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Liu B, Han J, Zhang H, Li Y, An Y, Ji S, Liu Z. The regulatory pathway of transcription factor MYB36 from Trichoderma asperellum Tas653 resistant to poplar leaf blight pathogen Alternaria alternata Aal004. Microbiol Res 2024; 282:127637. [PMID: 38382286 DOI: 10.1016/j.micres.2024.127637] [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: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
In fungi, MYB transcription factors (TFs) mainly regulate growth, development, and resistance to stress. However, as major disease-resistance TFs, they have rarely been studied in biocontrol fungi. In this study, MYB36 of Trichoderma asperellum Tas653 (Ta) was shown to respond strongly to the stress caused by Alternaria alternata Aa1004. Compared with wild-type Ta (Ta-Wt), the inhibition rate of the MYB36 knockout strain (Ta-Kn) on Aa1004 decreased by 11.06%; the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities decreased by 82.15 U/g, 0.19 OD470/min/g, and 1631.2 μmol/min/g, respectively. The MYB36 overexpression strain (Ta-Oe) not only enhanced hyperparasitism on Aa1004, caused its hyphae to swell, deform, or even rupture, but also reduced the incidence rate of poplar leaf blight. MYB36 regulates downstream (TFs, detoxification genes, defense genes, and other antifungal-related genes by binding to the cis-acting elements "ACAT" and "ATCG". Zinc finger TFs, as the main antifungal TFs, account for 90% of the total TFs, and Zn37.5 (23.24-) and Zn83.7 (23.18-fold) showed the greatest expression difference when regulated directly by MYB36. The detoxification genes mainly comprised 11 major major facilitator superfamily (MFS) genes, among which MYB36 directly increased the expression levels of three genes by more than 2-3.44-fold. The defense genes mainly encoded cytochrome P450 (P450) and hydrolases. e.g., P45061.3 (2-10.95-), P45060.2 (2-7.07-), and Hyd44.6 (2-2.30-fold). This study revealed the molecular mechanism of MYB36 regulation of the resistance of T. asperellum to A. alternata and provides theoretical guidance for the biocontrol of poplar leaf blight and the anti-disease mechanism of biocontrol fungi.
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Affiliation(s)
- Bin Liu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Han
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Huifang Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Modern Agricultural Industry Research Institute of Henan Zhoukou National Agricultural High-tech Industry Demonstration Zone, Zhoukou Normal University, Henan 466000, China
| | - Yuxiao Li
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Yibo An
- National Forestry and Grassland National Reserve Forest Engineering Technology Research Center, Chongqing Forestry Investment and Development Co., Ltd., Chongqing 401120, China
| | - Shida Ji
- Horticultural College of Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihua Liu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China.
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2
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van der Zee M, de Vries C, Masa M, Morales M, Rayo M, Hegger I. Regulatory aspects of a nanomaterial for imaging therapeutic cells. Drug Deliv Transl Res 2023; 13:2693-2703. [PMID: 37210426 PMCID: PMC10545613 DOI: 10.1007/s13346-023-01359-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
The ability to track therapeutic cells upon administration to the patient is of interest to both regulators and developers of cell therapy. The European Commission Horizon2020 project nTRACK from 2017-2022 aimed to develop a multi-modal nano-imaging agent to track therapeutic cells during development of a cell therapy. As part of this project, we investigated the regulatory pathway involved for such a product if marketed as a stand-alone product. An important regulatory hurdle appeared to be the appropriate regulatory classification of the nTRACK nano-imaging agent, as neither the definition for medicinal product nor the definition for medical device appeared to be a good fit for the purpose of the product and we were confronted with diverging views of competent authorities on the classification. As a consequence, the information requirements to fulfill before conducting a First in Human trial are not evident and can only be decided upon by closely collaborating and communicating with the relevant authorities throughout the development of the product. Moreover, standard test methods for demonstrating the quality and safety of a medicinal product or medical device are not always suitable for nanomaterials such as the nTRACK nano-imaging agent. Regulatory agility is therefore a great need to prevent delay of promising medical innovations, although regulatory guidance on these products will likely improve with more experience. In this article, we outline the lessons learnt related to the regulatory process of the nTRACK nano-imaging agent for tracking therapeutic cells and offer recommendations to both regulators and developers of similar products.
