Tag: iTOL

Dargie, G. C. et al. Age, extent and carbon storage of the central Congo Basin peatland complex. Nature 542, 86–90 (2017). Article  ADS  CAS  PubMed  Google Scholar  Page, S. E., Rieley, J. O. & Banks, C. J. Global and regional importance of the tropical peatland carbon pool. Global Change Biology…

Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…

Shock EL, Holland M, Meyer-Dombard DA, Amend JP, Osburn GR, Fischer TP. Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim Cosmochim Acta. 2010;74:4005–43. Article  CAS  Google Scholar  Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, et al. A comprehensive census…

Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…

Lederberg, J., Cavalli, L. L. & Lederberg, E. M. Sex compatibility in Escherichia Coli. Genetics 37, 720–730 (1952). Article  CAS  PubMed  PubMed Central  Google Scholar  Elisabeth, G., Günther, M. & Manuel, E. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003). Article  Google Scholar  de la…

United Nations Inter-agency Group for Child Mortality Estimation. Levels & Trends in Child Mortality: Report 2020, Estimates developed by the United Nations Inter-agency Group for Child Mortality Estimation. New York: United Nations Children’s Fund; 2020. Okomo, U. et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in…

Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69. CAS  PubMed  PubMed Central  Google Scholar  Konstantinidis K, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406. PubMed  PubMed Central  Google Scholar  Parks…

Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article  PubMed  PubMed Central  Google Scholar  Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…

Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article  CAS  PubMed  Google Scholar  Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…

Borzi, A. Le communicazioni intracellulari delle nostochinee. Malpighia – Rassegna mensuale di botanica 1 (1886–1887). Simon, R. D. Cyanophycin granules from the blue-green alga anabaena cylindrica: A reserve material consisting of copolymers of aspartic acid and arginine. Proc. Natl. Acad. Sci. U. S. A. 68, 265–267 (1971). Article  ADS  CAS …

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies Abstract The global sulfur cycle has implications for human health, climate change, biogeochemistry, and bioremediation. The organosulfur compounds that participate in this cycle not only represent a vast reservoir of sulfur,…

Dick G, Anantharaman K, Baker B, Li M, Reed D, Sheik C. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol. 2013;4:124. Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol. 2019;17:271–83. Article  CAS …

FAO. The State of World Fisheries and Aquaculture 2022. (FAO, 2022). doi.org/10.4060/cc0461en. Marinho-Neto, F. A. et al. Morphological, microbiological and ultrastructural aspects of sepsis by Aeromonas hydrophila in Piaractus mesopotamicus. PLoS ONE 14, 1–20 (2019). Google Scholar  Shirajum-Monir, M., Yusoff, S. M., Mohamad, A. & Ina-Salwany, M. Y. Vaccination of…

Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

Kopp, A. Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 28, 175–184 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Zarkower, D. DMRT genes in vertebrate gametogenesis. Curr. Top. Dev. Biol. 102, 327–356 (2013). Article  CAS  PubMed  Google Scholar  Zhang, T. & Zarkower, D. DMRT proteins…

La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef  CAS  PubMed  Google Scholar  Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…

Typhoid GBD, Paratyphoid C. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect Dis. 2019;19(4):369–81. Article  Google Scholar  Arndt MB, Mosites EM, Tian M, Forouzanfar MH, Mokhdad AH, Meller M, Ochiai RL, Walson JL. Estimating the burden of…

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….

PhnD1 proteins in picocyanobacteria are lineage partitioned The predicted phosphonate-binding protein (PhnD1) under study is found within the genome of all 97 sequenced picocyanobacteria strains in the Cyanorak database, comprising cluster CK_860 [20]. While the gene encoding PhnD1 is highly conserved among all picocyanobacterial genomes, our phylogenetic tree reveals it…

FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…

Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article  CAS  PubMed  Google Scholar  Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…

Faulde, M. K., Rueda, L. M. & Khaireh, B. A. First record of the Asian malaria vector Anopheles stephensi and its possible role in the resurgence of malaria in Djibouti Horn of Africa. Acta Trop. 139, 39–43 (2014). Article  PubMed  Google Scholar  R, A. et al. Confirmation of the presence…

Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Planet. Sci. 48, 205–231 (2020). Article  CAS  Google Scholar  Feng, D. et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth SCI 168, 3–16 (2018). Article  Google Scholar  Dubilier, N., Bergin, C….

Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66. Article  CAS  PubMed  Google Scholar  Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12. Article  CAS  PubMed  Google Scholar  Breitbart M. Marine viruses: truth or dare. Ann…

Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article  CAS  PubMed  Google Scholar  Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Croxen, M. A….

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article  CAS  PubMed  PubMed Central  Google Scholar  Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

Metal rich high-temperature venting on the northwest caldera wall of Brothers Volcano produces these black smoker chimneys. Credit: New Zealand-American Submarine Ring of Fire 2005 Exploration; NOAA Vents Program. A new study by researchers at Portland State University and the University of Wisconsin finds that a rich diversity of microorganisms…

Stairs CW, Leger MM, Roger AJ. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Philos Trans R Soc B: Biol Sci. 2015;370:20140326. Article  Google Scholar  Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. Nat Rev Microbiol. 2017;15:711–23. Article  CAS …

Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article  CAS  Google Scholar  Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…

Perkins EM, Donnellan SC, Bertozzi T, Whittington ID. Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infers evolution in the diet of parasitic flatworms. Int J Parasitol. 2010;40:1237–45. Article  CAS  PubMed  Google Scholar  Zhang D, Li WX, Zou H, Wu SG, Li M, Jakovlić I, et al. Homoplasy…

Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, et al. Processes and patterns of oceanic nutrient limitation. Nat Geosci. 2013;6:701–10. Article  CAS  Google Scholar  Sohm JA, Webb EA, Capone DG. Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol. 2011;9:499–508. Article  CAS  PubMed  Google Scholar  Zehr…

Figure 1a provides an overview of the experimental procedure and it is summarized in the following sections. Fig. 1: Schematic overview of high-resolution optical DNA mapping-based bacterial typing. a Experimental pipeline. The DNA, extracted via plug-lysis, is labelled with YOYO-1 and netropsin in a single step. The DNA is confined to…

Introduction Over the last decades, Proteus species infections have received special attention because of the emergence of some species resistant to various antimicrobial agents, particularly β-lactams.1 Proteus penneri, first recognized in 1982, is a member of the Enterobacteriaceae family, which is salicin- and esculin-negative and chloramphenicol-resistant.1,2 P. penneri is primarily…

SESSION 4: Gene Trees – HackMD ###### tags: `BOT3404` # SESSION 4: Gene Trees SESSION 4: Gene Tree [TOC] In this session we will be using the sequences retrieved from Session 3 and running a few commands to be able to arrange the sequences into a gene tree. ### MAFFT…

P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…

Characteristics of the study population Among the 200 DR-TB cases, 146 (73.0%) cases were male, the median age was 66 (interquartile range = 55–78) years, 165 (82.5%) were new cases and 182 (91.0%) cases showed pulmonary TB (Table 1). The majority of DR-TB cases came from northern (74, 37.0%) Taiwan. Among the…

Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…

Discovery of 11 new Cas12a candidates from a human gut microbiome database To discover new members of the Cas12a protein family, we built a pipeline that searches and sorts out new candidates from the National Center for Biotechnological Information (NCBI) human metagenome database. Using this search pipeline (Fig. 1a), we initially…

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India Pakistan, and the UK: A molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597–602 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella…

Cui, B., Smooker, P. M., Rouch, D. A., Daley, A. J. & Deighton, M. A. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling. J. Clin. Microbiol. 51, 9–14 (2013). CAS  PubMed  PubMed Central  Article  Google Scholar  Tevell, S., Hellmark, B.,…

In a recent study published in Travel Medicine and Infectious Disease, researchers phylogenomically analyzed the monkeypox virus (MPXV). Study: Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage? Image Credit: ART-ur/Shutterstock Background Since May 2022, there have been various reports of increasing MPVX infections…

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…

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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…

Previously, I have recommended two powered online tools for genomic analysis and data visualization here. I want to share with you other handy tools that I found recently. iTOL is perfect for beautifying genomic data. circos is useful for displaying the relationships between objects and positions. You could discover their…

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…