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Chen W, Newlands N, Hambleton S, Laroche A, Davoodi SM, Bakkeren G. Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada. Mol Ecol Resour 2024; 24:e13983. [PMID: 38840549 DOI: 10.1111/1755-0998.13983] [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: 02/21/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, Ontario, Canada
| | - Nathaniel Newlands
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Sarah Hambleton
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario, Canada
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | | - Guus Bakkeren
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
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2
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Brooks C, Mitchell E, Brown J, O'Donovan S, Carnaghan KA, Bleakney E, Arnscheidt J. Carbapenemase gene blaOXA-48 detected at six freshwater sites in Northern Ireland discharging onto identified bathing locations. Lett Appl Microbiol 2024; 77:ovae062. [PMID: 38925640 DOI: 10.1093/lambio/ovae062] [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: 01/11/2024] [Revised: 04/09/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
Faecal contamination of surface waters has the potential to spread not only pathogenic organisms but also antimicrobial resistant organisms. During the bathing season of 2021, weekly water samples, from six selected coastal bathing locations (n = 93) and their freshwater tributaries (n = 93), in Northern Ireland (UK), were examined for concentrations of faecal indicator bacteria Escherichia coli and intestinal enterococci. Microbial source tracking involved detection of genetic markers from the genus Bacteroides using PCR assays for the general AllBac marker, the human HF8 marker and the ruminant BacR marker for the detection of human, and ruminant sources of faecal contamination. The presence of beta-lactamase genes blaOXA-48, blaKPC, and blaNDM-1 was determined using PCR assays for the investigation of antimicrobial resistance genes that are responsible for lack of efficacy in major broad-spectrum antibiotics. The beta-lactamase gene blaOXA-48 was found in freshwater tributary samples at all six locations. blaOXA-48 was detected in 83% of samples that tested positive for the human marker and 69% of samples that tested positive for the ruminant marker over all six locations. This study suggests a risk of human exposure to antimicrobial resistant bacteria where bathing waters receive at least episodically substantial transfers from such tributaries.
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Affiliation(s)
- Catherine Brooks
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - Elaine Mitchell
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - James Brown
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - Sinéad O'Donovan
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - Kelly-Anne Carnaghan
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - Eoin Bleakney
- Bacteriology Department, Veterinary Sciences Division, Agri-food and Biosciences Institute, Stoney Road, Stormont, Belfast. BT4 3SD, UK
| | - Joerg Arnscheidt
- School of Geography and Environmental Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry. BT52 1SA, UK
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3
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Osathanunkul M. Species-specific eDNA assay development for enhanced box jellyfish risk management in coastal environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172900. [PMID: 38697547 DOI: 10.1016/j.scitotenv.2024.172900] [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: 02/05/2024] [Revised: 04/28/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Human interaction with marine creatures holds both positive and negative dimensions. Coastal communities benefit from marine environments, relying on them for sustenance and livelihoods. Fishing activities support economies, and marine biodiversity contributes to overall ecosystem health. However, challenges like overfishing, habitat destruction, and pollution pose threats to both marine life and human communities. Recently, there has been widespread concern regarding the potential increase in jellyfish populations across global marine ecosystems, attributed mainly to environmental factors such as climate drivers and anthropogenic forces, or their complex interactions. Encounters with hazardous marine species, such as box jellyfish, exemplify the dangers associated with coastal activities. Unintended interactions may lead to stings, injuries, and even fatalities, necessitating proactive measures and advanced technologies. This study addresses the inadequacies of existing measures in preventing box jellyfish incidents by introducing environmental DNA (eDNA) assays for detecting the deadly Chiropsoides buitendijki and focuses on developing qPCR and dPCR-based eDNA assays. Emphasising prevention over treatment, the study establishes a proactive system to assess C. buitendijki distribution across 63 tourist beaches in the Gulf of Thailand. Comparative analysis highlights the superior performance of dPCR over qPCR and traditional surveys. The dPCR experiment yielded positive results for all eDNA samples collected at sites where C. buitendijki had previously been identified. Remarkably, the eDNA testing also detected positive results in 16 additional sample locations where no physical specimens were collected, despite reported jellyfish stings at some of these sites. These findings underscore the precision and efficacy of the proposed eDNA detection technology in the early detection and assessment of box jellyfish distribution. This advancement therefore not only aids ecological research but also serves as a valuable tool for safeguarding public health, providing an early warning system for potential jellyfish encounters. Balancing positive human-marine interactions with effective risk mitigation strategies is crucial for sustainable coexistence, the preservation of marine ecosystems, and human well-being.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
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4
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Hachimi O, Falender R, Davis G, Wafula RV, Sutton M, Bancroft J, Cieslak P, Kelly C, Kaya D, Radniecki T. Evaluation of molecular-based methods for the detection and quantification of Cryptosporidium spp. in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174219. [PMID: 38917908 DOI: 10.1016/j.scitotenv.2024.174219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Cryptosporidium poses significant public health risks as a cause of waterborne disease worldwide. Clinical surveillance of cryptosporidiosis is largely underreported due to the asymptomatic and mildly symptomatic infections, clinical misdiagnoses, and barriers to access testing. Wastewater surveillance overcomes these limitations and could serve as an effective tool for identifying cryptosporidiosis at the population level. Despite its potential, the lack of standardized wastewater surveillance methods for Cryptosporidium spp. challenges implementation design and the comparability between studies. Thus, this study compared and contrasted Cryptosporidium wastewater surveillance methods for concentrating wastewater oocysts, extracting oocyst DNA, and detecting Cryptosporidium genetic markers. The evaluated concentration methods included electronegative membrane filtration, Envirocheck HV capsule filtration, centrifugation, and Nanotrap Microbiome Particles, with and without additional immunomagnetic separation purification (except for the Nanotrap Microbiome Particles). Oocyst DNA extraction by either the DNeasy Powersoil Pro kit and the QIAamp DNA Mini kit were evaluated and the impact of bead beating and freeze-thaw pretreatments on DNA recoveries was assessed. Genetic detection via qPCR assays targeting either the Cryptosporidium 18S rRNA gene or the Cryptosporidium oocyst wall protein gene were tested. Oocyst recovery percentages were highest for centrifugation (39-77 %), followed by the Nanotrap Microbiome Particles (24 %), electronegative filtration with a PBST elution (22 %), and Envirocheck HV capsule filtration (13 %). Immunomagnetic separation purification was found to be unsuitable due to interference from the wastewater matrix. Bead-beating pretreatment enhanced DNA recoveries from both the DNeasy Powersoil Pro kit (314 gc/μL DNA) and the QIAamp DNA Mini kit (238 gc/μL DNA). In contrast, freeze-thaw pretreatment reduced DNA recoveries to under 92 gc/μL DNA, likely through DNA degradation. Finally, while both qPCR assays were specific to Cryptosporidium spp., the 18S rRNA assay had a 5-fold lower detection limit and could detect a wider range of Cryptosporidium spp. than the Cryptosporidium oocyst wall protein assay.
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Affiliation(s)
- Oumaima Hachimi
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Rebecca Falender
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Gabriel Davis
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Rispa Vranka Wafula
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Melissa Sutton
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - June Bancroft
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Paul Cieslak
- Oregon Health Authority, 800 NE Oregon St, Portland, OR 97232, USA
| | - Christine Kelly
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA
| | - Tyler Radniecki
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall, Corvallis, OR 97331, USA.
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5
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Dye CK, Wu H, VanNoy B, Calluori S, Marfori CQ, Baccarelli AA, Zota AR. Psychosocial Stress and MicroRNA Expression Profiles in Myometrial Tissue of Women Undergoing Surgical Treatment for Uterine Fibroids. Reprod Sci 2024; 31:1651-1661. [PMID: 38379067 DOI: 10.1007/s43032-024-01482-2] [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: 09/20/2023] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Uterine leiomyomas (fibroids) are the most common non-cancerous tumors affecting women. Psychosocial stress is associated with fibroid risk and severity. The relationship between psychosocial stress and fibroid pathogenesis may involve alterations in microRNAs (miRNAs) although this has yet to be examined. We investigated associations between two psychosocial stress measures, a composite measure of recent stressful life events and perceived social status, with expression levels of 401 miRNAs in myometrium (n = 20) and fibroids (n = 44; 20 with paired fibroid and myometrium samples) among pre-menopausal women who underwent surgery for fibroid treatment. We used linear regressions to identify psychosocial stressors associated with miRNAs, adjusting for covariates (age, body mass index, race/ethnicity, and oral contraceptive use). The association between psychosocial stressors and miRNAs was considered statistically significant at an FDR p < 0.10 and showed a monotonic response (nominal p-trend < 0.05). In the myometrium, 21 miRNAs were significantly associated with a composite measure of recent stressful events, and two miRNAs were associated with perceived social status. No fibroid miRNAs were associated with either stress measure. Pathway analyses revealed miRNA-mRNA targets were significantly enriched (FDR p < 0.05) in pathways relevant to cancer/tumor development. Of the 74 differentially expressed miRNAs between myometrium and fibroids, miR-27a-5p and miR-301b were also associated with stress exposure. Our pilot analysis suggests that psychosocial stress is associated with myometrial miRNA expression and, thus, may have a role in the pathogenesis of fibroids from healthy myometrium.
