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Giaouris E. Comparing Gene Expression Between Planktonic and Biofilm Cells of Foodborne Bacterial Pathogens Through RT-qPCR. Methods Mol Biol 2025; 2852:143-158. [PMID: 39235742 DOI: 10.1007/978-1-0716-4100-2_10] [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: 09/06/2024]
Abstract
Like most microorganisms, important foodborne pathogenic bacteria, such as Salmonella enterica, Listeria monocytogenes, and several others as well, can attach to surfaces, of either abiotic or biotic nature, and create biofilms on them, provided the existence of supportive environmental conditions (e.g., permissive growth temperature, adequate humidity, and nutrient presence). Inside those sessile communities, the enclosed bacteria typically present a gene expression profile that differs from the one that would be displayed by the same cells growing planktonically in liquid media (free-swimming cells). This altered gene expression has important consequences on cellular physiology and behavior, including stress tolerance and induction of virulence. In this chapter, the methodology to use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to monitor and comparatively quantify expression changes in preselected genes of bacteria between planktonic and biofilm growth modes is presented.
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Affiliation(s)
- Efstathios Giaouris
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Nutrition, School of the Environment, University of the Aegean, Myrina, Lemnos, Greece.
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Sousa Severo DD, Martins WF, Miotto M, Verruck S, Rodrigues de Oliveira R, Aragão GMFD. Propidium monoazide (PMA) qPCR assay compared to the plate count method for quantifying the growth of Salmonella enterica serotypes in vacuum-packaged turkey breast combined with a mathematical modeling approach. Food Microbiol 2025; 125:104650. [PMID: 39448160 DOI: 10.1016/j.fm.2024.104650] [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: 05/30/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/26/2024]
Abstract
This study compares the plate count (PC) and the Propidium Monoazide-quantitative Polymerase Chain Reaction (PMA-qPCR) methods to assess the growth of a cocktail of three serotypes of Salmonella enterica (Heidelberg, Typhimurium, and Enteritidis) in cooked, sliced, and vacuum-packaged turkey breast (STB) under isothermal storage temperatures (8 °C-20 °C), using predictive models. Standard curves were developed for PMA-qPCR, demonstrating high efficiency (101%) and sensitivity, with quantification limits ranging from 1 to 2 log10 CFU/g for all temperatures studied. Comparative analysis revealed a significant correlation (R2 = 0.99; 95% CI) between the PC and PMA-qPCR methods; however, the agreement analysis indicated a mean difference (Bias) of -0.11 log10 CFU/g (p < 0.05), suggesting underestimation by the PC method. This indicates the presence of stressed or viable but nonculturable (VBNC) cells, detectable by PMA-qPCR but not by PC. The Baranyi and Roberts model showed a good ability to describe the behavior of S. enterica cocktail in STB for PC and PMA-qPCR data under all isothermal conditions. The exponential secondary model more accurately represented the temperature dependence of the maximum specific growth rate compared to the Ratkowsky square root model, with R2 values ≥ 0.984 and RMSE values ≤ 0.011 for both methods. These results suggest that combining PMA-qPCR with predictive modeling allows for a more accurate prediction of S. enterica growth, compared to PC method. In the event of cold chain disruptions of meat products, the use of PMA-qPCR method allow the quantification of VBNC cells, that can still pose a health risk to consumers, especially in ready-to-eat products.
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Affiliation(s)
- Danielle de Sousa Severo
- Department of Chemical Engineering and Food Engineering, Federal University of Santa Catarina, 88040-970, Florianópolis, SC, Brazil
| | - Wiaslan Figueiredo Martins
- Department of Food Technology, Goiano Federal Institute of Education, Science, and Technology, Morrinhos Campus, 75650-000, Morrinhos, GO, Brazil.
| | - Marília Miotto
- Department of Food Science and Technology, Agrarian Science Center, Federal University of Santa Catarina, 88034-001, Florianópolis, SC, Brazil
| | - Silvani Verruck
- Department of Food Science and Technology, Agrarian Science Center, Federal University of Santa Catarina, 88034-001, Florianópolis, SC, Brazil
| | | | - Gláucia Maria Falcão de Aragão
- Department of Chemical Engineering and Food Engineering, Federal University of Santa Catarina, 88040-970, Florianópolis, SC, Brazil
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Mizumoto-Teramura Y, Kamogashira T, Kondo K, Yamasoba T. Heterochronous multiplex real-time PCR with intercalating dye using uracil-DNA N-glycosylase (UNG) and multiple primer pairs to revaluate post PCR product. MethodsX 2024; 13:102818. [PMID: 39049931 PMCID: PMC11267051 DOI: 10.1016/j.mex.2024.102818] [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: 01/29/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Real-time PCR with intercalating dyes can only be performed once. The expensive fluorescent hydrolysis probes are target specific and are suitable to detect multiplex targets. Uracil-DNA N-glycosylase (UNG), which specifically hydrolyzes and degrades any uracil-containing PCR products, is often applied before PCR to reduce carryover contamination. We developed an optimized protocol for recovering DNA from PCR products and revaluating by real-time PCR with intercalating dye using UNG processing, which is particularly useful when the sample volume is very small and insufficient for multiple assays of real-time PCR.•A real-time PCR master mix with dUTP instead of dTTP was used.•UNG at 1 % and 10 % concentrations of PCR product volumes were used for the first and second processing.•The second real-time PCR was performed with different primer pairs than the first real-time PCR.
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Affiliation(s)
- Yui Mizumoto-Teramura
- Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Teru Kamogashira
- Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kenji Kondo
- Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Choi S, Piri A, Jung J, An S, Hwang J. Determination of airborne influenza virus and coronavirus infectivity using capsid integrity polymerase chain reaction. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135544. [PMID: 39216245 DOI: 10.1016/j.jhazmat.2024.135544] [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: 02/27/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Accurate airborne virus monitoring is important for preventing the spread of infectious diseases. Although standard reverse transcription-quantitative polymerase chain reaction (RT-qPCR) can efficiently detect viral ribonucleic acid (RNA), it cannot determine whether the RNA is associated with active (infectious) or inactive (non-infectious) viruses. Plaque assay is the gold standard for determining viral infectivity but is laborious and time-consuming. This study explored the viral infectivity of H1N1 influenza virus and human coronavirus (HCoV-229E) using capsid integrity RT-qPCR, where virus samples were pretreated with reagents penetrating viruses with damaged capsids, impeding amplification by binding to their RNA. Therefore, the amplified signals corresponded solely to active viruses with undamaged capsids. Propidium monoazide (PMA) and platinum (IV) chloride (PtCl4) were used to investigate the effects of reagent concentration. Feasibility tests revealed that PtCl4 was more efficient than PMA, with optimal concentrations of 125-250 μM and 250-500 μM for H1N1 influenza virus and HCoV-229E, respectively. The results of percentage of active virus showed that capsid integrity RT-qPCR provided a trend similar to that of plaque assay, indicating an accurate measure of viral infectivity. Virus sampling in the laboratory and field highlighted the precision of this methodology for determining viral infectivity. Therefore, this methodology enables rapid and accurate detection of infectious airborne H1N1 influenza virus and HCoV-229E, allowing swift response to outbreaks.
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Affiliation(s)
- Sangsoo Choi
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Amin Piri
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea; Institute of Engineering Research, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jiwoo Jung
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sanggwon An
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungho Hwang
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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Borgolte S, Menzel W, Varrelmann M. One-step TaqMan® RT-qPCR detection of sugar beet-infecting poleroviruses in Myzus persicae from yellow water pan traps opens up new possibilities for early risk assessment of virus yellows disease. J Virol Methods 2024; 331:115052. [PMID: 39423871 DOI: 10.1016/j.jviromet.2024.115052] [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: 08/06/2024] [Revised: 10/02/2024] [Accepted: 10/16/2024] [Indexed: 10/21/2024]
Abstract
Virus yellows disease (VY) is a major threat to sugar beet production in Europe. Beet chlorosis virus (BChV) and beet mild yellowing virus (BMYV) are of particular economic importance and are both persistently transmitted by the aphid vector Myzus persicae. As part of integrated pest management strategies, M. persicae influx into sugar beet fields is recorded weekly using yellow water pan traps. To date, only ELISA and RT-PCR assays have been described for BChV and BMYV detection in individual aphids. In this study, we describe for the first time two one-step TaqMan® RT-qPCR assays designed for the specific detection of BChV and BMYV in M. persicae after 7d incubation in water pan trap medium. Both viruses were reproducibly detected in individual aphids. After 7d incubation in trap medium, both viruses were reproducibly detected in individual aphids, as well as in one viruliferous aphid in a pool of 99 non-viruliferous aphids. Significant correlations can be shown between different mixing ratios of viruliferous to non-viruliferous aphids and Ct values of total RNA templates, allowing the percentage of viruliferous aphids in yellow water pan traps to be estimated using a standard curve. The described methodology provides a high sensitivity combined with a high sample throughput and can be used, after evaluation in the field, for practical monitoring, risk modelling and development of decision support systems for VY.
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Affiliation(s)
- Simon Borgolte
- Department of Phytopathology, Institute of Sugar Beet Research, Holtenser Landstraße 77, Göttingen D-37079, Germany.
| | - Wulf Menzel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany.
| | - Mark Varrelmann
- Department of Phytopathology, Institute of Sugar Beet Research, Holtenser Landstraße 77, Göttingen D-37079, Germany.
