Simple fluorescence-based high throughput cell viability assay for filamentous fungi.

PubMed

Chadha, S; Kale, S P

2015-09-01

Filamentous fungi are important model organisms to understand the eukaryotic process and have been frequently exploited in research and industry. These fungi are also causative agents of serious diseases in plants and humans. Disease management strategies include in vitro susceptibility testing of the fungal pathogens to environmental conditions and antifungal agents. Conventional methods used for antifungal susceptibilities are cumbersome, time-consuming and are not suitable for a large-scale analysis. Here, we report a rapid, high throughput microplate-based fluorescence method for investigating the toxicity of antifungal and stress (osmotic, salt and oxidative) agents on Magnaporthe oryzae and compared it with agar dilution method. This bioassay is optimized for the resazurin reduction to fluorescent resorufin by the fungal hyphae. Resazurin bioassay showed inhibitory rates and IC50 values comparable to the agar dilution method and to previously reported IC50 or MICs for M. oryzae and other fungi. The present method can screen range of test agents from different chemical classes with different modes of action for antifungal activities in a simple, sensitive, time and cost effective manner. A simple fluorescence-based high throughput method is developed to test the effects of stress and antifungal agents on viability of filamentous fungus Magnaporthe oryzae. This resazurin fluorescence assay can detect inhibitory effects comparable to those obtained using the growth inhibition assay with added advantages of simplicity, time and cost effectiveness. This high throughput viability assay has a great potential in large-scale screening of the chemical libraries of antifungal agents, for evaluating the effects of environmental conditions and hyphal kinetic studies in mutant and natural populations of filamentous fungi. © 2015 The Society for Applied Microbiology.

Changes in carbon footprint when integrating production of filamentous fungi in 1st generation ethanol plants.

PubMed

Brancoli, Pedro; Ferreira, Jorge A; Bolton, Kim; Taherzadeh, Mohammad J

2018-02-01

Integrating the cultivation of edible filamentous fungi in the thin stillage from ethanol production is presently being considered. This integration can increase the ethanol yield while simultaneously producing a new value-added protein-rich biomass that can be used for animal feed. This study uses life cycle assessment to determine the change in greenhouse gas (GHG) emissions when integrating the cultivation of filamentous fungi in ethanol production. The result shows that the integration performs better than the current scenario when the fungal biomass is used as cattle feed for system expansion and when energy allocation is used. It performs worse if the biomass is used as fish feed. Hence, integrating the cultivation of filamentous fungi in 1st generation ethanol plants combined with proper use of the fungi can lead to a reduction of GHG emissions which, considering the number of existing ethanol plants, can have a significant global impact. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vegan-mycoprotein concentrate from pea-processing industry byproduct using edible filamentous fungi.

PubMed

Souza Filho, Pedro F; Nair, Ramkumar B; Andersson, Dan; Lennartsson, Patrik R; Taherzadeh, Mohammad J

2018-01-01

Currently around one billion people in the world do not have access to a diet which provides enough protein and energy. However, the production of one of the main sources of protein, animal meat, causes severe impacts on the environment. The present study investigates the production of a vegan-mycoprotein concentrate from pea-industry byproduct (PpB), using edible filamentous fungi, with potential application in human nutrition. Edible fungal strains of Ascomycota ( Aspergillus oryzae , Fusarium venenatum , Monascus purpureus , Neurospora intermedia ) and Zygomycota ( Rhizopus oryzae ) phyla were screened and selected for their protein production yield. A. oryzae had the best performance among the tested fungi, with a protein yield of 0.26 g per g of pea-processing byproduct from the bench scale airlift bioreactor cultivation. It is estimated that by integrating the novel fungal process at an existing pea-processing industry, about 680 kg of fungal biomass attributing to about 38% of extra protein could be produced for each 1 metric ton of pea-processing byproduct. This study is the first of its kind to demonstrate the potential of the pea-processing byproduct to be used by filamentous fungi to produce vegan-mycoprotein for human food applications. The pea-processing byproduct (PpB) was proved to be an efficient medium for the growth of filamentous fungi to produce a vegan-protein concentrate. Moreover, an industrial scenario for the production of vegan-mycoprotein concentrate for human nutrition is proposed as an integrated process to the existing PPI production facilities.

Pyrene degradation by yeasts and filamentous fungi.

PubMed

Romero, M Cristina; Salvioli, Mónica L; Cazau, M Cecilia; Arambarri, A M

2002-01-01

The saprotrophic soil fungi Fusarium solani (Mart.) Sacc., Cylindrocarpon didymum (Hartig) Wollenw, Penicillium variabile Sopp. and the yeasts Rhodotorula glutinis (Fresenius) Harrison and Rhodotorula minuta (Saito) Harrison were cultured in mineral medium with pyrene. The remaining pyrene concentrations were periodically determined during 20 incubation days, using HPLC. To assess the metabolism of pyrene degradation we added 0.1 microCi of [4,5,9,10] 14C-pyrene to each fungi culture and measured the radioactivity in the volatile organic substances, extractable, aqueous phase, biomass and 14CO2 fractions. The assays demonstrated that F. solani and R. glutinis metabolized pyrene as a sole source of carbon. Differences in their activities at the beginning of the cultures disappeared by the end of the experiment, when 32 and 37% of the original pyrene concentration was detected, for the soil fungi and yeasts, respectively. Among the filamentous fungi, F. solani was highly active and oxidized pyrene; moreover, small but significant degradation rates were observed in C. didymum and P. variahile cultures. An increase in the 14CO2 evolution was observed at the 17th day with cosubstrate. R. glutinis and R. minuta cultures showed similar ability to biotransform pyrene, and that 35% of the initial concentration was consumed at the end of the assay. The same results were obtained in the experiments with or without glucose as cosubstrate.

CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art.

PubMed

Shi, Tian-Qiong; Liu, Guan-Nan; Ji, Rong-Yu; Shi, Kun; Song, Ping; Ren, Lu-Jing; Huang, He; Ji, Xiao-Jun

2017-10-01

In recent years, a variety of genetic tools have been developed and applied to various filamentous fungi, which are widely applied in agriculture and the food industry. However, the low efficiency of gene targeting has for many years hampered studies on functional genomics in this important group of microorganisms. The emergence of CRISPR/Cas9 genome-editing technology has sparked a revolution in genetic research due to its high efficiency, versatility, and easy operation and opened the door for the discovery and exploitation of many new natural products. Although the application of the CRISPR/Cas9 system in filamentous fungi is still in its infancy compared to its common use in E. coli, yeasts, and mammals, the deep development of this system will certainly drive the exploitation of fungal diversity. In this review, we summarize the research progress on CRISPR/Cas9 systems in filamentous fungi and finally highlight further prospects in this area.

Actinomycetes inhibit filamentous fungi from the cuticle of Acromyrmex leafcutter ants.

PubMed

Dângelo, Rômulo Augusto Cotta; de Souza, Danival José; Mendes, Thais Demarchi; Couceiro, Joel da Cruz; Lucia, Terezinha Maria Castro Della

2016-03-01

Actinomycetes bacteria associated with leafcutter ants produce secondary metabolites with antimicrobial properties against Escovopsis, a fungus specialized in attacking the gardens of fungus-growing ants, which denies the ants their food source. Because previous studies have used fungi isolated from fungus gardens but not from ant integument, the aims of the present study were to isolate actinomycetes associated with the cuticle of the Acromyrmex spp. and to quantify their inhibition abilities against the filamentous fungal species carried by these ants. The results demonstrated that actinomycetes had varied strain-dependent effects on several filamentous fungal species in addition to antagonistic activity against Escovopsis. The strain isolated from Acromyrmex balzani was identified as a Streptomyces species, whereas the remaining isolates were identified as different strains belonging to the genus Pseudonocardia. These findings corroborate the hypothesis that actinomycetes do not act specifically against Escovopsis mycoparasites and may have the ability to inhibit other species of pathogenic fungi. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Safety evaluation of filamentous fungi isolated from industrial doenjang koji.

PubMed

Lee, Jin Hee; Jo, Eun Hye; Hong, Eun Jin; Kim, Kyung Min; Lee, Inhyung

2014-10-01

A few starters have been developed and used for doenjang fermentation but often without safety evaluation. Filamentous fungi were isolated from industrial doenjang koji, and their potential for mycotoxin production was evaluated. Two fungi were isolated; one was more dominantly present (90%). Both greenish (SNU-G) and whitish (SNU-W) fungi showed 97% and 95% internal transcribed spacer sequence identities to Aspergillus oryzae/flavus, respectively. However, the SmaI digestion pattern of their genomic DNA suggested that both belong to A. oryzae. Moreover, both fungi had morphological characteristics similar to that of A. oryzae. SNU-G and SNU-W did not form sclerotia, which is a typical characteristic of A. oryzae. Therefore, both fungi were identified to be A. oryzae. In aflatoxin gene cluster analysis, both fungi had norB-cypA genes similar to that of A. oryzae. Consistent with this, aflatoxins were not detected in SNU-G and SNU-W using ammonia vapor, TLC, and HPLC analyses. Both fungi seemed to have a whole cyclopiazonic acid (CPA) gene cluster based on PCR of the maoA, dmaT, and pks-nrps genes, which are key genes for CPA biosynthesis. However, CPA was not detected in TLC and HPLC analyses. Therefore, both fungi seem to be safe to use as doenjang koji starters and may be suitable fungal candidates for further development of starters for traditional doenjang fermentation.

[Activity of butenafine against ocular pathogenic filamentous fungi in vitro].

PubMed

Xu, Yan; Pang, Guang-ren; Zhao, Dong-qing; Gao, Chuan-wen; Zhou, Lu-tan; Sun, Sheng-tao; Wang, Bing-liang; Chen, Zu-ji

2010-01-01

To investigate antifungal activity of butenafine in comparison with that of natamycin, amphotericin B and fluconazole against ocular pathogenic filamentous fungi in vitro. It was an experimental study. Susceptibility tests were performed against 260 isolates of ocular pathogenic filamentous fungi by broth dilution antifungal susceptibility test of filamentous fungi approved by the Clinical and Laboratory Standards Institute (CLSI) M38-A document. The isolates included Fusarium spp. (136), Aspergillus spp. (98), Alternaria alternata (9), Curvularia lunata (3), and unusual ocular pathogens (14). Final concentration ranged from 0.008 to 16.000 mg/L for butenafine, from 0.031 to 16.000 mg/L for amphotericin B and natamycin, and from 0.5 to 256.0 mg/L for fluconazole. Following incubation at 35 degrees C for 48 h, minimal inhibitory concentration (MIC) was determined according to the CLSI M38-A document. For amphotericin B and natamycin, the MIC was defined as the lowest drug concentration that prevented any discernible growth. For butenafine and fluconazole, the MIC was defined as the lowest concentration in which an approximately 75% reduction compared to the growth of the control was observed. Candida parapsilosis ATCC22019 was used as quality control strains to validated the results. Mean MIC and MIC range, the MIC at which 50% of the isolates tested were inhibited (MIC(50)) and the MIC at which 90% of the isolates tested were inhibited (MIC(90)), were provided for all the isolates tested by using descriptive statistical analysis with the statistical SPSS package (version 13.0). MIC(90) of butenafine, natamycin, amphotericin B and fluconazole were 4, 8, 2 and 512 mg/L for Fusarium spp., respectively; 0.063, 32.000, 2.000 and 256.000 mg/L for Aspergillus spp., respectively; 0.5, 8.0, 2.0 and 128.0 mg/L for Alternaria alternate, respectively; 0.125, 2.000, 0.500 and 4.000 mg/L for Curvularia lunata, respectively; and 1, 4, 1 and 256 mg/L for unusual ocular pathogens

Characterization of Yeasts and Filamentous Fungi using MALDI Lipid Phenotyping.

PubMed

Stübiger, Gerald; Wuczkowski, Michael; Mancera, Luis; Lopandic, Ksenija; Sterflinger, Katja; Belgacem, Omar

2016-11-01

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) becomes the method of choice for the rapid identification of microorganisms (i.e. protein biotyping). Although bacterial identification is already quite advanced, biotyping of other microbes including yeasts and fungi are still under development. In this context, lipids (e.g. membrane phospholipids) represent a very important group of molecules with essential functions for cell survival and adaptation to specific environments and habitats of the microorganisms. Therefore, lipids show the potential to serve as additional molecular parameters to be used for biotyping purposes. In this paper we present a molecular characterisation of yeasts and filamentous fungi based on the analysis of lipid composition by MALDI-MS (i.e. MALDI lipid phenotyping). Using a combination of Principal Component Analysis (PCA) and Hierarchical Clustering we could demonstrate that this approach allowed a classification and differentiation of several groups of yeasts (e.g. Saccharomyces) and filamentous fungi (e.g. Aspergillus, Penicillium, Trichoderma) at the species/strain level. By analysing the MALDI lipid profiles we were able to differentiate 26 closely related yeast strains, for which discrimination via genotypic methods like AFLP in this case are relatively more elaborate. Moreover, employing statistical analysis we could identify those lipid parameters (e.g. PCs and LPCs), which were responsible for the differentiation of the strains, thus providing insights into the molecular basis of our results. In summary, MALDI lipid phenotyping represents a suitable method for fungal characterization and shows the potential to be used as companion tool to genotyping and/or protein biotyping for the characterization and identification of yeasts and fungi in diverse areas (e.g. environmental, pharmaceutical, clinical applications, etc.). Copyright © 2016 Elsevier B.V. All rights reserved.

Filamentous fungi for production of food additives and processing aids.

PubMed

Archer, David B; Connerton, Ian F; MacKenzie, Donald A

2008-01-01

Filamentous fungi are metabolically versatile organisms with a very wide distribution in nature. They exist in association with other species, e.g. as lichens or mycorrhiza, as pathogens of animals and plants or as free-living species. Many are regarded as nature's primary degraders because they secrete a wide variety of hydrolytic enzymes that degrade waste organic materials. Many species produce secondary metabolites such as polyketides or peptides and an increasing range of fungal species is exploited commercially as sources of enzymes and metabolites for food or pharmaceutical applications. The recent availability of fungal genome sequences has provided a major opportunity to explore and further exploit fungi as sources of enzymes and metabolites. In this review chapter we focus on the use of fungi in the production of food additives but take a largely pre-genomic, albeit a mainly molecular, view of the topic.

Bio-Source of di-n-butyl phthalate production by filamentous fungi

NASA Astrophysics Data System (ADS)

Tian, Congkui; Ni, Jinren; Chang, Fang; Liu, Sitong; Xu, Nan; Sun, Weiling; Xie, Yuan; Guo, Yongzhao; Ma, Yanrong; Yang, Zhenxing; Dang, Chenyuan; Huang, Yuefei; Tian, Zhexian; Wang, Yiping

2016-02-01

Although DBP (di-n-butyl phthalate) is commonly encountered as an artificially-synthesized plasticizer with potential to impair fertility, we confirm that it can also be biosynthesized as microbial secondary metabolites from naturally occurring filamentous fungi strains cultured either in an artificial medium or natural water. Using the excreted crude enzyme from the fungi for catalyzing a variety of substrates, we found that the fungal generation of DBP was largely through shikimic acid pathway, which was assembled by phthalic acid with butyl alcohol through esterification. The DBP production ability of the fungi was primarily influenced by fungal spore density and incubation temperature. This study indicates an important alternative natural waterborne source of DBP in addition to artificial synthesis, which implied fungal contribution must be highlighted for future source control and risk management of DBP.

A-to-I RNA editing independent of ADARs in filamentous fungi

PubMed Central

Wang, Chenfang; Xu, Jin-Rong; Liu, Huiquan

2016-01-01

ABSTRACT ADAR mediated A-to-I RNA editing is thought to be unique to animals and occurs mainly in the non-coding regions. Recently filamentous fungi such as Fusarium graminearum were found to lack orthologs of animal ADARs but have stage-specific A-to-I editing during sexual reproduction. Unlike animals, majority of editing sites are in the coding regions and often result in missense and stop loss changes in fungi. Furthermore, whereas As in RNA stems are targeted by animal ADARs, RNA editing in fungi preferentially targets As in hairpin loops, implying that fungal RNA editing involves mechanisms related to editing of the anticodon loop by ADATs. Identification and characterization of fungal adenosine deaminases and their stage-specific co-factors may be helpful to understand the evolution of human ADARs. Fungi also can be used to study biological functions of missense and stop loss RNA editing events in eukaryotic organisms. PMID:27533598

[Filamentous fungi and mycotoxins as potential occupational risk factors among farmers harvesting various crops].

PubMed

Krysińska-Traczyk, Ewa; Perkowski, Juliusz; Kostecki, Marian; Dutkiewicz, Jacek; Kiecana, Irena

2003-01-01

The studies to determine the level of filamentous fungi and mycotoxins were carried out in samples of grain and grain dust during threshing of cereals by a combine harvester. High concentration of fungi was noted in grain and grain dust samples, it ranged from 5.0 to 520.0 cfu/g.10(3) and from 275.0 to 2825.0 cfu/g.10(3), respectively Allergizing and toxigenic fungi of Alternaria, Geotrichum, Cladosporium, Penicillium, Aspergillus and Fusarium species were observed in the study samples of grain and grain dust. In the samples of wheat grain, mycotoxins were also noted: moniliformin (MON), deoxynivalenol (DON) and ochratoxin A (OTA); their concentrations ranged from 0.025 to 0.088 microgram/g; 0.015-0.068 microgram/g; and from 0.0004 to 0.0008 microgram/g, respectively. The level of mycotoxins in the grain dust samples was within the range of 0.025-0.149 microgram/g-MON; 0.015-0.215 microgram/g-DON; 0.015-0.360 microgram/g-NIV; and 0.0004-0.0012 microgram/g-OTA. A significant correlation was observed between the occurrence of fungi of Fusarium species and the concentration of pathologic mycotoxins. The results confirm a considerable occupational risk among farmers engaged in grain threshing due to inhalation of pathogenic species of filamentous fungi and mycotoxins.

In vitro antifungal activity of silver nanoparticles against ocular pathogenic filamentous fungi.

PubMed

Xu, Yan; Gao, Chuanwen; Li, Xiaohua; He, Yi; Zhou, Lutan; Pang, Guangren; Sun, Shengtao

2013-03-01

Fungal keratitis is emerging as a major cause of vision loss in a developing country such as China because of higher incidence and the unavailability of effective antifungals. It is urgent to explore broad-spectrum antifungals to effectively suppress ocular fungal pathogens, and to develop new antifungal eye drops to combat this vision-threatening infection. The aim of this study is to investigate the antifungal activity of silver nanoparticles (nano-Ag) in comparison with that of natamycin against ocular pathogenic filamentous fungi in vitro. Susceptibility tests were performed against 216 strains of fungi isolated from patients with fungal keratitis from the Henan Eye Institute in China by broth dilution antifungal susceptibility test of filamentous fungi approved by the Clinical and Laboratory Standards Institute M38-A document. The isolates included 112 Fusarium isolates (82 Fusarium solani species complex, 20 Fusarium verticillioides species complex, and 10 Fusarium oxysporum species complex), 94 Aspergillus isolates (61 Aspergillus flavus species complex, 11 Aspergillus fumigatus species complex, 12 Aspergillus versicolor species complex, and 10 Aspergillus niger species complex), and 10 Alternaria alternata isolates. The minimum inhibitory concentration (MIC) range and mode, the MIC for 50% of the strains tested (MIC50 value), and the MIC90 value were provided for the isolates with the SPSS statistical package. MIC50 value of nano-Ag were 1, 0.5, and 0.5 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of nano-Ag were 1, 1, and 1 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC50 values of natamycin were 4, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of natamycin were 8, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. Nano-Ag, relative to natamycin, exhibits potent in vitro activity against

[Role of G-protein alpha sub-units in the morphogenic processes of filamentous Ascomycota fungi].

PubMed

García-Rico, Ramón O; Fierro, Francisco

The phylum Ascomycota comprises about 75% of all the fungal species described, and includes species of medical, phytosanitary, agricultural, and biotechnological importance. The ability to spread, explore, and colonise new substrates is a feature of critical importance for this group of organisms. In this regard, basic processes such as conidial germination, the extension of hyphae and sporulation, make up the backbone of development in most filamentous fungi. These processes require specialised morphogenic machinery, coordinated and regulated by mechanisms that are still being elucidated. In recent years, substantial progress has been made in understanding the role of the signalling pathway mediated by heterotrimericG proteins in basic biological processes of many filamentous fungi. This review focuses on the role of the alpha subunits of heterotrimericG proteins in the morphogenic processes of filamentous Ascomycota. Copyright © 2016 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Methodologies and Perspectives of Proteomics Applied to Filamentous Fungi: From Sample Preparation to Secretome Analysis

PubMed Central

Bianco, Linda; Perrotta, Gaetano

2015-01-01

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation. PMID:25775160

Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis.

PubMed

Bianco, Linda; Perrotta, Gaetano

2015-03-12

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi.

PubMed

Normand, Anne-Cécile; Cassagne, Carole; Ranque, Stéphane; L'ollivier, Coralie; Fourquet, Patrick; Roesems, Sam; Hendrickx, Marijke; Piarroux, Renaud

2013-04-08

The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera.Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for the identification of clinical filamentous fungi.

PubMed

Huang, Yanfei; Zhang, Mingxin; Zhu, Min; Wang, Mei; Sun, Yufeng; Gu, Haitong; Cao, Jingjing; Li, Xue; Zhang, Shaoya; Wang, Jinglin; Lu, Xinxin

2017-07-01

Infections caused by filamentous fungi have become a health concern, and require rapid and accurate identification in order for effective treatment of the pathogens. To compare the performance of two MALDI-TOF MS systems (Bruker Microflex LT and Xiamen Microtyper) in the identification of filamentous fungal species. A total of 374 clinical filamentous fungal isolates sequentially collected in the Clinical Laboratory at the Beijing Tongren Hospital between January 2014 and December 2015 were identified by traditional phenotypic methods, Bruker Microflex LT and Xiamen Microtyper MALDI-TOF MS, respectively. The discrepancy between these methods was resolved by sequencing for definitive identification. Bruker Microflex LT and Xiamen Microtyper had similar correct species ID (98.9 vs. 99.2%), genus ID (99.7 vs. 100%), mis-ID (0.3 vs. 0%) and no ID (0 vs. 0). The rate of correct species identification by both MALDI-TOF MS (98.9 and 99.2%, respectively) was much higher compared with phenotypic approach (91.9%). Both MALDI-TOF MS systems provide accurate identification of clinical filamentous fungi compared with conventional phenotypic method, and have the potential to replace identification for routine identification of these fungi in clinical mycology laboratories. Both systems have similar performance in the identification of clinical filamentous fungi.