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Affiliation(s)
- Christian K Dye
- Department of Environmental Health Sciences, Columbia University, 722, West 168Th St. 16Th Floor, New York, NY, 10032, USA.
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University, 722, West 168Th St. 16Th Floor, New York, NY, 10032, USA
| | - Brianna VanNoy
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Stephanie Calluori
- Department of Environmental Health Sciences, Columbia University, 722, West 168Th St. 16Th Floor, New York, NY, 10032, USA
| | - Cherie Q Marfori
- Minimally Invasive Gynecologic Surgery, Inova Health Systems, Arlington, VA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University, 722, West 168Th St. 16Th Floor, New York, NY, 10032, USA
| | - Ami R Zota
- Department of Environmental Health Sciences, Columbia University, 722, West 168Th St. 16Th Floor, New York, NY, 10032, USA
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6
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Rossi F, Del Matto I, Ricchiuti L, Marino L. Selection and Multiplexing of Reverse Transcription-Quantitative PCR Tests Targeting Relevant Honeybee Viral Pathogens. Microorganisms 2024; 12:1105. [PMID: 38930487 PMCID: PMC11205706 DOI: 10.3390/microorganisms12061105] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Verifying the inclusivity of molecular detection methods gives indications about the reliability of viral infection diagnosis because of the tendency of viral pathogens to undergo sequence variation. This study was aimed at selecting inclusive probes based on reverse transcription-quantitative PCR (RT-qPCR) assays for the diagnosis of the most widespread and detrimental viruses infecting honeybees, namely the acute bee paralysis virus (ABPV), the black queen cell virus (BQCV), the chronic paralysis bee virus (CBPV), the deformed wing virus variants A (DWVA) and B (DWVB), and the sacbrood virus (SBV). Therefore, previously described detection methods were re-evaluated in silico for their specificity and inclusivity. Based on this evaluation, selected methods were modified, or new ones were designed and tested in duplex RT-qPCR reactions. The limits of detection (LODs), effect of multiplexing on sensitivity and the viral RNA quantification potential in bees and hive debris were assessed. This study made available diagnostic assays able to detect an increased number of virus variants compared with previously described tests and two viral pathogens in a single PCR reaction.
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Affiliation(s)
- Franca Rossi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (I.D.M.); (L.R.); (L.M.)
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7
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Raines C, Lovy J, Phelps N, Mor S, Ng TFF, Iwanowicz L. Discovery and Genomic Characterization of a Novel Hepadnavirus from Asymptomatic Anadromous Alewife ( Alosa pseudoharengus). Viruses 2024; 16:824. [PMID: 38932117 PMCID: PMC11209213 DOI: 10.3390/v16060824] [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: 04/08/2024] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 06/28/2024] Open
Abstract
The alewife (Alosa pseudoharengus) is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015-2018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family: Hepadnaviridae; genus: Metahepadnavirus). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in this species, alewives are migratory interjurisdictional fishes of management concern. Identification of microbial agents using de novo sequencing and other advanced technologies is a critical aspect of understanding disease ecology for informed population management.
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Affiliation(s)
- Clayton Raines
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, 11649 Leetown Road, Kearneysville, WV 25430, USA;
- West Virginia Cooperative Fish and Wildlife Research Unit, Davis College of Agriculture, Natural Resources & Design, West Virginia University, 1 Waterfront Pl, Morgantown, WV 26506, USA
| | - Jan Lovy
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA;
- NJ Fish & Wildlife, Office of Fish and Wildlife Health and Forensics, 605 Pequest Rd, Oxford, NJ 07863, USA
| | - Nicolas Phelps
- Department of Fisheries, Wildlife, and Conservation Biology, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USA;
| | - Sunil Mor
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 570077, USA;
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55455, USA
| | - Terry Fei Fan Ng
- Department of Pathology, University of Georgia, Athens, GA 30602, USA;
| | - Luke Iwanowicz
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, 11649 Leetown Road, Kearneysville, WV 25430, USA;
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
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Starevich VA, Madueño L, Festa S, Agnello AC, Cecotti M, Layún MF, Oneto ME, Del Panno MT, Morelli IS. Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:566. [PMID: 38775858 DOI: 10.1007/s10661-024-12713-z] [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: 12/30/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024]
Abstract
Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.
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Affiliation(s)
| | - L Madueño
- CINDEFI, UNLP-CONICET, Bs. As., La Plata, Argentina.
| | - S Festa
- CINDEFI, UNLP-CONICET, Bs. As., La Plata, Argentina
| | - A C Agnello
- CINDEFI, UNLP-CONICET, Bs. As., La Plata, Argentina
| | | | - M F Layún
- CINDEFI, UNLP-CONICET, Bs. As., La Plata, Argentina
| | | | | | - I S Morelli
- CINDEFI, UNLP-CONICET, Bs. As., La Plata, Argentina
- CIC-PBA, Bs. As., La Plata, Argentina
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Shin JC, Jeong JY, Son SG, Choi SH, Nam HC, Yoon TH, Kim HJ, Choi DG, Lee H, Lee U, Yang SM, Kang I, Jung DY, Lee HW, Lee MK, Lee TJ, Kim G, Park HO, Lee SW. Developing centrifugal force real-time digital PCR for detecting extremely low DNA concentration. Sci Rep 2024; 14:11522. [PMID: 38769102 DOI: 10.1038/s41598-024-62199-5] [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: 04/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Digital PCR (dPCR) is a technique for absolute quantification of nucleic acid molecules. To develop a dPCR technique that enables more accurate nucleic acid detection and quantification, we established a novel dPCR apparatus known as centrifugal force real-time dPCR (crdPCR). This system is efficient than other systems with only 2.14% liquid loss by dispensing samples using centrifugal force. Moreover, we applied a technique for analyzing the real-time graph of the each micro-wells and distinguishing true/false positives using artificial intelligence to mitigate the rain, a persistent issue with dPCR. The limits of detection and quantification were 1.38 and 4.19 copies/μL, respectively, showing a two-fold higher sensitivity than that of other comparable devices. With the integration of this new technology, crdPCR will significantly contribute to research on next-generation PCR targeting absolute micro-analysis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ukyeol Lee
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | - Il Kang
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | | | - Moon-Keun Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Tae Jae Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Geehong Kim
- Nano-Convergence Systems Research Division, Korea Institute of Machinery & Materials, Daejeon, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon, Republic of Korea
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Perez-Bou L, Gonzalez-Martinez A, Cabrera JJ, Juarez-Jimenez B, Rodelas B, Gonzalez-Lopez J, Correa-Galeote D. Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR. MICROBIAL ECOLOGY 2024; 87:71. [PMID: 38748252 PMCID: PMC11096201 DOI: 10.1007/s00248-024-02385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.
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Affiliation(s)
- Lizandra Perez-Bou
- Environmental Microbiology Group, Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan J Cabrera
- Nitrogen Metabolism Group, Zaidín Experimental Station, Spanish National Research Council, EEZ-CSIC, Granada, Spain
| | - Belen Juarez-Jimenez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Belen Rodelas
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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11
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Dong TQ, Brown ER. A joint Bayesian hierarchical model for estimating SARS-CoV-2 genomic and subgenomic RNA viral dynamics and seroconversion. Biostatistics 2024; 25:336-353. [PMID: 37490631 DOI: 10.1093/biostatistics/kxad016] [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: 01/09/2023] [Revised: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 07/27/2023] Open
Abstract
Understanding the viral dynamics of and natural immunity to the severe acute respiratory syndrome coronavirus 2 is crucial for devising better therapeutic and prevention strategies for coronavirus disease 2019 (COVID-19). Here, we present a Bayesian hierarchical model that jointly estimates the genomic RNA viral load, the subgenomic RNA (sgRNA) viral load (correlated to active viral replication), and the rate and timing of seroconversion (correlated to presence of antibodies). Our proposed method accounts for the dynamical relationship and correlation structure between the two types of viral load, allows for borrowing of information between viral load and antibody data, and identifies potential correlates of viral load characteristics and propensity for seroconversion. We demonstrate the features of the joint model through application to the COVID-19 post-exposure prophylaxis study and conduct a cross-validation exercise to illustrate the model's ability to impute the sgRNA viral trajectories for people who only had genomic RNA viral load data.