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Golikova EA, Alshevskaya AA, Alrhmoun S, Sivitskaya NA, Sennikov SV. TCR-T cell therapy: current development approaches, preclinical evaluation, and perspectives on regulatory challenges. J Transl Med 2024; 22:897. [PMID: 39367419 PMCID: PMC11451006 DOI: 10.1186/s12967-024-05703-9] [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: 06/21/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024] Open
Abstract
TCR-T cell therapy represents a promising advancement in adoptive immunotherapy for cancer treatment. Despite its potential, the development and preclinical testing of TCR-T cells face significant challenges. This review provides a structured overview of the key stages in preclinical testing, including in silico, in vitro, and in vivo methods, within the context of the sequential development of novel therapies. This review aimed to systematically outline the processes for evaluating TCR-T cells at each stage: from in silico approaches used to predict target antigens, assess cross-reactivity, and minimize off-target effects, to in vitro assays designed to measure cell functionality, cytotoxicity, and activation. Additionally, the review discusses the limitations of in vivo testing in animal models, particularly in accurately reflecting the human tumor microenvironment and immune responses. Performed analysis emphasizes the importance of these preclinical stages in the safe and effective development of TCR-T cell therapies. While current models provide valuable insights, we identify critical gaps, particularly in in vivo biodistribution and toxicity assessments, and propose the need for enhanced standardization and the development of more representative models. This structured approach aims to improve the predictability and safety of TCR-T cell therapy as it advances towards clinical application.
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Affiliation(s)
- Elena A Golikova
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Alina A Alshevskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia.
| | - Saleh Alrhmoun
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
| | - Natalia A Sivitskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Sergey V Sennikov
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
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Ashraf MA, Irfan S, Baig A, Zeeshan SM, Khan H, Ahmed I, Virani N, Roshan R. Role of Xpert PCR kit in assessing MRSA colonization in medical and surgical units of a tertiary care teaching hospital. BMC Infect Dis 2024; 24:1096. [PMID: 39358697 PMCID: PMC11448093 DOI: 10.1186/s12879-024-09710-5] [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: 02/09/2024] [Accepted: 08/02/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND AND RATIONALE Methicillin resistant Staphylococcus aureus (MRSA) colonization increases the risk of MRSA infection. Detecting MRSA colonization can influence postoperative outcomes and prolong hospital stay. The conventional standard culture method for detecting MRSA colonization has limitations in terms of sensitivity and turnaround time. Hence, we sought out use of Xpert PCR kit for prompt evaluation of MRSA colonization to support MRSA prevention in a tertiary care hospital in Karachi, Pakistan. MATERIALS AND METHODS During 1st April-31st December 2022, 290 nasal and skin swab samples were collected from 257 patients and processed using routine culture (as gold standard method) and PCR-based MRSA detection assay (MRSA Xpert). RESULTS A total of two hundred and ninety (290) swab samples from 257 patients were obtained, 33 of which were paired. The overall prevalence of MRSA colonization was 12% by both methods, with 90% of cases classified as community-associated (CA-MRSA) whereas 10% as hospital-acquired (HA-MRSA). The colonized group showed a higher subsequent MRSA infection rate (11% vs. 3.5%) compared to the noncolonized group. Culture identified 11% of screening samples as MRSA positive, Xpert MRSA assay showed 100% sensitivity and 95% specificity. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50. CONCLUSION Our study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Both conventional culture and Xpert MRSA methods showed comparable efficacy for detection of MRSA colonization. Larger-scale studies are recommended to validate these findings conclusively.
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Affiliation(s)
- Muhammad Arsalan Ashraf
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Seema Irfan
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan.
| | - Ammarah Baig
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Syed Mohammad Zeeshan
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Hira Khan
- Aga Khan Medical College and University, Karachi, Pakistan
| | - Israr Ahmed
- Section Microbiology, Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Nazleen Virani
- Department of Infection Prevention and Hospital Epidemiology, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
| | - Rozina Roshan
- Department of Infection Prevention and Hospital Epidemiology, Aga Khan University Hospital, Box 3500, Stadium Road, Karachi, 74800, Pakistan
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Li G, Cao L, Liu K, Dong Y, Yang Z, Luo J, Gao W, Lei L, Song Y, Du X, Li X, Gao W, Liu G. Targeting PHB2-mediated mitophagy alleviates nonesterified fatty acid-induced mitochondrial dysfunction in bovine mammary epithelial cells. J Dairy Sci 2024; 107:8494-8507. [PMID: 38876225 DOI: 10.3168/jds.2024-24800] [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: 02/17/2024] [Accepted: 05/14/2024] [Indexed: 06/16/2024]
Abstract
Mitochondrial dysfunction has been reported to occur in the mammary gland of dairy cows suffering from ketosis. Prohibitin 2 (PHB2) plays a crucial role in regulating mitophagy, which clears impaired mitochondria to maintain normal mitochondrial function. Therefore, the current study aimed to investigate how PHB2 mediates mitophagy, thereby influencing mitochondrial function in the immortalized bovine mammary epithelial cell line (MAC-T cells). First, mammary gland tissue and blood samples were collected from healthy cows (n = 15, BHB <0.6 mM) and cows with clinical ketosis (n = 15, BHB >3.0 mM). Compared with healthy cows, cows with clinical ketosis exhibited lower DMI, milk production, milk protein, milk lactose, and serum glucose. In contrast, milk fat, serum nonesterified fatty acids (NEFA) and BHB were greater in cows with clinical ketosis. The protein abundance of PHB2, peroxisome proliferator activated receptor-γ coactivator-1α (PGC-1α), mitofusin 2 (MFN2) in whole cell lysates (WCL), as well as PHB2, sequestosome-1 (SQSTM1, also called p62), microtubule-associated protein 1 light chain 3-II (MAP1LC3-II, also called LC3-II), and ubiquitinated proteins in mitochondrial fraction were significantly lower in cows with clinical ketosis. The ATP content of mammary gland tissue in cows with clinical ketosis was lower than that of healthy cows. Second, MAC-T were cultured and treated with NEFA (0, 0.3, 0.6, 1.2 mM). The MAC-T treated with 1.2 mM NEFA displayed decreased protein abundance of PHB2, PGC-1α, and MFN2 in WCL, as well as protein abundance of PHB2, p62, LC3-II, and ubiquitinated proteins in mitochondrial fraction. The content of ATP and JC-1 aggregates in 1.2 mM NEFA group were lower than in the 0 mM NEFA group. Additionally, 1.2 mM NEFA disrupted the fusion between mitochondria and lysosomes. The MAC-T were then pretreated with 100 nM rapamycin, followed by treatment with or without NEFA. Rapamycin alleviated impaired mitophagy and mitochondria dysfunction induced by 1.2 mM NEFA. Third, MAC-T were transfected with small interfering RNA to silence PHB2 or a plasmid for overexpression of PHB2, followed by treatment with or without NEFA. The silencing of PHB2 aggravated 1.2 mM NEFA-induced impaired mitophagy and mitochondrial dysfunction, whereas the overexpression of PHB2 alleviated these effects. Overall, this study provides evidence that PHB2, in regulation of mitophagy, is a mechanism for bovine mammary epithelial cells to counteract NEFA-induced mitochondrial dysfunction.
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Affiliation(s)
- Guojin Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liguang Cao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Kai Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yifei Dong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zifeng Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jianchun Luo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenrui Gao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lin Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yuxiang Song
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiliang Du
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xinwei Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenwen Gao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Guowen Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Soorni A, Rezvani M, Bigdeli H. Transcriptome-guided selection of stable reference genes for expression analysis in spinach. Sci Rep 2024; 14:22113. [PMID: 39333266 PMCID: PMC11436919 DOI: 10.1038/s41598-024-73444-2] [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: 05/07/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Accurate measurement of gene expression levels is vital for advancing plant biology research. This study explores the identification and validation of stable reference genes (RGs) for gene expression analysis in Spinacia oleracea. Leveraging transcriptome data from various developmental stages, we employed rigorous statistical analyses to identify potential RGs. A total of 1196 candidate genes were initially screened based on expression variability, with subsequent refinement using criteria such as low variance and stability. Among 12 commonly used candidate RGs, EF1α and H3 emerged as the most stable across diverse experimental conditions, while GRP and PPR exhibited lower stability. These findings were further validated through qRT-PCR assays and comprehensive statistical analyses, including geNorm, NormFinder, BestKeeper, and RefFinder. Our study underscores the importance of systematic RG selection to ensure accurate normalization in gene expression studies, particularly in the context of S. oleracea developmental stages and physiological processes like flowering. These validated RGs provide a robust foundation for future gene expression analysis in S. oleracea and contribute to the advancement of molecular research in plant biology.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | - Maryam Rezvani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Haniye Bigdeli
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Chen Y, Wang X, Zhang J, Jiang Q, Qiao B, He B, Yin W, Qiao J, Liu Y. Split crRNA with CRISPR-Cas12a enabling highly sensitive and multiplexed detection of RNA and DNA. Nat Commun 2024; 15:8342. [PMID: 39333528 PMCID: PMC11436650 DOI: 10.1038/s41467-024-52691-x] [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: 01/12/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024] Open
Abstract
The CRISPR-Cas12a system has revolutionized nucleic acid testing (NAT) with its rapid and precise capabilities, yet it traditionally required RNA pre-amplification. Here we develop rapid fluorescence and lateral flow NAT assays utilizing a split Cas12a system (SCas12a), consisting of a Cas12a enzyme and a split crRNA. The SCas12a assay enables highly sensitive, amplification-free, and multiplexed detection of miRNAs and long RNAs without complex secondary structures. It can differentiate between mature miRNA and its precursor (pre-miRNA), a critical distinction for precise biomarker identification and cancer progression monitoring. The system's specificity is further highlighted by its ability to detect DNA and miRNA point mutations. Notably, the SCas12a system can quantify the miR-21 biomarker in plasma from cervical cancer patients and, when combined with RPA, detect HPV at attomole levels in clinical samples. Together, our work presents a simple and cost-effective SCas12a-based NAT platform for various diagnostic settings.
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Affiliation(s)
- Yichuan Chen
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Junqi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Qingyuan Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Bin Qiao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450001, China
| | - Baoxia He
- Department of pharmacy, Affiliated Cancer Hospital of Zhengzhou University and Henan cancer hospital, Zhengzhou, Henan, 450003, China
| | - Wenhao Yin
- BravoVax Co. Ltd., Wuhan, Hubei, 430075, China
| | - Jie Qiao
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China.
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China.
