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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Upadhyay M, Pogorevc N, Medugorac I. scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses. Mol Biol Evol 2024; 41:msae057. [PMID: 38507648 PMCID: PMC10994858 DOI: 10.1093/molbev/msae057] [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: 09/26/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved the problems associated with the installation of tools and their dependencies, population genomic analyses requiring multistep pipelines or complex data transformation can greatly be facilitated by the application of workflow management systems such as Nextflow and Snakemake. Here, we present scalepopgen, a collection of fully automated workflows that can carry out widely used population genomic analyses on the biallelic single nucleotide polymorphism data stored in either variant calling format files or the plink-generated binary files. scalepopgen is developed in Nextflow and can be run locally or on high-performance computing systems using either Conda, Singularity, or Docker. The automated workflow includes procedures such as (i) filtering of individuals and genotypes; (ii) principal component analysis, admixture with identifying optimal K-values; (iii) running TreeMix analysis with or without bootstrapping and migration edges, followed by identification of an optimal number of migration edges; (iv) implementing single-population and pair-wise population comparison-based procedures to identify genomic signatures of selection. The pipeline uses various open-source tools; additionally, several Python and R scripts are also provided to collect and visualize the results. The tool is freely available at https://github.com/Popgen48/scalepopgen.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Neža Pogorevc
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
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Oh R, Woo SJ, Joo K. Whole genome sequencing for inherited retinal diseases in the Korean National Project of Bio Big Data. Graefes Arch Clin Exp Ophthalmol 2024; 262:1351-1359. [PMID: 37947821 DOI: 10.1007/s00417-023-06309-5] [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: 06/25/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE This study aimed to analyze the genetic results of inherited retinal diseases (IRDs) and evaluate the diagnostic usefulness of whole genome sequencing (WGS) in the Korean National Project of Bio Big Data. METHODS As part of the Korean National Project of Bio Big Data, WGS was performed on 32 individuals with IRDs with no identified pathogenic variants through whole or targeted exome sequencing. RESULTS Individuals with retinitis pigmentosa (n = 23), cone dystrophy (n = 2), cone-rod dystrophy (n = 2), familial exudative vitreoretinopathy (n = 2), pigmented paravenous chorioretinal atrophy (n = 1), North Carolina macular dystrophy (n = 1), and bull's-eye macular dystrophy (n = 1) were included. WGS revealed genetic mutations in the IQCB1, PRPF31, USH2A, and GUCY2D genes in five cases (15.6%). Two large structural variations and an intronic variant were newly detected in three cases. Two individuals had biallelic missense mutations that were not identified in previous exome sequencing. CONCLUSION With WGS, the causative variants in 15.6% of unsolved IRDs from the Korean National Project of Bio Big Data were identified. Further research with a larger cohort might unveil the diagnostic usefulness of WGS in IRDs and other diseases.
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Affiliation(s)
- Richul Oh
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620.
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Chenhaka LH, Van Wyk DAB, Mienie C, Bezuidenhout CC, Lekota KE. The phylogenomic landscape of extended-spectrum β-lactamase producing Citrobacter species isolated from surface water. BMC Genomics 2023; 24:755. [PMID: 38062371 PMCID: PMC10704729 DOI: 10.1186/s12864-023-09867-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the North West Province, South Africa. RESULTS Phenotypic antimicrobial susceptibility profiles of the isolates demonstrated their ability to produce the extended-spectrum β-lactamase (ESBL). Whole genomes were sequenced to profile antibiotic resistance and virulence genes, as well as mobile genetic elements. In silico taxonomic identification was conducted by using multi-locus sequence typing and average nucleotide identity. A pangenome was used to determine the phylogenomic landscape of the Citrobacter species by using 109 publicly available genomes. The strains S21 and S23 were identified as C. braakii, while strains S24 and S25 were C. murliniae and C. portucalensis, respectively. Comparative genomics and sequenced genomes of the ESBL-producing isolates consisted of n = 91; 83% Citrobacter species in which bla-CMY-101 (n = 19; 32,2%) and bla-CMY-59 (n = 12; 38,7%) were prevalent in C. braakii, and C. portucalensis strains, respectively. Macrolide (acrAB-TolC, and mdtG) and aminoglycoside (acrD) efflux pumps genes were identified in the four sequenced Citrobacter spp. isolates. The quinolone resistance gene, qnrB13, was exclusive to the C. portucalensis S25 strain. In silico analysis detected plasmid replicon types IncHI1A, IncP, and Col(VCM04) in C. murliniae S24 and C. portucalensis S25, respectively. These potentially facilitate the T4SS secretion system in Citrobacter species. In this study, the C. braakii genomes could be distinguished from C. murliniae and C. portucalensis on the basis of gene encoding for cell surface localisation of the CPS (vexC) and identification of genes involved in capsule polymer synthesis (tviB and tviE). A cluster for the salmochelin siderophore system (iro-BCDEN) was found in C. murliniae S24. This is important when it comes to the pathogenicity pathway that confers an advantage in colonisation. CONCLUSIONS The emerging and genomic landscapes of these ESBL-producing Citrobacter species are of significant concern due to their dissemination potential in freshwater systems. The presence of these ESBL and multidrug-resistant (MDR) pathogens in aquatic environments is of One Health importance, since they potentially impact the clinical domain, that is, in terms of human health and the agricultural domain, that is, in terms of animal health and food production as well as the environmental domain.
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Affiliation(s)
- Lee-Hendra Chenhaka
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Deidré A B Van Wyk
- Unit for Environment Science and Management, Microbiology, North-West University, Mahikeng campus, Private Bag X2046, Mahikeng, 2745, South Africa.
| | - Charlotte Mienie
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Cornelius C Bezuidenhout
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Kgaugelo E Lekota
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
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Daniels BN, Nurge J, Sleeper O, Lee A, López C, Christie MR, Toonen RJ, White C, Davidson JM. Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk. PeerJ 2023; 11:e16510. [PMID: 38077446 PMCID: PMC10710129 DOI: 10.7717/peerj.16510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.
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Affiliation(s)
- Benjamin N. Daniels
- Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Jenna Nurge
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Olivia Sleeper
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Andy Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | - Cataixa López
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of America
| | - Mark R. Christie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States of America
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of America
| | - Crow White
- Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Jean M. Davidson
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
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Zhao R, Lukacsovich T, Gaut R, Emerson JJ. FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies. G3 (BETHESDA, MD.) 2023; 13:jkad162. [PMID: 37494033 PMCID: PMC10542570 DOI: 10.1093/g3journal/jkad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/26/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.
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Affiliation(s)
- Roy Zhao
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Tamas Lukacsovich
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Rebecca Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - J J Emerson
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Jaisamut K, Lisachov A, Thong T, Singchat W, Ahmad SF, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 2023; 31:29. [PMID: 37775555 DOI: 10.1007/s10577-023-09738-4] [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] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixes, Av. General Norton de Matos, S/N, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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Durbin MD, Fairman K, Helvaty LR, Huang M, Li M, Abreu D, Geddes GC, Helm BM, Landis BJ, McEntire A, Mitchell DK, Ware SM. Genetic Testing Guidelines Impact Care in Newborns with Congenital Heart Defects. J Pediatr 2023; 260:113495. [PMID: 37211210 PMCID: PMC10660555 DOI: 10.1016/j.jpeds.2023.113495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 05/23/2023]
Abstract
OBJECTIVE To evaluate genetic evaluation practices in newborns with the most common birth defect, congenital heart defects (CHD), we determined the prevalence and the yield of genetic evaluation across time and across patient subtypes, before and after implementation of institutional genetic testing guidelines. STUDY DESIGN This was a retrospective, cross-sectional study of 664 hospitalized newborns with CHD using multivariate analyses of genetic evaluation practices across time and patient subtypes. RESULTS Genetic testing guidelines for hospitalized newborns with CHD were implemented in 2014, and subsequently genetic testing increased (40% in 2013 and 75% in 2018, OR 5.02, 95% CI 2.84-8.88, P < .001) as did medical geneticists' involvement (24% in 2013 and 64% in 2018, P < .001). In 2018, there was an increased use of chromosomal microarray (P < .001), gene panels (P = .016), and exome sequencing (P = .001). The testing yield was high (42%) and consistent across years and patient subtypes analyzed. Increased testing prevalence (P < .001) concomitant with consistent testing yield (P = .139) added an estimated 10 additional genetic diagnoses per year, reflecting a 29% increase. CONCLUSIONS In patients with CHD, yield of genetic testing was high. After implementing guidelines, genetic testing increased significantly and shifted to newer sequence-based methods. Increased use of genetic testing identified more patients with clinically important results with potential to impact patient care.