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Affiliation(s)
- Tracy Q Dong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Elizabeth R Brown
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, 3980 15th Avenue NE, Seattle, WA 98195, USA
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12
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Royer C, Patin NV, Jesser KJ, Peña-Gonzalez A, Hatt JK, Trueba G, Levy K, Konstantinidis KT. Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections. mBio 2024; 15:e0342223. [PMID: 38488359 PMCID: PMC11005377 DOI: 10.1128/mbio.03422-23] [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: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
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Affiliation(s)
- C. Royer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N. V. Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - K. J. Jesser
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - A. Peña-Gonzalez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotà, Colombia
| | - J. K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G. Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - K. Levy
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - K. T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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13
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Salazar YEAR, Louzada J, Puça MCSDB, Guimarães LFF, Vieira JLF, de Siqueira AM, Gil JP, de Brito CFA, de Sousa TN. Delayed gametocyte clearance in Plasmodium vivax malaria is associated with polymorphisms in the cytochrome P450 reductase (CPR). Antimicrob Agents Chemother 2024; 68:e0120423. [PMID: 38411047 PMCID: PMC10989009 DOI: 10.1128/aac.01204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024] Open
Abstract
Primaquine (PQ) is the main drug used to eliminate dormant liver stages and prevent relapses in Plasmodium vivax malaria. It also has an effect on the gametocytes of Plasmodium falciparum; however, it is unclear to what extent PQ affects P. vivax gametocytes. PQ metabolism involves multiple enzymes, including the highly polymorphic CYP2D6 and the cytochrome P450 reductase (CPR). Since genetic variability can impact drug metabolism, we conducted an evaluation of the effect of CYP2D6 and CPR variants on PQ gametocytocidal activity in 100 subjects with P. vivax malaria. To determine gametocyte density, we measured the levels of pvs25 transcripts in samples taken before treatment (D0) and 72 hours after treatment (D3). Generalized estimating equations (GEEs) were used to examine the effects of enzyme variants on gametocyte densities, adjusting for potential confounding factors. Linear regression models were adjusted to explore the predictors of PQ blood levels measured on D3. Individuals with the CPR mutation showed a smaller decrease in gametocyte transcript levels on D3 compared to those without the mutation (P = 0.02, by GEE). Consistent with this, higher PQ blood levels on D3 were associated with a lower reduction in pvs25 transcripts. Based on our findings, the CPR variant plays a role in the persistence of gametocyte density in P. vivax malaria. Conceptually, our work points to pharmacogenetics as a non-negligible factor to define potential host reservoirs with the propensity to contribute to transmission in the first days of CQ-PQ treatment, particularly in settings and seasons of high Anopheles human-biting rates.
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Affiliation(s)
- Yanka Evellyn Alves Rodrigues Salazar
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Jaime Louzada
- Universidade Federal de Roraima, Boa Vista, Roraima, Brazil
| | - Maria Carolina Silva de Barros Puça
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Felipe Ferreira Guimarães
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | | | - André Machado de Siqueira
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Pedro Gil
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Solna, Sweden
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Tais Nobrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Solna, Sweden
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14
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Earland N, Semenkovich NP, Ramirez RJ, Gerndt SP, Harris PK, Gu Z, Hearn AI, Inkman M, Szymanski JJ, Whitfield D, Wahle BM, Xu Z, Chen K, Alahi I, Ni G, Chen A, Winckler W, Zhang J, Chaudhuri AA, Zevallos JP. Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer. Clin Cancer Res 2024; 30:1409-1421. [PMID: 37939112 PMCID: PMC10982646 DOI: 10.1158/1078-0432.ccr-23-1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE Our goal was to demonstrate that lymphatic drainage fluid (lymph) has improved sensitivity in quantifying postoperative minimal residual disease (MRD) in locally advanced human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) compared with plasma, and leverage this novel biofluid for patient risk stratification. EXPERIMENTAL DESIGN We prospectively collected lymph samples from neck drains of 106 patients with HPV (+) OPSCC, along with 67 matched plasma samples, 24 hours after surgery. PCR and next-generation sequencing were used to quantify cancer-associated cell-free HPV (cf-HPV) and tumor-informed variants in lymph and plasma. Next, lymph cf-HPV and variants were compared with TNM stage, extranodal extension (ENE), and composite definitions of high-risk pathology. We then created a machine learning model, informed by lymph MRD and clinicopathologic features, to compare with progression-free survival (PFS). RESULTS Postoperative lymph was enriched with cf-HPV compared with plasma (P < 0.0001) and correlated with pN2 stage (P = 0.003), ENE (P < 0.0001), and trial-defined pathologic risk criteria (mean AUC = 0.78). In addition, the lymph mutation number and variant allele frequency were higher in pN2 ENE (+) necks than in pN1 ENE (+) (P = 0.03, P = 0.02) or pN0-N1 ENE (-) (P = 0.04, P = 0.03, respectively). The lymph MRD-informed risk model demonstrated inferior PFS in high-risk patients (AUC = 0.96, P < 0.0001). CONCLUSIONS Variant and cf-HPV quantification, performed in 24-hour postoperative lymph samples, reflects single- and multifeature high-risk pathologic criteria. Incorporating lymphatic MRD and clinicopathologic feature analysis can stratify PFS early after surgery in patients with HPV (+) head and neck cancer. See related commentary by Shannon and Iyer, p. 1223.
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Affiliation(s)
- Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Nicholas P. Semenkovich
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Ricardo J. Ramirez
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Sophie P. Gerndt
- Division of Otolaryngology-Head and Neck Surgery, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Peter K. Harris
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Zhuosheng Gu
- Droplet Biosciences, Inc., Cambridge, Massachusetts
| | - Andrew I. Hearn
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew Inkman
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | | | - Benjamin M. Wahle
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Zhongping Xu
- Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kevin Chen
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Irfan Alahi
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Gabris Ni
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew Chen
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | | | - Jin Zhang
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Jose P. Zevallos
- Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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15
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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16
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Bustin SA, Kirvell S, Nolan T, Shipley GL. FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols. Int J Mol Sci 2024; 25:2773. [PMID: 38474020 DOI: 10.3390/ijms25052773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
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17
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Papin M, Philippot L, Breuil MC, Bru D, Dreux-Zigha A, Mounier A, Le Roux X, Rouard N, Spor A. Survival of a microbial inoculant in soil after recurrent inoculations. Sci Rep 2024; 14:4177. [PMID: 38378706 PMCID: PMC10879113 DOI: 10.1038/s41598-024-54069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.
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Affiliation(s)
- M Papin
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - L Philippot
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France.
| | - M C Breuil
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - D Bru
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Dreux-Zigha
- GreenCell Biopole Clermont Limagne, 63360, St Beauzire, France
| | - A Mounier
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - X Le Roux
- Universite Claude Bernard Lyon 1, Microbial Ecology Centre LEM, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, 43 Blvd 11 Novembre 1918, 69622, Villeurbanne, France
| | - N Rouard
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Spor
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
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18
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Kuzpınar E, Al Faysal A, Şenel P, Erdoğan T, Gölcü A. Quantification of mirtazapine in tablets via DNA binding mechanism; development of a new HPLC method. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1234:124019. [PMID: 38309044 DOI: 10.1016/j.jchromb.2024.124019] [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: 12/04/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024]
Abstract
Atypical antidepressant mirtazapine (MIR) is mostly prescribed for the management of major depressive disorder. The identification of MIR in pharmaceutical dosage forms was made possible by developing a novel, quick, sensitive high-performance liquid chromatography (HPLC) approach that was verified in accordance with ICH recommendations. In the first part of this study, HPLC investigations were optimized with regard to variables including pH, working column, mobile phase, temperature, and flow rate. The limit of detection (LOD) was 0.013 ppm, the limit of quantification (LOQ) was 0.044 ppm, and the linear range was computed as 0.5-15 ppm (R2 = 0.9998). The recovery investigation assessed the method's accuracy, which was shown to range between 98.82 and 100.97 %. In the second part, by using UV-vis spectroscopy, HPLC, thermal denaturation, and viscosity measurements, the mechanism of binding interaction of MIR with double-stranded fish sperm deoxyribonucleic acid (dsDNA) has been thoroughly studied. The DNA binding constants (Kb) were determined using UV-Vis absorption and HPLC methods. To investigate the interactions of MIR with dsDNA, molecular docking calculations and additionally, molecular dynamics simulations were performed. Results showed that MIR is located in the minor groove of dsDNA, and in addition to hydrogen bonding, electrostatic interaction is also formed between the aromatic ring of MIR and phosphate oxygen of dsDNA. Finally, a binding characterization study using MIR tablets was also conducted in order to assess the interaction mechanism of the DNA with the drug using the validated analytical procedure developed for the MIR molecule.
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Affiliation(s)
- Ecem Kuzpınar
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Abdullah Al Faysal
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Pelin Şenel
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Taner Erdoğan
- Kocaeli University, Kocaeli Vocational School, Department of Chemistry and Chemical Processing Technologies, Kocaeli, 41140, Türkiye
| | - Ayşegül Gölcü
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye.
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19
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Reinicke M, Braun SD, Diezel C, Lemuth O, Engelmann I, Liebe T, Ehricht R. From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification. Antibiotics (Basel) 2024; 13:161. [PMID: 38391548 PMCID: PMC10886392 DOI: 10.3390/antibiotics13020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.
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Affiliation(s)
- Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha Daniel Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Oliver Lemuth
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ines Engelmann
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Theresa Liebe
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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20
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Yi HW, Wang XM, Tan X, Ding CZ, Zhang CL, Wu JH, Li Q, Xin CQ, Fan W. Simultaneous detection of human norovirus GI, GII and SARS-CoV-2 by a quantitative one-step triplex RT-qPCR. Front Microbiol 2024; 14:1269275. [PMID: 38260899 PMCID: PMC10800780 DOI: 10.3389/fmicb.2023.1269275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Background There are many similarities in the clinical manifestations of human norovirus and SARS-CoV-2 infections, and nucleic acid detection is the gold standard for diagnosing both diseases. In order to expedite the identification of norovirus and SARS-CoV-2, a quantitative one-step triplex reverse transcription PCR (RT-qPCR) method was designed in this paper. Methods A one-step triplex RT-qPCR assay was developed for simultaneous detection and differentiation of human norovirus GI (NoV-GI), GII (NoV-GII) and SARS-CoV-2 from fecal specimens. Results The triplex RT-qPCR assay had high detection reproducibility (CV < 1%) and sensitivity. The lower limits of detection (LLOD95) of the triplex RT-qPCR assay for each target site were 128.5-172.8 copies/mL, and LLOD95 of the singleplex RT-qPCR assay were 110.3-142.0 copies/mL. Meanwhile, among the detection of clinical oropharyngeal swabs and fecal specimens, the results of the singleplex and triplex RT-qPCR assay showed high agreement. Conclusion The triplex RT-qPCR assay for simultaneous detection of NoV-GI, NoV-GII and SARS-CoV-2 from fecal specimens has high clinical application value.
