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Fungi molecular typing

María Ángeles Guevara, Nuria de María, Enrique Sáez-Laguna, María Dolores Vélez, María Teresa Cervera, José Antonio Cabezas
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme...
2017: Methods in Molecular Biology
Nhu Nguyen, Else C Vellinga, Thomas D Bruns, Peter Kennedy
The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. Here we present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available in public databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America...
October 19, 2016: Mycologia
Chen Chen, Gerard J M Verkley, Guangyu Sun, Johannes Z Groenewald, Pedro W Crous
Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated...
November 2016: Fungal Biology
Y J Fan, T Grebenc, J Wei, Y L Zhao, W Yan, L B Wang
We investigated the diversity of ectomycorrhiza associated with the endemic Picea crassifolia in Mount Helan National Nature Reserve in Inner Mongolia, China. Toward this objective, we conducted morphological and molecular identification of ectomycorrhizae in soil cubes taken from pure P. crassifolia stands. Eleven types of ectomycorrhizal (ECM) organisms were separated, briefly described, and identified. Nine morphotypes belonged to the phylum Basidiomycotina [Amphinema byssoides, Cortinarius sp (cf. limonius), Cortinarius vernus, Inocybe cf...
September 2, 2016: Genetics and Molecular Research: GMR
Marcel Zámocký, Hakim Tafer, Katarína Chovanová, Ksenija Lopandic, Anna Kamlárová, Christian Obinger
BACKGROUND: The ascomycetous family Chaetomiaceae (class Sordariomycetes) includes numerous soilborn, saprophytic, endophytic and pathogenic fungi which can adapt to various growth conditions and living niches by providing a broad armory of oxidative and antioxidant enzymes. RESULTS: We release the 34.7 Mbp draft genome of Chaetomium cochliodes CCM F-232 consisting of 6036 contigs with an average size of 5756 bp and reconstructed its phylogeny. We show that this filamentous fungus is closely related but not identical to Chaetomium globosum and Chaetomium elatum...
September 29, 2016: BMC Genomics
Franceli Rodrigues Kulcheski, Ana Paula Christoff, Rogerio Margis
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. The development of deep sequencing of ribosomal RNA (rRNA)-depleted RNA libraries, associated with improved computational tools, has provided the identification of several new circRNAs in all sorts of organisms, from protists, plants and fungi to animals. Recently, it was discovered that endogenous circRNAs can work as microRNA (miRNA) sponges. This means that the circRNAs bind to miRNAs and consequently repress their function, providing a new model of action for this class of ncRNA, as well as indicating another mechanism that regulates miRNA activity...
November 20, 2016: Journal of Biotechnology
Ren Na, Liu Jiajia, Yang Dongliang, Peng Yingzi, Hong Juan, Liu Xiong, Zhao Nana, Zhou Jing, Luo Yitian
Vincamine, a monoterpenoid indole alkaloid which had been marketed as nootropic drugs for the treatment of cerebral insufficiencies, is widely found in plants of the Apocynaceae family. Nerium indicum is a plant belonging to the Apocynaceae family. So, the purpose of this research was designed to investigate the vincamine alkaloids producing endophytic fungi from Nerium indicum, Apocynaceae. 11 strains of endophytic fungi, isolated from the stems and roots of the plant, were grouped into 5 genera on the basis of morphological characteristics...
November 2016: Microbiological Research
Manuel Ferrer, Celia Méndez-García, David Rojo, Coral Barbas, Andrés Moya
Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops...
September 15, 2016: Biochemical Pharmacology
M Sandoval-Denis, J Guarro, J F Cano-Lira, D A Sutton, N P Wiederhold, G S de Hoog, S P Abbott, C Decock, L Sigler, J Gené
The taxonomy of the synnematous genera Cephalotrichum, Doratomyces and Trichurus, and other related genera Gamsia, Wardomyces and Wardomycopsis, has been controversial and relies mainly on morphological criteria. These are microascaceous saprobic fungi mostly found in air and soil and with a worldwide distribution. In order to clarify their taxonomy and to delineate generic boundaries within the Microascaceae, we studied 57 isolates that include clinical, environmental and all the available ex-type strains of a large set of species by means of morphological, physiological and molecular phylogenetic analyses using DNA sequence data of four loci (the ITS region, and fragments of rDNA LSU, translation elongation factor 1α and β-tubulin)...
2016: Studies in Mycology
M Sandoval-Denis, J Gené, D A Sutton, J F Cano-Lira, G S de Hoog, C A Decock, N P Wiederhold, J Guarro
The genera Microascus and Scopulariopsis comprise species commonly isolated from soil, decaying plant material and indoor environments. A few species are also recognised as opportunistic pathogens of insects and animals, including humans. In the past, the taxonomy of these fungi has been based on morphology only. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied a large set of clinical and environmental isolates, including the available ex-type strains of numerous species, by means of morphological, physiological and molecular analyses...
June 2016: Persoonia
Agnes Agunos, F William Pierson, Bwalya Lungu, Patricia A Dunn, Nathaniel Tablante
Emerging and re-emerging diseases are continuously diagnosed in poultry species. A few of these diseases are known to cross the species barrier, thus posing a public health risk and an economic burden. We identified and synthesized global evidence for poultry nonfoodborne zoonoses to better understand these diseases in people who were exposed to different poultry-related characteristics (e.g., occupational or nonoccupational, operational types, poultry species, outbreak conditions, health status of flocks)...