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Affiliation(s)
- Margriet van der Zee
- National Institute of Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, the Netherlands
| | - Claudette de Vries
- National Institute of Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, the Netherlands.
| | | | | | | | - Ingrid Hegger
- National Institute of Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, the Netherlands
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3
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Yang Z, Yang F, Liu JL, Wu HT, Yang H, Shi Y, Liu J, Zhang YF, Luo YR, Chen KM. Heavy metal transporters: Functional mechanisms, regulation, and application in phytoremediation. Sci Total Environ 2022; 809:151099. [PMID: 34688763 DOI: 10.1016/j.scitotenv.2021.151099] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [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: 08/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 05/22/2023]
Abstract
Heavy metal pollution in soil is a global problem with serious impacts on human health and ecological security. Phytoextraction in phytoremediation, in which plants uptake and transport heavy metals (HMs) to the tissues of aerial parts, is the most environmentally friendly method to reduce the total amount of HMs in soil and has wide application prospects. However, the molecular mechanism of phytoextraction is still under investigation. The uptake, translocation, and retention of HMs in plants are mainly mediated by a variety of transporter proteins. A better understanding of the accumulation strategy of HMs via transporters in plants is a prerequisite for the improvement of phytoextraction. In this review, the biochemical structure and functions of HM transporter families in plants are systematically summarized, with emphasis on their roles in phytoremediation. The accumulation mechanism and regulatory pathways related to hormones, regulators, and reactive oxygen species (ROS) of HMs concerning these transporters are described in detail. Scientific efforts and practices for phytoremediation carried out in recent years suggest that creation of hyperaccumulators by transgenic or gene editing techniques targeted to these transporters and their regulators is the ultimate powerful path for the phytoremediation of HM contaminated soils.
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Affiliation(s)
- Zi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jia-Lan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hai-Tao Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yi Shi
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Jie Liu
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Yan-Feng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, Shaanxi, China
| | - Yan-Rong Luo
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Bassat Q, Maïga-Ascofaré O, May J, Clain J, Mombo-Ngoma G, Groger M, Adegnika AA, Agobé JCD, Djimde A, Mischlinger J, Ramharter M. Challenges in the clinical development pathway for triple and multiple drug combinations in the treatment of uncomplicated falciparum malaria. Malar J 2022; 21:61. [PMID: 35193586 PMCID: PMC8864855 DOI: 10.1186/s12936-022-04079-9] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/06/2022] [Indexed: 11/23/2022] Open
Abstract
The addition of a third anti-malarial drug matching the pharmacokinetic characteristics of the slowly eliminated partner drug in artemisinin-based combination therapy (ACT) has been proposed as new therapeutic paradigm for the treatment of uncomplicated falciparum malaria. These triple artemisinin-based combination therapy (TACT) should in theory more effectively prevent the development and spread of multidrug resistance than current ACT. Several clinical trials evaluating TACT—or other multidrug anti-malarial combination therapy (MDACT)—have been reported and more are underway. From a regulatory perspective, these clinical development programmes face a strategic dilemma: pivotal clinical trials evaluating TACT are designed to test for non-inferiority of efficacy compared to standard ACT as primary endpoint. While meeting the endpoint of non-inferior efficacy, TACT are consistently associated with a slightly higher frequency of adverse drug reactions than currently used ACT. Moreover, the prevention of the selection of specific drug resistance—one of the main reasons for TACT development—is beyond the scope of even large-scale clinical trials. This raises important questions: if equal efficacy is combined with poorer tolerability, how can then the actual benefit of these drug combinations be demonstrated? How should clinical development plans be conceived to provide objective evidence for or against an improved management of patients and effective prevention of anti-malarial drug resistance by TACT? What are the objective criteria to ultimately convince regulators to approve these new products? In this Opinion paper, the authors discuss the challenges for the clinical development of triple and multidrug anti-malarial combination therapies and the hard choices that need to be taken in the further clinical evaluation and future implementation of this new treatment paradigm.