- BravoVax Co. Ltd., Wuhan, Hubei, 430075, China.
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Kong Y, Jin P, Jia C, Qiao P, Zhang H, Dong Y, Yang Z, Zhou Y, Jung G, Hu J. A rapid real-time PCR assay for detecting Microdochium paspali causing sparse leaf patch on seashore paspalum and in environmental samples. PEST MANAGEMENT SCIENCE 2024. [PMID: 39300697 DOI: 10.1002/ps.8422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/29/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024]
Abstract
BACKGROUND Sparse leaf patch (SLP) is one of the most significant diseases affecting seashore paspalum (Paspalum vaginatum Sw.), caused by Microdochium paspali. Fast and accurate detection of this pathogen is crucial for effective disease management. However, conventional culture-based methods are time-consuming and often compromised by the presence of other saprophytic or endophytic fungi. RESULTS In this study, we developed a real-time fluorescent quantitative (q)PCR method based on the internal transcribed spacer (ITS) region of the ribosomal RNA gene to rapidly detect and quantify M. paspali. The qPCR assay demonstrated the ability to detect all 12 tested isolates of M. paspali, with no cross-reactions observed when tested against 30 isolates of other fungal pathogens from turfgrass samples. The detection limit of the qPCR method was as low as 3.65 × 102 copies μL-1 of M. paspali genomic DNA, and the entire detection process could be completed within 1 h. The fluorescence signal was detectable in the leaf tissues of seashore paspalum without apparent disease symptoms as early as 24 h postinoculation with M. paspali. Moreover, the qPCR method successfully detected M. paspali in both asymptomatic and symptomatic turfgrass samples, including leaf, stem, root and rhizosphere soil, indicating that this assay can significantly enhance the detection of M. paspali. CONCLUSION The study developed a rapid real-time qPCR assay for the detection of M. paspali causing SLP on seashore paspalum and in environmental samples, which has important implications for early warning and management of SLP. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yixuan Kong
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Peiyuan Jin
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Chenchen Jia
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Panpan Qiao
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Huangwei Zhang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yinglu Dong
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhimin Yang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yuxin Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Geunhwa Jung
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Jian Hu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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12
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Khademi P, Tukmechi A, Sgroi G, Ownagh A, Enferadi A, Khalili M, Mardani K. Molecular and genotyping techniques in diagnosis of Coxiella burnetii: An overview. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105655. [PMID: 39116951 DOI: 10.1016/j.meegid.2024.105655] [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: 05/18/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Although we live in the genomic era, the accessibility of the complete genome sequence of Coxiella burnetii, the etiological agent of Q fever, has increased knowledge in the field of genomic diversity of this agent However, it is still somewhat of a "question" microorganism. The epidemiology of Q fever is intricate due to its global distribution, repository and vector variety, as well as absence of surveys defining the dynamic interaction among these factors. Moreover, C. burnetii is a microbial agent that can be utilized as a bioterror weapon. Therefore, typing techniques used to recognize the strains can also be used to trace infections back to their source which is of great significance. In this paper, the latest and current typing techniques of C. burnetii spp. are reviewed illustrating their advantages and constraints. Recently developed multi locus VNTR analysis (MLVA) and single-nucleotide polymorphism (SNP) typing methods are promising in improving diagnostic capacity and enhancing the application of genotyping techniques for molecular epidemiologic surveys of the challenging pathogen. However, most of these studies did not differentiate between C. burnetii and Coxiella-like endosymbionts making it difficult to estimate the potential role that ticks play in the epidemiology of Q fever. Therefore, it is necessary to analyze the vector competence of different tick species to transmit C. burnetii. Knowledge of the vector and reservoir competence of ticks is important for taking adequate preventive measures to limit infection risks. The significant prevalence observed for the IS1111 gene underscores its substantial presence, while other genes display comparatively lower prevalence rates. Methodological variations, particularly between commercial and non-commercial kit-based methods, result in different prevalence outcomes. Variations in sample processing procedures also lead to significant differences in prevalence rates between mechanical and non-mechanical techniques.
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Affiliation(s)
- Peyman Khademi
- Department of Microbiology and Food Hygiene, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran; Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Amir Tukmechi
- Department of Microbiology and Food Hygiene, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran.
| | - Giovanni Sgroi
- Department of Animal Health, Experimental Zooprophylactic Institute of southern Italy, Portici, Naples, Italy
| | - Abdulghaffar Ownagh
- Department of Microbiology and Food Hygiene, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran
| | - Ahmad Enferadi
- Department of Microbiology and Food Hygiene, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Karim Mardani
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
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Zhan S, Zhang L, Zhong T, Wang L, Guo J, Cao J, Li L, Zhang H. Evaluation of Reference Gene Stability in Goat Skeletal Muscle Satellite Cells during Proliferation and Differentiation Phases. Animals (Basel) 2024; 14:2479. [PMID: 39272264 PMCID: PMC11394193 DOI: 10.3390/ani14172479] [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: 07/23/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
The process of skeletal muscle development is intricate and involves the regulation of a diverse array of genes. Accurate gene expression profiles are crucial for studying muscle development, making it essential to choose the right reference genes for real-time quantitative PCR (RT-qPCR). In the present study, eight candidate reference genes were identified from our previous transcriptome sequencing analysis of caprine skeletal muscle satellite cells (MuSCs), and two traditional reference genes (ACTB and GAPDH) were assessed. The quantitative levels of the candidate reference genes were determined through the RT-qPCR technique, while the stability of their expression was evaluated utilizing the GeNorm, NormFinder, BestKeeper, and RefFinder programs. Furthermore, the chosen reference genes were utilized for the normalization of the gene expression levels of PCNA and Myf5. It was determined that conventional reference genes, including ACTB and GAPDH, were not appropriate for normalizing target gene expression. Conversely, RPL14 and RPS15A, identified through RNA sequencing analysis, exhibited minimal variability and were identified as the optimal reference genes for normalizing gene expression during the proliferation and differentiation of goat MuSCs. Our research offers a validated panel of optimal reference genes for the detection of differentially expressed genes in goat muscle satellite cells using RT-qPCR.
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Affiliation(s)
- Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lufei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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14
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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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15
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de Brito MWD, de Carvalho SS, Mota MBDS, Mesquita RD. RNA-seq validation: software for selection of reference and variable candidate genes for RT-qPCR. BMC Genomics 2024; 25:697. [PMID: 39014352 PMCID: PMC11251314 DOI: 10.1186/s12864-024-10511-y] [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: 03/12/2024] [Accepted: 06/06/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is one of the most widely used gene expression analyses for validating RNA-seq data. This technique requires reference genes that are stable and highly expressed, at least across the different biological conditions present in the transcriptome. Reference and variable candidate gene selection is often neglected, leading to misinterpretation of the results. RESULTS We developed a software named "Gene Selector for Validation" (GSV), which identifies the best reference and variable candidate genes for validation within a quantitative transcriptome. This tool also filters the candidate genes concerning the RT-qPCR assay detection limit. GSV was compared with other software using synthetic datasets and performed better, removing stable low-expression genes from the reference candidate list and creating the variable-expression validation list. GSV software was used on a real case, an Aedes aegypti transcriptome. The top GSV reference candidate genes were selected for RT-qPCR analysis, confirming that eiF1A and eiF3j were the most stable genes tested. The tool also confirmed that traditional mosquito reference genes were less stable in the analyzed samples, highlighting the possibility of inappropriate choices. A meta-transcriptome dataset with more than ninety thousand genes was also processed successfully. CONCLUSION The GSV tool is a time and cost-effective tool that can be used to select reference and validation candidate genes from the biological conditions present in transcriptomic data.
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Affiliation(s)
- Márcio Wilson Dias de Brito
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- RioGen Tecnologia, Rio de Janeiro, Brazil
| | | | - Maria Beatriz Dos Santos Mota
- RioGen Tecnologia, Rio de Janeiro, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Dias Mesquita
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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16
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Jiao JY, Abdugheni R, Zhang DF, Ahmed I, Ali M, Chuvochina M, Dedysh SN, Dong X, Göker M, Hedlund BP, Hugenholtz P, Jangid K, Liu SJ, Moore ERB, Narsing Rao MP, Oren A, Rossello-Mora R, Rekadwad BN, Salam N, Shu W, Sutcliffe IC, Teo WFA, Trujillo ME, Venter SN, Whitman WB, Zhao G, Li WJ. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. Natl Sci Rev 2024; 11:nwae168. [PMID: 39071100 PMCID: PMC11275469 DOI: 10.1093/nsr/nwae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 07/30/2024] Open
Abstract
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig D-38124, Germany
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Kamlesh Jangid
- Bioenergy Group, MACS Collection of Microorganisms, Agharkar Research Institute, Pune 411004, India
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Edward R B Moore
- Department of Infectious Disease, Institute for Biomedicine, and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40234, Sweden
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles 070190, Spain
| | - Bhagwan Narayan Rekadwad
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nimaichand Salam
- National Agri-Food Biotechnology Institute, Knowledge City, Mohali 140306, India
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca 37008, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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17
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Sogore T, Guo M, Sun N, Jiang D, Shen M, Ding T. Microbiological and chemical hazards in cultured meat and methods for their detection. Compr Rev Food Sci Food Saf 2024; 23:e13392. [PMID: 38865212 DOI: 10.1111/1541-4337.13392] [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: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Cultured meat, which involves growing meat in a laboratory rather than breeding animals, offers potential benefits in terms of sustainability, health, and animal welfare compared to conventional meat production. However, the cultured meat production process involves several stages, each with potential hazards requiring careful monitoring and control. Microbial contamination risks exist in the initial cell collection from source animals and the surrounding environment. During cell proliferation, hazards may include chemical residues from media components such as antibiotics and growth factors, as well as microbial issues from improper bioreactor sterilization. In the differentiation stage where cells become muscle tissue, potential hazards include residues from scaffolding materials, microcarriers, and media components. Final maturation and harvesting stages risk environmental contamination from nonsterile conditions, equipment, or worker handling if proper aseptic conditions are not maintained. This review examines the key microbiological and chemical hazards that must be monitored and controlled during the manufacturing process for cultured meats. It describes some conventional and emerging novel techniques that could be applied for the detection of microbial and chemical hazards in cultured meat. The review also outlines the current evolving regulatory landscape around cultured meat and explains how thorough detection and characterization of microbiological and chemical hazards through advanced analytical techniques can provide crucial data to help develop robust, evidence-based food safety regulations specifically tailored for the cultured meat industry. Implementing new digital food safety methods is recommended for further research on the sensitive and effective detection of microbiological and chemical hazards in cultured meat.
