1
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Yang GS, Qiu Y, Yang ZA. The complete chloroplast genome of Keteleeria evelyniana Mast var. pendula Hsüeh (Pinaceae), a species with extremely small populations in China. Mitochondrial DNA B Resour 2024; 9:557-562. [PMID: 38686317 PMCID: PMC11057466 DOI: 10.1080/23802359.2024.2345780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Keteleeria evelyniana Mast var. pendula Hsüeh, a typical plant species of extremely small population, is faced to be endangered. The complete chloroplast (cp) genome of K. evelyniana var. pendula has been assembled and annotated for the first time in this study. The complete genome in length was found to be 117,139 bp. The genome annotation revealed a total of 118 genes, including 34 transfer RNA (tRNA) genes, 4 ribosomal RNA (rRNA) genes, and 80 protein-coding genes. The maximum-likelihood phylogenetic tree supported that K. evelyniana var. pendula, K. fortune, K. evelyniana, and K. davidiana are clustered in one branch. This complete chloroplast genome helped us to understand the evolution of K. evelyniana var. pendula. These results laid the foundation for future studies on the conservation of this species.
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Affiliation(s)
- Guan-Song Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Yu Qiu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Zheng-An Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
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2
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Sidstedt M, Gynnå AH, Kiesler KM, Jansson L, Steffen CR, Håkansson J, Johansson G, Österlund T, Bogestål Y, Tillmar A, Rådström P, Ståhlberg A, Vallone PM, Hedman J. Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method. Forensic Sci Int Genet 2024; 71:103047. [PMID: 38598919 DOI: 10.1016/j.fsigen.2024.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
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Affiliation(s)
- Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Arvid H Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Kevin M Kiesler
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Joakim Håkansson
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg SE-405 30, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Gustav Johansson
- SIMSEN Diagnostics, Sahlgrenska Science Park, Gothenburg, Sweden
| | - Tobias Österlund
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Yalda Bogestål
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping SE-587 58, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Anders Ståhlberg
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden.
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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4
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Wang Y, Wang J, Gruninger RJ, McAllister TA, Li M, Guan LL. Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas. RNA Biol 2024; 21:1-13. [PMID: 38797889 PMCID: PMC11135877 DOI: 10.1080/15476286.2024.2356334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Although circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification using six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3' ends degradation (RTP); ribosomal RNAs coupled with linear RNAs elimination (Ribo-R); ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3' ends elimination (Ribo-RTP), respectively. RNA-sequencing analysis revealed that different approaches led to varied ratio of uniquely mapped reads, false-positive rate of identifying circRNAs, and the number of circRNAs per million clean reads (Padj <0.05). Out of 2,285 and 2,939 highly confident circRNAs identified in liver and rumen tissues, respectively, 308 and 260 were commonly identified from five methods, with Ribo-RTP method identified the highest number of circRNAs. Besides, 507 of 4,051 identified bovine highly confident circRNAs had shared splicing sites with human circRNAs. The findings from this work provide optimized methods to identify bovine circRNAs from cattle tissues for downstream research of their biological roles in cattle.
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Affiliation(s)
- Yixin Wang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jian Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Robert J. Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Mingzhou Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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5
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Pérez-Bonilla M, Sánchez-Hidalgo M, González I, Oves-Costales D, Martín J, Murillo-Alba J, Tormo JR, Cho A, Byun SY, No JH, Shum D, Ioset JR, Genilloud O, Reyes F. Madurastatins with Imidazolidinone Rings: Natural Products or Side-Reaction Products from Extraction Solvents? Int J Mol Sci 2023; 25:301. [PMID: 38203471 PMCID: PMC10779116 DOI: 10.3390/ijms25010301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Madurastatins are a group of pentapeptides containing an oxazoline moiety, and, in a few cases, an imidazolidinone ring as an additional structural feature. In our search for new potential antiparasitic metabolites from natural sources, we studied the acetone extracts from a culture of Actinomadura sp. CA-135719. The LC/HRMS analysis of this extract identified the presence of the known madurastatins C1 (1), D1 (4), and D2 (5) together with additional members of the family that were identified as the new madurastatins H2 (2) and 33-epi-D1 (3) after isolation and spectroscopic analysis. The planar structures of the new compounds were established by HRMS, ESI-qTOF-MS/MS, and 1D and 2D NMR data, and their absolute configuration was proposed using Marfey's and bioinformatic analyses of the biosynthetic gene cluster (BGC). A revision of the absolute configuration of madurastatins D1 and D2 is proposed. Additionally, madurastatins containing imidazolidinone rings are proved to be artifacts originating during acetone extraction of the bacterial cultures.
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Affiliation(s)
- Mercedes Pérez-Bonilla
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Marina Sánchez-Hidalgo
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Ignacio González
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Daniel Oves-Costales
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Jesús Martín
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - José Murillo-Alba
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - José R. Tormo
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Ahreum Cho
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (A.C.); (S.-Y.B.); (J.-H.N.); (D.S.)
| | - Soo-Young Byun
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (A.C.); (S.-Y.B.); (J.-H.N.); (D.S.)
| | - Joo-Hwan No
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (A.C.); (S.-Y.B.); (J.-H.N.); (D.S.)
| | - David Shum
- Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea; (A.C.); (S.-Y.B.); (J.-H.N.); (D.S.)
| | - Jean-Robert Ioset
- Drugs for Neglected Diseases Initiative, 15 Chemin Camille-Vidart, 1202 Geneva, Switzerland;
| | - Olga Genilloud
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Granada, Spain; (M.S.-H.); (I.G.); (D.O.-C.); (J.M.); (J.M.-A.); (J.R.T.); (O.G.)
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6
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Chaves-Olarte E, Meza-Torres J, Herrera-Rodríguez F, Lizano-González E, Suárez-Esquivel M, Baker KS, Rivas-Solano O, Ruiz-Villalobos N, Villalta-Romero F, Cheng HP, Walker GC, Cloeckaert A, Thomson NR, Frisan T, Moreno E, Guzmán-Verri C. A sensor histidine kinase from a plant-endosymbiont bacterium restores the virulence of a mammalian intracellular pathogen. Microb Pathog 2023; 185:106442. [PMID: 37944675 PMCID: PMC10740080 DOI: 10.1016/j.micpath.2023.106442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/22/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Alphaproteobacteria include organisms living in close association with plants or animals. This interaction relies partly on orthologous two-component regulatory systems (TCS), with sensor and regulator proteins modulating the expression of conserved genes related to symbiosis/virulence. We assessed the ability of the exoS+Sm gene, encoding a sensor protein from the plant endosymbiont Sinorhizobium meliloti to substitute its orthologous bvrS in the related animal/human pathogen Brucella abortus. ExoS phosphorylated the B. abortus regulator BvrR in vitro and in cultured bacteria, showing conserved biological function. Production of ExoS in a B. abortus bvrS mutant reestablished replication in host cells and the capacity to infect mice. Bacterial outer membrane properties, the production of the type IV secretion system VirB, and its transcriptional regulators VjbR and BvrR were restored as compared to parental B. abortus. These results indicate that conserved traits of orthologous TCS from bacteria living in and sensing different environments are sufficient to achieve phenotypic plasticity and support bacterial survival. The knowledge of bacterial genetic networks regulating host interactions allows for an understanding of the subtle differences between symbiosis and parasitism. Rewiring these networks could provide new alternatives to control and prevent bacterial infection.
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Affiliation(s)
- Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica; Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Jazmín Meza-Torres
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Fabiola Herrera-Rodríguez
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Esteban Lizano-González
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica; Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Kate S Baker
- Parasites and Microbes from Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Olga Rivas-Solano
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Fabián Villalta-Romero
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Hai-Ping Cheng
- Biological Sciences Department, Lehman College, The City University of New York, New York, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Nicholas R Thomson
- Parasites and Microbes from Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Caterina Guzmán-Verri
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica; Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
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7
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Baker D, Godwin CM, Khanam M, Burtner AM, Dick GJ, Denef VJ. Variation in resource competition traits among Microcystis strains is affected by their microbiomes. MLIFE 2023; 2:401-415. [PMID: 38818269 PMCID: PMC10989160 DOI: 10.1002/mlf2.12094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 06/01/2024]
Abstract
Freshwater harmful algal blooms are often dominated by Microcystis, a phylogenetically cohesive group of cyanobacteria marked by extensive genetic and physiological diversity. We have previously shown that this genetic diversity and the presence of a microbiome of heterotrophic bacteria influences competitive interactions with eukaryotic phytoplankton. In this study, we sought to explain these observations by characterizing Monod equation parameters for resource usage (maximum growth rate μ max, half-saturation value for growth K s, and quota) as a function of N and P levels for four strains (NIES-843, PCC 9701, PCC 7806 [WT], and PCC 7806 ΔmcyB) in presence and absence of a microbiome derived from Microcystis isolated from Lake Erie. Results indicated limited differences in maximum growth rates but more pronounced differences in half-saturation values among Microcystis strains. The largest impact of the microbiome was reducing the minimal nitrogen concentration sustaining growth and reducing half saturation values, with variable results depending on the Microcystis strain. Microcystis strains also differed from each other in their N and P quotas and the extent to which microbiome presence affected them. Our data highlight the importance of the microbiome in altering Microcystis-intrinsic traits, strain competitive hierarchies, and thus bloom dynamics. As quota, μ max, and K s are commonly used in models for harmful algal blooms, our data suggest that model improvement may be possible by incorporating genotype dependencies of resource-use parameters.