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Affiliation(s)
- Matthew D Durbin
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN
| | - Korre Fairman
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Lindsey R Helvaty
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, Indiana University Bloomington School of Public Health, Bloomington, IN
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University Bloomington School of Public Health, Bloomington, IN
| | - Daniel Abreu
- Indiana University School of Medicine, Indianapolis, IN
| | - Gabrielle C Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Benjamin J Landis
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN; Division of Pediatric Cardiology, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN
| | - Alexis McEntire
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Dana K Mitchell
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN.
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Chu X, Wang Z, Wang W, Liu W, Cao Y, Feng L. Roles of hypoxic environment and M2 macrophage-derived extracellular vesicles on the progression of non-small cell lung cancer. BMC Pulm Med 2023; 23:239. [PMID: 37400770 DOI: 10.1186/s12890-023-02468-7] [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: 12/02/2022] [Accepted: 05/04/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Hypoxia contributes to the development of invasive and metastatic cancer cells, and is detrimental to cancer treatment. This study aimed to explore the molecular mechanisms by which hypoxic microenvironments affect hypoxic non-small cell lung cancer (NSCLC) development and the effects of M2 macrophage-derived extracellular vesicles (EVs) on NSCLC cells. METHODS A549 cells were cultured in an anoxic incubator for 48 h to construct hypoxic A549 cells, and then normal and hypoxic A549 cells were harvested for RNA sequencing. Next, THP-1 cells were used to induce M2 macrophages, and EVs were isolated from THP-1 cells and M2 macrophages. Cell counting kit-8 and transwell assays were used to determine the viability and migration of hypoxic A549 cells, respectively. RESULTS After sequencing, 2426 DElncRNAs and 501 DEmiRNAs were identified in normal A549 cells and hypoxic A549 cells. These DElncRNAs and DEmiRNAs were significantly enriched in "Wnt signaling pathway," "Hippo signaling pathway," "Rap1 signaling pathway," "calcium signaling pathway," "mTOR signaling pathway," and "TNF signaling pathway." Subsequently, ceRNA networks consisting of 4 lncRNA NDRG1 transcripts, 16 miRNAs and 221 target mRNAs were built, and the genes in the ceRNA networks were significantly associated with "Hippo signaling pathway" and "HIF-1 signaling pathway." EVs were successfully extracted from THP-1 cells and M2 macrophages, and M2 macrophage-derived EVs significantly enhanced the viability and migration of hypoxic A549 cells. Finally, M2 macrophage-derived EVs further upregulated the expression of NDRG1-009, NDRG1-006, VEGFA, and EGLN3, while downregulating miR-34c-5p, miR-346, and miR-205-5p in hypoxic A549 cells. CONCLUSIONS M2 macrophage-derived EVs may worsen the progression of NSCLC in a hypoxic microenvironment by regulating the NDRG1-009-miR-34c-5p-VEGFA, NDRG1-006-miR-346-EGLN3, NDRG1-009-miR-205-5p-VEGFA, and Hippo/HIF-1 signaling pathways.
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Affiliation(s)
- Xiao Chu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Zetian Wang
- Department of Trauma-Emergency & Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Weiqing Wang
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Wenjing Liu
- Department of Thoracic Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Yunyun Cao
- School of Medicine, The International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Department of Surgical Oncology, Minhang Branch, Fudan University Shanghai Cancer Center, NO.106, Ruili Road, Minhang District, Shanghai, 200240, China.
| | - Liang Feng
- Department of Surgical Oncology, Minhang Branch, Fudan University Shanghai Cancer Center, NO.106, Ruili Road, Minhang District, Shanghai, 200240, China.
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10
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Fernández-Caso B, Miqueleiz A, Alarcón T. Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1135. [PMID: 37508231 PMCID: PMC10376898 DOI: 10.3390/antibiotics12071135] [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: 05/28/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.
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Affiliation(s)
| | - Ana Miqueleiz
- Department of Microbiology, Hospital Universitario de Navarra, 31008 Pamplona, Spain
| | - Teresa Alarcón
- Department of Microbiology, Hospital Universitario La Princesa, 28006 Madrid, Spain
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11
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Piper M, Kluger H, Ruppin E, Hu-Lieskovan S. Immune Resistance Mechanisms and the Road to Personalized Immunotherapy. Am Soc Clin Oncol Educ Book 2023; 43:e390290. [PMID: 37459578 DOI: 10.1200/edbk_390290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
What does the future of cancer immunotherapy look like and how do we get there? Find out where we've been and where we're headed in A Report on Resistance: The Road to personalized immunotherapy.
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Affiliation(s)
- Miles Piper
- School of Medicine, University of Utah, Salt Lake City, UT
| | | | - Eytan Ruppin
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Siwen Hu-Lieskovan
- School of Medicine, University of Utah, Salt Lake City, UT
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
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12
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Wang Q, Li W, Liu H, Tan B, Dong X, Chi S, Yang Q, Zhang S, Fan D, Hu Y. The isolation, identification, whole-genome sequencing of Clostridium butyricum LV1 and its effects on growth performance, immune response, and disease-resistance of Litopenaeus vannamei. Microbiol Res 2023; 272:127384. [PMID: 37141852 DOI: 10.1016/j.micres.2023.127384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/01/2023] [Accepted: 04/08/2023] [Indexed: 05/06/2023]
Abstract
In this study, a strain of Clostridium butyricum was isolated from the intestine of Litopenaeus vannamei with the method of anaerobic microbial isolation and culture. Next, the probiotic properties of LV1 were evaluated with susceptibility tests, tolerance tests, and whole genome sequencing in vivo and in vitro, followed by the analysis of the effect of LV1 on the growth performance, immune response, and disease resistance of Litopenaeus vannamei. According to the results, the 16 S rDNA sequence of LV1 was 100% homolofgous to the reference sequence of Clostridium butyricum. Moreover, LV1 was resistant to several antibiotics including amikacin, streptomycin, and gentamicin and highly tolerated artificial gastric and artificial intestinal fluids. The whole genome of LV1 was 4625,068 bp in size and included 4336 coding genes. Among these genes, GO, KEGG, and COG databases exhibited the highest number of genes annotated to metabolic pathway classes and 105 genes annotated as glycoside hydrolases. Meanwhile, 176 virulence genes were predicted. The use of diets supplemented with 1.2 × 109 CFU/kg of LV1 live cells significantly increased the weight gain and specific growth rates of Litopenaeus vannamei and the activity of serum superoxide dismutase, glutathione peroxidase, acid phosphatase, and alkaline phosphatase (P < 0.05). Meanwhile, the use of these diets markedly improved the relative expression of intestinal immunity- and growth-related genes. In conclusion, LV1 has excellent probiotic properties. Specifically, the addition of 1.2 × 109 CFU/kg of LV1 live cells to the diet improved the growth performance, immune response, and disease-resistance of Litopenaeus vannamei.
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Affiliation(s)
- Qi Wang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China; Bio-Form Biotechnology (Guangdong) Co., Ltd, Foshan 528200, China
| | - Weikang Li
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China; Guangdong Evergreen Feed Industry Co., Ltd, Zhanjiang 524088, China
| | - Hongyu Liu
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China.
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China
| | - Xiaohui Dong
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China
| | - Shuyan Chi
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China
| | - Qihui Yang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China
| | - Shuang Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China; Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, Guangdong, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang 524025, China
| | - Depeng Fan
- Bio-Form Biotechnology (Guangdong) Co., Ltd, Foshan 528200, China
| | - Yadong Hu
- Bio-Form Biotechnology (Guangdong) Co., Ltd, Foshan 528200, China
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13
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Wen Y, Zeng L, Chen Q, Li Y, Fu M, Wang Z, Liu H, Li X, Huang P, Wu W, Zou Q, Yi W. RNA-Seq-based transcriptomics analysis during the photodynamic therapy of primary cells in secondary hyperparathyroidism. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:905-917. [PMID: 36750541 DOI: 10.1007/s43630-023-00361-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/02/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND The aim of this study was to identify changes in gene expression before and after 5-aminolevulinic acid-mediated photodynamic therapy (5-ALA-PDT) and to investigate the potential mechanism of 5-ALA-PDT based on ribonucleic acid sequencing (RNA-Seq) analysis. METHODS Secondary hyperparathyroidism (SHPT) primary cells were isolated from surgically excised specimens and exposed to laser light. The transcription profiles of SHPT primary cells were identified through RNA-Seq. Differentially expressed genes (DEGs) were identified. Enrichment of functions and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Quantitative real-time polymerase chain reaction (RT-qPCR) and western blot analysis were used to validate genes based on RNA-Seq results. RESULTS In total, 1320 DEGs were identified, of which 1019 genes were upregulated and 301 genes were downregulated. GO and KEGG pathway analyses identified significantly enriched pathways in DEGs, including TGF beta in extracellular matrix (ECM), negative regulation of triglyceride biosynthetic process, protein heterodimerization activity, systemic lupus erythematosus, ECM-receptor interaction, focal adhesion and protein digestion and absorption. Protein-protein interaction (PPI) network analyses identified potential heat shock protein (HSP) interactions among the DEGs. Eight HSP genes were also identified that were most likely involved in 5-ALA-PDT, which were further validated by RT-qPCR and western blotting. CONCLUSIONS The findings of this descriptive study reveal changes in the transcriptome profile during 5-ALA-PDT, suggesting that gene expression and mutation, signaling pathways, and the molecular network are altered in SHPT primary cells. The above findings provide new insight for further studies on the mechanisms underlying 5-ALA-PDT in SHPT.
