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de Castro Costa É, Bastos LS, Gomes TG, Miller RNG. Reference genes for RT-qPCR analysis in Musa acuminata genotypes contrasting in resistance to Fusarium oxysporum f. sp. cubense subtropical race 4. Sci Rep 2024; 14:16578. [PMID: 39020014 PMCID: PMC11255279 DOI: 10.1038/s41598-024-67538-0] [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: 06/06/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
Banana (Musa spp.) is the most widely consumed fruit globally. Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is a highly threatening disease to banana production. Resistance genes to Foc exist in wild Musa genotypes such as Musa acuminata subsp. burmannicoides var. Calcutta 4. Whilst real-time PCR (RT-qPCR) is appropriate for accurate analysis of gene expression in pathways involved in host defence responses, reference genes with stable expression under specific biotic stress conditions and host tissue types are necessary for normalization of sample variation. In this context, the stability in potential host reference genes ACT1, APT, EF1α, GAPDH, αTUB, RAN, UBIQ1, UBIQ2, βTUB1, βTUB3, L2 and ACTA1 was evaluated in total RNA samples from root tissues in Calcutta 4 (resistant) and Musa sp. cultivar Prata-anã (susceptible) extracted during interaction with Foc subtropical race 4 (STR4). Expression stability was calculated using the algorithms geNorm, NormFinder and BestKeeper. βTUB3 and L2 were identified as the most stable in Calcutta 4, with ACTA1 and GAPDH the most stable in Prata-anã. These reference genes for analysis of gene expression modulation in the Musa-Foc STR4 pathosystem are fundamental for advancing understanding of host defence responses to this important pathogen.
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Affiliation(s)
- Érica de Castro Costa
- Departamento de Fitopatologia, Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Lucas Santos Bastos
- Departamento de Fitopatologia, Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Taísa Godoy Gomes
- Departamento de Biologia Celular, Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Robert Neil Gerard Miller
- Departamento de Biologia Celular, Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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2
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Lee SJ, Kim Y, Kang K, Yoon H, Kang J, Cho SH, Paek NC. Rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE interacts with OsCRY2 and promotes flowering by upregulating Early heading date 1. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39012205 DOI: 10.1111/pce.15046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024]
Abstract
Flowering time is a crucial adaptive response to seasonal variation in plants and is regulated by environmental cues such as photoperiod and temperature. In this study, we demonstrated the regulatory function of rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE (OsCIBL1) in flowering time. Overexpression of OsCIB1L promoted flowering, whereas the oscib1l knockout mutation did not alter flowering time independent of photoperiodic conditions. Cryptochromes (CRYs) are blue light photoreceptors that enable plants to sense photoperiodic changes. OsCIBL1 interacted with OsCRY2, a member of the rice CRY family (OsCRY1a, OsCRY1b, and OsCRY2), and bound to the Early heading date 1 (Ehd1) promoter, activating the rice-specific Ehd1-Heading date 3a/RICE FLOWERING LOCUS T 1 pathway for flowering induction. Dual-luciferase reporter assays showed that the OsCIBL1-OsCRY2 complex required blue light to induce Ehd1 transcription. Natural alleles resulting from nonsynonymous single nucleotide polymorphisms in OsCIB1L and OsCRY2 may contribute to the adaptive expansion of rice cultivation areas. These results expand our understanding of the molecular mechanisms controlling rice flowering and highlight the importance of blue light-responsive genes in the geographic distribution of rice.
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Affiliation(s)
- Sang-Ji Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yunjeong Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kiyoon Kang
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Hyeryung Yoon
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jinku Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sung-Hwan Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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3
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Wang H, Wang H, Pian H, Su F, Tang F, Chen D, Chen J, Wen Y, Le XC, Li Z. CRISPR/Cas13a-Responsive and RNA-Bridged DNA Hydrogel Capillary Sensor for Point-of-Care Detection of RNA. Anal Chem 2024. [PMID: 39001804 DOI: 10.1021/acs.analchem.4c02087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Disease diagnostics and surveillance increasingly highlight the importance of portable, cost-effective, and sensitive point-of-care (POC) detection of nucleic acids. Here, we report a CRISPR/Cas13a-responsive and RNA-bridged DNA hydrogel capillary sensor for the direct and visual detection of specific RNA with high sensitivity. The capillary sensor was simply prepared by loading RNA-cross-linking DNA hydrogel film (∼0.2 mm ± 0.02 mm) at the end of a capillary. When CRISPR/Cas13a specifically recognizes the target RNA, the RNA bridge in the hydrogel film is cleaved by the trans-cleavage activity of CRISPR/Cas13a, increasing the permeability of the hydrogel film. Different concentrations of target RNA activate different amounts of Cas13a, cleaving different amounts of the RNA bridge in the hydrogel and causing corresponding changes in the permeability of the hydrogel. Therefore, samples containing different amounts of the target RNA travel to different distances in the capillary. Visual reading of the distance provides quantitative detection of the RNA target without the need for any nucleic acid amplification or auxiliary equipment. The technique was successfully used for the determination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical nasopharyngeal (NP) swab and saliva samples. Easily quantifiable distance using a ruler eliminates the need for any optical or electrochemical detection equipment, making this assay potentially useful for POC and on-site applications.
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Affiliation(s)
- Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Junjie Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yongqiang Wen
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
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4
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Chao Z, Selivanovitch E, Kallitsis K, Lu Z, Pachaury A, Owens R, Daniel S. Recreating the biological steps of viral infection on a cell-free bioelectronic platform to profile viral variants of concern. Nat Commun 2024; 15:5606. [PMID: 38961055 PMCID: PMC11222515 DOI: 10.1038/s41467-024-49415-6] [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: 09/13/2023] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Viral mutations frequently outpace technologies used to detect harmful variants. Given the continual emergence of SARS-CoV-2 variants, platforms that can identify the presence of a virus and its propensity for infection are needed. Our electronic biomembrane sensing platform recreates distinct SARS-CoV-2 host cell entry pathways and reports the progression of entry as electrical signals. We focus on two necessary entry processes mediated by the viral Spike protein: virus binding and membrane fusion, which can be distinguished electrically. We find that closely related variants of concern exhibit distinct fusion signatures that correlate with trends in cell-based infectivity assays, allowing us to report quantitative differences in their fusion characteristics and hence their infectivity potentials. We use SARS-CoV-2 as our prototype, but we anticipate that this platform can extend to other enveloped viruses and cell lines to quantifiably assess virus entry.
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Affiliation(s)
- Zhongmou Chao
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 124 Olin Hall, Ithaca, NY, 14853, USA
| | - Ekaterina Selivanovitch
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 124 Olin Hall, Ithaca, NY, 14853, USA
| | - Konstantinos Kallitsis
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr., Cambridge, CB3 0AS, UK
| | - Zixuan Lu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr., Cambridge, CB3 0AS, UK
| | - Ambika Pachaury
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 124 Olin Hall, Ithaca, NY, 14853, USA
| | - Róisín Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr., Cambridge, CB3 0AS, UK
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 124 Olin Hall, Ithaca, NY, 14853, USA.
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5
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Liu X, Bu S, Zhou H, Xu Y, Hao Z, Li Z, Wan J. Fluorescence biosensor to detect microRNAs via integrating DNA hairpins transition mediated strand displacement amplification with primer exchange reaction. Bioorg Med Chem Lett 2024; 106:129774. [PMID: 38688438 DOI: 10.1016/j.bmcl.2024.129774] [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: 02/21/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/02/2024]
Abstract
Herein, we constructed a fluorescence biosensor for the ultra-sensitive analysis of microRNAs (miRNAs) by combining DNA hairpins transition triggered strand displacement amplification (DHT-SDA) with primer exchange reaction (PER). Target miRNA initiated DHT-SDA to facilitate the generation of multiple single-stranded DNA (ssDNA) as PER primer, which was extended into a long ssDNA. The biosensor is successfully utilized in detecting miRNAs with high sensitivity (limit of detection for miRNA-21 was 58 fM) and a good linear relationship between 100 nM and 100 fM. By simply changing the DNA hairpin sequence, the constructed biosensor can be extended to analyze another miRNAs. Moreover, the biosensor has the feasibility of detecting miRNAs in real samples with satisfactory accuracy and reliability. Therefore, the fluorescent biosensor has great application potential in clinical diagnosis.
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Affiliation(s)
- Xiaoyu Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Shengjun Bu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130022, China
| | - Hongyu Zhou
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yao Xu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zhuo Hao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zehong Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China.
| | - Jiayu Wan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
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6
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Wei Y, Shen D, Nicholaus R, Wang Y, Lukwambe B, Zhu J, Yang W, Zheng Z. Exogenous compound bacteria enhance the nutrient removal efficiency of integrated bioremediation systems: Functional genes and microorganisms play key roles. ENVIRONMENTAL RESEARCH 2024; 252:118864. [PMID: 38574987 DOI: 10.1016/j.envres.2024.118864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/16/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
With the continuous development of intensive mariculture, the application of the integrated bioremediation system of aquaculture wastewater (IBSAW) is increasingly promoted. However, the process and nutrients removal performance of the IBSAW need to be further optimized due to its immature technologies. In this study, exogenous compound bacteria (ECB) were added to IBSAW to investigate its pollutants removal efficiency and the relevant mechanisms. High-throughput sequencing and Geochip gene array were used to analyze the correlation between nutrients and bacteria, and the abundance of N and P cycling genes were quantified. Multivariable statistics, dimensionality reduction analysis, and network analysis were applied to explore the mechanisms of IBSAW operation. The results showed that the nutrients decreased significantly after adding ECB, with the brush treatment group significantly outperforming the ceramsite in removing NO3- and PO43-. Ceramsite has an advantage in removing NO2--N. The addition of ECB and different substrates significantly affected the composition of bacterial communities. The contents of nosZ and nirKS related to denitrification in the treatment groups were significantly higher than those in the control group, and the contents in the brush treatment group were significantly higher than that of ceramsite. The biomarkers Psychroserpens and Ruegeria on the biofilm of the brush treatment group were positively correlated with nirKS, while Mycobacterium, Erythrobacter and Paracoccus, Pseudohaliea in the ceramsite group were positively correlated with nirS and nirK, respectively. Therefore, it is speculated that the ECB significantly promoted the increase of denitrification bacteria by affecting the composition of bacterial communities, and the ECB combined with functional genera improved the efficiency of nutrients removal in the system. This study provided a reference for understanding the process and mechanism of nutrients removal, optimizing the wastewater purification technology of the IBSAW and improving the performance of the system.