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Affiliation(s)
- Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ICREA, Passeig de Lluís Companys 23, 08010, Barcelona, 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
| | - Oumou Maïga-Ascofaré
- Kumasi Center for Collaborative Research, Kumasi, Ghana.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Jerôme Clain
- Université de Paris, Centre National de Référence du Paludisme, Hôpital Bichat- Claude Bernard, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Ghyslain Mombo-Ngoma
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany.,Centre de Recherches de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Ayôla A Adegnika
- Centre de Recherches de Lambaréné, Lambaréné, Gabon.,Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Abdoulaye Djimde
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Johannes Mischlinger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research, Partner Site Hamburg- Lübeck-Borstel-Riems, Hamburg- Lübeck-Borstel-Riems, Germany. .,Centre de Recherches de Lambaréné, Lambaréné, Gabon.
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Gupta P, Naithani S, Preece J, Kim S, Cheng T, D'Eustachio P, Elser J, Bolton EE, Jaiswal P. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol 2022; 2443:511-525. [PMID: 35037224 DOI: 10.1007/978-1-0716-2067-0_27] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/14/2023]
Abstract
Plant Reactome (https://plantreactome.gramene.org) and PubChem ( https://pubchem.ncbi.nlm.nih.gov ) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions. Plant Reactome knowledgebase, a conceptual plant pathway network, is built by biocuration and integrating (bio)chemical entities, gene products, and macromolecular interactions. It provides manually curated pathways for the reference species Oryza sativa (rice) and gene orthology-based projections that extend pathway knowledge to 106 plant species. Currently, it hosts 320 reference pathways for plant metabolism, hormone signaling, transport, genetic regulation, plant organ development and differentiation, and biotic and abiotic stress responses. In addition to the pathway browsing and search functions, the Plant Reactome provides the analysis tools for pathway comparison between reference and projected species, pathway enrichment in gene expression data, and overlay of gene-gene interaction data on pathways. PubChem, a popular reference database of (bio)chemical entities, provides information on small molecules and other types of chemical entities, such as siRNAs, miRNAs, lipids, carbohydrates, and chemically modified nucleotides. The data in PubChem is collected from hundreds of data sources, including Plant Reactome. This chapter provides a brief overview of the Plant Reactome and the PubChem knowledgebases, their association to other public resources providing accessory information, and how users can readily access the contents.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
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6
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Flanagan KL, MacIntyre CR, McIntyre PB, Nelson MR. SARS-CoV-2 Vaccines: Where Are We Now? J Allergy Clin Immunol Pract 2021; 9:3535-3543. [PMID: 34400116 PMCID: PMC8363243 DOI: 10.1016/j.jaip.2021.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/20/2022]
Abstract
The best and safest way to control the coronavirus disease 2019 (COVID-19) pandemic is by using vaccination to generate widespread immunity. The urgent need to develop safe and effective COVID-19 vaccines was met with unprecedented speed and action from the global community. There are now 289 vaccines in the development pipeline. More remarkably, there are 20 publicly available vaccines, and more than 3.3 billion doses of COVID-19 vaccines have been administered across 180 countries. This is just the beginning of our fight against the pandemic. Even at the current vaccination rate, it could take years to vaccinate the world's population; many high-income countries are focusing on their needs, whereas the poorer nations are waiting for vaccines. There is still much that we do not understand about immunity to this new disease, and we will have to contend with the emerging variants. In this commentary, we describe the current status of COVID-19 vaccine development and provide insights into how the development and approvals happened so quickly. We discuss the clinical trial data that led to rapid emergency use authorization and the many challenges of global rollout. We also comment on some of the key unanswered questions and future directions for COVID-19 vaccine development and deployment.
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Affiliation(s)
- Katie L Flanagan
- Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, Tas, Australia; School of Medicine, University of Tasmania, Launceston, Tas, Australia; School of Health and Biomedical Science, RMIT University, Bundoora, Vic, Australia; Department of Immunology and Pathology, Monash University, Melbourne, Vic, Australia.