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Affiliation(s)
- Hua-Wei Yi
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Xian-Mo Wang
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Xin Tan
- Health Science Center of Yangtze University, Jingzhou, Hubei, China
| | - Cai-Zhi Ding
- The People's Hospital of Songzi, Jingzhou, Hubei, China
| | - Chang-Li Zhang
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Jia-Hao Wu
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Qi Li
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Chen-Qi Xin
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
| | - Wen Fan
- The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- The First People's Hospital of Jingzhou, Jingzhou, Hubei, China
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21
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Porco D, Purnomo CA, Glesener L, Proess R, Lippert S, Jans K, Colling G, Schneider S, Stassen R, Frantz AC. eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account. BMC Ecol Evol 2024; 24:4. [PMID: 38178008 PMCID: PMC10768104 DOI: 10.1186/s12862-023-02189-9] [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: 08/07/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management. RESULTS Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA. CONCLUSIONS These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.
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Affiliation(s)
- David Porco
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg.
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg.
| | - Chanistya Ayu Purnomo
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Liza Glesener
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Roland Proess
- Umweltplanungsbüro Ecotop, 45, Schlassuecht, L-7435 Hollenfels, Luxembourg, Luxembourg
| | - Stéphanie Lippert
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Kevin Jans
- Natur&ëmwelt Fondation Hëllef fir d'Natur, 5, Route de Luxembourg, L-1899, Kockelscheuer, Luxembourg
| | - Guy Colling
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Simone Schneider
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Raf Stassen
- Biota.lu, 9a, Rue Principale, L-6990, Hostert, Luxembourg
| | - Alain C Frantz
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
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22
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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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23
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González-Torralva F, Norsworthy JK. Overexpression of Acetyl CoA Carboxylase 1 and 3 ( ACCase1 and ACCase3), and CYP81A21 were related to cyhalofop resistance in a barnyardgrass accession from Arkansas. PLANT SIGNALING & BEHAVIOR 2023; 18:2172517. [PMID: 36722712 PMCID: PMC9897766 DOI: 10.1080/15592324.2023.2172517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] is the most difficult-to-control weed species of rice production systems worldwide. It has evolved resistance to different herbicide sites of action, including the acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. Target-site mutations conferring resistance to ACCase-inhibiting herbicides are well documented; however, the role of the different ACCase genes in conferring resistance to cyhalofop-p-butyl (cyhalofop), an ACCase-inhibiting herbicide, remains poorly understood. This research assessed the contribution of gene amplification and expression of ACCase genes in a cyhalofop-resistant barnyardgrass accession. Additionally, the expression of glutathione-S-transferases (GSTs) and cytochrome P450 monooxygenases (P450s) genes as possible contributors to resistance to cyhalofop were investigated. Results demonstrated that ACCase gene amplification does not contribute to cyhalofop resistance. However, ACCase1 and ACCase3 were found to be overexpressed in the cyhalofop-resistant barnyardgrass accession. At 24 h after cyhalofop treatment, an overexpression of 2.0- and 2.8-fold was detected in ACCase1 and ACCase3, respectively. In addition, CYP81A21 (a P450 gene) was found to be 2.5-fold overexpressed compared to the susceptible accession in the same time period. These results suggest that ACCase1, ACCase3, and CYP81A21 are crucial genes in contributing cyhalofop resistance in this barnyardgrass accession.
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Affiliation(s)
- Fidel González-Torralva
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Jason K. Norsworthy
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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24
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Hernandez-Alvarado N, Bierle CJ, Schleiss MR. Droplet Digital PCR (ddPCR) Does Not Enhance the Sensitivity of Detection of Cytomegalovirus (CMV) DNA in Newborn Dried Blood Spots Evaluated in the Context of Newborn Congenital CMV (cCMV) Screening. Int J Neonatal Screen 2023; 10:1. [PMID: 38501568 PMCID: PMC10954086 DOI: 10.3390/ijns10010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 03/20/2024] Open
Abstract
Congenital cytomegalovirus (cCMV) infection is a leading cause of sensorineural hearing loss (SNHL) and neurodevelopmental disabilities in children worldwide. Some regions in the United States and Canada have implemented universal newborn screening for cCMV, which requires molecular diagnostic technologies for identifying cCMV, such as PCR testing of newborn dried blood spots (DBS). This study aimed to evaluate the sensitivity of droplet digital PCR (ddPCR) compared to quantitative real-time PCR to detect CMV DNA in newborn DBS. The limit of detection of various ddPCR primer/probe combinations (singleplex UL55-HEX, singleplex UL83-FAM, and multiplex UL55-HEX/UL83-FAM) was evaluated using the National Institute of Standards and Technology's (NIST) CMV quantitative standard. Singleplex UL55-HEX ddPCR exhibited the lowest limit of detection among the primer/probe combinations tested for ddPCR. UL55 ddPCR was then compared to real-time PCR in 49 infants with confirmed cCMV identified through newborn screening for CMV in saliva swabs and confirmed by a urine test. The results showed that ddPCR was only positive for 59% (29 out of 49) of the cCMV infants, while real-time PCR was positive for 80% (39 out of 49). Due to its lower sensitivity and throughput, ddPCR may not be suitable for cCMV newborn screening.
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Affiliation(s)
| | | | - Mark R. Schleiss
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Minnesota Medical School, Minneapolis, MN 55455, USA; (N.H.-A.); (C.J.B.)
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25
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Zhao B, Fujita T, Nihei Y, Yu Z, Chen X, Tanaka H, Ihara M. Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166420. [PMID: 37611711 DOI: 10.1016/j.scitotenv.2023.166420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in regions of low prevalence, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Here, we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to December 2022 during the third, fourth, fifth, sixth, seventh, and eighth waves of the COVID-19 outbreak in Japan. Viral RNA was below the limit of detection in all samples during the third and fourth waves. However, by counting the number of positive replicates in qPCR of each sample, we found that the positive ratio to all replicates in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during the third, fourth, and fifth waves. Time-step analysis indicated that, for 2 days either side of symptom onset, COVID-19 patients excreted in their feces large amounts of virus that wastewater surveillance could detect. We also demonstrated that the viral genome copy number in wastewater, as estimated from the positive ratio of SARSA-CoV-2 RNA, was correlated with the number of clinically confirmed cases. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.
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Affiliation(s)
- Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Tomonori Fujita
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Yoshiaki Nihei
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Water Agency Inc., 3-25 Higashi-Goken-cho, Shinjuku-ku, Tokyo 162-0813, Japan
| | - Zaizhi Yu
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Xiaohan Chen
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe-Otsu, Nankoku city, Kochi 783-8502, Japan.
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26
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Reyes GA, Chavez RA, Stasiewicz MJ. Modeling Preharvest Cyclospora cayetanensis Sampling and Testing for Various Water and Produce Sampling Plans. J Food Prot 2023; 86:100161. [PMID: 37742835 DOI: 10.1016/j.jfp.2023.100161] [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: 05/12/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/26/2023]
Abstract
As of August 2023, the two U.S. Food and Drug Administration (FDA) official detection methods for C. cayetanensis are outlined in the FDA Bacteriological Analytical Manual (BAM) Chapters 19b (produce testing) and 19c (agricultural water testing). These newly developed detection methods have been shown to not always detect contamination when present at low levels. Yet, industry and regulators may choose to use these methods as part of their monitoring and verification activities while detection methods continue to be improved. This study uses simulation to better understand the performance of these methods for various produce and water sampling plans. To do so, we used published FDA test validation data to fit a logistic regression model that predicts the methods' detection rate given the number of oocysts present in a 10-L agricultural water or 25 g produce sample. By doing so, we were able to determine contamination thresholds at which different numbers of samples (n = 1, 2, 4, 8, 16, and 32) would be adequate for detecting contamination. Furthermore, to evaluate sampling plans in use cases, a simulation was developed to represent C. cayetanensis contamination in agricultural water and on cilantro throughout a 45-day growth cycle. The model included uncertainty around the contamination sources, including scenarios of unintentionally contaminated irrigation water or in-field contamination. The results demonstrate that in cases where irrigation water was the contamination source, frequent water testing proved to be more powerful than produce testing. In scenarios where contamination occurred in-field, conducting frequent produce testing or testing produce toward the end of the season more reliably detected contamination. This study models the power of C. cayetanensis detection methods to understand the sampling plan performance and how these methods can be better used to monitor this emerging food safety hazard.