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Affiliation(s)
- Ying Wen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Yitong Li
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Mengdie Fu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Zixin Wang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China
| | - Hong Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Xiejia Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Peng Huang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Wei Wu
- Department of General Surgery, The Third Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Qiongyan Zou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China.
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, No. 139, Renmin Central Road, Changsha, 410011, People's Republic of China.
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14
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Wu T, Zhu D, Wu X, Zhang N, Zhang Q. Taxol‑resistant breast cancer cell‑derived exosome‑delivered miR‑187‑5p regulates the growth of breast cancer cells via ABCD2 and Wnt/β‑catenin signaling. Oncol Lett 2023; 25:119. [PMID: 36844629 PMCID: PMC9950341 DOI: 10.3892/ol.2023.13705] [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: 08/29/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Acquired resistance to Taxol (TAX) contributes to clinical treatment failure and significantly reduces the survival rate of patients. The present study aimed to explore the effects of exosomal microRNA (miR)-187-5p on TAX resistance in breast cancer cells and its underlying mechanisms. Exosomes were isolated from MCF-7 and TAX-resistant MCF-7/TAX cells, and the miR-187-5p and miR-106a-3p levels of the cells and exosomes were determined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Next, MCF-7 cells were treated with TAX for 48 h and either treated with exosomes or transfected with miR-187-5p mimics. Cell viability, apoptosis, migration, invasion and colony formation were determined using Cell Counting Kit-8, flow cytometry, Transwell and colony formation assays, and the expression levels of associated genes and proteins were detected by RT-qPCR and western blotting, respectively. Finally, a dual-luciferase reporter gene assay was performed to confirm the target of miR-187-5p. The results showed that miR-187-5p expression levels increased significantly in TAX-resistant MCF-7 cells and exosomes compared with normal MCF-7 cells and exosomes (P<0.05). However, miR-106a-3p was not detected in the cells or exosomes. Therefore, miR-187-5p was selected for subsequent experiments. A series of cell assays showed that TAX inhibited the viability, migration, invasion and colony formation of MCF-7 cells and promoted their apoptosis; however, these changes were reversed by resistant cell exosomes and miR-187-5p mimics. Additionally, TAX significantly upregulated ABCD2 and downregulated β-catenin, c-Myc and cyclin D1, whereas resistant exosomes and miR-187-5p mimics reversed the TAX-induced changes in expression. Finally, ABCD2 was confirmed to directly bind with miR-187-5p. It may be concluded that TAX-resistant cell-derived exosomes delivering miR-187-5p may affect the growth of TAX-induced breast cancer cells by targeting ABCD2 and c-Myc/Wnt/β-catenin signaling.
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Affiliation(s)
- Tieli Wu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150000, P.R. China
| | - Dandan Zhu
- Department of Medical Oncology, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163000, P.R. China
| | - Xingyi Wu
- Department of Internal Medicine, Qiqihar First Factory Hospital, Qiqihar, Heilongjiang 161000, P.R. China
| | - Ningning Zhang
- School of Basic Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161000, P.R. China
| | - Qingyuan Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150000, P.R. China,Correspondence to: Dr Qingyuan Zhang, Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang, Harbin, Heilongjiang 150000, P.R. China, E-mail:
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15
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Jang W, Kang JN, Jo IH, Lee SM, Park GH, Kim CK. The chromosome-level genome assembly of lance asiabell ( Codonopsis lanceolata), a medicinal and vegetable plant of the Campanulaceae family. Front Genet 2023; 14:1100819. [PMID: 36816041 PMCID: PMC9929348 DOI: 10.3389/fgene.2023.1100819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Codonopsis lanceolata (2n = 2x = 16) belongs to the Campanulaceae family and is a valuable medicinal and vegetable plant primarily found in East Asia. Several studies have demonstrated its excellent pharmacological effects, for example in bronchial treatment. However, genomic information of C. lanceolata is scarce, hindering studies on crop improvement of the species. Here, we report a high-quality chromosome-level genome assembly of C. lanceolata based on a hybrid method using Nanopore long-read, Illumina short-read, and Hi-C data. The assembled genome was completed as 1,273 Mb (84.5% of the estimated genome size), containing eight pseudo-chromosomes, ranging from 101.3 to 184.3 Mb. The genome comprised of 71.3% repeat sequences and 46,005 protein-coding genes, of which 85.7% genes were functionally annotated. Completeness of the assembled genome and genes was assessed to be 97.5% and 90.4%, respectively, by Benchmarking Universal Single-Copy Orthologs analysis. Phylogenetic and synteny analysis revealed that C. lanceolata was closely related to Platycodon grandiflorus in the Campanulaceae family. Gene family evolution revealed significant expansion of related genes involved in saponin biosynthesis in the C. lanceolata genome. This is the first reference genome reported for C. lanceolata. The genomic data produced in this study will provide essential information for further research to improve this medicinal plant and will broaden the understanding of the Campanulaceae family.
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Affiliation(s)
- Woojong Jang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, South Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, South Korea
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Gyu-Hwang Park
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea,*Correspondence: Chang-Kug Kim,
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16
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Chung HY, Jian M, Chang CK, Chen CS, Li SY, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Hung KS, Chang FY, Shang HS. The application of a novel 5-in-1 multiplex reverse transcriptase-polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern. Int J Infect Dis 2023; 127:56-62. [PMID: 36455809 PMCID: PMC9703862 DOI: 10.1016/j.ijid.2022.11.027] [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: 06/05/2022] [Revised: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). METHODS This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be used to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. RESULTS The limit of detection of each gene locus was 80 copies per polymerase chain reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. CONCLUSION The assay can also be applied in a commercial platform with the completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ming Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Yi Li
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Corresponding author
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17
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Shinn LM, Mansharamani A, Baer DJ, Novotny JA, Charron CS, Khan NA, Zhu R, Holscher HD. Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults. J Nutr 2023; 152:2956-2965. [PMID: 36040343 PMCID: PMC9840004 DOI: 10.1093/jn/nxac195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The fecal metabolome is affected by diet and includes metabolites generated by human and microbial metabolism. Advances in -omics technologies and analytic approaches have allowed researchers to identify metabolites and better utilize large data sets to generate usable information. One promising aspect of these advancements is the ability to determine objective biomarkers of food intake. OBJECTIVES We aimed to utilize a multivariate, machine learning approach to identify metabolite biomarkers that accurately predict food intake. METHODS Data were aggregated from 5 controlled feeding studies in adults that tested the impact of specific foods (almonds, avocados, broccoli, walnuts, barley, and oats) on the gastrointestinal microbiota. Fecal samples underwent GC-MS metabolomic analysis; 344 metabolites were detected in preintervention samples, whereas 307 metabolites were detected postintervention. After removing metabolites that were only detected in either pre- or postintervention and those undetectable in ≥80% of samples in all study groups, changes in 96 metabolites relative concentrations (treatment postintervention minus preintervention) were utilized in random forest models to 1) examine the relation between food consumption and fecal metabolome changes and 2) rank the fecal metabolites by their predictive power (i.e., feature importance score). RESULTS Using the change in relative concentration of 96 fecal metabolites, 6 single-food random forest models for almond, avocado, broccoli, walnuts, whole-grain barley, and whole-grain oats revealed prediction accuracies between 47% and 89%. When comparing foods with one another, almond intake was differentiated from walnut intake with 91% classification accuracy. CONCLUSIONS Our findings reveal promise in utilizing fecal metabolites as objective complements to certain self-reported food intake estimates. Future research on other foods at different doses and dietary patterns is needed to identify biomarkers that can be applied in feeding study compliance and clinical settings.
