Journal of Microbiology

Volume 58(8); August 2020

Review

Recent advances in the development of β-lactamase inhibitors: Shivakumar S. Jalde , Hyun Kyung Choi; J. Microbiol. 2020;58(8):633-647. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0285-z

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β-Lactam antibiotics are the most commonly prescribed antibiotics worldwide; however, antimicrobial resistance (AMR) is a global challenge. The β-lactam resistance in Gram-negative bacteria is due to the production of β-lactamases, including extended-spectrum β-lactamases, metallo-β-lactamases, and carbapenem-hydrolyzing class D β-lactamases. To restore the efficacy of BLAs, the most successful strategy is to use them in combination with β-lactamase inhibitors (BLI). Here we review the medically relevant β-lactamase families and penicillins, diazabicyclooctanes, boronic acids, and novel chemical scaffold-based BLIs, in particular approved and under clinical development.

Citations

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Functional and structural analyses of IMP-27 metallo-β-lactamase: evolution of IMP-type enzymes to overcome Zn(II) deprivation
Yoshiki Kato, Toshio Yamaguchi, Haruka Nakagawa-Kamura, Yoshikazu Ishii, Akiko Shimizu-Ibuka, Pablo Power
Microbiology Spectrum.2024;[Epub] CrossRef
Current Strategy for Targeting Metallo-β-Lactamase with Metal-Ion-Binding Inhibitors
Jessica L. Ortega-Balleza, Lenci K. Vázquez-Jiménez, Eyra Ortiz-Pérez, Guadalupe Avalos-Navarro, Alma D. Paz-González, Edgar E. Lara-Ramírez, Gildardo Rivera
Molecules.2024; 29(16): 3944. CrossRef
Understanding the Functional Dynamics of the TokK Enzyme in Carbapenem Biosynthesis via MD Simulations and QM/MM Calculations
Shakir Ali Siddiqui, Kshatresh Dutta Dubey
Inorganic Chemistry.2024; 63(40): 18963. CrossRef
Recent advances in functionalized macrocyclic polyamines for medicine applications
Hao Chang, Renzhong Qiao, Chao Li
Chinese Chemical Letters.2024; : 110675. CrossRef
Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis
Ying Luo, Taha Majid Mahmood Sheikh, Xin Li, YuMeng Yuan, Fen Yao, Meimei Wang, Xiaoling Guo, Jilong Wu, Muhammad Shafiq, Qingdong Xie, Xiaoyang Jiao
Virulence.2024;[Epub] CrossRef
Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species
Shida Ji, Bin Liu, Jing Han, Ning Kong, Yongfeng Yang, Yucheng Wang, Zhihua Liu
Fungal Genetics and Biology.2024; 172: 103889. CrossRef
Revisiting the Checkerboard to Inform Development of β-Lactam/β-Lactamase Inhibitor Combinations
Darren J. Bentley
Antibiotics.2024; 13(4): 337. CrossRef
Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria
Song Zhang, Xinyu Liao, Tian Ding, Juhee Ahn
Antibiotics.2024; 13(3): 260. CrossRef
The C5α-Methyl-Substituted Carbapenem NA-1-157 Exhibits Potent Activity against Klebsiella spp. Isolates Producing OXA-48-Type Carbapenemases
Clyde A. Smith, Nichole K. Stewart, Marta Toth, Pojun Quan, John D. Buynak, Sergei B. Vakulenko
ACS Infectious Diseases.2023; 9(5): 1123. CrossRef
Phenotypes, genotypes and breakpoints: an assessment of β-lactam/β-lactamase inhibitor combinations against OXA-48
Tomefa E Asempa, Abigail K Kois, Christian M Gill, David P Nicolau
Journal of Antimicrobial Chemotherapy.2023; 78(3): 636. CrossRef
Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli Derived from Food and Humans in Northern Xinjiang, China
Yushuang Wu, Shudi Huang, Donglai Zhang, Hua Ji, Yongqing Ni, Xueling Zhang, Juan Dong, Baokun Li
Foodborne Pathogens and Disease.2023; 20(7): 270. CrossRef
Sequential C−H Methylation Catalyzed by the B12‐Dependent SAM Enzyme TokK: Comprehensive Theoretical Study of Selectivities
Wen‐Hao Deng, Rong‐Zhen Liao
Chemistry – A European Journal.2023;[Epub] CrossRef
CMOS Spectrophotometric Microsystem for Malaria Detection
Gabriel M. Ferreira, Vitória Baptista, Vítor Silva, Maria I. Veiga, Graça Minas, Susana O. Catarino
IEEE Transactions on Biomedical Engineering.2023; 70(8): 2318. CrossRef
Synthesis and β-Lactamase Inhibition Activity of Imidates of Diazabicyclooctane
Lijuan Zhai, Jian Sun, Jingwen Ji, Lili He, Yuanyu Gao, Jinbo Ji, Yuanbai Liu, Yangxiu Mu, Xueqin Ma, Dong Tang, Haikang Yang, Zafar Iqbal, Zhixiang Yang
Russian Journal of Bioorganic Chemistry.2022; 48(5): 1059. CrossRef
Recent Developments to Cope the Antibacterial Resistance via β-Lactamase Inhibition
Zafar Iqbal, Jian Sun, Haikang Yang, Jingwen Ji, Lili He, Lijuan Zhai, Jinbo Ji, Pengjuan Zhou, Dong Tang, Yangxiu Mu, Lin Wang, Zhixiang Yang
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Retracted and replaced: Phenotypes, genotypes and breakpoints: an assessment of β-lactam/ β-lactamase inhibitor combinations against OXA-48
Tomefa E Asempa, Abigail K Kois, Christian M Gill, David P Nicolau
Journal of Antimicrobial Chemotherapy.2022; 77(10): 2622. CrossRef
Carbapenemase producing Klebsiella pneumoniae: implication on future therapeutic strategies
Ilias Karaiskos, Irene Galani, Vassiliki Papoutsaki, Lamprini Galani, Helen Giamarellou
Expert Review of Anti-infective Therapy.2022; 20(1): 53. CrossRef
Antimicrobial Activity of Dihydroisocoumarin Isolated from Wadi Lajab Sediment-Derived Fungus Penicillium chrysogenum: In Vitro and In Silico Study
Raha Orfali, Shagufta Perveen, Mohamed Fahad AlAjmI, Safina Ghaffar, Md Tabish Rehman, Abdullah R. AlanzI, Saja Bane Gamea, Mona Essa Khwayri
Molecules.2022; 27(11): 3630. CrossRef
The Odd Couple(s): An Overview of Beta-Lactam Antibiotics Bearing More Than One Pharmacophoric Group
Margherita De Rosa, Anna Verdino, Annunziata Soriente, Anna Marabotti
International Journal of Molecular Sciences.2021; 22(2): 617. CrossRef
Drugs That Changed Society: History and Current Status of the Early Antibiotics: Salvarsan, Sulfonamides, and β-Lactams
Søren Brøgger Christensen
Molecules.2021; 26(19): 6057. CrossRef
In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases
Nichole K. Stewart, Marta Toth, Anastasiya Stasyuk, Sergei B. Vakulenko, Clyde A. Smith
ACS Infectious Diseases.2021; 7(6): 1765. CrossRef
Inhibition of the Clostridioides difficile Class D β-Lactamase CDD-1 by Avibactam
Nichole K. Stewart, Marta Toth, Anastasiya Stasyuk, Mijoon Lee, Clyde A. Smith, Sergei B. Vakulenko
ACS Infectious Diseases.2021; 7(5): 1164. CrossRef