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Affiliation(s)
- Yingzhen Wei
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Ding Shen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Regan Nicholaus
- Department of Natural Sciences, Mbeya University of Science and Technology, Mbeya, Tanzania
| | - Yangcai Wang
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315048, China
| | - Betina Lukwambe
- School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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7
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Hu L, Zhang XT, Zeng X, Xiong LX, Ai Q, Liu CJ, Yang WW, Wu Y, Guo X, Li GQ, Liu L. ISAba1-mediated intrinsic chromosomal oxacillinase amplification confers carbapenem resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2024; 64:107258. [PMID: 38914142 DOI: 10.1016/j.ijantimicag.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 05/19/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Tandem amplification of carbapenemase genes increases gene copy number and enhances carbapenem resistance. These amplifications are often heterogeneous, transient, and located on plasmids, which also contribute to heteroresistance. Amplification of encoding genes is especially important for enzymes with low hydrolysis activity, which are often overlooked. Here, we reported an intrinsic oxacillinase oxaAb amplification flanked by ISAba1. The amplification is in the chromosome and contains up to 25 repeats. We provided genomic, transcriptomic, and proteomic evidence that the amplification resulted in oxacillinase overproduction. Notably, no point mutations of oxaAb were found during the amplification process. Strains of Acinetobacter baumannii with intrinsic amplified or external transformed ISAba1-oxaAb exhibited higher meropenem hydrolysis activity. Furthermore, the number of repeats in the amplification decreased gradually over a period of 21 d cultured with carbapenem withdrawal. However, upon re-exposure to meropenem, the ISAba1 flanked oxaAb responded rapidly, with repeat numbers reaching or exceeding pre-carbapenem withdrawal levels within 24 h. Taken together, these findings suggest that ISAba1-mediated gene amplification and overproduction of intrinsic low-activity oxacillinase oxaAb resulted in carbapenem resistance.
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Affiliation(s)
- Limiao Hu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiao-Tuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xi Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Lu-Xi Xiong
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Qi Ai
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Cai-Juan Liu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Wei-Wei Yang
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yuan Wu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.
| | - Xuemin Guo
- Meizhou People's Hospital, Meizhou, China; Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translation Research of Hakka Population, Meizhou, China.
| | - Guo-Qing Li
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China; Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, China.
| | - Logen Liu
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, China; Clinical Research Center, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.
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Noushahi HA, Khan AH, Khan HA, Kiedrzyński M, Akbar A, Shahzad R, Koerniati S, Alrefaei AF, Shu S. Optimizing liquid fermentation for Wolfiporia cocos: gene expression and biosynthesis of pachymic acid and mycelial biomass. Lett Appl Microbiol 2024; 77:ovae054. [PMID: 38866707 DOI: 10.1093/lambio/ovae054] [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: 10/30/2023] [Revised: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Wolfiporia cocos, a versatile fungus acclaimed for its nutritional and therapeutic benefits in Traditional Chinese Medicine, holds immense potential for pharmaceutical and industrial applications. In this study, we aimed to optimize liquid fermentation techniques and culture medium composition to maximize mycelial biomass (MB) yield, pachymic acid (PA) concentration, and overall PA production. Additionally, we investigated the molecular basis of our findings by quantifying the expression levels of genes associated with PA and MB biosynthesis using quantitative real-time polymerase chain reaction. Under the optimized fermentation conditions, significant results were achieved, with maximum MB reaching 6.68 g l-1, PA content peaking at 1.25 mg g-1, and a total PA yield of 4.76 g l-1. Notably, among the four examined genes, squalene monooxygenase, exhibited enhanced expression at 0.06 ratio under the optimized conditions. Furthermore, within the realm of carbohydrate-active enzymes, the glycoside hydrolases 16 family displayed elevated expression levels at 21 ratios, particularly during MB production. This study enhances understanding of genetic mechanism governing MB and PA production in W. cocos, highlighting the roles of squalene monooxygenase and glycoside hydrolases 16 carbohydrate-active enzymes.
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Affiliation(s)
- Hamza Armghan Noushahi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, Talca 3460000, Chile
| | - Aamir Hamid Khan
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Hamza Ali Khan
- Plant Breeding and Phenomic Centre, Faculty of Agricultural Sciences, University of Talca, Talca 3460000, Chile
| | - Marcin Kiedrzyński
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Adnan Akbar
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland
| | - Raheel Shahzad
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), KST-Cibinong, JI Raya Bogor KM46, Cibinong 16911, Indonesia
| | - Sri Koerniati
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), KST-Cibinong, JI Raya Bogor KM46, Cibinong 16911, Indonesia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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9
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Kofanova O, Paul S, Pexaras A, Bellora C, Petersons A, Schmitt M, Baker Berjaoui M, Qaoud Y, Kenk M, Wagner H, Fleshner N, Betsou F. Biospecimen Qualification in a Clinical Biobank of Urological Diseases. Biopreserv Biobank 2024; 22:257-267. [PMID: 37878356 DOI: 10.1089/bio.2022.0190] [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] [Indexed: 10/26/2023] Open
Abstract
Development of novel biomarkers for diagnosis of disease and assessment of treatment efficacy utilizes a wide range of biospecimens for discovery research. The fitness of biospecimens for the purpose of biomarker development depends on the clinical characteristics of the donor and on a number of critical and potentially uncontrolled pre-analytical variables. Pre-analytical factors influence the reliability of the biomarkers to be analyzed and can seriously impact analytic outcomes. Sample quality stratification assays and tools can be utilized by biorepositories to minimize bias resulting from samples' inconsistent quality. In this study, we evaluated the quality of biobanked specimens by comparing analytical outcomes at 1, 5, and 10 years after collection. Our results demonstrate that currently available assays and tools can be used by biobank laboratories to support objective biospecimen qualification. We have established a workflow to monitor the quality of different types of biospecimens and, in this study, present the results of a qualification exercise applied to fluid samples and their derivatives in the context of urological diseases.
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Affiliation(s)
- Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Sangita Paul
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Achilleas Pexaras
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Camille Bellora
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Ala Petersons
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Margaux Schmitt
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Mohamad Baker Berjaoui
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Yazan Qaoud
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Miran Kenk
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Heidi Wagner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Neil Fleshner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
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10
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Lynch CRH, Fleming R, Curran JM. Developing an interpretation model for body fluid identification. Forensic Sci Int 2024; 359:112032. [PMID: 38688209 DOI: 10.1016/j.forsciint.2024.112032] [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: 02/27/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
Criminal investigations, particularly sexual assaults, frequently require the identification of body fluid type in addition to body fluid donor to provide context. In most cases this can be achieved by conventional methods, however, in certain scenarios, alternative molecular methods are required. An example of this is the detection of menstrual fluid and vaginal material, which are not able to be identified using conventional techniques. Endpoint reverse-transcription PCR (RT-PCR) is currently used for this purpose to amplify body fluid specific messenger RNA (mRNA) transcripts in forensic casework. Real-time quantitative reverse-transcription PCR (RT-qPCR) is a similar method but utilises fluorescent markers to generate quantitative results in the form of threshold cycle (Cq) values. Despite the uncertainty surrounding body fluid identification, most interpretation guidelines utilise categorical statements. Probabilistic modelling is more realistic as it reflects biological variation as well as the known performance of the method. This research describes the application of various machine learning models to single-source mRNA profiles obtained by RT-qPCR and assesses their performance. Multinomial logistic regression (MLR), Naïve Bayes (NB), and linear discriminant analysis (LDA) were used to discriminate between the following body fluid categories: saliva, circulatory blood, menstrual fluid, vaginal material, and semen. We identified that the performance of MLR was somewhat improved when the quantitative dataset of the original Cq values was used (overall accuracy of approximately 0.95) rather than presence/absence coded data (overall accuracy of approximately 0.94). This indicates that the quantitative information obtained by RT-qPCR amplification is useful in assigning body fluid class. Of the three classification methods, MLR performed the best. When we utilised receiver operating characteristic curves to observe performance by body fluid class, it was clear that all methods found difficulty in classifying menstrual blood samples. Future work will involve the modelling of body fluid mixtures, which are common in samples analysed as part of sexual assault investigations.
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Affiliation(s)
- Courtney R H Lynch
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, New Zealand; School of Chemistry, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Rachel Fleming
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, New Zealand
| | - James M Curran
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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11
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Liu R, Guo L, Zhao Y, Wu D, Yu J, Liu P. Study on multi-target effects of the novel HDAC6 inhibitor W5 on Aβ/Cu 2+-induced Alzheimer's disease model of rats. Brain Res 2024; 1832:148847. [PMID: 38442843 DOI: 10.1016/j.brainres.2024.148847] [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: 08/28/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Histone deacetylase 6 (HDAC6) is a key therapeutic target in neurodegenerative diseases such as Alzheimer's disease (AD), which has been demonstrated to play an essential role in memory function and microtubule-associated tau physiology. In this study, W5 was used to treat AD model rats induced by Aβ/Cu2+ to study the improving effect of W5 on learning and memory impairment in AD rats and its related mechanism, to provide the basis for the subsequent development of W5 as an anti-AD drug. Results showed that W5 could decrease the expression of Aβ, Tau, and p-Tau proteins in the hippocampus of AD rats to inhibit the formation of senile plaques and neurofibrillary tangles, down-regulate the expression of Bax mRNA and Caspase-3 mRNA, and up-regulate the expression of Bcl-2 mRNA to reduce the apoptosis of neuron cells, reverse the expression of TNF-α, IL-1β and IL-6 mRNA to regulate neuroinflammatory response in AD rat brain. W5 also could regulate the oxidative stress state of AD rats, and balance the neurotransmitter disorder in AD rats' brain tissue. Overall, W5 could recover the morphology of hippocampal neurons and improve the learning and memory dysfunction in AD rats by regulating multiple targets in AD rats, providing a promising therapeutic avenue for the treatment of AD.
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Affiliation(s)
- Ruihua Liu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Linli Guo
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanan Zhao
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Dan Wu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jiasi Yu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ping Liu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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12
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Naatz A, Yeo CT, Hogg N, Corbett JA. β-Cell-selective regulation of gene expression by nitric oxide. Am J Physiol Regul Integr Comp Physiol 2024; 326:R552-R566. [PMID: 38586887 DOI: 10.1152/ajpregu.00240.2023] [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: 10/31/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Nitric oxide is produced at low micromolar levels following the induction of inducible nitric oxide synthase (iNOS) and is responsible for mediating the inhibitory actions of cytokines on glucose-stimulated insulin secretion by islets of Langerhans. It is through the inhibition of mitochondrial oxidative metabolism, specifically aconitase and complex 4 of the electron transport chain, that nitric oxide inhibits insulin secretion. Nitric oxide also attenuates protein synthesis, induces DNA damage, activates DNA repair pathways, and stimulates stress responses (unfolded protein and heat shock) in β-cells. In this report, the time- and concentration-dependent effects of nitric oxide on the expression of six genes known to participate in the response of β-cells to this free radical were examined. The genes included Gadd45α (DNA repair), Puma (apoptosis), Hmox1 (antioxidant defense), Hsp70 (heat shock), Chop (UPR), and Ppargc1α (mitochondrial biogenesis). We show that nitric oxide stimulates β-cell gene expression in a narrow concentration range of ∼0.5-1 µM or levels corresponding to iNOS-derived nitric oxide. At concentrations greater than 1 µM, nitric oxide fails to stimulate gene expression in β-cells, and this is associated with the inhibition of mitochondrial oxidative metabolism. This narrow concentration range of responses is β-cell selective, as the actions of nitric oxide in non-β-cells (α-cells, mouse embryonic fibroblasts, and macrophages) are concentration dependent. Our findings suggest that β-cells respond to a narrow concentration range of nitric oxide that is consistent with the levels produced following iNOS induction, and that these concentration-dependent actions are selective for insulin-containing cells.