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Affiliation(s)
- Tahirou Sogore
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Meimei Guo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Na Sun
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Donglei Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - Mofei Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
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18
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Mladenović M, Jarić S, Mundžić M, Pavlović A, Bobrinetskiy I, Knežević NŽ. Biosensors for Cancer Biomarkers Based on Mesoporous Silica Nanoparticles. BIOSENSORS 2024; 14:326. [PMID: 39056602 PMCID: PMC11274377 DOI: 10.3390/bios14070326] [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: 06/12/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Mesoporous silica nanoparticles (MSNs) exhibit highly beneficial characteristics for devising efficient biosensors for different analytes. Their unique properties, such as capabilities for stable covalent binding to recognition groups (e.g., antibodies or aptamers) and sensing surfaces, open a plethora of opportunities for biosensor construction. In addition, their structured porosity offers capabilities for entrapping signaling molecules (dyes or electroactive species), which could be released efficiently in response to a desired analyte for effective optical or electrochemical detection. This work offers an overview of recent research studies (in the last five years) that contain MSNs in their optical and electrochemical sensing platforms for the detection of cancer biomarkers, classified by cancer type. In addition, this study provides an overview of cancer biomarkers, as well as electrochemical and optical detection methods in general.
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Affiliation(s)
| | | | | | | | | | - Nikola Ž. Knežević
- BioSense Institute, University of Novi Sad, Dr Zorana Djindjica 1, 21000 Novi Sad, Serbia; (M.M.); (S.J.); (M.M.); (A.P.)
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19
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Jerala M, Remic T, Hauptman N, Homan P, Zajšek N, Petitjean M, Chen L, Zidar N. Thrombospondin 2, matrix Gla protein and digital analysis identified distinct fibroblast populations in fibrostenosing Crohn's disease. Sci Rep 2024; 14:13810. [PMID: 38877292 PMCID: PMC11178913 DOI: 10.1038/s41598-024-64672-7] [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: 12/20/2023] [Accepted: 06/11/2024] [Indexed: 06/16/2024] Open
Abstract
Fibrosis is an important complication in inflammatory bowel diseases. Previous studies suggest an important role of matrix Gla protein (MGP) and thrombospondin 2 (THBS2) in fibrosis in various organs. Our aim was to analyse their expression together with regulatory miRNAs in submucosal and subserosal fibroblasts in ulcerative colitis (UC) and Crohn's disease (CD) using immunohistochemistry and qPCR. Digital pathology was used to compare collagen fibre characteristics of submucosal and subserosal fibrosis. Immunohistochemistry showed expression of MGP, but not THBS2 in submucosa in UC and CD. In the subserosa, there was strong staining for both proteins in CD but not in UC. qPCR showed significant upregulation of THBS2 and MGP genes in CD subserosa compared to the submucosa. Digital pathology analysis revealed higher proportion of larger and thicker fibres that were more tortuous and reticulated in subserosal fibrosis compared to submucosal fibrosis. These results suggest distinct fibroblast populations in fibrostenosing CD, and are further supported by image analysis showing significant differences in the morphology and architecture of collagen fibres in submucosal fibrosis in comparison to subserosal fibrosis. Our study is the first to describe differences in submucosal and subserosal fibroblast populations, contributing to understanding of the pathogenesis of fibrostenosis in CD.
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Affiliation(s)
- Miha Jerala
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tinkara Remic
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Nina Hauptman
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Pia Homan
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Neža Zajšek
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | | | - Li Chen
- PharmaNest Inc., Princeton, NJ, 08540, USA
| | - Nina Zidar
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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20
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Mostufa S, Rezaei B, Ciannella S, Yari P, Gómez-Pastora J, He R, Wu K. Advancements and Perspectives in Optical Biosensors. ACS OMEGA 2024; 9:24181-24202. [PMID: 38882113 PMCID: PMC11170745 DOI: 10.1021/acsomega.4c01872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024]
Abstract
Optical biosensors exhibit immense potential, offering extraordinary possibilities for biosensing due to their high sensitivity, reusability, and ultrafast sensing capabilities. This review provides a concise overview of optical biosensors, encompassing various platforms, operational mechanisms, and underlying physics, and it summarizes recent advancements in the field. Special attention is given to plasmonic biosensors and metasurface-based biosensors, emphasizing their significant performance in bioassays and, thus, their increasing attraction in biosensing research, positioning them as excellent candidates for lab-on-chip and point-of-care devices. For plasmonic biosensors, we emphasize surface plasmon resonance (SPR) and its subcategories, along with localized surface plasmon resonance (LSPR) devices and surface enhance Raman spectroscopy (SERS), highlighting their ability to perform diverse bioassays. Additionally, we discuss recently emerged metasurface-based biosensors. Toward the conclusion of this review, we address current challenges, opportunities, and prospects in optical biosensing. Considering the advancements and advantages presented by optical biosensors, it is foreseeable that they will become a robust and widespread platform for early disease diagnostics.
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Affiliation(s)
- Shahriar Mostufa
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Bahareh Rezaei
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Parsa Yari
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jenifer Gómez-Pastora
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Rui He
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Kai Wu
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
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21
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Mir M, Khan AU, Khan A. Pharmacological investigation of taxifolin for its therapeutic potential in depression. Heliyon 2024; 10:e30467. [PMID: 38694040 PMCID: PMC11061746 DOI: 10.1016/j.heliyon.2024.e30467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
The current study aimed to investigate the influence of taxifolin on depression symptoms alleviation in Male Sprague-Dawley rats by targeting underlying pathways of depression. Molecular docking analyses were conducted to validate taxifolin's binding affinities against various targets. In silico analysis of taxifolin revealed various aspects of post docking interactions with different protein targets. Depression was induced in rats via intraperitoneal injection of Lipopolysaccharide (LPS; 500 μ g/Kg) for 14 alternative days. Rats (n = 6/group) were randomly assigned to four groups: (i) Saline/Control, (ii) Disease (LPS 500 μg/kg), (iii) Standard (fluoxetine 20 mg/kg), and (iv) Treatment (taxifolin 20 mg/kg). At the end of the in vivo study, brain samples were used for biochemical and morphological analysis. Taxifolin exhibited neuroprotective effects, as evidenced by behavioral studies, antioxidant analysis, histopathological examination, immunohistochemistry, ELISA and RT PCR, indicating an increase number of surviving neurons, normalization of cell size and shape, and reduction in vacuolization. Taxifolin also decreased inflammatory markers such as TNF-α, NF-κb, IL-6 and COX-2, while significantly upregulating and activating the protective PPAR-γ pathway, through which it reduces the oxidative stress, neuroinflammation, neurodegeneration, thereby ameliorating depression symptoms in experimental rat model of depression. Our finding suggests that taxifolin act as neuroprotective agent partially mediated through PPAR-γ pathway.
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Affiliation(s)
- Maha Mir
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Arif-ullah Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Aslam Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
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22
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Chang TD, Xu YZ, Wang YF, Wang XR, Tsai SH, Wu ZB, Tzean Y, Lin YH. Development of Rapid Detection Methods for Fusarium oysporum f. sp. melonis in Melon Seeds. Int J Mol Sci 2024; 25:5371. [PMID: 38791411 PMCID: PMC11121191 DOI: 10.3390/ijms25105371] [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: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Melon (Cucumis melo L.) is a global commercial crop that is sensitive to seed-borne wilt infections caused by Fusarium oxysporum f. sp. melonis (Fom). To address the challenge of detecting Fom contamination, we designed a probe-based real-time PCR method, TDCP2, in combination with rapid or column-based DNA extraction protocols to develop reliable molecular detection methods. Utilizing TDCP2, the detection rate reached 100% for both artificially Fom-inoculated (0.25-25%) and pod-inoculated melon seeds in conjunction with DNA samples from either the rapid or column-based extraction protocol. We performed analyses of precision, recall, and F1 scores, achieving a maximum F1 score of 1 with TDCP2, which highlights the robustness of the method. Additionally, intraday and interday assays were performed, which revealed the high reproducibility and stability of column-based DNA extraction protocols combined with TDCP2. These metrics confirm the reliability of our developed protocols, setting a foundation for future enhancements in seed pathology diagnostics and potentially broadening their applicability across various Fom infection levels. In the future, we hope that these methods will reduce food loss by improving the control and management of melon diseases.
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Affiliation(s)
- Tsai-De Chang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
| | - Ya-Zhen Xu
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
| | - Yu-Fen Wang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
| | - Xing-Ru Wang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
| | - Shang-Han Tsai
- Bachelor Program in Scientific Agriculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Zhong-Bin Wu
- Department of Horticulture and Landscape Architecture, National Taitung Jr. College, Taitung 95045, Taiwan;
| | - Yuh Tzean
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
| | - Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; (T.-D.C.); (Y.-Z.X.); (Y.-F.W.); (X.-R.W.)