Journal Articles

Production and characterization of melanin pigments derived from Amorphotheca resinae: Jeong-Joo Oh , Jee Young Kim , Sun Lul Kwon , Dong-Hyeok Hwang , Yoon-E Choi , Gyu-Hyeok Kim; J. Microbiol. 2020;58(8):648-656. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-0054-z

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Abstract

As melanin has emerged as functional pigment with cosmetic, health and food applications, the demand for the pigments is expected to increase. However, the conventional sources (e.g. mushroom, hair, and wool) of melanin production entail pigments inside the substrates which requires the costly extraction procedures, leading to inappropriate scalable production. In this study, we screened 102 of fungal isolates for their ability to produce melanin in the supernatant and selected the only Amorphotheca resinae as a promising candidate. In the peptone yeast extract glucose broth, A. resinae produced the melanin rapidly during the autolysis phase of growth, reaching up 4.5 g/L within 14 days. Structural characterization of the purified melanin from A. resinae was carried out by using elemental analysis, electron paramagnetic resonance, 13C solid-state nuclear magnetic resonance spectroscopy, and pyrolysis-gas chromatography-mass spectrometry in comparison with the standard melanins. The results indicate that the structural properties of A. resinae melanin is similar to the eumelanin which has a wide range of industrial uses. For example, the purified melanin from A. resinae has the potent antioxidant activities as a result of free radical scavenging assays. Consequently, A. resinae KUC3009 can be a promising candidate for scalable production of industrially applicable melanin.