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Affiliation(s)
- Aaron Naatz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Chay Teng Yeo
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Neil Hogg
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
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13
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Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
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14
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Hermanova Z, Valihrach L, Kriska J, Maheta M, Tureckova J, Kubista M, Anderova M. The deletion of AQP4 and TRPV4 affects astrocyte swelling/volume recovery in response to ischemia-mimicking pathologies. Front Cell Neurosci 2024; 18:1393751. [PMID: 38818517 PMCID: PMC11138210 DOI: 10.3389/fncel.2024.1393751] [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: 02/29/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction Astrocytic Transient receptor potential vanilloid 4 (TRPV4) channels, together with Aquaporin 4 (AQP4), are suspected to be the key players in cellular volume regulation, and therefore may affect the development and severity of cerebral edema during ischemia. In this study, we examined astrocytic swelling/volume recovery in mice with TRPV4 and/or AQP4 deletion in response to in vitro ischemic conditions, to determine how the deletion of these channels can affect the development of cerebral edema. Methods We used three models of ischemia-related pathological conditions: hypoosmotic stress, hyperkalemia, and oxygenglucose deprivation (OGD), and observed their effect on astrocyte volume changes in acute brain slices of Aqp4-/-, Trpv4-/- and double knockouts. In addition, we employed single-cell RT-qPCR to assess the effect of TRPV4 and AQP4 deletion on the expression of other ion channels and transporters involved in the homeostatic functioning of astrocytes. Results Quantification of astrocyte volume changes during OGD revealed that the deletion of AQP4 reduces astrocyte swelling, while simultaneous deletion of both AQP4 and TRPV4 leads to a disruption of astrocyte volume recovery during the subsequent washout. Of note, astrocyte exposure to hypoosmotic stress or hyperkalemia revealed no differences in astrocyte swelling in the absence of AQP4, TRPV4, or both channels. Moreover, under ischemia-mimicking conditions, we identified two distinct subpopulations of astrocytes with low and high volumetric responses (LRA and HRA), and their analyses revealed that mainly HRA are affected by the deletion of AQP4, TRPV4, or both channels. Furthermore, gene expression analysis revealed reduced expression of the ion transporters KCC1 and ClC2 as well as the receptors GABAB and NMDA in Trpv4-/- mice. The deletion of AQP4 instead caused reduced expression of the serine/cysteine peptidase inhibitor Serpina3n. Discussion Thus, we showed that in AQP4 or TRPV4 knockouts, not only the specific function of these channels is affected, but also the expression of other proteins, which may modulate the ischemic cascade and thus influence the final impact of ischemia.
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Affiliation(s)
- Zuzana Hermanova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine CAS, Prague, Czechia
- Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Lukas Valihrach
- Department of Cellular Neurophysiology, Institute of Experimental Medicine CAS, Prague, Czechia
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czechia
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine CAS, Prague, Czechia
| | - Mansi Maheta
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czechia
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine CAS, Prague, Czechia
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Vestec, Czechia
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine CAS, Prague, Czechia
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15
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Thapa R, Afzal M, Goyal A, Gupta G, Bhat AA, Almalki WH, Kazmi I, Alzarea SI, Shahwan M, Kukreti N, Ali H, Dureja H, Kumar P, Singh TG, Kuppusamy G, Singh SK, Dua K. Exploring ncRNA-mediated regulation of EGFR signalling in glioblastoma: From mechanisms to therapeutics. Life Sci 2024; 345:122613. [PMID: 38582393 DOI: 10.1016/j.lfs.2024.122613] [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: 02/15/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Glioblastoma (GBM) is the most prevalent and deadly primary brain tumor type, with a discouragingly low survival rate and few effective treatments. An important function of the EGFR signalling pathway in the development of GBM is to affect tumor proliferation, persistence, and treatment resistance. Advances in molecular biology in the last several years have shown how important ncRNAs are for controlling a wide range of biological activities, including cancer progression and development. NcRNAs have become important post-transcriptional regulators of gene expression, and they may affect the EGFR pathway by either directly targeting EGFR or by modifying important transcription factors and downstream signalling molecules. The EGFR pathway is aberrantly activated in response to the dysregulation of certain ncRNAs, which has been linked to GBM carcinogenesis, treatment resistance, and unfavourable patient outcomes. We review the literature on miRNAs, circRNAs and lncRNAs that are implicated in the regulation of EGFR signalling in GBM, discussing their mechanisms of action, interactions with the signalling pathway, and implications for GBM therapy. Furthermore, we explore the potential of ncRNA-based strategies to overcome resistance to EGFR-targeted therapies, including the use of ncRNA mimics or inhibitors to modulate the activity of key regulators within the pathway.
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Affiliation(s)
- Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, U.P., India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, 7, United Arab Emirates
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Punjab, India
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
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16
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Bissonnette N, Brousseau JP, Ollier S, Byrne AS, Ibeagha-Awemu EM, Tahlan K. Systematic assessment of the reliability of quantitative PCR assays targeting IS900 for the detection of Mycobacterium avium ssp. paratuberculosis presence in animal and environmental samples. J Dairy Sci 2024:S0022-0302(24)00788-4. [PMID: 38754821 DOI: 10.3168/jds.2023-24566] [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: 12/18/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the bacterium responsible for causing Johne's Disease (JD), which is endemic to dairy cattle and also incriminated in the etiology of Crohn's disease. The difficulty in diagnosing asymptomatic cows for JD makes this disease hard to control. JD is considered a priority under the One Health approach to prevent the spread of the causative agent to humans. Environmental screening is a strategic approach aimed at identifying dairy herds with animals infected with MAP. It serves as the initial step toward implementing more intensive actions to control the disease. Quantitative polymerase chain reaction (qPCR) technology is widely used for diagnosis. Given that genome sequencing is now much more accessible than ever before, it is possible to target regions of the MAP genome that allow for the greatest diagnostic sensitivity and specificity. The aim of this study was to identify among the published qPCR assays targeting IS900 the more cost-effective options to detect MAP and to validate them in the diagnostic context of JD disease. MAP IS900 is a prime target because it is a multicopy genetic element. A total of 136 publications have reported on the use of IS900 qPCR assays over the past 3 decades. Among these records, 29 used the SYBR Green chemistry and TaqMan technology was used in 107 reports. Aside from the 9 reports using commercial assays, 72 TaqMan reports cited previously published work, leaving us with 27 TaqMan qPCR designs. Upon closer examination, 5 TaqMan designs contained mismatches in primer or probe sequences. Additionally, others exhibited high similarity to environmental microorganisms or non-MAP mycobacteria. We assessed the performance of 6 IS900 qPCR designs and their sensitivity when applied to clinical or environmental samples, which varied from 4 to 56 fold overall. Additionally, we provide recommendations for testing clinical and environmental samples, as certain strategies used previously should be avoided due to poor qPCR design (e.g., the presence of mismatches) or a lack of specificity.
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Affiliation(s)
- N Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8.
| | - J-P Brousseau
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - S Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - A S Byrne
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
| | - E M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada J1M 0C8
| | - K Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada A1C 5S7
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17
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Sen P, Zhang Z, Sakib S, Gu J, Li W, Adhikari BR, Motsenyat A, L'Heureux-Hache J, Ang JC, Panesar G, Salena BJ, Yamamura D, Miller MS, Li Y, Soleymani L. High-Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer-Antigen Recognition in Clinical Samples and Machine Learning. Angew Chem Int Ed Engl 2024; 63:e202400413. [PMID: 38458987 DOI: 10.1002/anie.202400413] [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: 01/07/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High-precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single-pot and single-step electrochemical method that uses real-time kinetic profiling of the interaction between a high-affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS-CoV-2 and Influenza A viruses as model viruses with specifically engineered high-affinity aptamers. Utilizing this technique to diagnose COVID-19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method.
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Affiliation(s)
- Payel Sen
- Department of Engineering Physics, McMaster University, Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Sadman Sakib
- Department of Engineering Physics, McMaster University, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Wantong Li
- Department of Engineering Physics, McMaster University, Canada
| | | | - Ariel Motsenyat
- Department of Integrated Biomedical Engineering and Health Sciences, McMaster University, Canada
| | | | - Jann C Ang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Gurpreet Panesar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | | | - Debora Yamamura
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
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18
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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [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: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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19
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Alencar-Silva T, de Barcelos SM, Silva-Carvalho A, Sousa MGDC, Rezende TMB, Pogue R, Saldanha-Araújo F, Franco OL, Boroni M, Zonari A, Carvalho JL. Senotherapeutic Peptide 14 Suppresses Th1 and M1 Human T Cell and Monocyte Subsets In Vitro. Cells 2024; 13:813. [PMID: 38786036 PMCID: PMC11120033 DOI: 10.3390/cells13100813] [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: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Inflammation contributes to the onset and exacerbation of numerous age-related diseases, often manifesting as a chronic condition during aging. Given that cellular senescence fosters local and systemic inflammation, senotherapeutic interventions could potentially aid in managing or even reducing inflammation. Here, we investigated the immunomodulatory effects of the senotherapeutic Peptide 14 (Pep 14) in human peripheral blood mononuclear cells (PBMCs), monocytes, and macrophages. We found that, despite failing to significantly influence T cell activation and proliferation, the peptide promoted a Th2/Treg gene expression and cytokine signature in PBMCs, characterized by increased expression of the transcription factors GATA3 and FOXP3, as well as the cytokines IL-4 and IL-10. These observations were partially confirmed through ELISA, in which we observed increased IL-10 release by resting and PHA-stimulated PBMCs. In monocytes from the U-937 cell line, Pep 14 induced apoptosis in lipopolysaccharide (LPS)-stimulated cells and upregulated IL-10 expression. Furthermore, Pep 14 prevented LPS-induced activation and promoted an M2-like polarization in U-937-derived macrophages, evidenced by decreased expression of M1 markers and increased expression of M2 markers. We also showed that the conditioned media from Pep 14-treated macrophages enhanced fibroblast migration, indicative of a functional M2 phenotype. Taken together, our findings suggest that Pep 14 modulates immune cell function towards an anti-inflammatory and regenerative phenotype, highlighting its potential as a therapeutic intervention to alleviate immunosenescence-associated dysregulation.
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Affiliation(s)
- Thuany Alencar-Silva
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
| | - Stefhani Martins de Barcelos
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
- Multidisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
| | - Amandda Silva-Carvalho
- Hematology and Stem Cell Laboratory, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, Brazil; (A.S.-C.)
| | - Mauricio Gonçalves da Costa Sousa
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
| | - Taia Maria Berto Rezende
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
- Dentistry Department, University of Brasília, Brasília 70910-900, Brazil
- Post-Graduation Program in Health Sciences, University of Brasília, Brasília 70910-900, Brazil
| | - Robert Pogue
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
| | - Felipe Saldanha-Araújo
- Hematology and Stem Cell Laboratory, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, Brazil; (A.S.-C.)
| | - Octávio Luiz Franco
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
- Centre of Proteomic Analyses and Biochemistry, Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília 71966-700, Brazil
- S-Inova Biotech, Biotechnology Program, Catholic University Dom Bosco, Campo Grande 79117-900, Brazil
- Molecular Pathology Program, University of Brasília, Brasília 70910-900, Brazil
| | - Mariana Boroni
- OneSkin, Inc., San Francisco, CA 94107, USA
- Bioinformatics and Computational Biology Lab, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20230-130, Brazil
| | - Alessandra Zonari
- Molecular Pathology Program, University of Brasília, Brasília 70910-900, Brazil
| | - Juliana Lott Carvalho
- Post-Graduation Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília 71966-700, Brazil (S.M.d.B.); (M.G.d.C.S.); (T.M.B.R.); (R.P.)
- Multidisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
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20
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Zhang X, Li Y, Wang Q, Jiang C, Shan Y, Liu Y, Ma C, Guo Q, Shi C. Three-way junction structure-mediated reverse transcription-free exponential amplification reaction for pathogen RNA detection. Anal Bioanal Chem 2024; 416:3161-3171. [PMID: 38558309 DOI: 10.1007/s00216-024-05264-2] [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: 01/29/2024] [Revised: 02/27/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Since RNA is an important biomarker of many infectious pathogens, RNA detection of pathogenic organisms is crucial for disease diagnosis and environmental and food safety. By simulating the base mismatch during DNA replication, this study presents a novel three-way junction structure-mediated reverse transcription-free exponential amplification reaction (3WJ-RTF-EXPAR) for the rapid and sensitive detection of pathogen RNA. The target RNA served as a switch to initiate the reaction by forming a three-way junction (3WJ) structure with the ex-trigger strand and the ex-primer strand. The generated trigger strand could be significantly amplified through EXPAR to open the stem-loop structure of the molecular beacon to emit fluorescence signal. The proofreading activity of Vent DNA polymerase, in combination with the unique structure of 2+1 bases at the 3'-end of the ex-primer strand, could enhance the role of target RNA as a reaction switch to reduce non-specific amplification and ensure excellent specificity to differentiate target pathogen from those causing similar symptoms. Furthermore, detection of target RNA showed a detection limit of 1.0×104 copies/mL, while the time consumption was only 20 min, outperforming qRT-LAMP and qRT-PCR, the most commonly used RNA detection methods in clinical practice. All those indicates the great application prospects of this method in clinical diagnostic.
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Affiliation(s)
- Xinguang Zhang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yang Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Qing Wang
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Chao Jiang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yuting Shan
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yao Liu
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Biological Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao University of Science and Technology, QingdaoQingdao, 266042, China
| | - Qunqun Guo
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China.
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China.
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, People's Republic of China.
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, People's Republic of China.
- Qingdao JianMa Gene Technology Co., Ltd, Qingdao, 266114, People's Republic of China.
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21
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Zhang K, Jiang Z, Li X, Wang D, Hong J. Enhancing simultaneous saccharification and co-fermentation of corncob by Kluyveromyces marxianus through overexpression of putative transcription regulator. BIORESOURCE TECHNOLOGY 2024; 399:130627. [PMID: 38522677 DOI: 10.1016/j.biortech.2024.130627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
Overexpression of a gene with unknown function in Kluyveromyces marxianus markedly improved tolerance to lignocellulosic biomass-derived inhibitors. This overexpression also enhanced tolerance to elevated temperatures, ethanol, and high concentrations of NaCl and glucose. Inhibitor degradation and transcriptome analyses related this K. marxianusMultiple Stress Resistance (KmMSR) gene to the robustness of yeast cells. Nuclear localization and DNA-binding domain analyses indicate that KmMsr is a putative transcriptional regulator. Overexpression of a mutant protein with deletion in the flexible region between amino acids 100 and 150 further enhanced tolerance to multiple inhibitors during fermentation, with ethanol production and productivity increasing by 36.31 % and 80.22 %, respectively. In simultaneous saccharification co-fermentation of corncob without detoxification, expression of KmMSR with the deleted flexible region improved ethanol production by 5-fold at 42 °C and 2-fold at 37 °C. Overexpression of the KmMSR mutant provides a strategy for constructing robust lignocellulosic biomass using strains.
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Affiliation(s)
- Kehui Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Ziyun Jiang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Xingjiang Li
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, Anhui, China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China; Hefei National Laboratory for Physical Science at the Microscale, Hefei 230026, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, Anhui, China.
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22
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Rashid Z, Nabi A, Nabi N, Lateef I, Nisa Q, Fayaz T, Gulzar G, Bashir A, Shah MD, Zargar SM, Khan I, Nahvi AI, Itoo H, Shah RA, Padder BA. Selection of stable reference genes for qPCR expression of Colletotrichum lindemuthianum, the bean anthracnose pathogen. Fungal Biol 2024; 128:1771-1779. [PMID: 38796261 DOI: 10.1016/j.funbio.2024.03.008] [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: 01/04/2024] [Revised: 02/10/2024] [Accepted: 03/19/2024] [Indexed: 05/28/2024]
Abstract
Phaseolus vulgaris L., commonly known as the common bean, is a highly nutritious crop often called the "poor man's meat". However, it is susceptible to various diseases throughout the cropping season, with anthracnose caused by Colletotrichum lindemuthianum being a significant threat that leads to substantial losses. There is still a lack of understanding about the molecular basis of C. lindemuthianum pathogenicity. The first step in understanding this is to identify pathogenicity genes that express more during infection of common beans. A reverse transcription quantitative real-time PCR (qPCR) method can be used for virulence gene expression. However, this approach requires selecting appropriate reference genes to normalize relative gene expression data. Currently, there is no reference gene available for C. lindemuthianum. In this study, we selected eight candidate reference genes from the available genome of C. lindemuthianum to bridge the gap. These genes were ACT (Actin), β-tub (β-tubulin), EF (Elongation Factor), Cyt C (Cytochrome C), His H3 (Histone H3), CHS1 (Chitin synthetase), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and abfA (Alpha-l-Arabinofuranosidase A). The primers for these candidate reference genes were able to amplify cDNA only from the pathogen, demonstrating their specificity. The qPCR efficiency of the primers ranged from 80% to 103%. We analyzed the stability of gene expression in C. lindemuthianum by exposing the mycelium to nine different stress conditions. We employed algorithms, such as GeNorm, NormFinder, BestKeeper, and RefFinder tools, to identify the most stable gene. The analysis using these tools revealed that EF, GAPDH, and β-tub most stable genes, while ACT and CHS1 showed relatively low expression stability. A large number of potential effector genes have been identified through bioinformatics analysis in C. lindemuthianum. The stable genes for qPCR (EF and GAPDH) discovered in this study will aid the scientific community in determining the relative expression of C. lindemuthianum effector genes.
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Affiliation(s)
- Zainab Rashid
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Research Center for Residue and Quality Control Analysis, SKUAST-Kashmir, 190025, India
| | - Sajad M Zargar
- Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Imran Khan
- Division of Agricultural Statistics, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Afsah Iqbal Nahvi
- Extension Training Centre, Malangpora, Pulwama, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - H Itoo
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rafiq A Shah
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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23
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James DW, Quintela M, Lucini L, Alkafri NK, Healey GD, Younas K, Bunkheila A, Margarit L, Francis LW, Gonzalez D, Conlan RS. Homeobox regulator Wilms Tumour 1 is displaced by androgen receptor at cis-regulatory elements in the endometrium of PCOS patients. Front Endocrinol (Lausanne) 2024; 15:1368494. [PMID: 38745948 PMCID: PMC11091321 DOI: 10.3389/fendo.2024.1368494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Decidualisation, the process whereby endometrial stromal cells undergo morphological and functional transformation in preparation for trophoblast invasion, is often disrupted in women with polycystic ovary syndrome (PCOS) resulting in complications with pregnancy and/or infertility. The transcription factor Wilms tumour suppressor 1 (WT1) is a key regulator of the decidualization process, which is reduced in patients with PCOS, a complex condition characterized by increased expression of androgen receptor in endometrial cells and high presence of circulating androgens. Using genome-wide chromatin immunoprecipitation approaches on primary human endometrial stromal cells, we identify key genes regulated by WT1 during decidualization, including homeobox transcription factors which are important for regulating cell differentiation. Furthermore, we found that AR in PCOS patients binds to the same DNA regions as WT1 in samples from healthy endometrium, suggesting dysregulation of genes important to decidualisation pathways in PCOS endometrium due to competitive binding between WT1 and AR. Integrating RNA-seq and H3K4me3 and H3K27ac ChIP-seq metadata with our WT1/AR data, we identified a number of key genes involved in immune response and angiogenesis pathways that are dysregulated in PCOS patients. This is likely due to epigenetic alterations at distal enhancer regions allowing AR to recruit cofactors such as MAGEA11, and demonstrates the consequences of AR disruption of WT1 in PCOS endometrium.
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Affiliation(s)
- David W. James
- Swansea University Medical School, Swansea, United Kingdom
| | | | - Lisa Lucini
- Swansea University Medical School, Swansea, United Kingdom
| | | | | | - Kinza Younas
- Swansea University Medical School, Swansea, United Kingdom
- Swansea Bay University Health Board, Swansea, United Kingdom
| | - Adnan Bunkheila
- Swansea University Medical School, Swansea, United Kingdom
- Swansea Bay University Health Board, Swansea, United Kingdom
| | - Lavinia Margarit
- Swansea University Medical School, Swansea, United Kingdom
- Cwm Taf Morgannwg University Health Board, Bridgend, United Kingdom
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24
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Xu L, Chen Y, Ye J, Fan M, Weng G, Shen Y, Lin Z, Lin D, Xu Y, Feng S. Optical Nanobiosensor Based on Surface-Enhanced Raman Spectroscopy and Catalytic Hairpin Assembly for Early-Stage Lung Cancer Detection via Blood Circular RNA. ACS Sens 2024; 9:2020-2030. [PMID: 38602529 DOI: 10.1021/acssensors.3c02810] [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] [Indexed: 04/12/2024]
Abstract
Lung cancer has become the leading cause of cancer-related deaths globally. However, early detection of lung cancer remains challenging, resulting in poor outcomes for the patients. Herein, we developed an optical biosensor integrating surface-enhanced Raman spectroscopy (SERS) with a catalyzed hairpin assembly (CHA) to detect circular RNA (circRNA) associated with tumor formation and progression (circSATB2). The signals of the Raman reporter were considerably enhanced by generating abundant SERS "hot spots" with a core-shell nanoprobe and 2D SERS substrate with calibration capabilities. This approach enabled the sensitive (limit of detection: 0.766 fM) and reliable quantitative detection of the target circRNA. Further, we used the developed biosensor to detect the circRNA in human serum samples, revealing that patients with lung cancer had higher circRNA concentrations than healthy subjects. Moreover, we characterized the unique circRNA concentration profiles of the early stages (IA and IB) and subtypes (IA1, IA2, and IA3) of lung cancer. These results demonstrate the potential of the proposed optical sensing nanoplatform as a liquid biopsy and prognostic tool for the early screening of lung cancer.
