DOCSLIB.ORG

State of the World's Fungi 2018

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
State of the World's Fungi 2018 6 State of the World’s Fungi State of the World’s Fungi 2018 6. Fungal genomes: Exploring, understanding and utilising their diversity Ilia J. Leitcha, Pepijn W. Kooija, Timothy Cokera, Igor V. Grigorievb, László G. Nagyc, Francis Martind, Jason Stajiche, Bryn T. M. Dentingerf, Ester Gayaa a Royal Botanic Gardens, Kew, UK; b U.S. Department of Energy Joint Genome Institute, USA; c Biological Research Centre, Hungarian Academy of Sciences, Hungary; d INRA, Université de Lorraine, France; e University of California-Riverside, USA; f Natural History Museum of Utah & School of Biological Sciences, University of Utah, USA 40 Positive interactions and insights Fungal genomes: exploring, understanding and utilising their diversity How many whole fungal genomes have been sequenced to date? How is this information being used to enhance our insights into medicine and climate change resilience and to find new fungi for use in everyday life, from food to antibiotics and biofuels? stateoftheworldsfungi.org/2018/fungal-genomes.html Fungal genomes: Exploring, understanding and utilising their diversity 41 Whole genomes have been sequenced for over 1,500 species of fungi, more than the number sequenced for plant and animal species combined 42 Positive interactions and insights FIGURE 1: CUMULATIVE NUMBER OF FUNGAL THE GENOMES OF FUNGI HAVE LONG SPECIES WITH WHOLE-GENOME SEQUENCES [Data collated from online genome databases including NCBI Genome BEEN OF INTEREST TO GENETICISTS database (ncbi.nlm.nih.gov/genome), JGI Genome Portal: MycoCosm BECAUSE MANY SPECIES ARE QUICK (genome.jgi.doe.gov/fungi), and EnsembleFungi (fungi.ensembl.org)] 1600 AND EASY TO GROW, THEIR DNA CAN BE Basidiomycota 1400 EASILY MANIPULATED, AND BECAUSE Ascomycota 1200 MANY OF THEIR ESSENTIAL CELL Mucoromycota 1000 PROCESSES ARE THE SAME AS IN ALL Zoopagomycota 800 EUKARYOTES*, INCLUDING HUMANS. Chytridiomycota 600 Blastocladiomycota Indeed, some of the earliest insights into how DNA encodes 400 Cummulative number of species the information needed to build life came from research on Cryptomycota & Microsporidia† the fungus Neurospora crassa[1]. More recent studies using 200 baker’s yeast (Saccharomyces cerevisiae) and fission yeast 0 (Schizosaccharomyces pombe) have led to many further breakthroughs in our understanding of human biology and 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 disease[2,3] (see Box 1 and Chapter 4). In this chapter, we Year review the current status of our knowledge of fungal DNA † The current fungal status of species belonging to Cryptomycota and and how this is being utilised to address some of the Microsporidia is still debated by some mycologists as they possess some characters that suggest they fall outside Kingdom Fungi. However, increasing most pressing challenges facing humanity, such as climate amounts of genomic data support the inclusion of these phyla within Kingdom change, food security and human health[4–8]. Fungi (see Chapter 2: Box 2). WHOLE-GENOME SEQUENCING Baker’s yeast was the first eukaryote to have its whole across the fungal tree of life, with data for species from all genome sequenced (published in 1996[9]). Since then, the eight phyla (see Figure 1) and all 12 subphyla[18,19]. number of whole-genome sequences available for fungi has In addition to ensuring full coverage across the spectrum risen exponentially (see Figure 1). This has been driven of fungal diversity, many other factors have been important in by several factors, including: (i) rapid advances in DNA driving the choice of species for sequencing. The insights that sequencing technologies; (ii) the drop in sequencing costs; can arise from a knowledge of fungal genomes can be applied (iii) the typically small size of fungal genomes compared with to many different challenges, as we now describe. other eukaryotes (see Box 2); and (iv) several large-scale sequencing initiatives (e.g. the Fungal Genome Initiative by the Broad Institute[10] and projects like the 1000 Fungal 1. INSIGHTS THAT ENHANCE OUR Genomes[11,12] and the Mycorrhizal Genomics Initiative[13] from UNDERSTANDING OF FUNGAL DISEASES the US Department of Energy Joint Genome Institute (JGI)). AND HOW TO TREAT THEM Currently there are more whole-genome sequences for Applications in medicine and human health species of fungi than for plants and animals combined. By Many of the first fungal species sequenced were those of 31 March 2018, the number of fungal species