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Affiliation(s)
- Gustavo A Reyes
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ruben A Chavez
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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27
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Carvalho D, Marques S, Siqueira G, Ferreira A, Santos J, Geraldo D, Castro CR, Machado AV, Vaz F, Lopes C. Enhancing the Longevity and Functionality of Ti-Ag Dry Electrodes for Remote Biomedical Applications: A Comprehensive Study. SENSORS (BASEL, SWITZERLAND) 2023; 23:8321. [PMID: 37837150 PMCID: PMC10575150 DOI: 10.3390/s23198321] [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: 09/11/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
This study aims to evaluate the lifespan of Ti-Ag dry electrodes prepared using flexible polytetrafluoroethylene (PTFE) substrates. Following previous studies, the electrodes were designed to be integrated into wearables for remote electromyography (EMG) monitoring and electrical stimulation (FES) therapy. Four types of Ti-Ag electrodes were prepared by DC magnetron sputtering, using a pure-Ti target doped with a growing number of Ag pellets. After extensive characterization of their chemical composition and (micro)structural evolution, the Ti-Ag electrodes were immersed in an artificial sweat solution (standard ISO-3160-2) at 37 °C with constant stirring. Results revealed that all the Ti-Ag electrodes maintained their integrity and functionality for 24 h. Although there was a notable increase in electrical resistivity beyond this timeframe, the acquisition and transmission of (bio)signals remained viable for electrodes with Ag/Ti ratios below 0.23. However, electrodes with higher Ag content (Ag/Ti = 0.31) became insulators after 7 days of immersion due to excessive Ag release into the sweat solution. This study concludes that higher Ag/Ti atomic ratios result in heightened corrosion processes on the electrode's surface, consequently diminishing their lifespan despite the advantages of incorporating Ag into their composition. This research highlights the critical importance of evaluating electrode longevity, especially in remote biomedical applications like smart wearables, where electrode performance over time is crucial for reliable and sustained monitoring and stimulation.
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Affiliation(s)
- Daniel Carvalho
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
| | - Sandra Marques
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
| | - Giorgia Siqueira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
| | - Armando Ferreira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
- LaPMET—Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057 Braga, Portugal
| | - João Santos
- Chemistry Centre, University of Minho, 4710-057 Braga, Portugal
| | - Dulce Geraldo
- Chemistry Centre, University of Minho, 4710-057 Braga, Portugal
| | - Cidália R. Castro
- Institute for Polymers and Composites, University of Minho, 4800-058 Guimarães, Portugal
| | - Ana V. Machado
- Polymer Engineering Department, Institute for Polymers and Composites, University of Minho, 4800-058 Guimarães, Portugal
| | - Filipe Vaz
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
- LaPMET—Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057 Braga, Portugal
| | - Cláudia Lopes
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, 4710-057 Braga, Portugal (C.L.)
- LaPMET—Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057 Braga, Portugal
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28
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D'Agnese E, Chase D, Andruszkiewicz-Allan E. ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES. J Wildl Dis 2023; 59:545-556. [PMID: 37791744 DOI: 10.7589/jwd-d-22-00128] [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: 09/02/2022] [Accepted: 06/01/2023] [Indexed: 10/05/2023]
Abstract
Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.
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Affiliation(s)
- Erin D'Agnese
- University of Washington, School of Marine and Environmental Affairs, 3737 Brooklyn Ave. NE, Seattle, Washington 98105, USA
- Wild EcoHealth LLC, Tacoma, Washington 98465, USA
| | - Dorothy Chase
- U.S. Geological Survey, Western Fisheries Research Center, 6505 Northeast 65th St., Seattle, Washington 98115, USA
| | - Elizabeth Andruszkiewicz-Allan
- University of Washington, School of Marine and Environmental Affairs, 3737 Brooklyn Ave. NE, Seattle, Washington 98105, USA
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29
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E Z, Luo P, Ren C, Cheng C, Pan W, Jiang X, Jiang F, Ma B, Yu S, Zhang X, Chen T, Hu C. Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:778-789. [PMID: 37658250 DOI: 10.1007/s10126-023-10239-y] [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: 06/05/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The tropical sea cucumber Holothuria scabra is naturally found in the Indo-West Pacific. However, due to their commercial value, natural H. scabra populations have declined significantly in recent years, resulting in its status as an endangered species. Surveys of H. scabra resource pose a challenge due to its specific characteristics, such as sand-burrowing behavior. To overcome this problem, our study established a convenient and feasible method for assessing H. scabra resources using environmental DNA (eDNA) monitoring technology. First, H. scabra-specific TaqMan primers and probe were designed based on its cox1 gene, followed by the development of an eDNA monitoring method for H. scabra in two separate sea areas (Xuwen and Daya Bay). The method was subsequently employed to investigate the distribution of H. scabra and assess the effects of aquaculture stock enhancement through juvenile releasing in the Weizhou Island sea area. The H. scabra eDNA monitoring approach was found to be more appropriate and credible than traditional methods, and a positive impact of stocking on H. scabra populations was observed. In summary, this is the first report to quantify eDNA concentration in a Holothuroidea species, and it provides a convenient and accurate method for surveying H. scabra resources. This study introduces novel concepts for eDNA-based detection of endangered marine benthic animals and monitoring their population distribution and abundance.
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Affiliation(s)
- Zixuan E
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Chuhang Cheng
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Wenjie Pan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Fajun Jiang
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Suzhong Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China.
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da Silva BKNI, Alves Cortez AC, Oliveira LA, de Almeida JDR, de Souza ÉS, Cruz KS, Jackisch Matsuura AB, Ogusku MM, Solórzano Chavarría KJ, Baía-da-Silva D, Bassat Q, Guimarães Lacerda MV, Frickmann H, de Souza JVB. Design and optimization of an improved qPCR assay for the detection of Histoplasma capsulatum. Eur J Microbiol Immunol (Bp) 2023; 13:37-44. [PMID: 37738109 PMCID: PMC10578137 DOI: 10.1556/1886.2023.00026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 09/01/2023] [Indexed: 09/24/2023] Open
Abstract
Background This study aimed at improving a real-time polymerase-chain-reaction (qPCR) assay for the detection of Histoplasma capsulatum, a fungal pathogen that can cause severe respiratory infections in humans, in clinical and soil samples. Methods Primer and probes were in-silico designed, in-silico and in-vitro evaluated including clinical biopsy materials and finally subjected to a real-world application with collected soil samples. Results Applying the qPCR assay with liver and lung biopsies from 71 patients each, including 59 patients infected with human immunodeficiency virus (HIV), as well as with Sabouraud (SAB) agar culture as the diagnostic reference standard, diagnostic accuracy of the qPCR assay of 100% (5/5) sensitivity and 96% (63/66) specificity for liver samples and 100% (4/4) sensitivity and 94% (63/67) specificity for the lung samples was recorded. When applying the assay with soil samples from caves near of Presidente Figueiredo city, Amazonas, Brazil, one sample from the Maroaga cave was confirmed as positive. Conclusions The improved qPCR assessed in this study was successful in detecting H. capsulatum with high efficiency and accuracy in in-vitro evaluation, including the identification of the target pathogen in both clinical and environmental samples.
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Affiliation(s)
| | | | | | | | | | - Katia Santana Cruz
- Medical Mycology Laboratory, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
| | - Ani Beatriz Jackisch Matsuura
- Microbial Diversity Laboratory of the Amazon with Health Importance, Leônidas and Maria Deane Institute-Fiocruz-AM, Manaus, Amazonas, Brazil
| | - Mauricio Morishi Ogusku
- Mycobacteriology Laboratory, Instituto Nacional de Pesquisas da Amazonia–INPA, Manaus, Brazil
| | - Karolina Jeaneth Solórzano Chavarría
- Graduate Program in Tropical Medicine, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
- Carlos Borborema Clinical Research Unit, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
| | - Djane Baía-da-Silva
- Graduate Program in Pharmaceutical Sciences, Universidade Federal do Amazonas-UFAM, Manaus, Brazil
- Graduate Program in Tropical Medicine, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
- Carlos Borborema Clinical Research Unit, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
- Instituto Leônidas Maria Deane- ILMD, Fiocruz-AM, Manaus, Brazil
- Pharmacy Faculty, Universidade Nilton Lins, Manaus, Brazil
| | - Quique Bassat
- ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, 080100Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marcus Vinícius Guimarães Lacerda
- Graduate Program in Tropical Medicine, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
- Carlos Borborema Clinical Research Unit, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado-FMT-HVD, Manaus, Brazil
- Instituto Leônidas Maria Deane- ILMD, Fiocruz-AM, Manaus, Brazil
- University of Texas Medical Branch, Galveston, USA
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital, Hamburg, Germany
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Dye CK, Wu H, VanNoy B, Calluori S, Marfori CQ, Baccarelli AA, Zota AR. Psychosocial stress and microRNA expression profiles in myometrial tissue of women undergoing surgical treatment for uterine fibroids. RESEARCH SQUARE 2023:rs.3.rs-3373251. [PMID: 37790535 PMCID: PMC10543257 DOI: 10.21203/rs.3.rs-3373251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Uterine leiomyomas (fibroids) are the most common non-cancerous tumor affecting women. Psychosocial stress is associated with fibroid risk and severity. The relationship between psychosocial stress and fibroid pathogenesis may involve alterations in microRNAs (miRNAs) although this has yet to be examined. We investigated associations between two psychosocial stress measures, a composite measure of recent stressful life events and perceived social status, with expression levels of 401 miRNAs in myometrium (n = 20) and fibroids (n = 44; 20 matched between tissues) from pre-menopausal women who underwent surgery for fibroid treatment. We used linear regressions to identify psychosocial stressors associated with miRNAs, adjusting for covariates (age, body mass index, and race/ethnicity). Psychosocial stressors were modeled as ordinal variables and results were considered statistically significant if the overall variable significant was below false discovery threshold (FDR < 0.10) and showed a monotonic dose-response (nominal p-trend < 0.05). In the myometrium, 16 miRNAs were significantly associated with total stressful events and two miRNAs were associated with perceived social status. No fibroid miRNAs were associated with either stress measure. Pathway analyses revealed miRNA-mRNA targets were significantly enriched (FDR < 0.05) in pathways relevant to cancer/tumor development. Of the 74 differentially expressed miRNAs between myometrium and fibroids (p < 0.05), miR-27a-5p was also associated with stress exposure. Our pilot analysis suggests that psychosocial stress is associated with changes in myometrium miRNAs, and thus, plays a role in the pathogenesis of fibroids from healthy myometrium.