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Affiliation(s)
- Leila M Shinn
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aditya Mansharamani
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David J Baer
- Beltsville Human Nutrition Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Janet A Novotny
- Beltsville Human Nutrition Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Craig S Charron
- Beltsville Human Nutrition Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Naiman A Khan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Kinesiology & Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruoqing Zhu
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hannah D Holscher
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Kinesiology & Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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18
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Player RA, Aguinaldo AM, Merritt BB, Maszkiewicz LN, Adeyemo OE, Forsyth ER, Verratti KJ, Chee BW, Grady SL, Bradburne CE. The META tool optimizes metagenomic analyses across sequencing platforms and classifiers. FRONTIERS IN BIOINFORMATICS 2023; 2:969247. [PMID: 36685333 PMCID: PMC9852826 DOI: 10.3389/fbinf.2022.969247] [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: 06/14/2022] [Accepted: 12/14/2022] [Indexed: 01/09/2023] Open
Abstract
A major challenge in the field of metagenomics is the selection of the correct combination of sequencing platform and downstream metagenomic analysis algorithm, or "classifier". Here, we present the Metagenomic Evaluation Tool Analyzer (META), which produces simulated data and facilitates platform and algorithm selection for any given metagenomic use case. META-generated in silico read data are modular, scalable, and reflect user-defined community profiles, while the downstream analysis is done using a variety of metagenomic classifiers. Reported results include information on resource utilization, time-to-answer, and performance. Real-world data can also be analyzed using selected classifiers and results benchmarked against simulations. To test the utility of the META software, simulated data was compared to real-world viral and bacterial metagenomic samples run on four different sequencers and analyzed using 12 metagenomic classifiers. Lastly, we introduce "META Score": a unified, quantitative value which rates an analytic classifier's ability to both identify and count taxa in a representative sample.
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Affiliation(s)
- Robert A. Player
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States
| | | | - Brian B. Merritt
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States
| | - Lisa N. Maszkiewicz
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States
| | | | - Ellen R. Forsyth
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States
| | | | - Brant W. Chee
- Division of General Internal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States,Armstrong Institute for Patient Safety and Quality, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sarah L. Grady
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States
| | - Christopher E. Bradburne
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States,*Correspondence: Christopher E. Bradburne,
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19
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Lim SW, Jeon JH, Lim B, Jang MJ, Kim DH, Kim CH, Kim JM. Blood transcriptomic differences in the immune response under stressful environmental according to stocking density in pigs. J Anim Sci 2023; 101:skad336. [PMID: 37798138 PMCID: PMC10655785 DOI: 10.1093/jas/skad336] [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: 06/20/2023] [Accepted: 10/05/2023] [Indexed: 10/07/2023] Open
Abstract
The implementation of animal welfare in the pig industry is becoming a global trend, and welfare can be improved through livestock management. In modern and intensive farming systems, it has become important to find a reasonable compromise between stocking density and productivity. The simultaneous detection of behavioral and physiological parameters is helpful when considering welfare levels for stocking density. This study aimed to confirm the effect of stocking density through transcriptome linkage. A comparison of three groups according to stocking density (low density, eight pigs and 1.0 m2 per head; normal density, eight pigs and 0.8 m2 per head; and high density, eight pigs and 0.6 m2 per head) was performed, and their transcriptomic changes were observed using the RNA-Seq method. Differentially expressed genes were identified for each comparison group (low density vs. normal density, 95 upregulated genes and 112 downregulated genes; high density vs. normal density, 133 upregulated genes and 217 downregulated genes; and high density vs. low density, 245 upregulated genes and 237 downregulated genes). Biological mechanisms according to stocking density were identified through functional annotation. T-cell differentiation and immune disease pathway enriched in the high-density group caused immune imbalance through dysregulated T-cell signaling. Moreover, oxidative stress, together with DNA damage, can lead to high susceptibility to disease. Our study confirmed the biological mechanisms through immunological expression patterns according to stocking density. The study results are expected to provide comprehensive insight into systematic operation strategies considering stocking density and biomarkers for use in welfare evaluation.
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Affiliation(s)
- Seok-Won Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Jung Hwan Jeon
- Animal Welfare Research Team, National Institute of Animal Science, Rural Development Agriculture, Wanju 55365, Republic of Korea
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Min-Jae Jang
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
| | - Doo-Hwan Kim
- Division of Animal Science, Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Chan Ho Kim
- Animal Welfare Research Team, National Institute of Animal Science, Rural Development Agriculture, Wanju 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do 17546, Republic of Korea
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20
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The impact of modifier genes on cone-rod dystrophy heterogeneity: An explorative familial pilot study and a hypothesis on neurotransmission impairment. PLoS One 2022; 17:e0278857. [PMID: 36490268 PMCID: PMC9733859 DOI: 10.1371/journal.pone.0278857] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Cone-rod dystrophies (CORDs) are a heterogeneous group of inherited retinopathies (IRDs) with more than 30 already known disease-causing genes. Uncertain phenotypes and extended range of intra- and interfamilial heterogenicity make still difficult to determine a precise genotype-phenotype correlation. Here, we used a next-generation sequencing approach to study a Sicilian family with a suspected form of CORD. Affected family members underwent ophthalmological examinations and a proband, blind from 50 years, underwent whole genome and exome sequencing. Variant analysis was enriched by pathway analysis and relevant variants were, then, investigated in other family members and in 100 healthy controls from Messina. CORD diagnosis with an intricate pattern of symptoms was confirmed by ophthalmological examinations. A total of about 50,000 variants were identified in both proband's genome and exome. All affected family members presented specific genotypes mainly determined by mutated GUCY2D gene, and different phenotypical traits, mainly related to focus and color perception. Thus, we looked for possible modifier genes. According to relationship with GUCY2D, predicted functional effects, eye localization, and ocular disease affinity, only 9 variants, carried by 6 genes (CACNG8, PAX2, RXRG, CCDC175, PDE4DIP and LTF), survived the filtering. These genes encode key proteins involved in cone development and survival, and retina neurotransmission. Among analyzed variants, CACNG8c.*6819A>T and the new CCDC175 c.76C>T showed extremely low frequency in the control group, suggesting a key role on disease phenotypes. Such discovery could enforce the role of modifier genes into CORD onset/progression, contributing to improve diagnostic test towards a better personalized medicine.
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21
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Du M, Hou Z, Liu L, Xuan Y, Chen X, Fan L, Li Z, Xu B. 1Progress, applications, challenges and prospects of protein purification technology. Front Bioeng Biotechnol 2022; 10:1028691. [PMID: 36561042 PMCID: PMC9763899 DOI: 10.3389/fbioe.2022.1028691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Protein is one of the most important biological macromolecules in life, which plays a vital role in cell growth, development, movement, heredity, reproduction and other life activities. High quality isolation and purification is an essential step in the study of the structure and function of target proteins. Therefore, the development of protein purification technologies has great theoretical and practical significance in exploring the laws of life activities and guiding production practice. Up to now, there is no forthcoming method to extract any proteins from a complex system, and the field of protein purification still faces significant opportunities and challenges. Conventional protein purification generally includes three steps: pretreatment, rough fractionation, and fine fractionation. Each of the steps will significantly affect the purity, yield and the activity of target proteins. The present review focuses on the principle and process of protein purification, recent advances, and the applications of these technologies in the life and health industry as well as their far-reaching impact, so as to promote the research of protein structure and function, drug development and precision medicine, and bring new insights to researchers in related fields.
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Affiliation(s)
- Miao Du
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Zhuru Hou
- Science and Technology Centre, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
| | - Yan Xuan
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Xiaocong Chen
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Lei Fan
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Zhuoxi Li
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
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22
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Su XZ, Wu J, Xu F, Pattaradilokrat S. Genetic mapping of determinants in drug resistance, virulence, disease susceptibility, and interaction of host-rodent malaria parasites. Parasitol Int 2022; 91:102637. [PMID: 35926693 PMCID: PMC9452477 DOI: 10.1016/j.parint.2022.102637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/31/2022]
Abstract
Genetic mapping has been widely employed to search for genes linked to phenotypes/traits of interest. Because of the ease of maintaining rodent malaria parasites in laboratory mice, many genetic crosses of rodent malaria parasites have been performed to map the parasite genes contributing to malaria parasite development, drug resistance, host immune response, and disease pathogenesis. Drs. Richard Carter, David Walliker, and colleagues at the University of Edinburgh, UK, were the pioneers in developing the systems for genetic mapping of malaria parasite traits, including characterization of genetic markers to follow the inheritance and recombination of parasite chromosomes and performing the first genetic cross using rodent malaria parasites. Additionally, many genetic crosses of inbred mice have been performed to link mouse chromosomal loci to the susceptibility to malaria parasite infections. In this chapter, we review and discuss past and recent advances in genetic marker development, performing genetic crosses, and genetic mapping of both parasite and host genes. Genetic mappings using models of rodent malaria parasites and inbred mice have contributed greatly to our understanding of malaria, including parasite development within their hosts, mechanism of drug resistance, and host-parasite interaction.
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Affiliation(s)
- Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Fangzheng Xu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
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23
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Segura-Alabart N, Serratosa F, Gómez S, Fernández A. Nonunique UPGMA clusterings of microsatellite markers. Brief Bioinform 2022; 23:6652780. [PMID: 35915053 PMCID: PMC9487649 DOI: 10.1093/bib/bbac312] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/15/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.