with publicly medical importance, including Candida albicans – the most available whole-genome sequences was 1,532 (most available commonly encountered human fungal pathogen, causing, for [14] online in JGI’s MycoCosm ). This is in comparison to just 326 example, skin and mucosal infections such as nappy rash plant and 868 animal species with whole genome sequences and thrush[20]. Whole-genome sequences have since been available in the National Center for Biotechnology Information generated for over 100 additional fungal pathogens of humans. [15] (NCBI) genome database . However these fungal data still They include genome sequences for the top ten invasive represent just a tiny fraction of the estimated 2.2 to 3.8 fungal species, such as Pneumocystis jirovecii, which causes [16] million species . Most data come from species in the phyla a type of pneumonia with mortality rates that can reach 80% in Ascomycota and Basidiomycota (see Figure 1), which is hardly immunocompromised patients[21]. Together it is estimated that surprising since together they contain >90% of the currently these ten species may be responsible for more human deaths [17] described species (see Chapter 1). Nevertheless, species each year than are caused by either tuberculosis or malaria[21]. with whole-genome sequences also include representatives The emerging knowledge of the underpinning genes and metabolic pathways is also proving to be invaluable * Eukaryotes comprise any organism that packages the bulk of its DNA for designing effective therapies that target the fungus into chromosomes located within a membrane-bound nucleus. Eukaryotes while minimising toxic side effects in humans[22], and in include animals, fungi, plants and a huge diversity of single-celled organisms that are loosely referred to as protists. Eukaryotes are distinct the search for new antibiotics and other bioactive from prokaryotes, which include Bacteria and Archaea. compounds with potential as new pharmaceuticals[23]. Fungal genomes: Exploring, understanding and utilising their diversity 43 BOX 1: FUNGAL GENOMES AS GATEWAYS yeast and humans, these findings are now being explored TO UNDERSTANDING HUMAN BIOLOGY to identify potential features of the genome that can be AND DISEASE used to focus the development of new approaches for [41] Fungi, in particular the unicellular yeasts such as baker’s extending the lifespans of humans . yeast (Saccharomyces cerevisiae) and fission yeast As several major drugs have been shown to hit the (Schizosaccharomyces pombe), have been hugely important same gene targets and elicit the same responses in for understanding many aspects of human biology. This is Saccharomyces cerevisiae as they do in humans, this yeast because many of the genes involved in regulating molecular, is currently being used as a living test tube to test the metabolic and cellular processes in humans have efficacy of possible therapeutic toxins in the treatment of [3] equivalent genes in these yeasts[2,40]. They can therefore be Parkinson’s disease . used as powerful models to shed light on a diverse range of biological processes and on how errors in these genes Cells of the fission yeast Schizosaccharomyces pombe[2] and processes lead to diseases. The study of genes that are involved in controlling when cells divide in Saccharomyces cerevisiae and Schizosaccharomyces pombe has been pivotal in revealing how the cell cycle is regulated at the genomic level. Such discoveries have pioneered the development of a diverse array of treatments for cancer that are widely used today. Saccharomyces cerevisiae was recently used to uncover some of the molecular processes underpinning ageing and 15 μm longevity. Given the high similarity of these processes in 44 Positive interactions and insights In addition, the increasing availability of multiple genome which forms mycorrhizal associations with pine species and is sequences for different strains of the same species is used in commercial forestry to inoculate plantations in order providing insights into the rapid genomic evolution that can to enhance their growth and health. The growing volumes of occur during disease progression and treatment. This enables genomic data are opening up new opportunities to explore how the development of rapid diagnostic tools and identification mycorrhizal fungi can be manipulated to enhance plant health, of drug resistance and hence the delivery of tailor-made environmental sustainability and ecosystem resilience in the treatments for patients[24]. face of environmental change[34]. In the field of public health, recent analysis of genomic While mycorrhizal species have been targeted for whole- data from studies of the gut microbiome (the sum of all the genome sequencing[13], the genomes of endophytic fungi (i.e. microbes such as bacteria and fungi that live in the gut) those that grow inside plants – see Chapter 5) have received suggests that changes in the abundance of specific fungi and less attention. However, some endophytes, particularly those their