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The Enigmatic World of Fungal Melanin: A Comprehensive Review
Malika Suthar, Laurent Dufossé, Sanjay K. Singh
Journal of Fungi.2023; 9(9): 891. CrossRef
Fungi as a source of eumelanin: current understanding and prospects
William Beeson, Kyle Gabriel, Christopher Cornelison
Journal of Industrial Microbiology and Biotechnology.2023;[Epub] CrossRef
Melanin biopolymers from microbial world with future perspectives—a review
Helan Soundra Rani Michael, Shri Ranjani Subiramanian, Divyavaahini Thyagarajan, Nazneen Bobby Mohammed, Venkatesh Kumar Saravanakumar, Mageswari Govindaraj, Kalpanadevi Murugasamy Maheswari, Naresh Karthikeyan, Charu Ramesh Kumar
Archives of Microbiology.2023;[Epub] CrossRef
Microbial Melanin: Renewable Feedstock and Emerging Applications in Food-Related Systems
Erminta Tsouko, Eirini Tolia, Dimitris Sarris
Sustainability.2023; 15(9): 7516. CrossRef
Fungi-derived natural antioxidants
Nazli Pinar Arslan, Pranav Dawar, Seyda Albayrak, Meryem Doymus, Fakhrul Azad, Nevzat Esim, Mesut Taskin
Critical Reviews in Food Science and Nutrition.2023; : 1. CrossRef
Comparative Biophysical and Ultrastructural Analysis of Melanins Produced by Clinical Strains of Different Species From the Trichosporonaceae Family
Iara Bastos de Andrade, Glauber Ribeiro de Sousa Araújo, Fábio Brito-Santos, Maria Helena Galdino Figueiredo-Carvalho, Rosely Maria Zancopé-Oliveira, Susana Frases, Rodrigo Almeida-Paes
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Preparation and characterization of natural melanin and its nanocomposite formed by copper doping
Ghada Khouqeer, Mawadda Alghrably, Nawal Madkhali, Manel Dhahri, Mariusz Jaremko, Abdul‐Hamid Emwas
Nano Select.2022; 3(12): 1598. CrossRef
Natural Melanin: Current Trends, and Future Approaches, with Especial Reference to Microbial Source
Noura El-Ahmady El-Naggar, WesamEldin I. A. Saber
Polymers.2022; 14(7): 1339. CrossRef
Eco-evolutionary impact of ultraviolet radiation (UVR) exposure on microorganisms, with a special focus on our skin microbiome
Sandhya Rai, Gunjan Rai, Amod Kumar
Microbiological Research.2022; 260: 127044. CrossRef
An Evaluation of Different Types of Peptone as Partial Substitutes for Animal-derived Serum in Vero Cell Culture
Chloe Lezin, Philippe Mauduit, Georges Uzan, Mohamed Essameldin Abdelgawad
Alternatives to Laboratory Animals.2022; 50(5): 339. CrossRef
Analytical Pyrolysis of the Fungal Melanins from Ochroconis spp. Isolated from Lascaux Cave, France
Cesareo Saiz-Jimenez, Pedro M. Martin-Sanchez, Jose A. Gonzalez-Perez, Bernardo Hermosin
Applied Sciences.2021; 11(3): 1198. CrossRef
Bioprocess of Microbial Melanin Production and Isolation
Kwon-Young Choi
Frontiers in Bioengineering and Biotechnology.2021;[Epub] CrossRef
Genomic Analysis and Assessment of Melanin Synthesis in Amorphotheca resinae KUC3009
Jeong-Joo Oh, Young Jun Kim, Jee Young Kim, Sun Lul Kwon, Changsu Lee, Myeong-Eun Lee, Jung Woo Kim, Gyu-Hyeok Kim
Journal of Fungi.2021; 7(4): 289. CrossRef
Fungal melanin as a biocompatible broad-spectrum sunscreen with high antioxidant activity
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Short-term effects of returning granulated straw on soil microbial community and organic carbon fractions in dryland farming: Wei Fan , Jinggui Wu; J. Microbiol. 2020;58(8):657-667. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-9266-5

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Abstract

We conducted a 2-year field experiment which was comprised of five treatments, namely no straw returning (CK), straw mulching (SM), straw plowed into the soil (SP), and straw returned in granulated form (SG). The aim of this study was to investigate the effects of different straw returning modes on soil bacterial and fungal community structure and their relationships to soil organic carbon (SOC) fractions at three different soil depths (0–20, 20–40, and 40–60 cm) in a dryland under maize cultivation in Northeast (NE) China. SM, SP, and SG treatments significantly increased SOC content. Compared with SM and SP treatments, SG treatment significantly increased the content of SOC and easily oxidizable carbon (EOC) in the topsoil (0–20 cm depth), and increased dissolved organic carbon (DOC) and SOC content of the light fraction (LFOC) in the 20–40 cm layer. Meanwhile, SG treatment exhibited the highest microbial biomass C (MBC) content in all of the three soil depths. SG treatment also enhanced bacterial richness as well as fungal richness and diversity in the upper 40 cm of soil. In addition, SG treatment increased the relative abundance of Proteobacteria in all depths, and had the highest relative abundance of Basidiomycota in the first 20 cm of soil. SP treatment showed the lowest soil organic carbon content in all fractions and soil microbial community composition. SM treatment exhibited similar results to SG treatment in SOC, DOC, and LFOC contents, and bacterial diversity in the topsoil and subsoil. As a whole, treatment SG improved soil quality and maize yield, hence we recommend returning granulated straw as the most effective practice for enhancing labile SOC fractions as well as maintaining soil diversity and microbial richness of arid farmlands in NE China.