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Affiliation(s)
- Luyun Xu
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Yuanmei Chen
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, PR China
| | - Jianqing Ye
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Min Fan
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Guibin Weng
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, PR China
| | - Yongshi Shen
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, PR China
| | - Zhizhong Lin
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, PR China
| | - Duo Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Yuanji Xu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, PR China
| | - Shangyuan Feng
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
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25
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Kaur G, Tintelott M, Suranglikar M, Masurier A, Vu XT, Gines G, Rondelez Y, Ingebrandt S, Coffinier Y, Pachauri V, Vlandas A. Time-encoded electrical detection of trace RNA biomarker by integrating programmable molecular amplifier on chip. Biosens Bioelectron 2024; 257:116311. [PMID: 38677018 DOI: 10.1016/j.bios.2024.116311] [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: 12/31/2023] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
One of the serious challenges facing modern point-of-care (PoC) molecular diagnostic platforms relate to reliable detection of low concentration biomarkers such as nucleic acids or proteins in biological samples. Non-specific analyte-receptor interactions due to competitive binding in the presence of abundant molecules, inefficient mass transport and very low number of analyte molecules in sample volume, in general pose critical hurdles for successful implementation of such PoC platforms for clinical use. Focusing on these specific challenges, this work reports a unique PoC biosensor that combines the advantages of nanoscale biologically-sensitive field-effect transistor arrays (BioFET-arrays) realized in a wafer-scale top-down nanofabrication as high sensitivity electrical transducers with that of sophisticated molecular programs (MPs) customized for selective recognition of analyte miRNAs and amplification resulting in an overall augmentation of signal transduction strategy. The MPs realize a programmable universal molecular amplifier (PUMA) in fluidic matrix on chip and provide a biomarker-triggered exponential release of small nucleic acid sequences easily detected by receptor-modified BioFETs. A common miRNA biomarker LET7a was selected for successful demonstration of this novel biosensor, achieving limit of detection (LoD) down to 10 fM and wide dynamic ranges (10 pM-10 nM) in complex physiological solutions. As the determination of biomarker concentration is implemented by following the electrical signal related to analyte-triggered PUMA in time-domain instead of measuring the threshold shifts of BioFETs, and circumvents direct hybridization of biomarkers at transducer surface, this new strategy also allows for multiple usage (>3 times) of the biosensor platform suggesting exceptional cost-effectiveness for practical use.
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Affiliation(s)
- Gurpreet Kaur
- Institut D'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR CNRS 8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq, Cedex, 59652, France
| | - Marcel Tintelott
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Mohit Suranglikar
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Antoine Masurier
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Xuan-Thang Vu
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Guillaume Gines
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, Ecole Supérieure de Physique et de Chimie Industrielles, PSL Research University, and CNRS, Paris, France
| | - Sven Ingebrandt
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Yannick Coffinier
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany
| | - Vivek Pachauri
- Institute of Materials in Electrical Engineering 1, RWTH Aachen University, Sommerfeldstrasse 24, 52074, Aachen, Germany.
| | - Alexis Vlandas
- Institut D'Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR CNRS 8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq, Cedex, 59652, France
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26
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Ji CH, Je HW, Kim H, Kang HS. Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications. Nat Prod Rep 2024; 41:672-699. [PMID: 38259139 DOI: 10.1039/d3np00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
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27
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Earl CC, Javier AJ, Richards AM, Markham LW, Goergen CJ, Welc SS. Functional cardiac consequences of β-adrenergic stress-induced injury in the mdx mouse model of Duchenne muscular dystrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589650. [PMID: 38659739 PMCID: PMC11042272 DOI: 10.1101/2024.04.15.589650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cardiomyopathy is the leading cause of death in Duchenne muscular dystrophy (DMD), however, in the mdx mouse model of DMD, the cardiac phenotype differs from that seen in DMD-associated cardiomyopathy. Although some have used pharmacologic stress to enhance the cardiac phenotype in the mdx model, many methods lead to high mortality, variable cardiac outcomes, and do not recapitulate the structural and functional cardiac changes seen in human disease. Here, we describe a simple and effective method to enhance the cardiac phenotype model in mdx mice using advanced 2D and 4D high-frequency ultrasound to monitor cardiac dysfunction progression in vivo. For our study, mdx and wild-type (WT) mice received daily low-dose (2 mg/kg/day) isoproterenol injections for 10 days. Histopathologic assessment showed that isoproterenol treatment increased myocyte injury, elevated serum cardiac troponin I levels, and enhanced fibrosis in mdx mice. Ultrasound revealed reduced ventricular function, decreased wall thickness, increased volumes, and diminished cardiac reserve in mdx mice compared to wild-type. Our findings highlight the utility of low-dose isoproterenol in mdx mice as a valuable model for exploring therapies targeting DMD-associated cardiac complications.
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Affiliation(s)
- Conner C. Earl
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette IN, USA
- Indiana University School of Medicine, IN, USA
| | - Areli J. Javier
- Musculoskeletal Health Sciences Program, Indiana University School of Medicine, Indianapolis, IN USA
| | - Alyssa M. Richards
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette IN, USA
| | - Larry W. Markham
- Division of Pediatric Cardiology, Riley Children’s Hospital at Indiana University Health, Indiana University School of Medicine, Indianapolis, IN
| | - Craig J. Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette IN, USA
- Indiana University School of Medicine, IN, USA
| | - Steven S. Welc
- Division of Pediatric Cardiology, Riley Children’s Hospital at Indiana University Health, Indiana University School of Medicine, Indianapolis, IN
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis IN, USA
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28
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Jin D, Liang S, Shmatko A, Arnold A, Horst D, Grünewald TGP, Gerstung M, Bai X. Teacher-student collaborated multiple instance learning for pan-cancer PDL1 expression prediction from histopathology slides. Nat Commun 2024; 15:3063. [PMID: 38594278 PMCID: PMC11004138 DOI: 10.1038/s41467-024-46764-0] [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: 07/30/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
Programmed cell death ligand 1 (PDL1), as an important biomarker, is quantified by immunohistochemistry (IHC) with few established histopathological patterns. Deep learning aids in histopathological assessment, yet heterogeneity and lacking spatially resolved annotations challenge precise analysis. Here, we present a weakly supervised learning approach using bulk RNA sequencing for PDL1 expression prediction from hematoxylin and eosin (H&E) slides. Our method extends the multiple instance learning paradigm with the teacher-student framework, which assigns dynamic pseudo-labels for intra-slide heterogeneity and retrieves unlabeled instances using temporal ensemble model distillation. The approach, evaluated on 12,299 slides across 20 solid tumor types, achieves a weighted average area under the curve of 0.83 on fresh-frozen and 0.74 on formalin-fixed specimens for 9 tumors with PDL1 as an established biomarker. Our method predicts PDL1 expression patterns, validated by IHC on 20 slides, offering insights into histologies relevant to PDL1. This demonstrates the potential of deep learning in identifying diverse histological patterns for molecular changes from H&E images.
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Affiliation(s)
- Darui Jin
- Image Processing Center, Beihang University, Beijing, 102206, China
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Shen Yuan Honors College, Beihang University, Beijing, 100191, China
| | - Shangying Liang
- Image Processing Center, Beihang University, Beijing, 102206, China
| | - Artem Shmatko
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Arnold
- Charité - Universitätsmedizin Berlin, Institute of Pathology, 10117, Berlin, Germany
| | - David Horst
- Charité - Universitätsmedizin Berlin, Institute of Pathology, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas G P Grünewald
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| | - Moritz Gerstung
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Xiangzhi Bai
- Image Processing Center, Beihang University, Beijing, 102206, China.
- State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, 100191, China.
- Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China.
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [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: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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30
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Huynh TQ, Tran NBV, Pham TTV, Le VBT, Truong TP, Huynh VA, Tong TH, Trinh TTL, Nguyen VD, Pham LNM, Nguyen TH, Lin Q, Lim TK, Lin Q, Nguyen TTH. Adaptive response of Pseudomonas aeruginosa under serial ciprofloxacin exposure. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001443. [PMID: 38568202 PMCID: PMC11084610 DOI: 10.1099/mic.0.001443] [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: 10/18/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Understanding the evolution of antibiotic resistance is important for combating drug-resistant bacteria. In this work, we investigated the adaptive response of Pseudomonas aeruginosa to ciprofloxacin. Ciprofloxacin-susceptible P. aeruginosa ATCC 9027, CIP-E1 (P. aeruginosa ATCC 9027 exposed to ciprofloxacin for 14 days) and CIP-E2 (CIP-E1 cultured in antibiotic-free broth for 10 days) were compared. Phenotypic responses including cell morphology, antibiotic susceptibility, and production of pyoverdine, pyocyanin and rhamnolipid were assessed. Proteomic responses were evaluated using comparative iTRAQ labelling LC-MS/MS to identify differentially expressed proteins (DEPs). Expression of associated genes coding for notable DEPs and their related regulatory genes were checked using quantitative reverse transcriptase PCR. CIP-E1 displayed a heterogeneous morphology, featuring both filamentous cells and cells with reduced length and width. By contrast, although filaments were not present, CIP-E2 still exhibited size reduction. Considering the MIC values, ciprofloxacin-exposed strains developed resistance to fluoroquinolone antibiotics but maintained susceptibility to other antibiotic classes, except for carbapenems. Pyoverdine and pyocyanin production showed insignificant decreases, whereas there was a significant decrease in rhamnolipid production. A total of 1039 proteins were identified, of which approximately 25 % were DEPs. In general, there were more downregulated proteins than upregulated proteins. Noted changes included decreased OprD and PilP, and increased MexEF-OprN, MvaT and Vfr, as well as proteins of ribosome machinery and metabolism clusters. Gene expression analysis confirmed the proteomic data and indicated the downregulation of rpoB and rpoS. In summary, the response to CIP involved approximately a quarter of the proteome, primarily associated with ribosome machinery and metabolic processes. Potential targets for bacterial interference encompassed outer membrane proteins and global regulators, such as MvaT.
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Affiliation(s)
- Thuc Quyen Huynh
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Bao Vy Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Thi Thuy Vy Pham
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Vo Bao Tran Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | | | - Van An Huynh
- Gia Dinh People’s Hospital, Ho Chi Minh City, Vietnam
| | - Thi Hang Tong
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Thi Truc Ly Trinh
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Van Dung Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
| | - Le Nhat Minh Pham
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
- Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Thi Hiep Nguyen
- Viet Nam National University, Ho Chi Minh City, Vietnam
- School of Biomedical Engineering, International University, Ho Chi Minh City, Vietnam
| | - Qifeng Lin
- Protein and Proteomics Centre, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Teck Kwang Lim
- Protein and Proteomics Centre, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Protein and Proteomics Centre, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thi Thu Hoai Nguyen
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University, Ho Chi Minh City, Vietnam
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31
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Vega-García E, Palacios G, Pérez JA, Vélez-Tobarias M, Torres-Vega AM, Ascaso-Terrén C, Carmelo E. A molecular toolbox for fast and convenient diagnosis of emerging and reemerging bacterial pathogens causing fever of intermediate duration. Eur J Clin Microbiol Infect Dis 2024; 43:649-657. [PMID: 38270806 DOI: 10.1007/s10096-024-04760-8] [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: 12/18/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
PURPOSE Fever of intermediate duration (FID) is defined as a fever in the community without a specific origin or focus, with a duration between 7 and 28 days. FID is often caused by pathogens associated with animal contact or their arthropods parasites, such as ticks, fleas, or lice. The purpose of this work is to design a collection of molecular tools to promptly and accurately detect common bacterial pathogens causing FID, including bacteria belonging to genera Rickettsia, Bartonella, Anaplasma, and Ehrlichia, as well as Coxiella burnetii. METHODS Reference DNA sequences from a collection of Rickettsia, Bartonella, Anaplasma, and Ehrlichia species were used to design genus-specific primers and FRET probes targeted to conserved genomic regions. For C. burnetii, primers previously described were used, in combination with a newly designed specific probe. Real-time PCR assays were optimized using reference bacterial genomic DNA in a background of human genomic DNA. RESULTS The four real-time PCR assays can detect as few as ten copies of target DNA from those five genera of FDI-causing bacteria in a background of 300 ng of human genomic DNA, mimicking the low microbial load generally found in patient's blood. CONCLUSION These assays constitute a fast and convenient "toolbox" that can be easily implemented in diagnostic laboratories to provide timely and accurate detection of bacterial pathogens that are typical etiological causes of febrile syndromes such as FID in humans.