Load more

Recommended publications
  • Sequence and Phylogenetic Analysis of SSU Rrna Gene of Five Microsporidia
    Curr Microbiol (2010) 60:30–37 DOI 10.1007/s00284-009-9495-7 Sequence and Phylogenetic Analysis of SSU rRNA Gene of Five Microsporidia ShiNan Dong Æ ZhongYuan Shen Æ Li Xu Æ Feng Zhu Received: 21 May 2009 / Accepted: 24 August 2009 / Published online: 19 September 2009 Ó The Author(s) 2009. This article is published with open access at Springerlink.com Abstract The complete small subunit rRNA (SSU to elucidate phylogenetic relationships and taxonomic rRNA) gene sequences of five microsporidia including status of microsporidian species by analyzing information Nosema heliothidis, and four novel microsporidia isolated from SSU rRNA sequences of microsporidia. from Pieris rapae, Phyllobrotica armta, Hemerophila atrilineata, and Bombyx mori, respectively, were obtained by PCR amplification, cloning, and sequencing. Two Introduction phylogenetic trees based on SSU rRNA sequences had been constructed by using Neighbor-Joining of Phylip Microsporidia are obligate intracellular parasites that infect software and UPGMA of MEGA4.0 software. The taxo- a broad range of invertebrates and humans, they were nomic status of four novel microsporidia was determined recognized as a causative agent for many hosts including by analysis of phylogenetic relationship, length, G?C insects, fishes, rodents, and primates. In 1857, the first content, identity, and divergence of the SSU rRNA microsporidian species—N. bombycis was described by sequences. The results showed that the microsporidia iso- Nageli [1]. Until now, more than 1,200 microsporidia lated from Pieris rapae, Phyllobrotica armta, and He- species belonging to *150 genera have been reported merophila atrilineata have close phylogenetic relationship [2, 3]. with the Nosema, while another microsporidium isolated The adaptation of microsporidia to a parasitic lifestyle from Bombyx mori is closely related to the Endoreticulatus.
    [Show full text]
  • Filling Gaps in the Microsporidian Tree: Rdna Phylogeny of Chytridiopsis Typographi (Microsporidia: Chytridiopsida)
    Parasitology Research (2019) 118:169–180 https://doi.org/10.1007/s00436-018-6130-1 GENETICS, EVOLUTION, AND PHYLOGENY - ORIGINAL PAPER Filling gaps in the microsporidian tree: rDNA phylogeny of Chytridiopsis typographi (Microsporidia: Chytridiopsida) Daniele Corsaro1 & Claudia Wylezich2 & Danielle Venditti1 & Rolf Michel3 & Julia Walochnik4 & Rudolf Wegensteiner5 Received: 7 August 2018 /Accepted: 23 October 2018 /Published online: 12 November 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Microsporidia are intracellular eukaryotic parasites of animals, characterized by unusual morphological and genetic features. They can be divided in three main groups, the classical microsporidians presenting all the features of the phylum and two putative primitive groups, the chytridiopsids and metchnikovellids. Microsporidia originated from microsporidia-like organisms belong- ing to a lineage of chytrid-like endoparasites basal or sister to the Fungi. Genetic and genomic data are available for all members, except chytridiopsids. Herein, we filled this gap by obtaining the rDNA sequence (SSU-ITS-partial LSU) of Chytridiopsis typographi (Chytridiopsida), a parasite of bark beetles. Our rDNA molecular phylogenies indicate that Chytridiopsis branches earlier than metchnikovellids, commonly thought ancestral, forming the more basal lineage of the Microsporidia. Furthermore, our structural analyses showed that only classical microsporidians present 16S-like SSU rRNA and 5.8S/LSU rRNA gene fusion, whereas the standard eukaryote rRNA gene structure, although slightly reduced, is still preserved in the primitive microsporidians, including 18S-like SSU rRNA with conserved core helices, and ITS2-like separating 5.8S from LSU. Overall, our results are consistent with the scenario of an evolution from microsporidia-like rozellids to microsporidians, however suggesting for metchnikovellids a derived position, probably related to marine transition and adaptation to hyperparasitism.