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Synergizing production and ecology: innovations in sustainable dryland agriculture
Xining Zhao, Honghua He, Kadambot H. M. Siddique, Xiaodong Gao
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Han Lin, Mingyong Li, Jiangtao Ji, Chao Zhang, Guangyuan Zhong, Hongjian Wu, Zhaohui Du, Qianwen Li, Lu Tan, Haopeng Han
Agronomy.2024; 14(12): 2885. CrossRef
Successive Years of Rice Straw Return Increased the Rice Yield and Soil Nutrients While Decreasing the Greenhouse Gas Intensity
Meikang Wu, Min Nuo, Zixian Jiang, Ruiyao Xu, Hongcheng Zhang, Xiao Lu, Liqun Yao, Man Dou, Xu Xing, Xin Meng, Dongchao Wang, Xiaoshuang Wei, Ping Tian, Guan Wang, Zhihai Wu, Meiying Yang
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Ting Fan, Yulin Zhang, Kexin Hu, Shiqi Xu, Afeng Zhang, Shaoqi Xue, Jiale Han, Xudong Wang
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Guizhong Xu, Fahong Wu, Weijuan Geng
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Jian Xiao, Jianglin Zhang, Peng Li, Youyun Tang, Yanhong Lu, Yulin Liao, Jun Nie
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Effects of Maize Straw Return Modes on Soil Organic Carbon Content and Aggregate Stability in a Mollisol in Northeast China
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Ting Fan, Yulin Zhang, Xudong Wang, Yonghua Zhao, Andong Shi, Xia Zhang
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Returned straw reduces nitrogen runoff loss by influencing nitrification process through modulating soil C:N of different paddy systems
Shaopeng Wang, Limei Zhai, Shufang Guo, Fulin Zhang, Lingling Hua, Hongbin Liu
Agriculture, Ecosystems & Environment.2023; 354: 108438. CrossRef
Effects of rumen microorganisms on straw returning to soil at different depths
Kailun Song, Chunhuo Zhou, Hengpei Li, Zicheng Zhou, Guorong Ni, Xin Yin
European Journal of Soil Biology.2023; 114: 103454. CrossRef
Stover return and nitrogen application affect soil organic carbon and nitrogen in a double‐season maize field
Y. X. Liu, Y. Q. Pan, L. Yang, S. Ahmad, X. B. Zhou, M. Zhou
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Native soil organic-carbon contents shape distinct bacterial communities associated with priming effect
Xu Chen, Mengyang You, Xiaozeng Han, Xinchun Lu, Wenxiu Zou, Jun Yan
Pedobiologia.2022; 95: 150842. CrossRef
Straw Return and Nitrogen Fertilization to Maize Regulate Soil Properties, Microbial Community, and Enzyme Activities Under a Dual Cropping System
Li Yang, Ihsan Muhammad, Yu Xin Chi, Dan Wang, Xun Bo Zhou
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Liwei Wang, Cheng Wang, Fangyuan Feng, Zhengniu Wu, Hongkui Yan
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Labile organic carbon fractions drive soil microbial communities after long-term fertilization
Zhiming Zhang, Jun Yan, Xiaozeng Han, Wenxiu Zou, Xu Chen, Xinchun Lu, Yutian Feng
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Straw incorporation plus biochar addition improved the soil quality index focused on enhancing crop yield and alleviating global warming potential
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Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR: Guoyang Xie , Shuang Yu , Wen Li , Dan Mu , Zoraida P. Aguilar , Hengyi Xu; J. Microbiol. 2020;58(8):668-674. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-0084-6

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Abstract

A multiplex polymerase chain reaction (mPCR) with propidium monoazide (PMA) and internal amplification control (IAC) for the simultaneous detection of waterborne pathogens Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7, was developed. This PMA-IAC-mPCR assay used four new specific primers based on the genes for invA, ecfX, cesB, and fliC, respectively. A 16S rRNA primer was chosen for IAC to eliminate false negative
results
. The photosensitive dye, propidium monoazide (PMA) was used to exclude signals from dead bacteria that could lead to false positive results. In pure culture, the limits of detection (LOD) were 101 CFU/ml for P. aeruginosa, 102 CFU/ml for both Salmonella spp. and E. coli O157:H7, and 103 CFU/ml for B. cereus, respectively. In addition, with a 6–8 h enrichment of all four bacteria that were combined in a mixture that was spiked in water sample matrix, the LOD was 3 CFU/ml for Salmonella spp., 7 CFU/ml for E. coli O157:H7, 10 CFU/ml for B. cereus and 2 CFU/ml for P. aeruginosa. This PMA-IAC-mPCR assay holds potential for application in the multiplex assay of waterborne pathogens.

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In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei: Peizhuo Zou , Qian Yang , Hailiang Wang , Guosi Xie , Zhi Cao , Xing Chen , Wen Gao , Jie Huang; J. Microbiol. 2020;58(8):675-686. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9537-1

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Abstract

Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 106 CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 105 CFU/ml, 104 CFU/ml, and 103 CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.

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Basigin binds bacteria and activates Dorsal signaling to promote antibacterial defense in Penaeus vannamei
Linwei Yang, Zi-ang Wang, Yushi Gan, Hongliang Zuo, Hengwei Deng, Shaoping Weng, Jianguo He, Xiaopeng Xu
Fish & Shellfish Immunology.2023; 142: 109123. CrossRef
Clinical protective effects of polyhexamethylene biguanide hydrochloride (PHMB) against Vibrio parahaemolyticus causing translucent post-larvae disease (VTPD) in Penaeus vannamei
Tianchang Jia, Tingting Xu, Jitao Xia, Shuang Liu, Wenqiang Li, Ruidong Xu, Jie Kong, Qingli Zhang
Journal of Invertebrate Pathology.2023; 201: 108002. CrossRef

The effects of deletion of cellobiohydrolase genes on carbon source-dependent growth and enzymatic lignocellulose hydrolysis in Trichoderma reesei: Meibin Ren , Yifan Wang , Guoxin Liu , Bin Zuo , Yuancheng Zhang , Yunhe Wang , Weifeng Liu , Xiangmei Liu , Yaohua Zhong; J. Microbiol. 2020;58(8):687-695. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-9630-5