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Affiliation(s)
- Elva Vega-García
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez S/N, 38200, La Laguna, Tenerife, Spain
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Génesis Palacios
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez S/N, 38200, La Laguna, Tenerife, Spain
| | - José A Pérez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez S/N, 38200, La Laguna, Tenerife, Spain.
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Facultad de Ciencias, Universidad de La Laguna, La Laguna, Tenerife, Spain.
| | - Mónica Vélez-Tobarias
- Servicio de Medicina Interna, Hospital Universitario de La Palma (HULP), Breña Alta, La Palma, Spain
| | - Ana María Torres-Vega
- Servicio de Medicina Interna, Hospital Insular Ntra. Sra. de los Reyes (HINSR), Valverde, El Hierro, Spain
| | | | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez S/N, 38200, La Laguna, Tenerife, Spain.
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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32
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Goncalves D, Duy DL, Peffer S, Morano KA. Cytoplasmic redox imbalance in the thioredoxin system activates Hsf1 and results in hyperaccumulation of the sequestrase Hsp42 with misfolded proteins. Mol Biol Cell 2024; 35:ar53. [PMID: 38381577 PMCID: PMC11064659 DOI: 10.1091/mbc.e23-07-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Cells employ multiple systems to maintain homeostasis when experiencing environmental stress. For example, the folding of nascent polypeptides is exquisitely sensitive to proteotoxic stressors including heat, pH, and oxidative stress, and is safeguarded by a network of protein chaperones that concentrate potentially toxic misfolded proteins into transient assemblies to promote folding or degradation. The redox environment itself is buffered by both cytosolic and organellar thioredoxin and glutathione pathways. How these systems are linked is poorly understood. Here, we determine that specific disruption of the cytosolic thioredoxin system resulted in constitutive activation of the heat shock response in Saccharomyces cerevisiae and accumulation of the sequestrase Hsp42 into an exaggerated and persistent juxtanuclear quality control (JUNQ) compartment. Terminally misfolded proteins also accumulated in this compartment in thioredoxin reductase (TRR1)-deficient cells, despite apparently normal formation and dissolution of transient cytoplasmic quality control (CytoQ) bodies during heat shock. Notably, cells lacking TRR1 and HSP42 exhibited severe synthetic slow growth exacerbated by oxidative stress, signifying a critical role for Hsp42 under redox-challenged conditions. Finally, we demonstrated that Hsp42 localization patterns in trr1∆ cells mimic those observed in chronically aging and glucose-starved cells, linking nutrient depletion and redox imbalance with management of misfolded proteins via a process of long-term sequestration.
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Affiliation(s)
- Davi Goncalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Duong Long Duy
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Sara Peffer
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
- Microbiology and Infectious Disease Program, MD Anderson UTHealth Graduate School at UTHealth Houston, Houston, TX 77030
| | - Kevin A. Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
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Carey A, Nguyen K, Kandikonda P, Kruglov V, Bradley C, Dahlquist KJV, Cholensky S, Swanson W, Badovinac VP, Griffith TS, Camell CD. Age-associated accumulation of B cells promotes macrophage inflammation and inhibits lipolysis in adipose tissue during sepsis. Cell Rep 2024; 43:113967. [PMID: 38492219 PMCID: PMC11014686 DOI: 10.1016/j.celrep.2024.113967] [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: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Non-canonical lipolysis induced by inflammatory cytokines or Toll-like receptor ligands is required for the regulation of inflammation during endotoxemia and sepsis. Canonical lipolysis induced by catecholamines declines during aging due to factors including an expansion of lymphocytes, pro-inflammatory macrophage polarization, and an increase in chronic low-grade inflammation; however, the extent to which the non-canonical pathway of lipolysis is active and impacted by immune cells during aging remains unclear. Therefore, we aimed to define the extent to which immune cells from old mice influence non-canonical lipolysis during sepsis. We identified age-associated impairments of non-canonical lipolysis and an accumulation of dysfunctional B1 B cells in the visceral white adipose tissue (vWAT) of old mice. Lifelong deficiency of B cells results in restored non-canonical lipolysis and reductions in pro-inflammatory macrophage populations. Our study suggests that targeting the B cell-macrophage signaling axis may resolve metabolic dysfunction in aged vWAT and attenuate septic severity in older individuals.
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Affiliation(s)
- Anna Carey
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA; Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Katie Nguyen
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pranathi Kandikonda
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Victor Kruglov
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Claire Bradley
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Korbyn J V Dahlquist
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephanie Cholensky
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Whitney Swanson
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Urology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Thomas S Griffith
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Urology, University of Minnesota, Minneapolis, MN 55455, USA; Minneapolis VA Health Care System, Minneapolis, MN 55417, USA
| | - Christina D Camell
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA; Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
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LaBute B, Fong J, Ziaee F, Gombar R, Stover M, Beaudin T, Badalova M, Geng Q, Corchis-Scott R, Podadera A, Lago K, Xu Z, Lim F, Chiu F, Fu M, Nie X, Wu Y, Quan C, Hamm C, McKay RM, Ng K, Porter LA, Tong Y. Evaluating and optimizing Acid-pH and Direct Lysis RNA extraction for SARS-CoV-2 RNA detection in whole saliva. Sci Rep 2024; 14:7017. [PMID: 38527999 DOI: 10.1038/s41598-024-54183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
COVID-19 has been a global public health and economic challenge. Screening for the SARS-CoV-2 virus has been a key part of disease mitigation while the world continues to move forward, and lessons learned will benefit disease detection beyond COVID-19. Saliva specimen collection offers a less invasive, time- and cost-effective alternative to standard nasopharyngeal swabs. We optimized two different methods of saliva sample processing for RT-qPCR testing. Two methods were optimized to provide two cost-efficient ways to do testing for a minimum of four samples by pooling in a 2.0 mL tube and decrease the need for more highly trained personnel. Acid-pH-based RNA extraction method can be done without the need for expensive kits. Direct Lysis is a quick one-step reaction that can be applied quickly. Our optimized Acid-pH and Direct Lysis protocols are reliable and reproducible, detecting the beta-2 microglobulin (B2M) mRNA in saliva as an internal control from 97 to 96.7% of samples, respectively. The cycle threshold (Ct) values for B2M were significantly higher in the Direct Lysis protocol than in the Acid-pH protocol. The limit of detection for N1 gene was higher in Direct Lysis at ≤ 5 copies/μL than Acid-pH. Saliva samples collected over the course of several days from two COVID-positive individuals demonstrated Ct values for N1 that were consistently higher from Direct Lysis compared to Acid-pH. Collectively, this work supports that each of these techniques can be used to screen for SARS-CoV-2 in saliva for a cost-effective screening platform.
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Affiliation(s)
- Brayden LaBute
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Jackie Fong
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Farinaz Ziaee
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Robert Gombar
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Mathew Stover
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Terry Beaudin
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Maria Badalova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kyle Lago
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - ZhenHuan Xu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Fievel Lim
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Felix Chiu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Minghua Fu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Xiaofeng Nie
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Yuanmin Wu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | | | - Caroline Hamm
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
- Windsor Regional Hospital, Windsor, ON, Canada
| | - R Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Kenneth Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
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35
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Biase FH, Schettini G. Protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes. STAR Protoc 2024; 5:102940. [PMID: 38460133 PMCID: PMC10941008 DOI: 10.1016/j.xpro.2024.102940] [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: 09/25/2023] [Revised: 01/09/2024] [Accepted: 02/21/2024] [Indexed: 03/11/2024] Open
Abstract
The use of CRISPR-Cas9 ribonucleoproteins has revolutionized manipulation of genomes. Here, we present a protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes. First, we describe steps for production and preparation of presumptive zygotes for electroporation. The first electroporation introduces ribonucleoproteins formed by Cas9D10A with two guide RNAs to target DNA, and the second introduces the same ribonucleoprotein complex to target DNA plus Cas13a with one guide RNA to target RNAs. For complete details on the use and execution of this protocol, please refer to Nix et al.1.
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Affiliation(s)
- Fernando H Biase
- Virginia Polytechnique Institute and State University, Blacksburg, VA 24061, USA.
| | - Gustavo Schettini
- Virginia Polytechnique Institute and State University, Blacksburg, VA 24061, USA
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36
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Jahun AS, Sorgeloos F, Goodfellow IG. An optimized protocol for the extraction and quantification of cytosolic DNA in mammalian cells. STAR Protoc 2024; 5:102913. [PMID: 38393950 PMCID: PMC10901131 DOI: 10.1016/j.xpro.2024.102913] [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: 10/24/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Leakage of mitochondrial or nuclear DNA into the cytosol can occur following viral infections, radiation damage, and some cancers. Here, we present an optimized protocol for isolating and quantifying cytosolic DNA from mammalian cells. We describe steps for collecting cytosolic fractions from cells, extracting DNA using columns, and quantifying extracted DNA using qPCR. This straightforward protocol can be completed in as little as 5 hours, and allows for the identification of the source of DNA. For complete details on the use and execution of this protocol, please refer to Jahun et al.1.
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Affiliation(s)
- Aminu S Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK.
| | - Frederic Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK; Université catholique de Louvain, de Duve Institute, MIPA-VIRO 74-49, 74 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK.
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Xu H, Zheng Y, Xie J, Duan W, Yu L, Lin R, Li CC, Jia L. Imaging mRNA in vitro and in vivo with nanofirecracker probes via intramolecular hybridization chain reaction. Biosens Bioelectron 2024; 248:115973. [PMID: 38150797 DOI: 10.1016/j.bios.2023.115973] [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: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/24/2023] [Indexed: 12/29/2023]
Abstract
Hybridization chain reaction (HCR) based enzyme-free amplification techniques have recently been developed for the visualization of intracellular messenger RNA (mRNA). However, the slow kinetics and potential interference with the intricate biological environments hinder its application in the clinic and in vivo. Herein, we designed a nanofirecracker probe-based strategy using intramolecular hybridization chain reaction (IHCR) amplifier for rapid, efficient, sensitive, specific detection and imaging of survivin mRNA both in vitro and vivo. Two probes, HP1 and HP2, in IHCR were simultaneously incorporated into a DNA nanowire scaffolds to bring HP1 and HP2 to close proximity on the assembled nanowire scaffolds. Empowered by the DNA nanowire scaffolds and spatial confinement effect, the nanofirecracker probe-based IHCR sensing system exhibited improved biostability, accelerated reaction kinetics, and enhanced signal amplification. This new strategy has been successfully applied to imaging mRNA in both cultured cells and in mice. Importantly, this novel sensing method was capable of detecting survivin mRNA in clinical blood samples from subjects with colorectal cancer. Thus, this novel nanofirecracker probe-based IHCR strategy holds great potential in advancing both biomedical research and in molecular diagnostics.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China.
| | - Yanhui Zheng
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China
| | - Jingjing Xie
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Wei Duan
- School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Lixue Yu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ruimiao Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Chen-Chen Li
- Shandong Key Laboratory of Biochemical Analysis, Qingdao University of Science and Technology, Qingdao, Shangdong, 266042, China
| | - Lee Jia
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China
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Lv PL, Jia C, Wei CH, Zhao HP, Chen R. Efficient perchlorate reduction in microaerobic environment facilitated by partner methane oxidizers. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133683. [PMID: 38310847 DOI: 10.1016/j.jhazmat.2024.133683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
The conventional perchlorate (ClO4-) reduction typically necessitates anaerobic conditions. However, in this study, we observed efficient ClO4- reduction using CH4 as the electron donor in a microaerobic environment. The maximum ClO4- removal flux of 2.18 g/m2·d was achieved in CH4-based biofilm. The kinetics of ClO4- reduction showed significant differences, with trace oxygen increasing the reduction rate of ClO4-, whereas oxygen levels exceeding 2 mg/L decelerated the ClO4- reduction. In the absence of exogenous oxygen, anaerobic methanotrophic (ANME) archaea contribute more than 80% electrons through the reverse methanogenesis pathway for ClO4- reduction. Simultaneously, microorganisms activate CH4 by utilizing oxygen generated from chlorite (ClO2-) disproportionation. In the presence of exogenous oxygen, methane oxidizers predominantly consume oxygen to drive the aerobic oxidation of methane. It is indicated that methane oxidizers and perchlorate reducing bacteria can form aggregates to resist external oxygen shocks and achieve efficient ClO4- reduction under microaerobic condition. These findings provide new insights into biological CH4 mitigation and ClO4- removal in hypoxic environment.
