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Shu HY, Zhao L, Jia Y, Liu FF, Chen J, Chang CM, Jin T, Yang J, Shu WS. CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5024-5034. [PMID: 38454313 PMCID: PMC10956431 DOI: 10.1021/acs.est.3c11096] [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] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.
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Affiliation(s)
- Hao-Yue Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Liang Zhao
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
| | - Yanyan Jia
- School
of Ecology, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Fei-Fei Liu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Jiang Chen
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Chih-Min Chang
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
| | - Tao Jin
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- One
Health Biotechnology (Suzhou) Co., Ltd., Suzhou 215009, PR China
| | - Jian Yang
- School
of Food and Drug, Shenzhen Polytechnic, Shenzhen 518081, PR China
| | - Wen-Sheng Shu
- Guangdong
Magigene Biotechnology Co., Ltd., Shenzhen 518081, PR China
- Institute
of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity
and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology
for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510006, PR China
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Matveeva OV, Ogurtsov AY, Nazipova NN, Shabalina SA. Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes. PLoS One 2018; 13:e0199162. [PMID: 29928000 PMCID: PMC6013149 DOI: 10.1371/journal.pone.0199162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/02/2018] [Indexed: 12/20/2022] Open
Abstract
Off-target oligoprobe's interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array. The database included two types of probes with signals derived from (i) a combination of specific signal and cross-hybridization and (ii) genomic cross-hybridization only. All probes from the database were grouped into bins according to their sequence characteristics, where both hybridization signals were averaged separately. For selection of specific probes, we analyzed the following sequence characteristics: vulnerability to self-folding, nucleotide composition bias, numbers of G nucleotides and GGG-blocks, and occurrence of probe's k-mers in the human genome. Increases in bin ranges for these characteristics are simultaneously accompanied by a decrease in hybridization specificity-the ratio between specific and cross-hybridization signals. However, both averaged hybridization signals exhibit growing trends along with an increase of probes' binding energy, where the hybridization specific signal increases significantly faster in comparison to the cross-hybridization. The same trend is evident for the S function, which serves as a combined evaluation of probe binding energy and occurrence of probe's k-mers in the genome. Application of S allows extracting a larger number of specific probes, as compared to using only binding energy. Thus, we showed that high values of specific and cross-hybridization signals are not mutually exclusive for probes with high values of binding energy and S. In this study, the application of a new set of sequence characteristics allows detection of probes that are highly specific to their targets for array design and other bio-techniques that require selection of specific probes.
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Affiliation(s)
- Olga V. Matveeva
- Biopolymer Design LLC, Acton, Massachusetts, United States of America
- * E-mail: (OVM); (SAS)
| | - Aleksey Y. Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nafisa N. Nazipova
- Institute of Mathematical Problems of Biology, RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Svetlana A. Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (OVM); (SAS)
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Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB. MICROARRAYS 2017; 6:microarrays6020009. [PMID: 28555058 PMCID: PMC5487956 DOI: 10.3390/microarrays6020009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/22/2017] [Accepted: 05/26/2017] [Indexed: 11/29/2022]
Abstract
Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131).
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Affiliation(s)
- Ahsan Munir
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48823, USA.
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48823, USA.
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
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Yu C, Wales SQ, Mammel MK, Hida K, Kulka M. Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets. J Virol Methods 2016; 234:54-64. [PMID: 27033182 DOI: 10.1016/j.jviromet.2016.03.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022]
Abstract
Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250-500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples.
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Affiliation(s)
- Christine Yu
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Samantha Q Wales
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Mark K Mammel
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Kaoru Hida
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Michael Kulka
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA.
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Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array. MICROARRAYS 2014; 3:263-81. [PMID: 27600348 PMCID: PMC4979054 DOI: 10.3390/microarrays3040263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/22/2014] [Accepted: 11/03/2014] [Indexed: 11/20/2022]
Abstract
Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.
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Lê Cao KA, Rohart F, McHugh L, Korn O, Wells CA. YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses. Genomics 2014; 103:239-51. [DOI: 10.1016/j.ygeno.2014.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 01/09/2023]
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He W, Qi B, Zhou Q, Lu C, Huang Q, Xian L, Chen M. Key genes and pathways in thyroid cancer based on gene set enrichment analysis. Oncol Rep 2013; 30:1391-7. [PMID: 23784086 DOI: 10.3892/or.2013.2557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/15/2013] [Indexed: 11/06/2022] Open
Abstract
The incidence of thyroid cancer and its associated morbidity has shown the most rapid increase among all cancers since 1982, but the mechanisms involved in thyroid cancer, particularly significant key genes induced in thyroid cancer, remain undefined. In many studies, gene probes have been used to search for key genes involved in causing and facilitating thyroid cancer. As a result, many possible virulence genes and pathways have been identified. However, these studies lack a case contrast for selecting the most possible virulence genes and pathways, as well as conclusive results with which to clarify the mechanisms of cancer development. In the present study, we used gene set enrichment and meta-analysis to select key genes and pathways. Based on gene set enrichment, we identified 5 downregulated and 4 upregulated mixed pathways in 6 tissue datasets. Based on the meta-analysis, there were 17 common pathways in the tissue datasets. One pathway, the p53 signaling pathway, which includes 13 genes, was identified by both the gene set enrichment analysis and meta-analysis. Genes are important elements that form key pathways. These pathways can induce the development of thyroid cancer later in life. The key pathways and genes identified in the present study can be used in the next stage of research, which will involve gene elimination and other methods of experimentation.
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Affiliation(s)
- Wenwu He
- Department of Cardiothoracic Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, P.R. China
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