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Affiliation(s)
- Dylan Baker
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Casey M. Godwin
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
| | - Muhtamim Khanam
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Ashley M. Burtner
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
| | - Gregory J. Dick
- Cooperative Institute for Great Lakes Research, School for Environment and SustainabilityUniversity of MichiganAnn ArborMichiganUSA
- Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichiganUSA
| | - Vincent J. Denef
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
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8
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Oliveira DS, Fablet M, Larue A, Vallier A, Carareto CA, Rebollo R, Vieira C. ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements. Nucleic Acids Res 2023; 51:9764-9784. [PMID: 37615575 PMCID: PMC10570057 DOI: 10.1093/nar/gkad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.
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Affiliation(s)
- Daniel S Oliveira
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Institut Universitaire de France (IUF), Paris, Île-de-FranceF-75231, France
| | - Anaïs Larue
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Claudia M A Carareto
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
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Kulkarni CC, Cholin SS, Bajpai AK, Ondrasek G, Mesta RK, Rathod S, Patil HB. Comparative Root Transcriptome Profiling and Gene Regulatory Network Analysis between Eastern and Western Carrot ( Daucus carota L.) Cultivars Reveals Candidate Genes for Vascular Tissue Patterning. PLANTS (BASEL, SWITZERLAND) 2023; 12:3449. [PMID: 37836190 PMCID: PMC10575051 DOI: 10.3390/plants12193449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Carrot (Daucus carota L.) is a highly consumed vegetable rich in carotenoids, known for their potent antioxidant, anti-inflammatory, and immune-protecting properties. While genetic and molecular studies have largely focused on wild and Western carrot cultivars (cvs), little is known about the evolutionary interactions between closely related Eastern and Western cvs. In this study, we conducted comparative transcriptome profiling of root tissues from Eastern (UHSBC-23-1) and Western (UHSBC-100) carrot cv. to better understand differentially expressed genes (DEGs) associated with storage root development and vascular cambium (VC) tissue patterning. Through reference-guided TopHat mapping, we achieved an average mapping rate of 73.87% and identified a total of 3544 DEGs (p < 0.05). Functional annotation and gene ontology classification revealed 97 functional categories, including 33 biological processes, 19 cellular components, 45 metabolic processes, and 26 KEGG pathways. Notably, Eastern cv. exhibited enrichment in cell wall, plant-pathogen interaction, and signal transduction terms, while Western cv. showed dominance in photosynthesis, metabolic process, and carbon metabolism terms. Moreover, constructed gene regulatory network (GRN) for both cvs. obtained orthologs with 1222 VC-responsive genes of Arabidopsis thaliana. In Western cv, GRN revealed VC-responsive gene clusters primarily associated with photosynthetic processes and carbon metabolism. In contrast, Eastern cv. exhibited a higher number of stress-responsive genes, and transcription factors (e.g., MYB15, WRKY46, AP2/ERF TF connected via signaling pathways with NAC036) were identified as master regulators of xylem vessel differentiation and secondary cell wall thickening. By elucidating the comparative transcriptome profiles of Eastern and Western cvs. for the first time, our study provides valuable insights into the differentially expressed genes involved in root development and VC tissue patterning. The identification of key regulatory genes and their roles in these processes represents a significant advancement in our understanding of the evolutionary relations and molecular mechanisms underlying secondary growth of carrot and regulation by vascular cambium.
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Affiliation(s)
- Chaitra C. Kulkarni
- Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India;
- Kittur Rani Chennamma College of Horticulture, Arabhavi, Gokak 591218, Belgaum Dt., Karnataka, India
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Sarvamangala S. Cholin
- Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India;
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Akhilesh K. Bajpai
- Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase-I, Bengaluru 560100, Karnataka, India
| | - Gabrijel Ondrasek
- Department of Soil Amelioration, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - R. K. Mesta
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Santosha Rathod
- Indian Institute of Rice Research, Hyderabad 500030, Telangana, India
| | - H. B. Patil
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
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10
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Ma Y, Gan J, Bai Y, Cao D, Jiao Y. Minimal residual disease in solid tumors: an overview. Front Med 2023; 17:649-674. [PMID: 37707677 DOI: 10.1007/s11684-023-1018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/24/2023] [Indexed: 09/15/2023]
Abstract
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Affiliation(s)
- Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jingbo Gan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yinlei Bai
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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11
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Wang Y, Li J, Cao Y, Chen W, Xing H, Guo X, Shi Y, Wang Y, Liang T, Ye L, Liu D, Yang T, Wang Y, Ma W. Characteristic analysis and identification of novel molecular biomarkers in elderly glioblastoma patients using the 2021 WHO Classification of Central Nervous System Tumors. Front Neurosci 2023; 17:1165823. [PMID: 37360159 PMCID: PMC10288210 DOI: 10.3389/fnins.2023.1165823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Elderly glioblastoma (GBM) patients is characterized by high incidence and poor prognosis. Currently, however, there is still a lack of adequate molecular characterization of elderly GBM patients. The fifth edition of the WHO Classification of Central Nervous System Tumors (WHO5) gives a new classification approach for GBM, and the molecular characteristics of elderly GBM patients need to be investigated under this new framework. Methods The clinical and radiological features of patients with different classifications and different ages were compared. Potential prognostic molecular markers in elderly GBM patients under the WHO5 classification were found using Univariate Cox regression and Kaplan-Meier survival analysis. Results A total of 226 patients were included in the study. The prognostic differences between younger and elderly GBM patients were more pronounced under the WHO5 classification. Neurological impairment was more common in elderly patients (p = 0.001), while intracranial hypertension (p = 0.034) and epilepsy (p = 0.038) were more common in younger patients. Elderly patients were more likely to have higher Ki-67(p = 0.013), and in elderly WHO5 GBM patients, KMT5B (p = 0.082), KRAS (p = 0.1) and PPM1D (p = 0.055) were each associated with overall survival (OS). Among them, KRAS and PPM1D were found to be prognostic features unique to WHO5 elderly GBM patients. Conclusion Our study demonstrates that WHO5 classification can better distinguish the prognosis of elderly and younger GBM. Furthermore, KRAS and PPM1D may be potential prognostic predictors in WHO5 elderly GBM patients. The specific mechanism of these two genes in elderly GBM remains to be further studied.
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Affiliation(s)
- Yaning Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junlin Li
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaning Cao
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenlin Chen
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Xing
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaopeng Guo
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
| | - Yixin Shi
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuekun Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Ye
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Delin Liu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianrui Yang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
| | - Wenbin Ma
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
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12
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Hashimoto Y, Masunaga N, Kagara N, Abe K, Yoshinami T, Tsukabe M, Sota Y, Miyake T, Tanei T, Shimoda M, Shimazu K. Detection of Ultra-Rare ESR1 Mutations in Primary Breast Cancer Using LNA-Clamp ddPCR. Cancers (Basel) 2023; 15:cancers15092632. [PMID: 37174098 PMCID: PMC10177270 DOI: 10.3390/cancers15092632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
ESR1 mutations in breast cancer are one of the mechanisms of resistance to aromatase inhibitors. These mutations are common in metastatic breast cancer; however, these are rare in primary breast cancer. However, these data have been analyzed mainly in formalin-fixed, paraffin-embedded tissue; thus, rare mutations that may be present in primary breast cancer may be overlooked. In this study, we developed a highly sensitive mutation detection method called locked nucleic acid (LNA)-clamp droplet digital PCR (ddPCR) and validated it. The mutation detection sensitivity was substantiated to 0.003%. Then, we used this method to analyze ESR1 mutations in fresh-frozen (FF) tissues of primary breast cancer. cDNA extracted from the FF tissues of 212 patients with primary breast cancers were measured. Twenty-eight ESR1 mutations were found in twenty-seven (12.7%) patients. Sixteen (7.5%) patients had Y537S mutations and twelve (5.7%) had D538G mutations. Two mutations with a variant allele frequency (VAF) of ≥0.1% and twenty-six mutations with a VAF of <0.1% were found. By using this LNA-clamp ddPCR, this study demonstrated the presence of minor clones with a VAF of <0.1% in primary breast cancer.