    [Show full text]
  • Effects of Genotypic and Phenotypic Variation on Establishment Are Important for Conservation, Invasion, and Infection Biology
    Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology Anders Forsman1 Ecology and Evolution in Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar, Sweden Edited by Ilkka Hanski, University of Helsinki, Helsinki, Finland, and approved December 2, 2013 (received for review September 20, 2013) There is abundant evidence that the probability of successful that more diverse groups harbor preadapted phenotypes, i.e., establishment in novel environments increases with number of a sampling effect (15, 16), niche complementarity resulting from individuals in founder groups and with number of repeated intro- reduced competition in groups where different phenotypes ex- ductions. Theory posits that the genotypic and phenotypic variation ploit different resources (17, 18), and facilitation, i.e., when the among individuals should also be important, but few studies have presence of one genotype or phenotype promotes the success of examined whether founder diversity influences establishment in- other phenotypes (19, 20). In addition, diverse populations of dependent of propagule pressure, nor whether the effect is model animals and plants may be less vulnerable to predators, diseases, or context dependent. I summarize the results of 18 experimental and pathogens (21, 22). Finally, genetic and phenotypic variation studies and report on a metaanalysis that provides strong evidence may promote population persistence because it buffers against that higher levels of genotypic and phenotypic diversity in founder selection in changing environments and enables adaptations to groups increase establishment success in plants and animals. The novel and changing conditions (10, 23–25). The above mecha- effect of diversity is stronger in experiments carried out under nisms are neither exhaustive nor mutually exclusive.
    [Show full text]
  • Evolutionary and Functional Studies on Microsporidian ATP-Binding
    Infection, Genetics and Evolution 68 (2019) 136–144 Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Evolutionary and functional studies on microsporidian ATP-binding T cassettes: Insights into the adaptation of microsporidia to obligated intracellular parasitism Qiang Hea, Charles R. Vossbrinckc, Qiong Yangd, Xian-Zhi Menga, Jian Luoa, Guo-Qing Pana, ⁎ ⁎ Ze-Yang Zhoua,b, , Tian Lia, a State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China b College of Life Science, Chongqing Normal University, Chongqing 400047, China c Department of Soil and Water, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA d Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China ARTICLE INFO ABSTRACT Keywords: ATP-binding cassette (ABC) transporters comprise the largest family of transmembrane proteins and are found in Microsporidian all domains of life. The ABCs are involved in a variety of biological processes and as exporters play important ABC transporter roles in multidrug resistance. However, the ABC transporters have not been addressed in microsporidia, which Genome are a very large group of obligate intracellular parasites that can infect nearly all animals, including humans. Evolution Here, a total of 234 ABC transporters were identified from 18 microsporidian genomes and classified intofive Nosema bombycis subfamilies, including 74 ABCBs, 2 ABCCs, 18 ABCEs, 15 ABCFs, 102 ABCGs and 23 uncategorized members. Two subfamilies, ABCA and ABCD, are found in most organisms, but lost in microsporidia. Phylogenetic analysis indicated that microsporidian ABCB and ABCG subfamilies expanded by recent gene duplications, which re- sulted in the two largest subfamilies in microsporidia.
    [Show full text]
  • Bringing a Trait‐Based Approach to Plant‐Associated Fungi
    Biol. Rev. (2020), 95, pp. 409–433. 409 doi: 10.1111/brv.12570 Fungal functional ecology: bringing a trait-based approach to plant-associated fungi Amy E. Zanne1,∗ , Kessy Abarenkov2, Michelle E. Afkhami3, Carlos A. Aguilar-Trigueros4, Scott Bates5, Jennifer M. Bhatnagar6, Posy E. Busby7, Natalie Christian8,9, William K. Cornwell10, Thomas W. Crowther11, Habacuc Flores-Moreno12, Dimitrios Floudas13, Romina Gazis14, David Hibbett15, Peter Kennedy16, Daniel L. Lindner17, Daniel S. Maynard11, Amy M. Milo1, Rolf Henrik Nilsson18, Jeff Powell19, Mark Schildhauer20, Jonathan Schilling16 and Kathleen K. Treseder21 1Department of Biological Sciences, George Washington University, Washington, DC 20052, U.S.A. 2Natural History Museum, University of Tartu, Vanemuise 46, Tartu 51014, Estonia 3Department of Biology, University of Miami, Coral Gables, FL 33146, U.S.A. 4Freie Universit¨at-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195 Berlin, Germany 5Department of Biological Sciences, Purdue University Northwest, Westville, IN 46391, U.S.A. 6Department of Biology, Boston University, Boston, MA 02215, U.S.A. 7Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, U.S.A. 8Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, U.S.A. 9Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A. 10Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia 11Department of Environmental Systems Science, Institute of Integrative Biology, ETH Z¨urich, 8092, Z¨urich, Switzerland 12Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN 55108, U.S.A.