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Abstract

The saprophytic fungus Trichoderma reesei has long been used as a model to study microbial degradation of lignocellulosic biomass. The major cellulolytic enzymes of T. reesei are the cellobiohydrolases CBH1 and CBH2, which constitute more than 70% of total proteins secreted by the fungus. However, their physiological functions and effects on enzymatic hydrolysis of cellulose substrates are not sufficiently elucidated. Here, the cellobiohydrolase-encoding genes cbh1 and cbh2 were deleted, individually or combinatively, by using an auxotrophic marker-recycling technique in T. reesei. When cultured on media with different soluble carbon sources, all three deletion strains (Δcbh1, Δcbh2, and Δcbh1Δcbh2) exhibited no dramatic variation in morphological phenotypes, but their growth rates increased apparently when cultured on soluble cellulase-inducing carbon sources. In addition, Δcbh1 showed dramatically reduced growth and Δcbh1Δcbh2 could hardly grew on microcrystalline cellulose (MCC), whereas all strains grew equally on sodium carboxymethyl cellulose (CMC-Na), suggesting that the influence of the CBHs on growth was carbon source-dependent. Moreover, five representative cellulose substrates were used to analyse the influence of the absence of CBHs on saccharification efficiency. CBH1 deficiency significantly affected the enzymatic hydrolysis rates of various cellulose substrates, where acid pre-treated corn stover (PCS) was influenced the least. CBH2 deficiency reduced the hydrolysis of MCC, PCS, and acid pre-treated and delignified corncob but improved the hydrolysis ability of filter paper. These results demonstrate the specific contributions of CBHs to the hydrolysis of different types of biomass, which could facilitate the development of tailor-made strains with highly efficient hydrolysis enzymes for certain biomass types in the biofuel industry.

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An efficient CRISPR/Cas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production
Jiaxin Zhang, Kehang Li, Yu Sun, Cheng Yao, Weifeng Liu, Hong Liu, Yaohua Zhong
Biotechnology for Biofuels and Bioproducts.2024;[Epub] CrossRef
Transcriptome-wide analysis of a superior xylan degrading isolate Penicillium oxalicum 5–18 revealed active lignocellulosic degrading genes
Shuang Hu, Pei Han, Bao-Teng Wang, Long Jin, Hong-Hua Ruan, Feng-Jie Jin
Archives of Microbiology.2024;[Epub] CrossRef
Engineering the secretome of Aspergillus niger for cellooligosaccharides production from plant biomass
Fernanda Lopes de Figueiredo, Fabiano Jares Contesini, César Rafael Fanchini Terrasan, Jaqueline Aline Gerhardt, Ana Beatriz Corrêa, Everton Paschoal Antoniel, Natália Sayuri Wassano, Lucas Levassor, Sarita Cândida Rabelo, Telma Teixeira Franco, Uffe Hasb
Microbial Cell Factories.2024;[Epub] CrossRef
Constitutive overexpression of cellobiohydrolase 2 in Trichoderma reesei reveals its ability to initiate cellulose degradation
Yubo Wang, Meibin Ren, Yifan Wang, Lu Wang, Hong Liu, Mei Shi, Yaohua Zhong
Engineering Microbiology.2023; 3(1): 100059. CrossRef
Inducer-free recombinant protein production in Trichoderma reesei: secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source
Toshiharu Arai, Mayumi Wada, Hiroki Nishiguchi, Yasushi Takimura, Jun Ishii
Microbial Cell Factories.2023;[Epub] CrossRef
The Influence of Trctf1 Gene Knockout by CRISPR–Cas9 on Cellulase Synthesis by Trichoderma reesei with Various Soluble Inducers
Yudian Chen, Yushan Gao, Zancheng Wang, Nian Peng, Xiaoqin Ran, Tingting Chen, Lulu Liu, Yonghao Li
Fermentation.2023; 9(8): 746. CrossRef
The effect of cellobiohydrolase 1 gene knockout for composition and hydrolytic activity of the enzyme complex secreted by filamentous fungus Penicillium verruculosum
Valeriy Yu. Kislitsin, Andrey M. Chulkin, Ivan N. Zorov, Yuri А. Denisenko, Arkadiy P. Sinitsyn, Alexandra M. Rozhkova
Bioresource Technology Reports.2022; 18: 101023. CrossRef
Deciphering the efficient cellulose degradation by the thermophilic fungus Myceliophthora thermophila focused on the synergistic action of glycoside hydrolases and lytic polysaccharide monooxygenases
Xing Qin, Jiahuan Zou, Kun Yang, Jinyang Li, Xiaolu Wang, Tao Tu, Yuan Wang, Bin Yao, Huoqing Huang, Huiying Luo
Bioresource Technology.2022; 364: 128027. CrossRef

WasC, a WASP family protein, is involved in cell adhesion and migration through regulation of F-actin polymerization in Dictyostelium: Pyeonghwa Jeon , Taeck Joong Jeon; J. Microbiol. 2020;58(8):696-702. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0138-9

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Abstract

The actin cytoskeleton is involved in the regulation of cell morphology and migration. Wiskott-Aldrich Syndrome proteins (WASPs) play an important role in controlling actin polymerization by activating the Arp2/3 complex. The present study investigated the roles of WasC, one of the 3 WASPs in Dictyostelium, in cellular processes. Cells lacking WasC displayed strong cell adhesion and approximately 1.5-fold increase in F-actin levels as compared to the wild-type cells. Loss of wasC caused defects in phagocytosis and decreased the migration speed in chemoattractant-mediated cell migration but did not affect directionality. WasC was localized to the protruding region in migrating cells and, transiently and rapidly translocated to the cell cortex in response to chemoattractant stimulation, in an F-actin dependent manner. Our
results
suggest that WasC is involved in cell adhesion and migration by regulating F-actin polymerization at the leading edge of migrating cells, probably as a negative regulator. The increased strength of adhesion in wasC null cells is likely to decrease the migration speed but not the directionality.