September 2016: Avian Diseases
Absar Alum, Galahad Zachariah Isaacs
BACKGROUND: The modern built environment (BE) design creates unique ecological niches ideal for the survival and mutual interaction of microbial communities. This investigation focused on the synergistic relations between Legionella and the fungal species commonly found in BEs and the impact of these synergistic relationships on the survival and transmission of Legionella. METHODS: A field study was conducted to identify the types and concentrations of fungi in BEs...
September 2, 2016: American Journal of Infection Control
William J Davis, Peter M Letcher, Martha J Powell
Zoospore ultrastructural characters combined with molecular phylogenetic hypotheses have been used to revise the taxonomy of zoosporic true fungi. An example is the reclassification of Rhizophlyctis rosea-like fungal strains into four new families and three new genera within the order Rhizophlyctidales. One genus was Borealophlyctis, which included a Canadian isolate, DAOMC 229843. A recent survey of chytrid diversity in Alabama (USA) yielded additional strains (WJD 170, WJD 171) in the Borealophlyctis lineage...
July 2016: Mycologia
Aimee C McKinnon
The identification of fungal endophytes often relies on culturing isolates from surface-sterilized plant tissue. However, molecular techniques have enabled the rapid detection and identification of targeted endophyte species, and next-generation sequencing technology provides an opportunity to obtain comprehensive information on endophytic communities, directly from plant tissue. In order to achieve accurate detection from internal tissues, surface microbes and associated deoxyribonucleic acid (DNA) must be eliminated, with particular consideration for the type of plant tissue and the efficacy of the surface sterilization procedure used...
2016: Methods in Molecular Biology
Jonas Hanske, Stevan Aleksić, Martin Ballaschk, Marcel Jurk, Elena Shanina, Monika Beerbaum, Peter Schmieder, Bettina G Keller, Christoph Rademacher
Antigen uptake and processing by innate immune cells is crucial to initiate the immune response. Therein, the endocytic C-type lectin receptors serve as pattern recognition receptors, detecting pathogens by their glycan structures. Herein, we studied the carbohydrate recognition domain of Langerin, a C-type lectin receptor involved in the host defense against viruses such as HIV and influenza as well as bacteria and fungi. Using a combination of nuclear magnetic resonance and molecular dynamics simulations, we unraveled the molecular determinants underlying cargo capture and release encoded in the receptor architecture...
September 21, 2016: Journal of the American Chemical Society
Liya He, Jiao Feng, Sha Lu, Zhiwen Chen, Chunmei Chen, Ya He, Xiuwen Yi, Liyan Xi
Transferring DNA into cells is an essential method of research on molecular cloning and gene function. As the molecular biology and materials physics develop, more and more new transformation methods have been applied in mammalian cells. Some techniques have been successfully developed for several types of fungi, but their efficiencies are extremely low. To better study on functional genes of fungi, and to improve the characteristics of fungi in an easy, safe and reliable way, many research are made to effectively develop such technologies in a wide variety of species and to increase the efficiency and reproducibility of genetic transformation...
August 16, 2016: International Journal of Developmental Biology
Jay M Portnoy, P Brock Williams, Charles S Barnes
PURPOSE OF REVIEW: In this review, we describe innate immunity to fungi and the ability of pattern recognition receptors (PRRs) to recognize fungal-associated molecular patterns (FAMPs) and danger-associated molecular patterns (DAMPs). RECENT FINDINGS: Protective responses against fungal antigens can be divided into two parts: innate immunity and adaptive immunity. Detection of foreign substance by the innate immune system is mediated by a variety of genetically encoded receptors known as pattern recognition receptors (PRRs)...
September 2016: Current Allergy and Asthma Reports
Nor Azizah Kusai, Madihah Mior Zakuan Azmi, Nur Ain Izzati Mohd Zainudin, Mohd Termizi Yusof, Azmi Abd Razak
Setosphaeria rostrata, a common plant pathogen causing leaf spot disease, affects a wide range of plant species, mainly grasses. Fungi were isolated from brown spots on rice leaves throughout Peninsular Malaysia, and 45 isolates were identified as Setosphaeria rostrata The isolates were then characterized using morphological and molecular approaches. The mating type was determined using PCR amplification of the mating type alleles, and isolates of opposite mating types were crossed to examine sexual reproduction...
September 2016: Mycologia
Nancy Van Prooyen, C Allen Henderson, Davina Hocking Murray, Anita Sil
Innate immune cells shape the host response to microbial pathogens. Here we elucidate critical differences in the molecular response of macrophages vs. dendritic cells (DCs) to Histoplasma capsulatum, an intracellular fungal pathogen of humans. It has long been known that macrophages are permissive for Histoplasma growth and succumb to infection, whereas DCs restrict fungal growth and survive infection. We used murine macrophages and DCs to identify host pathways that influence fungal proliferation and host-cell viability...
July 2016: PLoS Pathogens
Guo Wei, Peng Tian, Fengxia Zhang, Hao Qin, Han Miao, Qingwen Chen, Zhongyi Hu, Li Cao, Meijiao Wang, Xingfang Gu, Sanwen Huang, Mingsheng Chen, Guodong Wang
Plant volatile organic compounds, which are generated in a tissue-specific manner, play important ecological roles in the interactions between plants and their environments, including the well-known functions of attracting pollinators and protecting plants from herbivores/fungi attacks. However, to date, there have not been reports of holistic volatile profiling of the various tissues of a single plant species, even for the model plant species. In this study, we qualitatively and quantitatively analyzed 85 volatile chemicals, including 36 volatile terpenes, in 23 different tissues of cucumber (Cucumis sativus) plants using solid-phase microextraction combined with gas chromatography-mass spectrometry...
September 2016: Plant Physiology
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