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Affiliation(s)
- Yoko Hashimoto
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Nanae Masunaga
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Naofumi Kagara
- Department of Breast Surgery, Osaka General Medical Center, 3-1-56, Bandai-Higashi, Sumiyoshi-ku, Osaka 558-8558, Osaka, Japan
| | - Kaori Abe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tetsuhiro Yoshinami
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Masami Tsukabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
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13
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Yang T, Wu Z, Li L, Jiang M, Fang X, Huang W, Zhou Y. Identification and analysis of toxins in novel Bacillus thuringiensis strain Bt S3076-1 against Spodoptera frugiperda and Helicoverpa armigera (Lep.: Noctuidae). Arch Microbiol 2023; 205:168. [PMID: 37017772 DOI: 10.1007/s00203-023-03490-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 04/06/2023]
Abstract
Despite the successful application of toxins from Bacillus thuringiensis as biological control agents against pests, pests are showing resistance against an increasing number of Bacillus thuringiensis toxins due to evolution; thus, new toxins with higher toxicity and broad-spectrum activity against insects are being increasingly identified. To find new toxins, whole genome sequencing of the novel B. thuringiensis strain Bt S3076-1 was performed, and ten predicted toxic genes were identified in this study, including six cry genes, two tpp genes, one cyt gene and one vip gene, among which six were novel toxins. Subsequently, SDS‒PAGE analysis showed that the major proteins at the spore maturation stage were approximately 120 kDa, 70 kDa, 67 kDa, 60 kDa and 40 kDa, while active proteins after trypsin digestion (approximately 70 kDa and 40 kDa) exhibited LC50 values of 149.64 μg/g and 441.47 μg/g against Spodoptera frugiperda and Helicoverpa armigera larvae, respectively. Furthermore, pathological observation results showed that the peritrophic membrane of Spodoptera frugiperda and Helicoverpa armigera larvae was degraded. These findings will provide an experimental reference for further research on the insecticidal activity, toxicity spectrum and synergism of these toxins in Bt S3076-1.
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Affiliation(s)
- Tianbao Yang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Zhongqi Wu
- Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, People's Republic of China
- Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, People's Republic of China
| | - Liuping Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Xuanjun Fang
- Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, People's Republic of China
- Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, People's Republic of China
| | - Wenshan Huang
- Guangxi Lvyounong Biological Technology Co., Ltd, Nanning, 537100, People's Republic of China
| | - Yan Zhou
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, 530008, People's Republic of China.
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14
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Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
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Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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15
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Li W, Fan G, Sun K, Liu J, Liu J, Wang Y, Li E, Wu X, Shen L, Pan T. Microbial community structure dynamics of invasive bullfrog with meningitis-like infectious disease. Front Microbiol 2023; 14:1126195. [PMID: 36992930 PMCID: PMC10040567 DOI: 10.3389/fmicb.2023.1126195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/23/2023] [Indexed: 03/14/2023] Open
Abstract
Meningitis-like infectious disease (MID) (also known as frog cataract and torticollis) is a disease prone to occur in amphibians and reptiles. It is highly contagious and has a high mortality rate. In this study, we sampled and sequenced microbiomes from oral and intestinal samples of five normal and five diseased bullfrogs. The analysis found that the richness, uniformity, and abundance of the microbial community of the diseased bullfrogs were significantly higher than those of the normal bullfrogs in both the oral cavity and the gut. In the diseased group, the abundance of Elizabethkingia significantly increased and that of Lactococcus significantly decreased. It showed that the structure of the microbial community had changed a lot in diseased frogs. After the pathogenic bacteria infected the body, it might be make the decline in the immune function of the body declined, and resulting in some conditional pathogenic bacteria in the water body further infecting the body. As a result, the richness and composition of the microbial community significantly changed. This study can provide a theoretical basis for the control of MID of bullfrogs.
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Affiliation(s)
- Wengang Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
| | - Guangwei Fan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
| | - Ke Sun
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
| | - Jingru Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jinyan Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Yu Wang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - En Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
| | - Xiaobing Wu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- *Correspondence: Liang Shen,
| | - Tao Pan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Wuhu, China
- Tao Pan,
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16
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Yang Y, Dev A, Sychugov I, Hägglund C, Zhang SL. Plasmon-Enhanced Fluorescence of Single Quantum Dots Immobilized in Optically Coupled Aluminum Nanoholes. J Phys Chem Lett 2023; 14:2339-2346. [PMID: 36847590 PMCID: PMC10009806 DOI: 10.1021/acs.jpclett.3c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Fluorescence-based optical sensing techniques have continually been explored for single-molecule detection targeting myriad biomedical applications. Improving signal-to-noise ratio remains a prioritized effort to enable unambiguous detection at single-molecule level. Here, we report a systematic simulation-assisted optimization of plasmon-enhanced fluorescence of single quantum dots based on nanohole arrays in ultrathin aluminum films. The simulation is first calibrated by referring to the measured transmittance in nanohole arrays and subsequently used for guiding their design. With an optimized combination of nanohole diameter and depth, the variation of the square of simulated average volumetric electric field enhancement agrees excellently with that of experimental photoluminescence enhancement over a large range of nanohole periods. A maximum 5-fold photoluminescence enhancement is statistically achieved experimentally for the single quantum dots immobilized at the bottom of simulation-optimized nanoholes in comparison to those cast-deposited on bare glass substrate. Hence, boosting photoluminescence with optimized nanohole arrays holds promises for single-fluorophore-based biosensing.
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Affiliation(s)
- Yupeng Yang
- Division
of Solid-State Electronics, Department of Electrical Engineering,
The Ångström Laboratory, Uppsala
University, SE-751 03 Uppsala, Sweden
| | - Apurba Dev
- Division
of Solid-State Electronics, Department of Electrical Engineering,
The Ångström Laboratory, Uppsala
University, SE-751 03 Uppsala, Sweden
| | - Ilya Sychugov
- Division
of Photonics, Department of Applied Physics, School of Engineering
Sciences, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Carl Hägglund
- Division
of Solar Cell Technology, Department of Materials Science and Engineering,
The Ångström Laboratory, Uppsala
University, SE-751 03 Uppsala, Sweden
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Electrical Engineering,
The Ångström Laboratory, Uppsala
University, SE-751 03 Uppsala, Sweden
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17
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Zhang Y, Tang Y, Sun Z, Jia J, Fang Y, Wan X, Fang D. Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing. Genome Res 2023; 33:412-426. [PMID: 36958795 PMCID: PMC10078286 DOI: 10.1101/gr.277213.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/01/2023] [Indexed: 03/25/2023]
Abstract
Tn5 transposon tagments double-stranded DNA and RNA/DNA hybrids to generate nucleic acids that are ready to be amplified for high-throughput sequencing. The nucleic acid substrates for the Tn5 transposon must be explored to increase the applications of Tn5. Here, we found that the Tn5 transposon can transpose oligos into the 5' end of single-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA sequencing, starting with as little as 30 pg of total RNA. Moreover, compared with traditional dUTP-based strand-specific RNA sequencing, this method detects more genes, has a higher strand specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.