Production and chemical characterization of pigments in filamentous fungi.

PubMed

Souza, Patrícia Nirlane da Costa; Grigoletto, Tahuana Luiza Bim; de Moraes, Luiz Alberto Beraldo; Abreu, Lucas M; Guimarães, Luís Henrique Souza; Santos, Cledir; Galvão, Luciano Ribeiro; Cardoso, Patrícia Gomes

2016-01-01

Production of pigments by filamentous fungi is gaining interest owing to their use as food colourants, in cosmetics and textiles, and because of the important biological activities of these compounds. In this context, the objectives of this study were to select pigment-producing fungi, identify these fungi based on internal transcribed spacer sequences, evaluate the growth and pigment production of the selected strains on four different media, and characterize the major coloured metabolites in their extracts. Of the selected fungal strains, eight were identified as Aspergillus sydowii (CML2967), Aspergillus aureolatus (CML2964), Aspergillus keveii (CML2968), Penicillium flavigenum (CML2965), Penicillium chermesinum (CML2966), Epicoccum nigrum (CML2971), Lecanicillium aphanocladii (CML2970) and Fusarium sp. (CML2969). Fungal pigment production was influenced by medium composition. Complex media, such as potato dextrose and malt extract, favoured increased pigment production. The coloured compounds oosporein, orevactaene and dihydrotrichodimerol were identified in extracts of L. aphanocladii (CML2970), E. nigrum (CML2971), and P. flavigenum (CML2965), respectively. These results indicate that the selected fungal strains can serve as novel sources of pigments that have important industrial applications.

Capillary electrophoresis of conidia from cultivated microscopic filamentous fungi.

PubMed

Horká, Marie; Růzicka, Filip; Kubesová, Anna; Holá, Veronika; Slais, Karel

2009-05-15

In immunocompromised people fungal agents are able to cause serious infections with high mortality rate. An early diagnosis can increase the chances of survival of the affected patients. Simultaneously, the fungi produce toxins and they are frequent cause of allergy. Currently, various methods are used for detection and identification of these pathogens. They use microscopic examination and growth characteristic of the fungi. New methods are based on the analysis of structural elements of the target microorganisms such as proteins, polysaccharides, glycoproteins, nucleic acids, etc. for the construction of antibodies, probes, and primers for detection. The above-mentioned methods are time-consuming and elaborate. Here hydrophobic conidia from the cultures of different strains of the filamentous fungi were focused and separated by capillary zone electrophoresis and capillary isoelectric focusing. The detection was optimized by dynamic modifying of conidia by the nonionogenic tenside on the basis of pyrenebutanoate. Down to 10 labeled conidia of the fungal strains were fluorometrically detected, and isoelectric points of conidia were determined. The observed isoelectric points were compared with those obtained from the separation of the cultured clinical samples, and they were found to be not host-specific.

Organic Acid Production by Filamentous Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magnuson, Jon K.; Lasure, Linda L.

Many of the commercial production processes for organic acids are excellent examples of fungal biotechnology. However, unlike penicillin, the organic acids have had a less visible impact on human well-being. Indeed, organic acid fermentations are often not even identified as fungal bioprocesses, having been overshadowed by the successful deployment of the β-lactam processes. Yet, in terms of productivity, fungal organic acid processes may be the best examples of all. For example, commercial processes using Aspergillus niger in aerated stirred-tank-reactors can convert glucose to citric acid with greater than 80% efficiency and at final concentrations in hundreds of grams per liter.more » Surprisingly, this phenomenal productivity has been the object of relatively few research programs. Perhaps a greater understanding of this extraordinary capacity of filamentous fungi to produce organic acids in high concentrations will allow greater exploitation of these organisms via application of new knowledge in this era of genomics-based biotechnology. In this chapter, we will explore the biochemistry and modern genetic aspects of the current and potential commercial processes for making organic acids. The organisms involved, with a few exceptions, are filamentous fungi, and this review is limited to that group. Although yeasts including Saccharomyces cerevisiae, species of Rhodotorula, Pichia, and Hansenula are important organisms in fungal biotechnology, they have not been significant for commercial organic acid production, with one exception. The yeast, Yarrowia lipolytica, and related yeast species, may be in use commercially to produce citric acid (Lopez-Garcia, 2002). Furthermore, in the near future engineered yeasts may provide new commercial processes to make lactic acid (Porro, Bianchi, Ranzi, Frontali, Vai, Winkler, & Alberghina, 2002). This chapter is divided into two parts. The first contains a review of the commercial aspects of current and potential large

Centromeres of filamentous fungi.

PubMed

Smith, Kristina M; Galazka, Jonathan M; Phatale, Pallavi A; Connolly, Lanelle R; Freitag, Michael

2012-07-01

How centromeres are assembled and maintained remains one of the fundamental questions in cell biology. Over the past 20 years, the idea of centromeres as precise genetic loci has been replaced by the realization that it is predominantly the protein complement that defines centromere localization and function. Thus, placement and maintenance of centromeres are excellent examples of epigenetic phenomena in the strict sense. In contrast, the highly derived "point centromeres" of the budding yeast Saccharomyces cerevisiae and its close relatives are counter-examples for this general principle of centromere maintenance. While we have learned much in the past decade, it remains unclear if mechanisms for epigenetic centromere placement and maintenance are shared among various groups of organisms. For that reason, it seems prudent to examine species from many different phylogenetic groups with the aim to extract comparative information that will yield a more complete picture of cell division in all eukaryotes. This review addresses what has been learned by studying the centromeres of filamentous fungi, a large, heterogeneous group of organisms that includes important plant, animal and human pathogens, saprobes, and symbionts that fulfill essential roles in the biosphere, as well as a growing number of taxa that have become indispensable for industrial use.

Centromeres of filamentous fungi

PubMed Central

Smith, Kristina M.; Galazka, Jonathan M.; Phatale, Pallavi A.; Connolly, Lanelle R.; Freitag, Michael

2012-01-01

How centromeres are assembled and maintained remains one of the fundamental questions in cell biology. Over the past 20 years the idea of centromeres as precise genetic loci has been replaced by the realization that it is predominantly the protein complement that defines centromere localization and function. Thus, placement and maintenance of centromeres are excellent examples of epigenetic phenomena in the strict sense. In contrast, the highly derived “point centromeres” of the budding yeast Saccharomyces cerevisiae and its close relatives are counterexamples for this general principle of centromere maintenance. While we have learned much in the past decade, it remains unclear if mechanisms for epigenetic centromere placement and maintenance are shared amongst various groups of organisms. For that reason it seems prudent to examine species from many different phylogenetic groups with the aim to extract comparative information that will yield a more complete picture of cell division in all eukaryotes. This review addresses what has been learned by studying the centromeres of filamentous fungi, a large, heterogeneous group of organisms that includes important plant, animal and human pathogens, saprobes and symbionts that fulfill essential roles in the biosphere, as well as a growing number of taxa that have become indispensable for industrial use. PMID:22752455

The Ecological Genomics of Fungi: Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murat, Claude; Payen, Thibaut; Petitpierre, Denis

2013-01-01

In the last decade, the genome of several dozen filamentous fungi have been sequenced. Interestingly, vast diversity in genome size was observed (Fig. 2.1) with 14-fold differences between the 9 Mb of the human pathogenic dandruff fungus (Malassezia globosa; Xu, Saunders, et al., 2007) and the 125 Mb of the ectomycorrhizal black truffle of P rigord (Tuber melanosporum; Martin, Kohler, et al., 2010). Recently, Raffaele and Kamoun (2012) highlighted that the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansion. Indeed, repeated elements are ubiquitous in all prokaryote and eukaryote genomes; however, their frequencies canmore » vary from just a minor percentage of the genome to more that 60 percent of the genome. Repeated elements can be classified in two major types: satellites DNA and transposable elements. In this chapter, the different types of repeated elements and how these elements can impact genome and gene repertoire will be described. Also, an intriguing link between the transposable elements richness and diversity and the ecological niche will be highlighted.« less

Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

PubMed

Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

2012-04-10

Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry. Copyright © 2012 Elsevier B.V. All rights reserved.

Waste biorefineries using filamentous ascomycetes fungi: Present status and future prospects.

PubMed

Ferreira, Jorge A; Mahboubi, Amir; Lennartsson, Patrik R; Taherzadeh, Mohammad J

2016-09-01

Filamentous ascomycetes fungi have had important roles in natural cycles, and are already used industrially for e.g. supplying of citric, gluconic and itaconic acids as well as many enzymes. Faster human activities result in higher consumption of our resources and producing more wastes. Therefore, these fungi can be explored to use their capabilities to convert back wastes to resources. The present paper reviews the capabilities of these fungi in growing on various residuals, producing lignocellulose-degrading enzymes and production of organic acids, ethanol, pigments, etc. Particular attention has been on Aspergillus, Fusarium, Neurospora and Monascus genera. Since various species are used for production of human food, their biomass can be considered for feed applications and so biomass compositional characteristics as well as aspects related to culture in bioreactor are also provided. The review has been further complemented with future research avenues. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Tolerance and biosorption of copper (Cu) and lead (Pb) by filamentous fungi isolated from a freshwater ecosystem.

PubMed

Iskandar, Nur Liyana; Zainudin, Nur Ain Izzati Mohd; Tan, Soon Guan

2011-01-01

Filamentous fungi are able to accumulate significant amount of metals from their environment. The potential of fungal biomass as agents for biosorption of heavy metals from contaminated sediments is currently receiving attention. In the present study, a total of 41 isolates of filamentous fungi obtained from the sediment of the Langat River, Selangor, Malaysia were screened for their tolerance and uptake capability of copper (Cu) and lead (Pb). The isolates were identified as Aspergillus niger, A. fumigatus, Trichoderma asperellum, Penicillium simplicissimum and P. janthinellum. A. niger and P. simplicissimum, were able to survive at 1000 mg/L of Cu(II) concentration on Potato Dextrose Agar (PDA) while for Pb, only A. niger survived at 5000 mg/L concentration. The results showed that A. niger, P. simplicissimum and T. asperellum have a better uptake capacity for Pb compared to Cu and the findings indicated promising biosorption of Cu and Pb by these filamentous fungi from aqueous solution. The present study was also determined the maximum removal of Cu(II) and Pb(II) that was performed by A. niger. The metal removal which occurred at Cu(II) 200 mg/L was (20.910 +/- 0.581) mg/g and at 250 mg/L of Pb(II) was (54.046 +/- 0.328) mg/g.

Incidence and distribution of filamentous fungi during fermentation, drying and storage of coffee (Coffea arabica L.) beans

PubMed Central

Silva, Cristina Ferreira; Batista, Luis Roberto; Schwan, Rosane Freitas

2008-01-01

The objective of this work was to isolate and characterize filamentous fungi present in different stages of harvest, fermentation, drying and storage of coffee beans processed by natural method. The cherries were hand-picked and then placed on a cement drying platform where they remained until reached 11% of humidity. Microbial counts were found in all samples during fermentation and drying of the coffee beans. Counts of fungi in the coffee cherries collected from the tree (time 0) were around 1.5 x 103 CFU/g. This number increased slowly during the fermentation and drying reaching values of 2 x 105 CFU/g within 22 days of processing. Two hundred and sixty three isolates of filamentous fungi were identified. The distribution of species during fermentation and drying was very varied while there was a predominance of Aspergillus species during storage period. The genera found were Pestalotia (4), Paecelomyces (4), Cladosporium (26), Fusarium (34), Penicillium (81) and Aspergillus (112) and comprised 38 different species. PMID:24031259

Aluminium leaching from red mud by filamentous fungi.

PubMed

Urík, Martin; Bujdoš, Marek; Milová-Žiaková, Barbora; Mikušová, Petra; Slovák, Marek; Matúš, Peter

2015-11-01

This contribution investigates the efficient and environmentally friendly aluminium leaching from red mud (bauxite residue) by 17 species of filamentous fungi. Bioleaching experiments were examined in batch cultures with the red mud in static, 7-day cultivation. The most efficient fungal strains in aluminium bioleaching were Penicillium crustosum G-140 and Aspergillus niger G-10. The A. niger G-10 strain was capable to extract up to approximately 141 mg·L(-1) of aluminium from 0.2 g dry weight red mud. Chemical leaching with organic acids mixture, prepared according to A. niger G-10 strain's respective fungal excretion during cultivation, proved that organic acids significantly contribute to aluminium solubilization from red mud. Copyright © 2015 Elsevier Inc. All rights reserved.

In Vitro Antifungal Activities of the New Triazole UR-9825 against Clinically Important Filamentous Fungi

PubMed Central

Capilla, Javier; Ortoneda, Montserrat; Pastor, Francisco Javier; Guarro, Josep

2001-01-01

We used a modified reference microdilution method (the M-38P method) to evaluate the in vitro activities of the new triazole UR-9825 in comparison with those of amphotericin B against 77 strains of opportunistic filamentous fungi. UR-9825 was clearly more active than amphotericin B against all fungi except Fusarium solani and Scytalidium spp. Notably, UR-9825 had low MICs for Aspergillus fumigatus and Paecilomyces lilacinus (MICs at which 90% of isolates are inhibited, 0.125 μg/ml for both species). PMID:11502542

Enhanced antioxidative activity of soybean koji prepared with various filamentous fungi.

PubMed

Lin, Chia-Hung; Wei, Yi-Tien; Chou, Cheng-Chun

2006-10-01

In the present study, soybean koji fermented with various GRAS filamentous fungi, including Aspergillus sojae BCRC 30103, Aspergillus oryzae BCRC 30222, Aspergillus awamori, Actinomucor taiwanensis and Rhizopus sp. These organisms are commonly used as starters in the fermentation of many traditional, oriental food products. The growth of starter organisms, total phenolic content, and antioxidative activities of the methanol extract of these kojis are compared with specific reference to alpha-diphenyl-2-picryl-hydrozyl (DPPH) radicals scavenging effects, Fe2+-chelating ability, and reducing power. Depending on starter organism, various extents of mycelia propagation (35.23-86.29 mg/g koji) were noted after 3 days of fermentation. Total phenolic content increased in soybean after fermentation. Koji also displayed enhanced antioxidative activates in comparison with the non-fermented soybean. Among the five kinds of koji tested, those fermented with Asp. awamori exhibited the highest levels of DPPH-free radicals scavenging activity, Fe2+-chelating ability and reducing power. The DPPH-free radicals scavenging activity and Fe2+-chelating ability of this soybean koji was ca. 8.9 and 6.7 fold that of the control. Analysis of the dose-response effect also revealed that before reaching a threshold point, there is a linear relationship between increases in antioxidative activity and increases in the concentration of the koji extract. These results show the potential for developing a healthy food supplement with soybean fermented by the GRAS filamentous fungi.

Survey and significance of filamentous fungi from tap water.

PubMed

Gonçalves, Ana B; Paterson, R Russell M; Lima, Nelson

2006-05-01

Fungi in drinking water are involved in the production of tastes and odours in water. Health problems are possible, originating from mycotoxins, animal pathogens and allergies. This report concerns the surveillance of mesophilic fungi in tap water and assessment of their potential for causing problems. The methods for the determination of the filamentous fungi (ff) were filtering, swabbing and baiting. Tap water, half-strength corn meal, neopeptone-glucose rose Bengal aureomycin (NGRBA) and oomycete selective agars for the enumeration of colony forming units (cfu) were used. Samples were taken consecutively over 16 months. Filtration and NGRBA gave the highest ff counts. A total of 340 taxa were isolated. There appeared to be a negative correlation between bacterial and yeast (b/y) and ff counts. Highest counts were found in winter months for ff and in the warmer months for b/y. Penicillium (40.6%) and Acremonium (38.8%) were the most frequently isolated ff. There was a difference in the pattern of isolation of the key taxa with season: penicillia predominated in early summer and Acremonium in winter. P. expansum was isolated in high numbers in May 2004. This species is associated with the production of the mycotoxin patulin and the odour secondary metabolite geosmin. P. brevicompactum was detected throughout the sampling period and is known to produce the immunosuppressive drug mycophenolic acid. Acremonium is associated with ocentol production which is responsible for bad tastes and flavours. The remaining taxa were Phialophora sp. (4.1%), Cladosporium sp. (3.5%), Rhizopus stolonifer (2.9%), Chaetomium sp. (0.6%), Alternaria sp. (0.3%), Aspergillus sp. (0.3%), mycelia sterilia (2.6%) and unidentified (6.2%). It is emphasised that few Aspergillus and no Fusarium strains were isolated. Rhizopus stolonifer was obtained. However, none of the fungi isolated at mesophilic temperature used could be described as being involved with pathogenicity per se.

Filamentous fungi associated with natural infection of noble rot on withered grapes.

PubMed

Lorenzini, M; Simonato, B; Favati, F; Bernardi, P; Sbarbati, A; Zapparoli, G

2018-05-02

The effects of noble rot infection of grapes on the characteristics of different types of wine, including Italian passito wine, are well known. Nevertheless, there is still little information on filamentous fungi associated with noble-rotten grapes. In this study, withered Garganega grapes for passito wine production, naturally infected by noble rot, were analyzed and compared to sound grapes. Skin morphology and fungal population on berry surfaces were analyzed. Scanning electron microscopy analysis revealed microcracks, germination conidia and branched hyphae on noble-rotten berries. Penicillium, Aureobasidium and Cladosporium were the most frequent genera present. Analysis of single berries displayed higher heterogeneity of epiphytic fungi in those infected by noble-rot than in sound berries. Penicillium adametzoides, Cladosporium cladospoirioides and Coniochaeta polymorpha were recovered. These, to the best of our knowledge, had never been previously isolated from withered grapes and, for C. polymorpha, from grapevine. This study provided novel data on noble rot mycobiota and suggests that fungi that co-habit with B. cinerea could have an important role on grape and wine quality. Copyright © 2018 Elsevier B.V. All rights reserved.

The importance of connections between the cell wall integrity pathway and the unfolded protein response in filamentous fungi.

PubMed

Malavazi, Iran; Goldman, Gustavo Henrique; Brown, Neil Andrew

2014-11-01

In the external environment, or within a host organism, filamentous fungi experience sudden changes in nutrient availability, osmolality, pH, temperature and the exposure to toxic compounds. The fungal cell wall represents the first line of defense, while also performing essential roles in morphology, development and virulence. A polarized secretion system is paramount for cell wall biosynthesis, filamentous growth, nutrient acquisition and interactions with the environment. The unique ability of filamentous fungi to secrete has resulted in their industrial adoption as fungal cell factories. Protein maturation and secretion commences in the endoplasmic reticulum (ER). The unfolded protein response (UPR) maintains ER functionality during exposure to secretion and cell wall stress. UPR, therefore, influences secretion and cell wall homeostasis, which in turn impacts upon numerous fungal traits important to pathogenesis and biotechnology. Subsequently, this review describes the relevance of the cell wall and UPR systems to filamentous fungal pathogens or industrial microbes and then highlights interconnections between the two systems. Ultimately, the possible biotechnological applications of an enhanced understanding of such regulatory systems in combating fungal disease, or the removal of natural bottlenecks in protein secretion in an industrial setting, are discussed. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A SIMPLE POLYMERASE CHAIN REACTION/RESTRICTION FRAGMENT LENGTH POLYMORPHISM ASSAY CAPABLE OF IDENTIFYING MEDICALLY RELEVANT FILAMENTOUS FUNGI

EPA Science Inventory

The accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result of abnormal growth of the filamentous fungi (mold) in and on buildign surfaces. In order to accurately reflect the organisms responsible for these maladies it is of...

Filamentous fungi as a source of natural antioxidants.

PubMed

Smith, Helen; Doyle, Sean; Murphy, Richard

2015-10-15

Ten species of filamentous fungi grown in submerged flask cultures were investigated for antioxidant capacity. Effective antioxidant activity was demonstrated in terms of β-carotene/linoleic acid bleaching, radical scavenging, reduction of metal ions and chelating abilities against ferrous ions. Different extraction methods affected antioxidant activities through their effect on biologically active compounds produced in fungal mycelia. The methanolic extract of each fungus was typically more effective in antioxidant properties. Phenolic content was established in the range of 0.44-9.33 mg/g, flavonoid contents were in the range of 0.02-3.90 mg/g and condensed tannin contents were in the range of 1.77-18.83 mg/g. Total phenol content of each extract was attributed to overall antioxidant capacity (r ⩾ 0.883-1.000). Submerged cultivation of Grifola frondosa, Monascus purpureus, Pleurotus spp., Lentinula edodes and Trametes versicolor proved to be an effective method for the production of natural antioxidants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conversion of Agricultural Streams and Food-Processing By-Products to Value-Added Compounds Using Filamentous Fungi.

PubMed

Chan, Lauryn G; Cohen, Joshua L; de Moura Bell, Juliana Maria Leite Nobrega

2018-03-25

The design of new food products and increased agricultural activities have produced a diversity of waste streams or by-products that contain a high load of organic matter. The underutilization of these streams presents a serious threat to the environment and to the financial viability of the agricultural sector and the food industry. Oleaginous microorganisms, such as yeast and microalgae, have been used to convert the organic matter present in many agricultural waste streams into an oil-rich biomass. Filamentous fungi are promising oleaginous microorganisms because of their high lipid accumulation potential and simple biomass recovery, the latter being related to their pellet-like growth morphology in submerged cultivation. This review highlights the use of oleaginous filamentous fungi to convert food by-products into value-added components, including the effect of cultivation conditions on biomass yield and composition. Special attention is given to downstream processing for the commercial production of fungal oil. Also discussed are innovative techniques to optimize the biomass oil yield and to minimize the challenges associated with biomass harvesting and oil extraction at industrial scale.