| | - C Raina MacIntyre
- Biosecurity Research Program, Kirby Institute, UNSW Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Peter B McIntyre
- Women's and Children's Health, University of Otago, Dunedin, New Zealand
| | - Michael R Nelson
- Division of Asthma, Allergy and Immunology, University of Virginia, Charlottesville, Va
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Mousavian Z, Khodabandeh M, Sharifi-Zarchi A, Nadafian A, Mahmoudi A. StrongestPath: a Cytoscape application for protein-protein interaction analysis. BMC Bioinformatics 2021; 22:352. [PMID: 34187355 PMCID: PMC8244221 DOI: 10.1186/s12859-021-04230-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can also identify any activating or inhibitory regulatory paths between two distinct sets of transcription factors and target genes. This application can be used on the built-in human and mouse PPI or signaling databases, or any user-provided database for some organism. RESULTS Our results on 12 signaling pathways from the NetPath database demonstrate that the application can be used for indicating proteins which may play significant roles in a pathway by finding the strongest path(s) in the PPI or signaling network. CONCLUSION Easy access to multiple public large databases, generating output in a short time, addressing some key challenges in one platform, and providing a user-friendly graphical interface make StrongestPath an extremely useful application.
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Affiliation(s)
- Zaynab Mousavian
- Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.
| | - Mehran Khodabandeh
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.,Department of Stem cells and Developmental Biology at the Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Alireza Nadafian
- Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
| | - Alireza Mahmoudi
- Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
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González-Moro I, Santin I. Long non-coding RNA-regulated pathways in pancreatic β cells: Their role in diabetes. Int Rev Cell Mol Biol 2021; 359:325-355. [PMID: 33832652 DOI: 10.1016/bs.ircmb.2021.02.007] [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] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides that have not coding potential, but act as gene expression regulators through several molecular mechanisms. Several studies have identified tons of lncRNAs that are expressed in pancreatic β cells and many of them have been shown to have β cell-specific expression, suggesting a potential role in the regulation of basal β cell functions. Indeed, accumulating evidence based on numerous studies, has highlighted the implication of lncRNAs in the regulation of pancreatic β cell differentiation and proliferation, insulin synthesis and secretion, and apoptosis. In addition, several lncRNAs have shown to be implicated in pancreatic β cell dysfunction linked to different types of diabetes, including type 1 and type 2 diabetes, and monogenic forms of the disease. Pathogenic conditions linked to diabetes (inflammation or lipoglucotoxicity, for example) dysregulate the expression of several lncRNAs, suggesting that changes in lncRNA may alter potentially important pathways for β cell function, and eventually leading to β cell dysfunction and diabetes development. In this sense, functional characterization of some lncRNAs has demonstrated that these non-coding molecules participate in the regulation of several crucial pathways at the pancreatic β cell level, and dysregulation of these pathways leads to pathogenic phenotypes. In this review, we provide an overview of the action mechanisms of functionally characterized lncRNAs in healthy β cells and describe the contribution of some diabetes-associated lncRNAs to pancreatic β cell failure.
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Affiliation(s)
- Itziar González-Moro
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; CIBER (Centro de Investigación Biomédica en Red) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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Hu Y, Zhou X, Zhang B, Li S, Fan X, Zhao H, Zhang J, Liu H, He Q, Li Q, Ayaad M, You A, Xing Y. OsPRR37 Alternatively Promotes Heading Date Through Suppressing the Expression of Ghd7 in the Japonica Variety Zhonghua 11 under Natural Long-Day Conditions. Rice (N Y) 2021; 14:20. [PMID: 33630174 PMCID: PMC7907330 DOI: 10.1186/s12284-021-00464-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/12/2021] [Indexed: 05/24/2023]
Abstract
Heading date is an important agronomic trait of rice (Oryza sativa L.) and is regulated by numerous genes, some of which exhibit functional divergence in a genetic background-dependent manner. Here, we identified a late heading date 7 (lhd7) mutant that flowered later than wild-type Zhonghua 11 (ZH11) under natural long-day (NLD) conditions. Map-based cloning facilitated by the MutMap strategy revealed that LHD7 was on the same locus as OsPRR37 but exhibited a novel function as a promoter of heading date. A single-nucleotide mutation of G-to-A in the coding region caused a substitution of aspartic acid for glycine at site 159 within the pseudo-receiver (PR) domain of OsPRR37. Transcriptional analysis revealed that OsPRR37 suppressed Ghd7 expression in both ZH11 background under NLD conditions and the Zhenshan 97 background under natural short-day conditions. Consistently, the expression of Ehd1, Hd3a and RFT1 was enhanced by OsPRR37 in the ZH11 background. Genetic analysis indicated that the promotion of heading date and reduction in grain yield by OsPRR37 were partially dependent on Ghd7. Further investigation showed that the alternative function of OsPRR37 required an intact Ghd7-related regulatory pathway involving not only its upstream regulators OsGI and PhyB but also its interacting partner Hd1. Our study revealed the distinct role of OsPRR37 in the ZH11 background, which provides a more comprehensive understanding of OsPRR37 function and enriches the theoretical bases for improvement of rice heading date in the future.
