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Lin CP, Huang CH, Padgett T, Bucay MAC, Chen CW, Shen ZY, Chiu L, Tseng YC, Yu JK, Wang J, Wang MC, Hoh DZ. Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan. Biodivers Data J 2024; 12:e116921. [PMID: 38694844 PMCID: PMC11061556 DOI: 10.3897/bdj.12.e116921] [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: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Background This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.
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Affiliation(s)
- Chieh-Ping Lin
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, TaiwanGenome and Systems Biology Degree Program, Academia Sinica and National Taiwan UniversityTaipeiTaiwan
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Chung-Hsin Huang
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Trevor Padgett
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Mark Angelo C. Bucay
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Cheng-Wei Chen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Zong-Yu Shen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Ling Chiu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Oceanography, National Taiwan University, Taipei, TaiwanInstitute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | - Yung-Che Tseng
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
| | - Jr-Kai Yu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, TaiwanInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
| | - Min-Chen Wang
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel, GermanyZoological Institute, Christian-Albrechts University of KielKielGermany
| | - Daphne Z. Hoh
- Taiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia Sinica, Taipei, TaiwanTaiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia SinicaTaipeiTaiwan
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Abstract
It is known that extracellular vesicles (EVs) are shed from cells of almost every type of cell or organism, showing their ubiquity in all empires of life. EVs are defined as naturally released particles from cells, delimited by a lipid bilayer, and cannot replicate. These nano- to micrometer scaled spheres shuttle a set of bioactive molecules. EVs are of great interest as vehicles for drug targeting and in fundamental biological research, but in vitro culture of animal cells usually achieves only small yields. The exploration of other biological kingdoms promises comprehensive knowledge on EVs broadening the opportunities for basic understanding and therapeutic use. Thus, plants might be sustainable biofactories producing nontoxic and highly specific nanovectors, whereas bacterial and fungal EVs are promising vaccines for the prevention of infectious diseases. Importantly, EVs from different eukaryotic and prokaryotic kingdoms are involved in many processes including host-pathogen interactions, spreading of resistances, and plant diseases. More extensive knowledge of inter-species and interkingdom regulation could provide advantages for preventing and treating pests and pathogens. In this review, we present a comprehensive overview of EVs derived from eukaryota and prokaryota and we discuss how better understanding of their intercommunication role provides opportunities for both fundamental and applied biology.
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Affiliation(s)
- Eric Woith
- Institute of Pharmacy, Pharmaceutical Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195 Berlin, Germany;
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection Research (HZI), Biogenic Nanotherapeutics Group (BION), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Matthias F. Melzig
- Institute of Pharmacy, Pharmaceutical Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195 Berlin, Germany;
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Marchais A, Chevalier C, Voinnet O. Extensive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including AGO5-dependent pseudogene-derived siRNAs. RNA 2019; 25:1098-1117. [PMID: 31138671 PMCID: PMC6800511 DOI: 10.1261/rna.069294.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/07/2019] [Indexed: 05/19/2023]
Abstract
In a reductionist perspective, plant silencing small (s)RNAs are often classified as mediating nuclear transcriptional gene silencing (TGS) or cytosolic posttranscriptional gene silencing (PTGS). Among the PTGS diagnostics is the association of AGOs and their sRNA cargos with the translation apparatus. In Arabidopsis, this is observed for AGO1 loaded with micro(mi)RNAs and, accordingly, translational-repression (TR) is one layer of plant miRNA action. Using AGO1:miRNA-mediated TR as a paradigm, we explored, with two unrelated polysome-isolation methods, which, among the ten Arabidopsis AGOs and numerous sRNA classes, interact with translation. We found that representatives of all three AGO-clades associate with polysomes, including the TGS-effector AGO4 and stereotypical 24-nt sRNAs that normally mediate TGS of transposons/repeats. Strikingly, approximately half of these annotated 24-nt siRNAs displayed unique matches in coding regions/introns of genes, and in pseudogenes, but not in transposons/repeats commonly found in their vicinity. Protein-coding gene-derived 24-nt sRNAs correlate with gene-body methylation. Those derived from pseudogenes belong to two main clusters defined by their parental-gene expression patterns, and are vastly enriched in AGO5, itself found on polysomes. Based on their tight expression pattern in developing and mature siliques, their biogenesis, and genomic/epigenomic features of their loci-of-origin, we discuss potential roles for these hitherto unknown polysome-enriched, pseudogene-derived siRNAs.