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Affiliation(s)
- Natàlia Segura-Alabart
- Departament d'Enginyeria Informática i Matemátiques, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007, Tarragona, Spain
| | - Francesc Serratosa
- Departament d'Enginyeria Informática i Matemátiques, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007, Tarragona, Spain
| | - Sergio Gómez
- Departament d'Enginyeria Informática i Matemátiques, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007, Tarragona, Spain
| | - Alberto Fernández
- Departament d'Enginyeria Quámica, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007, Tarragona, Spain
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24
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Yang Y, La TC, Gillman JD, Lyu Z, Joshi T, Usovsky M, Song Q, Scaboo A. Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. FRONTIERS IN PLANT SCIENCE 2022; 13:938100. [PMID: 35968122 PMCID: PMC9372550 DOI: 10.3389/fpls.2022.938100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line ('Osage') with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ∼16.5 to ∼4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars, was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits.
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Affiliation(s)
- Yia Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Thang C. La
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Jason D. Gillman
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Columbia, MO, United States
| | - Zhen Lyu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
| | - Trupti Joshi
- Department of Health Management and Informatics, MU Institute of Data Science and Informatics and Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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25
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The Urobiome and Its Role in Overactive Bladder. Int Neurourol J 2022; 26:190-200. [PMID: 35468617 PMCID: PMC9537439 DOI: 10.5213/inj.2244016.008] [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: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.
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26
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Grenni P. Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:687-714. [PMID: 35191071 DOI: 10.1002/etc.5289] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 11/11/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
River ecosystems are very important parts of the water cycle and an excellent habitat, food, and drinking water source for many organisms, including humans. Antibiotics are emerging contaminants which can enter rivers from various sources. Several antibiotics and their related antibiotic resistance genes (ARGs) have been detected in these ecosystems by various research programs and could constitute a substantial problem. The presence of antibiotics and other resistance cofactors can boost the development of ARGs in the chromosomes or mobile genetic elements of natural bacteria in rivers. The ARGs in environmental bacteria can also be transferred to clinically important pathogens. However, antibiotics and their resistance genes are both not currently monitored by national or international authorities responsible for controlling the quality of water bodies. For example, they are not included in the contaminant list in the European Water Framework Directive or in the US list of Water-Quality Benchmarks for Contaminants. Although ARGs are naturally present in the environment, very few studies have focused on non-impacted rivers to assess the background ARG levels in rivers, which could provide some useful indications for future environmental regulation and legislation. The present study reviews the antibiotics and associated ARGs most commonly measured and detected in rivers, including the primary analysis tools used for their assessment. In addition, other factors that could enhance antibiotic resistance, such as the effects of chemical mixtures, the effects of climate change, and the potential effects of the coronavirus disease 2019 pandemic, are discussed. Environ Toxicol Chem 2022;41:687-714. © 2022 SETAC.
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Affiliation(s)
- Paola Grenni
- Water Research Institute, National Research Council of Italy, via Salaria km 29.300, Monterotondo, Rome, 00015, Italy
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27
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Wan X, Xie B, Sun H, Gu W, Wang C, Deng Q, Zhou S. Exosomes derived from M2 type tumor-associated macrophages promote osimertinib resistance in non-small cell lung cancer through MSTRG.292666.16-miR-6836-5p-MAPK8IP3 axis. Cancer Cell Int 2022; 22:83. [PMID: 35168607 PMCID: PMC8845243 DOI: 10.1186/s12935-022-02509-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background Osimertinib resistance limits the treatment of epidermal growth factor receptor-(EGFR)-mutated non-small-cell lung carcinoma (NSCLC). The mechanisms of osimertinib resistance need to be elucidated to determine alternative treatment strategies. This study explores the role of M2 type tumor-associated macrophage (TAM)-derived exosomal MSTRG.292666.16 in osimertinib resistance, and its related competing endogenous RNA (ceRNA) mechanism. Methods M2 type TAMs were induced with 200 ng/mL phorbol 12-myristate 13-acetate, 20 ng/mL IL-4 and IL-13, and M2 type macrophage markers were measured by RT-qPCR. Next, the exosomes were isolated and characterized. Tumor formation in nude mice was conducted using H1975 cells under different treatment conditions. Small RNA sequencing was performed on exosomes derived from sensitive and resistant plasma, and ceRNA networks were constructed. Fluorescence in situ hybridization was used to observe the localization of MSTRG.292666.16, and a ceRNA network (MSTRG.292666.16-miR-6836-5p-MAPK8IP3) was selected for further validation. Results M2 type TAMs, and M2 type TAM-derived exosomes were successfully induced and isolated. Nude mice results showed that M2 type TAM-derived exosomes and MSTRG.292666.16 overexpression significantly increased tumor volume after administration of osimertinib for 4 weeks. M2 type TAMs were found in the resistant plasma, and MSTRG.292666.16 localized in the cytoplasm of H1975 cells. In addition, the genes in the ceRNA networks were significantly enriched in eight GO terms and seven KEGG pathways, including the MAPK signaling pathway. Subsequently, the levels of MSTRG.292666.16 and MAPK8IP3 significantly increased in both resistant plasma-derived exosomes and M2 type TAM-derived exosomes, while miR-6836-5p levels were significantly reduced. Finally, MSTRG.292666.16, miR-6836-5p, and MAPK8IP3 were part of the same network. Conclusions M2 type TAM-derived exosomes promoted osimertinib resistance in NSCLC by regulating the MSTRG.292666.16/miR-6386-5p/MAPK8IP3 axis. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02509-x.
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Affiliation(s)
- Xiaoying Wan
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China.,Medical College of Tongji University, Shanghai, 200433, China
| | - Boxiong Xie
- Department of Thoracic, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Hui Sun
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China
| | - Weiqing Gu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China
| | - Chunyan Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China
| | - Qinfang Deng
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China.
| | - Songwen Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Yangpu District, Shanghai, 200433, China.
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28
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Ohmomo H, Harada S, Komaki S, Ono K, Sutoh Y, Otomo R, Umekage S, Hachiya T, Katanoda K, Takebayashi T, Shimizu A. DNA Methylation Abnormalities and Altered Whole Transcriptome Profiles after Switching from Combustible Tobacco Smoking to Heated Tobacco Products. Cancer Epidemiol Biomarkers Prev 2022; 31:269-279. [PMID: 34728466 PMCID: PMC9398167 DOI: 10.1158/1055-9965.epi-21-0444] [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: 04/07/2021] [Revised: 08/29/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The use of heated tobacco products (HTP) has increased exponentially in Japan since 2016; however, their effects on health remain a major concern. METHODS Tsuruoka Metabolome Cohort Study participants (n = 11,002) were grouped on the basis of their smoking habits as never smokers (NS), past smokers (PS), combustible tobacco smokers (CS), and HTP users for <2 years. Peripheral blood mononuclear cells were collected from 52 participants per group matched to HTP users using propensity scores, and DNA and RNA were purified from the samples. DNA methylation (DNAm) analysis of the 17 smoking-associated DNAm biomarker genes (such as AHRR, F2RL3, LRRN3, and GPR15), as well as whole transcriptome analysis, was performed. RESULTS Ten of the 17 genes were significantly hypomethylated in CS and HTP users compared with NS, among which AHRR, F2RL3, and RARA showed intermediate characteristics between CS and NS; nonetheless, AHRR expression was significantly higher in CS than in the other three groups. Conversely, LRRN3 and GPR15 were more hypomethylated in HTP users than in NS, and GPR15 expression was markedly upregulated in all the groups when compared with that in NS. CONCLUSIONS HTP users (switched from CS <2 years) display abnormal DNAm and transcriptome profiles, albeit to a lesser extent than the CS. However, because the molecular genetic effects of long-term HTP use are still unknown, long-term molecular epidemiologic studies are needed. IMPACT This study provides new insights into the molecular genetic effects on DNAm and transcriptome profiles in HTP users who switched from CS.
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Affiliation(s)
- Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Kanako Ono
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Ryo Otomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - So Umekage
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Kota Katanoda
- Division of Cancer Statistics Integration, National Cancer Center Research Institute, Chuo, Tokyo, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan.,Corresponding Author: Atsushi Shimizu, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate 028-3694, Japan. Phone: 81-19-651-5110, ext. 5473; E-mail:
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Jang MJ, Lim C, Lim B, Kim JM. Integrated multiple transcriptomes in oviductal tissue across the porcine oestrous cycle reveal functional roles in oocyte maturation and transport. J Anim Sci 2021; 100:6464098. [PMID: 34918099 DOI: 10.1093/jas/skab364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding the changes in the swine female reproductive system is important for solving issues related to reproductive failure and litter size. Elucidating the regulatory mechanisms of the natural oestrous cycle in the oviduct under non-fertilisation conditions can improve our understanding of its role in the reproductive system. Herein, whole transcriptome RNA sequencing of oviduct tissue samples was performed. The differentially expressed genes (DEGs) were identified for each time point relative to Day 0 and classified into three clusters based on their expression patterns. Clusters 1 and 2 included genes involved in the physiological changes through the oestrous cycle. Cluster 1 genes were mainly involved in PI3K-Akt signalling and steroid hormone biosynthesis pathways. Cluster 2 genes were involved in extracellular matrix-receptor interactions and protein digestion pathways. In Cluster 3, the DEGs were downregulated in the luteal phase; they were strongly associated with cell cycle, calcium signalling, and oocyte meiosis. The gene expression in the oviduct during the oestrous cycle influenced oocyte transport and fertilisation. Our findings provide a basis for successfully breeding pigs and elucidating the mechanisms underlying the changes in the pig oviduct during the oestrous cycle.