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Affiliation(s)
- Yong Hu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiuping Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal, 13759, Egypt
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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Braynen J, Yang Y, Yuan J, Xie Z, Cao G, Wei X, Shi G, Zhang X, Wei F, Tian B. Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa. Cell Biosci 2021; 11:17. [PMID: 33436051 PMCID: PMC7802129 DOI: 10.1186/s13578-021-00528-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/03/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa. RESULTS The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin's biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated. CONCLUSION Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.
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Affiliation(s)
- Janeen Braynen
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Jiachen Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Gangqiang Cao
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaochun Wei
- Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaowei Zhang
- Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Fang Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. .,Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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11
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Yao J, Du H, Zhou H, Leng X, Wu J, He S, Luo J, Liang X, Liu H, Wang Q, Wei Q, Tan Q. Molecular characterization and expression profiles of six genes involved in vitellogenic deposition and hydrolysis of Chinese sturgeon (Acipenser sinensis) suggesting their transcriptional regulation on ovarian development. Theriogenology 2021; 162:59-66. [PMID: 33444917 DOI: 10.1016/j.theriogenology.2020.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/18/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 01/02/2023]
Abstract
Ovary development of Chinese sturgeon (Acipenser sinensis) in controlled breeding has been reported to respond to dietary lipid levels. However, the corresponding molecular regulatory mechanism about ovary development of Chinese sturgeon is still unclear. To elucidate the molecular mechanism of vitellogenic deposition and hydrolysis, six key genes, namely, vtgr (vitellogenin receptor), atp6v1c1 (Vacuolar H+-ATPase subunit c1), atp6v1h (Vacuolar H+-ATPase subunit h), ctsb (cathepsin B), ctsd (cathepsin D) and ctsl (cathepsin L) involved in vitellogenic deposition and hydrolysis of Chinese sturgeon were cloned and characterized, and their spatio-temporal mRNA expression profiles as well as transcriptional responses to dietary lipid level were investigated. The full-length cDNA sequences of these six genes showed similar domain structure to their respective orthologous genes from other vertebrates. Tissue-specific expression patterns of these genes were observed in ovary, liver, muscle, spleen, brain, gill, intestine, heart, stomach and kidney. Ovarian expression level of vtgr was the highest in stage II, and ctsl expression was the highest in stage IV, while the mRNA expressions of other 4 genes were the highest in stage III. The increase of dietary lipid level promoted ovary development and elevated the expressions of vtgr, atp6v1c1, atp6v1h, ctsb and ctsd in the ovary. The results of the present study indicated that these genes are crucial for vitellogenic deposition, and provided a preliminary understanding on the molecular regulation of vitellogenic deposition and hydrolysis during ovary development of Chinese sturgeon.
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Affiliation(s)
- Junpeng Yao
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization, Ministry of Agriculture/Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China
| | - Hai Zhou
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Xiaoqian Leng
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization, Ministry of Agriculture/Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China
| | - Jinping Wu
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization, Ministry of Agriculture/Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China
| | - Shan He
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Jiang Luo
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization, Ministry of Agriculture/Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China
| | - Xufang Liang
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Hong Liu
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Qingchao Wang
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization, Ministry of Agriculture/Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China.
| | - Qingsong Tan
- College of Fisheries, Huazhong Agricultural University/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture/Hubei Collaborative Innovation Center for Freshwater Aquaculture/Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China.