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Affiliation(s)
- Antonin Marchais
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Clément Chevalier
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
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Teng J, Loukin S, Zhou X, Kung C. Yeast luminometric and Xenopus oocyte electrophysiological examinations of the molecular mechanosensitivity of TRPV4. J Vis Exp 2013:50816. [PMID: 24637628 PMCID: PMC4396860 DOI: 10.3791/50816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
TRPV4 (Transient Receptor Potentials, vanilloid family, type 4) is widely expressed in vertebrate tissues and is activated by several stimuli, including by mechanical forces. Certain TRPV4 mutations cause complex hereditary bone or neuronal pathologies in human. Wild-type or mutant TRPV4 transgenes are commonly expressed in cultured mammalian cells and examined by Fura-2 fluorometry and by electrodes. In terms of the mechanism of mechanosensitivity and the molecular bases of the diseases, the current literature is confusing and controversial. To complement existing methods, we describe two additional methods to examine the molecular properties of TRPV4. (1) Rat TRPV4 and an aequorin transgene are transformed into budding yeast. A hypo-osmtic shock of the transformant population yields a luminometric signal due to the combination of aequorin with Ca(2+), released through the TRPV4 channel. Here TRPV4 is isolated from its usual mammalian partner proteins and reveals its own mechanosensitivity. (2) cRNA of TRPV4 is injected into Xenopus oocytes. After a suitable period of incubation, the macroscopic TRPV4 current is examined with a two-electrode voltage clamp. The current rise upon removal of inert osmoticum from the oocyte bath is indicative of mechanosensitivity. The microAmpere (10(-6) to 10(-4) A) currents from oocytes are much larger than the subnano- to nanoAmpere (10(-10) to 10(-9) A) currents from cultured cells, yielding clearer quantifications and more confident assessments. Microscopic currents reflecting the activities of individual channel proteins can also be directly registered under a patch clamp, in on-cell or excised mode. The same oocyte provides multiple patch samples, allowing better data replication. Suctions applied to the patches can activate TRPV4 to directly assess mechanosensitivity. These methods should also be useful in the study of other types of TRP channels.
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Affiliation(s)
- Jinfeng Teng
- Laboratory of Cell and Molecular Biology, University of Wisconsin - Madison
| | - Stephen Loukin
- Laboratory of Cell and Molecular Biology, University of Wisconsin - Madison
| | - Xinliang Zhou
- Laboratory of Cell and Molecular Biology, University of Wisconsin - Madison
| | - Ching Kung
- Laboratory of Cell and Molecular Biology, University of Wisconsin - Madison; Department of Genetics, University of Wisconsin - Madison;
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Abstract
Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.
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Affiliation(s)
- Patrick J Cummings
- Center for Biotechnology Education, Krieger School of Arts and Sciences, Johns Hopkins University, USA.
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Abstract
Increasing protein expression enables researchers to better understand the functional role of that protein in regulating key biological processes(1). In the lung, this has been achieved typically through genetic approaches that utilize transgenic mice(2,3) or viral or non-viral vectors that elevate protein levels via increased gene expression(4). Transgenic mice are costly and time-consuming to generate and the random insertion of a transgene or chronic gene expression can alter normal lung development and thus limit the utility of the model(5). While conditional transgenics avert problems associated with chronic gene expression(6), the reverse tetracycline-controlled transactivator (rtTA) mice, which are used to generate conditional expression, develop spontaneous air space enlargement(7). As with transgenics, the use of viral and non-viral vectors is expensive(8) and can provoke dose-dependent inflammatory responses that confound results(9) and hinder expression(10). Moreover, the efficacy of repeated doses are limited by enhanced immune responses to the vector(11,12). Researchers are developing adeno-associated viral (AAV) vectors that provoke less inflammation and have longer expression within the lung(13). Using β-galactosidase, we present a method for rapidly and effectively increasing protein expression within the lung using a direct protein transfection technique. This protocol mixes a fixed amount of purified protein with 20 μl of a lipid-based transfection reagent (Pro-Ject, Pierce Bio) to allow penetration into the lung tissue itself. The liposomal protein mixture is then injected into the lungs of the mice via the trachea using a microsprayer (Penn Century, Philadelphia, PA). The microsprayer generates a fine plume of liquid aerosol throughout the lungs. Using the technique we have demonstrated uniform deposition of the injected protein throughout the airways and the alveoli of mice(14). The lipid transfection technique allows the use of a small amount of protein to achieve effect. This limits the inflammatory response that otherwise would be provoked by high protein administration. Indeed, using this technique we published that we were able to significantly increase PP2A activity in the lung without affecting lung lavage cellularity(15). Lung lavage cellularity taken 24 hr after challenge was comparable to controls (27 ± 4 control vs. 31 ± 5 albumin transfected; N=6 per group). Moreover, it increases protein levels without inducing lung developmental changes or architectural changes that can occur in transgenic models. However, the need for repeated administrations may make this technique less favorable for studies examining the effects of long-term increases in protein expression. This would be particularly true for proteins with short half-lives.
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Williams RW, Xue B, Uversky VN, Dunker AK. Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. Intrinsically Disord Proteins 2013; 1:e25724. [PMID: 28516017 PMCID: PMC5424788 DOI: 10.4161/idp.25724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 11/19/2022]
Abstract
The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information.
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Affiliation(s)
- Robert W Williams
- Department of Biomedical Informatics; Uniformed Services University; Bethesda, MD USA
| | - Bin Xue
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA
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