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Affiliation(s)
- Pan-Long Lv
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - Chuan Jia
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - Chi-Hang Wei
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China
| | - He-Ping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Rong Chen
- Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, China.
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Zhang P, Chen S, Chen S, Zhu Y, Lin Y, Xu X, Liu Z, Zou S. Selection and Validation of qRT-PCR Internal Reference Genes to Study Flower Color Formation in Camellia impressinervis. Int J Mol Sci 2024; 25:3029. [PMID: 38474274 DOI: 10.3390/ijms25053029] [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: 01/16/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Real-time quantitative PCR (qRT-PCR) is a pivotal technique for gene expression analysis. To ensure reliable and accurate results, the internal reference genes must exhibit stable expression across varied experimental conditions. Currently, no internal reference genes for Camellia impressinervis have been established. This study aimed to identify stable internal reference genes from eight candidates derived from different developmental stages of C. impressinervis flowers. We employed geNorm, NormFinder, and BestKeeper to evaluate the expression stability of these candidates, which was followed by a comprehensive stability analysis. The results indicated that CiTUB, a tubulin gene, exhibited the most stable expression among the eight reference gene candidates in the petals. Subsequently, CiTUB was utilized as an internal reference for the qRT-PCR analysis of six genes implicated in the petal pigment synthesis pathway of C. impressinervis. The qRT-PCR results were corroborated by transcriptome sequencing data, affirming the stability and suitability of CiTUB as a reference gene. This study marks the first identification of stable internal reference genes within the entire genome of C. impressinervis, establishing a foundation for future gene expression and functional studies. Identifying such stable reference genes is crucial for advancing molecular research on C. impressinervis.
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Affiliation(s)
- Peilan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuying Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyu Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanming Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqing Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Bustin SA, Kirvell S, Nolan T, Shipley GL. FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols. Int J Mol Sci 2024; 25:2773. [PMID: 38474020 DOI: 10.3390/ijms25052773] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
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Li R, Su P, Shi Y, Shi H, Ding S, Su X, Chen P, Wu D. Gene doping detection in the era of genomics. Drug Test Anal 2024. [PMID: 38403949 DOI: 10.1002/dta.3664] [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: 10/03/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Recent progress in gene editing has enabled development of gene therapies for many genetic diseases, but also made gene doping an emerging risk in sports and competitions. By delivery of exogenous transgenes into human body, gene doping not only challenges competition fairness but also places health risk on athletes. World Anti-Doping Agency (WADA) has clearly inhibited the use of gene and cell doping in sports, and many techniques have been developed for gene doping detection. In this review, we will summarize the main tools for gene doping detection at present, highlight the main challenges for current tools, and elaborate future utilizations of high-throughput sequencing for unbiased, sensitive, economic and large-scale gene doping detections. Quantitative real-time PCR assays are the widely used detection methods at present, which are useful for detection of known targets but are vulnerable to codon optimization at exon-exon junction sites of the transgenes. High-throughput sequencing has become a powerful tool for various applications in life and health research, and the era of genomics has made it possible for sensitive and large-scale gene doping detections. Non-biased genomic profiling could efficiently detect new doping targets, and low-input genomics amplification and long-read third-generation sequencing also have application potentials for more efficient and straightforward gene doping detection. By closely monitoring scientific advancements in gene editing and sport genetics, high-throughput sequencing could play a more and more important role in gene detection and hopefully contribute to doping-free sports in the future.
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Affiliation(s)
- Ruihong Li
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Shanghai Center of Agri-Products Quality and Safety, Shanghai, China
| | - Peipei Su
- Innovative Program of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Shi
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Shi
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Department of Rheumatology and Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengqian Ding
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
| | - Xianbin Su
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peijie Chen
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Die Wu
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
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42
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Phan T, Ye Q, Stach C, Lin YC, Cao H, Bowen A, Langlois RA, Hu WS. Synthetic Cell Lines for Inducible Packaging of Influenza A Virus. ACS Synth Biol 2024; 13:546-557. [PMID: 38259154 PMCID: PMC10878389 DOI: 10.1021/acssynbio.3c00526] [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: 08/27/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024]
Abstract
Influenza A virus (IAV) is a negative-sense RNA virus that causes seasonal infections and periodic pandemics, inflicting huge economic and human costs on society. The current production of influenza virus for vaccines is initiated by generating a seed virus through the transfection of multiple plasmids in HEK293 cells followed by the infection of seed viruses into embryonated chicken eggs or cultured mammalian cells. We took a system design and synthetic biology approach to engineer cell lines that can be induced to produce all viral components except hemagglutinin (HA) and neuraminidase (NA), which are the antigens that specify the variants of IAV. Upon the transfection of HA and NA, the cell line can produce infectious IAV particles. RNA-Seq transcriptome analysis revealed inefficient synthesis of viral RNA and upregulated expression of genes involved in host response to viral infection as potential limiting factors and offered possible targets for enhancing the productivity of the synthetic cell line. Overall, we showed for the first time that it was possible to create packaging cell lines for the production of a cytopathic negative-sense RNA virus. The approach allows for the exploitation of altered kinetics of the synthesis of viral components and offers a new method for manufacturing viral vaccines.
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Affiliation(s)
- Thu Phan
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Qian Ye
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Christopher Stach
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yu-Chieh Lin
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Haoyu Cao
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Annika Bowen
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ryan A. Langlois
- Department
of Microbiology and Immunology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wei-Shou Hu
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Liu Y, Zhang L, Meng S, Zhang H, Wang S, Xu C, Liu Y, Xu T, He Y, Cui Y, Tan C, Li T, Qi M. Galactinol Regulates JA Biosynthesis to Enhance Tomato Cold Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2547-2559. [PMID: 38286812 DOI: 10.1021/acs.jafc.3c08710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Low temperatures can inhibit plant growth and development and reduce fruit yield. This study demonstrated that the expression of AnGolS1 from Ammopiptanthus nanus (A. nanus) encoding a galactinol synthase enhanced tomato cold tolerance. In AnGolS1-overexpressing plants, the jasmonic acid (JA) biosynthesis substrates 13-hydroperoxylinolenicacid and 12,13-epoxylinolenicacid were significantly accumulated, and the expression levels of the ethylene response factor (SlERF4-7) and serine protease inhibitor (SlSPI5) were increased. We speculated that there may be correlations among galactinol, ethylene signaling, the protease inhibitor, protease, and JA levels. The expression levels of SlERF4-7 and SlSPI5 as well as the JA content were significantly increased under exogenous galactinol treatment. Additionally, the expression of SlSPI5 was reduced in SlERF4-7-silenced plants, and SlERF4-7 was confirmed to bind to the dehydration-responsive element (DRE) of the SlSPI5 promoter. These results suggest that SlSPI5 is a target gene of the SlERF4-7 transcription factor. In addition, SlSPI5 interacted with cysteine protease (SlCPase), while SlCPase interacted with lipoxygenase (SlLOX5) and allene oxide synthase (SlAOS2). When SlCPase was silenced, JA levels increased and plant cold tolerance was enhanced. Therefore, galactinol regulates JA biosynthesis to enhance tomato cold tolerance through the SlERF4-7-SlSPI5-SlCPase-SlLOX5/SlAOS2 model. Overall, our study provides new perspectives on the role of galactinol in the JA regulatory network in plant adaptation to low-temperature stress.
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Affiliation(s)
- YuDong Liu
- College of Agriculture, Shihezi University, Shihezi 832003, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi 832003, China
| | - Li Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang 110161, China
| | - SiDa Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - HuiDong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - Shuo Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - ChuanQiang Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - YuFeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - Yi He
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang Agricultural University, Shenyang 110161, China
| | - YiQing Cui
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang Agricultural University, Shenyang 110161, China
| | - ChangHua Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang Agricultural University, Shenyang 110161, China
| | - TianLai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
| | - MingFang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Key Laboratory of Protected Horticulture, Ministry of Education, Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang 110161, China
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He L, Wang JY, Su QJ, Chen ZH, Xie F. Selection and validation of reference genes for RT-qPCR in ophiocordyceps sinensis under different experimental conditions. PLoS One 2024; 19:e0287882. [PMID: 38319940 PMCID: PMC10846742 DOI: 10.1371/journal.pone.0287882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/14/2023] [Indexed: 02/08/2024] Open
Abstract
The Chinese caterpillar mushroom, Ophiocordyceps sinensis (O. sinensis), is a rarely medicinal fungus in traditional chinese herbal medicine due to its unique medicinal values, and the expression stability of reference genes is essential to normalize its gene expression analysis. In this study, BestKeeper, NormFinder and geNorm, three authoritative statistical arithmetics, were applied to evaluate the expression stability of sixteen candidate reference genes (CRGs) in O. sinensis under different stress [low temperature (4°C), light treatment (300 lx), NaCl (3.8%)] and different development stages (mycelia, primordia and fruit bodies) and formation of morphologic mycelium (aeriasubstrate, hyphae knot mycelium). The paired variation values indicated that two genes could be enough to accurate standardization exposed to different conditions of O.sinensis. Among these sixteen CRGs, 18S ribosomal RNA (18S rRNA) and beta-Tubulin (β-TUB) showed the topmost expression stability in O.sinensis exposed to all conditions, while glutathione hydrolase proenzym (GGT) and Phosphoglucose isomerase (PGI) showed the least expression stability. The optimal reference gene in different conditions was various. β-TUB and Ubiquitin (UBQ) were identified as the two most stable genes in different primordia developmental stage, while phosphoglucomutase (PGM) with elongation factor 1-alpha (EF1-α) and 18S rRNA with UBQ were the most stably expressed for differentially morphologic mycelium stages and different stresses, respectively. These results will contribute to more accurate evaluation of the gene relative expression levels in O.sinensis under different conditions using the optimal reference gene in real-time quantitative PCR (RT-qPCR) analysis.