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12
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Farinha AP, Schrama D, Silva T, Conceição LEC, Colen R, Engrola S, Rodrigues P, Cerqueira M. Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics. J Proteomics 2021; 232:104047. [PMID: 33217584 DOI: 10.1016/j.jprot.2020.104047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Plant protein sources play an essential role in aquaculture by reducing the use of fish meal to sustainable levels, although further supplementation is needed to fulfill fish nutritional requirements. This work addressed fish growth performance and proteome changes to dietary methionine in European seabass juveniles. A dose-dependent response to methionine (Met) was observed on fish growth consistent with proteomic analyses, suggesting Met requirement ≥0.9% (w/w). Fish fed at 0.77% (w/w) exhibited reduced growth and an enrichment in proteins involved in cellular homeostasis. Proteomics data suggest an optimal nutritional status at 1.36% Met (w/w), together with putative beneficial effects on the immune system up to 1.66% Met (w/w). The response to dietary Met involved the convergence of different metabolic and signalling pathways implicated in cell growth and immune response e.g., mTOR, Hedgehog or the T Cell receptor signalling, coupled with a fine-tuning regulation of amino acid metabolism and translation.
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Abstract
Currently, the majority of medical devices are designed for adults; some are then miniaturized for use in neonates. This process neglects population-specific testing that would ensure that the medical devices used for neonates are actually safe and effective for that group. Incorporating human-centered design principles and utilizing methods to evaluate devices that include simulation and clinical testing can improve the safety of devices used in caring for neonates. However, significant regulatory, financial, social and ethical barriers to development remain. In order to overcome these barriers and create a pipeline of safe and effective neonatal medical devices, specific incentives are required.
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Affiliation(s)
- Janene H Fuerch
- Division of Neonatal and Developmental Medicine, Stanford University Medical Center, United States.
| | | | - Immanuel Barshi
- Human System Integration Division, NASA Ames Research Center, United States
| | - Helen Liley
- Mater Mothers' Hospital and Mater Research - The University of Queensland, Faculty of Medicine, The University of Queensland, Australia
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14
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Wang K, Zhang H, Zhang J, Jia E, Zhu G. Prediction of immune factors and signaling pathways in lung injury induced by LPS based on network analysis. Saudi J Biol Sci 2019; 26:2068-2073. [PMID: 31889796 PMCID: PMC6923448 DOI: 10.1016/j.sjbs.2019.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/23/2022] Open
Abstract
Objective To construct a regulatory network involved in acute lung injury, so as to provide a new theoretical basis and research ideas for studying the relationship between inflammatory factors and immune proteins to collectively regulate the occurrence of acute lung injury. Method By using Meta-analysis, GO, KEGG and other methods notarized and constructed the regulatory network pathways of cytokine cascade and lung injury induced by LPS. Results The result of Meta-analysis showed that the correlation between CD14, TNF-α, IL-6 gene and acute lung injury was statistically significant. GO analysis and KEGG analysis showed that acute lung injury contained CD14, TNF-α, IL-6 and other involved factors in the induced process of LPS, these inflammatory factors and immune proteins jointly regulate the process of disease development. Conclusion CD14 receptor is an important receptor involved in mediating LPS-activated cells, and is a high-affinity LPS receptor. LPS stimulates inflammatory effector cells to bind to LPS receptor- CD14 to activate intracellular signal cascade. Direct or indirect involvement of pathogenic factors enable cytokine caused by induction form a particularly complex network of cytokine regulatory pathways, of which the inflammatory factors TNF-α and IL-6 are simultaneously involved in LPS-mediated and CD14-mediated cytokine cascades.