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Affiliation(s)
- Christian K Dye
- Department of Environmental Health Sciences, Columbia University
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University
| | | | | | | | | | - Ami R Zota
- Department of Environmental Health Sciences, Columbia University
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Wong CH, Zhang Z, Eid W, Plaza-Diaz J, Kabir P, Wan S, Jia JJ, Mercier E, Thakali O, Pisharody L, Hegazy N, Stephenson SE, Fang W, Nguyen TB, Ramsay NT, McKay RM, Corchis-Scott R, MacKenzie AE, Graber TE, D' Aoust PM, Delatolla R. Rapidly developed, optimized, and applied wastewater surveillance system for real-time monitoring of low-incidence, high-impact MPOX outbreak. JOURNAL OF WATER AND HEALTH 2023; 21:1264-1276. [PMID: 37756194 PMCID: wh_2023_145 DOI: 10.2166/wh.2023.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Recent MPOX viral resurgences have mobilized public health agencies around the world. Recognizing the significant risk of MPOX outbreaks, large-scale human testing, and immunization campaigns have been initiated by local, national, and global public health authorities. Recently, traditional clinical surveillance campaigns for MPOX have been complemented with wastewater surveillance (WWS), building on the effectiveness of existing wastewater programs that were built to monitor SARS-CoV-2 and recently expanded to include influenza and respiratory syncytial virus surveillance in wastewaters. In the present study, we demonstrate and further support the finding that MPOX viral fragments agglomerate in the wastewater solids fraction. Furthermore, this study demonstrates that the current, most commonly used MPOX assays are equally effective at detecting low titers of MPOX viral signal in wastewaters. Finally, MPOX WWS is shown to be more effective at passively tracking outbreaks and/or resurgences of the disease than clinical testing alone in smaller communities with low human clinical case counts of MPOX.
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Affiliation(s)
- Chandler H Wong
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada E-mail:
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Lakshmi Pisharody
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Sean E Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Tram B Nguyen
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Nathan T Ramsay
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - R Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Patrick M D' Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
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Dunn FB, Silverman AI. Sunlight photolysis of SARS-CoV-2 N1 gene target in the water environment: considerations for the environmental surveillance of wastewater-impacted surface waters. JOURNAL OF WATER AND HEALTH 2023; 21:1228-1241. [PMID: 37756191 PMCID: wh_2023_091 DOI: 10.2166/wh.2023.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 has been used around the world to supplement clinical testing data for situational awareness of COVID-19 disease trends. Many regions of the world lack centralized wastewater collection and treatment infrastructure, which presents additional considerations for wastewater surveillance of SARS-CoV-2, including environmental decay of the RT-qPCR gene targets used for quantification of SARS-CoV-2 virions. Given the role of sunlight in the environmental decay of RNA, we evaluated sunlight photolysis kinetics of the N1 gene target in heat-inactivated SARS-CoV-2 with a solar simulator under laboratory conditions. Insignificant photolysis of the N1 target was observed in a photosensitizer-free matrix. Conversely, significant decay of the N1 target was observed in wastewater at a shallow depth (<1 cm). Given that sunlight irradiance is affected by several environmental factors, first-order decay rate models were used to evaluate the effect of water column depth, time of the year, and latitude on decay kinetics. Decay rate constants were found to decrease significantly with greater depth of the well-mixed water column, at high latitudes, and in the winter. Therefore, sunlight-mediated decay of the N1 gene target is likely to be minimal, and is unlikely to confound results from wastewater-based epidemiology programs utilizing wastewater-impacted surface waters.
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Affiliation(s)
- Fiona B Dunn
- Department of Civil and Urban Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA E-mail:
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA
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Ganjalizadeh V, Hawkins AR, Schmidt H. Adaptive time modulation technique for multiplexed on-chip particle detection across scales. OPTICA 2023; 10:812-818. [PMID: 38818330 PMCID: PMC11138143 DOI: 10.1364/optica.489068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Integrated optofluidic biosensors have demonstrated ultrasensitivity down to single particle detection and attomolar target concentrations. However, a wide dynamic range is highly desirable in practice and can usually only be achieved by using multiple detection modalities or sacrificing linearity. Here, we demonstrate an analysis technique that uses temporal excitation at two different time scales to simultaneously enable digital and analog detection of fluorescent targets. We demonstrated the seamless detection of nanobeads across eight orders of magnitude from attomolar to nanomolar concentration. Furthermore, a combination of spectrally varying modulation frequencies and a closed-loop feedback system that provides rapid adjustment of excitation laser powers enables multiplex analysis in the presence of vastly different concentrations. We demonstrated this ability to detect across scales via an analysis of a mixture of fluorescent nanobeads at femtomolar and picomolar concentrations. This technique advances the performance and versatility of integrated biosensors, especially toward point-of-use applications.
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Affiliation(s)
- Vahid Ganjalizadeh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Aaron R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
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Rajab N, Ibrahim H, Hassan RYA, Youssef AFA. Selective determination of nitrite in water and food samples using zirconium oxide (ZrO 2)@MWCNTs modified screen printed electrode. RSC Adv 2023; 13:21259-21270. [PMID: 37465573 PMCID: PMC10350638 DOI: 10.1039/d3ra03448h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Nitrite ions are being used in different forms as food preservatives acting as flavor enhancers or coloring agents for food products. However, continuous ingestion of nitrite may have severe health implications due to its mutagenic and carcinogenic effects. Thus, this study constructed an electrochemical assay using disposable nano-sensor chip ZrO2@MWCNTs screen printed electrodes (SPE) for the rapid, selective, and sensitive determination of nitrite in food and water samples. As a sensing platform, the use of nanomaterials, including metal oxide nanostructures and carbon nanotubes, exhibited a superior electrocatalytic activity and conductivity. Morphological, structural, and electrochemical analyses were performed using electron microscopy (SEM and TEM), Fourier-transform infrared (FTIR) spectroscopy, electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and chronoamperometry (CA). Accordingly, a wide dynamic linear range (5.0 μM to 100 μM) was obtained with a limit of detection of 0.94 μM by the chronoamperometric technique. In addition, the sensor's selectivity was tested when several non-target species were exposed to the sensor chips while no obvious electrochemical signals were generated when the nitrite ions were not present. Eventually, real food and water sample analysis was conducted, and a high recovery was achieved.
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Affiliation(s)
- Nadeen Rajab
- University of Science and Technology (UST), Zewail City of Science and Technology Giza 12578 Egypt
| | - Hosny Ibrahim
- Chemistry Department, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Rabeay Y A Hassan
- University of Science and Technology (UST), Zewail City of Science and Technology Giza 12578 Egypt
| | - Ahmed F A Youssef
- University of Science and Technology (UST), Zewail City of Science and Technology Giza 12578 Egypt
- Chemistry Department, Faculty of Science, Cairo University Giza 12613 Egypt
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Rodgers BD, Herring SK, Carias DR, Chen J, Rocha AG. Development and validation of a model gene therapy biodistribution assay for AVGN7 using digital droplet polymerase chain reaction. Mol Ther Methods Clin Dev 2023; 29:494-503. [PMID: 37273901 PMCID: PMC10236005 DOI: 10.1016/j.omtm.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/08/2023] [Indexed: 06/06/2023]
Abstract
Biodistribution assays are integral to gene therapy commercialization and have traditionally used real-time qPCR. Droplet digital PCR (ddPCR), however, has distinct advantages including higher sensitivity and absolute quantification but is underused because of lacking regulatory guidance and meaningful examples in the literature. We report a fit-for-purpose model process to validate a good laboratory practice (GLP)-compliant ddPCR assay for AVGN7, a Smad7 gene therapeutic for muscle wasting. Duplexed primer/probe sets for Smad7 and mouse TATA-box binding protein were optimized using gBlock DNA over a dynamic range of 10-80,000 copies/reaction in 250 ng mouse gDNA. Linearized plasmid and mouse gDNA were used for validation, which determined precision, accuracy, ruggedness/robustness, selectivity, recovery, specificity, dilution linearity, and stability. Inter-run precision and accuracy met previously established criteria with bias between -5% and 15%, coefficient of variation (CV) less than 19%, and total error within 8%-35%. The limit of detection was 2.5 copies/reaction, linearity was confirmed at 40-80,000 copies/reaction, specificity was demonstrated by single droplet populations and assay stability was demonstrated for benchtop, refrigerated storage, and repeated freeze-thaw cycles. The procedural road map provided exceeds recently established standards. It is also relevant to many IND-enabling processes, as validated ddPCR assays can be used in biodistribution studies and with vector titering and manufacturing quality control.
