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Xu D, Metz J, Harmody D, Peterson T, Winder P, Guzmán EA, Russo R, McCarthy PJ, Wright AE, Wang G. Brominated and Sulfur-Containing Angucyclines Derived from a Single Pathway: Identification of Nocardiopsistins D-F. Org Lett 2022; 24:7900-7904. [PMID: 36269561 DOI: 10.1021/acs.orglett.2c02879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One novel brominated nocardiopsistin D (1) and two new sulfur-containing nocardiopsistins E-F (2-3) were identified from Nocardiopsis sp. HB-J378. The biosynthetic gene cluster ncd featuring a brominase was identified. Compounds 1-3 exhibited significant anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) activities with minimum inhibitory concentrations (MICs) of 0.098, 3.125, and 0.195 μg/mL, respectively. The single bromination in 1 drastically enhanced the anti-MRSA activity by 128-fold without altering cell toxicity and acquired new activities against the bacterial pathogens vancomycin-resistant S. aureus (VRSA), Enterococcus faecium, and Bacillus cereus.
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Affiliation(s)
- Dongbo Xu
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Jackie Metz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Dedra Harmody
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Tara Peterson
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Priscilla Winder
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Esther A Guzmán
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Riccardo Russo
- Regional Bio-Containment Laboratory, Department of Medicine, Rutgers University, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Peter J McCarthy
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Amy E Wright
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, Florida 34946, United States
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Polyhydroxyalkanoate (PHA) Biopolymer Synthesis by Marine Bacteria of the Malaysian Coral Triangle Region and Mining for PHA Synthase Genes. Microorganisms 2022; 10:microorganisms10102057. [PMID: 36296332 PMCID: PMC9607975 DOI: 10.3390/microorganisms10102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource depletion, and global waste issues. This has spurred the isolation and characterisation of novel PHA-producing strains through cultivation and non-cultivation approaches, with a particular interest in genes encoding PHA synthesis pathways. Since sea sponges and sediment are marine benthic habitats known to be rich in microbial diversity, sponge tissues (Xestospongia muta and Aaptos aaptos) and sediment samples were collected in this study from Redang and Bidong islands located in the Malaysian Coral Triangle region. PHA synthase (phaC) genes were identified from sediment-associated bacterial strains using a cultivation approach and from sponge-associated bacterial metagenomes using a non-cultivation approach. In addition, phylogenetic diversity profiling was performed for the sponge-associated bacterial community using 16S ribosomal ribonucleic acid (16S rRNA) amplicon sequencing to screen for the potential presence of PHA-producer taxa. A total of three phaC genes from the bacterial metagenome of Aaptos and three phaC genes from sediment isolates (Sphingobacterium mizutaii UMTKB-6, Alcaligenes faecalis UMTKB-7, Acinetobacter calcoaceticus UMTKB-8) were identified. Produced PHA polymers were shown to be composed of 5C to nC monomers, with previously unreported PHA-producing ability of the S. mizutaii strain, as well as a 3-hydroxyvalerate-synthesising ability without precursor addition by the A. calcoaceticus strain.
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Kawamura Y, Mori K, Amachi S. Reductive deiodination of 2,4,6-triiodophenol by Vallitalea sp. strain TIP-1 isolated from the marine sponge. J Biosci Bioeng 2021; 132:154-160. [PMID: 34024749 DOI: 10.1016/j.jbiosc.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
An anaerobic microbial consortium capable of reductively dehalogenating 2,4,6-triiodophenol (2,4,6-TIP) was enriched from the marine sponge Hymeniacidon sinapium. The enrichment reductively deiodinated 100 μM of 2,4,6-TIP to 4-iodophenol (4-IP) and 2-iodophenol (2-IP) in the presence of sterile sponge tissue as the sole carbon source and electron donor. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis revealed that bacteria closely related with Vallitalea guaymasensis and Oceanirhabdus sediminicola, both of which are members of the order Clostridiales, were predominant in the enrichment. When glucose was added to the enrichment as alternative carbon source, one of these bacteria grew predominantly, which was subsequently isolated as a pure culture. The strain, designated as TIP-1, showed 99.7% 16S rRNA gene sequence similarity with V. guaymasensis. In the presence of glucose, strain TIP-1 reductively deiodinated 2,4,6-TIP to 2-IP and 4-IP at a molar ratio of 3:1, during which 2,4-diiodophenol (2,4-DIP) and 2,6-diiodophenol (2,6-DIP) were observed as deiodinated intermediates. Glucose was required for 2,4,6-TIP deiodination, but 2,4,6-TIP was not essential for growth of strain TIP-1. The strain also deiodinated 2,4-DIP to 2-IP and 4-IP at a molar ratio of 1:1, and 2,6-DIP to 2-IP, but further deiodination of the monoiodophenols was not observed. These results suggest that strain TIP-1 removed both ortho- and para-substituted iodines equally. Such deiodinating bacteria could be applied to the mineralization or dehalogenation of triiodobenzene derivatives, which are widely used as X-ray contrast media.
