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Kravtsova LS, Peretolchina TE, Triboy TI, Nebesnykh IA, Tupikin AE, Kabilov MR. A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding. Vavilovskii Zhurnal Genet Selektsii 2023; 27:694-702. [PMID: 38213463 PMCID: PMC10782034 DOI: 10.18699/vjgb-23-80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 01/13/2024] Open
Abstract
The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p<0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius gregarius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring.
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Affiliation(s)
- L S Kravtsova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T I Triboy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - I A Nebesnykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A E Tupikin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Babovskaya AA, Trifonova EA, Serebrova VN, Svarovskaya MG, Zarubin AA, Zhilyakova OV, Gabidulina TV, Poltanova AA, Rychkova LV, Stepanov VA. [Protocol of Transcriptome Analysis of Decidual Placenta Cells]. Mol Biol (Mosk) 2022; 56:325-333. [PMID: 35403625 DOI: 10.31857/s0026898422020045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/13/2021] [Indexed: 06/14/2023]
Abstract
The advent of high-throughput sequencing technologies has expanded our understanding of the biological significance of non-coding regions of the genome. In recent years, more and more studies have been devoted to studying the role of noncoding RNAs in the development of diseases, as well as their participation in various cellular processes. Until now, all transcriptome studies of native placental tissue with the description of the noncoding RNA region were carried out without isolating individual cell populations. This approach, due to the high cellular heterogeneity of the placental tissue, significantly complicates the ability to determine the molecular-biological functions of individual cells and their role in the molecular pathogenesis of reproductive disorders. In this work, we propose a technique for obtaining total RNA from single decidual cells of frozen placental tissue obtained by laser-capture microdissection technology for transcriptome sequencing, including a cluster of noncoding RNAs. This technique can be successfully used to study the full-genome expression profile of other placental cell populations. The high accuracy of results on the transcriptome profiling of decidual cells obtained using the developed technique was additionally confirmed by an integrative analysis with the results of a 10x Genomics experiment.
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Affiliation(s)
- A A Babovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | - E A Trifonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
- Siberian State Medical University, Tomsk, 634050 Russia
| | - V N Serebrova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | - M G Svarovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
- Siberian State Medical University, Tomsk, 634050 Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | | | | | - A A Poltanova
- Siberian State Medical University, Tomsk, 634050 Russia
| | - L V Rychkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, 664003 Russia
| | - V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
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Chakravorty S, Afzali B, Kazemian M. EBV-associated diseases: Current therapeutics and emerging technologies. Front Immunol 2022; 13:1059133. [PMID: 36389670 PMCID: PMC9647127 DOI: 10.3389/fimmu.2022.1059133] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
EBV is a prevalent virus, infecting >90% of the world's population. This is an oncogenic virus that causes ~200,000 cancer-related deaths annually. It is, in addition, a significant contributor to the burden of autoimmune diseases. Thus, EBV represents a significant public health burden. Upon infection, EBV remains dormant in host cells for long periods of time. However, the presence or episodic reactivation of the virus increases the risk of transforming healthy cells to malignant cells that routinely escape host immune surveillance or of producing pathogenic autoantibodies. Cancers caused by EBV display distinct molecular behaviors compared to those of the same tissue type that are not caused by EBV, presenting opportunities for targeted treatments. Despite some encouraging results from exploration of vaccines, antiviral agents and immune- and cell-based treatments, the efficacy and safety of most therapeutics remain unclear. Here, we provide an up-to-date review focusing on underlying immune and environmental mechanisms, current therapeutics and vaccines, animal models and emerging technologies to study EBV-associated diseases that may help provide insights for the development of novel effective treatments.