The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi.

PubMed

Frisvad, Jens C; Andersen, Birgitte; Thrane, Ulf

2008-02-01

A secondary metabolite is a chemical compound produced by a limited number of fungal species in a genus, an order, or even phylum. A profile of secondary metabolites consists of all the different compounds a fungus can produce on a given substratum and includes toxins, antibiotics and other outward-directed compounds. Chemotaxonomy is traditionally restricted to comprise fatty acids, proteins, carbohydrates, or secondary metabolites, but has sometimes been defined so broadly that it also includes DNA sequences. It is not yet possible to use secondary metabolites in phylogeny, because of the inconsistent distribution throughout the fungal kingdom. However, this is the very quality that makes secondary metabolites so useful in classification and identification. Four groups of organisms are particularly good producers of secondary metabolites: plants, fungi, lichen fungi, and actinomycetes, whereas yeasts, protozoa, and animals are less efficient producers. Therefore, secondary metabolites have mostly been used in plant and fungal taxonomy, whereas chemotaxonomy has been neglected in bacteriology. Lichen chemotaxonomy has been based on few biosynthetic families (chemosyndromes), whereas filamentous fungi have been analysed for a wide array of terpenes, polyketides, non-ribosomal peptides, and combinations of these. Fungal chemotaxonomy based on secondary metabolites has been used successfully in large ascomycete genera such as Alternaria, Aspergillus, Fusarium, Hypoxylon, Penicillium, Stachybotrys, Xylaria and in few basidiomycete genera, but not in Zygomycota and Chytridiomycota.

Identification and characterization of filamentous fungi isolated from fermentation starters for Hong Qu glutinous rice wine brewing.

PubMed

Lv, Xu-Cong; Huang, Zhi-Qing; Zhang, Wen; Rao, Ping-Fan; Ni, Li

2012-01-01

Hong Qu glutinous rice wine is one of the most popular traditional rice wines in China. Traditionally, this wine is brewed from glutinous rice with the addition of wine fermentation starters (Hong Qu (also called red yeast rice) and White Qu). The objective of this study was to investigate the variability of filamentous fungi associated with traditional fermentation starters through a traditional culture-dependent method and a molecular identification approach. In this study, forty-three filamentous fungi were separated by traditional culture-dependent means (macro- and microscopic characteristics) from 10 fermentation starters and classified into 16 different species based on morphological examination and the internal transcribed spacer (ITS) sequences analysis. It was observed that the genus Aspergillus had the highest number (14 isolates) of isolates followed by Rhizopus (11 isolates), Monascus (5 isolates) and Penicillium (4 isolates). The species R. oryzae, A. niger, A. flavus and M. purpureus were frequently found in wine starter samples, among which R. oryzae was the most frequent species. The enzyme-producing properties (glucoamylase, α-amylase and protease) of all fungal isolates from different starters were also evaluated. A. flavus, R. oryzae and M. purpureus were found to be better glucoamylase producers. A. flavus, R. oryzae and A.oryzae exhibited higher activity of α-amylase. A. flavus and A. oryzae had higher protease activity. However, some fungal isolates of the same species exhibited a significant variability in the production levels for all determined enzyme activity. This study is the first to identify filamentous fungi associated with the starter of Hong Qu glutinous rice wine using both traditional and molecular methods. The results enrich our knowledge of liquor-related micro-organisms, and can be used to promote the development of the traditional fermentation technology.

Mycelial pellet formation by edible ascomycete filamentous fungi, Neurospora intermedia.

PubMed

Nair, Ramkumar B; Lennartsson, Patrik R; Taherzadeh, Mohammad J

2016-12-01

Pellet formation of filamentous fungi in submerged culture is an imperative topic of fermentation research. In this study, we report for the first time the growth of filamentous ascomycete fungus, Neurospora intermedia in its mycelial pellet form. In submerged culture, the growth morphology of the fungus was successfully manipulated into growing as pellets by modifying various cultivation conditions. Factors such as pH (2.0-10.0), agitation rate (100-150 rpm), carbon source (glucose, arabinose, sucrose, and galactose), the presence of additive agents (glycerol and calcium chloride) and trace metals were investigated for their effect on the pellet formation. Of the various factors screened, uniform pellets were formed only at pH range 3.0-4.0, signifying it as the most influential factor for N. intermedia pellet formation. The average pellet size ranged from 2.38 ± 0.12 to 2.86 ± 0.38 mm. The pellet formation remained unaffected by the inoculum type used and its size showed an inverse correlation with the agitation rate of the culture. Efficient glucose utilization was observed with fungal pellets, as opposed to the freely suspended mycelium, proving its viability for fast-fermentation processes. Scale up of the pelletization process was also carried out in bench-scale airlift and bubble column reactors (4.5 L).

[The research and application of pretreatment method for matrix-assisted laser desorption ionization-time of flight mass spectrometry identification of filamentous fungi].

PubMed

Huang, Y F; Chang, Z; Bai, J; Zhu, M; Zhang, M X; Wang, M; Zhang, G; Li, X Y; Tong, Y G; Wang, J L; Lu, X X

2017-08-08

Objective: To establish and evaluate the feasibility of a pretreatment method for matrix-assisted laser desorption ionization-time of flight mass spectrometry identification of filamentous fungi developed by the laboratory. Methods: Three hundred and eighty strains of filamentous fungi from January 2014 to December 2016 were recovered and cultured on sabouraud dextrose agar (SDA) plate at 28 ℃ to mature state. Meanwhile, the fungi were cultured in liquid sabouraud medium with a vertical rotation method recommended by Bruker and a horizontal vibration method developed by the laboratory until adequate amount of colonies were observed. For the strains cultured with the three methods, protein was extracted with modified magnetic bead-based extraction method for mass spectrum identification. Results: For 380 fungi strains, it took 3-10 d to culture with SDA culture method, and the ratio of identification of the species and genus was 47% and 81%, respectively; it took 5-7 d to culture with vertical rotation method, and the ratio of identification of the species and genus was 76% and 94%, respectively; it took 1-2 d to culture with horizontal vibration method, and the ratio of identification of the species and genus was 96% and 99%, respectively. For the comparison between horizontal vibration method and SDA culture method comparison, the difference was statistically significant (χ(2)=39.026, P <0.01); for the comparison between horizontal vibration method and vertical rotation method recommended by Bruker, the difference was statistically significant(χ(2)=11.310, P <0.01). Conclusion: The horizontal vibration method and modified magnetic bead-based extraction method developed by the laboratory is superior to the method recommended by Bruker and SDA culture method in terms of the identification capacity for filamentous fungi, which can be applied in clinic.

NEW OBSERVATION OF FAILED FILAMENT ERUPTIONS: THE INFLUENCE OF ASYMMETRIC CORONAL BACKGROUND FIELDS ON SOLAR ERUPTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Y.; Xu, Z.; Su, J.

2009-05-01

Failed filament eruptions not associated with a coronal mass ejection (CME) have been observed and reported as evidence for solar coronal field confinement on erupting flux ropes. In those events, each filament eventually returns to its origin on the solar surface. In this Letter, a new observation of two failed filament eruptions is reported which indicates that the mass of a confined filament can be ejected to places far from the original filament channel. The jetlike mass motions in the two failed filament eruptions are thought to be due to the asymmetry of the background coronal magnetic fields with respectmore » to the locations of the filament channels. The asymmetry of the coronal fields is confirmed by an extrapolation based on a potential field model. The obvious imbalance between the positive and negative magnetic flux (with a ratio of 1:3) in the bipolar active region is thought to be the direct cause of the formation of the asymmetric coronal fields. We think that the asymmetry of the background fields can not only influence the trajectories of ejecta, but also provide a relatively stronger confinement for flux rope eruptions than the symmetric background fields do.« less

Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds.

PubMed

Lecellier, A; Gaydou, V; Mounier, J; Hermet, A; Castrec, L; Barbier, G; Ablain, W; Manfait, M; Toubas, D; Sockalingum, G D

2015-02-01

Filamentous fungi may cause food and feed spoilage and produce harmful metabolites to human and animal health such as mycotoxins. Identification of fungi using conventional phenotypic methods is time-consuming and molecular methods are still quite expensive and require specific laboratory skills. In the last two decades, it has been shown that Fourier transform infrared (FTIR) spectroscopy was an efficient tool for microorganism identification. The aims of this study were to use a simple protocol for the identification of filamentous fungi using FTIR spectroscopy coupled with a partial least squares discriminant analysis (PLS-DA), to implement a procedure to validate the obtained results, and to assess the transferability of the method and database. FTIR spectra of 486 strains (43 genera and 140 species) were recorded. An IR spectral database built with 288 strains was used to identify 105 different strains. It was found that 99.17% and 92.3% of spectra derived from these strains were correctly assigned at the genus and species levels, respectively. The establishment of a score and a threshold permitted to validate 80.79% of the results obtained. A standardization function (SF) was also implemented and tested on FTIR data from another instrument on a different site and permitted to increase the percentage of well predicted spectra for this set from 72.15% to 89.13%. This study confirms the good performance of high throughput FTIR spectroscopy for fungal identification using a spectral library of molds of industrial relevance. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of phenanthrene removal by Aspergillus niger ATC 16404 (filamentous fungi) and Pseudomonas putida KT2442 (bacteria) in enriched nutrient-liquid medium

NASA Astrophysics Data System (ADS)

Hamzah, N.; Kamil, N. A. F. M.; Singhal, N.; Padhye, L.; Swift, S.

2018-04-01

Polycyclic Aromatic Hydrocarbons (PAHs) is one of the persistent and carcinogenic pollutants that needs to be eliminated from the environment. The study on degradation of PAHs by bacteria is thoroughly discussed in literature. Many strains of bacteria were chosen in order to eliminate the PAHs compound in the environment. However, there are less study on the filamentous fungi although fungi appears to be an abundant population and as dominant group in PAHs contaminated soil habitats [1], [2]. This study was conducted to determine and compare the Phenanthrene (PHE) removal by fungi and bacteria in excessive nutrient-liquid culture. Then, the survival for both strains was investigated in the presence of PHE and finally, the analysis on the fungi-PHE interaction was carried out. In condition of excessive nutrient, the removal of PHE was evaluated for fungi and bacteria in batch experiment for 5 days. PHE removal for A.niger and P.putida were found to be 97% and 20% respectively after 5 days. The presence of PHE was negatively inhibits the grow of the bacteria and the fungus. The PHE uptake mechanism for A.niger was observed to be a passive transport mechanism with 45 μg per g fungus dry weight within 24 hr of incubation. As a conclusion, filamentous fungi have the potent role in the removal of PHE as well as bacteria but depending on the strains and the condition of the environment. Fungi is known to co-metabolize the PHE meanwhile, PHE can be used as sole carbon for bacteria. This preliminary result is significant in understanding the bacteria-fungi-PHE interaction to enhance the degradation of PAHs for co-culture study in the future.

Secretome-based Manganese(II) Oxidation by Filamentous Ascomycete Fungi

NASA Astrophysics Data System (ADS)

Zeiner, C. A.; Purvine, S.; Zink, E.; Paša-Tolić, L.; Chaput, D.; Wu, S.; Santelli, C. M.; Hansel, C. M.

2017-12-01

Manganese (Mn) oxides are among the strongest oxidants in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and Mn peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Through a combination of chemical and in-gel assays, bulk mass spectrometry, and iTRAQ proteomics, we demonstrate enzymatic Mn(II) oxidation in the secretomes of three phylogenetically diverse Ascomycetes that were isolated from Mn-laden sediments. Candidate Mn(II)-oxidizing enzymes were species-specific and included bilirubin oxidase and tyrosinase in Stagonospora sp. SRC1lsM3a, GMC oxidoreductase in Paraconiothyrium sporulosum AP3s5-JAC2a, and FAD-binding oxidoreductases in Pyrenochaeta sp. DS3sAY3a. These findings were supported by full proteomic characterization of the secretomes, which revealed a lack of Mn, lignin, and versatile peroxidases in these Ascomycetes but a substantially higher proportion of LMCOs and GMC oxidoreductases compared to wood-rot Basidiomycetes. We also identified the potential for indirect enzymatic Mn(II) oxidation by hydroxyl radical, as the secretomes were rich in diverse lignocellulose-degrading enzymes that could participate in Fenton chemistry. A link between Mn(II) oxidation and carbon oxidation analogous to white-rot Basidiomycetes remains unknown in these Ascomycetes. Interestingly, growth rates on rich medium were unaffected by the presence of Mn(II), and the production of Mn(II)-oxidizing proteins in the secretome was constitutive and not inducible by Mn(II). Thus, no physiological benefit of Mn(II) oxidation in these Ascomycetes has yet been identified, and Mn(II) oxidation appears to be a side reaction. Future work will explore the lignin-degrading capacity of

Emerging infections due to filamentous fungi in humans and animals: only the tip of the iceberg?

PubMed

Debourgogne, Anne; Dorin, Joséphine; Machouart, Marie

2016-06-01

Over the last few decades, the number of patients susceptible to invasive filamentous fungal infections has steadily increased, especially in populations suffering from hematological diseases. The pathogens responsible for such mycoses are now quite well characterized, such as Aspergillus spp. - the most commonly isolated mold -, Mucorales, Fusarium spp., Scedosporium spp. or melanized fungi. An increase in the incidence of this category of 'emerging' fungi has been recently highlighted, evoking a shift in fungal ecology. Starting from these medical findings, taking a step back and adopt a wider perspective offers possible explanations of this phenomenon on an even larger scale than previously reported. In this review, we illustrate the link between emerging fungi in medicine and changes in ecology or human behaviours, and we encourage integrative approaches to apprehend the adverse effects of progress and develop preventive measures in vast domains, such as agriculture or medicine. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Biotransformation of labdane and halimane diterpenoids by two filamentous fungi strains

PubMed Central

Seidl, Cláudia; Severino, Vanessa G. P.; Cardoso, Carmen Lúcia; Castro-Gamboa, Ian

2017-01-01

Biotransformation of natural products by filamentous fungi is a powerful and effective approach to achieve derivatives with valuable new chemical and biological properties. Although diterpenoid substrates usually exhibit good susceptibility towards fungi enzymes, there have been no studies concerning the microbiological transformation of halimane-type diterpenoids up to now. In this work, we investigated the capability of Fusarium oxysporum (a fungus isolated from the rhizosphere of Senna spectabilis) and Myrothecium verrucaria (an endophyte) to transform halimane (1) and labdane (2) acids isolated from Hymenaea stigonocarpa (Fabaceae). Feeding experiments resulted in the production of six derivatives, including hydroxy, oxo, formyl and carboxy analogues. Incubation of 1 with F. oxysporum afforded 2-oxo-derivative (3), while bioconversion with M. verrucaria provided 18,19-dihydroxy (4), 18-formyl (5) and 18-carboxy (6) bioproducts. Transformation of substrate 2 mediated by F. oxysporum produced a 7α-hydroxy (7) derivative, while M. verrucaria yielded 7α- (7) and 3β-hydroxy (8) metabolites. Unlike F. oxysporum, which showed a preference to transform ring B, M. verrucaria exhibited the ability to hydroxylate both rings A and B from substrate 2. Additionally, compounds 1–8 were evaluated for inhibitory activity against Hr-AChE and Hu-BChE enzymes through ICER-IT-MS/MS assay. PMID:29291077

Biotransformation of labdane and halimane diterpenoids by two filamentous fungi strains.

PubMed

Monteiro, Afif F; Seidl, Cláudia; Severino, Vanessa G P; Cardoso, Carmen Lúcia; Castro-Gamboa, Ian

2017-11-01

Biotransformation of natural products by filamentous fungi is a powerful and effective approach to achieve derivatives with valuable new chemical and biological properties. Although diterpenoid substrates usually exhibit good susceptibility towards fungi enzymes, there have been no studies concerning the microbiological transformation of halimane-type diterpenoids up to now. In this work, we investigated the capability of Fusarium oxysporum (a fungus isolated from the rhizosphere of Senna spectabilis ) and Myrothecium verrucaria (an endophyte) to transform halimane ( 1 ) and labdane ( 2 ) acids isolated from Hymenaea stigonocarpa (Fabaceae). Feeding experiments resulted in the production of six derivatives, including hydroxy, oxo, formyl and carboxy analogues. Incubation of 1 with F. oxysporum afforded 2-oxo-derivative ( 3 ), while bioconversion with M. verrucaria provided 18,19-dihydroxy ( 4 ), 18-formyl ( 5 ) and 18-carboxy ( 6 ) bioproducts. Transformation of substrate 2 mediated by F. oxysporum produced a 7 α -hydroxy ( 7 ) derivative, while M. verrucaria yielded 7 α - ( 7 ) and 3 β -hydroxy ( 8 ) metabolites. Unlike F. oxysporum , which showed a preference to transform ring B, M. verrucaria exhibited the ability to hydroxylate both rings A and B from substrate 2 . Additionally, compounds 1 - 8 were evaluated for inhibitory activity against Hr-AChE and Hu-BChE enzymes through ICER-IT-MS/MS assay.

Proteome studies of filamentous fungi.

PubMed

Baker, Scott E; Panisko, Ellen A

2011-01-01

The continued fast pace of fungal genome sequence generation has enabled proteomic analysis of a wide variety of organisms that span the breadth of the Kingdom Fungi. There is some phylogenetic bias to the current catalog of fungi with reasonable DNA sequence databases (genomic or EST) that could be analyzed at a global proteomic level. However, the rapid development of next generation sequencing platforms has lowered the cost of genome sequencing such that in the near future, having a genome sequence will no longer be a time or cost bottleneck for downstream proteomic (and transcriptomic) analyses. High throughput, nongel-based proteomics offers a snapshot of proteins present in a given sample at a single point in time. There are a number of variations on the general methods and technologies for identifying peptides in a given sample. We present a method that can serve as a "baseline" for proteomic studies of fungi.

[Identification of filamentous fungi isolated from clinical samples by two different methods and their susceptibility results].

PubMed

Direkel, Sahin; Otağ, Feza; Aslan, Gönül; Ulger, Mahmut; Emekdaş, Gürol

2012-01-01

Molds are widely distributed in nature. Aspergillus spp. represent the most frequently observed causative agents, however less frequent pathogens Fusarium, Scedosporium and Zygomycetes have also been considered the most important causes of morbidity and mortality in profoundly immunosuppressed hosts. The aims of this study were to identify filamentous fungi isolated from clinical specimens by conventional and molecular methods, and to detect their antifungal susceptibilities. A total of 6742 clinical specimens obtained from hospitalized patients at critical units of Mersin University Medical Faculty Hospital and sent to our laboratory between April 2008-January 2010 were included in the study. The isolates were identified by classical mycological methods and polymerase chain reaction-based DNA sequencing. Susceptibilities to fluconazole and voriconazole were tested by disk diffusion method and to fluconazole, voriconazole, amfoterisin B, caspofungin and posaconazole by E-test. Filamentous fungi were isolated from 71 (1.05%) samples (13 sputum, 4 wound, 4 peritoneal fluid, 3 extrenal ear discharge, 3 abscess and one of each cerebrospinal fluid, blood, tissue biopsy, nasal swab and conjunctival swab) which belonged to 32 patients (13 female, 19 male; age range 7 months-77 years, mean age: 46.6 years). Of the patients 62.3% presented one or more risk factors such as chronic renal failure (n= 8), chronic obstructive lung disease (n= 6), malignancy (n= 6), diabetes mellitus (n= 5) and peripheral vascular disease (n= 5). Of the isolates six were identified as Aspergillus niger, six as Aspergillus flavus, five as Aspergillus fumigatus, four as Aspergillus terreus, five as Fusarium spp., two as Bipolaris spp., and one of each as Acremonium spp., Aurebasidium spp., Mucor spp., and Scedosporium spp. By conventional methods. Three isolates exhibited different identities by DNA sequencing. All Aspergillus isolates were correctly identified at species level by both methods

Toxins of filamentous fungi.

PubMed

Bhatnagar, Deepak; Yu, Jiujiang; Ehrlich, Kenneth C

2002-01-01

Mycotoxins are low-molecular-weight secondary metabolites of fungi. The most significant mycotoxins are contaminants of agricultural commodities, foods and feeds. Fungi that produce these toxins do so both prior to harvest and during storage. Although contamination of commodities by toxigenic fungi occurs frequently in areas with a hot and humid climate (i.e. conditions favorable for fungal growth), they can also be found in temperate conditions. Production of mycotoxins is dependent upon the type of producing fungus and environmental conditions such as the substrate, water activity (moisture and relative humidity), duration of exposure to stress conditions and microbial, insect or other animal interactions. Although outbreaks of mycotoxicoses in humans have been documented, several of these have not been well characterized, neither has a direct correlation between the mycotoxin and resulting toxic effect been well established in vivo. Even though the specific modes of action of most of the toxins are not well established, acute and chronic effects in prokaryotic and eukaryotic systems, including humans have been reported. The toxicity of the mycotoxins varies considerably with the toxin, the animal species exposed to it, and the extent of exposure, age and nutritional status. Most of the toxic effects of mycotoxins are limited to specific organs, but several mycotoxins affect many organs. Induction of cancer by some mycotoxins is a major concern as a chronic effect of these toxins. It is nearly impossible to eliminate mycotoxins from the foods and feed in spite of the regulatory efforts at the national and international levels to remove the contaminated commodities. This is because mycotoxins are highly stable compounds, the producing fungi are ubiquitous, and food contamination can occur both before and after harvest. Nevertheless, good farm management practices and adequate storage facilities minimize the toxin contamination problems. Current research is

Similar is not the same: differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi.