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Affiliation(s)
- Yuki Kawamura
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba 271-8510, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-city, Chiba 271-8510, Japan.
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Lascu I, Mereuță I, Chiciudean I, Hansen H, Avramescu SM, Tănase A, Stoica I. Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. Microbiologyopen 2021; 10:e1182. [PMID: 33970538 PMCID: PMC8087987 DOI: 10.1002/mbo3.1182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical-based plastics. Here, we describe the complete genome of a new marine PHA-producing bacterium-Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA-producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open-source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3-ketothiolase, and an acetoacetyl-CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl-CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.
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Affiliation(s)
- Irina Lascu
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ioana Mereuță
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Iulia Chiciudean
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Hilde Hansen
- Department of ChemistryFaculty of Science and TechnologyUiT The Arctic University of NorwayTromsøNorway
| | - Sorin Marius Avramescu
- Department of Organic Chemistry, Biochemistry and CatalysisFaculty of ChemistryUniversity of BucharestBucharestRomania
| | - Ana‐Maria Tănase
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ileana Stoica
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
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Kumar V, Kumar S, Singh D. Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges. Int J Biol Macromol 2019; 147:1255-1267. [PMID: 31739043 DOI: 10.1016/j.ijbiomac.2019.09.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India.
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Bioremediation of Mercury through Encapsulation of the Clone Carrying Meroperon. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.1.62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Shady NH, Fouad MA, Salah Kamel M, Schirmeister T, Abdelmohsen UR. Natural Product Repertoire of the Genus Amphimedon. Mar Drugs 2018; 17:md17010019. [PMID: 30598005 PMCID: PMC6357078 DOI: 10.3390/md17010019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 01/23/2023] Open
Abstract
Marine sponges are a very attractive and rich source in the production of novel bioactive compounds. The sponges exhibit a wide range of pharmacological activities. The genus Amphimedon consists of various species, such as viridis, compressa, complanata, and terpenensis, along with a handful of undescribed species. The Amphimedon genus is a rich source of secondary metabolites containing diverse chemical classes, including alkaloids, ceramides, cerebrososides, and terpenes, with various valuable biological activities. This review covers the literature from January 1983 until January 2018 and provides a complete survey of all the compounds isolated from the genus Amphimedon and the associated microbiota, along with their corresponding biological activities, whenever applicable.
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Affiliation(s)
- Nourhan Hisham Shady
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, 61519 Minia, Egypt.
| | - Mostafa A Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt.
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, 61519 Minia, Egypt.
| | - Tanja Schirmeister
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Staudingerweg 5, 55128 Mainz, Germany.
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Butt FI, Muhammad N, Hamid A, Moniruzzaman M, Sharif F. Recent progress in the utilization of biosynthesized polyhydroxyalkanoates for biomedical applications – Review. Int J Biol Macromol 2018; 120:1294-1305. [DOI: 10.1016/j.ijbiomac.2018.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/20/2018] [Accepted: 09/02/2018] [Indexed: 01/10/2023]
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Muller KE, Denison RF. Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181124. [PMID: 30662731 PMCID: PMC6304121 DOI: 10.1098/rsos.181124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/13/2018] [Indexed: 05/07/2023]
Abstract
Resources that microbial symbionts obtain from hosts may enhance fitness during free-living stages when resources are comparatively scarce. For rhizobia in legume root nodules, diverting resources from nitrogen fixation to polyhydroxybutyrate (PHB) has been discussed as a source of host-symbiont conflict. Yet, little is known about natural variation in PHB storage and its implications for rhizobial evolution. We therefore measured phenotypic variation in natural rhizobia populations and investigated how PHB might contribute to fitness in the free-living stage. We found that natural populations of rhizobia from Glycine max and Chamaecrista fasciculata had substantial, heritable variation in PHB acquisition during symbiosis. A model simulating temperature-dependent metabolic activity showed that the observed range of stored PHB per cell could support survival for a few days, for active cells, or over a century for sufficiently dormant cells. Experiments with field-isolated Bradyrhizobium in starvation culture suggest PHB is partitioned asymmetrically in dividing cells, consistent with individual-level bet-hedging previously demonstrated in E. meliloti. High-PHB isolates used more PHB over the first month, yet still retained more PHB for potential long-term survival in a dormant state. These results suggest that stored resources like PHB may support both short-term and long-term functions that contribute to fitness in the free-living stage.
