Tag: NAR

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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An inducible system for expression and validation of the specificity of short hairpin RNA in mammalian cells – HKUST SPD

Bibliographic Details Author Ma, Hoi Tang On, Kin Fan Tsang, Yiu Huen Poon, Randy Yat Choi Issue Date 2007 Source Nucleic acids research, v. 35, (4), 2007, FEB, Article number e22 Abstract RNA interference (RNAi) by means of short hairpin RNA (shRNA) has developed into a powerful tool for loss-of-function…

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A desirable transgenic strategy using GGTA1 endogenous promoter-mediated knock-in for xenotransplantation model

Lai, L. et al. Production of alpha-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science 295, 1089–1092. doi.org/10.1126/science.1068228 (2002). ADS  CAS  Article  PubMed  Google Scholar  Kuwaki, K. et al. Heart transplantation in baboons using alpha1,3-galactosyltransferase gene-knockout pigs as donors: initial experience. Nat. Med. 11, 29–31. doi.org/10.1038/nm1171 (2005). CAS  Article  PubMed  Google…

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Frontiers | A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae

Introduction The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) protein systems naturally exist in prokaryotes. They are RNA-mediated defense mechanisms to protect bacteria and archaea from invading nucleic acids (Barrangou et al., 2007). CRISPR–Cas systems are classified into two classes (1 and 2). Class 2 CRISPR–Cas require a single…

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Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

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In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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Team develops method to increase gene editing efficiency while minimizing DNA deletion sizes

Targeting E. coli DNA pol I to DSBs increased the ratio of 1-bp deletions versus >1-bp deletions and TIS versus non-TIS. (A) Counteracting DNA resection (e.g. MRE11) by pol I fused to Cas9. The expected result is suppression of the MMEJ and SSA DNA repair pathways, which require DNA resection. (B)…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information

doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Zhong-Hao Ren et al. Front Genet. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations 1 School…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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LAMP-CRISPR-Cas12a-lateral flow immunochromatographic strip | IDR

Introduction About 700,000 people die from “superbugs” globally every year. Antibiotic abuse is the culprit of extensive spread of superbugs. Currently, carbapenemase-producing organisms are among the most important pathogens of hospital infections. Especially the plasmid-mediated highly transmissible carbapenem-resistant Enterobacterales (CRE) has become an important public health issue of global concern….

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Bacterial 23S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 23S Ribosomal RNA RefSeq Targeted Loci Project We’re sorry, but GBIF doesn’t work properly without JavaScript enabled. Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. Citation National Center for…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Dataset for manuscript “The use of comparative genomic analysis for the development of subspecies-specific PCR assays for the Mycobacterium abscessus complex” by Winifred Akwani et al. A core genome MLST scheme was developed for Mycobacterium abscessus complex (MABC) subspecies M. abscessus, M. bolletii and M. massiliense, using chewBBACA version 2.8.5…

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Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

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Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

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(PDF) Pstl RFLP at the medium chain acyl-Coenzyme A dehydrogenase locus (ACADM chromsome 1) | Paul Engel

(PDF) Pstl RFLP at the medium chain acyl-Coenzyme A dehydrogenase locus (ACADM chromsome 1) | Paul Engel – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn…

Continue Reading (PDF) Pstl RFLP at the medium chain acyl-Coenzyme A dehydrogenase locus (ACADM chromsome 1) | Paul Engel

Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs

doi: 10.1093/nar/gkac019. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. 2 Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA. 3 Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA….

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Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project

Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project We’re sorry, but GBIF doesn’t work properly without JavaScript enabled. Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. Citation McVeigh R (2013)….

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Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

Continue Reading Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Efficient target cleavage by Type V Cas12a effectors programmed with split CRISPR RNA

doi: 10.1093/nar/gkab1227. Online ahead of print. Regina Shebanova  1 , Natalia Nikitchina  1   2 , Nikita Shebanov  1 , Vladimir Mekler  3 , Konstantin Kuznedelov  3 , Egor Ulashchik  4 , Ruslan Vasilev  5   6 , Olga Sharko  4 , Vadim Shmanai  4 , Ivan Tarassov  2 , Konstantin Severinov  1   3   7 , Nina Entelis  2…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

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Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress

doi: 10.1093/nar/gkab1224. Online ahead of print. Affiliations Expand Affiliations 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland. 2 Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland. 3 Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria. 4 Rieveschl Laboratories…

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HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

doi: 10.1093/nar/gkab1221. Online ahead of print. Yang Yang  1   2 , Liwei Zhang  3 , Chaoyang Xiong  2 , Jun Chen  2   4   5 , Li Wang  6 , Zengqi Wen  2   5 , Juan Yu  2 , Ping Chen  4 , Yanhui Xu  6 , Jingji Jin  1   7   8 , Yong Cai …

Continue Reading HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium | BMC Biotechnology

1. Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, et al. Positive selection driving cytoplasmic genome evolution of the medicinally important ginseng plant genus Panax. Front Plant Sci. 2018;9:359. doi.org/10.3389/fpls.2018.00359. Article  PubMed  PubMed Central  Google Scholar  2. Takeshi T, Marouane B, Takuya I, Kazusato O, Kimiko…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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Next Generation Sequencing in tissues: Fully in situ methods

Here, Synthetic Biology Platform Lead at the Wyss Institute for Biologically Inspired Engineering, Richie Kohman, continues exploring the breakthroughs of Next Generation Sequencing (NGS) Exploring the locations and identities of RNA within biological tissues can uncover important information about cell types and states as well as give insight into cellular…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Infective endocarditis caused by ESBL-EC

Tsuneaki Kenzaka,1,2 Yuto Shinkura,1 Shizuo Kayama,3– 5 Liansheng Yu,3– 5 Sayoko Kawakami,3 Motoyuki Sugai,3– 5 Satoru Kawasaki1 1Department of Internal Medicine, Hyogo Prefectural Tamba Medical Center, Tanba, Japan; 2Division of Community Medicine and Career Development, Kobe University Graduate School of Medicine, Kobe, Japan; 3Antimicrobial Resistance Research Center, National Institute of…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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