Citations

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Wiskott-Aldrich syndrome gene as a prognostic biomarker correlated with immune infiltrates in clear cell renal cell carcinoma
Guixin Ding, Tianqi Wang, Shangjing Liu, Zhongbao Zhou, Jian Ma, Jitao Wu
Frontiers in Immunology.2023;[Epub] CrossRef
Dual regulation of the actin cytoskeleton by CARMIL-GAP
Goeh Jung, Miao Pan, Christopher J. Alexander, Tian Jin, John A. Hammer
Journal of Cell Science.2022;[Epub] CrossRef
Regulation of the Actin Cytoskeleton via Rho GTPase Signalling in Dictyostelium and Mammalian Cells: A Parallel Slalom
Vedrana Filić, Lucija Mijanović, Darija Putar, Antea Talajić, Helena Ćetković, Igor Weber
Cells.2021; 10(7): 1592. CrossRef

Performance comparison of fecal preservative and stock solutions for gut microbiome storage at room temperature: Chanhyeok Park , Kyeong Eui Yun , Jeong Min Chu , Ji Yeon Lee , Chang Pyo Hong , Young Do Nam , Jinuk Jeong , Kyudong Han , Yong Ju Ahn; J. Microbiol. 2020;58(8):703-710. Published online June 25, 2020; DOI: https://doi.org/10.1007/s12275-020-0092-6

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Abstract

The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different
methods
, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.

Citations

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Omnigene-Guttm ensures fecal microbiome stability in the pediatric population
Raoull Hoogendijk, Thijs J. M. van den Broek, Hyunju Lee, Sabine Mueller, Cassie Kline, John Bianco, Janetta Top, Marcel R. de Zoete, Lennart Kester, Friso Calkoen, Jasper van der Lugt
AMB Express.2024;[Epub] CrossRef
Microbes for lung cancer detection: feasibility and limitations
Sirui Zhou, Weijian Zhu, Hehua Guo, Yalan Nie, Jiazheng Sun, Ping Liu, Yulan Zeng
Frontiers in Oncology.2024;[Epub] CrossRef
Importance of Human Faecal Biobanking: From Collection to Storage
Izabela Lewandowska, Katarzyna Grzech, Jolanta Krzysztoń-Russjan
Advancements of Microbiology.2024; 63(4): 181. CrossRef
Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis
Xin-meng Li, Xiao Shi, Yao Yao, Yi-cun Shen, Xiang-ling Wu, Ting Cai, Lun-xi Liang, Fen Wang, Po-Yu Liu
Microbiology Spectrum.2023;[Epub] CrossRef
Microbial Composition and Stool Short Chain Fatty Acid Levels in Fibromyalgia
Yunkyung Kim, Geun-Tae Kim, Jihun Kang
International Journal of Environmental Research and Public Health.2023; 20(4): 3183. CrossRef
Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations
Leigh Combrink, Ian R. Humphreys, Quinn Washburn, Holly K. Arnold, Keaton Stagaman, Kristin D. Kasschau, Anna E. Jolles, Brianna R. Beechler, Thomas J. Sharpton
Frontiers in Microbiology.2023;[Epub] CrossRef
Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence
Taobing Yu, Lang Cheng, Qi Liu, Shasha Wang, Yuan Zhou, Hongbin Zhong, Meifang Tang, Hai Nian, Tengxiang Lian, Cheng Gao, Glade Dlott
Microbiology Spectrum.2022;[Epub] CrossRef
Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis
Xin-meng Li, Xiao Shi, Yao Yao, Yi-cun Shen, Xiang-ling Wu, Fen Wang
SSRN Electronic Journal .2022;[Epub] CrossRef
Trialling a microbiome-targeted dietary intervention in children with ADHD—the rationale and a non-randomised feasibility study
Kate Lawrence, Kyriaki Myrissa, Miguel Toribio-Mateas, Lori Minini, Alice M. Gregory
Pilot and Feasibility Studies.2022;[Epub] CrossRef
Can the genetic variability of Blastocystis sp. be associated with the climatic region of its human carriers?
B. Ake-Canche, E. Rodriguez-Bataz, J.Y Esquivel-Piña, A. Tolentino-Loreto, S. Arroyo-Escalante, J. Martínez-Ocaña, M. Romero-Valdovinos, O. Valenzuela, G.E. Orozco-Mosqueda, F. Martinez-Hernandez, P. Maravilla, A. Martinez
Infection, Genetics and Evolution.2022; 106: 105383. CrossRef
Critical evaluation of faecal microbiome preservation using metagenomic analysis
Alena L Pribyl, Donovan H Parks, Nicola Z Angel, Joel A Boyd, Alexander G Hasson, Liang Fang, Samantha L MacDonald, Blake A Wills, David L A Wood, Lutz Krause, Gene W Tyson, Philip Hugenholtz
ISME Communications.2021;[Epub] CrossRef
The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology
Jinuk Jeong, Kyeongeui Yun, Seyoung Mun, Won-Hyong Chung, Song-Yi Choi, Young-do Nam, Mi Young Lim, Chang Pyo Hong, ChanHyeok Park, Yong Ju Ahn, Kyudong Han
Scientific Reports.2021;[Epub] CrossRef
Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
Christine N. Spencer, Jennifer L. McQuade, Vancheswaran Gopalakrishnan, John A. McCulloch, Marie Vetizou, Alexandria P. Cogdill, Md A. Wadud Khan, Xiaotao Zhang, Michael G. White, Christine B. Peterson, Matthew C. Wong, Golnaz Morad, Theresa Rodgers, Jona
Science.2021; 374(6575): 1632. CrossRef
Impact of Plant-Based Meat Alternatives on the Gut Microbiota of Consumers: A Real-World Study
Miguel A. Toribio-Mateas, Adri Bester, Natalia Klimenko
Foods.2021; 10(9): 2040. CrossRef