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Affiliation(s)
- Yanjun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yin Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhongxing Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junqi Jia
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuan Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinyi Wan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dong Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China;
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
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18
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Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F. Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research. Microbiol Spectr 2023; 11:e0428222. [PMID: 36744896 PMCID: PMC10101064 DOI: 10.1128/spectrum.04282-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lu Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Guoqing Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Ze Zhao
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Hui Wang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
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19
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Liu K, Xie N, Wang Y, Liu X. Contribution bias of parental genomes to the hybrid lineages of black Amur bream and topmouth culter revealed by low-coverage whole-genome sequencing. Gene 2023; 852:147058. [PMID: 36423776 DOI: 10.1016/j.gene.2022.147058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Interspecific hybridization has the potential to increase animal genetic diversity, enable the introgression of advantageous genetic variation, and even create hybrid lineages. Using the low-coverage whole-genome sequencing data of black Amur bream (Megalobrama terminalis [SJ]), topmouth culter (Culter alburnus [QZ]), and their hybrid progeny, we focused on the sequence variation and contribution bias to the genomic composition of the hybrid lineages of SJ♀ × QZ♂ [ZJ] and QZ♀ × SJ♂ [FJ]. Both mash-based genetic distance analysis and variant analysis based on various reference genomes revealed that the hybrid lineages' genomes are more prone to QZ composition. Furthermore, we assess the degree of subgenomic intermixing between parents QZ and SJ in the FJ and ZJ hybrid lineages. In the Jaccard index-zero genomic area, 89.41% of the genomic region in ZJ and 90.23% in FJ are entirely from one of the parental genomes. This genomic area is primarily from QZ, regardless of FJ or ZJ. In FJ, the proportion is 55.70%; in ZJ, the proportion is 54.60%. Using the reference-free variant discovery tool, we identified two InDel markers (Both were SSR-type InDel markers) and one (T/A)-type SNP marker that displayed differences in agarose electrophoresis. Our current findings suggest that parental genomic contribution bias leads to an imbalance in the genomic composition of hybrid lineages. The genomic composition bias is connected to species but not maternal effects, giving insights into the development of vertebrate genomes shortly after hybridization.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Yuxi Wang
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Xinyi Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
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20
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Cheng C, Fei Z, Xiao P. Methods to improve the accuracy of next-generation sequencing. Front Bioeng Biotechnol 2023; 11:982111. [PMID: 36741756 PMCID: PMC9895957 DOI: 10.3389/fbioe.2023.982111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023] Open
Abstract
Next-generation sequencing (NGS) is present in all fields of life science, which has greatly promoted the development of basic research while being gradually applied in clinical diagnosis. However, the cost and throughput advantages of next-generation sequencing are offset by large tradeoffs with respect to read length and accuracy. Specifically, its high error rate makes it extremely difficult to detect SNPs or low-abundance mutations, limiting its clinical applications, such as pharmacogenomics studies primarily based on SNP and early clinical diagnosis primarily based on low abundance mutations. Currently, Sanger sequencing is still considered to be the gold standard due to its high accuracy, so the results of next-generation sequencing require verification by Sanger sequencing in clinical practice. In order to maintain high quality next-generation sequencing data, a variety of improvements at the levels of template preparation, sequencing strategy and data processing have been developed. This study summarized the general procedures of next-generation sequencing platforms, highlighting the improvements involved in eliminating errors at each step. Furthermore, the challenges and future development of next-generation sequencing in clinical application was discussed.
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21
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Kim JY, Jelinek J, Lee YH, Kim DH, Kang K, Ryu SH, Moon HR, Cho K, Rha SH, Cha JK, Issa JPJ, Kim J. Hypomethylation in MTNR1B: a novel epigenetic marker for atherosclerosis profiling using stenosis radiophenotype and blood inflammatory cells. Clin Epigenetics 2023; 15:11. [PMID: 36658621 PMCID: PMC9854223 DOI: 10.1186/s13148-023-01423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Changes in gene-specific promoter methylation may result from aging and environmental influences. Atherosclerosis is associated with aging and environmental effects. Thus, promoter methylation profiling may be used as an epigenetic tool to evaluate the impact of aging and the environment on atherosclerosis development. However, gene-specific methylation changes are currently inadequate epigenetic markers for predicting atherosclerosis and cardiovascular disease pathogenesis. RESULTS We profiled and validated changes in gene-specific promoter methylation associated with atherosclerosis using stenosis radiophenotypes of cranial vessels and blood inflammatory cells rather than direct sampling of atherosclerotic plaques. First, we profiled gene-specific promoter methylation changes using digital restriction enzyme analysis of methylation (DREAM) sequencing in peripheral blood mononuclear cells from eight samples each of cranial vessels with and without severe-stenosis radiophenotypes. Using DREAM sequencing profiling, 11 tags were detected in the promoter regions of the ACVR1C, ADCK5, EFNA2, ENOSF1, GLS2, KNDC1, MTNR1B, PACSIN3, PAX8-AS1, TLDC1, and ZNF7 genes. Using methylation evaluation, we found that EFNA2, ENOSF1, GLS2, KNDC1, MTNR1B, PAX8-AS1, and TLDC1 showed > 5% promoter methylation in non-plaque intima, atherosclerotic vascular tissues, and buffy coats. Using logistic regression analysis, we identified hypomethylation of MTNR1B as an independent variable for the stenosis radiophenotype prediction model by combining it with traditional atherosclerosis risk factors including age, hypertension history, and increases in creatinine, lipoprotein (a), and homocysteine. We performed fivefold cross-validation of the prediction model using 384 patients with ischemic stroke (50 [13%] no-stenosis and 334 [87%] > 1 stenosis radiophenotype). For the cross-validation, the training dataset included 70% of the dataset. The prediction model showed an accuracy of 0.887, specificity to predict stenosis radiophenotype of 0.940, sensitivity to predict no-stenosis radiophenotype of 0.533, and area under receiver operating characteristic curve of 0.877 to predict stenosis radiophenotype from the test dataset including 30% of the dataset. CONCLUSIONS We identified and validated MTNR1B hypomethylation as an epigenetic marker to predict cranial vessel atherosclerosis using stenosis radiophenotypes and blood inflammatory cells rather than direct atherosclerotic plaque sampling.
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Affiliation(s)
- Jee Yeon Kim
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Jaroslav Jelinek
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ USA
| | - Young Ho Lee
- grid.254230.20000 0001 0722 6377Department of Anatomy, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Dae Hyun Kim
- grid.412048.b0000 0004 0647 1081Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Keunsoo Kang
- grid.411982.70000 0001 0705 4288Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, South Korea
| | - Su Hyun Ryu
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Hye Rin Moon
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Kwangjo Cho
- grid.412048.b0000 0004 0647 1081Department of Thoracic and Cardiovascular Surgery, Dong-A University Hospital, Busan, South Korea
| | - Seo Hee Rha
- grid.412048.b0000 0004 0647 1081Department of Pathology, Dong-A University Hospital, Busan, South Korea
| | - Jae Kwan Cha
- grid.254230.20000 0001 0722 6377Department of Anatomy, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jean-Pierre J. Issa
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ USA
| | - Jei Kim
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea ,grid.411665.10000 0004 0647 2279Daejeon-Chungnam Regional Cerebrovascular Center, Chungnam National University Hospital, Daejeon, South Korea
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22
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Sánchez-Hidalgo M, García MJ, González I, Oves-Costales D, Genilloud O. Complete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene Clusters. Microorganisms 2023; 11:microorganisms11020265. [PMID: 36838228 PMCID: PMC9962454 DOI: 10.3390/microorganisms11020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Minor genera actinomycetes are considered a promising source of new secondary metabolites. The strain Kribbella sp. CA-293567 produces sandramycin and kribbellichelins A & B In this work, we describe the complete genome sequencing of this strain and the in silico identification of biosynthetic gene clusters (BGCs), focusing on the pathways encoding sandramycin and kribbellichelins A-B. We also present a comparative analysis of the biosynthetic potential of 38 publicly available genomes from Kribbella strains.
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23
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Barszcz M, Tuśnio A, Taciak M. Poultry nutrition. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Nutrition is the most important environmental factor affecting development, health status, growth performance and profitability of poultry production. Feeds for poultry constitute up to 70–75% of total production costs. Poultry nutrition differs considerably from that of other livestock, which is determined by the specific anatomy of the gastrointestinal tract. Protein, energy, fat, fiber, minerals, vitamins, and water are of basic importance for poultry nutrition and their content in feeds must cover the requirement that differ depending on the bird’s age and species. In general, feed protein must be of good value including the content of essential amino acids. Among them lysine, methionine, cysteine, threonine and tryptophan are the limiting ones. The main ingredient of poultry feeds are cereal grains, i.e. wheat and maize, which predominantly constitute an energy source because their protein content is insufficient for birds. Because of that cereals cannot be the only feed for poultry and must be combined with protein sources such as soybean or rapeseed meal, legume seeds or protein concentrates. Despite birds’ requirement for nutrients and chemical composition of feeds are well known, nutrition must face many problems. One of the most important issues is to find alternatives to antibiotic growth promoters.