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Affiliation(s)
- Katherine E. Muller
- Graduate Program in Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - R. Ford Denison
- Department of Ecology Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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Bayari SH, Şen EH, Ide S, Topaloglu B. Structural studies on Demospongiae sponges from Gökçeada Island in the Northern Aegean Sea. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:368-377. [PMID: 29179087 DOI: 10.1016/j.saa.2017.11.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/23/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
The Demospongiae is the largest Class in the phylum Porifera (sponges). Most sponge species in the Class Demospongiae have a skeleton of siliceous spicules and/or protein spongin or both. The first aim of this study was to perform the morphological and structural characterization of the siliceous spicules of four species belonging to Class Demospongiae (Suberites domuncula, Axinella polypoides, Axinella damicornis and Agelas oroides) collected around Gökçeada Island-Turkey (Northern Aegean Sea). The characterizations were carried out using a combination of Scanning Electron Microscopy with Energy Dispersive X-ray Spectroscopy (SEM/EDX), Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy (ATR-FTIR) and Small Angle X-ray Scattering (SAXS) techniques. The sponge Chondrosia reniformis (Porifera, Demospongiae) lacks a structural skeleton of spicules or the spongin. It consists mainly of a collagenous tissue. The collagen with sponge origin is an important source in biomedical and pharmaceutical applications. The second aim of this study was to provide more information on the molecular structure of collagen of outer (ectosome) and inner (choanosome) regions of the Chondrosia reniformis using ATR-FTIR spectroscopy. Hierarchical clustering analysis (HCA) was also used for the discrimination of ATR-FTIR spectra of species.
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Affiliation(s)
- Sevgi Haman Bayari
- Department of Physics Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800 Ankara, Turkey.
| | - Elif Hilal Şen
- Department of Physics Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800 Ankara, Turkey
| | - Semra Ide
- Department of Physics Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800 Ankara, Turkey
| | - Bülent Topaloglu
- Department of Marine Biology, Faculty of Fisheries, Istanbul University, 34480 Istanbul, Turkey
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Sugappriya M, Sudarsanam D, Bhaskaran R, Joseph J, Suresh A. Druggability and Binding Site Interaction Studies of Potential Metabolites Isolated from Marine Sponge Aurora globostellata against Human Epidermal Growth Factor Receptor-2. Bioinformation 2017; 13:261-268. [PMID: 28959095 PMCID: PMC5609291 DOI: 10.6026/97320630013261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
To study the involvement of compounds stigmasterol and oleic acid isolated from marine sponge Aurora globostellata and docking
against the Human Epidermal Growth Factor Receptor-2 in breast cancer. The comparative molecular docking was performed with
the natural compounds from marine sponge and the synthetic drugs used in breast cancer treatment against the target HER2. The
molecular docking analysis was done using GLIDE in Schrodinger software package. The ADME properties were calculated using the
Qikprop. The observation of the common binding site for all the ligands confirms the binding pocket; where the isolated compound
Stigmasterol agrees well with the binding residues and thus can be optimized further to arrive at a molecule that has a high binding
affinity and low binding constant. The results of the docking studies carried out on HER2 provide an insight for the compound
stigmasterol to have drug like properties than oleic acid. These results are supportive to confirm the marine sponges as a better lead for
cancer therapeutics.
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Affiliation(s)
- M Sugappriya
- Research and development centre, Bharathiar University, Coimbatore 641 046, Tamilnadu, India
| | - D Sudarsanam
- Department of Zoology and Advanced Biotechnology, Loyola college, Chennai 600034,Tamil nadu, India
| | - Raj Bhaskaran
- School of Biotechnology and genetic engineering Bharathiar University, Coimbatore 641 046, Tamilnadu, India
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Jeppiaar Research park, Sathyabama University, Chennai 600119,Tamilnadu, India
| | - Arumugam Suresh
- Centre for Drug Discovery and Development, Jeppiaar Research park, Sathyabama University, Chennai 600119,Tamilnadu, India
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Sathiyanarayanan G, Bhatia SK, Song HS, Jeon JM, Kim J, Lee YK, Kim YG, Yang YH. Production and characterization of medium-chain-length polyhydroxyalkanoate copolymer from Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620. Int J Biol Macromol 2017; 97:710-720. [DOI: 10.1016/j.ijbiomac.2017.01.053] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 02/03/2023]
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