Development of a real-time loop-mediated isothermal amplification method for the detection of severe fever with thrombocytopenia syndrome virus: Jae Woong Lee , Yu-Jung Won , Lae Hyung Kang , Sung-Geun Lee , Seung-Won Park , Soon-Young Paik; J. Microbiol. 2020;58(8):711-715. Published online May 18, 2020; DOI: https://doi.org/10.1007/s12275-020-0109-1

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Abstract

Severe fever with thrombocytopenia syndrome (SFTS) is being reported annually in South Korea since its first detection there in 2010. The causal agent is a negative-strand RNA virus 80–100 nm in diameter. It causes fever, thrombocytopenia, leukocytopenia, gastrointestinal symptoms, and neural symptoms. The mortality rate of SFTS was 32.6% among 172
case
s reported from 2012 to 2015 in South Korea. Thus, is necessary to develop an effective diagnostic method that selectively identifies the isolates circulating in South Korea. The real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay is a simple, rapid, and sensitive approach for molecular diagnosis. Here, we designed novel primers for this assay and found that the technique had very high specificity, sensitivity, and efficiency. This real-time RTLAMP approach using the novel primers developed herein can be applied for early diagnosis of SFTSV strains in South Korea to reduce the mortality rate of SFTS.

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Long-Term Detection and Isolation of Severe Fever with Thrombocytopenia Syndrome (SFTS) Virus in Dog Urine
Yumiko Saga, Toshikazu Yoshida, Rieko Yoshida, Shunsuke Yazawa, Takahisa Shimada, Noriko Inasaki, Masae Itamochi, Emiko Yamazaki, Kazunori Oishi, Hideki Tani
Viruses.2023; 15(11): 2228. CrossRef
Advancements in the Worldwide Detection of Severe Fever with Thrombocytopenia Syndrome Virus Infection from 2009 to 2023
Lin Ai, Wei Wang, Zheng Teng
China CDC Weekly.2023; 5(31): 687. CrossRef
Molecular detection of “Candidatus Rickettsia tarasevichiae” by Loop-mediated Isothermal Amplification (LAMP) of the ompA gene
Jing Xue, Qing Ren, Rui Jian, Guang-Cheng Xie, Yongliang Chen, Jiangli Wang, Luanying Du, Wen-Ping Guo
Journal of Microbiological Methods.2022; 202: 106601. CrossRef
Dual-gene detection in a single-tube system based on CRISPR-Cas12a/Cas13a for severe fever thrombocytopenia syndrome virus
Yating Zhu, Chen Xing, Li Yang, Qian Li, Xiaofeng Wang, Jing Zhou, Cong Zhang, Cuiping Ren, Fahu Liu, Jun He, Bing Shen, Yinan Du, Yan Liu
Frontiers in Microbiology.2022;[Epub] CrossRef
CRISPR/Cas12a Technology Combined With RPA for Rapid and Portable SFTSV Detection
Mengqian Huang, Sihua Liu, Yanan Xu, Aqian Li, Wei Wu, Mifang Liang, Guoyu Niu, Zhiyun Wang, Tao Wang
Frontiers in Microbiology.2022;[Epub] CrossRef
Development of monoclonal antibody based IgG and IgM ELISA for diagnosis of severe fever with thrombocytopenia syndrome virus infection
Mei Zhang, Yanhua Du, Li Yang, Lin Zhan, Bin Yang, Xueyong Huang, Bianli Xu, Koichi Morita, Fuxun Yu
The Brazilian Journal of Infectious Diseases.2022; 26(4): 102386. CrossRef
Development of an RT-LAMP Assay for the Rapid Detection of SFTS Virus
Shiori Sano, Shuetsu Fukushi, Souichi Yamada, Shizuko Harada, Hitomi Kinoshita, Satoko Sugimoto, Tomoki Yoshikawa, Takeshi Kurosu, Yuki Takamatsu, Masayuki Shimojima, Shoichi Toda, Yuka Hamada, Naoki Fujisawa, Takayuki Sugimoto, Masayuki Saijo
Viruses.2021; 13(4): 693. CrossRef
A Real-Time Loop-Mediated Isothermal Amplification for Detection of the Wheat Dwarf Virus in Wheat and the Insect VectorPsammotettix alienus
Xingan Hao, Licheng Wang, Xudong Zhang, Qinrong Zhong, Jamal-U-Ddin Hajano, Liangsheng Xu, Yunfeng Wu
Plant Disease.2021; 105(12): 4113. CrossRef
Baseline mapping of severe fever with thrombocytopenia syndrome virology, epidemiology and vaccine research and development
Nathen E. Bopp, Jaclyn A. Kaiser, Ashley E. Strother, Alan D. T. Barrett, David W. C. Beasley, Virginia Benassi, Gregg N. Milligan, Marie-Pierre Preziosi, Lisa M. Reece
npj Vaccines.2020;[Epub] CrossRef

