Journal of Microbiology

Review

Armored RNA technology as a clinical diagnostics tool for future pandemic preparedness: Jin Hao Tan, Prashant Mainali, Wei Zhang, Dave Siak-Wei Ow; J. Microbiol. 2026;64(2):e2510016. Published online February 28, 2026; DOI: https://doi.org/10.71150/jm.2510016

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Abstract PDF: The COVID-19 pandemic highlighted the critical role of reliable molecular diagnostics in outbreak response and the vulnerabilities of existing systems to delays and reagent instability. Armored RNA technology, which packages RNA within bacteriophage-derived capsids, offers a robust solution by combining nuclease resistance, safety, and versatility into a single platform. Armored RNA has become a trusted internal and external control for RT-qPCR and RT-LAMP, enabling accurate detection across a wide range of viral pathogens. Also, recent advances in alternative expression systems, such as plant-based and cell-free platforms, as well as the use of more stable scaffolds from bacteriophage Qβ, are enhancing yield, stability, and accessibility of armored RNA. Engineering innovations, including capsid polymorphism and optimized downstream purification, further improve efficiency and broaden possible applications. Looking ahead, armored RNA holds promise not only as a diagnostic standard but also as a delivery vehicle for vaccines and therapeutics. Encapsulation of self-amplifying RNA, small interfering RNA, or microRNA could open new pathways for rapid-response vaccines and targeted therapies, aligning this technology with the future of precision medicine. By uniting stability, scalability, and adaptability, armored RNA represents a critical component of global health preparedness, with the potential to strengthen diagnostic resilience and accelerate biomedical countermeasures in future pandemics.

Journal Articles

Whole-Genome Sequencing Reveals the Population Structure and Genetic Diversity of Salmonella Typhimurium ST34 and ST19 Lineages: Zhen-Xu Zhuo, Yu-Lian Feng, Xi-Wei Zhang, Hao Liu, Fang-Yin Zeng, Xiao-Yan Li; J. Microbiol. 2024;62(10):859-870. Published online November 4, 2024; DOI: https://doi.org/10.1007/s12275-024-00170-9

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Salmonella Typhimurium is an invasive gastrointestinal pathogen for both humans and animals. To investigate the genetic framework and diversity of S. Typhimurium, a total of 194 S. Typhimurium isolates were collected from patients in a tertiary hospital between 2020 and 2021. Antimicrobial susceptibility testing was used to confirm the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were performed to determine the sequence type, phylogenetic relationships, resistance gene profiles, Salmonella pathogenicity island (SPI) and the diversity of the core and pan genome. The result showed that 57.22% of S. Typhimurium isolates were multidrug resistant and resistance of total isolates to the first-line drug ciprofloxacin was identified in 60.82%. The population structure of S. Typhimurium was categorized into three lineages: ST19 (20.10%, 39/194), ST34-1 (47.42%, 92/194) and ST34-2 (40.65%, 63/194), with the population size exhibiting increasing trends. All lineages harbored variety of fimbrial operons, prophages, SPIs and effectors that contributed to the virulence and long-term infections of S. Typhimurium. Importantly, ST34-1 lineage might potentially be more invasive due to the possession of SPI1-effector gene sopE which was essential for the proliferation, internalization and intracellular presence of S. Typhimurium in hosts. Multiple antimicrobial resistance genes were characteristically distributed across three lineages, especially carbapenem genes only detected in ST34-1&2 lineages. The distinct functional categories of pan genome among three lineages were observed in metabolism, signaling and gene information processing. This study provides a theoretical foundation for the evolved adaptation and genetic diversity of S. Typhimurium ST19 and ST34, among which ST34 lineages with multidrug resistance and potential hypervirulence need to pay more attention to epidemiological surveillance.

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Genomic Evidence for the Rise of Salmonella Typhimurium ST34 with Increased Plasmid-Mediated Resistance in the Thailand Pork Chain
Hongmei Liu, Ning Wang, Sunpetch Angkititrakul, Wengui Li, Zhongyang Luo, Mingpeng Hou, Yi Wu, Yubo Shi, Yuelin Wang, Fengyun Li, Yaowen Liu, Xin Wu, Fanan Suksawat
Pathogens.2025; 14(12): 1190. CrossRef

Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest: Mao Tian, Shiyu Wu, Wei Zhang, Gaosen Zhang, Xue Yu, Yujie Wu, Puchao Jia, Binglin Zhang, Tuo Chen, Guangxiu Liu; J. Microbiol. 2024;62(4):277-284. Published online March 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00108-1

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Abstract PDF: We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038(T), from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C(15:0) and iso-C(17:0). Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038(T) has the highest similarity with Spelaeicoccus albus DSM 26341( T) (96.02%). ZFBP1038(T) formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038(T) was 63.65 mol% and the genome size was 4.05 Mb. Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038(T) and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively. Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038(T) represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038(T) (= EE 014( T) = GDMCC 1.3024( T) = JCM 35335( T)).