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Affiliation(s)
| | | | - Dereck R Carias
- Smithers Pharmaceutical Development Services, Ewing, NJ 08628, USA
| | - Joyce Chen
- Smithers Pharmaceutical Development Services, Ewing, NJ 08628, USA
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Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
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Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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Shim KY, Shin H, Yeo IC, Kim KR, Kwak IS, Jeong CB. Environmental DNA surveillance of biocontamination in a drinking water treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131656. [PMID: 37236104 DOI: 10.1016/j.jhazmat.2023.131656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
A clean and adequate supply of drinking water is essential to life and good health. However, despite the risk of biologically derived contamination of drinking water, monitoring of invertebrate outbreaks has relied primarily on naked-eye inspections that are prone to errors. In this study, we applied environmental DNA (eDNA) metabarcoding as a biomonitoring tool at seven different stages of drinking water treatment, from prefiltration to release from household faucets. While the composition of invertebrate eDNA communities reflected the communities of the source water in earlier stages of the treatment, several predominant invertebrate taxa (e.g., rotifer) were shown to be introduced during purification, but most were eliminated in later treatment stages. In addition, the limit of detection/quantification of PCR assay and read capacity of high-throughput sequencing was assessed with further microcosm experiments to estimate the applicability eDNA metabarcoding to the biocontamination surveillance in drinking water treatment plants (DWTPs). Here we propose a novel eDNA-based approach for sensitive and efficient surveillance of invertebrate outbreaks in DWTPs.
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Affiliation(s)
- Kyu-Young Shim
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Heesang Shin
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - In-Cheol Yeo
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Kyu Ri Kim
- Hoseo Toxicology Research Center, Hoseo University, Asan 31499, Republic of Korea
| | - Ihn-Sil Kwak
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Chang-Bum Jeong
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea.
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Shan J, Jia Y, Hickenbotham P, Teulières L, Clokie MRJ. Combining citizen science and molecular diagnostic methods to investigate the prevalence of Borrelia burgdorferi s.l. and Borrelia miyamotoi in tick pools across Great Britain. Front Microbiol 2023; 14:1126498. [PMID: 37180256 PMCID: PMC10169747 DOI: 10.3389/fmicb.2023.1126498] [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: 12/17/2022] [Accepted: 03/31/2023] [Indexed: 05/16/2023] Open
Abstract
Lyme disease is the most common tick-borne disease and is caused by a group of bacteria known as Borrelia burgdorferi sensu lato (s.l.) complex. Sharing the same genus as B. burgdorferi, Borrelia miyamotoi is a distinct genotype that causes relapsing fever disease. This emerging tick-borne disease is increasingly becoming a concern in public health. To investigate the prevalence of B. burgdorferi s.l. and B. miyamotoi in ticks first, we developed a PCR (Bmer-qPCR) that targets the phage terminase large subunit (terL) gene carried by B. miyamotoi. A similar approach had been used successfully in developing Ter-qPCR for detecting B. burgdorferi s.l. The terL protein functions as an enzyme in packaging phage DNA. Analytical validation of the Bmer-qPCR confirmed its specificity, efficiency and sensitivity. Second, we designed a citizen science-based approach to detect 838 ticks collected from numerous sites across Great Britain. Finally, we applied Bmer-qPCR and Ter-qPCR to 153 tick pools and revealed that the prevalence of B. burgdorferi s.l. and B. miyamotoi was dependent on their geographical locations, i.e. Scotland showed a higher rate of B. burgdorferi s.l. and lower rate of B. miyamotoi carriage as compared to those of the England data. A pattern of diminishing rate of B. miyamotoi carriage from southern England to northern Scotland was visible. Together, the citizen science-based approach provided an estimation of the carriage rate of B. burgdorferi s.l. and B. miyamotoi in tick pools and a potential spreading pattern of B. miyamotoi from the south to the north of Great Britain. Our findings underscore the power of combining citizen science with the molecular diagnostic method to reveal hidden pattern of pathogen-host-environment interplay. Our approach can provide a powerful tool to elucidate the ecology of tick-borne diseases and may offer guidance for pathogen control initiatives. In an era of limited resources, monitoring pathogens requires both field and laboratory support. Citizen science approaches provide a method to empower the public for sample collection. Coupling citizen science approaches with laboratory diagnostic tests can make real-time monitoring of pathogen distribution and prevalence possible.
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Affiliation(s)
- Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ying Jia
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Peter Hickenbotham
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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Berger CS, Bougas B, Côté G, Dumont JF, Bernatchez L. A qPCR-based method to detect the eel parasitic nematode Anguillicola crassus in intermediate and final hosts. Parasitol Res 2023; 122:1435-1443. [PMID: 37071205 DOI: 10.1007/s00436-023-07843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Being able to systematically detect parasitic infection, even when no visual signs of infection are present, is crucial to the establishment of accurate conservation policies. The nematode Anguillicola crassus infects the swimbladder of anguillid species and is a potential threat for eel populations. In North America, naïve hosts such as the American eel Anguilla rostrata are affected by this infection. The accidental introduction of A. crassus following restocking programs may contribute to the actual decline of the American eel in Canada. We present a quantitative real time PCR-based method to detect A. crassus infection in final and intermediate hosts. We tested two protocols on samples from different geographical origins in Canada: 1) a general detection of A. crassus DNA in pools of young final hosts (glass eels) or crustacean intermediate hosts 2) a detection at the individual scale by analyzing swim bladders from elvers, or from adult yellow and silver eels. The DNA of A. crassus was detected in one pool of zooplankton (intermediate host) from the Richelieu River (Montérégie-Québec), as well as in individual swim bladders of 13 elvers from Grande and Petite Trinité rivers (Côte-Nord-Québec). We suggest that our qPCR approach could be used in a quantitative way to estimate the parasitic burden in individual swim bladders of elvers. Our method, which goes beyond most of previous developed protocols that restricted the diagnosis of A. crassus to the moment when it was fully established in its final host, should help to detect early A. crassus infection in nature.
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Affiliation(s)
- Chloé Suzanne Berger
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Bérénice Bougas
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Guillaume Côté
- Ministère de L'Environnement, de La Lutte Contre Les Changements Climatiques, de La Faune Et Des Parcs (MELCCFP), Québec, QC, Canada
| | - Jean-François Dumont
- Ministère de L'Environnement, de La Lutte Contre Les Changements Climatiques, de La Faune Et Des Parcs (MELCCFP), Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Pfuderer L, Stark WJ, Grass RN. Synthetic Microbial Surrogates Consisting of Lipid Nanoparticles Encapsulating DNA for the Validation of Surface Disinfection Procedures. ACS APPLIED BIO MATERIALS 2023; 6:1252-1259. [PMID: 36854082 PMCID: PMC10031560 DOI: 10.1021/acsabm.3c00004] [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: 03/02/2023]
Abstract
Effective cleaning and disinfection procedures are an integral part of good manufacturing practice and in maintaining hygiene standards in health-care facilities. In this study, a method to validate such cleaning and disinfection procedures of surfaces was established employing lipid nanoparticles (LNPs) encapsulating DNA. It was possible to determine and distinguish between the physical cleaning effect (dilution) and the chemical cleaning effect (disintegration) on the LNPs during the cleaning and disinfection procedure (wiping). After treatment with 70 v % ethanol as a disinfectant and SDS solution as a cleaning agent, LNPs showed log10 reductions of 4.5 and 4.0, respectively. These values are similar to the log10 reductions exhibited by common bacteria, such as Escherichia coli and Serratia marcescens. Therefore, LNPs pose as useful tools for cleaning validation with advantages over the already existing tools and enable a separate detection of dilution and chemical disinfectant action.
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Affiliation(s)
- Lara Pfuderer
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Wendelin J Stark
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Robert N Grass
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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Assessment of virus concentration methods for detecting SARS-CoV-2 IN wastewater. Braz J Microbiol 2023:10.1007/s42770-023-00941-3. [PMID: 36877444 PMCID: PMC9987392 DOI: 10.1007/s42770-023-00941-3] [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: 11/16/2022] [Accepted: 02/24/2023] [Indexed: 03/07/2023] Open
Abstract
Wastewater-based epidemiology has been described as a valuable tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a community. However, there is no consensus on the best concentration method to allow reliable detection of SARS-CoV-2 in this matrix, considering different laboratory facilities. This study compares two viral concentration methods, ultracentrifugation (ULT) and skimmed-milk flocculation (SMF), for detecting SARS-CoV-2 in wastewater samples. The analytical sensitivity (limits of detection and quantification [LoD/LoQ]) of both methods was evaluated using a bovine respiratory syncytial virus (BRSV) as a surrogate. Three different approaches were conducted to establish LoD of each method based on the assays on the standard curve (ALoDsc), on the dilution of internal control (ALoDiC), and the processing steps (PLoD). For PLoD, ULT method had the lowest value (1.86 × 103 genome copy/microliter [GC/µL]) when compared to the SMF method (1.26 × 107 GC/µL). The LoQ determination showed a mean value of 1.55 × 105 GC/µL and 3.56 × 108 GC/µL to ULT and SMF, respectively. The detection of SARSCoV-2 in naturally contaminated wastewater revealed 100% (12/12) and 25% (3/12) of detection using ULT and SMF with quantification ranging from 5.2 to 7.2 log10 genome copy/liter (GC/L) and 5.06 to 5.46 log10 GC/L, respectively. The detection success rate of BRSV used as an internal control process was 100% (12/12) for ULT and 67% (8/12) for SMF, with an efficiency recovery rate ranging from 12 to 38% and 0.1 to 5%, respectively. Our data consolidates the importance of assessing the methods used; however, further analysis should be carried out to improve low-cost concentration methodologies, essential for use in low-income and developing countries.