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23
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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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24
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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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25
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Kalita A, Das M. Aquaporins (AQPs) as a marker in the physiology of inflammation and its interaction studies with garcinol. Inflammopharmacology 2024; 32:1575-1592. [PMID: 38267609 DOI: 10.1007/s10787-023-01412-9] [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: 06/13/2023] [Accepted: 10/17/2023] [Indexed: 01/26/2024]
Abstract
Aquaporins like AQP1, AQP3, and AQP4 are known to be involved in the pathophysiology of inflammation based on earlier reports. This study aimed to evaluate the involvement of Aquaporins as a potential target of inflammation. The study also investigates the efficacy of methanolic extract of Garcinia (GME) and its potent phytocompound (garcinol) against the Aquaporins involved in inflammation. siRNA silencing of AQP3 was carried out in RAW264.7 cells followed by LPS stimulation (1 µg/ml) and assessment of important markers of inflammation including NO, PGE2, TNF-α, IL-6, IL-1β, CCL20, iNOS and COX-2. To assess the anti-inflammatory potential of Garcinia extract and garcinol, cells were stimulated with 1 µg/ml LPS in the absence and presence of increasing concentrations of GME and garcinol. During the experimental period, extract concentrations (115 µg/ml and 230 µg/ml for RAW264.7; 118 µg/ml and 236 µg/ml for THP-1) and garcinol concentrations (6 µM and 12 µM for RAW264.7; 3 µM and 6 µM for THP-1) were selected based on the IC50. The anti-inflammatory effects were assessed by measuring the levels of TNF-α, IL-1β, IL-6, and CCL20 in LPS-stimulated cells. The AQP expression was studied at transcriptional and translational levels using qPCR and Western blot analysis respectively. AQP3 knockdown significantly decreased the NO, PGE2, TNF-α, IL-1β levels along with iNOS and COX-2 mRNA expression. LPS stimulation led to a significant increase in the mRNA and protein level expression AQP1, AQP3, and AQP4 in RAW264.7 cells; and AQP1 and AQP3 in THP-1 cells indicating their role as markers of inflammation. GME and garcinol effectively suppressed the LPS-induced proinflammatory cytokine production in both cell lines. The results indicate that AQP1, AQP3, and AQP4 could play a crucial role as markers of inflammation. Anti-inflammatory agents like Garcinia could potentially decrease the expression of such AQPs, thus inhibiting the inflammatory process.
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Affiliation(s)
- Anuradha Kalita
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, Assam, 781014, India
| | - Manas Das
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, Assam, 781014, India.
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26
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Lim J, Han W, Thang LTH, Lee YW, Shin JH. Customizable Nichrome Wire Heaters for Molecular Diagnostic Applications. BIOSENSORS 2024; 14:152. [PMID: 38534259 DOI: 10.3390/bios14030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Accurate sample heating is vital for nucleic acid extraction and amplification, requiring a sophisticated thermal cycling process in nucleic acid detection. Traditional molecular detection systems with heating capability are bulky, expensive, and primarily designed for lab settings. Consequently, their use is limited where lab systems are unavailable. This study introduces a technique for performing the heating process required in molecular diagnostics applicable for point-of-care testing (POCT), by presenting a method for crafting customized heaters using freely patterned nichrome (NiCr) wire. This technique, fabricating heaters by arranging protrusions on a carbon black-polydimethylsiloxane (PDMS) cast and patterning NiCr wire, utilizes cost-effective materials and is not constrained by shape, thereby enabling customized fabrication in both two-dimensional (2D) and three-dimensional (3D). To illustrate its versatility and practicality, a 2D heater with three temperature zones was developed for a portable device capable of automatic thermocycling for polymerase chain reaction (PCR) to detect Escherichia coli (E. coli) O157:H7 pathogen DNA. Furthermore, the detection of the same pathogen was demonstrated using a customized 3D heater surrounding a microtube for loop-mediated isothermal amplification (LAMP). Successful DNA amplification using the proposed heater suggests that the heating technique introduced in this study can be effectively applied to POCT.
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Affiliation(s)
- Juhee Lim
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Won Han
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Le Tran Huy Thang
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Yong Wook Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- School of Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Joong Ho Shin
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence, Pukyong National University, Busan 48513, Republic of Korea
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27
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Hosseinzadeh S, Masoudi AA. Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries. Genome 2024; 67:78-89. [PMID: 37983732 DOI: 10.1139/gen-2023-0055] [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: 11/22/2023]
Abstract
Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE-LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility.
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Affiliation(s)
- Shahram Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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28
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Hays A, Wissel M, Colletti K, Soon R, Azadeh M, Smith J, Doddareddy R, Chalfant M, Adamowicz W, Ramaswamy SS, Dholakiya SL, Guelman S, Gullick B, Durham J, Rennier K, Nagilla P, Muruganandham A, Diaz M, Tierney C, John K, Valentine J, Lockman T, Liu HY, Moritz B, Ouedraogo JP, Piche MS, Smet M, Murphy J, Koenig K, Zybura A, Vyhlidal C, Mercier J, Jani N, Kubista M, Birch D, Morse K, Johansson O. Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. AAPS J 2024; 26:24. [PMID: 38316745 DOI: 10.1208/s12248-023-00880-9] [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: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.
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Affiliation(s)
- Amanda Hays
- BioAgilytix Laboratories, Durham, North Carolina, USA.
| | - Mark Wissel
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | - Russell Soon
- BioMarin Pharmaceutical Inc., Novato, California, USA
| | - Mitra Azadeh
- Ultragenyx Pharmaceutical Inc., Novato, Calfornia, USA
| | | | | | | | - Wendy Adamowicz
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | | | | | | | - Bryan Gullick
- BioAgilytix Laboratories, Durham, North Carolina, USA
| | | | | | - Pruthvi Nagilla
- Asher Biotherapeutics, Inc., South San Francisco, California, USA
| | | | - Manisha Diaz
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | | | | | - Timothy Lockman
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | - Hsing-Yin Liu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | | | | | - Jacqueline Murphy
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kaylyn Koenig
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Agnes Zybura
- Labcorp Drug Development, Greenfield, Indiana, USA
| | - Carrie Vyhlidal
- KCAS Bioanalytical and Biomarker Services, Shawnee, Kansas, USA
| | | | - Niketa Jani
- BioAgilytix Laboratories, Boston, Massachusetts, USA
| | - Mikael Kubista
- Institute of Biotechnology Czech Academy of Sciences, Prague, Czech Republic
| | - Donald Birch
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Karlin Morse
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
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29
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Shang L, Liang P, Xu L, Xue Y, Liu K, Wang Y, Bao X, Chen F, Peng H, Wang Y, Ju J, Li B. Stable SERS Detection of Lactobacillus fermentum Using Optical Tweezers in a Microfluidic Environment. Anal Chem 2024; 96:248-255. [PMID: 38113377 DOI: 10.1021/acs.analchem.3c03852] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Rapid identification of fermented lactic acid bacteria has long been a challenge in the brewing industry. This study combined label-free surface-enhanced Raman scattering (SERS) and optical tweezer technology to construct a test platform within a microfluidic environment. Six kinds of lactic acid bacteria common in industry were tested to prove the stability of the SERS spectra. The results demonstrated that the utilization of optical tweezers to securely hold the bacteria significantly enhanced the stability of the SERS spectra. Furthermore, SVM and XGBoost machine learning algorithms were utilized to analyze the obtained Raman spectra for identification, and the identification accuracies exceeded 95% for all tested lactic acid bacteria. The findings of this study highlight the crucial role of optical tweezers in improving the stability of SERS spectra by capturing bacteria in a microfluidic environment, prove that this technology could be used in the rapid identification of lactic acid bacteria, and show great significance in expanding the applicability of the SERS technique for other bacterial testing purposes.
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Affiliation(s)
- Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lei Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, P. R. China
| | - Ying Xue
- HOOKE Instruments Ltd, Changchun 130031, P. R. China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yuntong Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaodong Bao
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fuyuan Chen
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hao Peng
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yu Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Ju
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, P. R. China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- HOOKE Instruments Ltd, Changchun 130031, P. R. China
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Selvakesavan RK, Nuc M, Kolarčik V, Krajewski P, Franklin G. Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures. Sci Data 2024; 11:42. [PMID: 38184679 PMCID: PMC10771467 DOI: 10.1038/s41597-023-02878-6] [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: 07/17/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
Hypericum is a large genus that includes more than 500 species of pharmacological, ecological and conservation value. Although latest advances in sequencing technologies were extremely exploited for generating and assembling genomes of many living organisms, annotated whole genome sequence data is not publicly available for any of the Hypericum species so far. Bioavailability of secondary metabolites varies for different tissues and the data derived from different cultures will be a valuable tool for comparative studies. Here, we report the single molecule real-time sequencing (SMRT) data sets of Hypericum perforatum L. plantlets and cell suspension cultures for the first time. Sequencing data from cell suspension cultures yielded more than 33,000 high-quality transcripts from 20 Gb of raw data, while more than 55,000 high-quality transcripts were obtained from 35 Gb of raw data from plantlets. This dataset is a valuable tool for comparative transcriptomic analysis and will help to understand the unknown biosynthetic pathways of high medicinal value in the Hypericum genus.
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Affiliation(s)
- Rajendran K Selvakesavan
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
- Department of Biotechnology, PSGR Krishnammal College for Women, Coimbatore, 641004, India
| | - Maria Nuc
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-041 54, Košice, Slovakia
| | - Paweł Krajewski
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Holmes AE, Baerwald MR, Rodzen J, Schreier BM, Mahardja B, Finger AJ. Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches. PeerJ 2024; 12:e16453. [PMID: 38188170 PMCID: PMC10768661 DOI: 10.7717/peerj.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/23/2023] [Indexed: 01/09/2024] Open
Abstract
Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.