Proteome analysis reveals global response to deletion of mrflbA in Monascus ruber: Qingqing Yan , Zhouwei Zhang , Yishan Yang , Fusheng Chen , Yanchun Shao; J. Microbiol. 2018;56(4):255-263. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7425-8

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Abstract PDF

Monascus spp. are commonly used for a wide variety of applications in the food and pharmaceutical industries. In previous studies, the knock-out of mrflbA (a putative regulator of the G protein α subunit) in M. ruber led to autolysis of the mycelia, decreased pigmentation and lowered mycotoxin production. Therefore, we aimed to obtain a comprehensive overview of the underlying mechanism of mrflbA deletion at the proteome level. A two-dimensional gel electrophoresis analysis of mycelial proteins indicated that the abundance of 178 proteins was altered in the ΔmrflbA strain, 33 of which were identified with high confidence. The identified proteins are involved in a range of activities, including carbohydrate and amino acid metabolism, hyphal development and the oxidative stress response, protein modification, and the regulation of cell signaling. Consistent with these findings, the activity of antioxidative enzymes and chitinase was elevated in the supernatant of the ΔmrflbA strain. Furthermore, deletion of mrflbA resulted in the transcriptional reduction of secondary metabolites (pigment and mycotoxin). In short, the mutant phenotypes induced by the deletion of mrflbA were consistent with changes in the expression levels of associated proteins, providing direct evidence of the regulatory functions mediated by mrflbA in M. ruber.

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Histone deacetylase MrHos3 negatively regulates the production of citrinin and pigments in Monascus ruber
Qianrui Liu, Yunfan Zheng, Baixue Liu, Fufang Tang, Yanchun Shao
Journal of Basic Microbiology.2023; 63(10): 1128. CrossRef
Histone deacetylase MrRpd3 plays a major regulational role in the mycotoxin production of Monascus ruber
Yunfan Zheng, Yueyan Huang, Zejing Mao, Yanchun Shao
Food Control.2022; 132: 108457. CrossRef
Characterization of key upstream asexual developmental regulators in Monascus ruber M7
Lili Jia, Yuyun Huang, Jae-Hyuk Yu, Marc Stadler, Yanchun Shao, Wanping Chen, Fusheng Chen
Food Bioscience.2022; 50: 102153. CrossRef
Quantitative Proteomics Analysis by Sequential Window Acquisition of All Theoretical Mass Spectra–Mass Spectrometry Reveals Inhibition Mechanism of Pigments and Citrinin Production of Monascus Response to High Ammonium Chloride Concentration
Bo Zhou, Yifan Ma, Yuan Tian, Jingbo Li, Haiyan Zhong
Journal of Agricultural and Food Chemistry.2020; 68(3): 808. CrossRef

Review

Minireview] The molecular mechanism of azole resistance in Aspergillus fumigatus: from bedside to bench and back: Xiaolei Wei , Yuanwei Zhang Zhang , Ling Lu; J. Microbiol. 2015;53(2):91-99. Published online January 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5014-7

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Abstract PDF

The growing use of immunosuppressive therapies has resulted in a dramatic increased incidence of invasive fungal infections (IFIs) caused by Aspergillus fumigatus, a common pathogen, and is also associated with a high mortality rate. Azoles are the primary guideline-recommended therapy agents for first-line treatment and prevention of IFIs. However, increased azole usage in medicinal and agricultural settings has caused azole-resistant isolates to repeatedly emerge in the environment, resulting in a significant threat to human health. In this review, we present and summarize current research on the resistance mechanisms of azoles in A. fumigatus as well as efficient susceptibility testing methods. Moreover, we analyze and discuss the putative clinical (bedside) indication of these findings from bench work.