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Affiliation(s)
- Marcin Barszcz
- Department of Animal Nutrition , The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences , Instytucka 3, 05-110 Jabłonna , Poland
| | - Anna Tuśnio
- Department of Animal Nutrition , The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences , Instytucka 3, 05-110 Jabłonna , Poland
| | - Marcin Taciak
- Department of Animal Nutrition , The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences , Instytucka 3, 05-110 Jabłonna , Poland
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24
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A genetically novel avian Hepatitis E virus in China. Virus Genes 2022; 58:589-593. [PMID: 36183048 DOI: 10.1007/s11262-022-01937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/25/2022] [Indexed: 10/07/2022]
Abstract
Hepatitis E virus (HEV) infection has a global distribution with diverse hosts, including mammals and avians. In this study, an avian Hepatitis E virus (aHEV) strain with a high mortality rate of about 30%, designated as SDXT20, was obtained from the liver of 30-week-old Hubbard chickens with severe hepatosplenomegaly in 2020 in Eastern China and HEV was proved to be the only pathogen by next-generation sequencing. Its complete genome, which encodes three open reading frames (ORFs), is 6649 nt in length. ORF1-3 encodes three proteins with lengths of 1532 aa, 606 aa, and 82 aa, respectively, and ORF2 and ORF3 overlap with each other. BLAST-based similarity analysis of the complete viral genome demonstrated that SDXT20 had merely 80.5-92.2% similarity with avian Avihepevirus magniiecur strains and 50.4%-54.8% lower similarity with Paslahepevirus balayani, Rocahepevirus ratti, and Chirohepevirus eptesici species. Further genetic evolution analysis of the complete genome and ORF2 revealed that the isolate was genetically distinct from known aHEVs, and it belonged to a novel genetically distinct aHEV. This study provides data for further analysis of the multi-host and cross-host genetic evolution of HEVs.
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25
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Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
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26
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Hansen J, Siddiq MM, Yadaw AS, Tolentino RE, Rabinovich V, Jayaraman G, Jain MR, Liu T, Li H, Xiong Y, Goldfarb J, Iyengar R. Whole cell response to receptor stimulation involves many deep and distributed subcellular biochemical processes. J Biol Chem 2022; 298:102325. [PMID: 35926710 PMCID: PMC9520007 DOI: 10.1016/j.jbc.2022.102325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Neurite outgrowth is an integrated whole cell response triggered by the cannabinoid-1 receptor. We sought to identify the many different biochemical pathways that contribute to this whole cell response. To understand underlying mechanisms, we identified subcellular processes (SCPs) composed of one or more biochemical pathways and their interactions required for this response. Differentially expressed genes and proteins were obtained from bulk transcriptomics and proteomic analysis of extracts from cells stimulated with a cannabinoid-1 receptor agonist. We used these differentially expressed genes and proteins to build networks of interacting SCPs by combining the expression data with prior pathway knowledge. From these SCP networks, we identified additional genes that when ablated, experimentally validated the SCP involvement in neurite outgrowth. Our experiments and informatics modeling allowed us to identify diverse SCPs such as those involved in pyrimidine metabolism, lipid biosynthesis, and mRNA splicing and stability, along with more predictable SCPs such as membrane vesicle transport and microtubule dynamics. We find that SCPs required for neurite outgrowth are widely distributed among many biochemical pathways required for constitutive cellular functions, several of which are termed ‘deep’, since they are distal to signaling pathways and the key SCPs directly involved in extension of the neurite. In contrast, ‘proximal’ SCPs are involved in microtubule growth and membrane vesicle transport dynamics required for neurite outgrowth. From these bioinformatics and dynamical models based on experimental data, we conclude that receptor-mediated regulation of subcellular functions for neurite outgrowth is both distributed, that is, involves many different biochemical pathways, and deep.
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Affiliation(s)
- Jens Hansen
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mustafa M Siddiq
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Arjun Singh Yadaw
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Rosa E Tolentino
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Vera Rabinovich
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mohit Raja Jain
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, Newark, NY, 07103, United States
| | - Tong Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, Newark, NY, 07103, United States
| | - Hong Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, Newark, NY, 07103, United States
| | - Yuguang Xiong
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Joseph Goldfarb
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Ravi Iyengar
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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27
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Orchestrated translation specializes dinoflagellate metabolism three times per day. Proc Natl Acad Sci U S A 2022; 119:e2122335119. [PMID: 35858433 PMCID: PMC9335273 DOI: 10.1073/pnas.2122335119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many cells specialize for different metabolic tasks at different times over their normal ZT cycle by changes in gene expression. However, in most cases, circadian gene expression has been assessed at the mRNA accumulation level, which may not faithfully reflect protein synthesis rates. Here, we use ribosome profiling in the dinoflagellate Lingulodinium polyedra to identify thousands of transcripts showing coordinated translation. All of the components in carbon fixation are concurrently regulated at ZT0, predicting the known rhythm of carbon fixation, and many enzymes involved in DNA replication are concurrently regulated at ZT12, also predicting the known rhythm in this process. Most of the enzymes in glycolysis and the TCA cycle are also regulated together, suggesting rhythms in these processes as well. Surprisingly, a third cluster of transcripts show peak translation at approximately ZT16, and these transcripts encode enzymes involved in transcription, translation, and amino acid biosynthesis. The latter has physiological consequences, as measured free amino acid levels increase at night and thus represent a previously undocumented rhythm in this model. Our results suggest that ribosome profiling may be a more accurate predictor of changed metabolic state than transcriptomics.
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28
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He B, Li B, Chen X, Zhang Q, Lu C, Yang S, Long J, Ning L, Chen H, Huang J. PDL1Binder: Identifying programmed cell death ligand 1 binding peptides by incorporating next-generation phage display data and different peptide descriptors. Front Microbiol 2022; 13:928774. [PMID: 35910615 PMCID: PMC9335124 DOI: 10.3389/fmicb.2022.928774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Monoclonal antibody drugs targeting the PD-1/PD-L1 pathway have showed efficacy in the treatment of cancer patients, however, they have many intrinsic limitations and inevitable drawbacks. Peptide inhibitors as alternatives might compensate for the drawbacks of current PD-1/PD-L1 interaction blockers. Identifying PD-L1 binding peptides by random peptide library screening is a time-consuming and labor-intensive process. Machine learning-based computational models enable rapid discovery of peptide candidates targeting the PD-1/PD-L1 pathway. In this study, we first employed next-generation phage display (NGPD) biopanning to isolate PD-L1 binding peptides. Different peptide descriptors and feature selection methods as well as diverse machine learning methods were then incorporated to implement predictive models of PD-L1 binding. Finally, we proposed PDL1Binder, an ensemble computational model for efficiently obtaining PD-L1 binding peptides. Our results suggest that predictive models of PD-L1 binding can be learned from deep sequencing data and provide a new path to discover PD-L1 binding peptides. A web server was implemented for PDL1Binder, which is freely available at http://i.uestc.edu.cn/pdl1binder/cgi-bin/PDL1Binder.pl.
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Affiliation(s)
- Bifang He
- Medical College, Guizhou University, Guiyang, China
| | - Bowen Li
- Medical College, Guizhou University, Guiyang, China
| | - Xue Chen
- Medical College, Guizhou University, Guiyang, China
| | | | - Chunying Lu
- Medical College, Guizhou University, Guiyang, China
| | | | - Jinjin Long
- Medical College, Guizhou University, Guiyang, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Heng Chen
- Medical College, Guizhou University, Guiyang, China
- *Correspondence: Heng Chen,
| | - Jian Huang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Jian Huang,
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29
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Oh B, Santhanam S, Azadian M, Swaminathan V, Lee AG, McConnell KW, Levinson A, Song S, Patel JJ, Gardner EE, George PM. Electrical modulation of transplanted stem cells improves functional recovery in a rodent model of stroke. Nat Commun 2022; 13:1366. [PMID: 35292643 PMCID: PMC8924243 DOI: 10.1038/s41467-022-29017-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Stroke is a leading cause of long-term disability worldwide, intensifying the need for effective recovery therapies. Stem cells are a promising stroke therapeutic, but creating ideal conditions for treatment is essential. Here we developed a conductive polymer system for stem cell delivery and electrical modulation in animals. Using this system, electrical modulation of human stem cell transplants improve functional stroke recovery in rodents. Increased endogenous stem cell production corresponds with improved function. Transcriptome analysis identified stanniocalcin 2 (STC2) as one of the genes most significantly upregulated by electrical stimulation. Lentiviral upregulation and downregulation of STC2 in the transplanted stem cells demonstrate that this glycoprotein is an essential mediator in the functional improvements seen with electrical modulation. Moreover, intraventricular administration of recombinant STC2 post-stroke confers functional benefits. In summation, our conductive polymer system enables electrical modulation of stem cells as a potential method to improve recovery and identify important therapeutic targets. Paul George and colleagues developed a conductive polymer system to enable stem cell delivery and electrical modulation in vivo. Employing this system improved functional stroke recovery in rodents and identified important repair pathways.