PubMed

Klaubauf, Sylvia; Narang, Hari Mander; Post, Harm; Zhou, Miaomiao; Brunner, Kurt; Mach-Aigner, Astrid R; Mach, Robert L; Heck, Albert J R; Altelaar, A F Maarten; de Vries, Ronald P

2014-11-01

The transcriptional activator XlnR (Xlr1/Xyr1) is a major regulator in fungal xylan and cellulose degradation as well as in the utilization of d-xylose via the pentose catabolic pathway. XlnR homologs are commonly found in filamentous ascomycetes and often assumed to have the same function in different fungi. However, a comparison of the saprobe Aspergillus niger and the plant pathogen Magnaporthe oryzae showed different phenotypes for deletion strains of XlnR. In this study wild type and xlnR/xlr1/xyr1 mutants of five fungi were compared: Fusarium graminearum, M. oryzae, Trichoderma reesei, A. niger and Aspergillus nidulans. Growth profiling on relevant substrates and a detailed analysis of the secretome as well as extracellular enzyme activities demonstrated a common role of this regulator in activating genes encoding the main xylanolytic enzymes. However, large differences were found in the set of genes that is controlled by XlnR in the different species, resulting in the production of different extracellular enzyme spectra by these fungi. This comparison emphasizes the functional diversity of a fine-tuned (hemi-)cellulolytic regulatory system in filamentous fungi, which might be related to the adaptation of fungi to their specific biotopes. Data are available via ProteomeXchange with identifier PXD001190. Copyright © 2014 Elsevier Inc. All rights reserved.

Unfolded protein response in filamentous fungi-implications in biotechnology.

PubMed

Heimel, Kai

2015-01-01

The unfolded protein response (UPR) represents a mechanism to preserve endoplasmic reticulum (ER) homeostasis that is conserved in eukaryotes. ER stress caused by the accumulation of potentially toxic un- or misfolded proteins in the ER triggers UPR activation and the induction of genes important for protein folding in the ER, ER expansion, and transport from and to the ER. Along with this adaptation, the overall capacity for protein secretion is markedly increased by the UPR. In filamentous fungi, various approaches to employ the UPR for improved production of homologous and heterologous proteins have been investigated. As the effects on protein production were strongly dependent on the expressed protein, generally applicable strategies have to be developed. A combination of transcriptomic approaches monitoring secretion stress and basic research on the UPR mechanism provided novel and important insight into the complex regulatory cross-connections between UPR signalling, cellular physiology, and developmental processes. It will be discussed how this increasing knowledge on the UPR might stimulate the development of novel strategies for using the UPR as a tool in biotechnology.

Proteome Studies of Filamentous Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, Scott E.; Panisko, Ellen A.

2011-04-20

The continued fast pace of fungal genome sequence generation has enabled proteomic analysis of a wide breadth of organisms that span the breadth of the Kingdom Fungi. There is some phylogenetic bias to the current catalog of fungi with reasonable DNA sequence databases (genomic or EST) that could be analyzed at a global proteomic level. However, the rapid development of next generation sequencing platforms has lowered the cost of genome sequencing such that in the near future, having a genome sequence will no longer be a time or cost bottleneck for downstream proteomic (and transcriptomic) analyses. High throughput, non-gel basedmore » proteomics offers a snapshot of proteins present in a given sample at a single point in time. There are a number of different variations on the general method and technologies for identifying peptides in a given sample. We present a method that can serve as a “baseline” for proteomic studies of fungi.« less

Comparison of six extraction techniques for isolation of DNA from filamentous fungi.

PubMed

van Burik, J A; Schreckhise, R W; White, T C; Bowden, R A; Myerson, D

1998-10-01

Filamentous fungi have a sturdy cell wall which is resistant to the usual DNA extraction procedures. We determined the DNA extraction procedure with the greatest yield of high quality fungal DNA and the least predilection for cross-contamination of equipment between specimens. Each of six extraction methods was performed using Aspergillus fumigatus hyphae. The six methods were: (1) glass bead pulverization with vortexing; (2) grinding with mortar and pestle followed by glass bead pulverization; (3) glass bead pulverization using 1% hydroxyacetyl trimethyl ammonium bromide (CTAB) buffer in a water bath sonicator; (4) water bath sonication in CTAB buffer; (5) grinding followed by incubation with CTAB; and (6) lyticase enzymatic cell lysis. Genomic DNA yields were measured by spectrophotometry and by visual reading of 2% agarose gels, with shearing assessed by the migration of the DNA on the gel. Genomic fungal DNA yields were highest for Method 1, followed by Methods 5 approximately = to 2 >3 approximately = to 4 approximately = to 6. Methods 2 and 5, both of which involved grinding with mortar and pestle, led to shearing of the genomic DNA in one of two trials each. We conclude that the use of glass beads with extended vortexing is optimal for extraction of microgramme amounts of DNA from filamentous fungal cultures.

Potential bioremediation of mercury-contaminated substrate using filamentous fungi isolated from forest soil.

PubMed

Kurniati, Evi; Arfarita, Novi; Imai, Tsuyoshi; Higuchi, Takaya; Kanno, Ariyo; Yamamoto, Koichi; Sekine, Masahiko

2014-06-01

The use of filamentous fungi in bioremediation of heavy metal contamination has been developed recently. This research aims to observe the capability of filamentous fungi isolated from forest soil for bioremediation of mercury contamination in a substrate. Six fungal strains were selected based on their capability to grow in 25 mg/L Hg(2+)-contaminated potato dextrose agar plates. Fungal strain KRP1 showed the highest ratio of growth diameter, 0.831, thus was chosen for further observation. Identification based on colony and cell morphology carried out by 18S rRNA analysis gave a 98% match to Aspergillus flavus strain KRP1. The fungal characteristics in mercury(II) contamination such as range of optimum pH, optimum temperature and tolerance level were 5.5-7 and 25-35°C and 100 mg/L respectively. The concentration of mercury in the media affected fungal growth during lag phases. The capability of the fungal strain to remove the mercury(II) contaminant was evaluated in 100 mL sterile 10 mg/L Hg(2+)-contaminated potato dextrose broth media in 250 mL Erlenmeyer flasks inoculated with 10(8) spore/mL fungal spore suspension and incubation at 30°C for 7 days. The mercury(II) utilization was observed for flasks shaken in a 130 r/min orbital shaker (shaken) and non-shaken flasks (static) treatments. Flasks containing contaminated media with no fungal spores were also provided as control. All treatments were done in triplicate. The strain was able to remove 97.50% and 98.73% mercury from shaken and static systems respectively. A. flavus strain KRP1 seems to have potential use in bioremediation of aqueous substrates containing mercury(II) through a biosorption mechanism. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Potentially toxic filamentous fungi associated to the economically important Nodipecten nodosus (Linnaeus, 1758) scallop farmed in southeastern Rio de Janeiro, Brazil.

PubMed

Santos, Antônia; Hauser-Davis, Rachel Ann; Santos, Manoel José Soares; De Simone, Salvatore Giovani

2017-02-15

Numerous countries have been confronted with infectious diseases in mariculture activities, including fungi infections, although reports in scallops are scarce. Thus, this study aimed to investigate the occurrence of filamentous fungi in Nodipecten nodosus specimens from three marine farms in Southeastern Brazil. Eight fungi genera were observed in the branchial arches, intestine and muscle tissue of the scallop specimens. These include potentially toxin-producing species, such as Aspergillus, Penicillium and Fusarium. Their presence may lead to potential public health concerns, since all sampling sites showed the presence of fungi in all scallop organs, with special concern regarding edible muscle tissue. A significant number of species was observed at one of the study areas, which could indicate a previously unknown source of contamination, since increases in fungi species richness in polluted coastal waters have been reported. This is also, to the best of our knowledge, the first report of Pestalotiopsis in shellfish. Copyright © 2016 Elsevier Ltd. All rights reserved.

Current state and future perspectives of loop-mediated isothermal amplification (LAMP)-based diagnosis of filamentous fungi and yeasts.

PubMed

Niessen, Ludwig

2015-01-01

Loop-mediated isothermal amplification is a rather novel method of enzymatic deoxyribonucleic acid amplification which can be applied for the diagnosis of viruses, bacteria, and fungi. Although firmly established in viral and bacterial diagnosis, the technology has only recently been applied to a noteworthy number of species in the filamentous fungi and yeasts. The current review gives an overview of the literature so far published on the topic by discussing the different groups of fungal organisms to which the method has been applied. Moreover, the method is described in detail as well as the different possibilities available for signal detection and quantification and sample preparation. Future perspective of loop-mediated isothermal amplification-based assays is discussed in the light of applicability for fungal diagnostics.

Aspergillus oryzae AoSO is a novel component of stress granules upon heat stress in filamentous fungi.

PubMed

Huang, Hsiang-Ting; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

2013-01-01

Stress granules are a type of cytoplasmic messenger ribonucleoprotein (mRNP) granule formed in response to the inhibition of translation initiation, which typically occurs when cells are exposed to stress. Stress granules are conserved in eukaryotes; however, in filamentous fungi, including Aspergillus oryzae, stress granules have not yet been defined. For this reason, here we investigated the formation and localization of stress granules in A. oryzae cells exposed to various stresses using an EGFP fusion protein of AoPab1, a homolog of Saccharomyces cerevisiae Pab1p, as a stress granule marker. Localization analysis showed that AoPab1 was evenly distributed throughout the cytoplasm under normal growth conditions, and accumulated as cytoplasmic foci mainly at the hyphal tip in response to stress. AoSO, a homolog of Neurospora crassa SO, which is necessary for hyphal fusion, colocalized with stress granules in cells exposed to heat stress. The formation of cytoplasmic foci of AoSO was blocked by treatment with cycloheximide, a known inhibitor of stress granule formation. Deletion of the Aoso gene had effects on the formation and localization of stress granules in response to heat stress. Our results suggest that AoSO is a novel component of stress granules specific to filamentous fungi. The authors would specially like to thank Hiroyuki Nakano and Kei Saeki for generously providing experimental and insightful opinions.

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi.

PubMed

Hilber-Bodmer, Maja; Schmid, Michael; Ahrens, Christian H; Freimoser, Florian M

2017-01-05

While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes. Overall, this competition screen of 640 pairwise combinations revealed a broad range of outcomes, ranging from small stimulatory effects of some yeasts up to a growth inhibition of more than 80% by individual species. On average, yeasts isolated from soil suppressed filamentous fungi more strongly than phyllosphere yeasts and the antagonistic activity was a species-/isolate-specific property and not dependent on the filamentous fungus a yeast was interacting with. The isolates with the strongest antagonistic activity were Metschnikowia pulcherrima, Hanseniaspora sp., Cyberlindnera sargentensis, Aureobasidium pullulans, Candida subhashii, and Pichia kluyveri. Among these, the soil yeasts (C. sargentensis, A. pullulans, C. subhashii) assimilated and/or oxidized more di-, tri- and tetrasaccharides and organic acids than yeasts from the phyllosphere. Only the two yeasts C. subhashii and M. pulcherrima were able to grow with N-acetyl-glucosamine as carbon source. The competition assays and physiological experiments described here identified known antagonists that have been implicated in the biological control of plant pathogenic fungi in the past, but also little characterised species such as C. subhashii. Overall, soil yeasts were more antagonistic and metabolically versatile than yeasts from

How peroxisomes partition between cells. A story of yeast, mammals and filamentous fungi.

PubMed

Knoblach, Barbara; Rachubinski, Richard A

2016-08-01

Eukaryotic cells are subcompartmentalized into discrete, membrane-enclosed organelles. These organelles must be preserved in cells over many generations to maintain the selective advantages afforded by compartmentalization. Cells use complex molecular mechanisms of organelle inheritance to achieve high accuracy in the sharing of organelles between daughter cells. Here we focus on how a multi-copy organelle, the peroxisome, is partitioned in yeast, mammalian cells, and filamentous fungi, which differ in their mode of cell division. Cells achieve equidistribution of their peroxisomes through organelle transport and retention processes that act coordinately, although the strategies employed vary considerably by organism. Nevertheless, we propose that mechanisms common across species apply to the partitioning of all membrane-enclosed organelles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Light regulation on growth, development, and secondary metabolism of marine-derived filamentous fungi.

PubMed

Cai, Menghao; Fang, Zhe; Niu, Chuanpeng; Zhou, Xiangshan; Zhang, Yuanxing

2013-11-01

Effects of different light conditions on development, growth, and secondary metabolism of three marine-derived filamentous fungi were investigated. Darkness irritated sexual development of Aspergillus glaucus HB1-19, while white, red, and blue lights improved its asexual behavior. The red and blue lights improved asexual stroma formation of Xylaria sp. (no. 2508), but the darkness and white light inhibited it. Differently, development of Halorosellinia sp. (no. 1403) turned out to be insensitive to any tested light irradiation. Upon the experimental data, no regularity was observed linking development with secondary metabolism. However, fungal growth showed inversely correlation with productions of major bioactive compounds (aspergiolide A, 1403C, and xyloketal B) from various strains. The results indicated that aspergiolide A biosynthesis favored blue light illumination, while 1403C and xyloketal B preferred red light irradiation. With the favorite light sensing conditions, productions of aspergiolide A, 1403C, and xyloketal B were enhanced by 32.9, 21.9, and 30.8 % compared with those in the dark, respectively. The phylogenetic analysis comparing the light-responding proteins of A. glaucus HB 1-19 with those in other systems indicated that A. glaucus HB 1-19 was closely related to Aspergillus spp. especially A. nidulans in spite of its role of marine-derived fungus. It indicated that marine fungi might conserve its light response system when adapting the marine environment. This work also offers useful information for process optimization involving light regulation on growth and metabolism for drug candidate production from light-sensitive marine fungi.

Controlling filamentous fungi morphology with microparticles to enhanced β-mannanase production.

PubMed

Yatmaz, Ercan; Karahalil, Ercan; Germec, Mustafa; Ilgin, Merve; Turhan, İrfan

2016-09-01

β-mannanase was produced mainly by Aspergillus species and can degrade the β-1,4-mannose linkages of galactomannans. This study was undertaken to enhance mannanase production using talcum and aluminum oxide as the microparticles, which control cell morphology of recombinant Aspergillus sojae in glucose and carob extract medium. Both microparticles improved fungal growth in glucose and carob pod extract medium. Aluminum oxide (1 g/L) was the best agent for glucose medium which resulted in 514.0 U/ml. However, the highest mannanase activity was found as 568.7 U/ml with 5 g/L of talcum in carob extract medium. Increase in microparticle concentration resulted in decreasing the pellet size diameter. Furthermore, more than 10 g/L of talcum addition changed the filamentous fungi growth type from pellet to pellet/mycelium mixture. Results showed that right type and concentration of microparticle in fermentation media improved the mannanase activity and production rate by controlling the growth morphology.

Transformation in fungi.

PubMed Central

Fincham, J R

1989-01-01

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater

In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Mosier, Annika

2018-01-22

Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, CA.

Use of Laccase as a Novel, Versatile Reporter System in Filamentous Fungi

PubMed Central

Mander, Gerd J.; Wang, Huaming; Bodie, Elizabeth; Wagner, Jens; Vienken, Kay; Vinuesa, Claudia; Foster, Caroline; Leeder, Abigail C.; Allen, Gethin; Hamill, Valerie; Janssen, Giselle G.; Dunn-Coleman, Nigel; Karos, Marvin; Lemaire, Hans Georg; Subkowski, Thomas; Bollschweiler, Claus; Turner, Geoffrey; Nüsslein, Bernhard; Fischer, Reinhard

2006-01-01

Laccases are copper-containing enzymes which oxidize phenolic substrates and transfer the electrons to oxygen. Many filamentous fungi contain several laccase-encoding genes, but their biological roles are mostly not well understood. The main interest in laccases in biotechnology is their potential to be used to detoxify phenolic substances. We report here on a novel application of laccases as a reporter system in fungi. We purified a laccase enzyme from the ligno-cellulolytic ascomycete Stachybotrys chartarum. It oxidized the artificial substrate 2,2′-azino-di-(3-ethylbenzthiazolinsulfonate) (ABTS). The corresponding gene was isolated and expressed in Aspergillus nidulans, Aspergillus niger, and Trichoderma reesei. Heterologously expressed laccase activity was monitored in colorimetric enzyme assays and on agar plates with ABTS as a substrate. The use of laccase as a reporter was shown in a genetic screen for the isolation of improved T. reesei cellulase production strains. In addition to the laccase from S. charatarum, we tested the application of three laccases from A. nidulans (LccB, LccC, and LccD) as reporters. Whereas LccC oxidized ABTS (Km = 0.3 mM), LccD did not react with ABTS but with DMA/ADBP (3,5-dimethylaniline/4-amino-2,6-dibromophenol). LccB reacted with DMA/ADBP and showed weak activity with ABTS. The different catalytic properties of LccC and LccD allow simultaneous use of these two laccases as reporters in one fungal strain. PMID:16820501

Use of laccase as a novel, versatile reporter system in filamentous fungi.

PubMed

Mander, Gerd J; Wang, Huaming; Bodie, Elizabeth; Wagner, Jens; Vienken, Kay; Vinuesa, Claudia; Foster, Caroline; Leeder, Abigail C; Allen, Gethin; Hamill, Valerie; Janssen, Giselle G; Dunn-Coleman, Nigel; Karos, Marvin; Lemaire, Hans Georg; Subkowski, Thomas; Bollschweiler, Claus; Turner, Geoffrey; Nüsslein, Bernhard; Fischer, Reinhard

2006-07-01

Laccases are copper-containing enzymes which oxidize phenolic substrates and transfer the electrons to oxygen. Many filamentous fungi contain several laccase-encoding genes, but their biological roles are mostly not well understood. The main interest in laccases in biotechnology is their potential to be used to detoxify phenolic substances. We report here on a novel application of laccases as a reporter system in fungi. We purified a laccase enzyme from the ligno-cellulolytic ascomycete Stachybotrys chartarum. It oxidized the artificial substrate 2,2'-azino-di-(3-ethylbenzthiazolinsulfonate) (ABTS). The corresponding gene was isolated and expressed in Aspergillus nidulans, Aspergillus niger, and Trichoderma reesei. Heterologously expressed laccase activity was monitored in colorimetric enzyme assays and on agar plates with ABTS as a substrate. The use of laccase as a reporter was shown in a genetic screen for the isolation of improved T. reesei cellulase production strains. In addition to the laccase from S. charatarum, we tested the application of three laccases from A. nidulans (LccB, LccC, and LccD) as reporters. Whereas LccC oxidized ABTS (Km = 0.3 mM), LccD did not react with ABTS but with DMA/ADBP (3,5-dimethylaniline/4-amino-2,6-dibromophenol). LccB reacted with DMA/ADBP and showed weak activity with ABTS. The different catalytic properties of LccC and LccD allow simultaneous use of these two laccases as reporters in one fungal strain.

Identification and characterization of thermostable glucose dehydrogenases from thermophilic filamentous fungi.

PubMed

Ozawa, Kazumichi; Iwasa, Hisanori; Sasaki, Noriko; Kinoshita, Nao; Hiratsuka, Atsunori; Yokoyama, Kenji

2017-01-01

FAD-dependent glucose dehydrogenase (FAD-GDH), which contains FAD as a cofactor, catalyzes the oxidation of D-glucose to D-glucono-1,5-lactone, and plays an important role in biosensors measuring blood glucose levels. In order to obtain a novel FAD-GDH gene homolog, we performed degenerate PCR screening of genomic DNAs from 17 species of thermophilic filamentous fungi. Two FAD-GDH gene homologs were identified and cloned from Talaromyces emersonii NBRC 31232 and Thermoascus crustaceus NBRC 9129. We then prepared the recombinant enzymes produced by Escherichia coli and Pichia pastoris. Absorption spectra and enzymatic assays revealed that the resulting enzymes contained oxidized FAD as a cofactor and exhibited glucose dehydrogenase activity. The transition midpoint temperatures (T m ) were 66.4 and 62.5 °C for glycosylated FAD-GDHs of T. emersonii and T. crustaceus prepared by using P. pastoris as a host, respectively. Therefore, both FAD-GDHs exhibited high thermostability. In conclusion, we propose that these thermostable FAD-GDHs could be ideal enzymes for use as thermotolerant glucose sensors with high accuracy.

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi.

PubMed

McMullen, Allison R; Wallace, Meghan A; Pincus, David H; Wilkey, Kathy; Burnham, C A

2016-08-01

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Diagnostic utility of melanin production by fungi: study on tissue sections and culture smears with Masson-Fontana stain.

PubMed

Sundaram, Challa; Shantveer, G Uppin; Umabala, Pamidi; Lakshmi, Vemu

2014-01-01

Dematiaceous fungi appear brown in tissue section due to melanin in their cell walls. When the brown color is not seen on routine H and E and culture is not available, differentiation of dematiaceous fungi from other fungi is difficult on morphology alone. To study if melanin production by dematiaceous fungi can help differentiate them from other types of fungi. Fifty tissue sections of various fungal infections and 13 smears from cultures of different species of fungi were stained with Masson Fontana stain to assess melanin production. The tissue sections included biopsies from 26 culture-proven fungi and 24 biopsies of filamentous fungi diagnosed on morphology alone with no culture confirmation. All culture-proven dematiaceous fungi and Zygomycetes showed strong positivity in sections and culture smears. Aspergillus sp showed variable positivity and intensity. Cryptococcus neoformans showed strong positivity in tissue sections and culture smears. Tissue sections of septate filamentous fungi (9/15), Zygomycetes (4/5), and fungi with both hyphal and yeast morphology (4/4) showed positivity for melanin. The septate filamentous fungi negative for melanin were from biopsy samples of fungal sinusitis including both allergic and invasive fungal sinusitis and colonizing fungal balls. Melanin is produced by both dematiaceous and non-dematiaceous fungi. Masson-Fontana stain cannot reliably differentiate dematiaceous fungi from other filamentous fungi like Aspergillus sp; however, absence of melanin in the hyphae may be used to rule out dematiaceous fungi from other filamentous fungi. In the differential diagnosis of yeast fungi, Cryptococcus sp can be differentiated from Candida sp by Masson-Fontana stain in tissue sections.

Diesel pollution biodegradation: synergetic effect of Mycobacterium and filamentous fungi.