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Affiliation(s)
- Min-Jae Jang
- Functional Genomics and Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Chiwoong Lim
- Functional Genomics and Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Byeonghwi Lim
- Functional Genomics and Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun-Mo Kim
- Functional Genomics and Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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Zhou Z, Eichner C, Nilsen F, Jonassen I, Dondrup M. A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis). BMC Genomics 2021; 22:832. [PMID: 34789144 PMCID: PMC8600823 DOI: 10.1186/s12864-021-08054-7] [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: 05/03/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08054-7).
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Affiliation(s)
- Zhaoran Zhou
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Christiane Eichner
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Frank Nilsen
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Inge Jonassen
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
| | - Michael Dondrup
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway.
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [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] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Chitosan oligosaccharides packaged into rat adipose mesenchymal stem cells-derived extracellular vesicles facilitating cartilage injury repair and alleviating osteoarthritis. J Nanobiotechnology 2021; 19:343. [PMID: 34702302 PMCID: PMC8549296 DOI: 10.1186/s12951-021-01086-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023] Open
Abstract
Objectives This study aimed to investigate the roles of adipose mesenchymal stem cell (AMSC)-derived extracellular vesicles (EVs) binding with chitosan oligosaccharides (COS) in cartilage injury, as well as the related mechanisms. Results IL-1β treatment significantly inhibited the viability and migration of chondrocytes and enhanced cell apoptosis (P < 0.05), while chitosan oligosaccharides and extracellular vesicles-chitosan oligosaccharide conjugates (EVs-COS/EVs-COS conjugates) reversed the changes induced by IL-1β (P < 0.05), and the effects of extracellular vesicles-chitosan oligosaccharide conjugates were better than those of chitosan oligosaccharides (P < 0.05). After cartilage damage, IL-1β, OPN, and p53 were significantly upregulated, COL1A1, COL2A1, OCN, RUNX2, p-Akt/Akt, PI3K, c-Myc, and Bcl2 were markedly downregulated, and extracellular vesicles-chitosan oligosaccharide conjugates reversed the expression induced by cartilage injury. Through sequencing, 760 differentially expressed genes (DEGs) clustered into four expression patterns were associated with negative regulation of the canonical Wnt, PI3K-Akt, AMPK, and MAPK signaling pathways. Conclusion Extracellular vesicles-chitosan oligosaccharide conjugates may serve as a new cell-free biomaterial to facilitate cartilage injury repair and improve osteoarthritis. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-01086-x.
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Khalil AIS, Chattopadhyay A, Sanyal A. Analysis of Aneuploidy Spectrum From Whole-Genome Sequencing Provides Rapid Assessment of Clonal Variation Within Established Cancer Cell Lines. Cancer Inform 2021; 20:11769351211049236. [PMID: 34671179 PMCID: PMC8521761 DOI: 10.1177/11769351211049236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The revolution in next-generation sequencing (NGS) technology has allowed easy access and sharing of high-throughput sequencing datasets of cancer cell lines and their integrative analyses. However, long-term passaging and culture conditions introduce high levels of genomic and phenotypic diversity in established cell lines resulting in strain differences. Thus, clonal variation in cultured cell lines with respect to the reference standard is a major barrier in systems biology data analyses. Therefore, there is a pressing need for a fast and entry-level assessment of clonal variations within cell lines using their high-throughput sequencing data. RESULTS We developed a Python-based software, AStra, for de novo estimation of the genome-wide segmental aneuploidy to measure and visually interpret strain-level similarities or differences of cancer cell lines from whole-genome sequencing (WGS). We demonstrated that aneuploidy spectrum can capture the genetic variations in 27 strains of MCF7 breast cancer cell line collected from different laboratories. Performance evaluation of AStra using several cancer sequencing datasets revealed that cancer cell lines exhibit distinct aneuploidy spectra which reflect their previously-reported karyotypic observations. Similarly, AStra successfully identified large-scale DNA copy number variations (CNVs) artificially introduced in simulated WGS datasets. CONCLUSIONS AStra provides an analytical and visualization platform for rapid and easy comparison between different strains or between cell lines based on their aneuploidy spectra solely using the raw BAM files representing mapped reads. We recommend AStra for rapid first-pass quality assessment of cancer cell lines before integrating scientific datasets that employ deep sequencing. AStra is an open-source software and is available at https://github.com/AISKhalil/AStra.
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Affiliation(s)
| | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [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: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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Pedrosa MC, Lima L, Heleno S, Carocho M, Ferreira ICFR, Barros L. Food Metabolites as Tools for Authentication, Processing, and Nutritive Value Assessment. Foods 2021; 10:foods10092213. [PMID: 34574323 PMCID: PMC8465241 DOI: 10.3390/foods10092213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022] Open
Abstract
Secondary metabolites are molecules with unlimited applications that have been gaining importance in various industries and studied from many angles. They are mainly used for their bioactive capabilities, but due to the improvement of sensibility in analytical chemistry, they are also used for authentication and as a quality control parameter for foods, further allowing to help avoid food adulteration and food fraud, as well as helping understand the nutritional value of foods. This manuscript covers the examples of secondary metabolites that have been used as qualitative and authentication molecules in foods, from production, through processing and along their shelf-life. Furthermore, perspectives of analytical chemistry and their contribution to metabolite detection and general perspectives of metabolomics are also discussed.
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Wei L, Wang G, Yang C, Zhang Y, Chen Y, Zhong C, Li Q. MicroRNA-550a-3-5p controls the brain metastasis of lung cancer by directly targeting YAP1. Cancer Cell Int 2021; 21:491. [PMID: 34530822 PMCID: PMC8444378 DOI: 10.1186/s12935-021-02197-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/06/2021] [Indexed: 02/08/2023] Open
Abstract
Background This study aimed to explore the potential regulatory mechanisms of brain metastasis and to identify novel underlying targets of lung cancer with brain metastasis. Methods Exosomes were isolated from the plasma of lung cancer patients with or without brain metastasis and low or high metastatic lung cancer cells, and small RNA from plasma-derived exosomes were sequenced. Differentially expressed miRNAs (DE-miRNAs) were identified. Human brain microvascular endothelial cells (HBMECs) were transfected with miR-550a-3-5p mimics or inhibitors and exosomes. Cell viability, migration, and apoptosis/cycle were determined using Cell Counting Kit-8 (CCK-8), Transwell, and flow cytometry, respectively. Western blotting was used to measure the expression of the associated proteins. Finally, a dual-luciferase reporter gene assay was performed to confirm the miR-550a-3-5p target. Results Transmission electron microscopy, NanoSight, and western blotting showed that exosomes were successfully isolated and cell-derived exosomes could be taken up by HBMECs. Sequencing identified 22 DE-miRNAs which were enriched in the MAPK, chemokine, PPAR, and Wnt signaling pathways. MiR-550a-3-5p was significantly enriched in brain metastatic exosomes. Cellular experiments showed that miR-550a-3-5p and exosome enrichment significantly inhibited cell viability and migration, promoted apoptosis, and regulated the cell cycle of HBMECs compared with the controls (P < 0.05). Compared with the controls, high levels of both miR-550a-3-5p and exosomes markedly upregulated cleaved-PARP expression, but downregulated the expression of pRB, CDK6, YAP1, CTGF, and CYR61 (P < 0.05). Finally, YAP1 was confirmed to bind directly to miR-550a-3-5p. Conclusion Our results indicate that miR-550a-3-5p and YAP1 may be novel potential targets for controlling brain metastasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02197-z.
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Affiliation(s)
- Liang Wei
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Guangxue Wang
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Cheng Yang
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Yanfei Zhang
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Yiming Chen
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China
| | - Chunlong Zhong
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China.
| | - Qinchuan Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China. .,Department of Cardiothoracic Surgery, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China.
