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Wang Y, Zhou D, Feng Y, Chen G, Li N. T-UCRs with digestive and respiratory diseases. Bioorg Med Chem Lett 2020; 30:127306. [PMID: 32631526 DOI: 10.1016/j.bmcl.2020.127306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
From the perspective of histoembryology, the lung, gaster, and intestines that derived from the endoderm of the gastrula are structurally homologous. The interplay of intestines and lung in many pathologic changes is called the gut-lung axis. RNAs transcribed from ultraconserved regions (T-UCRs) are highly evolutionarily conserved in many mammalian genomes and have been found to be important in the pathogenesis and diagnosis of many diseases. More and more studies in recent years have shown that T-UCRs play important roles both in digestive and respiratory diseases. Taking the gut-lung axis as the entry point, this review summarizes the T-UCRs related to digestive and respiratory diseases in recent years. Meanwhile, these T-UCRs and their targets can lay a foundation for future drug research.
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Affiliation(s)
- Yajun Wang
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Storck V, Nikolaki S, Perruchon C, Chabanis C, Sacchi A, Pertile G, Baguelin C, Karas PA, Spor A, Devers-Lamrani M, Papadopoulou ES, Sibourg O, Malandain C, Trevisan M, Ferrari F, Karpouzas DG, Tsiamis G, Martin-Laurent F. Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community. Front Microbiol 2018; 9:1412. [PMID: 30008705 PMCID: PMC6034002 DOI: 10.3389/fmicb.2018.01412] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 06/08/2018] [Indexed: 01/03/2023] Open
Abstract
Pesticides are intentionally applied to agricultural fields for crop protection. They can harm non-target organisms such as soil microorganisms involved in important ecosystem functions with impacts at the global scale. Within the frame of the pesticide registration process, the ecotoxicological impact of pesticides on soil microorganisms is still based on carbon and nitrogen mineralization tests, despite the availability of more extensive approaches analyzing the abundance, activity or diversity of soil microorganisms. In this study, we used a high-density DNA microarray (PhyloChip) and 16S rDNA amplicon next-generation sequencing (NGS) to analyze the impact of the organophosphate insecticide chlorpyrifos (CHL), the phenyl-urea herbicide isoproturon (IPU), or the triazole fungicide tebuconazole (TCZ) on the diversity and composition of the soil bacterial community. To our knowledge, it is the first time that the combination of these approaches are applied to assess the impact of these three pesticides in a lab-to-field experimental design. The PhyloChip analysis revealed that although no significant changes in the composition of the bacterial community were observed in soil microcosms exposed to the pesticides, significant differences in detected operational taxonomic units (OTUs) were observed in the field experiment between pesticide treatments and control for all three tested pesticides after 70 days of exposure. NGS revealed that the bacterial diversity and composition varied over time. This trend was more marked in the microcosm than in the field study. Only slight but significant transient effects of CHL or TCZ were observed in the microcosm and the field study, respectively. IPU was not found to significantly modify the soil bacterial diversity or composition. Our results are in accordance with conclusions of the Environmental Food Safety Authority (EFSA), which concluded that these three pesticides may have a low risk toward soil microorganisms.
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Affiliation(s)
- Veronika Storck
- AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
| | - Sofia Nikolaki
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | | | - Angela Sacchi
- Aeiforia srl, Spinoff Università Cattolica del Sacro Cuore, Fidenza, Italy
| | - Giorgia Pertile
- Aeiforia srl, Spinoff Università Cattolica del Sacro Cuore, Fidenza, Italy
| | | | - Panagiotis A. Karas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Aymé Spor
- AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
| | - Marion Devers-Lamrani
- AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
| | - Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | | | | | - Marco Trevisan
- Department of Agronomy and Environmental and Chemistry, Catholic University of the Sacred Heart, Piacenza, Italy
| | - Federico Ferrari
- Aeiforia srl, Spinoff Università Cattolica del Sacro Cuore, Fidenza, Italy
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Fabrice Martin-Laurent
- AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
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Zhang Y, Patel K, Endrawis T, Bowers A, Sun Y. A FASTQ compressor based on integer-mapped k-mer indexing for biologist. Gene 2015; 579:75-81. [PMID: 26743127 DOI: 10.1016/j.gene.2015.12.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/03/2015] [Accepted: 12/23/2015] [Indexed: 12/20/2022]
Abstract
Next generation sequencing (NGS) technologies have gained considerable popularity among biologists. For example, RNA-seq, which provides both genomic and functional information, has been widely used by recent functional and evolutionary studies, especially in non-model organisms. However, storing and transmitting these large data sets (primarily in FASTQ format) have become genuine challenges, especially for biologists with little informatics experience. Data compression is thus a necessity. KIC, a FASTQ compressor based on a new integer-mapped k-mer indexing method, was developed (available at http://www.ysunlab.org/kic.jsp). It offers high compression ratio on sequence data, outstanding user-friendliness with graphic user interfaces, and proven reliability. Evaluated on multiple large RNA-seq data sets from both human and plants, it was found that the compression ratio of KIC had exceeded all major generic compressors, and was comparable to those of the latest dedicated compressors. KIC enables researchers with minimal informatics training to take advantage of the latest sequence compression technologies, easily manage large FASTQ data sets, and reduce storage and transmission cost.
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Affiliation(s)
- Yeting Zhang
- Department of Research, Synblex LLC, State College, PA 16801, USA.
| | - Khyati Patel
- New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA.
| | - Tony Endrawis
- New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA.
| | - Autumn Bowers
- New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA.
| | - Yazhou Sun
- New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA.
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Nagamine K, Hung GC, Li B, Lo SC. DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays. Microbiol Insights 2015; 8:7-14. [PMID: 26279626 PMCID: PMC4515919 DOI: 10.4137/mbi.s29736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/05/2022] Open
Abstract
Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani, and Staphylococcus aureus, which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5-50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.
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Affiliation(s)
- Kenjiro Nagamine
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Guo-Chiuan Hung
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Bingjie Li
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Shyh-Ching Lo
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies and Division of Human Tissues, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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