PubMed

Li, You-Qing; Liu, Hong-Fang; Tian, Zhen-Le; Zhu, Li-Hua; Wu, Ying-Hui; Tang, He-Qing

2008-06-01

To biodegrade the diesel pollution in aqueous solution inoculated with Mycobacterium and filamentous fungi. Bacteria sampled from petroleum hydrocarbons contaminated sites in Karamay Oilfield were isolated and identified as Mycobacterium hyalinum (MH) and cladosporium. Spectrophotometry and gas chromatography (GC) were used to analyze of the residual concentrations of diesel oil and its biodegradation products. From the GC data, the values of apparent biodegradation ratio of the bacterial strain MH to diesel oil were close to those obtained in the control experiments. Moreover, the number of MH did not increase with degradation time. However, by using n-octadecane instead of diesel oil, the real biotic degradation ratio increased to 20.9% over 5 days of degradation. Cladosporium strongly biodegraded diesel oil with a real degradation ratio of up to 34% after 5 days treatment. When the two strains were used simultaneously, a significant synergistic effect between them resulted in almost complete degradation of diesel oil, achieving a total diesel removal of 99% over 5 days of treatment, in which one part of about 80% and another part of about 19% were attributed to biotic and abiotic processes, respectively. The observed synergistic effect was closely related to the aromatics-degrading ability of Cladosporium, which favored the growth of MH and promoted the bioavailability of diesel oil.

One-pot strategy for on-site enzyme production, biomass hydrolysis, and ethanol production using the whole solid-state fermentation medium of mixed filamentous fungi.

PubMed

Maehara, Larissa; Pereira, Sandra C; Silva, Adilson J; Farinas, Cristiane S

2018-02-01

The efficient use of renewable lignocellulosic feedstocks to obtain biofuels and other bioproducts is a key requirement for a sustainable biobased economy. This requires novel and effective strategies to reduce the cost contribution of the cellulolytic enzymatic cocktails needed to convert the carbohydrates into simple sugars, in order to make large-scale commercial processes economically competitive. Here, we propose the use of the whole solid-state fermentation (SSF) medium of mixed filamentous fungi as an integrated one-pot strategy for on-site enzyme production, biomass hydrolysis, and ethanol production. Ten different individual and mixed cultivations of commonly used industrial filamentous fungi (Aspergillus niger, Aspergillus oryzae, Trichoderma harzianum, and Trichoderma reesei) were performed under SSF and the whole media (without the extraction step) were used in the hydrolysis of pretreated sugarcane bagasse. The cocultivation of T. reesei with A. oryzae increased the amount of glucose released by around 50%, compared with individual cultivations. The release of glucose and reducing sugars achieved using the whole SSF medium was around 3-fold higher than obtained with the enzyme extract. The addition of soybean protein (0.5% w/w) during the hydrolysis reaction further significantly improved the saccharification performance by blocking the lignin and avoiding unproductive adsorption of enzymes. The results of the alcoholic fermentation validated the overall integrated process, with a volumetric ethanol productivity of 4.77 g/L.h, representing 83.5% of the theoretical yield. These findings demonstrate the feasibility of the proposed one-pot integrated strategy using the whole SSF medium of mixed filamentous fungi for on-site enzymes production, biomass hydrolysis, and ethanol production. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

DOE PAGES

McCluskey, Kevin; Baker, Scott E.

2017-02-17

As model organisms filamentous fungi have been important since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycetemore » filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Likewise, shared data has contributed to the success of model systems. Furthermore, the scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.« less

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCluskey, Kevin; Baker, Scott E.

As model organisms filamentous fungi have been important since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycetemore » filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Likewise, shared data has contributed to the success of model systems. Furthermore, the scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.« less

Identification of filamentous fungi isolates by MALDI-TOF mass spectrometry: clinical evaluation of an extended reference spectra library.

PubMed

Becker, Pierre T; de Bel, Annelies; Martiny, Delphine; Ranque, Stéphane; Piarroux, Renaud; Cassagne, Carole; Detandt, Monique; Hendrickx, Marijke

2014-11-01

The identification of filamentous fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) relies mainly on a robust and extensive database of reference spectra. To this end, a large in-house library containing 760 strains and representing 472 species was built and evaluated on 390 clinical isolates by comparing MALDI-TOF MS with the classical identification method based on morphological observations. The use of MALDI-TOF MS resulted in the correct identification of 95.4% of the isolates at species level, without considering LogScore values. Taking into account the Brukers' cutoff value for reliability (LogScore >1.70), 85.6% of the isolates were correctly identified. For a number of isolates, microscopic identification was limited to the genus, resulting in only 61.5% of the isolates correctly identified at species level while the correctness reached 94.6% at genus level. Using this extended in-house database, MALDI-TOF MS thus appears superior to morphology in order to obtain a robust and accurate identification of filamentous fungi. A continuous extension of the library is however necessary to further improve its reliability. Indeed, 15 isolates were still not represented while an additional three isolates were not recognized, probably because of a lack of intraspecific variability of the corresponding species in the database. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Modeling the Growth of Filamentous Fungi at the Particle Scale in Solid-State Fermentation Systems.

PubMed

Sugai-Guérios, Maura Harumi; Balmant, Wellington; Furigo, Agenor; Krieger, Nadia; Mitchell, David Alexander

2015-01-01

Solid-state fermentation (SSF) with filamentous fungi is a promising technique for the production of a range of biotechnological products and has the potential to play an important role in future biorefineries. The performance of such processes is intimately linked with the mycelial mode of growth of these fungi: Not only is the production of extracellular enzymes related to morphological characteristics, but also the mycelium can affect bed properties and, consequently, the efficiency of heat and mass transfer within the bed. A mathematical model that describes the development of the fungal mycelium in SSF systems at the particle scale would be a useful tool for investigating these phenomena, but, as yet, a sufficiently complete model has not been proposed. This review presents the biological and mass transfer phenomena that should be included in such a model and then evaluates how these phenomena have been modeled previously in the SSF and related literature. We conclude that a discrete lattice-based model that uses differential equations to describe the mass balances of the components within the system would be most appropriate and that mathematical expressions for describing the individual phenomena are available in the literature. It remains for these phenomena to be integrated into a complete model describing the development of fungal mycelia in SSF systems.

[Filamentous and phosphate solubilizing fungi relationships with some edaphic parameters and coffee plantations management].

PubMed

Posada, Raúl Hernando; Sánchez de Prager, Marina; Sieverding, Ewald; Aguilar Dorantes, Karla; Heredia-Abarca, Gabriela Patricia

2012-09-01

Soil properties and the environment have multiple outcomes on fungal communities. Although, the interaction effects between management intensity, pH, available phosphorus, organic carbon, soil texture and different fractions of water stable macro-aggregates on the communities of microscopic filamentous fungi (MFF), iron phosphate solubilizing fungi (PSF-Fe), and iron and calcium phosphate solubilizing fungi (PSF-(Fe+Ca)), have been previously evaluated in field conditions, this has never been performed in terms of their combined effects, neither with phosphate solubilizing fungi. To assess this, we collected 40 composite soil samples from eight Mexican and Colombian coffee plantations, with different management intensities and physico-chemical edaphic parameters, during 2008-2009. We isolated different communities of MFF, PSF-Fe and PSF-(Fe+Ca), by wet sieving and soil particles culture in Potato-Dextrose-Agar from soil samples, and we classified isolates in terms of their phosphate solubilizing ability. Following the principal component analysis results, we decided to analyze fungal communities and abiotic factors interactions for each country separately. Structural Equation Models revealed that organic carbon was positively associated to MFF richness and number of isolates (lambda>0.58), but its relationship with PSF-Fe and PSF-(Fe+Ca) were variable; while the available phosphorus, pH and water stable macro-aggregate fractions did not show a clear pattern. Management intensity was negatively related to PSF-Fe (lambda < or = -0.21) morphotype richness and the number of isolates in Colombian coffee plantations. We found that the relationships of clay and organic carbon content, and available phosphorus and soil pH, with the species richness and number of isolates of MFF, PSF-Fe and PSF-(Fe+Ca) were highly variable; this made impossible to generalize the responses between saprotrophic fungal groups and geographic zones. The management intensity was not related to

Distribution and abundance of fungi in the soils of Taylor Valley, Antarctica

USGS Publications Warehouse

Connell, L.; Redman, R.; Craig, S.; Rodriguez, R.

2006-01-01

The occurrence and distribution of culturable fungi in Taylor Valley, Antarctica was assessed in terms of soil habitat. Soil transects throughout the valley revealed differential habitat utilization between filamentous and non-filamentous (yeast and yeast-like) fungi. In addition, there were significant differences in species distribution patterns with respect to soil pH, moisture, distance from marine coastline, carbon, chlorophyll a, salinity, elevation and solar inputs. Filamentous fungal abundance is most closely associated with habitats having higher pH, and soil moistures. These close associations were not found with yeast and yeast-like fungi demonstrating that yeast and yeast-like fungi utilize a broader range of habitat. An intensive survey of the Victoria Land is necessary to gain a better understanding of their role in soil functioning and nutrient cycling processes. ?? 2006 Elsevier Ltd. All rights reserved.

One step N-glycosylation by filamentous fungi biofilm in bioreactor of a new phosphodiesterase-3 inhibitor tetrazole.

PubMed

de Melo Souza, Paula L; Arruda, Evilanna L; Pazini, Francine; Menegatti, Ricardo; Vaz, Boniek G; Lião, Luciano M; de Oliveira, Valéria

2016-07-01

An efficient and rapid process for N-glycosylation of 5-(1-(3-fluorophenyl)-1H-pyrazol-4-yl)-2H-tetrazole-LQFM 021 (1), a new synthetic derivative of pyrazole with phosphodiesterase-3 (PDE-3) inhibitory action, vasorelaxant activity and low toxicity catalyzed by filamentous fungi biofilm in bioreactor was successfully developed. A maximum N-glycosyl yield of 68% was obtained with Cunninghamella echinulata ATCC 9244 biofilm in bioreactor with conditions of 25mgml(-1) of 1 in PDSM medium at 28°C for 96h. After extraction with ethyl acetate, the derivative was identified by Ultrahigh Resolution Mass Spectrometry and (1)H-(13)C HSQC/HMBC. Copyright © 2016 Elsevier Ltd. All rights reserved.

The detection of the imprint of filaments on cosmic microwave background lensing

NASA Astrophysics Data System (ADS)

He, Siyu; Alam, Shadab; Ferraro, Simone; Chen, Yen-Chi; Ho, Shirley

2018-05-01

Galaxy redshift surveys, such as the 2-Degree-Field Survey (2dF)1, Sloan Digital Sky Survey (SDSS)2, 6-Degree-Field Survey (6dF)3, Galaxy And Mass Assembly survey (GAMA)4 and VIMOS Public Extragalactic Redshift Survey (VIPERS)5, have shown that the spatial distribution of matter forms a rich web, known as the cosmic web6. Most galaxy survey analyses measure the amplitude of galaxy clustering as a function of scale, ignoring information beyond a small number of summary statistics. Because the matter density field becomes highly non-Gaussian as structure evolves under gravity, we expect other statistical descriptions of the field to provide us with additional information. One way to study the non-Gaussianity is to study filaments, which evolve non-linearly from the initial density fluctuations produced in the primordial Universe. In our study, we report the detection of lensing of the cosmic microwave background (CMB) by filaments, and we apply a null test to confirm our detection. Furthermore, we propose a phenomenological model to interpret the detected signal, and we measure how filaments trace the matter distribution on large scales through filament bias, which we measure to be around 1.5. Our study provides new scope to understand the environmental dependence of galaxy formation. In the future, the joint analysis of lensing and Sunyaev-Zel'dovich observations might reveal the properties of `missing baryons', the vast majority of the gas that resides in the intergalactic medium, which has so far evaded most observations.

Selection of filamentous fungi of the Beauveria genus able to metabolize quercetin like mammalian cells

PubMed Central

de M. B. Costa, Eula Maria; Pimenta, Fabiana Cristina; Luz, Wolf Christian; de Oliveira, Valéria

2008-01-01

Microbial biotransformations constitute an important alternative as models for drug metabolism study in mammalians and have been used for the industrial synthesis of chemicals with pharmaceutical purposes. Several microorganisms with unique biotransformation ability have been found by intensive screening and put in commercial applications. Ten isolates of Beauveria sp genus filamentous fungi, isolated from soil in the central Brazil, and Beauveria bassiana ATCC 7159 were evaluated for their capability of quercetin biotransformation. Biotransformation processes were carried out for 24 up to 96 hours and monitored by mass spectrometry analyses of the culture broth. All strains were able to metabolize quercetin, forming mammalian metabolites. The results were different from those presented by other microorganisms previously utilized, attrackting attention because of the great diversity of reactions. Methylated, sulphated, monoglucuronidated, and glucuronidated conjugated metabolites were simultaneously detected. PMID:24031237

In vitro susceptibility of filamentous fungi from mycotic keratitis to azole drugs.

PubMed

Shobana, C S; Mythili, A; Homa, M; Galgóczy, L; Priya, R; Babu Singh, Y R; Panneerselvam, K; Vágvölgyi, C; Kredics, L; Narendran, V; Manikandan, P

2015-03-01

The in vitro antifungal activities of azole drugs viz., itraconazole, voriconazole, ketoconazole, econazole and clotrimazole were investigated in order to evaluate their efficacy against filamentous fungi isolated from mycotic keratitis. The specimen collection was carried out from fungal keratitis patients attending Aravind eye hospital and Post-graduate institute of ophthalmology, Coimbatore, India and was subsequently processed for the isolation of fungi. The dilutions of antifungal drugs were prepared in RPMI 1640 medium. Minimum inhibitory concentrations (MICs) were determined and MIC50 and MIC90 were calculated for each drug tested. A total of 60 fungal isolates were identified as Fusarium spp. (n=30), non-sporulating moulds (n=9), Aspergillus flavus (n=6), Bipolaris spp. (n=6), Exserohilum spp. (n=4), Curvularia spp. (n=3), Alternaria spp. (n=1) and Exophiala spp. (n=1). The MICs of ketoconazole, clotrimazole, voriconazole, econazole and itraconazole for all the fungal isolates ranged between 16 μg/mL and 0.03 μg/mL, 4 μg/mL and 0.015 μg/mL, 8 μg/mL and 0.015 μg/mL, 8 μg/mL and 0.015 μg/mL and 32 μg/mL and 0.06 μg/mL respectively. From the MIC50 and MIC90 values, it could be deciphered that in the present study, clotrimazole was more active against the test isolates at lower concentrations (0.12-5 μg/mL) when compared to other drugs tested. The results suggest that amongst the tested azole drugs, clotrimazole followed by voriconazole and econazole had lower MICs against moulds isolated from mycotic keratitis. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Lipid production in association of filamentous fungi with genetically modified cyanobacterial cells.

PubMed

Miranda, Ana F; Taha, Mohamed; Wrede, Digby; Morrison, Paul; Ball, Andrew S; Stevenson, Trevor; Mouradov, Aidyn

2015-01-01

Numerous strategies have evolved recently for the generation of genetically modified or synthetic microalgae and cyanobacteria designed for production of ethanol, biodiesel and other fuels. In spite of their obvious attractiveness there are still a number of challenges that can affect their economic viability: the high costs associated with (1) harvesting, which can account for up to 50 % of the total biofuel's cost, (2) nutrients supply and (3) oil extraction. Fungal-assisted bio-flocculation of microalgae is gaining increasing attention due to its high efficiency, no need for added chemicals and low energy inputs. The implementation of renewable alternative carbon, nitrogen and phosphorus sources from agricultural wastes and wastewaters for growing algae and fungi makes this strategy economically attractive. This work demonstrates that the filamentous fungi, Aspergillus fumigatus can efficiently flocculate the unicellular cyanobacteria Synechocystis PCC 6803 and its genetically modified derivatives that have been altered to enable secretion of free fatty acids into growth media. Secreted free fatty acids are potentially used by fungal cells as a carbon source for growth and ex-novo production of lipids. For most of genetically modified strains the total lipid yields extracted from the fungal-cyanobacterial pellets were found to be higher than additive yields of lipids and total free fatty acids produced by fungal and Synechocystis components when grown in mono-cultures. The synergistic effect observed in fungal-Synechocystis associations was also found in bioremediation rates when animal husbandry wastewater was used an alternative source of nitrogen and phosphorus. Fungal assisted flocculation can complement and assist in large scale biofuel production from wild-type and genetically modified Synechocystis PCC 6803 strains by (1) efficient harvesting of cyanobacterial cells and (2) producing of high yields of lipids accumulated in fungal-cyanobacterial pellets.

Nuclear movement in fungi.

PubMed

Xiang, Xin

2017-12-11

Nuclear movement within a cell occurs in a variety of eukaryotic organisms including yeasts and filamentous fungi. Fungal molecular genetic studies identified the minus-end-directed microtubule motor cytoplasmic dynein as a critical protein for nuclear movement or orientation of the mitotic spindle contained in the nucleus. Studies in the budding yeast first indicated that dynein anchored at the cortex via its anchoring protein Num1 exerts pulling force on an astral microtubule to orient the anaphase spindle across the mother-daughter axis before nuclear division. Prior to anaphase, myosin V interacts with the plus end of an astral microtubule via Kar9-Bim1/EB1 and pulls the plus end along the actin cables to move the nucleus/spindle close to the bud neck. In addition, pushing or pulling forces generated from cortex-linked polymerization or depolymerization of microtubules drive nuclear movements in yeasts and possibly also in filamentous fungi. In filamentous fungi, multiple nuclei within a hyphal segment undergo dynein-dependent back-and-forth movements and their positioning is also influenced by cytoplasmic streaming toward the hyphal tip. In addition, nuclear movement occurs at various stages of fungal development and fungal infection of plant tissues. This review discusses our current understanding on the mechanisms of nuclear movement in fungal organisms, the importance of nuclear positioning and the regulatory strategies that ensure the proper positioning of nucleus/spindle. Published by Elsevier Ltd.

Peroxide accumulation and cell death in filamentous fungi induced by contact with a contestant.

PubMed

Silar, Philippe

2005-02-01

Podospora anserina and Coprinopsis cinerea (syn. Coprinus cinereus) are endowed with a defence system able to differentiate self vs. non-self and involving the generation of peroxide. Indeed, they produce peroxide when confronted with a filamentous fungus, only in non-self confrontations. Both species are not able to recognize yeasts and show a differential response to bacteria. The accumulation of peroxides in the ascomycete Podospora anserina requires an NADPH oxidase and a MAP kinase cascade, previously shown to be involved in fruit body formation, cell differentiation and cell degeneration. Confrontation is accompanied by the death of the contestant hyphae only in specific combinations of species. As in animals and plants, data suggest that peroxide is likely involved in signalling rather than playing a direct toxic role. Fungi display more complex behaviours than generally acknowledged, i.e. they are able to recognize potential contestants and built up defence reactions involving evolutionary conserved enzymes.

Abundance and dynamics of filamentous fungi in the complex ambrosia gardens of the primitively eusocial beetle Xyleborinus saxesenii Ratzeburg (Coleoptera: Curculionidae, Scolytinae).

PubMed

Biedermann, Peter H W; Klepzig, Kier D; Taborsky, Michael; Six, Diana L

2013-03-01

Insect fungus gardens consist of a community of interacting microorganisms that can have either beneficial or detrimental effects to the farmers. In contrast to fungus-farming ants and termites, the fungal communities of ambrosia beetles and the effects of particular fungal species on the farmers are largely unknown. Here, we used a laboratory rearing technique for studying the filamentous fungal garden community of the ambrosia beetle, Xyleborinus saxesenii, which cultivates fungi in tunnels excavated within dead trees. Raffaelea sulfurea and Fusicolla acetilerea were transmitted in spore-carrying organs by gallery founding females and established first in new gardens. Raffaelea sulfurea had positive effects on egg-laying and larval numbers. Over time, four other fungal species emerged in the gardens. Prevalence of one of them, Paecilomyces variotii, correlated negatively with larval numbers and can be harmful to adults by forming biofilms on their bodies. It also comprised the main portion of garden material removed from galleries by adults. Our data suggest that two mutualistic, several commensalistic and one to two pathogenic filamentous fungi are associated with X. saxesenii. Fungal diversity in gardens of ambrosia beetles appears to be much lower than that in gardens of fungus-culturing ants, which seems to result from essential differences in substrates and behaviours. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Production of mycotoxins by filamentous fungi in untreated surface water.

PubMed

Oliveira, Beatriz R; Mata, Ana T; Ferreira, João P; Barreto Crespo, Maria T; Pereira, Vanessa J; Bronze, Maria R

2018-04-16

Several research studies reported that mycotoxins and other metabolites can be produced by fungi in certain matrices such as food. In recent years, attention has been drawn to the wide occurrence and identification of fungi in drinking water sources. Due to the large demand of water for drinking, watering, or food production purposes, it is imperative that further research is conducted to investigate if mycotoxins may be produced in water matrices. This paper describes the results obtained when a validated analytical method was applied to detect and quantify the presence of mycotoxins as a result of fungi inoculation and growth in untreated surface water. Aflatoxins B1 and B2, fumonisin B3, and ochratoxin A were detected at concentrations up to 35 ng/L. These results show that fungi can produce mycotoxins in water matrices in a non-negligible quantity and, as such, attention must be given to the presence of fungi in water.

Identification of fungi isolated from banana rachis and characterization of their surface activity.

PubMed

Méndez-Castillo, L; Prieto-Correa, E; Jiménez-Junca, C

2017-03-01

Filamentous fungi are an unexplored source for the production of biosurfactants, but over a decade one of the most surface active molecules called hydrophobins was discovered. There are few techniques to determine the surface activity of fungi without any kind of manipulation that can affect the final results. In this work, we identified 33 strains of filamentous fungi isolated from banana rachis which may have potential in producing biosurfactants. Further, the production of surface active compounds by the strains was measured by two techniques. First, the surface tension of supernatants was evaluated in liquid cultures of the strains. We found that three strains belonging to the genus Fusarium, Penicillium and Trichoderma showed activity in the reduction of surface tension, which indicate a putative production of biosurfactants. Second, we measured the contact angle between the drop of water and the solid culture of strains to determine the surface activity of cells, classifying the strains as hydrophilic or hydrophobic. These techniques can be used as a quantitative measurement of the surface activity of fungi without cell manipulation. Biosurfactants are an alternative to petrochemical derivatives, and filamentous fungi are a promising source of these molecules. This work identified 33 strains of filamentous fungi in agroindustrial wastes. This is important because these results open the opportunity of finding new biosurfactants (hydrophobins) with unique properties. We propose the evaluation of surface tension in the supernatant as a quantitative screening to determine the production of biosurfactants from the strains of fungi. © 2017 The Society for Applied Microbiology.