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Affiliation(s)
- Ann E. Holmes
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
- Graduate Group in Ecology, University of California, Davis, Davis, California, United States
| | - Melinda R. Baerwald
- California Department of Water Resources, West Sacramento, California, United States
| | - Jeff Rodzen
- Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, United States
| | - Brian M. Schreier
- California Department of Water Resources, West Sacramento, California, United States
| | - Brian Mahardja
- Bureau of Reclamation, US Department of the Interior, Sacramento, California, United States
| | - Amanda J. Finger
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
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Li WX, Cai LT, Huang YP, Huang YQ, Pan SH, Liu ZL, Ndandala CB, Shi G, Deng SP, Shi HJ, Li GL, Jiang DN. Sequence identification and expression characterization of leptin in the spotted scat, Scatophagus argus. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110882. [PMID: 37562672 DOI: 10.1016/j.cbpb.2023.110882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Scatophagus argus is an important marine culture fish in South and South-East Asia, including Southeast coastal areas of China. Artificial propagation technology for S. argus is not optimum; thus further studies on its reproduction biology are required. Although previous studies have shown that leptin (Lep) can regulate fish reproduction, the role of lep genes in S. argus is unknown. Herein, in silico analysis showed that S. argus has two lep genes (lepa and lepb). Protein 3D-structure prediction showed that Lepa has four α-helices (similar to mammals), while Lepb only has three. Tissue distribution analysis showed that lepa is highly expressed in the liver, whereas lepb was not detected in any tissue. Notably, lepr was expressed in all tissues. Lepa mRNA expression levels in the liver and serum Lep, estradiol (E2) and vitellogenin (Vtg) levels of female fish were significantly higher in ovaries at stage IV than in ovaries at stage II. Serum E2 levels were significantly positively correlated with Vtg levels in female fish at different development stages, while serum E2 was not correlated with Lep levels. Consistently, in vitro incubation of the liver with E2 significantly up-regulated vtga, while it did not affect lepa expression. Recombinant Lep (10 nM) significantly up-regulated chicken gonadotropin-releasing hormone (cGnRH/GnRH-II) in the hypothalamus and GnRH receptor (GnRHR) and luteinizing hormone beta (Lhb) in the pituitary. These results suggest that lepa regulates female reproduction in S. argus.
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Affiliation(s)
- Wan-Xin Li
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Li-Ting Cai
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Yan-Ping Huang
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Yuan-Qing Huang
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Shu-Hui Pan
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Zhi-Long Liu
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Charles Brighton Ndandala
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Gang Shi
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Si-Ping Deng
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Hong-Juan Shi
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Guang-Li Li
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China
| | - Dong-Neng Jiang
- Fisheries College of Guangdong Ocean University, Guangdong Province Famous Fish Reproduction Regulation and Breeding Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, 524088 Zhanjiang, China.
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Wendelboe Olsen K, Hedley PL, Hagen CM, Rode L, Placing S, Wøjdemann KR, Shalmi AC, Sundberg K, Nørremølle A, Tabor A, Elson JL, Christiansen M. The significance of mitochondrial haplogroups in preeclampsia risk. Pregnancy Hypertens 2023; 34:146-151. [PMID: 37979242 DOI: 10.1016/j.preghy.2023.11.001] [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: 06/27/2023] [Revised: 10/02/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
OBJECTIVE To determine whether mitochondrial haplogroups function as disease-modifiers or as susceptibility factors in preeclampsia using a traditional haplogroup association model. METHODS This retrospective study haplotyped 235 control and 78 preeclamptic pregnancies from Denmark using either real-time PCR or Sanger sequencing depending on the rarity of the haplogroup. RESULTS No significant association between haplogroups and the risk of preeclampsia was found, nor was any role for haplogroups in disease severity uncovered. CONCLUSION Mitochondrial haplogroups are not associated with preeclampsia or the severity of preeclampsia in the Danish population. However, this study cannot exclude a role for less common mtDNA variation. Models that can examine these should be applied in preeclamptic patients.
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Affiliation(s)
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark; Brazen Bio, Los Angeles, CA, USA
| | - Christian M Hagen
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Rode
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, 2600 Glostrup, Denmark
| | - Sophie Placing
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Karen R Wøjdemann
- Department of Gynecology and Obstetrics, Bornholm Hospital, 3700 Rønne, Bornholm, Denmark
| | | | - Karin Sundberg
- Center of Fetal Medicine, Department of Obstetrics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne Nørremølle
- Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Ann Tabor
- Center of Fetal Medicine, Department of Obstetrics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Medical and Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Joanna L Elson
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark; Biosciences Institute Newcastle University, Newcastle, UK; The Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa.
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Chen J, Chen Z, Zhang J, Zhuang W, Zheng X. Screening of reliable reference genes for the normalization of RT-qPCR in chicken gastrointestinal tract. Poult Sci 2023; 102:103169. [PMID: 37918133 PMCID: PMC10641542 DOI: 10.1016/j.psj.2023.103169] [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: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
The application of reverse transcription quantitative real-time PCR technology for the production of gene tissue expression profiles is a widely employed approach in molecular biology research. It is imperative to ascertain internal reference genes that exhibit stable expression across diverse tissues to ensure the precision of tissue gene expression profiles. While there have been studies documenting the most suitable reference genes for various tissues in chickens, there is a dearth of research on the identification of reference genes in the gastrointestinal (GI) tract of chickens. This study utilized 4 different algorithms (Delta CT, BestKeeper, NormFinder, and Genorm) to assess the stability of 19 internal reference genes in various GI tract tissues, including individual GI tract tissues, the anterior and posterior GI tract, and the entire GI tissue. The RefFinder software was employed to comprehensively rank these genes. The research findings successfully identified the most appropriate internal reference genes for each type of GI tissue. Furthermore, TBP, DNAJC24, Polr2b, RPL13, andAp2m exhibited stable expression in the entire and posterior GI tract, whereas HMBS, TBP, Ap2m, GUSB, DNAJC24, and RPL13 demonstrated stable expression in the anterior GI tract. However, the internal reference genes commonly utilized, namely β-Actin, 18s RNA, and ALB, exhibit poor stability and are not advised for future investigations concerning gene expression in the GI region. Consequently, MUC2 and CDX1, 2 genes that specifically express in the gut, were chosen for examination to ascertain the stability of the aforementioned internal reference genes in this particular study. In summary, this study presents a relatively stable set of internal reference genes that can be employed to enhance the precision of quantifying mRNA expression levels in functional genes within the chicken GI tract.
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Affiliation(s)
- Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ziwei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jilong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Wuchao Zhuang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xiaotong Zheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China.
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Guo X, Ma Y, Wang H, Yin H, Shi X, Chen Y, Gao G, Sun L, Wang J, Wang Y, Fan D. Status and developmental trends in recombinant collagen preparation technology. Regen Biomater 2023; 11:rbad106. [PMID: 38173768 PMCID: PMC10761200 DOI: 10.1093/rb/rbad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Recombinant collagen is a pivotal topic in foundational biological research and epitomizes the application of critical bioengineering technologies. These technological advancements have profound implications across diverse areas such as regenerative medicine, organ replacement, tissue engineering, cosmetics and more. Thus, recombinant collagen and its preparation methodologies rooted in genetically engineered cells mark pivotal milestones in medical product research. This article provides a comprehensive overview of the current genetic engineering technologies and methods used in the production of recombinant collagen, as well as the conventional production process and quality control detection methods for this material. Furthermore, the discussion extends to foresee the strides in physical transfection and magnetic control sorting studies, envisioning an enhanced preparation of recombinant collagen-seeded cells to further fuel recombinant collagen production.
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Affiliation(s)
- Xiaolei Guo
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Yuan Ma
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Hang Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hongping Yin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xinli Shi
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Yiqin Chen
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Guobiao Gao
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Lei Sun
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Jiadao Wang
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials & College of Biomedical Engineering, Sichuan University, Chengdu 610064, China
| | - Daidi Fan
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
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36
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Gu M, Yi X, Shang Z, Nong X, Lin M, Xia F. A fuel-initiated DNA molecular machine for microRNA detection in serum via poly-adenine-mediated spherical nucleic acids. J Mater Chem B 2023; 11:11052-11063. [PMID: 37946538 DOI: 10.1039/d3tb02361c] [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: 11/12/2023]
Abstract
MicroRNAs (miRNAs) have been identified as promising disease diagnostic biomarkers. However, it is challenging to sensitively detect miRNAs, especially in complex biological environments, due to their low abundance and small size. Herein, we have developed a DNA-fueled molecular machine for sensitive detection of miRNA-22 (miR-22) in undiluted serum by combining poly-adenine-mediated spherical nucleic acids (polyA-SNAs) with a toehold mediated strand displacement reaction (TMSDR). The polyA-SNAs are constructed by the assembly of diblock DNA probes on a AuNP surface through the high binding affinity of polyA to AuNPs. The surface density of the diblock DNA probe can be controlled by tuning the length of the polyA block, and the orientation of the diblock DNA probe can adopt an upright conformation, which is beneficial to target hybridization and TMSDRs. TMSDR is an enzyme-free target recycling amplification approach. Taking advantage of polyA-mediated SNAs and TMSDR, the operation of the molecular machine based on two successive TMSDRs on polyA20-SNAs is rapid and efficient, which can significantly amplify the fluorescence response for detection of miR-22 in an undiluted complex matrix. The developed sensor can detect as low as 10 pM of target miRNA/DNA in undiluted fetal bovine serum within 30 min. The synergetic effect of polyA-mediated SNAs and TMSDR presents a potential alternative tool for the detection of biomarkers in real biological samples.