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Savadi S, Mangalassery S, Sandesh MS. Advances in genomics and genome editing for breeding next generation of fruit and nut crops. Genomics 2021; 113:3718-3734. [PMID: 34517092 DOI: 10.1016/j.ygeno.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/21/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India.
| | | | - M S Sandesh
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India
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Boev AS, Rakitko AS, Usmanov SR, Kobzeva AN, Popov IV, Ilinsky VV, Kiktenko EO, Fedorov AK. Genome assembly using quantum and quantum-inspired annealing. Sci Rep 2021; 11:13183. [PMID: 34162895 PMCID: PMC8222255 DOI: 10.1038/s41598-021-88321-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/09/2021] [Indexed: 02/05/2023] Open
Abstract
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the [Formula: see text]X 174 bacteriophage. Our results pave a way for a significant increase in the efficiency of solving bioinformatics problems with the use of quantum computing technologies and, in particular, quantum annealing might be an effective method. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.
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Affiliation(s)
- A S Boev
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | | | - S R Usmanov
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | - A N Kobzeva
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
| | - I V Popov
- Genotek ltd., Moscow, 105120, Russia
| | | | - E O Kiktenko
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - A K Fedorov
- Russian Quantum Center, Skolkovo, Moscow, 143025, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.
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Wang X, Li Z, Cui Y, Cui X, Chen C, Wang Z. Exosomes Isolated From Bone Marrow Mesenchymal Stem Cells Exert a Protective Effect on Osteoarthritis via lncRNA LYRM4-AS1-GRPR-miR-6515-5p. Front Cell Dev Biol 2021; 9:644380. [PMID: 34124036 PMCID: PMC8193855 DOI: 10.3389/fcell.2021.644380] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
Objectives The aim of this study was to investigate the effects of exosomes isolated from human bone marrow mesenchymal stem cells (BMSCs) on osteoarthritis (OA) and a competitive endogenous RNA (ceRNA) network. Methods Exosomes were isolated from human BMSCs and characterized by transmission electron microscopy (TEM), Nanosight (NTA), and western blotting. Chondrocytes were treated with interleukin-1β (IL-1β) and then transfected with exosomes. Cell viability and apoptosis were determined using Cell Counting Kit-8 (CCK-8) and flow cytometry, respectively. Cells with IL-1β and exosomes were sequenced, and differentially expressed lncRNAs (DE-lncRNAs) and miRNAs (DE-miRNAs) were identified. Thereafter, a ceRNA network (LYRM4-AS1-GRPR-miR-6515-5p) was chosen for further validation. Results TEM, NTA, and western blotting showed that exosomes were successfully isolated, and PKH67 staining showed that exosomes could be taken up by IL-1β-induced chondrocytes. Compared with the control group, IL-1β significantly decreased cell viability and promoted apoptosis (P < 0.05), while exosomes reversed the changes induced by IL-1β. For MMP3, AKT, and GRPR, IL-1β upregulated their expression, while exosomes downregulated their expression. For PTEN, there was no significant difference in PTEN expression between the control and IL-1β groups; however, exosomes markedly upregulated PTEN expression. By sequencing, 907 DE-lncRNAs and 25 DE-miRNAs were identified, and a ceRNA network was constructed. The dual-luciferase reporter gene indicated that LYRM4-AS1, miR-6515-5, and GRPR interacted with each other. The results of cell experiments showed that LYRM4-AS1 regulated the growth of IL-1β-induced chondrocytes by GRPR/miR-6515-5p. Conclusion Exosomes may alleviate OA inflammation by regulating the LYRM4-AS1/GRPR/miR-6515-5p signaling pathway.
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Affiliation(s)
- Xiuhui Wang
- Department of Orthopedics, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Zhuokai Li
- Department of Orthopedics, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Yin Cui
- Department of Orthopedics, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Xu Cui
- Department of Orthopedics, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Cheng Chen
- Department of Orthopedics, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Zhe Wang
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China
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LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ 2021; 9:e11359. [PMID: 34123583 PMCID: PMC8166240 DOI: 10.7717/peerj.11359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.
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Affiliation(s)
- Michael G LaMontagne
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Phi L Tran
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Alexander Benavidez
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
| | - Lisa D Morano
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
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The Full-Length Transcriptome Sequencing and Identification of Na +/H + Antiporter Genes in Halophyte Nitraria tangutorum Bobrov. Genes (Basel) 2021; 12:genes12060836. [PMID: 34071650 PMCID: PMC8227117 DOI: 10.3390/genes12060836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 01/20/2023] Open
Abstract
Nitraria tangutorum Bobrov is a halophyte that is resistant to salt and alkali and is widely distributed in northwestern China. However, its genome has not been sequenced, thereby limiting studies on this particular species. For species without a reference genome, the full-length transcriptome is a convenient and rapid way to obtain reference gene information. To better study N. tangutorum, we used PacBio single-molecule real-time technology to perform full-length transcriptome analysis of this halophyte. In this study, a total of 21.83 Gb of data were obtained, and 198,300 transcripts, 51,875 SSRs (simple sequence repeats), 55,574 CDS (coding sequence), and 74,913 lncRNAs (long non-coding RNA) were identified. In addition, using this full-length transcriptome, we identified the key Na+/H+ antiporter (NHX) genes that maintain ion balance in plants and found that these are induced to express under salt stress. The results indicate that the full-length transcriptome of N. tangutorum can be used as a database and be utilized in elucidating the salt tolerance mechanism of N. tangutorum.
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Citterio CE, Rivolta CM, Targovnik HM. Structure and genetic variants of thyroglobulin: Pathophysiological implications. Mol Cell Endocrinol 2021; 528:111227. [PMID: 33689781 DOI: 10.1016/j.mce.2021.111227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Thyroglobulin (TG) plays a main role in the biosynthesis of thyroid hormones (TH), and, thus, it is involved in a wide range of vital functions throughout the life cycle of all vertebrates. Deficiency of TH production due to TG genetic variants causes congenital hypothyroidism (CH), with devastating consequences such as intellectual disability and impaired growth if untreated. To this day, 229 variations in the human TG gene have been identified while the 3D structure of TG has recently appeared. Although TG deficiency is thought to be of autosomal recessive inheritance, the introduction of massive sequencing platforms led to the identification of a variety of monoallelic TG variants (combined with mutations in other thyroid gene products) opening new questions regarding the possibility of oligogenic inheritance of the disease. In this review we discuss remarkable advances in the understanding of the TG architecture and the pathophysiology of CH associated with TG defects, providing new insights for the management of congenital disorders as well as counseling benefits for families with a history of TG abnormalities. Moreover, we summarize relevant aspects of TH synthesis within TG and offer an updated analysis of animal and cellular models of TG deficiency for pathophysiological studies of thyroid dyshormonogenesis while highlighting perspectives for new investigations. All in all, even though there has been sustained progress in understanding the role of TG in thyroid pathophysiology during the past 50 years, functional characterization of TG variants remains an important area of study for future advancement in the field.
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Affiliation(s)
- Cintia E Citterio
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Carina M Rivolta
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina
| | - Héctor M Targovnik
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética/Cátedra de Genética, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Inmunología, Genética y Metabolismo (INIGEM), Buenos Aires, Argentina.
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Tillmar A, Fagerholm SA, Staaf J, Sjölund P, Ansell R. Getting the conclusive lead with investigative genetic genealogy - A successful case study of a 16 year old double murder in Sweden. Forensic Sci Int Genet 2021; 53:102525. [PMID: 33991867 DOI: 10.1016/j.fsigen.2021.102525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
On the morning of October 19, 2004, an eight-year-old boy and a 56-year-old woman were stabbed to death on an open street in the city of Linköping, Sweden. The perpetrator left his DNA at the crime scene, and after 15 years of various investigation efforts, including more than 9000 interrogations and mass DNA screening of more than 6000 men, there were still no clues about the identity of the unknown murderer. The successful application of investigative genetic genealogy (IGG) in the US raised the interest for this tool within the Swedish Police Authority. After legal consultations it was decided that IGG could be applied in this double murder case as a pilot case study. From extensive DNA analysis, including whole-genome sequencing and genotype imputation, DNA data sets were established and searched within both GEDmatch and FamilyTree DNA genealogy databases. A number of fairly distant relatives were found from which family trees were created. The genealogy work resulted in two candidates, two brothers, one of whom matched the crime scene samples by routine STR profiling. The suspect confessed the murders at the initial police hearing and was later convicted of the murders. In this paper we describe the successful application of an emerging technology. We disclose details of the DNA analyses which, due to the poor quality and low quantity of the DNA, required reiterative sequencing and genotype imputation efforts. The successful application of IGG in this double murder case exemplifies its applicability not only in the US but also in Europe. The pressure is now high on the involved authorities to establish IGG as a tool for cold case criminal investigations and for missing person identifications. There is, however, a continuous need to accommodate legal, social and ethical aspects as well.