    [Show full text]
  • Genome-Resolved Metagenomics of Eukaryotic Populations During Early Colonization of Premature Infants and in Hospital Rooms Matthew R
    Olm et al. Microbiome (2019) 7:26 https://doi.org/10.1186/s40168-019-0638-1 RESEARCH Open Access Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms Matthew R. Olm1†, Patrick T. West1†, Brandon Brooks1,8, Brian A. Firek2, Robyn Baker3, Michael J. Morowitz2 and Jillian F. Banfield4,5,6,7* Abstract Background: Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment. Results: Genome-resolved analysis of 1174 time-series fecal metagenomes from 161 premature infants revealed fungal colonization of 10 infants. Relative abundance levels reached as high as 97% and were significantly higher in the first weeks of life (p = 0.004). When fungal colonization occurred, multiple species were present more often than expected by random chance (p = 0.008). Twenty-four metagenomic samples were analyzed from hospital rooms of six different infants. Compared to floor and surface samples, hospital sinks hosted diverse and highly variable communities containing genomically novel species, including from Diptera (fly) and Rhabditida (worm) for which genomes were assembled. With the exception of Diptera and two other organisms, zygosity of the newly assembled diploid eukaryote genomes was low.
    [Show full text]
  • Virtual 2-D Map of the Fungal Proteome
    www.nature.com/scientificreports OPEN Virtual 2‑D map of the fungal proteome Tapan Kumar Mohanta1,6*, Awdhesh Kumar Mishra2,6, Adil Khan1, Abeer Hashem3,4, Elsayed Fathi Abd‑Allah5 & Ahmed Al‑Harrasi1* The molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in diferent parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome‑wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2‑D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non‑ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identifed as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes.
    [Show full text]
  • Four QTL Underlie Resistance to a Microsporidian Parasite That May Drive Genome Evolution in Its 2 Daphnia Host
    bioRxiv preprint doi: https://doi.org/10.1101/847194; this version posted November 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Four QTL underlie resistance to a microsporidian parasite that may drive genome evolution in its 2 Daphnia host 3 Devon Keller1, Devin Kirk1,2, Pepijn Luijckx1,3 4 1 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, 5 M5S 3G5. 6 2 Current address: Department of Biology, Stanford University, Stanford, USA. 7 3 School of Natural Sciences, Zoology, Trinity College Dublin, Dublin 2, Ireland 8 Author contributions 9 DK, DK and PL designed the study and conducted experiments. PL conducted the analysis. PL wrote the 10 first draft of the manuscript, and all authors significantly contributed to revisions. 11 Abstract: 12 Despite its pivotal role in evolutionary and ecological processes the genetic architecture underlying host- 13 parasite interactions remains understudied. Here we use a quantitative trait loci approach to identify 14 regions in the Daphnia magna genome that provide resistance against its microsporidium parasite 15 Ordospora colligata. The probability that Daphnia became infected was affected by a single locus and an 16 interaction between two additional loci. A fourth locus influenced the number of spores that grew within 17 the host. Comparing our findings to previously published genetic work on Daphnia magna revealed that 18 two of these loci may be the same as detected for another microsporidium parasite, suggesting a general 19 immune response to this group of pathogens.
    [Show full text]
  • Purified Bioactive Compounds from Mentha Spp. Oils As a Source of Candidosis Treatment
    Incentivo governamental para Arranjos Produtivos Locais de Plantas Medicinais e Fitoterápicos no âmbito do SUS REVISÃO FARMACOLOGIA Purified bioactive compounds from Mentha spp. oils as a source of Candidosis treatment. A brief review Compostos bioativos purificados de óleos de Mentha spp. como fonte de tratamento de candidose. Uma breve revisão DOI 10.5935/2446-4775.20170009 1BONI, Giovana C.*; 1FEIRIA, Simone N. B. de; 1HÖFLING, José F. 1University of Campinas - UNICAMP, Piracicaba Dental School, Piracicaba, SP, Brazil. *Correspondência: [email protected] Abstract Medicinal plants have been the subject of many studies in an attempt to discovery alternative drugs, since they are sources of potentially bioactive compounds that may act in the maintenance of human health. The discovery of new antimicrobial substances or biocomponents derived from natural products has been important in the control of microorganisms, especially due to the increase of cases of resistance to conventional antimicrobials. In parallel, yeasts of the genus Candida are becoming a public health problem in the last decades due to the increase of infections denominated candidosis. Candida spp. has mechanisms of virulence, such as polymorphism and biofilm formation, that facilitate the development of the infection and difficult the treatment. In this sense, studies found in the literature with bioactive compounds from Mentha spp. essential oil, describe their antifungal action, especially from the isolated compounds as carvone, mentone, menthofuran and pulegone. In this sense, this review describes studies about antimicrobial activity of these compounds especially against yeasts of Candida species and some particularities of this genus such as virulence mechanisms once these themes are crucial for the development of new alternative drugs and/or antifungal agents that may act as adjuncts to conventional treatments against these microorganisms.