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Affiliation(s)
- Kaiwei Wang
- Department of Anesthesia and Perioperative Medicine, Henan Provincial International Coalition Laboratory of Basic Research on Anaesthetics and Pain, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Haoran Zhang
- Department of Anesthesia and Perioperative Medicine, Henan Provincial International Coalition Laboratory of Basic Research on Anaesthetics and Pain, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Jiaqiang Zhang
- Department of Anesthesia and Perioperative Medicine, Henan Provincial International Coalition Laboratory of Basic Research on Anaesthetics and Pain, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Erju Jia
- Department of Anesthesia, Henan Provincial Yexian People's Hospital, Yexian 467200, China
| | - Guosong Zhu
- Department of Anesthesia and Perioperative Medicine, Henan Provincial International Coalition Laboratory of Basic Research on Anaesthetics and Pain, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
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15
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Hou B, Tao L, Zhu X, Wu W, Guo M, Ye J, Wu H, Zhang H. Global regulator BldA regulates morphological differentiation and lincomycin production in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2018; 102:4101-15. [PMID: 29549449 DOI: 10.1007/s00253-018-8900-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Global regulator BldA, the only tRNA for a rare leucine codon UUA, is best known for its ability to affect morphological differentiation and secondary metabolism in the genus Streptomyces. In this study, we confirmed the regulatory function of the bldA gene (Genbank accession no. EU124663.1) in Streptomyces lincolnensis. Disruption of bldA hinders the sporulation and lincomycin production, that can recur when complemented with a functional bldA gene. Western blotting assays demonstrate that translation of the lmbB2 gene which encodes a L-tyrosine hydroxylase is absolutely dependent on BldA; however, mistranslation of the lmbU gene which encodes a cluster-situated regulator (CSR) is observed in a bldA mutant. Intriguingly, when the preferential cognate codon CTG was used, the expression level of LmbU was not the highest compared to the usage of rare codon TTA or CTA, indicating the rare codon in this position is significant for the regulation of lmbU expression. Moreover, replacement of TTA codons in both genes with another leucin codon in the bldA mutant did not restore lincomycin production. Thus, we believe that the bldA gene regulates lincomycin production via controlling the translation of not only lmbB2 and lmbU, but also the other TTA-containing genes. In conclusion, the present study demonstrated the importance of the bldA gene in morphological differentiation and lincomycin production in S. lincolnensis.
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16
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Zheng X, Su Y, Chen Y, Huang H, Shen Q. Global transcriptional responses of denitrifying bacteria to functionalized single-walled carbon nanotubes revealed by weighted gene-coexpression network analysis. Sci Total Environ 2018; 613-614:1240-1249. [PMID: 28958131 DOI: 10.1016/j.scitotenv.2017.09.193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 06/04/2017] [Revised: 09/18/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
Functionalized single-walled carbon nanotubes (f-SWNTs) are widely used in many fields due to the unique structure and the excellent properties. Although these nanomaterials have been reported to enable to cause negative effects on denitrifying bacteria once they enter the environment, the toxic behaviors and regulatory mechanisms of f-SWNTs to denitrification remain unclear. In this study, the denitrification performance of a model denitrifier exposed to pristine and functionalized SWNTs was investigated, and the global transcriptional responses were comprehensively explored by RNA-seq and weighted gene-coexpression network analysis (WGCNA). Although both hydroxyl SWNTs (SWNTs-OH) and carboxyl SWNTs (SWNTs-COOH) showed inhibitory effects on bacterial denitrification, the former more severely inhibited denitrification than the latter. Transcriptional profiles showed that compared with SWNTs-COOH, SWNTs-OH much more strongly influenced the expressions of the key genes related to signal transduction, substance transport, electron transfer and transcriptional regulation. Functional analysis further indicated that the genes associated with substrate transport, carbon source metabolism and electron transfer underwent dramatic down-regulation. Using WGCNA, 12 gene modules were established corresponding to various types of carbon nanotubes, and eigengene adjacency analysis revealed the key gene modules related to denitrification performance under different conditions. Hub gene network analysis revealed the key regulatory factors of bacterial denitrification induced by f-SWNTs. The results suggested that f-SWNTs modulated the key genes responsible for the glycerolipid/free fatty acid (GL/FFA) cycle, and thus disturb processes associated with denitrification, including signaling process, energy homeostasis, intracellular redox balance and transportation.