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Affiliation(s)
- Menghan Gu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
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Xu S, Wang W, Meng T, Wang F, Wang G, Huang F, Wang G, Yu X, Wu R, Hou L, Ye Z, Zhang X, Zhao H, Shen Y. Construction and validation of a immune-related prognostic gene DHRS1 in hepatocellular carcinoma based on bioinformatic analysis. Medicine (Baltimore) 2023; 102:e35268. [PMID: 37861541 PMCID: PMC10589603 DOI: 10.1097/md.0000000000035268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
A member of the short-chain dehydrogenase/reductase superfamily (DHRS1, SDR19C1) is a member of the short-chain dehydrogenase/reductase superfamily and a potential predictor of hepatocellular carcinoma (HCC). However, the role of DHRS1 in HCC immunity remains unclear. We systematically analyzed the association between DHRS1 and HCC immunity with transcriptional and clinical data from the Tumor Immune Estimation Resource, an integrated repository portal for tumor immune system interactions, and cBioPortal databases. Six DHRS1-associated immunomodulators strongly correlated with survival and were uncovered by exploiting univariate and multivariate Cox analyses. We created a risk score for each patient by adding the points from each immunomodulator and then classified them into high and low risk categories. Survival analysis were used to compare the overall survival between the 2 groups, and the receiver operating characteristic curve was applied to assess the accuracy of the risk score. Data from our center were adopted as the external validation set, the risk score was calculated using the risk coefficient of the 6 genes in the training cohort, and survival analysis were executed to verify the experimental group results. A nomogram was ultimately constructed with the R package. Our data revealed a correlation between the levels of immune cell infiltration and either the DHRS1 gene copy numbers or mRNA levels in HCC. Second, we generated a signature based on the 6 DHRS1-related immunomodulators (KDR, TNFRSF4, CD276, TNFSF4, SLAMF6, and SIGLEC9). We postulate that the generated risk scores would serve as an independent indicator of HCC prognosis, with an area under the receiver operating characteristic curve for the risk score of 0.743. We further established external validation sets to reconfirm the predictive validity of the risk score. Finally, a prognostic nomogram and calibration curve were created. The DHRS1 gene may exert an impact on HCC immunity. We posit that the nominated immune signature based on DHRS1-associated immunomodulators could constitute a promising prognostic biomarker in HCC.
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Affiliation(s)
- Sa Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Wei Wang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Meng
- Department of General Surgery, Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fuyan Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Guoxing Wang
- Anhui BioX-Vision Biological Technology Co., Ltd, Hefei, China
| | - Fan Huang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Guobin Wang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaojun Yu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruolin Wu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Liujin Hou
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenghui Ye
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xinghua Zhang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hongchuan Zhao
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Organ Transplant Center of The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuxian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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Barr J, Colpaert G, Cadoni E, Madder A. Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting. Methods 2023; 218:189-197. [PMID: 37597698 DOI: 10.1016/j.ymeth.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Oligonucleotides (ODNs) find applications as diagnostic and therapeutic tools due to their unique ability to interact, thanks to Watson-Crick base pairing, with a specific DNA or RNA target strand. Although most of the tools available today rely on mere hydrogen bond formation, chemical modifications to enable covalent interstrand-crosslinking (ICL) have been reported, and are gaining a place under the spotlight as they potentially offer a series of advantages over the state of the art, including a higher potency and selectivity. This methodological paper focuses on the use of a pro-reactive furan moiety and its subsequent oxidation for applications in ODN targeting. The design of effective capture and targeting probes to ensure high ICL yields is discussed and the mechanisms underlying the (photo)chemical oxidation of furan are explained. Furthermore, examples of furan-containing DNAs designed for different applications, including DNA-DNA or DNA-RNA ICL and DNA-peptide/protein targeting, are provided. The paper highlights the advantages of using different oxidative chemical triggers, such as N-bromosuccinimide or singlet oxygen, to offer additional selectivity control over the ICL reaction.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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Filgueira CPB, Pitta-Pereira D, Cantanhêde LM, Ferreira GEM, Dos Reis S, Cupolillo E, Moreira OC, Britto C, Boité MC. HRM Accuracy and Limitations as a Species Typing Tool for Leishmania Parasites. Int J Mol Sci 2023; 24:14784. [PMID: 37834232 PMCID: PMC10573552 DOI: 10.3390/ijms241914784] [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: 08/22/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
High Resolution Melting Analysis (HRM) has been pointed out as a suitable alternative method to detect and identify Leishmania species. Herein, we aimed to evaluate the sensitivity, specificity, accuracy, and limitations of a HSP70-HRM protocol both as a diagnostic scheme applied in clinical samples and as a species typing tool for laboratory research and reference services. Our data reveal the pronounced species-typing potential of the HSP70-HRM in DNA from cultured parasites. For clinical samples, however, we advise caution due to parasite load-dependent accuracy. In light of these findings and considering the importance of parasite load determination for clinical and research purposes, we recommend the integration of the presented typing scheme and the previously published Leishmania quantifying approach as combined tools for clinicians, surveillance, and research.
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Affiliation(s)
- Camila Patricio Braga Filgueira
- Leishmaniasis Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (C.P.B.F.); (L.M.C.); (E.C.)
| | - Daniela Pitta-Pereira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, FIOCRUZ, Pavilhão Leônidas Deane, Sala 209, Avenida Brasil 4365, Manguinhos, Rio de Janeiro 21045-900, Brazil; (D.P.-P.); (C.B.)
| | - Lilian Motta Cantanhêde
- Leishmaniasis Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (C.P.B.F.); (L.M.C.); (E.C.)
- Laboratório de EpiGenética, Fiocruz Rondônia, Rua da Beira, 7671, Porto Velho 76812-245, Brazil; (G.E.M.F.); (S.D.R.)
- Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental, INCT EpiAmO, Porto Velho 76812-100, Brazil
| | | | - Sayonara Dos Reis
- Laboratório de EpiGenética, Fiocruz Rondônia, Rua da Beira, 7671, Porto Velho 76812-245, Brazil; (G.E.M.F.); (S.D.R.)
| | - Elisa Cupolillo
- Leishmaniasis Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (C.P.B.F.); (L.M.C.); (E.C.)
- Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental, INCT EpiAmO, Porto Velho 76812-100, Brazil
| | - Otacilio C. Moreira
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Constança Britto
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, FIOCRUZ, Pavilhão Leônidas Deane, Sala 209, Avenida Brasil 4365, Manguinhos, Rio de Janeiro 21045-900, Brazil; (D.P.-P.); (C.B.)
| | - Mariana Côrtes Boité
- Leishmaniasis Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (C.P.B.F.); (L.M.C.); (E.C.)
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Renganathan VG, Renuka R, Vanniarajan C, Raveendran M, Elangovan A. Selection and validation of reliable reference genes for quantitative real-time PCR in Barnyard millet (Echinochloa spp.) under varied abiotic stress conditions. Sci Rep 2023; 13:15573. [PMID: 37731036 PMCID: PMC10511452 DOI: 10.1038/s41598-023-40526-6] [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: 12/16/2022] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (RT-qPCR) using a stable reference gene is widely used for gene expression research. Barnyard millet (Echinochloa spp.) is an ancient crop in Asia and Africa that is widely cultivated for food and fodder. It thrives well under drought, salinity, cold, and heat environmental conditions, besides adapting to any soil type. To date, there are no gene expression studies performed to identify the potential candidate gene responsible for stress response in barnyard millet, due to lack of reference gene. Here, 10 candidate reference genes, Actin (ACT), α-tubulin (α-TUB), β-tubulin (β-TUB), RNA pol II (RP II), elongation factor-1 alpha (EF-1α), adenine phosphoribosyltransferase (APRT), TATA-binding protein-like factor (TLF), ubiquitin-conjugating enzyme 2 (UBC2), ubiquitin-conjugating enzyme E2L5 (UBC5) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were selected from mRNA sequences of E. crus-galli and E. colona var frumentacea. Five statistical algorithms (geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder) were applied to determine the expression stabilities of these genes in barnyard millet grown under four different abiotic stress (drought, salinity, cold and heat) exposed at different time points. The UBC5 and ɑ-TUB in drought, GAPDH in salinity, GAPDH and APRT in cold, and EF-1α and RP II in heat were the most stable reference genes, whereas ß-TUB was the least stable irrespective of stress conditions applied. Further Vn/Vn + 1 analysis revealed two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with Cu-ZnSOD (SOD1) in the plants exposed to different abiotic stress conditions. The results revealed that the relative quantification of the SOD1 gene varied according to reference genes and the number of reference genes used, thus highlighting the importance of the choice of a reference gene in such experiments. This study provides a foundational framework for standardizing RT-qPCR analyses, enabling accurate gene expression profiling in barnyard millet.
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Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Raman Renuka
- Department of Biotechnology, Centre of Excellence for Innovations, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Chockalingam Vanniarajan
- Anbil Dharmalingam Agricultural College & Research Institute, Tamil Nadu Agricultural University, Tiruchirappalli, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Allimuthu Elangovan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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Pronkin PG, Tatikolov AS. Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules. Int J Mol Sci 2023; 24:13954. [PMID: 37762255 PMCID: PMC10531095 DOI: 10.3390/ijms241813954] [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: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye-HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy.
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Affiliation(s)
| | - Alexander S. Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia;
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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Gonçales RA, Portis IG, dos Reis TF, Basso Júnior LR, Martinez R, Zhu H, Pereira M, Soares CMDA, Coelho PSR. Identification and immunogenic potential of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides brasiliensis. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1243475. [PMID: 37746134 PMCID: PMC10512324 DOI: 10.3389/ffunb.2023.1243475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023]
Abstract
In fungal pathogens the cell wall plays an important role in host-pathogen interactions because its molecular components (e.g., polysaccharides and proteins) may trigger immune responses during infection. GPI-anchored proteins represent the main protein class in the fungal cell wall where they can perform several functions, such as cell wall remodeling and adhesion to host tissues. Genomic analysis has identified the complement of GPI-anchored proteins in many fungal pathogens, but the function has remained unknown for most of them. Here, we conducted an RNA expression analysis of GPI-anchored proteins of Paracoccidioides brasiliensis which causes paracoccidioidomycosis (PCM), an important human systemic mycosis endemic in Latin America. The expression of the GPI-anchored proteins was analyzed by quantitative PCR in both the mycelium and yeast forms. qPCR analysis revealed that the transcript levels of 22 of them were increased in hyphae and 10 in yeasts, respectively, while 14 did not show any significant difference in either form. Furthermore, we cloned 46 open reading frames and purified their corresponding GPI-anchored proteins in the budding yeast. Immunoblot and ELISA analysis of four purified GPI-anchored proteins revealed immune reactivity of these proteins against sera obtained from PCM patients. The information obtained in this study provides valuable information about the expression of many GPI-anchored proteins of unknown function. In addition, based on our immune analysis, some GPI-anchored proteins are expressed during infection and therefore, they might serve as good candidates for the development of new diagnostic methods.