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Affiliation(s)
- Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
| | | | - Jan Staaf
- Polisregion Öst, Swedish Police Authority, Linköping, Sweden
| | | | - Ricky Ansell
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
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Identification of functional cytochrome P450 and ferredoxin from Streptomyces sp. EAS-AB2608 by transcriptional analysis and their heterologous expression. Appl Microbiol Biotechnol 2021; 105:4177-4187. [PMID: 33944982 DOI: 10.1007/s00253-021-11304-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/21/2021] [Accepted: 04/18/2021] [Indexed: 01/02/2023]
Abstract
Bioconversion using microorganisms and their enzymes is an important tool in many industrial fields. The discovery of useful new microbial enzymes contributes to the development of industries utilizing bioprocesses. Streptomyces sp. EAS-AB2608, isolated from a soil sample collected in Japan, can convert the tetrahydrobenzotriazole CPD-1 (a selective positive allosteric modulator of metabotropic glutamate receptor 5) to its hydroxylated form at the C4-(R) position. The current study was performed to identify the genes encoding the enzymes involved in CPD-1 bioconversion and to verify their function. To identify gene products responsible for the conversion of CPD-1, we used RNA sequencing to analyze EAS-AB2608; from its 8333 coding sequences, we selected two genes, one encoding cytochrome P450 (easab2608_00800) and the other encoding ferredoxin (easab2608_00799), as encoding desirable gene products involved in the bioconversion of CPD-1. The validity of this selection was tested by using a heterologous expression approach. A bioconversion assay using genetically engineered Streptomyces avermitilis SUKA24 ∆saverm3882 ∆saverm7246 co-expressing the two selected genes (strain ES_SUKA_63) confirmed that these gene products had hydroxylation activity with respect to CPD-1, indicating that they are responsible for the conversion of CPD-1. Strain ES_SUKA_63 also showed oxidative activity toward other compounds and therefore might be useful not only for bioconversion of CPD-1 but also as a tool for synthesis of drug metabolites and in optimization studies of various pharmaceutical lead compounds. We expect that this approach will be useful for bridging the gap between the latest enzyme optimization technologies and conventional enzyme screening using microorganisms. KEY POINTS: • Genes easab2608_00800 (cyp) and easab2608_00799 (fdx) were selected by RNA-Seq. • Selection validity was evaluated by an engineered S. avermitilis expression system. • Strain ES_SUKA_63 showed oxidative activity toward CPD-1 and other compounds.
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Wernick AI, Walton RL, Soto-Beasley AI, Koga S, Ren Y, Heckman MG, Milanowski LM, Valentino RR, Kondru N, Uitti RJ, Cheshire WP, Wszolek ZK, Dickson DW, Ross OA. Investigating ELOVL7 coding variants in multiple system atrophy. Neurosci Lett 2021; 749:135723. [PMID: 33600908 DOI: 10.1016/j.neulet.2021.135723] [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: 11/13/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Multiple system atrophy (MSA) is a rare sporadic, progressive parkinsonism characterised by autonomic dysfunction. A recent genome-wide association study reported an association at the Elongation of Very Long Fatty Acids Protein 7 (ELOVL7) locus with MSA risk. In the current study four independent and unrelated cohorts were assessed, consisting of pathologically confirmed MSA cases, Parkinson's disease (PD) cases, and two unrelated, healthy control groups. All exons of ELOVL7 were sequenced in pathologically confirmed MSA cases; data for PPMI samples and Biobank controls was extracted from whole genome sequence. Coding variants in ELOVL7 were extremely rare, and we observed no significant association of ELOVL7 coding variants with risk of MSA.
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Affiliation(s)
- Anna I Wernick
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; School of Biological Sciences, University of Manchester, Manchester, UK; Queen Square Institute of Neurology, University College London, London, UK
| | - Ronald L Walton
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yingxue Ren
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Lukasz M Milanowski
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Naveen Kondru
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Mayo Graduate School Neuroscience Track, Mayo Clinic, Jacksonville, FL, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.
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46
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Dias CAR, Santos Júnior JE, Pinto CM, Santos FR, Perini FA. Mitogenomics of
Didelphis
(Mammalia; Didelphimorphia; Didelphidae) and insights into character evolution in the genus. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cayo Augusto Rocha Dias
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - José Eustáquio Santos Júnior
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Christian Miguel Pinto
- Departamento de Biologia Facultad de Ciencias Escuela Politécnica Nacional Quito Ecuador
| | - Fabrício Rodrigues Santos
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Fernando Araújo Perini
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
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47
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Fader KA, Zhang J, Menetski JP, Thadhani RI, Antman EM, Friedman GS, Ramaiah SK, Vaidya VS. A Biomarker-Centric Approach to Drug Discovery and Development: Lessons Learned from the Coronavirus Disease 2019 Pandemic. J Pharmacol Exp Ther 2021; 376:12-20. [PMID: 33115823 PMCID: PMC11046728 DOI: 10.1124/jpet.120.000204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 11/22/2022] Open
Abstract
Faced with the health and economic consequences of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the biomedical community came together to identify, diagnose, prevent, and treat the novel disease at breathtaking speeds. The field advanced from a publicly available viral genome to a commercialized globally scalable diagnostic biomarker test in less than 2 months, and first-in-human dosing with vaccines and repurposed antivirals followed shortly thereafter. This unprecedented efficiency was driven by three key factors: 1) international multistakeholder collaborations, 2) widespread data sharing, and 3) flexible regulatory standards tailored to meet the urgency of the situation. Learning from the remarkable success achieved during this public health crisis, we are proposing a biomarker-centric approach throughout the drug development pipeline. Although all therapeutic areas would benefit from end-to-end biomarker science, efforts should be prioritized to areas with the greatest unmet medical needs, including neurodegenerative diseases, chronic lower respiratory diseases, metabolic disorders, and malignant neoplasms. SIGNIFICANCE STATEMENT: Faced with the unprecedented threat of the severe acute respiratory syndrome coronavirus 2 pandemic, the biomedical community collaborated to develop a globally scalable diagnostic biomarker (viral DNA) that catalyzed therapeutic development at breathtaking speeds. Learning from this remarkable efficiency, we propose a multistakeholder biomarker-centric approach to drug development across therapeutic areas with unmet medical needs.
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Affiliation(s)
- Kelly A Fader
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Jiangwei Zhang
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Joseph P Menetski
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Ravi I Thadhani
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Elliott M Antman
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Gary S Friedman
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Shashi K Ramaiah
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
| | - Vishal S Vaidya
- Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts (K.A.F., J.Z., G.S.F., S.K.R., V.S.V.); Foundation for the National Institutes of Health, Bethesda, Maryland (J.P.M.); Mass General Brigham, Boston, Massachusetts (R.I.T.); and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (E.M.A.)
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Abstract
Protein Biotechnology is an exciting and fast- growing area of research, with numerous industrial applications. The growing demand for developing efficient and rapid protein purification methods is driving research and growth in this area. Advances and progress in the techniques and methods of protein purification have been such that one can reasonably expect that any protein of a given order of stability may be purified to currently acceptable standards of homogeneity. However, protein manufacturing cost remains extremely high, with downstream processing constituting a substantial proportion of the overall cost. Understanding of the methods and optimization of the experimental conditions have become critical to the manufacturing industry in order to minimize production costs while satisfying the quality as well as all regulatory requirements. New purification processes exploiting specific, effective and robust methods and chromatographic materials are expected to guide the future of the protein purification market.
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Krokidis MG. Biomarker-Driven Analysis Using High-Throughput Approaches in Neuroinflammation and Neurodegenerative Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1339:51-58. [DOI: 10.1007/978-3-030-78787-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Qiu YL, Zheng H, Devos A, Selby H, Gevaert O. A meta-learning approach for genomic survival analysis. Nat Commun 2020; 11:6350. [PMID: 33311484 PMCID: PMC7733508 DOI: 10.1038/s41467-020-20167-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
RNA sequencing has emerged as a promising approach in cancer prognosis as sequencing data becomes more easily and affordably accessible. However, it remains challenging to build good predictive models especially when the sample size is limited and the number of features is high, which is a common situation in biomedical settings. To address these limitations, we propose a meta-learning framework based on neural networks for survival analysis and evaluate it in a genomic cancer research setting. We demonstrate that, compared to regular transfer-learning, meta-learning is a significantly more effective paradigm to leverage high-dimensional data that is relevant but not directly related to the problem of interest. Specifically, meta-learning explicitly constructs a model, from abundant data of relevant tasks, to learn a new task with few samples effectively. For the application of predicting cancer survival outcome, we also show that the meta-learning framework with a few samples is able to achieve competitive performance with learning from scratch with a significantly larger number of samples. Finally, we demonstrate that the meta-learning model implicitly prioritizes genes based on their contribution to survival prediction and allows us to identify important pathways in cancer.
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Affiliation(s)
- Yeping Lina Qiu
- Department of Electrical Engineering, Stanford University, Stanford, USA
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA
| | - Hong Zheng
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA
| | - Arnout Devos
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Heather Selby
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, USA.
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