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Lindsay DL, Guan X, Harms NE, Cronin JT, Meyerson LA, Lance RF. DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11512. [PMID: 37051584 PMCID: PMC10083467 DOI: 10.1002/aps3.11512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
PREMISE To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real-time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. METHODS AND RESULTS Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies. CONCLUSIONS The newly developed assays were validated using P. australis samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing.
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Affiliation(s)
- Denise L. Lindsay
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
| | - Xin Guan
- Bennett AerospaceVicksburgMississippi39180USA
- Present address:
ModernaTX, Moderna Technology CenterNorwoodMarylandUSA
| | - Nathan E. Harms
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
| | | | | | - Richard F. Lance
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
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Yeh SC, Strilets T, Tan WL, Castillo D, Medkour H, Rey-Cadilhac F, Serrato-Pomar IM, Rachenne F, Chowdhury A, Chuo V, Azar SR, Singh MK, Hamel R, Missé D, Kini RM, Kenney LJ, Vasilakis N, Marti-Renom MA, Nir G, Pompon J, Garcia-Blanco MA. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLoS Pathog 2023; 19:e1011224. [PMID: 36996041 PMCID: PMC10062553 DOI: 10.1371/journal.ppat.1011224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3'UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3'UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission.
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Affiliation(s)
- Shih-Chia Yeh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tania Strilets
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Wei-Lian Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Hacène Medkour
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | | | | | | | - Avisha Chowdhury
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Vanessa Chuo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Sasha R. Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rodolphe Hamel
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Tropical Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Preventive Medicine and Population Health, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center for Emerging Viruses and Arboviruses, University of University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Mariano A. Garcia-Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
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Anderson SD, Gleason CA. A molecular beacon real-time polymerase chain reaction assay for the identification of M. chitwoodi, M. fallax, and M. minor. FRONTIERS IN PLANT SCIENCE 2023; 14:1096239. [PMID: 36909438 PMCID: PMC9994647 DOI: 10.3389/fpls.2023.1096239] [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: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are major pests of many important crops around the world. In the Northwestern region of the United States of America (USA), Meloidogyne chitwoodi causes economic losses in potatoes because the nematodes can infect the tubers, which leads to potato galling and reductions in marketable yield. Meloidogyne chitwoodi is a quarantine pathogen in certain potato export markets, and there is little industry tolerance for the presence of this nematode. Recently, two Meloidogyne species that are not known to be present in agricultural fields in the USA were detected on golf turfgrasses in California and Washington. These species, M. fallax and M. minor, are morphologically similar to M. chitwoodi and can infect potatoes and cause tuber damage. Their detection in the USA means that they could potentially infest potato fields and become a problem in potato production. Additionally, M. fallax is a regulated plant pest in the USA, which makes the correct identification of potato-infecting root-knot nematodes important. Previously, there was no single-tube assay that could determine whether M. chitwoodi, M. fallax, and/or M. minor were present in a sample. Thus, a molecular beacon real-time PCR assay which can reliably detect M. chitwoodi, M. fallax, or M. minor from crude nematode extracts was designed and characterized.
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Early detection of local SARS-CoV-2 outbreaks by wastewater surveillance: a feasibility study. Epidemiol Infect 2023; 151:e28. [PMID: 36722251 PMCID: PMC9990400 DOI: 10.1017/s0950268823000146] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Wastewater surveillance and quantitative analysis of SARS-CoV-2 RNA are increasingly used to monitor the spread of COVID-19 in the community. We studied the feasibility of applying the surveillance data for early detection of local outbreaks. A Monte Carlo simulation model was constructed, applying data on reported variation in RNA gene copy concentration in faeces and faecal masses shed. It showed that, even with a constant number of SARS-CoV-2 RNA shedders, the variation in concentrations found in wastewater samples will be large, and that it will be challenging to translate viral concentrations into incidence estimates, especially when the number of shedders is low. Potential signals for early detection of hypothetical outbreaks were analysed for their performance in terms of sensitivity and specificity of the signals. The results suggest that a sudden increase in incidence is not easily identified on the basis of wastewater surveillance data, especially in small sampling areas and in low-incidence situations. However, with a high number of shedders and when combining data from multiple consecutive tests, the performance of wastewater sampling is expected to improve considerably. The developed modelling approach can increase our understanding of the results from wastewater surveillance of SARS-CoV-2.
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Kechin A, Oscorbin I, Cherednichenko A, Khrapov E, Schwartz Y, Stavitskaya N, Filipenko M. Selection of IS6110 conserved regions for the detection of Mycobacterium tuberculosis using qPCR and LAMP. Arch Microbiol 2023; 205:71. [PMID: 36688992 DOI: 10.1007/s00203-023-03410-5] [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: 08/24/2022] [Revised: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
IS6110 insertion sequence is a frequently used target for Mycobacterium tuberculosis detection. However, its sequence variability is studied insufficiently. We aimed to identify the most conservative and variable regions in IS6110 sequences and develop qPCR and LAMP oligonucleotide sets for the conservative regions. Using in-house Python scripts, 3609 M. tuberculosis genome sequences from the NCBI database were aligned; conservative regions were identified to design oligonucleotide sets. IS6110 fragments located within the 31-231 bp region were the most conservative and represented in genomes and were used to design qPCR and LAMP oligonucleotides. The in silico sensitivity of the qPCR oligonucleotides on the whole genome set was 99.1% and 98.4%. For the LAMP primers developed, the sensitivity was 96.9%. For qPCR, the limit of detection with 95% confidence (LoD95%) was four IS6110 copies per reaction, with LoD90% being 200 BCG cells per ml of artificial sputum. For LAMP, LoD95% was 16 copies per reaction, with LoD90% being 400 Mycobacterium bovis Bacille Calmette-Guerin (BCG) cells per ml of artificial sputum. We have demonstrated the IS6110 sequence variability and designed highly sensitive qPCR and LAMP oligonucleotides to detect M. tuberculosis.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation.
| | - Igor Oscorbin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Andrey Cherednichenko
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Yakov Schwartz
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Nataliya Stavitskaya
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Maksim Filipenko
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
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Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [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: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
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Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
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Schmidt PJ, Acosta N, Chik AHS, D’Aoust PM, Delatolla R, Dhiyebi HA, Glier MB, Hubert CRJ, Kopetzky J, Mangat CS, Pang XL, Peterson SW, Prystajecky N, Qiu Y, Servos MR, Emelko MB. Realizing the value in "non-standard" parts of the qPCR standard curve by integrating fundamentals of quantitative microbiology. Front Microbiol 2023; 14:1048661. [PMID: 36937263 PMCID: PMC10020645 DOI: 10.3389/fmicb.2023.1048661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The real-time polymerase chain reaction (PCR), commonly known as quantitative PCR (qPCR), is increasingly common in environmental microbiology applications. During the COVID-19 pandemic, qPCR combined with reverse transcription (RT-qPCR) has been used to detect and quantify SARS-CoV-2 in clinical diagnoses and wastewater monitoring of local trends. Estimation of concentrations using qPCR often features a log-linear standard curve model calibrating quantification cycle (Cq) values obtained from underlying fluorescence measurements to standard concentrations. This process works well at high concentrations within a linear dynamic range but has diminishing reliability at low concentrations because it cannot explain "non-standard" data such as Cq values reflecting increasing variability at low concentrations or non-detects that do not yield Cq values at all. Here, fundamental probabilistic modeling concepts from classical quantitative microbiology were integrated into standard curve modeling approaches by reflecting well-understood mechanisms for random error in microbial data. This work showed that data diverging from the log-linear regression model at low concentrations as well as non-detects can be seamlessly integrated into enhanced standard curve analysis. The newly developed model provides improved representation of standard curve data at low concentrations while converging asymptotically upon conventional log-linear regression at high concentrations and adding no fitting parameters. Such modeling facilitates exploration of the effects of various random error mechanisms in experiments generating standard curve data, enables quantification of uncertainty in standard curve parameters, and is an important step toward quantifying uncertainty in qPCR-based concentration estimates. Improving understanding of the random error in qPCR data and standard curve modeling is especially important when low concentrations are of particular interest and inappropriate analysis can unduly affect interpretation, conclusions regarding lab performance, reported concentration estimates, and associated decision-making.
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Affiliation(s)
- Philip J. Schmidt
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | | | - Patrick M. D’Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Hadi A. Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Melissa B. Glier
- Public Health Laboratory, BC Centre for Disease Control, Vancouver, BC, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer Kopetzky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chand S. Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Alberta Health Services, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Shelley W. Peterson
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Natalie Prystajecky
- Public Health Laboratory, BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Mark R. Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Monica B. Emelko
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Monica B. Emelko,
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