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Affiliation(s)
- Relber Aguiar Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s – PT Government Associate Laboratory, Braga, Portugal
| | - Igor Godinho Portis
- Laboratorio de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Luiz Roberto Basso Júnior
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto Medical School, Universidade de São Paulo (FMRP/USP), Ribeirão Preto, SP, Brazil
| | - Roberto Martinez
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Maristela Pereira
- Laboratorio de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Célia Maria de Almeida Soares
- Laboratorio de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Paulo Sergio Rodrigues Coelho
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto Medical School, Universidade de São Paulo (FMRP/USP), Ribeirão Preto, SP, Brazil
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Wang S, Kang Y, Qi F, Jin H. Genetics of hair graying with age. Ageing Res Rev 2023; 89:101977. [PMID: 37276979 DOI: 10.1016/j.arr.2023.101977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/17/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023]
Abstract
Hair graying is an early and obvious phenotypic and physiological trait with age in humans. Several recent advances in molecular biology and genetics have increased our understanding of the mechanisms of hair graying, which elucidate genes related to the synthesis, transport, and distribution of melanin in hair follicles, as well as genes regulating these processes above. Therefore, we review these advances and examine the trends in the genetic aspects of hair graying from enrichment theory, Genome-Wide association studies, whole exome sequencing, gene expression studies, and animal models for hair graying with age, aiming to overview the changes in hair graying at the genetic level and establish the foundation for future research. Meanwhile, by summarizing the genetics, it's of great value to explore the possible mechanism, treatment, or even prevention of hair graying with age.
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Affiliation(s)
- Sifan Wang
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China
| | - Yuanbo Kang
- Department of Plastic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Shuaifuyuan1#, Dongcheng District, Beijing 100730, P.R.China
| | - Fei Qi
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China
| | - Hongzhong Jin
- Department of Dermatology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing 100730, China.
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Yu H, Gao X, Ge Q, Tai W, Hao X, Shao Q, Fang Z, Chen M, Song Y, Gao W, Liu G, Du X, Li X. Tumor necrosis factor-α reduces adiponectin production by decreasing transcriptional activity of peroxisome proliferator-activated receptor-γ in calf adipocytes. J Dairy Sci 2023; 106:5182-5195. [PMID: 37268580 DOI: 10.3168/jds.2022-22919] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/24/2023] [Indexed: 06/04/2023]
Abstract
Adiponectin (encoded by ADIPOQ) is an adipokine that orchestrates energy homeostasis by modulating glucose and fatty acid metabolism in peripheral tissues. During the periparturient period, dairy cows often develop adipose tissue inflammation and decreased plasma adiponectin levels. Proinflammatory cytokine tumor necrosis factor-α (TNF-α) plays a pivotal role in regulating the endocrine functions of adipocytes, but whether it affects adiponectin production in calf adipocytes remains obscure. Thus, the present study aimed to determine whether TNF-α could affect adiponectin production in calf adipocytes and to identify the underlying mechanism. Adipocytes isolated from Holstein calves were differentiated and used for (1) BODIPY493/503 staining; (2) treatment with 0.1 ng/mL TNF-α for different times (0, 8, 16, 24, or 48 h); (3) transfection with peroxisome proliferator-activated receptor-γ (PPARG) small interfering RNA for 48 h followed by treatment with or without 0.1 ng/mL TNF-α for 24 h; and (4) overexpression of PPARG for 48 h followed by treatment with or without 0.1 ng/mL TNF-α for 24 h. After differentiation, obvious lipid droplets and secretion of adiponectin were observed in adipocytes. Treatment with TNF-α did not alter mRNA abundance of ADIPOQ but reduced the total and high molecular weight (HMW) adiponectin content in the supernatant of adipocytes. Quantification of mRNA abundance of endoplasmic reticulum (ER)/Golgi resident chaperones involved in adiponectin assembly revealed that ER protein 44 (ERP44), ER oxidoreductase 1α (ERO1A), and disulfide bond-forming oxidoreductase A-like protein (GSTK1) were downregulated in TNF-α-treated adipocytes, while 78-kDa glucose-regulated protein and Golgi-localizing γ-adaptin ear homology domain ARF binding protein-1 were unaltered. Moreover, TNF-α diminished nuclear translocation of PPARγ and downregulated mRNA abundance of PPARG and its downstream target gene fatty acid synthase, suggesting that TNF-α suppressed the transcriptional activity of PPARγ. In the absence of TNF-α, overexpression of PPARG enhanced the total and HMW adiponectin content in supernatant and upregulated the mRNA abundance of ADIPOQ, ERP44, ERO1A, and GSTK1 in adipocytes. However, knockdown of PPARG reduced the total and HMW adiponectin content in supernatant and downregulated the mRNA abundance of ADIPOQ, ERP44, ERO1A, and GSTK1 in adipocytes. In the presence of TNF-α, overexpression of PPARG decreased, while knockdown of PPARG further exacerbated TNF-α-induced reductions in total and HMW adiponectin secretion and gene expression of ERP44, ERO1A, and GSTK1. Overall, TNF-α reduces adiponectin assembly in the calf adipocyte, which may be partly mediated by attenuation of PPARγ transcriptional activity. Thus, locally elevated levels of TNF-α in adipose tissue may be one reason for the decrease in circulating adiponectin in periparturient dairy cows.
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Affiliation(s)
- Hao Yu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Xinxing Gao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Qilai Ge
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Wenjun Tai
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Xue Hao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Qi Shao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Zhiyuan Fang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Meng Chen
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Yuxiang Song
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Wenwen Gao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Guowen Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China
| | - Xiliang Du
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China.
| | - Xinwei Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, 130062, Jilin, China.
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [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: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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Ramos-Gómez S, Busto MD, Ortega N. Detection of Hazelnut and Almond Adulteration in Olive Oil: An Approach by qPCR. Molecules 2023; 28:molecules28104248. [PMID: 37241987 DOI: 10.3390/molecules28104248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023] Open
Abstract
Virgin olive oil (VOO), characterized by its unique aroma, flavor, and health benefits, is subject to adulteration with the addition of oils obtained from other edible species. The consumption of adulterated olive oil with nut species, such as hazelnut or almond, leads to health and safety issues for consumers, due to their high allergenic potential. To detect almond and hazelnut in olive oil, several amplification systems have been analyzed by qPCR assay with a SYBR Green post-PCR melting curve analysis. The systems selected were Cora1F2/R2 and Madl, targeting the genes coding the allergenic protein Cor a 1 (hazelnut) and Pru av 1 (almond), respectively. These primers revealed adequate specificity for each of the targeted species. In addition, the result obtained demonstrated that this methodology can be used to detect olive oil adulteration with up to 5% of hazelnut or almond oil by a single qPCR assay, and with a level as low as 2.5% by a nested-qPCR assay. Thus, the present research has shown that the SYBR-based qPCR assay can be a rapid, precise, and accurate method to detect adulteration in olive oil.
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Affiliation(s)
- Sonia Ramos-Gómez
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - María D Busto
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natividad Ortega
- Department of Biotechnology and Food Science, Area of Biochemistry and Molecular Biology, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
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Chen J, Wang Y, Yang Z, Liu D, Jin Y, Li X, Deng Y, Wang B, Zhang Z, Ma Y. Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data. BMC Genomics 2023; 24:248. [PMID: 37165306 PMCID: PMC10170059 DOI: 10.1186/s12864-023-09358-6] [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: 01/30/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. RESULTS In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. CONCLUSION Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
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Affiliation(s)
- Jiao Chen
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunjian Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Jin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuhang Deng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Boya Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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Chauhan RP, Fogel R, Limson J. Overview of Diagnostic Methods, Disease Prevalence and Transmission of Mpox (Formerly Monkeypox) in Humans and Animal Reservoirs. Microorganisms 2023; 11:1186. [PMID: 37317160 DOI: 10.3390/microorganisms11051186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mpox-formerly monkeypox-is a re-emerging zoonotic virus disease, with large numbers of human cases reported during multi-country outbreaks in 2022. The close similarities in clinical symptoms that Mpox shares with many orthopoxvirus (OPXV) diseases make its diagnosis challenging, requiring laboratory testing for confirmation. This review focuses on the diagnostic methods used for Mpox detection in naturally infected humans and animal reservoirs, disease prevalence and transmission, clinical symptoms and signs, and currently known host ranges. Using specific search terms, up to 2 September 2022, we identified 104 relevant original research articles and case reports from NCBI-PubMed and Google Scholar databases for inclusion in the study. Our analyses observed that molecular identification techniques are overwhelmingly being used in current diagnoses, especially real-time PCR (3982/7059 cases; n = 41 studies) and conventional PCR (430/1830 cases; n = 30 studies) approaches being most-frequently-used to diagnose Mpox cases in humans. Additionally, detection of Mpox genomes, using qPCR and/or conventional PCR coupled to genome sequencing methods, offered both reliable detection and epidemiological analyses of evolving Mpox strains; identified the emergence and transmission of a novel clade 'hMPXV-1A' lineage B.1 during 2022 outbreaks globally. While a few current serologic assays, such as ELISA, reported on the detection of OPXV- and Mpox-specific IgG (891/2801 cases; n = 17 studies) and IgM antibodies (241/2688 cases; n = 11 studies), hemagglutination inhibition (HI) detected Mpox antibodies in human samples (88/430 cases; n = 6 studies), most other serologic and immunographic assays used were OPXV-specific. Interestingly, virus isolation (228/1259 cases; n = 24 studies), electron microscopy (216/1226 cases; n = 18 studies), and immunohistochemistry (28/40; n = 7 studies) remain useful methods of Mpox detection in humans in select instances using clinical and tissue samples. In animals, OPXV- and Mpox-DNA and antibodies were detected in various species of nonhuman primates, rodents, shrews, opossums, a dog, and a pig. With evolving transmission dynamics of Mpox, information on reliable and rapid detection methods and clinical symptoms of disease is critical for disease management.
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Affiliation(s)
- Ravendra P Chauhan
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
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