    [Show full text]
  • I've Gut a Feeling: Microbiota Impacting the Conceptual And
    International Journal of Molecular Sciences Review I’ve Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine Amedeo Amedei 1,2,* and Federico Boem 1 1 Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, 03 50134, Firenze, Italy; [email protected] 2 Department of Biomedicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Largo Brambilla, 03 50134, Firenze, Italy * Correspondence: amedeo.amedei@unifi.it Received: 21 September 2018; Accepted: 16 November 2018; Published: 27 November 2018 Abstract: In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call “health” and in generating and/or favoring (those cases in which the microbiota’s complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as “health” and “individual,” do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine. Keywords: microbiome; health; precision medicine; genomics 1.
    [Show full text]
  • Science Citation Indexed Journal List
    SCIENCE CITATION INDEXED JOURNAL LIST Sr.No. Journal Title ISSN E-ISSN Publisher 1 2D MATERIALS 2053-1583 2053-1583 IOP PUBLISHING LTD 2 3 BIOTECH 2190-572X 2190-5738 SPRINGER HEIDELBERG 3 3D PRINTING AND ADDITIVE MANUFACTURING 2329-7662 2329-7670 MARY ANN LIEBERT, INC 4 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH 1619-4500 1614-2411 SPRINGER HEIDELBERG 5 AAPG BULLETIN 0149-1423 1558-9153 AMER ASSOC PETROLEUM GEOLOGIST 6 AAPS JOURNAL 1550-7416 1550-7416 SPRINGER 7 AAPS PHARMSCITECH 1530-9932 1530-9932 SPRINGER 8 AATCC JOURNAL OF RESEARCH 2330-5517 2330-5517 AMER ASSOC TEXTILE CHEMISTS COLORISTS-AATCC 9 AATCC REVIEW 1532-8813 1532-8813 AMER ASSOC TEXTILE CHEMISTS COLORISTS-AATCC 10 ABDOMINAL RADIOLOGY 2366-004X 2366-0058 SPRINGER ABHANDLUNGEN AUS DEM MATHEMATISCHEN SEMINAR DER 11 0025-5858 1865-8784 SPRINGER HEIDELBERG UNIVERSITAT HAMBURG 12 ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 0065-7727 AMER CHEMICAL SOC 13 ACADEMIC EMERGENCY MEDICINE 1069-6563 1553-2712 WILEY 14 ACADEMIC MEDICINE 1040-2446 1938-808X LIPPINCOTT WILLIAMS & WILKINS 15 ACADEMIC PEDIATRICS 1876-2859 1876-2867 ELSEVIER SCIENCE INC 16 ACADEMIC RADIOLOGY 1076-6332 1878-4046 ELSEVIER SCIENCE INC 17 ACAROLOGIA 0044-586X 2107-7207 ACAROLOGIA-UNIVERSITE PAUL VALERY 18 ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE 0898-9621 1545-5815 TAYLOR & FRANCIS INC 19 ACCOUNTS OF CHEMICAL RESEARCH 0001-4842 1520-4898 AMER CHEMICAL SOC 20 ACCREDITATION AND QUALITY ASSURANCE 0949-1775 1432-0517 SPRINGER 21 ACI MATERIALS JOURNAL 0889-325X 1944-737X AMER CONCRETE
    [Show full text]
  • Discovery of New Mycoviral Genomes Within Publicly Available Fungal Transcriptomic Datasets
    bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets 1 1 1,2 1 Kerrigan B. Gilbert ,​ Emily E. Holcomb ,​ Robyn L. Allscheid ,​ James C. Carrington *​ ​ ​ ​ ​ 1 ​ Donald Danforth Plant Science Center, Saint Louis, Missouri, USA 2 ​ Current address: National Corn Growers Association, Chesterfield, Missouri, USA * Address correspondence to James C. Carrington E-mail: [email protected] Short title: Virus discovery from RNA-seq data ​ bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. ​ ​ Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina.
    [Show full text]