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Antifungal and fungicide susceptibility of clinical, animal, and environmental Fusarium and Neocosmospora species from Colombia: a one-health approach
Valeri Saenz, Andrés Felipe Lizcano-Salas, Patrice Le Pape, Adriana Marcela Celis Ramírez
Scientific Reports.2025;[Epub] CrossRef
Azole resistance in Aspergillus fumigatus- comprehensive review
Mthokozisi Dladla, Marieka Gyzenhout, Gert Marias, Soumya Ghosh
Archives of Microbiology.2024;[Epub] CrossRef
Unveiling environmental transmission risks: comparative analysis of azole resistance in Aspergillus fumigatus clinical and environmental isolates from Yunnan, China
Jianchuan Gong, Jiarui Huang, Yongju Liu, Ying Zhang, Yuhong Gao, Gustavo H. Goldman
Microbiology Spectrum.2024;[Epub] CrossRef
The mitochondrial protein Bcs1A regulates antifungal drug tolerance by affecting efflux pump expression in the filamentous pathogenic fungus Aspergillus fumigatus
Guorong Yang, Weiwei Shi, Wenlin He, Jing Wu, Sutao Huang, Li Mo, Junjie Zhang, Huaxue Wang, Xiaogang Zhou, Gustavo H. Goldman
Microbiology Spectrum.2024;[Epub] CrossRef
The expression pattern, subcellular localization and function of three sterol 14α-demethylases in Aspergillus oryzae
Qi Jin, Ganghua Li, Kunhai Qin, Yitong Shang, Huanhuan Yan, Hongliang Liu, Bin Zeng, Zhihong Hu
Frontiers in Genetics.2023;[Epub] CrossRef
Mitochondrial Membrane-Associated Protein Mba1 Confers Antifungal Resistance by Affecting the Production of Reactive Oxygen Species in Aspergillus fumigatus
Guoxing Zhu, Shu Chen, Yuanwei Zhang, Ling Lu
Antimicrobial Agents and Chemotherapy.2023;[Epub] CrossRef
Drug-Resistant Aspergillus spp.: A Literature Review of Its Resistance Mechanisms and Its Prevalence in Europe
Maria Antonia De Francesco
Pathogens.2023; 12(11): 1305. CrossRef
Deletion of cox7c Results in Pan-Azole Resistance in Aspergillus fumigatus
Mingcong Chen, Guowei Zhong, Sha Wang, Peiying Chen, Lei Li
Antimicrobial Agents and Chemotherapy.2022;[Epub] CrossRef
Cannabis and the Cancer Patient
Ilana M Braun, Donald I Abrams, Stacey E Blansky, Steven A Pergam
JNCI Monographs.2021; 2021(58): 68. CrossRef
Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
Yuying Fan, Yue Wang, Gregory A. Korfanty, Meagan Archer, Jianping Xu
Pathogens.2021; 10(6): 701. CrossRef
Analysis of the prochloraz‐Mn resistance risk and its molecular basis in Mycogone rosea from Agaricus bisporus
Yixin Du, Niuniu Shi, Hongchun Ruan, Jianqiang Miao, He Yan, Chunxi Shi, Furu Chen, Xili Liu
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Electron Donor Cytochrome b 5 Is Required for Hyphal Tip Accumulation of Sterol-Rich Plasma Membrane Domains and Membrane Fluidity in Aspergillus fumigatus
Chi Zhang, Yiran Ren, Lu Gao, Huiyu Gu, Ling Lu, Rebecca E. Parales
Applied and Environmental Microbiology.2021;[Epub] CrossRef
Examining Signatures of Natural Selection in Antifungal Resistance Genes Across Aspergillus Fungi
Renato Augusto Corrêa dos Santos, Matthew E. Mead, Jacob L. Steenwyk, Olga Rivero-Menéndez, Ana Alastruey-Izquierdo, Gustavo Henrique Goldman, Antonis Rokas
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Uncovering New Mutations Conferring Azole Resistance in the Aspergillus fumigatus cyp51A Gene
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Synergistic Effect of Pyrvinium Pamoate and Azoles Against Aspergillus fumigatus in vitro and in vivo
Yi Sun, Lujuan Gao, Youwen Zhang, Ji Yang, Tongxiang Zeng
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Recent trends in the epidemiology, diagnosis, treatment, and mechanisms of resistance in clinical Aspergillus species: A general review with a special focus on the Middle Eastern and North African region
Ayate Zakaria, Marwan Osman, Fouad Dabboussi, Rayane Rafei, Hassan Mallat, Nicolas Papon, Jean-Philippe Bouchara, Monzer Hamze
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Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis
Renato A. C. dos Santos, Jacob L. Steenwyk, Olga Rivero-Menendez, Matthew E. Mead, Lilian P. Silva, Rafael W. Bastos, Ana Alastruey-Izquierdo, Gustavo H. Goldman, Antonis Rokas
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Azole resistance mechanisms in Aspergillus: update and recent advances
Alba Pérez-Cantero, Loida López-Fernández, Josep Guarro, Javier Capilla
International Journal of Antimicrobial Agents.2020; 55(1): 105807. CrossRef
Calcium signaling pathway is involved in non-CYP51 azole resistance in Aspergillus fumigatus
Yeqi Li, Yuanwei Zhang, Ling Lu
Medical Mycology.2019; 57(Supplement): S233. CrossRef
Fungal cytochrome P450 protein Cyp51: What we can learn from its evolution, regulons and Cyp51-based azole resistance
Jinxing Song, Shizhu Zhang, Ling Lu
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Identification and Characterization of Key Charged Residues in the Cofilin Protein Involved in Azole Susceptibility, Apoptosis, and Virulence of Aspergillus fumigatus
Zhongyi Lu, Xiaodong Jia, Yong Chen, Xuelin Han, Fangyan Chen, Shuguang Tian, Xueting Su, Zongwei Li, Jingya Zhao, Xi Zhang, Mandong Hu, Liuyu Huang, Li Han
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Aspergillus fumigatus Afssn3-Afssn8 Pair Reverse Regulates Azole Resistance by Conferring Extracellular Polysaccharide, Sphingolipid Pathway Intermediates, and Efflux Pumps to Biofilm
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Screening and Characterization of a Non- cyp51A Mutation in an Aspergillus fumigatus cox10 Strain Conferring Azole Resistance
Xiaolei Wei, Peiying Chen, Rongsui Gao, Yeqi Li, Anxue Zhang, Feifei Liu, Ling Lu
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A Putative Mitochondrial Iron Transporter MrsA in Aspergillus fumigatus Plays Important Roles in Azole-, Oxidative Stress Responses and Virulence
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Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus
Chi Zhang, Xiuhua Meng, Xiaolei Wei, Ling Lu
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Triazole Susceptibilities in Thermotolerant Fungal Isolates from Outdoor Air in the Seoul Capital Area in South Korea
Seungeun Lee, Siyu Xu, Chemmeri Padasseri Bivila, Hyeyoung Lee, Myung Soo Park, Young Woon Lim, Naomichi Yamamoto, Kap-Hoon Han
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Research Support, Non-U.S. Gov'ts