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Affiliation(s)
- Li He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Jin Yi Wang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Qiang Jun Su
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Zhao He Chen
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Fang Xie
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
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Dai Y, Gao X, Zhang S, Li F, Zhang H, Li G, Sun R, Zhang S, Hou X. Exploring the Regulatory Dynamics of BrFLC-Associated lncRNA in Modulating the Flowering Response of Chinese Cabbage. Int J Mol Sci 2024; 25:1924. [PMID: 38339202 PMCID: PMC10856242 DOI: 10.3390/ijms25031924] [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: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs exhibited an inverse expression pattern to the flowering repressor genes FLOWERING LOCUS C 1 (BrFLC1) and FLOWERING LOCUS C 2 (BrFLC2) during vernalization, suggesting a complex regulatory mechanism. Notably, their expression in the shoot apex and leaves was confirmed through in fluorescent in situ hybridization (FISH). Furthermore, when these lncRNAs were overexpressed in Arabidopsis, a noticeable acceleration in flowering was observed, unveiling functional similarities to Arabidopsis's COLD ASSISTED INTRONIC NONCODING RNA (COOLAIR). This resemblance suggests a potentially conserved regulatory mechanism across species. This study not only enhances our understanding of lncRNAs in flowering regulation, but also opens up new possibilities for their application in agricultural practices.
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Affiliation(s)
- Yun Dai
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xinyu Gao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shifan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Fei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Hui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Guoliang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Rifei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shujiang Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
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46
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Sankar K, Lee KY, Kwak KW, Lee SJ, Lee YB. Seasonal Stability Assessment of Reference Genes for Quantitative Real-Time Polymerase Chain Reaction Normalization in Bombus terrestris. Curr Issues Mol Biol 2024; 46:1335-1347. [PMID: 38392203 PMCID: PMC10887669 DOI: 10.3390/cimb46020085] [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: 12/07/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
Bumblebees (B. terrestris) play a crucial role as highly efficient biological agents in commercial pollination. Understanding the molecular mechanisms governing their adaptation to diverse seasonal environments may pave the way for effective management strategies in the future. With the burgeoning advancement in post-genetic studies focusing on B. terrestris, there is a critical need to normalize quantitative real-time PCR (qRT-PCR) data using suitable reference genes. To address this necessity, we employed RefFinder, a software-based tool, to assess the suitability of several candidate endogenous control genes, including actin (ACT), arginine kinase (AK), elongation factor 1 alpha (EF1), glyceraldehyde-3-phosphate (GAPDH), phospholipase (PLA2), and ribosomal proteins (S18, S28). These genes were evaluated for their efficacy as biological endogenous controls by examining their expression patterns across various environmental conditions corresponding to different seasons (Spring, Summer, Autumn, Winter) and tissues (ovary, fat body, thorax, head) in bumblebees. Moreover, the study investigated the significance of selecting appropriate reference genes for three key genes involved in the juvenile hormone (JH) signaling pathways: Krüppel homolog 1 (Kr-h1), methyl farnesoate epoxidase (MFE), and Vitellogenin (Vg). Our research identifies specific genes suitable for normalization in B. terrestris, thereby offering valuable insights into gene expression and functional metabolic genetics under varying seasonal conditions. This catalog of reference genes will serve as a valuable resource for future research endeavors.
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Affiliation(s)
- Kathannan Sankar
- Agricultural Biology Department, National Institute of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Kyeong-Yong Lee
- Agricultural Biology Department, National Institute of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Kyu-Won Kwak
- Agricultural Biology Department, National Institute of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Su-Jin Lee
- Agricultural Biology Department, National Institute of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Young-Bo Lee
- Agricultural Biology Department, National Institute of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
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47
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Wang Z, She D, Liu L, Hua X, Zhu H, Yu L, Wang H, Zhu Y, Fan G, Wang Y, Xu M, Zhou G. Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1. Cell Signal 2024; 114:110977. [PMID: 37984605 DOI: 10.1016/j.cellsig.2023.110977] [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: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs which take part in the regulation of the initiation and development of different types of cancer. Numerous studies have demonstrated that circRNAs are involved in the progression of osteosarcoma (OS) as well. Thus, we put our emphasis on the exploration of crucial circRNAs in the process of OS initiation and progression. Using RNA sequencing, we found that circSATB2 was highly expressed in OS tissues compared with adjacent normal tissues. Then, we confirmed the high expression of circSATB2 in OS cell lines and OS tissues and its high expression was related to poor prognosis of OS patients. Functional experiments exhibited that circSATB2 promoted OS proliferation and migration in vitro, primary OS model and OS lung metastasis model showed that circSATB2 aggravated OS progression in vivo. Mechanistically, circSATB2 was found to promote OS progression through sponging miR-661 and FUS regulating the mRNA of ZNFX1. Therefore, circSATB2 could act as a prognostic marker and a therapeutic target for osteosarcoma in the future.
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Affiliation(s)
- Zhen Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China; Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Diankun She
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Lei Liu
- Department of Orthopedics,The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu, China
| | - Xianming Hua
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Hao Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Lingfeng Yu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Han Wang
- Department of Pharmacy, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Gentao Fan
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yicun Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Meng Xu
- Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China.
| | - Guangxin Zhou
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China.
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48
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Cao L, Zhang Q, Miao R, Zhao X, Ni Y, Li W, Feng R, Yang D. Reference gene selection for quantitative real-time PCR analysis of Hymenopellis radicata under abiotic stress. Fungal Biol 2024; 128:1567-1577. [PMID: 38341262 DOI: 10.1016/j.funbio.2023.11.004] [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: 08/09/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 02/12/2024]
Abstract
Hymenopellis radicata (H. radicata) is an edible fungus rich in protein and mineral elements, with high edible and medical value. And reference genes suitable for normalization of qRT-PCR data from this species have not been investigated. In this study, therefore, we selected 11 housekeeping genes common in biology. The expression levels of these housekeeping genes were measured in three different tissues and six different abiotic stress treatments in mycelium. They were evaluated for expression stability using online tools. The results showed that gene ACT could be stable expressed in all samples. The expressions of genes TUB and UBQ10 are the most stable under heat stress, ACT and EF are the most stable genes under salt stress, ACT and TUB are the most stable genes under oxidation stress, RPL6 and EF are the most stable genes under pH condition, ACT and RPB2 are the most stable genes under cadmium stress, and RPB2 and UBC are the most stable genes under drought condition. ACT and PP2A are the most stable genes at different tissue sites. This study is of great help to explore the gene expression pattern of H. radicata, and also provides reference for internal reference gene screening under other conditions.
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Affiliation(s)
- Luping Cao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Renyun Miao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Xu Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China.
| | - Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu 610299, Sichuan, China
| | - Delong Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China.
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49
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Tsai S, Tikekar RV. The effect of emulsifier type and oil inclusion on stress-related gene expression of Salmonella typhimurium in oil-in-water emulsion. J Food Sci 2024; 89:1211-1224. [PMID: 38224194 DOI: 10.1111/1750-3841.16908] [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: 07/27/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Salmonella has been associated with numerous outbreaks from contaminated food products, including emulsions. Emulsions are influenced by emulsifier type and oil presence, which can have varying degrees of stress or protection on bacteria. Although our previous research has shown that emulsifier solutions, rather than emulsions, provide a protective effect on Salmonella typhimurium after thermal treatment, the underlying mechanism remains unclear. This study selected S. typhimurium as the model microorganism and utilized the same emulsifiers (Tween 20, Tween 80, Triton X-100) to create emulsifier solutions and emulsions with the same oil fraction (60% (v/v)) to examine their effect on the expression of nine selected genes (rpoE, rpoH, otsB, proV, fadA, fabA, dnaK, ibpA, ompC) associated with stress response. Specifically, the study observed variations in gene expression under normal and thermal stress at 55°C. After 20-h incubation, Triton X-100 emulsion caused an upregulation of stress-related genes, rpoE, otsB, and fabA, suggesting stressful environment. After thermal treatment, S. typhimurium in Triton X-100 solution showed a longer 5-log reduction time with increased proV and decreased fabA and ompC expression, suggesting enhanced thermal protection compared to its emulsion. Conversely, Tween 80 solution increased fabA and ompC expression, indicating greater membrane fluidity and passive diffusion, potentially reducing thermal resistance. However, according to the upregulation of ibpA, this effect was likely mitigated by the overproduction of heat shock proteins. Notably, Triton X-100 environments exhibited the most significant gene expression changes after heat treatment, whereas Tween 80 without oil was the most inhospitable for bacterial survival. These findings inform bacterial responses under various conditions, aiding food safety strategies.
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Affiliation(s)
- Shawn Tsai
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Rohan V Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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50
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Daude MM, Ságio SA, Rodrigues JN, Lima NMP, Lima AA, Sarmento MI, Sarmento RA, Barreto HG. Reference genes for Eucalyptus spp. under Beauveria bassiana inoculation and subsequently infestation by the galling wasp Leptocybe invasa. Sci Rep 2024; 14:2556. [PMID: 38297150 PMCID: PMC10830493 DOI: 10.1038/s41598-024-52948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
Relative gene expression analysis through RT-qPCR is an important molecular technique that helps understanding different molecular mechanisms, such as the plant defense response to insect pests. However, the use of RT-qPCR for gene expression analysis can be affected by factors that directly affect the reliability of the results. Among these factors, the appropriate choice of reference genes is crucial and can strongly impact RT-qPCR relative gene expression analyses, highlighting the importance in correctly choosing the most suitable genes for the success of the analysis. Thus, this study aimed to select and validate reference genes for relative gene expression studies through RT-qPCR in hybrids of Eucalyptus tereticornis × Eucalyptus camaldulensis (drought tolerant and susceptible to Leptocybe invasa) under conditions of inoculation by the Beauveria bassiana fungus and subsequent infestation by L. invasa. The expression level and stability of eleven candidate genes were evaluated. Stability was analyzed using the RefFinder tool, which integrates the geNorm, NormFinder, BestKeeper, and Delta-Ct algorithms. The selected reference genes were validated through the expression analysis of the transcriptional factor EcDREB2 (dehydration-responsive element-binding protein 2). For all treatments evaluated, EcPTB, EcPP2A-1, and EcEUC12 were the best reference genes. The triplets EcPTB/EcEUC12/EcUBP6, EcPP2A-1/EcEUC12/EcPTB, EcIDH/EcSAND/Ecα-TUB, EcPP2A-1/Ecα-TUB/EcPTB, and EcPP2A-1/EcUPL7/EcSAND were the best reference genes for the control plants, mother plants, plants inoculated with B. bassiana, plants infested with L. invasa, and plants inoculated with B. bassiana and subsequently infested with L. invasa, respectively. The best determined reference genes were used to normalize the RT-qPCR expression data for each experimental condition evaluated. The results emphasize the importance of this type of study to ensure the reliability of relative gene expression analyses. Furthermore, the findings of this study can be used as a basis for future research, comprising gene expression analysis of different eucalyptus metabolic pathways.
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Affiliation(s)
- Matheus Martins Daude
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil
| | - Solange Aparecida Ságio
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Digital Agroenergy, Federal University of Tocantins, Palmas, TO, Brazil
| | - Jovielly Neves Rodrigues
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | | | - André Almeida Lima
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil
| | - Maíra Ignacio Sarmento
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | - Renato Almeida Sarmento
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil
- Postgraduate Program in Forest and Environmental Sciences, Federal University of Tocantins, Palmas, TO, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analysis (LAM), Life Sciences Department, Faculty of Medicine, Federal University of Tocantins, Palmas, TO, Brazil.
- Postgraduate Program in Biodiversity and Biotechnology, Rede Bionorte, Federal University of Tocantins, Palmas, TO, Brazil.
- Postgraduate Program in Digital Agroenergy, Federal University of Tocantins, Palmas, TO, Brazil.
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