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Affiliation(s)
- Byeongtaek Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sruthi Santhanam
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matine Azadian
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Vishal Swaminathan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alex G Lee
- Department of Pediatrics, University of California, San Francisco, CA, 94305, USA
| | - Kelly W McConnell
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexa Levinson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shang Song
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jainith J Patel
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emily E Gardner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Paul M George
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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30
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Ghaffari SR, Rafati M, Shadnoush M, Pourbabaee S, Aghighi M, Samiee SM, Kermanchi J, Alaei MR, Salehpour S, Amirkashani D, Setoodeh A, Sarkhail P, Badv RS, Aminzadeh M, Shiva S, Eshraghi P, Moravej H, Hashemipour M, Rostampour N, Hamidieh AA, Shamsian BS, Shams S, Zamanfar D, Ebrahimi A, Otadi A, Tara SZ, Barati Z, Fakhri L, Hoseini A, Amiri H, Ramandi S, Mostofinezhad N, Kani ZP, Mohammadyari E, Khosravi M, Saadati M, Hoseininasab F, Khorshid HRK, Modaberisaber Y. Molecular characterization of a large cohort of Mucopolysaccharidosis patients: Iran Mucopolysaccharidosis RE-diagnosis Study (IMPRESsion). Hum Mutat 2022; 43:e1-e23. [PMID: 35005816 DOI: 10.1002/humu.24328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 01/05/2022] [Indexed: 01/30/2023]
Abstract
Mucopolysaccharidoses (MPSs) are rare, heterogeneous inborn errors of metabolism (IEM) diagnosed through a combination of clinical, biochemical, and genetic investigations. The aim of this study was molecular characterization of the largest cohort of Iranian MPS patients (302 patients from 289 unrelated families), along with tracking their ethnicity and geographical origins. 185/289 patients were studied using an IEM-targeted NGS panel followed by complementary Sanger sequencing, which led to the diagnosis of 154 MPS patients and 5 non-MPS IEMs (diagnostic yield: 85.9%). Furthermore, 106/289 patients who were referred with positive findings went through re-analysis and confirmatory tests which confirmed MPS diagnosis in 104. Among the total of 258 MPS patients, 225 were homozygous, 90 harbored novel variants, and 9 had copy number variations. MPS IV was the most common type (34.8%) followed by MPS I (22.7%) and MPS VI (22.5%). Geographical origin analysis unveiled a pattern of distribution for frequent variants in ARSB (c.430G>A, c.962T>C [p.Leu321Pro], c.281C>A [p.Ser94*]), GALNS (c.319G>A [p.Ala107Thr], c.860C>T [p.Ser287Leu], c.1042A>G [p.Thr348Ala]), and IDUA (c.1A>C [p.Met1Leu], c.1598C>G [p.Pro533Arg], c.1562_1563insC [p.Gly522Argfs*50]). Our extensive patient cohort reveals the genetic and geographic landscape of MPS in Iran, which provides insight into genetic epidemiology of MPS and can facilitate a more cost-effective, time-efficient diagnostic approach based on the region-specific variants. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Saeed Reza Ghaffari
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Gene Clinic, Tehran, Iran
| | - Maryam Rafati
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mahdi Shadnoush
- Department of Clinical Nutrition, Faculty of Nutrition & Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shokooh Pourbabaee
- Deputy of Curative Affairs, Ministry of Health and Medical Education, Tehran, Iran
| | - Mohammad Aghighi
- Transplantation and Diseases Administrationو Deputy of Curative Affairs, Ministry of Health and Medical Education, Tehran, Iran
| | - Siamak Mirab Samiee
- Food and Drug Laboratory Research Center, Tehran, Iran.,General Reference Health Laboratory, Ministry of Health and Medical Education, Tehran, IR
| | - Jamshid Kermanchi
- Transplantation and Diseases Administrationو Deputy of Curative Affairs, Ministry of Health and Medical Education, Tehran, Iran
| | | | | | - Davoud Amirkashani
- Division of Endocrinology and Metabolism, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, IR
| | - Aria Setoodeh
- Children's Medical Center, Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Tehran, IR
| | - Peymaneh Sarkhail
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - Reza Shervin Badv
- Department of Pediatrics, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Tehran, IR
| | - Majid Aminzadeh
- Diabetes Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Khuzestan, IR
| | - Siamak Shiva
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, East Azerbaijan, IR
| | - Peyman Eshraghi
- Mashhad University of Medical Sciences, Mashhad, Khorasan Razavi, IR
| | - Hossein Moravej
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Fars, IR
| | - Mahin Hashemipour
- Metabolic Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Isfahan, IR
| | - Noushin Rostampour
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences Isfahan, Isfahan, Isfahan, IR
| | - Amir Ali Hamidieh
- Pediatric Cell and Gene Therapy Research Center, Tehran University of Medical Sciences, Tehran, Tehran, IR
| | - Bibi Shahin Shamsian
- Pediatric Congenital Hematologic Disorders Research Center, Research, Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sedigheh Shams
- Department of Pathology, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Tehran, IR
| | - Daniel Zamanfar
- Diabetes Research Center, Mazandaran University of Medical Sciences, Sari, IR
| | - Ayoub Ebrahimi
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, East Azerbaijan, IR
| | - Ali Otadi
- The University of British Columbia, Faculty of Science, Vancouver, BC, Canada
| | - Seyedeh Zahra Tara
- Pediatric Endocrinology Department, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zeinab Barati
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Laya Fakhri
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Azadeh Hoseini
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hosna Amiri
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Somayeh Ramandi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Niusha Mostofinezhad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | | | | | - Mahsa Khosravi
- Islamic Azad University Tehran Medical Sciences, Tehran, Tehran, IR
| | - Masoome Saadati
- Islamic Azad University Tehran North Branch, Tehran, Tehran, IR
| | - Fatemeh Hoseininasab
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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31
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RNA-seq for revealing the function of the transcriptome. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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Alser M, Lindegger J, Firtina C, Almadhoun N, Mao H, Singh G, Gomez-Luna J, Mutlu O. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures. Comput Struct Biotechnol J 2022; 20:4579-4599. [PMID: 36090814 PMCID: PMC9436709 DOI: 10.1016/j.csbj.2022.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023] Open
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33
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Bagal UR, Phan J, Welsh RM, Misas E, Wagner D, Gade L, Litvintseva AP, Cuomo CA, Chow NA. MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. Methods Mol Biol 2022; 2517:215-228. [PMID: 35674957 DOI: 10.1007/978-1-0716-2417-3_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.
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Affiliation(s)
- Ujwal R Bagal
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Phan
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth Misas
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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34
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A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. INSECTS 2021; 12:insects12121066. [PMID: 34940154 PMCID: PMC8706918 DOI: 10.3390/insects12121066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/16/2021] [Accepted: 11/25/2021] [Indexed: 01/23/2023]
Abstract
Simple Summary We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. Abstract White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.
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35
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Bossé JT, Li Y, Cohen LM, Stegger M, Angen Ø, Lacouture S, Gottschalk M, Lei L, Koene M, Kuhnert P, Bandara AB, Inzana TJ, Holden MTG, Harris D, Oshota O, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR, On Behalf Of The BRaDP T Consortium. Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation. Microb Genom 2021; 7. [PMID: 34818145 PMCID: PMC8743550 DOI: 10.1099/mgen.0.000687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report here the complete genome sequence of the widely studied Actinobacillus pleuropneumoniae serovar 8 reference strain 405, generated using the Pacific Biosciences (PacBio) RS II platform. Furthermore, we compared draft sequences generated by Illumina sequencing of six stocks of this strain, including the same original stock used to generate the PacBio sequence, held in different countries and found little genetic variation, with only three SNPs identified, all within the degS gene. However, sequences of two small plasmids, pARD3079 and p405tetH, detected by Illumina sequencing of the draft genomes were not identified in the PacBio sequence of the reference strain.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Yanwen Li
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Liza Miriam Cohen
- Department of Production Animal Clinical Sciences Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, Changchun, P.R China
| | - Miriam Koene
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, Universität Bern, Bern, Switzerland
| | - Aloka B Bandara
- Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA
| | - Thomas J Inzana
- Present address: College of Veterinary Medicine, Long Island University, Brookville, USA.,Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA
| | - Matthew T G Holden
- Present address: School of Medicine, University of St Andrews, St Andrews, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK
| | - David Harris
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Olusegun Oshota
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, UK
| | - Paul R Langford
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
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36
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Porath‐Krause A, Strauss AT, Henning JA, Seabloom EW, Borer ET. Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anita Porath‐Krause
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Alexander T. Strauss
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Jeremiah A. Henning
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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37
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Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma. Nat Commun 2021; 12:6726. [PMID: 34795254 PMCID: PMC8602403 DOI: 10.1038/s41467-021-26974-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/26/2021] [Indexed: 02/08/2023] Open
Abstract
Cutaneous T cell lymphomas (CTCL) are rare but aggressive cancers without effective treatments. While a subset of patients derive benefit from PD-1 blockade, there is a critically unmet need for predictive biomarkers of response. Herein, we perform CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions from 14 advanced CTCL patients enrolled in a pembrolizumab clinical trial (NCT02243579). We find no differences in the frequencies of immune or tumor cells between responders and non-responders. Instead, we identify topographical differences between effector PD-1+ CD4+ T cells, tumor cells, and immunosuppressive Tregs, from which we derive a spatial biomarker, termed the SpatialScore, that correlates strongly with pembrolizumab response in CTCL. The SpatialScore coincides with differences in the functional immune state of the tumor microenvironment, T cell function, and tumor cell-specific chemokine recruitment and is validated using a simplified, clinically accessible tissue imaging platform. Collectively, these results provide a paradigm for investigating the spatial balance of effector and suppressive T cell activity and broadly leveraging this biomarker approach to inform the clinical use of immunotherapies.