Halomonas alkalitolerans sp. nov., a Novel Moderately Halophilic Bacterium Isolated from Soda Meadow Saline Soil in Daqing, China: Shuang Wang , Qian Yang , Zhi-Hua Liu , Lei Sun , Dan Wei , Jun-Zheng Zhang , Jin-Zhu Song , Yun Wang , Jia Song , Jin-Xia Fan , Xian-Xin Meng , Wei Zhang; J. Microbiol. 2011;49(1):24-28. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0197-z

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Abstract PDF

A moderately halophilic bacterial strain 15-13T, which was isolated from soda meadow saline soil in Daqing City, Heilongjiang Province, China, was subjected to a polyphasic taxonomic study. The cells of strain 15-13T were found to be Gram-negative, rod-shaped, and motile. The required growth conditions for strain 15-13T were: 1-23% NaCl (optimum, 7%), 10-50°C (optimum, 35°C), and pH 7.0-11.0 (optimum, pH 9.5). The predominant cellular fatty acids were C18:1 ω7c (60.48%) and C16:0 (13.96%). The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain 15-13T clustered within a branch comprising species of the genus Halomonas. The closest phylogenetic neighbor of strain 15-13T was Halomonas pantelleriensis DSM 9661T (98.9% 16S rRNA gene sequence similarity). The level of DNA-DNA relatedness between the novel isolated strain and H. pantelleriensis DSM 9661T was 33.8%. On the basis of the phenotypic and phylogenetic data, strain 15-13T represents a novel species of the genus Halomonas, for which the name Halomonas alkalitolerans sp. nov. is proposed. The type strain for this novel species is 15-13T (=CGMCC 1.9129T =NBRC 106539T).