Inhibitory effects of piceatannol on human cytomegalovirus (hCMV) in vitro: San-Ying Wang , Jing Zhang , Xiao-Gang Xu , Hui-Li Su , Wen-Min Xing , Zhong-Shan Zhang , Wei-Hua Jin , Ji-Huan Dai , Ya-Zhen Wang , Xin-Yue He , Chuan Sun , Jing Yan , Gen-Xiang Mao; J. Microbiol. 2020;58(8):716-723. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-9528-2

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Abstract

Human cytomegalovirus (hCMV) is a ubiquitous herpesvirus, which results in the establishment of a latent infection that persists throughout the life of the host and can be reactivated when the immunity is low. Currently, there is no vaccine for hCMV infection, and the licensed antiviral drugs mainly target the viral enzymes and have obvious adverse reactions. Thus, it is important to search for compounds with antihCMV properties. The present study aimed to investigate the suppressive effects of piceatannol on hCMV Towne strain infection and the putative underlying mechanisms using human diploid fibroblast WI-38 cells. Piceatannol supplementation prevented the lytic changes induced by hCMV infection in WI-38 cells. Furthermore, piceatannol suppressed the expression of hCMV immediate-early (IE) and early (E) proteins as well as the replication of hCMV DNA in a dose-dependent manner. Moreover, hCMV-induced cellular senescence was suppressed by piceatannol, as shown by a decline in the senescence-associated β-galactosidase (SA-β-Gal) activity and decreased production of intracellular reactive oxygen species (ROS). p16INK4a, a major senescence-associated molecule, was dramatically elevated by current hCMV infection that was attenuated by pre-incubation with piceatannol in a dose-dependent manner. These results demonstrated that piceatannol suppressed the hCMV infection via inhibition of the activation of p16INK4a and cellular senescence induced by hCMV. Together, these findings indicate piceatannol as a novel and potent anti-hCMV agent with the potential to be developed as an effective treatment for chronic hCMV infection.

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Hala I. Al-Jaber, Ashok K. Shakya, Mahmoud A. Al-Qudah, Lina M. Barhoumi, Hana E. Abu-Sal, Hazem S. Hasan, Nezar Al-Bataineh, Sultan Abu-Orabi, Mohammad S. Mubarak
Arabian Journal of Chemistry.2024; 17(9): 105939. CrossRef
Mechanism of PRRSV infection and antiviral role of polyphenols
Fructueux Modeste Amona, Yipeng Pang, Xingyu Gong, Yanhong Wang, Xingtang Fang, Chunlei Zhang, Xi Chen
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Predicting phase-I metabolism of piceatannol: an in silico study
Ravi Kumar Rajan, Maida Engels, Muthiah Ramanathan
In Silico Pharmacology.2024;[Epub] CrossRef
Inhibition of influenza a virus infection by natural stilbene piceatannol targeting virus hemagglutinin
Lianghao Huang, Jinyu Wang, Xiaoyao Ma, Lishan Sun, Cui Hao, Wei Wang
Phytomedicine.2023; 120: 155058. CrossRef
Latin American Plants against Microorganisms
Sofía Isabel Cuevas-Cianca, Cristian Romero-Castillo, José Luis Gálvez-Romero, Eugenio Sánchez-Arreola, Zaida Nelly Juárez, Luis Ricardo Hernández
Plants.2023; 12(23): 3997. CrossRef
Piceatannol as an Antiviral Inhibitor of PRV Infection In Vitro and In Vivo
Zhiying Wang, Xiaojing Cai, Zhiyuan Ren, Yi Shao, Yongkang Xu, Lian Fu, Yan Zhu
Animals.2023; 13(14): 2376. CrossRef
Recent Advances in Antiviral Activities of Triterpenoids
Yue Liu, Liangyu Yang, Hong Wang, Yongai Xiong
Pharmaceuticals.2022; 15(10): 1169. CrossRef
Insights into Antiviral Properties and Molecular Mechanisms of Non-Flavonoid Polyphenols against Human Herpesviruses
Sherif T. S. Hassan, Miroslava Šudomová, Alena Mazurakova, Peter Kubatka
International Journal of Molecular Sciences.2022; 23(22): 13891. CrossRef
Suppressive effects of pterostilbene on human cytomegalovirus (HCMV) infection and HCMV-induced cellular senescence
Sanying Wang, Xuqiang Zhou, Xinyue He, Shushu Ma, Chuan Sun, Jing Zhang, Xiaogang Xu, Weihua Jin, Jin Yan, Ping Lin, Genxiang Mao
Virology Journal.2022;[Epub] CrossRef
Sulphated glucuronomannan tetramer and hexamer from Sargassum thunbergii exhibit anti-human cytomegalovirus activity by blocking viral entry
Sanying Wang, Xiaogang Xu, Chuan Sun, Jing Zhang, Xinyue He, Zhongshan Zhang, Hong Huang, Jing Yan, Weihua Jin, Genxiang Mao
Carbohydrate Polymers.2021; 273: 118510. CrossRef
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Marwa Elsbaey, Mahmoud A.A. Ibrahim, Fatma Abdel Bar, Abdullah A. Elgazar
South African Journal of Botany.2021; 141: 278. CrossRef

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