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38
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Liu K, Xie N, Ma HJ. Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855). Mol Biol Rep 2021; 49:943-950. [PMID: 34727288 DOI: 10.1007/s11033-021-06913-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known. METHODS AND RESULTS This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent. CONCLUSIONS This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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39
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Gadad SS, Camacho CV, Malladi V, Hutti CR, Nagari A, Kraus WL. PARP-1 Regulates Estrogen-Dependent Gene Expression in Estrogen Receptor α-Positive Breast Cancer Cells. Mol Cancer Res 2021; 19:1688-1698. [PMID: 34158394 PMCID: PMC8492518 DOI: 10.1158/1541-7786.mcr-21-0103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/01/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) has gained considerable attention as a target for therapeutic inhibitors in breast cancers. Previously we showed that PARP-1 localizes to active gene promoters to regulate histone methylation and RNA polymerase II activity (Pol II), altering the expression of various tumor-related genes. Here we report a role for PARP-1 in estrogen-dependent transcription in estrogen receptor alpha (ERα)-positive (ER+) breast cancers. Global nuclear run-on and sequencing analyses functionally linked PARP-1 to the direct control of estrogen-regulated gene expression in ER+ MCF-7 breast cancer cells by promoting transcriptional elongation by Pol II. Furthermore, chromatin immunoprecipitation sequencing analyses revealed that PARP-1 regulates the estrogen-dependent binding of ERα and FoxA1 to a subset of genomic ERα binding sites, promoting active enhancer formation. Moreover, we found that the expression levels of the PARP-1- and estrogen-coregulated gene set are enriched in the luminal subtype of breast cancer, and high PARP-1 expression in ER+ cases correlates with poor survival. Finally, treatment with a PARP inhibitor or a transcriptional elongation inhibitor attenuated estrogen-dependent growth of multiple ER+ breast cancer cell lines. Taken together, our results show that PARP-1 regulates critical molecular pathways that control the estrogen-dependent gene expression program underlying the proliferation of ER+ breast cancer cells. IMPLICATIONS: PARP-1 regulates the estrogen-dependent genomic binding of ERα and FoxA1 to regulate critical gene expression programs by RNA Pol II that underlie the proliferation of ER+ breast cancers, providing a potential therapeutic opportunity for PARP inhibitors in estrogen-responsive breast cancers.
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Affiliation(s)
- Shrikanth S Gadad
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, Texas
| | - Cristel V Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Venkat Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Charles R Hutti
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
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40
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Liu K, Feng XY, Ma HJ, Xie N. Comparative mitochondrial genome analysis of the Mongolian redfin, Chanodichthys mongolicus (Xenocyprididae) from China reveals heteroplasmy. Mitochondrial DNA B Resour 2021; 6:2601-2604. [PMID: 34409154 PMCID: PMC8366642 DOI: 10.1080/23802359.2021.1961627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study determined the mitochondrial genome (mitogenome) of Chanodichthys mongolicus from China's Qiantang River and analyzed its phylogenetic history in the Subfamily Cultrinae. Next-generation sequencing was used to obtain the mitogenome of C. mongolicus, GenBank Accession Number MZ032228. The mitochondrial genome length of C. mongolicus from China's Qiantang River is 16,622 bp. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two central noncoding regions (the control region and the origin of light strand replication). Based on BLAST comparisons, the sequence identity of C. mongolicus MZ032228 from China's Qiantang River was 99.84% to that of Ancherythroculter wangi MG783573 from China's Nei River, 99.75% to C. mongolicus AP009060 from Russia's Black River. The phylogenetic analysis is consistent with BLAST comparisons in confirming that A. wangi MG783573 and C. mongolicus MZ032228 show a high genetic similarity. This study also confirms mitochondrial DNA heteroplasmy in C. mongolicus for the first time and documents 35 heterogeneous loci that were detected.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiao-yu Feng
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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Abstract
CircRNAs are a subclass of lncRNAs that have been found to be abundantly present in a wide range of species, including humans. CircRNAs are generally produced by a noncanonical splicing event called backsplicing that is dependent on the canonical splicing machinery, giving rise to circRNAs classified into three main categories: exonic circRNA, circular intronic RNA, and exon-intron circular RNA. Notably, circRNAs possess functional importance and display their functions through different mechanisms of action including sponging miRNAs, or even being translated into functional proteins. In addition, circRNAs also have great potential as biomarkers, particularly in cancer, thanks to their high stability, tissue type and developmental stage specificity, and their presence in biological fluids, which make them promising candidates as noninvasive biomarkers. In this chapter, we describe the most commonly used techniques for the study of circRNAs as cancer biomarkers, including high-throughput techniques such as RNA-Seq and microarrays, and other methods to analyze the presence of specific circRNAs in patient samples.
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Affiliation(s)
- Carla Solé
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Gartze Mentxaka
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain. .,Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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43
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Lu P, Foley J, Zhu C, McNamara K, Sirinukunwattana K, Vennam S, Varma S, Fehri H, Srivastava A, Zhu S, Rittscher J, Mallick P, Curtis C, West R. Transcriptome and genome evolution during HER2-amplified breast neoplasia. Breast Cancer Res 2021; 23:73. [PMID: 34266469 PMCID: PMC8281634 DOI: 10.1186/s13058-021-01451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/03/2021] [Indexed: 01/05/2023] Open
Abstract
Background The acquisition of oncogenic drivers is a critical feature of cancer progression. For some carcinomas, it is clear that certain genetic drivers occur early in neoplasia and others late. Why these drivers are selected and how these changes alter the neoplasia’s fitness is less understood. Methods Here we use spatially oriented genomic approaches to identify transcriptomic and genetic changes at the single-duct level within precursor neoplasia associated with invasive breast cancer. We study HER2 amplification in ductal carcinoma in situ (DCIS) as an event that can be both quantified and spatially located via fluorescence in situ hybridization (FISH) and immunohistochemistry on fixed paraffin-embedded tissue. Results By combining the HER2-FISH with the laser capture microdissection (LCM) Smart-3SEQ method, we found that HER2 amplification in DCIS alters the transcriptomic profiles and increases diversity of copy number variations (CNVs). Particularly, interferon signaling pathway is activated by HER2 amplification in DCIS, which may provide a prolonged interferon signaling activation in HER2-positive breast cancer. Multiple subclones of HER2-amplified DCIS with distinct CNV profiles are observed, suggesting that multiple events occurred for the acquisition of HER2 amplification. Notably, DCIS acquires key transcriptomic changes and CNV events prior to HER2 amplification, suggesting that pre-amplified DCIS may create a cellular state primed to gain HER2 amplification for growth advantage. Conclusion By using genomic methods that are spatially oriented, this study identifies several features that appear to generate insights into neoplastic progression in precancer lesions at a single-duct level. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01451-6.
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Affiliation(s)
- Peipei Lu
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Joseph Foley
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Katherine McNamara
- Department of Medicine and Genetics, Stanford University, Stanford, CA, USA
| | - Korsuk Sirinukunwattana
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Big Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Sujay Vennam
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hamid Fehri
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Big Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jens Rittscher
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Parag Mallick
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Christina Curtis
- Department of Medicine and Genetics, Stanford University, Stanford, CA, USA
| | - Robert West
- Department of Pathology, Stanford University, Stanford, CA, USA
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44
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Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA, Puerta T, Keše D, Balla E, Zákoucká H, Rob F, Morré SA, de Barbeyrac B, Galán JC, de Vries HJC, Thomson NR, Goldenberger D, Egli A. Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains. Microb Genom 2021; 7. [PMID: 34184981 PMCID: PMC8461462 DOI: 10.1099/mgen.0.000599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis, is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.