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Developments in extremophilic bacterial genomics: A post next generation sequencing era
Digvijay Verma, Swati Joshi, Priyanka Ghimire, Archana Mishra, Vinay Kumar
Ecological Genetics and Genomics.2024; 32: 100255. CrossRef
Two Novel Alkaliphilic Species Isolated from Saline-Alkali Soil in China: Halalkalibacter flavus sp. nov., and Halalkalibacter lacteus sp. nov
Pin-Jiao Jin, Lei Sun, Yong-Hong Liu, Kang-Kang Wang, Manik Prabhu Narsing Rao, Osama Abdalla Abdelshafy Mohamad, Bao-Zhu Fang, Li Li, Lei Gao, Wen-Jun Li, Shuang Wang
Microorganisms.2024; 12(5): 950. CrossRef
Alteribacter salitolerans sp. nov., isolated from a saline-alkaline soil
Shuang Wang, Lei Sun, Manik Prabhu Narsing Rao, Guo-Hong Liu, Pin-Jiao Jin, Zhou-Yan Dong, Zheng-Han Lian, Xiao-Yu Hao, Ming-Yi Zhang, Wen-Jun Li
Archives of Microbiology.2022;[Epub] CrossRef
Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated fromSaline-sodic soil in Daqing, China
Shuang Wang, Lei Sun, Dan Wei, Baoku Zhou, Junzheng Zhang, Xuejia Gu, Lei Zhang, Ying Liu, Yidan Li, Wei Guo, Shuang Jiang, Yaqing Pan, Yufeng Wang
Journal of Microbiology.2014; 52(7): 548. CrossRef
Microbiology and Epidemiology ofHalomonasSpecies
Kwang Kyu Kim, Jung-Sook Lee, David A Stevens
Future Microbiology.2013; 8(12): 1559. CrossRef

Cloning, Expression, and Characterization of Xylose Reductase with Higher Activity from Candida tropicalis: Feiwei Zhang , Dairong Qiao , Hui Xu , Chong Liao , Shilin Li , Yi Cao; J. Microbiol. 2009;47(3):351-357. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0225-9

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Abstract PDF

Xylose reductase (XR) is a key enzyme in xylose metabolism because it catalyzes the reduction of xylose to xylitol. In order to study the characteristics of XR from Candida tropicalis SCTCC 300249, its XR gene(xyl1) was cloned and expressed in Escherichia coli BL21 (DE3). The fusion protein was purified effectively by Ni2+-chelating chromatography, and the kinetics of the recombinant XR was investigated. The Km values of the C. tropicalis XR for NADPH and NADH were 45.5 uM and 161.9 uM, respectively, which demonstrated that this XR had dual coenzyme specificity. Moreover, this XR showed the highest catalytic efficiency (kcat=1.44x04 min-1) for xylose among the characterized aldose reductases. Batch fermentation was performed with Saccharomyces serivisiae W303-1A:pYES2XR, and resulted in 7.63 g/L cell mass, 93.67 g/L xylitol, and 2.34 g/Lh xylitol productivity. This XR coupled with its dual coenzyme specificity, high activity, and catalytic efficiency proved its utility in in vitro xylitol production.

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Enhancing the production of xylitol in recombinant Escherichia coli BL21 by metabolic engineering
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Kinetics and Predicted Structure of a Novel Xylose Reductase from Chaetomium thermophilum
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Yirong Xu, Ping Chi, Muhammad Bilal, Hairong Cheng
Applied Microbiology and Biotechnology.2019; 103(13): 5143. CrossRef
A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization
Bhaskar Paidimuddala, Gopala Krishna Aradhyam, Sathyanarayana N. Gummadi
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Inhibition of Debaryomyces nepalensis xylose reductase by lignocellulose derived by-products
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Seiya Watanabe, Yuki Utsumi, Shigeki Sawayama, Yasuo Watanabe
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Sequence analysis of KmXYL1 genes and verification of thermotolerant enzymatic activities of xylose reductase from four Kluyveromyces marxianus strains
Jae-Bum Park, Jin-Seong Kim, Seung-Won Jang, Deok-Ho Kweon, Eock Kee Hong, Won Cheol Shin, Suk-Jin Ha
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Biao Zhang, Ling Zhang, Dongmei Wang, Xiaolian Gao, Jiong Hong
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