Occurrence and hygienic relevance of fungi in drinking water.

PubMed

Kanzler, D; Buzina, W; Paulitsch, A; Haas, D; Platzer, S; Marth, E; Mascher, F

2008-03-01

Fungi, above all filamentous fungi, can occur almost everywhere, even in water. They can grow in such a quantity in water that they can affect the health of the population or have negative effects on food production. There are several reports of fungal growth in water from different countries, but to our knowledge none from Austria so far. The aim of this study was to gain an overview of the spectrum of filamentous fungi and yeasts in drinking water systems. Thirty-eight water samples from drinking water and groundwater were analysed. Fungi were isolated by using membrane filtration and plating method with subsequent cultivation on agar plates. The different taxa of fungi were identified using routine techniques as well as molecular methods. Fungi were isolated in all water samples examined. The mean value for drinking water was 9.1 CFU per 100 ml and for groundwater 5400 CFU per 100 ml. Altogether 32 different taxa of fungi were found. The taxa which occurred most frequently were Cladosporium spp., Basidiomycetes and Penicillium spp. (74.6%, 56.4% and 48.7%, respectively). This study shows that drinking water can be a reservoir for fungi, among them opportunists, which can cause infections in immunosuppressed patients.

Polymorphism and phylogenetic species delimitation in filamentous fungi from predominant mycobiota in withered grapes.

PubMed

Lorenzini, M; Cappello, M S; Logrieco, A; Zapparoli, G

2016-12-05

Filamentous fungi are the main pathogens of withered grapes destined for passito wine production. Knowledge of which species inhabit these post-harvest fruits and their pathogenicity is essential in order to develop strategies to control infection, but is still scarce. This study investigated the predominant mycobiota of withered grapes through a cultivation-dependent approach. Strain and species heterogeneity was evidenced on examining isolates collected over three consecutive years. Colony morphology and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis revealed the occurrence of several phenotypes and haplotypes, respectively. Strains were phylogenetically analyzed based on sequence typing of different genes or regions (e.g. calmodulin, β-tubulin and internal transcribed spacer region). Beside the most common necrotrophic-saprophytic species of Penicillium, Aspergillus, Alternaria and Botrytis species responsible for fruit rot, other saprobic species were identified (e.g. Trichoderma atroviride, Sarocladium terricola, Arthrinium arundinis and Diaporthe eres) generally not associated with post-harvest fruit diseases. Species such as Penicillium ubiquetum, Cladosporium pseudocladosporioides, Lichtheimia ramosa, Sarocladium terricola, Diaporthe nobilis, Bipolaris secalis, Paraconiothyrium fuckelii and Galactomyces reessii that had never previously been isolated from grapevine or grape were also identified. Moreover, it was not possible to assign a species to some isolates, while some members of Didymosphaeriaceae and Didymellaceae remained unclassified even at genus level. This study provides insights into the diversity of the epiphytic fungi inhabiting withered grapes and evidences the importance of their identification to understand the causes of fruit diseases. Finally, phylogenetic species delimitation furnished data of interest to fungal taxonomy. Copyright © 2016 Elsevier B.V. All rights reserved.

A Sensitive Method for Examining Whole Cell Biochemical Composition in Single Cells of Filamentous Fungi using Synchrotron FTIR Spectromicroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konstantin,J.; Gough, K.; Julian, R.

2008-01-01

Cell function is related to cell composition. The asexual state of filamentous fungi (molds and mildews) has two main life cycle stages: vegetative hyphae for substrate colonization and nutrient acquisition, and asexual spores for survival and dispersal. Hyphal composition changes over a few tens of microns during growth and maturation; spores are different from hyphae. Most biochemical analyses are restricted to studying a few components at high spatial resolution (e.g. histochemistry) or many compounds at low spatial resolution (e.g. GC-MS). Synchrotron FTIR spectromicroscopy can be used to study fungal cell biology by fingerprinting varieties of carbohydrates, proteins, and lipids atmore » about 6 microm spatial resolution. FTIR can distinguish fungal species and changes during hyphal growth, and reveals that even fungi grown under optimal vs mildly stressed conditions exhibit dramatic biochemical changes without obvious morphological effects. Here we compare hypha and spore composition of two fungi, Neurospora and Rhizopus. There are clear biochemical changes when Neurospora hyphae commit to spore development, during spore maturation and following germination, many of which are consistent with results from molecular genetics, but have not been shown before at high spatial resolution. Rhizopus spores develop within a fluid-containing sporangium that becomes dry at maturity. Rhizopus spores had similar protein content and significantly more carbohydrate than the sporangial fluid, both of which are novel findings.« less

Filamentous fungi isolated from sand and water of "Bairro Novo" and "Casa Caiada" beaches, Olinda, Pernambuco, Brazil.

PubMed

Gomes, D N F; Cavalcanti, M A Q; Fernandes, M J S; Lima, D M M; Passavante, J Z O

2008-08-01

Fungi comprehend a heterogeneous group of heterotrophic microorganisms that act as saprobes or parasites or, less frequently, as symbionts living in association with other organisms. They are cosmopolitan and important components of ecosystems. Considering the small number of Brazilian papers on the filamentous mycota in marine environments, and the need to improve knowledge of the diversity of these microfungi in "Casa Caiada" and "Bairro Novo" beaches, Olinda, PE, the aim of this work was to isolate and identify the fungi from sand and water samples of these ecosystems. Thirty two samplings of sand (surface and 20 cm deep) and water (surface and 1 m deep) were carried out during the dry and rainy seasons, in low and high tide. From each sand sample, a suspension was made with 50 g of sand diluted in 90 mL of sterilized distilled water. From each sand suspension and water sample, 0.5 mL was spread, in triplicate, onto Petri dishes containing Sabouraud Agar added of chloramphenicol. The plates were incubated at 28 degrees C (+/-2 degrees C). Fifty seven species were isolated, identified, and classified in 20 genera. Aspergillus and Penicillium were the most frequent genera in both sand and water, with a total of 11 and 19 species, respectively.

Antifungal susceptibility and pathogenic potential of environmental isolated filamentous fungi compared with colonizing agents in immunocompromised patients.

PubMed

Teixeira, A B A; Silva, M; Lyra, L; Luz, E A; Uno, J; Takada, H; Miyaji, M; Nishimura, K; Schreiber, A Z

2005-09-01

Infection is a major cause of morbidity and mortality in bone marrow transplant recipients and in patients with hematological malignancies. The source of infection is almost always endogenous flora or the hospital environment. The present study evaluated bone marrow transplant recipients and patients with hematological malignancies colonized and/or infected with filamentous fungi. During 1 year, environmental air samples were also taken from the bone marrow transplant unit by a modification of gravity air-setting plate (GASP) methodology. Fusarium spp. were the most prevalent genus in the fall and Cladosporium spp. in the winter. Clinically isolated strains grew better at 37 degrees C than environmental strains. According to NCCLS M-38P methods, environmental Aspergillus strains showed higher MICs to miconazol and itraconazol, and clinical Fusarium strains were less susceptible to fluconazole.

Cloning, sequencing, and transgenic expression of Podospora curvicolla and Sordaria macrospora eEF1A genes: relationship between cytosolic translation and longevity in filamentous fungi.

PubMed

Gagny, B; Rossignol, M; Silar, P

1997-12-01

We have cloned and sequenced the gene encoding the translation elongation factor eEF1A from two filamentous fungi, Podospora curvicolla and Sordaria macrospora. These fungi are close relatives of Podospora anserina and also show senescence syndromes. Comparison of the sequences of the deduced proteins with that of P. anserina reveals that the three proteins differ in several positions. Replacement of the P. anserina gene by either of the two exogenous genes does not entail any modification in P. anserina physiology; the longevity of the fungus is not affected. No alteration of in vivo translational accuracy was detected; however, the exogenous proteins nonetheless promoted a modification of the resistance to the aminoglycoside antibiotic paromomycin. These data suggest that optimization of life span between these closely related fungi has likely not been performed during evolution through modifications of eEF1A activity, despite the fact that mutations in this factor can drastically affect longevity. Copyright 1997 Academic Press.

Fungi isolated from flue-cured tobacco sold in Southeast United States, 1968-1970.

PubMed

Welty, R E

1972-09-01

Flue-cured tobacco leaves, from low- and middle-stalk positions, offered for sale in each of two markets, within each of five tobacco types, were evaluated for moisture content (MC) and filamentous fungi during August through October in 1968, 1969, and 1970. Alternaria alternata, Penicillium cyclopium, Aspergillus niger, Aspergillus repens, and Aspergillus flavus were most frequently isolated from cultured tissue. Other filamentous fungi that grew from the tissue included species from four genera of field fungi and seven species of storage fungi. Although the MC ranged from 11.0 to 22.5%, it averaged 16.4, 16.8, and 15.9% for samples taken in 1968, 1969, and 1970, respectively. Average populations of fungi per sample over the three years ranged from 0 to 1,528,500 colonies/g of tobacco.

Fungi Isolated from Flue-Cured Tobacco Sold in Southeast United States, 1968-1970

PubMed Central

Welty, Ronald E.

1972-01-01

Flue-cured tobacco leaves, from low- and middle-stalk positions, offered for sale in each of two markets, within each of five tobacco types, were evaluated for moisture content (MC) and filamentous fungi during August through October in 1968, 1969, and 1970. Alternaria alternata, Penicillium cyclopium, Aspergillus niger, Aspergillus repens, and Aspergillus flavus were most frequently isolated from cultured tissue. Other filamentous fungi that grew from the tissue included species from four genera of field fungi and seven species of storage fungi. Although the MC ranged from 11.0 to 22.5%, it averaged 16.4, 16.8, and 15.9% for samples taken in 1968, 1969, and 1970, respectively. Average populations of fungi per sample over the three years ranged from 0 to 1,528,500 colonies/g of tobacco. PMID:4627970

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

PubMed

Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Microparticle based morphology engineering of filamentous microorganisms for industrial bio-production.

PubMed

Walisko, Robert; Krull, Rainer; Schrader, Jens; Wittmann, Christoph

2012-11-01

Filamentous microorganisms are important work horses in industrial biotechnology and supply enzymes, antibiotics, pharmaceuticals, bulk and fine chemicals. Here we highlight recent findings on the use of microparticles in the cultivation of filamentous bacteria and fungi, with the aim of enabling a more precise control of their morphology towards better production performance. First examples reveal a broad application range of microparticle based processes, since multiple filamentous organisms are controllable in their growth characteristics and respond by enhanced product formation.

Morphology and rheology in filamentous cultivations.

PubMed

Wucherpfennig, T; Kiep, K A; Driouch, H; Wittmann, C; Krull, R

2010-01-01

Because of their metabolic diversity, high production capacity, secretion efficiency, and capability of carrying out posttranslational modifications, filamentous fungi are widely exploited as efficient cell factories in the production of metabolites, bioactive substances, and native or heterologous proteins, respectively. There is, however, a complex relationship between the morphology of these microorganisms, transport phenomena, the viscosity of the cultivation broth, and related productivity. The morphological characteristics vary between freely dispersed mycelia and distinct pellets of aggregated biomass, every growth form having a distinct influence on broth rheology. Hence, the advantages and disadvantages for mycelial or pellet cultivation have to be balanced out carefully. Because of the still inadequate understanding of the morphogenesis of filamentous microorganisms, fungal morphology is often a bottleneck of productivity in industrial production. To obtain an optimized production process, it is of great importance to gain a better understanding of the molecular and cell biology of these microorganisms as well as the relevant approaches in biochemical engineering. In this chapter, morphology and growth of filamentous fungi are described, with special attention given to specific problems as they arise from fungal growth forms; growth and mass transfer in fungal biopellets are discussed as an example. To emphasize the importance of the flow behavior of filamentous cultivation broths, an introduction to rheology is also given, reviewing important rheological models and recent studies concerning rheological parameters. Furthermore, current knowledge on morphology and productivity in relation to the environom is outlined in the last section of this review. Copyright 2010 Elsevier Inc. All rights reserved.

In vitro susceptibility of filamentous fungi to copper nanoparticles assessed by rapid XTT colorimetry and agar dilution method.

PubMed

Ghasemian, E; Naghoni, A; Tabaraie, B; Tabaraie, T

2012-12-01

Metal nanoparticles and their uses in various aspects have recently drawn a great deal of attention. One of the major applications is that it can be used as an antimicrobial agent. They can be considered in approaches targeted to decrease the harms caused by microorganisms, specifically fungi, threatening the medical and industrial areas. The aim of this study was to investigate the antifungal activity of synthesized copper nanoparticles (CuNPs) against four filamentous fungi including Alternaria alternata, Aspergillus flavus, Fusarium solani, and Penicillium chrysogenum. Zerovalent copper nanoparticles of mean size 8nm were synthesized by inert gas condensation (IGC) method. The antifungal activity of these synthesized copper nanoparticles was measured against selected fungi by using two different techniques including agar dilution method and XTT reduction assay. The minimal inhibitory concentrations (MICs) for copper nanoparticles by agar dilution method were less or equal to 40mg/L for P. chrysogenum, less or equal to 60mg/L for A. alternata, less or equal to 60mg/L for F. solani, and less or equal to 80mg/L for A. flavus. And also MICs obtained by XTT reduction assay ranged from 40 to 80mg/L. Our data demonstrated that the copper nanoparticles inhibited fungal growth, but the fungal sensitivity to copper nanoparticles varies depending on the fungal species. Therefore, it is advisable that the minimal inhibitory concentrations (MICs) be examined before using these compounds. It is hoped that, in future, copper nanoparticles could replace some antifungal agents, making them applicable to many different medical devices and antimicrobial control system. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Thermophilic Fungi to Dominate Aflatoxigenic/Mycotoxigenic Fungi on Food under Global Warming

PubMed Central

Paterson, Robert Russell M.; Lima, Nelson

2017-01-01

Certain filamentous fungi produce mycotoxins that contaminate food. Mycotoxin contamination of crops is highly influenced by environmental conditions and is already affected by global warming, where there is a succession of mycotoxigenic fungi towards those that have higher optimal growth temperatures. Aflatoxigenic fungi are at the highest limit of temperature although predicted increases in temperature are beyond that constraint. The present paper discusses what will succeed these fungi and represents the first such consideration. Aflatoxins are the most important mycotoxins and are common in tropical produce, much of which is exported to temperate regions. Hot countries may produce safer food under climate change because aflatoxigenic fungi will be inhibited. The same situation will occur in previously temperate regions where these fungi have recently appeared, although decades later. Existing thermotolerant and thermophilic fungi (TTF) will dominate, in contrast to the conventional mycotoxigenic fungi adapting or mutating, as it will be quicker. TTF produce a range of secondary metabolites, or potential mycotoxins and patulin which may become a new threat. In addition, Aspergillus fumigatus will appear more frequently, a serious human pathogen, because it is (a) thermotolerant and (b) present on crops: hence this is an even greater problem. An incubation temperature of 41 °C needs employing forthwith to detect TTF. Finally, TTF in crops requires study because of the potential for diseases in humans and animals under climate change. PMID:28218685

Thermophilic Fungi to Dominate Aflatoxigenic/Mycotoxigenic Fungi on Food under Global Warming.

PubMed

Paterson, Robert Russell M; Lima, Nelson

2017-02-17

Certain filamentous fungi produce mycotoxins that contaminate food. Mycotoxin contamination of crops is highly influenced by environmental conditions and is already affected by global warming, where there is a succession of mycotoxigenic fungi towards those that have higher optimal growth temperatures. Aflatoxigenic fungi are at the highest limit of temperature although predicted increases in temperature are beyond that constraint. The present paper discusses what will succeed these fungi and represents the first such consideration. Aflatoxins are the most important mycotoxins and are common in tropical produce, much of which is exported to temperate regions. Hot countries may produce safer food under climate change because aflatoxigenic fungi will be inhibited. The same situation will occur in previously temperate regions where these fungi have recently appeared, although decades later. Existing thermotolerant and thermophilic fungi (TTF) will dominate, in contrast to the conventional mycotoxigenic fungi adapting or mutating, as it will be quicker. TTF produce a range of secondary metabolites, or potential mycotoxins and patulin which may become a new threat. In addition, Aspergillus fumigatus will appear more frequently, a serious human pathogen, because it is (a) thermotolerant and (b) present on crops: hence this is an even greater problem. An incubation temperature of 41 °C needs employing forthwith to detect TTF. Finally, TTF in crops requires study because of the potential for diseases in humans and animals under climate change.

Marine Fungi: Their Ecology and Molecular Diversity

NASA Astrophysics Data System (ADS)

Richards, Thomas A.; Jones, Meredith D. M.; Leonard, Guy; Bass, David

2012-01-01

Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

Monitoring of Microscopic Filamentous Fungi in Indoor Air of Transplant Unit.

PubMed

Holý, Ondřej; Matoušková, Ivanka; Kubátová, Alena; Hamal, Petr; Svobodová, Lucie; Jurásková, Eva; Raida, Luděk

2015-12-01

The aim of the study was to control the microbial contamination of indoor air monitored monthly at the Transplant Unit of the University Hospital Olomouc from August 2010 to July 2011. The unit is equipped with a three-stage air filtration system with HEPA filters. The MAS-100 air sampler (Merck, GER) was used. Twenty locations were singled out for the purposes of collecting a total of 720 samplings of the indoor air. Swabs of the HVAC diffusers at the sampling locations were always carried out after the sampling of the indoor air. In total, 480 samples of the indoor air were taken for Sabouraud chloramphenicol agar. In 11 cases (2.29%) the cultivation verified the presence of microscopic filamentous fungi. Only two cases involved the sanitary facilities of a patient isolation box; the other positive findings were from the facilities. The most frequent established genus was Aspergillus spp. (4x), followed by Trichoderma spp. (2x) and Penicillium spp. (2x), Paecilomyces spp., Eurotium spp., and Chrysonilia spp. (1x each). In 2 cases the cultivation established sterile aerial mycelium, unfortunately no further identification was possible. A total of 726 swabs of HVAC diffusers were collected (2 positive-0.28%). The study results demonstrated the efficacy of the HVAC equipment. With the continuing increase in the number of severely immunocompromised patients, hospitals are faced with the growing problem of invasive aspergillosis and other opportunistic infections. Preventive monitoring of microbial air contaminants is of major importance for the control of invasive aspergillosis. Copyright© by the National Institute of Public Health, Prague 2015.

Valorization of sugar-to-ethanol process waste vinasse: A novel biorefinery approach using edible ascomycetes filamentous fungi.

PubMed

Nair, Ramkumar B; Taherzadeh, Mohammad J

2016-12-01

The aim of the present work was to study the integration of edible ascomycetes filamentous fungi into the existing sugar- or molasses-to-ethanol processes, to grow on vinasse or stillage and produce ethanol and protein-rich fungal biomass. Two fungal strains, Neurospora intermedia and Aspergillus oryzae were examined in shake flasks and airlift-bioreactors, resulting in reduction of vinasse COD by 34% and viscosity by 21%. Utilization of glycerol and sugars were observed, yielding 202.4 or 222.8g dry fungal biomass of N. intermedia or A. oryzae respectively, per liter of vinasse. Integration of the current process at an existing ethanol facility producing about 100,000m 3 of ethanol per year could produce around 200,000-250,000tons of dry fungal biomass (40-45% protein) together with about 8800-12,600m 3 extra ethanol (8.8-12.6% of production-rate improvement). Copyright © 2016 Elsevier Ltd. All rights reserved.

Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.

PubMed

Meerupati, Tejashwari; Andersson, Karl-Magnus; Friman, Eva; Kumar, Dharmendra; Tunlid, Anders; Ahrén, Dag

2013-11-01

Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity

Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi

PubMed Central

Meerupati, Tejashwari; Andersson, Karl-Magnus; Friman, Eva; Kumar, Dharmendra; Tunlid, Anders; Ahrén, Dag

2013-01-01

Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity

Effect of low shear modeled microgravity on phenotypic and central chitin metabolism in the filamentous fungi Aspergillus niger and Penicillium chrysogenum.

PubMed

Sathishkumar, Yesupatham; Velmurugan, Natarajan; Lee, Hyun Mi; Rajagopal, Kalyanaraman; Im, Chan Ki; Lee, Yang Soo

2014-08-01

Phenotypic and genotypic changes in Aspergillus niger and Penicillium chrysogenum, spore forming filamentous fungi, with respect to central chitin metabolism were studied under low shear modeled microgravity, normal gravity and static conditions. Low shear modeled microgravity (LSMMG) response showed a similar spore germination rate with normal gravity and static conditions. Interestingly, high ratio of multiple germ tube formation of A. niger in LSMMG condition was observed. Confocal laser scanning microscopy images of calcofluor flurophore stained A. niger and P. chrysogenum showed no significant variations between different conditions tested. Transmission electron microscopy images revealed number of mitochondria increased in P. chrysogenum in low shear modeled microgravity condition but no stress related-woronin bodies in fungal hyphae were observed. To gain additional insight into the cell wall integrity under different conditions, transcription level of a key gene involved in cell wall integrity gfaA, encoding the glutamine: fructose-6-phosphate amidotransferase enzyme, was evaluated using qRT-PCR. The transcription level showed no variation among different conditions. Overall, the results collectively indicate that the LSMMG has shown no significant stress on spore germination, mycelial growth, cell wall integrity of potentially pathogenic fungi, A. niger and P. chrysogenum.

A novel 96-well gel-based assay for determining antifungal activity against filamentous fungi.