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Affiliation(s)
- Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Key Laboratory for Urban and Ecological Restoration of Shanghai, School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Qiuting Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Jia M, Yu X, Jiang J, Li Z, Feng Y. The cytidine repressor participates in the regulatory pathway of indole in Pantoea agglomerans. Res Microbiol 2017; 168:636-43. [PMID: 28483441 DOI: 10.1016/j.resmic.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 11/23/2022]
Abstract
Indole, an important signal molecule in both intraspecies and interspecies, regulates a variety of bacterial behaviors, but its regulatory mechanism is still unknown. Pantoea agglomerans YS19, a preponderant endophytic bacterium isolated from rice, does not produce indole, yet it senses exogenous indole. In this study, a mutant of YS19-Rpr whose target gene expression was downregulated by indole was selected through mTn5 transposon mutagenesis. Using the TAIL-PCR technique, the mutation gene was identified as a cytR homologue, which encodes a cytidine repressor (CytR) protein, a bacterial transcription factor involved in a complex regulation scheme. The negative regulation of indole in cytR, which is equivalent to the mutation in cytR, promotes the expression of a downstream gene deoC, which encodes the key enzyme deoxyribose-phosphate aldolase in participating in pentose metabolism. We found that DeoC is one of the regulatory proteins of P. agglomerans that is involved in counteracting starvation. Furthermore, the expression of deoC was induced by starvation conditions, accompanied by a decrease in cytR expression. This finding suggests that the indole signal and the mutation of cytR relieve inhibition of CytR in the transcription of deoC, facilitating better adaptation of the bacterium to the adverse conditions of the environment.
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Chaccour C, Rabinovich NR. Ivermectin to reduce malaria transmission III. Considerations regarding regulatory and policy pathways. Malar J 2017; 16:162. [PMID: 28434407 PMCID: PMC5402052 DOI: 10.1186/s12936-017-1803-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/06/2017] [Indexed: 11/05/2022] Open
Abstract
Vector control is a task previously relegated to products that (a) kill the mosquitoes directly at different stages (insecticides, larvicides, baited traps), or (b) avoid/reduce human-mosquito contact (bed nets, repellents, house screening), thereby reducing transmission. The potential community-based administration of the endectocide ivermectin with the intent to kill mosquitoes that bite humans, and thus reduce malaria transmission, offers a novel approach using a well-known drug, but additional steps are required to address technical, regulatory and policy gaps. The proposed community administration of this drug presents dual novel paradigms; first, indirect impact on the community rather than on individuals, and second, the use of a drug for vector control. In this paper, the main questions related to the regulatory and policy pathways for such an application are identified. Succinct answers are proposed for how the efficacy, safety, acceptability, cost-effectiveness and programmatic suitability could result in regulatory approval and ultimately policy recommendations on the use of ivermectin as a complementary vector control tool.
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Affiliation(s)
- Carlos Chaccour
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain. .,Centro de Investigação Em Saúde de Manhiça, Maputo, Mozambique. .,Instituto de Salud Tropical Universidad de Navarra, Pamplona, Spain.
| | - N Regina Rabinovich
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Zhang Y, Liu D, Wang L, Wang S, Yu X, Dai E, Liu X, Luo S, Jiang W. Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. J Mol Med (Berl) 2015. [PMID: 26208504 DOI: 10.1007/s00109-015-1315-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
UNLABELLED Coronary artery disease (CAD) is the most common type of heart disease. However, the molecular mechanisms of CAD remain elusive. Regulatory pathways are known to play crucial roles in many pathogenic processes. Thus, inferring risk regulatory pathways is an important step toward elucidating the mechanisms underlying CAD. With advances in high-throughput data, we developed an integrated systems approach to identify CAD risk regulatory pathways and key regulators. Firstly, a CAD-related core subnetwork was identified from a curated transcription factor (TF) and microRNA (miRNA) regulatory network based on a random walk algorithm. Secondly, candidate risk regulatory pathways were extracted from the subnetwork by applying a breadth-first search (BFS) algorithm. Then, risk regulatory pathways were prioritized based on multiple CAD-associated data sources. Finally, we also proposed a new measure to prioritize upstream regulators. We inferred that phosphatase and tensin homolog (PTEN) may be a key regulator in the dysregulation of risk regulatory pathways. This study takes a closer step than the identification of disease subnetworks or modules. From the risk regulatory pathways, we could understand the flow of regulatory information in the initiation and progression of the disease. Our approach helps to uncover its potential etiology. KEY MESSAGES We developed an integrated systems approach to identify risk regulatory pathways. We proposed a new measure to prioritize the key regulators in CAD. PTEN may be a key regulator in dysregulation of the risk regulatory pathways.
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Affiliation(s)
- Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dianming Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lihong Wang
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China
| | - Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Enyu Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xinyi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shanshun Luo
- Department of Gerontology, The First Hospital of Harbin Medical University, Harbin Medical University, Harbin, China.
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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