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Affiliation(s)
- Srishti Chakravorty
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Department of Computer Science, Purdue University, West Lafayette IN, United States
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. Front Plant Sci 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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Chalot M, Puschenreiter M. Editorial: Exploring Plant Rhizosphere, Phyllosphere and Endosphere Microbial Communities to Improve the Management of Polluted Sites. Front Microbiol 2021; 12:763566. [PMID: 34691011 PMCID: PMC8527027 DOI: 10.3389/fmicb.2021.763566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Michel Chalot
- UMR Chrono-environnement, CNRS 6249 - Université de Bourgogne-Franche-Comté, Besançon, France.,Université de Lorraine, Faculté des Sciences et Technologies, Nancy, France
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García-Gómez C, Yebra L, Cortés D, Sánchez A, Alonso A, Valcárcel-Pérez N, Gómez-Jakobsen F, Herrera I, Johnstone C, Mercado JM. Shifts in the protist community associated with an anticyclonic gyre in the Alboran Sea (Mediterranean Sea). FEMS Microbiol Ecol 2021; 96:5911576. [PMID: 32975560 DOI: 10.1093/femsec/fiaa197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone to the core of an oligotrophic anticyclonic gyre (AG). Sampling was performed during summer, when the water column was stratified. The superphyla Alveolata, Stramenopila and Rhizaria accounted for 84% of the total operational taxonomic units (OTUs). The most diverse groups were Dinophyceae (21% of OTUs), Marine Alveolates-II (MALV-II; 20%), Ciliophora (9%) and MALV-I (6%). In terms of read abundance, the predominant groups were Dinophyceae (29%), Bacillariophyta (14%), MALV-II (11%) and Ciliophora (11%). Samples were clustered into three groups according to the sampling depth and position. The shallow community in coastal stations presented distinguishable patterns of diatoms and ciliates compared with AG stations. These results indicate that there was a strong horizontal coupling between phytoplankton and ciliate communities. Abundance of Radiolaria and Syndiniales increased with depth. Our analyses demonstrate that the stratification disruption produced by the AG caused shifts in the trophic ecology of the plankton assemblages inducing a transition from bottom-up to top-down control.
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Affiliation(s)
- Candela García-Gómez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Lidia Yebra
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Dolores Cortés
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Antonio Sánchez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Aitor Alonso
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Nerea Valcárcel-Pérez
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Francisco Gómez-Jakobsen
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Inma Herrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Carolina Johnstone
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
| | - Jesús M Mercado
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Puerto Pesquero s/n, 29640 Fuengirola, Spain
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Zhong LY, Hao RX, Wang WD, Wan JJ, Zhu XX. [Combined Process of DNBF-O 3-GAC for Nitrogen and Phosphorus and Metabolite Advanced Removal]. Huan Jing Ke Xue 2018; 39:247-255. [PMID: 29965689 DOI: 10.13227/j.hjkx.201706070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To improve the quality of the tailings water from a wastewater treatment plant (WWTP), a denitrification biofilter (DNBF) with a composite filler composed of a new slow-release organic-carbon source (SOC-F), sponge iron, and activated carbon was tested. Studies were conducted in the combined process of DNBF-O3-GAC to explore the efficiency of the advanced removal of nitrogen, phosphorus, and microbial metabolite by using synthetic effluent made from running water and chemicals. Corresponding comparative studies were conducted by using the secondary effluent from the WWTP. The microbial population structure in the biofilm of the denitrification biofilter was analyzed by adopting MiSeq high-throughput sequencing technologies. The results indicated that the combination process achieved high efficiency removal of nitrogen, phosphorus, and microbial metabolite. The average removal rate of NO3--N in the simulated and actual water period reached 88.87% and 79.99%, respectively; the average removal rate of TP reached 87.67% and 65.51%, respectively; and the average removal rate of UV254 reached 45.51% and 49.23%, respectively. Each processing unit had different functions. The changes in NO3--N, TN, TP, and TFe mainly occurred in the denitrification biofilter, and the removal of UV254 and the change in the three-dimensional fluorescence intensity mainly occurred in the ozone-activated carbon reactor. The cluster analysis at the genus level indicated that the denitrification system had sulfur autotrophic denitrifying bacteria and heterotrophic denitrifying bacteria. Sulfur autotrophic denitrification increased obviously in the actual water period when relatively lack of carbon sources, and the proportion of Thiobacillus increased from 7.44% to 29.62%. The complementary effect of sulfur autotrophic denitrification and heterotrophic denitrification had extended the use of the new slow-release carbon source.
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Affiliation(s)
- Li-Yan Zhong
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
- Huizhou City Huayu Water Resources and Hydropower Engineering Survey and Design Co., Ltd., Huizhou 516003, China
| | - Rui-Xia Hao
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Wei-Dong Wang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jing-Jing Wan
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Xia Zhu
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, College of Architectural Engineering, Beijing University of Technology, Beijing 100124, China
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