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Affiliation(s)
- Helena M B Seth-Smith
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angèle Bénard
- Present address: Healthcare Systems Research Group, VHIR, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sylvia M Bruisten
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Bart Versteeg
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Olivia Peuchant
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Cécile Bébéar
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - David A Lewis
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, Parramatta, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Teresa Puerta
- Unidad de ITS/VIH, Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Darja Keše
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Eszter Balla
- Bacterial STI Reference Laboratory, National Public Health Center (former National Center for Epidemiology), Budapest, Hungary
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of Syphilis and Chlamydia Infections, National Institute of Public Health, Srobarova 48, 100 42, Prague 10, Czech Republic
| | - Filip Rob
- Department of Dermatovenereology, Second Faculty of Medicine, Charles University and Hospital Bulovka, Budinova 2, 180 81, Prague 8, Czech Republic
| | - Servaas A Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.,Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research Institute GROW, University of Maastricht, Maastricht, The Netherlands
| | - Bertille de Barbeyrac
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Henry J C de Vries
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Daniel Goldenberger
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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Evaluating coverage bias in next-generation sequencing of Escherichia coli. PLoS One 2021; 16:e0253440. [PMID: 34166413 PMCID: PMC8224930 DOI: 10.1371/journal.pone.0253440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/05/2021] [Indexed: 01/18/2023] Open
Abstract
Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.
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46
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New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies. Neural Comput Appl 2021; 33:15669-15692. [PMID: 34155424 PMCID: PMC8208613 DOI: 10.1007/s00521-021-06188-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
During the last (15) years, improved omics sequencing technologies have expanded the scale and resolution of various biological applications, generating high-throughput datasets that require carefully chosen software tools to be processed. Therefore, following the sequencing development, bioinformatics researchers have been challenged to implement alignment algorithms for next-generation sequencing reads. However, nowadays selection of aligners based on genome characteristics is poorly studied, so our benchmarking study extended the “state of art” comparing 17 different aligners. The chosen tools were assessed on empirical human DNA- and RNA-Seq data, as well as on simulated datasets in human and mouse, evaluating a set of parameters previously not considered in such kind of benchmarks. As expected, we found that each tool was the best in specific conditions. For Ion Torrent single-end RNA-Seq samples, the most suitable aligners were CLC and BWA-MEM, which reached the best results in terms of efficiency, accuracy, duplication rate, saturation profile and running time. About Illumina paired-end osteomyelitis transcriptomics data, instead, the best performer algorithm, together with the already cited CLC, resulted Novoalign, which excelled in accuracy and saturation analyses. Segemehl and DNASTAR performed the best on both DNA-Seq data, with Segemehl particularly suitable for exome data. In conclusion, our study could guide users in the selection of a suitable aligner based on genome and transcriptome characteristics. However, several other aspects, emerged from our work, should be considered in the evolution of alignment research area, such as the involvement of artificial intelligence to support cloud computing and mapping to multiple genomes.
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47
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Kelil A, Gallo E, Banerjee S, Adams JJ, Sidhu SS. CellectSeq: In silico discovery of antibodies targeting integral membrane proteins combining in situ selections and next-generation sequencing. Commun Biol 2021; 4:561. [PMID: 33980972 PMCID: PMC8115320 DOI: 10.1038/s42003-021-02066-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
Synthetic antibody (Ab) technologies are efficient and cost-effective platforms for the generation of monoclonal Abs against human antigens. Yet, they typically depend on purified proteins, which exclude integral membrane proteins that require the lipid bilayers to support their native structure and function. Here, we present an Ab discovery strategy, termed CellectSeq, for targeting integral membrane proteins on native cells in complex environment. As proof of concept, we targeted three transmembrane proteins linked to cancer, tetraspanin CD151, carbonic anhydrase 9, and integrin-α11. First, we performed in situ cell-based selections to enrich phage-displayed synthetic Ab pools for antigen-specific binders. Then, we designed next-generation sequencing procedures to explore Ab diversities and abundances. Finally, we developed motif-based scoring and sequencing error-filtering algorithms for the comprehensive interrogation of next-generation sequencing pools to identify Abs with high diversities and specificities, even at extremely low abundances, which are very difficult to identify using manual sampling or sequence abundances.
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Affiliation(s)
- Abdellali Kelil
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Eugenio Gallo
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Toronto Recombinant Antibody Centre, University of Toronto, Toronto, Canada
| | - Sunandan Banerjee
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Toronto Recombinant Antibody Centre, University of Toronto, Toronto, Canada
| | - Jarrett J. Adams
- grid.17063.330000 0001 2157 2938Toronto Recombinant Antibody Centre, University of Toronto, Toronto, Canada
| | - Sachdev S. Sidhu
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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Canine brucellosis in Costa Rica reveals widespread Brucella canis infection and the recent introduction of foreign strains. Vet Microbiol 2021; 257:109072. [PMID: 33965789 DOI: 10.1016/j.vetmic.2021.109072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/13/2021] [Indexed: 01/31/2023]
Abstract
Brucellosis is a prevalent disease in Costa Rica (CR), with an increasing number of human infections. Close to half of homes in CR have one or more dogs, corresponding to ∼1.4 million canines, most of them in the Central Valley within or near the cities of San José, Heredia, and Alajuela. From 302 dog sera collected from this region, 19 were positive for Brucella canis antigens, and five had antibodies against smooth lipopolysaccharide, suggesting infections by both B. canis and other Brucella species. B. canis strains were isolated in the Central Valley from 26 kennel dogs and three pet dogs, all displaying clinical signs of canine brucellosis. We detected three recent introductions of different B. canis strains in kennels: two traced from Mexico and one from Panama. Multiple locus-variable number tandem repeats (MLVA-16) and whole-genome sequencing (WGSA) analyses showed that B. canis CR strains comprise three main lineages. The tree topologies obtained by WGSA and MLVA-16 just partially agreed, indicating that the latter analysis is not suitable for phylogenetic studies. The fatty acid methyl ester analysis resolved five different B. canis groups, showing less resolution power than the MLVA-16 and WGSA. Lactobacillic acid was absent in linages I and II but present in linage III, supporting the recent introductions of B. canis strains from Mexico. B. canis displaying putative functional cyclopropane synthase for the synthesis of lactobacillic acid are phylogenetically intertwined with B. canis with non-functional protein, indicating that mutations have occurred independently in the various lineages.
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49
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Li Z, Liang F, Zhang T, Fu N, Pei X, Long Y. Enhanced tolerance to drought stress resulting from Caragana korshinskii CkWRKY33 in transgenic Arabidopsis thaliana. BMC Genom Data 2021; 22:11. [PMID: 33691617 PMCID: PMC7945665 DOI: 10.1186/s12863-021-00965-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/28/2021] [Indexed: 11/23/2022] Open
Abstract
Background It is well known that WRKY transcription factors play important roles in plant growth and development, defense regulation and stress responses. Results In this study, a WRKY transcription factor, WRKY33, was cloned from Caragana korshinskii. A sequence structure analysis showed that it belonged to the Group-I type. Subcellular localization experiments in tobacco epidermal cells showed the presence of CkWRKY33 in the nucleus. Additionally, CkWRKY33 was overexpressed in Arabidopsis thaliana. A phenotypic investigation revealed that compared with wild-type plants, CkWRKY33-overexpressing transgenic plants had higher survival rates, as well as relative soluble sugar, proline and peroxidase contents, but lower malondialdehyde contents, following a drought stress treatment. Conclusions This suggested that the overexpression of CkWRKY33 led to an enhanced drought-stress tolerance in transgenic A. thaliana. Thus, CkWRKY33 may act as a positive regulator involved in the drought-stress responses in Caragana korshinskii. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00965-4.
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Affiliation(s)
- Zhen Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengping Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Tianbao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Na Fu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yan Long
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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50
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Guan-Song Y, Peng L, Yang ZA, Zhang J, Zhu YA, Xie JJ. The complete chloroplast genome of Pterospermum menglunense (Sterculiaceae), an endangered species. Mitochondrial DNA B Resour 2021; 6:1276-1278. [PMID: 33829107 PMCID: PMC8008881 DOI: 10.1080/23802359.2021.1907251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pterospermum menglunense is the endangered plant species of the genus Pterospermum in the family Sterculiaceae. In the study, the complete genome was 162,421bp in length, including of two inverted repeats (IRA and IRB, 25,572 bp), separated by a large single-copy region (LSC, 90,754 bp) and a small single-copy region (SSC, 20,523 bp). The genome annotation reveals a total of 132 genes, including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 87 protein-coding (PCG) genes. The phylogenetic tree showed P. menglunense is closely related to Pterospermum kingtungense.
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Affiliation(s)
- Yang Guan-Song
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Lei Peng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Zheng-An Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jie Zhang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Ying-An Zhu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jun-Jun Xie
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
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