PubMed

Troskie, Anscha Mari; Vlok, Nicolas Maré; Rautenbach, Marina

2012-12-01

In recent years the global rise in antibiotic resistance and environmental consciousness lead to a renewed fervour to find and develop novel antibiotics, including antifungals. However, the influence of the environment on antifungal activity is often disregarded and many in vitro assays may cause the activity of certain antifungals to be overestimated or underestimated. The general antifungal test assays that are economically accessible to the majority of scientists primarily rely on visual examination or on spectrophotometric analysis. The effect of certain morphogenic antifungals, which may lead to hyperbranching of filamentous fungi, unfortunately renders these methods unreliable. To minimise the difficulties experienced as a result of hyperbranching, we developed a straightforward, economical 96-well gel-based method, independent of spectrophotometric analysis, for highly repeatable determination of antifungal activity. For the calculation of inhibition parameters, this method relies on the visualisation of assay results by digitisation. The antifungal activity results from our novel micro-gel dilution assay are comparable to that of the micro-broth dilution assay used as standard reference test of The Clinical and Laboratory Standard Institute. Furthermore, our economical assay is multifunctional as it permits microscopic analysis of the preserved assay results, as well as rendering highly reliable data. Copyright © 2012 Elsevier B.V. All rights reserved.

Filamentous fungal diversity and community structure associated with the solid state fermentation of Chinese Maotai-flavor liquor.

PubMed

Chen, Bi; Wu, Qun; Xu, Yan

2014-06-02

Maotai-flavor liquor is produced by simultaneous saccharification and fermentation (SSF) process under solid state conditions, including Daqu (starter) making, stacking fermentation and alcohol fermentation stages. Filamentous fungi produce many enzymes to degrade the starch material into fermentable sugar during liquor fermentation. This study investigated the filamentous fungal community associated with liquor making process. Eight and seven different fungal species were identified by using culture-dependent and -independent method (PCR-denaturing gradient gel electrophoresis, DGGE) analyses, respectively. The traditional enumeration method showed that Daqu provided 7 fungal species for stacking fermentation. The total population of filamentous fungi increased from 3.4 × 10(3)cfu/g to 1.28 × 10(4)cfu/g in the first 3 days of stacking fermentation, and then decreased till the end. In alcohol fermentation in pits, the population continuously decreased and few fungal species survived (lower than 1 × 10(3)cfu/g) after 10 days. Therefore, stacking fermentation is an essential stage for the growth of filamentous fungi. Paecilomyces variotii, Aspergillus oryzae and Aspergillus terreus were detected by both methods, and P. variotii and A. oryzae were the predominant species. Meanwhile, P. variotii possessed the highest glucoamylase (3252 ± 526 U/g) and A. oryzae exhibited the highest α-amylase (1491 ± 324 U/g) activity among the cultivable fungal species. Furthermore, the variation of starch and reducing sugar content was consistent with the growth of P. variotii and A. oryzae in Zaopei (fermented grains) during stacking fermentation, which implied that the two filamentous fungi played an important role in producing amylase for hydrolyzing the starch. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomics of industrial fungi: trends and insights for biotechnology.

PubMed

de Oliveira, José Miguel P Ferreira; de Graaff, Leo H

2011-01-01

Filamentous fungi are widely known for their industrial applications, namely, the production of food-processing enzymes and metabolites such as antibiotics and organic acids. In the past decade, the full genome sequencing of filamentous fungi increased the potential to predict encoded proteins enormously, namely, hydrolytic enzymes or proteins involved in the biosynthesis of metabolites of interest. The integration of genome sequence information with possible phenotypes requires, however, the knowledge of all the proteins in the cell in a system-wise manner, given by proteomics. This review summarises the progress of proteomics and its importance for the study of biotechnological processes in filamentous fungi. A major step forward in proteomics was to couple protein separation with high-resolution mass spectrometry, allowing accurate protein quantification. Despite the fact that most fungal proteomic studies have been focused on proteins from mycelial extracts, many proteins are related to processes which are compartmentalised in the fungal cell, e.g. β-lactam antibiotic production in the microbody. For the study of such processes, a targeted approach is required, e.g. by organelle proteomics. Typical workflows for sample preparation in fungal organelle proteomics are discussed, including homogenisation and sub-cellular fractionation. Finally, examples are presented of fungal organelle proteomic studies, which have enlarged the knowledge on areas of interest to biotechnology, such as protein secretion, energy production or antibiotic biosynthesis.

Proteomics of industrial fungi: trends and insights for biotechnology

PubMed Central

de Oliveira, José Miguel P. Ferreira

2010-01-01

Filamentous fungi are widely known for their industrial applications, namely, the production of food-processing enzymes and metabolites such as antibiotics and organic acids. In the past decade, the full genome sequencing of filamentous fungi increased the potential to predict encoded proteins enormously, namely, hydrolytic enzymes or proteins involved in the biosynthesis of metabolites of interest. The integration of genome sequence information with possible phenotypes requires, however, the knowledge of all the proteins in the cell in a system-wise manner, given by proteomics. This review summarises the progress of proteomics and its importance for the study of biotechnological processes in filamentous fungi. A major step forward in proteomics was to couple protein separation with high-resolution mass spectrometry, allowing accurate protein quantification. Despite the fact that most fungal proteomic studies have been focused on proteins from mycelial extracts, many proteins are related to processes which are compartmentalised in the fungal cell, e.g. β-lactam antibiotic production in the microbody. For the study of such processes, a targeted approach is required, e.g. by organelle proteomics. Typical workflows for sample preparation in fungal organelle proteomics are discussed, including homogenisation and sub-cellular fractionation. Finally, examples are presented of fungal organelle proteomic studies, which have enlarged the knowledge on areas of interest to biotechnology, such as protein secretion, energy production or antibiotic biosynthesis. PMID:20922379

The evolution of compositionally and functionally distinct actin filaments.

PubMed

Gunning, Peter W; Ghoshdastider, Umesh; Whitaker, Shane; Popp, David; Robinson, Robert C

2015-06-01

The actin filament is astonishingly well conserved across a diverse set of eukaryotic species. It has essentially remained unchanged in the billion years that separate yeast, Arabidopsis and man. In contrast, bacterial actin-like proteins have diverged to the extreme, and many of them are not readily identified from sequence-based homology searches. Here, we present phylogenetic analyses that point to an evolutionary drive to diversify actin filament composition across kingdoms. Bacteria use a one-filament-one-function system to create distinct filament systems within a single cell. In contrast, eukaryotic actin is a universal force provider in a wide range of processes. In plants, there has been an expansion of the number of closely related actin genes, whereas in fungi and metazoa diversification in tropomyosins has increased the compositional variety in actin filament systems. Both mechanisms dictate the subset of actin-binding proteins that interact with each filament type, leading to specialization in function. In this Hypothesis, we thus propose that different mechanisms were selected in bacteria, plants and metazoa, which achieved actin filament compositional variation leading to the expansion of their functional diversity. © 2015. Published by The Company of Biologists Ltd.

Interactions between a Sap Beetle, Sabal Palm, Scale Insect, Filamentous Fungi and Yeast, with Discovery of Potential Antifungal Compounds

PubMed Central

Cline, Andrew R.; Skelley, Paul E.; Kinnee, Scott A.; Rooney-Latham, Suzanne; Winterton, Shaun L.; Borkent, Christopher J.; Audisio, Paolo

2014-01-01

The multi-trophic relationship between insects, yeast, and filamentous fungi is reported on sabal palm (Sabal palmetto (Walter) Lodd. ex Schult. & Schult. f.). Gut content analyses and observations of adult and larval feeding of the sap beetle Brachypeplus glaber LeConte indicate that niche partitioning of fungal food substrata occurs between adults and larvae. This is the first report of specific mycophagous niche partitioning among beetle life stages based on gut content analyses. Fungi isolated from the beetle gut of adults, larvae, and pupae include species of Fusarium Link, Cladosporium Link, and Penicillium Link, which were differentially ingested by larvae and adults; Fusarium solani and Penicillium species in larvae, whereas F. oxysoproum, F. verticillioides, and Cladosporium in adults. These data indicate the first species-level host data for Brachypeplus Erichson species. Fusarium proliferatum (Matsush.) Nirenberg was the most commonly occurring fungal gut component, being isolated from the palm as well as gut of larvae, pupae, and adults; representing a commonly shared food resource. One species of yeast, Meyerozyma caribbica (Vaughan-Mart. et al.) Kurtzman & Suzuki (basionym = Pichia caribbica), was isolated from all life stages and is likely responsible for anti-fungal properties observed in the pupae and represents a promising source of antifungal compounds; rearing and diagnostic protocols are provided to aid biomedical researchers. Feeding and cleaning behaviors are documented using time-lapse video-micrography, and discussed in a behavioral and functional morphological context. Adults spent long periods feeding, often >1/3 of the two-hour observation period. A generic adult body posture was observed during feeding, and included substrate antennation before and after ingestion. Adult grooming behaviors were manifested in distinct antennal and tarsal cleaning mechanisms. Larval behaviors were different from adults, and larvae feeding on Fusarium

In vitro susceptibility of filamentous fungi to itraconazole, voriconazole and posaconazole by Clinical and Laboratory Standards Institute reference method and E-test.

PubMed

Kondori, N; Svensson, E; Mattsby-Baltzer, I

2011-09-01

The use of anti-fungal agents has increased dramatically in recent years and new drugs have been developed. Several methods are available for determinations of their specific biological activities, i.e. the standard method for minimum inhibitory concentration-determination is described in M-38 [Clinical and Laboratory Standards Institute document M-38 (CLSI M-38)]. However, alternative methods, such as the E-test, are currently available in Mycology laboratories. The susceptibilities of clinical isolates of Aspergillus spp. (n = 29), Fusarium spp. (n = 5), zygomycetes (n = 21) and Schizophyllum (n = 1) were determined for itraconazole, voriconazole and posaconazole, using the CLSI M-38-A broth dilution method and also by the E-test. A good overall agreement (83.7%) between the two methods for all drugs and organisms was observed. Analyses of voriconazole showed a better agreement (93%) between the methods than posaconazole and itraconazole (85% and 74% respectively). Aspergillus spp. were the most susceptible fungi to the anti-fungal agents tested in this study. Posaconazole was the most active drug against filamentous fungi in vitro, followed by itraconazole and voriconazole. The latter (voriconazole) demonstrated no significant in vitro activity against zygomycetes. © 2010 Blackwell Verlag GmbH.

Antioxidants produced by Eurotium herbariorum of filamentous fungi used for the manufacture of karebushi, dried bonito (Katsuobushi).

PubMed

Miyake, Yoshiaki; Ito, Chihiro; Itoigawa, Masataka; Osawa, Toshihiko

2009-06-01

Extracts prepared by culturing ten filamentous fungi from Aspergillus and Eurotium species isolated from dried bonito (katsuobushi) were examined for 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging capacity. The extracts prepared by culturing E. herbariorum NE-1 and NE-4, which are used in the molding process for the manufacture of karebushi (a kind of katsuobushi), were shown to have higher activity than the others. Five antioxidants were isolated from the extracts and identified as isodihydroauroglaucin (IDAG), auroglaucin (AG), dihydroauroglaucin (DAG), tetrahydroauroglaucin (TAG), and flavoglaucin (FG) by (1)H-NMR, (13)C-NMR, and EI-MS analyses. Compared with alpha-tocopherol, the isolated antioxidants exhibited high antioxidative activity for the radical scavenging capacity of DPPH and superoxide, but low activity for inhibiting the autoxidation of docosahexaenoic acid (DHA). The isolated antioxidants were produced by the Eurotium species, but not by the Aspergillus species. DAG and TAG exhibited higher radical scavenging capacity than the other antioxidants and were abundantly contained in the extracts of E. herbariorum NE-1 and NE-4.

Galactic cold cores. VIII. Filament formation and evolution: Filament properties in context with evolutionary models

NASA Astrophysics Data System (ADS)

Rivera-Ingraham, A.; Ristorcelli, I.; Juvela, M.; Montillaud, J.; Men'shchikov, A.; Malinen, J.; Pelkonen, V.-M.; Marston, A.; Martin, P. G.; Pagani, L.; Paladini, R.; Paradis, D.; Ysard, N.; Ward-Thompson, D.; Bernard, J.-P.; Marshall, D. J.; Montier, L.; Tóth, L. V.

2017-05-01

Context. The onset of star formation is intimately linked with the presence of massive unstable filamentary structures. These filaments are therefore key for theoretical models that aim to reproduce the observed characteristics of the star formation process in the Galaxy. Aims: As part of the filament study carried out by the Herschel Galactic Cold Cores Key Programme, here we study and discuss the filament properties presented in GCC VII (Paper I) in context with theoretical models of filament formation and evolution. Methods: A conservatively selected sample of filaments located at a distance D< 500 pc was extracted from the GCC fields with the getfilaments algorithm. The physical structure of the filaments was quantified according to two main components: the central (Gaussian) region of the filament (core component), and the power-law-like region dominating the filament column density profile at larger radii (wing component). The properties and behaviour of these components relative to the total linear mass density of the filament and the column density of its environment were compared with the predictions from theoretical models describing the evolution of filaments under gravity-dominated conditions. Results: The feasibility of a transition from a subcritical to supercritical state by accretion at any given time is dependent on the combined effect of filament intrinsic properties and environmental conditions. Reasonably self-gravitating (high Mline,core) filaments in dense environments (AV≳ 3 mag) can become supercritical on timescales of t 1 Myr by accreting mass at constant or decreasing width. The trend of increasing Mline,tot (Mline,core and Mline,wing) and ridge AV with background for the filament population also indicates that the precursors of star-forming filaments evolve coevally with their environment. The simultaneous increase of environment and filament AV explains the observed association between dense environments and high Mline,core values

Clonal reproduction in fungi

PubMed Central

Taylor, John W.; Hann-Soden, Christopher; Branco, Sara; Sylvain, Iman; Ellison, Christopher E.

2015-01-01

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest. PMID:26195774

Antifungal Activity against Filamentous Fungi of Ts1, a Multifunctional Toxin from Tityus serrulatus Scorpion Venom

PubMed Central

Santussi, Welligton M.; Bordon, Karla C. F.; Rodrigues Alves, Ana P. N.; Cologna, Camila T.; Said, Suraia; Arantes, Eliane C.

2017-01-01

Antimicrobial peptides (AMPs) are ubiquitous and multipotent components of the innate immune defense arsenal used by both prokaryotic and eukaryotic organisms. The search for new AMPs has increased in recent years, due to the growing development of microbial resistance to therapeutical drugs. In this work, we evaluate the effects of Tityus serrulatus venom (Tsv), its fractions and its major toxin Ts1, a beta-neurotoxin, on fungi growth. The fractions were obtained by ion-exchange chromatography of Tsv. The growth inhibition of 11 pathogenic and non-pathogenic filamentous fungi (Aspergillus fumigatus, A. nidulans, A. niger, A. terreus, Neurospora crassa, Penicillium corylophilum, P. ochrochloron, P. verrucosum, P. viridicatum, P. waksmanii, and Talaromyces flavus) was evaluated by quantitative microplate reader assay. Tsv (100 and 500 μg/well, which correspond to 1 and 5 mg/mL, respectively, of total soluble protein) was active in inhibiting growth of A. nidulans, A. terreus, P. corylophilum, and P. verrucosum, especially in the higher concentration used and at the first 30 h. After this period, fungi might have used Tsv components as alternative sources of nutrients, and therefore, increased their growth tax. Only fractions IX, X, XI, XIIA, XIIB (3 and 7.5 μg/well, which correspond to 30 and 75 μg/mL, respectively, of total soluble protein) and Ts1 (1.5, 3, and 6 μg/well, which correspond to 2.18, 4.36, and 8.72 μM, respectively) showed antifungal activity. Ts1 showed to be a non-morphogenic toxin with dose-dependent activity against A. nidulans, inhibiting 100% of fungal growth from 3 μg/well (4.36 μM). The inhibitory effect of Ts1 against A. nidulans growth was accompanied by fungistatic effects and was not amended by 1 mM CaCl2 or tetrodotoxin (46.98 and 93.96 μM). The structural differences between Ts1 and drosomycin, a potent cysteine-rich antifungal peptide, are discussed here. Our results highlight the antifungal potential of the first cysteine

Selective isolation of dematiaceous fungi from the workers of Atta laevigata (Formicidae: Attini).

PubMed

Guedes, F L A; Attili-Angelis, D; Pagnocca, F C

2012-01-01

Leaf-cutting ants (Formicidae: Attini) are considered pests in agriculture for their impact in human crops, as they utilize leaf fragments to raise their fungal mutualist (Agaricales: Lepiotaceae). Basically, the basidiomycetous fungus is cultivated to supply food to adult workers and broads; in return, the ants protect it against natural enemies. However, recent studies have claimed that other microorganisms are associated to ant nests where a wide range of interactions may take place. To investigate the occurrence of dematiaceous fungi on the cuticle of Atta laevigata ants, 30 workers were sampled from an adult nest located in the surroundings of the Center for the Studies of Social Insects, UNESP-Rio Claro, SP, Brazil. The use of selective techniques to avoid high-sporulation fungi has been recommended and was tested in this study. To favor the isolation of the desired fungi, heads and cuticle scrapings of ant bodies were inoculated on Mycosel agar and incubated for 3 weeks at 35°C. Morphological and molecular methods were used to identify the filamentous fungi recovered. From 56 isolates, 19 were hyaline filamentous species, and among the remaining 37, some are mentioned as phyto-associated fungi like Alternaria arborescens, Bipolaris sorokiniana, Bipolaris eleusines, Bipolaris zeae, Curvularia trifolii, and Paraphaeosphaeria michotii. These species are reported from A. laevigata bodies for the first time. None of the isolation trials revealed the presence of the parasite Escovopsis or entomopathogenic fungi. The possible spread of the fungi in nature by the ants is discussed.

Population-Based Survey of Filamentous Fungi and Antifungal Resistance in Spain (FILPOP Study)

PubMed Central

Mellado, E.; Peláez, T.; Pemán, J.; Zapico, S.; Alvarez, M.; Rodríguez-Tudela, J. L.; Cuenca-Estrella, M.

2013-01-01

A population-based survey was conducted to investigate the epidemiology of and antifungal resistance in Spanish clinical strains of filamentous fungi isolated from deep tissue samples, blood cultures, and respiratory samples. The study was conducted in two different periods (October 2010 and May 2011) to analyze seasonal variations. A total of 325 strains were isolated in 29 different hospitals. The average prevalence was 0.0016/1,000 inhabitants. Strains were identified by sequencing of DNA targets and susceptibility testing by the European Committee for Antimicrobial Susceptibility Testing reference procedure. The most frequently isolated genus was Aspergillus, accounting for 86.3% of the isolates, followed by Scedosporium at 4.7%; the order Mucorales at 2.5%; Penicillium at 2.2%, and Fusarium at 1.2%. The most frequent species was Aspergillus fumigatus (48.5%), followed by A. flavus (8.4%), A. terreus (8.1%), A. tubingensis (6.8%), and A. niger (6.5%). Cryptic/sibling Aspergillus species accounted for 12% of the cases. Resistance to amphotericin B was found in 10.8% of the isolates tested, while extended-spectrum triazole resistance ranged from 10 to 12.7%, depending on the azole tested. Antifungal resistance was more common among emerging species such as those of Scedosporium and Mucorales and also among cryptic species of Aspergillus, with 40% of these isolates showing resistance to all of the antifungal compounds tested. Cryptic Aspergillus species seem to be underestimated, and their correct classification could be clinically relevant. The performance of antifungal susceptibility testing of the strains implicated in deep infections and multicentric studies is recommended to evaluate the incidence of these cryptic species in other geographic areas. PMID:23669377

SYMPATHETIC SOLAR FILAMENT ERUPTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Rui; Liu, Ying D.; Zimovets, Ivan

2016-08-10

The 2015 March 15 coronal mass ejection as one of the two that together drove the largest geomagnetic storm of solar cycle 24 so far was associated with sympathetic filament eruptions. We investigate the relations between the different filaments involved in the eruption. A surge-like small-scale filament motion is confirmed as the trigger that initiated the erupting filament with multi-wavelength observations and using a forced magnetic field extrapolation method. When the erupting filament moved to an open magnetic field region, it experienced an obvious acceleration process and was accompanied by a C-class flare and the rise of another larger filamentmore » that eventually failed to erupt. We measure the decay index of the background magnetic field, which presents a critical height of 118 Mm. Combining with a potential field source surface extrapolation method, we analyze the distributions of the large-scale magnetic field, which indicates that the open magnetic field region may provide a favorable condition for F2 rapid acceleration and have some relation with the largest solar storm. The comparison between the successful and failed filament eruptions suggests that the confining magnetic field plays an important role in the preconditions for an eruption.« less

Comparative study of the effects of solid-state fermentation with three filamentous fungi on the total phenolics content (TPC), flavonoids, and antioxidant activities of subfractions from oats (Avena sativa L.).

PubMed

Cai, Shengbao; Wang, Ou; Wu, Wei; Zhu, Songjie; Zhou, Feng; Ji, Baoping; Gao, Fengyi; Zhang, Di; Liu, Jia; Cheng, Qian

2012-01-11

The aim of present work was to investigate the effect of solid-state fermentation with filamentous fungi (Aspergillus oryzae var. effuses, Aspergillus oryzae, and Aspergillus niger) on total phenolics content (TPC), flavonoids, and antioxidant activities of four subfractions of oat, namely, n-hexane, ethyl acetate (EA), n-butanol, and water, and compare them to their corresponding subfractions of unfermented oat. The TPC and total flavonoids increased dramatically, especially in EA subfractions (p < 0.05). The levels of antioxidant activity of subfractions were also significantly enhanced (p < 0.05). The highest antioxidant activities were also found in the EA subfractions. The polyphenols in EA were analyzed by high-performance liquid chromatography at 280 nm. Most polyphenols were increased remarkably, especially ferulic and caffeic acids. There was a clear correlation between the TPC and antioxidant activity. In conclusion, fungi fermentation is a potential bioprocess for increasing the TPC, flavonoids, and antioxidant activities of oat-based food.

Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi.

PubMed

Carroll, Emily; Trinh, Tran Ngoc; Son, Hokyoung; Lee, Yin-Won; Seo, Jeong-Ah

2017-05-01

Nuruk is a fermenting starter that is involved in the production of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several companies and persons in 2013 to 2014, and obtained 364 isolates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharomycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lichtheimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces anomalus were counted with maximum 1.3-1.8 × 10 8 CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were isolated in much higher numbers than Rhizopus and Rhizomucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applications, 27 fungal strains were chosen based on isolation frequencies from nuruk, and the ability to produce useful enzyme.

Ecology and identification of environmental fungi and metabolic processes involved in the biodeterioration of Brazilian soapstone historical monuments.

PubMed

Boniek, D; de Castro Mendes, I; Paiva, C A O; de Paula Lana, U G; Dos Santos, A F B; de Resende Stoianoff, M A

2017-11-01

This study aimed to evaluate the action of organic acids produced by the fungal population associated with the biodeterioration process of the Twelve Prophets of Aleijadinho, a set of soapstone sculptures in Congonhas, state of Minas Gerais, Brazil. For this, samples of fungi were obtained from the surface of each of the 12 outdoor stone sculptures that comprise the set of Prophets. The identification of the colonizing filamentous fungi was performed by classical microbiology and molecular methods. Some species of filamentous fungi-dependent cultivation were detected, and the presence of species Aspergillus versicolor, Curvularia lunata, Epicoccum nigrum, Penicillium citrinum and Pseudocercospora norchiensis indicated a connection with the excretion of organic acids. The acids produced by each of these fungal species were analysed quantitatively by chromatographic methods, revealing potential biodeterioration by the action of acidic metabolites excreted in the stone. Minas Gerais, Brazil, is vulnerable to the activities of mineral extraction industries, posing an imminent risk to United Nations Educational, Scientific and Cultural Organization (UNESCO) recognized cities, e.g. Congonhas. Many of these municipalities hold many soapstone religious sculptures and historical monuments. Consequently, soapstone is susceptible to filamentous fungi attack causing irreversible biodeterioration. Despite the concern related to nondestructive sampling of 18th century sculptures, in this study, we have discussed the factors that lead to biodeterioration of soapstone due to organic acid excretion by the fungi that damage the stone, thereby providing an insight in conserving and preserving the soapstone monuments. © 2017 The Society for Applied Microbiology.

Methods for transforming and expression screening of filamentous fungal cells with a DNA library

DOEpatents

Teter, Sarah; Lamsa, Michael; Cherry, Joel; Ward, Connie

2015-06-02

The present invention relates to methods for expression screening of filamentous fungal transformants, comprising: (a) isolating single colony transformants of a DNA library introduced into E. coli; (b) preparing DNA from each of the single colony E. coli transformants; (c) introducing a sample of each of the DNA preparations of step (b) into separate suspensions of protoplasts of a filamentous fungus to obtain transformants thereof, wherein each transformant contains one or more copies of an individual polynucleotide from the DNA library; (d) growing the individual filamentous fungal transformants of step (c) on selective growth medium, thereby permitting growth of the filamentous fungal transformants, while suppressing growth of untransformed filamentous fungi; and (e) measuring activity or a property of each polypeptide encoded by the individual polynucleotides. The present invention also relates to isolated polynucleotides encoding polypeptides of interest obtained by such methods, to nucleic acid constructs, expression vectors, and recombinant host cells comprising the isolated polynucleotides, and to methods of producing the polypeptides encoded by the isolated polynucleotides.

Glass bead cultivation of fungi: combining the best of liquid and agar media.

PubMed

Droce, Aida; Sørensen, Jens Laurids; Giese, Henriette; Sondergaard, Teis Esben

2013-09-01

Production of bioactive compounds and enzymes from filamentous fungi is highly dependent on cultivation conditions. Here we present an easy way to cultivate filamentous fungi on glass beads that allow complete control of nutrient supply. Secondary metabolite production in Fusarium graminearum and Fusarium solani cultivated on agar plates, in shaking liquid culture or on glass beads was compared. Agar plate culture and glass bead cultivation yielded comparable results while liquid culture had lower production of secondary metabolites. RNA extraction from glass beads and liquid cultures was easier than from agar plates and the quality was superior. The system allows simple control of nutrient availability throughout fungal cultivation. This combined with the ease of extraction of nucleic acids and metabolites makes the system highly suitable for the study of gene regulation in response to specific nutrient factors. © 2013.

Fungi in the healthy human gastrointestinal tract

PubMed Central

Hallen-Adams, Heather E.; Suhr, Mallory J.

2017-01-01

ABSTRACT Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors. PMID:27736307

Fungi in the healthy human gastrointestinal tract.

PubMed

Hallen-Adams, Heather E; Suhr, Mallory J

2017-04-03

Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors.

Comparative evaluation of lignocellulolytic activities of filamentous cultures of monocentric and polycentric anaerobic fungi.

PubMed

Dagar, Sumit Singh; Kumar, Sanjay; Mudgil, Priti; Puniya, Anil Kumar

2018-04-01

Sixteen strains of monocentric and polycentric anaerobic fungi were evaluated for cellulase, xylanase and esterase activities. Though strain level variations were observed among all genera, Neocallimastix and Orpinomyces strains exhibited the highest lignocellulolytic activities. The esterase activities of monocentric group of anaerobic fungi were better than the polycentric group. Copyright © 2018 Elsevier Ltd. All rights reserved.

Two Types of Long-duration Quasi-static Evolution of Solar Filaments

NASA Astrophysics Data System (ADS)

Xing, C.; Li, H. C.; Jiang, B.; Cheng, X.; Ding, M. D.

2018-04-01

In this Letter, we investigate the long-duration quasi-static evolution of 12 pre-eruptive filaments (four active region (AR) and eight quiescent filaments), mainly focusing on the evolution of the filament height in 3D and the decay index of the background magnetic field. The filament height in 3D is derived through two-perspective observations of Solar Dynamics Observatory (SDO) and Solar TErrestrial RElations Observatory (STEREO). The coronal magnetic field is reconstructed using the potential field source surface model. A new finding is that the filaments we studied show two types of long-duration evolution: one type comprises a long-duration static phase and a short, slow rise phase with a duration of less than 12 hr and a speed of 0.1–0.7 km s‑1, while the other one only presents a slow rise phase but with an extremely long duration of more than 60 hr and a smaller speed of 0.01–0.2 km s‑1. At the moment approaching the eruption, the decay index of the background magnetic field at the filament height is similar for both AR and quiescent filaments. The average value and upper limit are ∼0.9 and ∼1.4, close to the critical index of torus instability. Moreover, the filament height and background magnetic field strength are also found to be linearly and exponentially related with the filament length, respectively.

[Keratinophilic fungi in soils of parks of Corrientes city, Argentina].

PubMed

Sarmiento, María Mercedes; Mangiaterra, Magdalena; Bojanich, María Viviana; Basualdo, Juan Ángel; Giusiano, Gustavo

2016-01-01

The soil is a natural reservoir of keratinophilic fungi, which are a small but important group of filamentous fungi, some of which typically develop on keratinized tissues of living animals. There are numerous species of saprophytic fungi with recognized keratinophilic abilities, and several studies have been undertaken in order to link their presence to possible human disease. To know the biota of geophilic fungi in general and of keratinophilic fungi particularly in soils from two public parks. Soil samples from two public parks of Corrientes city, Argentina, were studied during two seasons, using the hook technique and serial dilutions for fungal isolation. Using the hook technique, 170 isolates were classified into 17 genera and 21 species, among which it is worth mentioning the presence of Microsporum canis. Shannon index for keratinophilic fungi in autumn was 2.27, and 1.92 in spring. By means of the serial dilutions technique, 278 fungi isolated were identified into 33 genera and 71 species. Shannon index in autumn was 3.9, and 3.5 in spring. The soils studied have particularly favorable conditions for the survival of pathogens and opportunistic geophilic fungi for humans and animals. Copyright © 2014 Asociación Española de Micología. Published by Elsevier Espana. All rights reserved.

Methods to preserve potentially toxigenic fungi.

PubMed

Guimarães, Lucas Costa; Fernandes, Ana Paula; Chalfoun, Sara Maria; Batista, Luís Roberto

2014-01-01

Microorganisms are a source of many high-value compounds which are useful to every living being, such as humans, plants and animals. Since the process of isolating and improving a microorganism can be lengthy and expensive, preserving the obtained characteristic is of paramount importance, so the process does not need to be repeated. Fungi are eukaryotic, achlorophyllous, heterotrophic organisms, usually filamentous, absorb their food, can be either macro or microscopic, propagate themselves by means of spores and store glycogen as a source of storage. Fungi, while infesting food, may produce toxic substances such as mycotoxins. The great genetic diversity of the Kingdom Fungi renders the preservation of fungal cultures for many years relevant. Several international reference mycological culture collections are maintained in many countries. The methodologies that are most fit for preserving microorganisms for extended periods are based on lowering the metabolism until it reaches a stage of artificial dormancy. The goal of this study was to analyze three methods for potentially toxigenic fungal conservation (Castellani's, continuous subculture and lyophilization) and to identify the best among them.

Diversity of micro-fungi in an Antarctic dry valley

NASA Technical Reports Server (NTRS)

Baublis, J. A.; Wharton, R. A. Jr; Volz, P. A.; Wharton RA, J. r. (Principal Investigator)

1991-01-01

The fungal microflora of a dry valley in Southern Victoria Land near McMurdo Sound, Antarctica, was investigated. Samples were collected from introduced objects such as a mummified penguin and spent chewing tobacco in addition to the sparse soil found in rock fissures, isolated moss colonies, shoreline deposit materials, CaCO3 precipitates, and microbial mat debris obtained from the frozen surface of the lake in the basin of Taylor Valley. Using conventional media and techniques, all collection sites yielded populations of yeasts and filamentous fungi. Water samples and live microbial mats from beneath the lake ice yielded species of fungi along with an abundance of bacteria.

Putative fossilized fungi from the lithified volcaniclastic apron of Gran Canaria, Spain.

PubMed

Ivarsson, Magnus; Broman, Curt; Holmström, Sara J M; Ahlbom, Marianne; Lindblom, Sten; Holm, Nils G

2011-09-01

We report the discovery of fossilized filamentous structures in samples of the lithified, volcaniclastic apron of Gran Canaria, which were obtained during Leg 157 of the Ocean Drilling Program (ODP). These filamentous structures are 2-15 μm in diameter and several hundred micrometers in length and are composed of Si, Al, Fe, Ca, Mg, Na, Ti, and C. Chitin was detected in the filamentous structures by staining with wheat germ agglutinin dye conjugated with fluorescein isothiocyanate (WGA-FITC), which suggests that they are fossilized fungal hyphae. The further elucidation of typical filamentous fungal morphological features, such as septa, hyphal bridges, and anastomosis and their respective sizes, support this interpretation. Characteristic structures that we interpreted as fossilized spores were also observed in association with the putative hyphae. The fungal hyphae were found in pyroxene phenocrysts and in siderite pseudomorphs of a basalt breccia. The fungal colonization of the basalt clasts occurred after the brecciation but prior to the final emplacement and lithification of the sediment at ∼16-14 Ma. The siderite appears to have been partially dissolved by the presence of fungal hyphae, and the fungi preferentially colonized Fe-rich carbonates over Fe-poor carbonates (aragonite). Our findings indicate that fungi may be an important geobiological agent in subseafloor environments and an important component of the deep subseafloor biosphere, and that hydrothermal environments associated with volcanism can support a diverse ecosystem, including eukaryotes.

Distribution of sterigmatocystin in filamentous fungi.

PubMed

Rank, Christian; Nielsen, Kristian F; Larsen, Thomas O; Varga, Janos; Samson, Rob A; Frisvad, Jens C

2011-01-01

During the last 50y, the carcinogenic mycotoxin sterigmatocystin (ST) has been reported in several phylogenetically and phenotypically different genera: Aschersonia, Aspergillus, Bipolaris, Botryotrichum, Chaetomium, Emericella, Eurotium, Farrowia, Fusarium, Humicola, Moelleriella, Monocillium and Podospora. We have reexamined all available strains of the original producers, in addition to ex type and further strains of each species reported to produce ST and the biosynthetically derived aflatoxins. We also screened strains of all available species in Penicillium and Aspergillus for ST and aflatoxin. Six new ST producing fungi were discovered: Aspergillus asperescens, Aspergillus aureolatus, Aspergillus eburneocremeus, Aspergillus protuberus, Aspergillus tardus, and Penicillium inflatum and one new aflatoxin producer: Aspergillus togoensis (=Stilbothamnium togoense). ST was confirmed in 23 Emericella, four Aspergillus, five Chaetomium, one Botryotrichum and one Humicola species grown on a selection of secondary metabolite inducing media, and using multiple detection methods: HPLC-UV/Vis DAD, - HRMS and - MS/MS. The immediate precursor for aflatoxin, O-methylsterigmatocystin was found in Chaetomium cellulolyticum, Chaetomium longicolleum, Chaetomium malaysiense and Chaetomium virescens, but aflatoxin was not detected from any Chaetomium species. In all 55 species, representing more than 11 clades throughout the Pezizomycotina, can be reliably claimed to be ST producers and 13 of these can also produce aflatoxins. It is not known yet whether the ST/aflatoxin pathway has been developed independently 11 times, or is the result of partial horizontal gene transfer. Copyright © 2011 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Unwinding motion of a twisted active region filament

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, X. L.; Xue, Z. K.; Kong, D. F.

To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament,more » we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.« less

Contribution of filamentous fungi to the musty odorant 2,4,6-trichloroanisole in water supply reservoirs and associated drinking water treatment plants.

PubMed

Bai, Xiuzhi; Zhang, Ting; Qu, Zhipeng; Li, Haipu; Yang, Zhaoguang

2017-09-01

In this study, the distribution of 2,4,6-trichloroanisole (2,4,6-TCA) in two water supply reservoirs and four associated drinking water treatment plants (DWTPs) were investigated. The 2,4,6-TCA concentrations were in the range of 1.53-2.36 ng L -1 in water supply reservoirs and 0.76-6.58 ng L -1 at DWTPs. To determine the contribution of filamentous fungi to 2,4,6-TCA in a full-scale treatment process, the concentrations of 2,4,6-TCA in raw water, settled water, post-filtration water, and finished water were measured. The results showed that 2,4,6-TCA levels continuously increased until chlorination, suggesting that 2,4,6-TCA could form without a chlorination reaction and fungi might be the major contributor to the 2,4,6-TCA formation. Meanwhile, twenty-nine fungal strains were isolated and identified by morphological and molecular biological methods. Of the seventeen isolated fungal species, eleven showed the capability to convert 2,4,6-trichlorophenol (2,4,6-TCP) to 2,4,6-TCA. The highest level of 2,4,6-TCA formation was carried out by Aspergillus versicolor voucher BJ1-3: 40.5% of the original 2,4,6-TCP was converted to 2,4,6-TCA. There was a significant variation in the capability of different species to generate 2,4,6-TCA. The results from the proportions of cell-free, cell-attached, and cell-bound 2,4,6-TCA suggested that 2,4,6-TCA generated by fungi was mainly distributed in their extracellular environment. In addition to 2,4,6-TCA, five putative volatile by-products were also identified by gas chromatography and mass spectrometry. These findings increase our understanding on the mechanisms involved in the formation of 2,4,6-TCA and provide insights into managing and controlling 2,4,6-TCA-related problems in drinking water. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

PubMed

Mäkelä, Miia R; Marinović, Mila; Nousiainen, Paula; Liwanag, April J M; Benoit, Isabelle; Sipilä, Jussi; Hatakka, Annele; de Vries, Ronald P; Hildén, Kristiina S

2015-01-01

The biological conversion of plant lignocellulose plays an essential role not only in carbon cycling in terrestrial ecosystems but also is an important part of the production of second generation biofuels and biochemicals. The presence of the recalcitrant aromatic polymer lignin is one of the major obstacles in the biofuel/biochemical production process and therefore microbial degradation of lignin is receiving a great deal of attention. Fungi are the main degraders of plant biomass, and in particular the basidiomycete white rot fungi are of major importance in converting plant aromatics due to their ability to degrade lignin. However, the aromatic monomers that are released from lignin and other aromatic compounds of plant biomass are toxic for most fungi already at low levels, and therefore conversion of these compounds to less toxic metabolites is essential for fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting aromatic monomers. In this review we provide an overview of the aromatic components of plant biomass, and their release and conversion by fungi. Finally, we will summarize the applications of fungal systems related to plant aromatics. Copyright © 2015 Elsevier Inc. All rights reserved.

A SIMPLE POLYMERASE CHAIN REACTION-SEQUENCING ANALYSIS CAPABLE OF IDENTIFYING MULTIPLE MEDICALLY RELEVANT FILAMENTOUS FUNGAL SPECIES

EPA Science Inventory

Due to the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result of abnormal growth of the filamentous fungi (mold) in and on building surfaces, it is necessary to accurately determine the organisms responsible for these m...

Thermophilic Fungi: Their Physiology and Enzymes†

PubMed Central

Maheshwari, Ramesh; Bharadwaj, Girish; Bhat, Mahalingeshwara K.

2000-01-01

Thermophilic fungi are a small assemblage in mycota that have a minimum temperature of growth at or above 20°C and a maximum temperature of growth extending up to 60 to 62°C. As the only representatives of eukaryotic organisms that can grow at temperatures above 45°C, the thermophilic fungi are valuable experimental systems for investigations of mechanisms that allow growth at moderately high temperature yet limit their growth beyond 60 to 62°C. Although widespread in terrestrial habitats, they have remained underexplored compared to thermophilic species of eubacteria and archaea. However, thermophilic fungi are potential sources of enzymes with scientific and commercial interests. This review, for the first time, compiles information on the physiology and enzymes of thermophilic fungi. Thermophilic fungi can be grown in minimal media with metabolic rates and growth yields comparable to those of mesophilic fungi. Studies of their growth kinetics, respiration, mixed-substrate utilization, nutrient uptake, and protein breakdown rate have provided some basic information not only on thermophilic fungi but also on filamentous fungi in general. Some species have the ability to grow at ambient temperatures if cultures are initiated with germinated spores or mycelial inoculum or if a nutritionally rich medium is used. Thermophilic fungi have a powerful ability to degrade polysaccharide constituents of biomass. The properties of their enzymes show differences not only among species but also among strains of the same species. Their extracellular enzymes display temperature optima for activity that are close to or above the optimum temperature for the growth of organism and, in general, are more heat stable than those of the mesophilic fungi. Some extracellular enzymes from thermophilic fungi are being produced commercially, and a few others have commercial prospects. Genes of thermophilic fungi encoding lipase, protease, xylanase, and cellulase have been cloned and

Tropomyosin inhibits ADF/cofilin-dependent actin filament dynamics.

PubMed

Ono, Shoichiro; Ono, Kanako

2002-03-18

Tropomyosin binds to actin filaments and is implicated in stabilization of actin cytoskeleton. We examined biochemical and cell biological properties of Caenorhabditis elegans tropomyosin (CeTM) and obtained evidence that CeTM is antagonistic to ADF/cofilin-dependent actin filament dynamics. We purified CeTM, actin, and UNC-60B (a muscle-specific ADF/cofilin isoform), all of which are derived from C. elegans, and showed that CeTM and UNC-60B bound to F-actin in a mutually exclusive manner. CeTM inhibited UNC-60B-induced actin depolymerization and enhancement of actin polymerization. Within isolated native thin filaments, actin and CeTM were detected as major components, whereas UNC-60B was present at a trace amount. Purified UNC-60B was unable to interact with the native thin filaments unless CeTM and other associated proteins were removed by high-salt extraction. Purified CeTM was sufficient to restore the resistance of the salt-extracted filaments from UNC-60B. In muscle cells, CeTM and UNC-60B were localized in different patterns. Suppression of CeTM by RNA interference resulted in disorganized actin filaments and paralyzed worms in wild-type background. However, in an ADF/cofilin mutant background, suppression of CeTM did not worsen actin organization and worm motility. These results suggest that tropomyosin is a physiological inhibitor of ADF/cofilin-dependent actin dynamics.

Function and Biosynthesis of Cell Wall α-1,3-Glucan in Fungi.

PubMed

Yoshimi, Akira; Miyazawa, Ken; Abe, Keietsu

2017-11-18

Although α-1,3-glucan is a major cell wall polysaccharide in filamentous fungi, its biological functions remain unclear, except that it acts as a virulence factor in animal and plant pathogenic fungi: it conceals cell wall β-glucan on the fungal cell surface to circumvent recognition by hosts. However, cell wall α-1,3-glucan is also present in many of non-pathogenic fungi. Recently, the universal function of α-1,3-glucan as an aggregation factor has been demonstrated. Applications of fungi with modified cell wall α-1,3-glucan in the fermentation industry and of in vitro enzymatically-synthesized α-1,3-glucan in bio-plastics have been developed. This review focuses on the recent progress in our understanding of the biological functions and biosynthetic mechanism of cell wall α-1,3-glucan in fungi. We briefly consider the history of studies on α-1,3-glucan, overview its biological functions and biosynthesis, and finally consider the industrial applications of fungi deficient in α-1,3-glucan.

Function and Biosynthesis of Cell Wall α-1,3-Glucan in Fungi

PubMed Central

Yoshimi, Akira; Miyazawa, Ken; Abe, Keietsu

2017-01-01

Although α-1,3-glucan is a major cell wall polysaccharide in filamentous fungi, its biological functions remain unclear, except that it acts as a virulence factor in animal and plant pathogenic fungi: it conceals cell wall β-glucan on the fungal cell surface to circumvent recognition by hosts. However, cell wall α-1,3-glucan is also present in many of non-pathogenic fungi. Recently, the universal function of α-1,3-glucan as an aggregation factor has been demonstrated. Applications of fungi with modified cell wall α-1,3-glucan in the fermentation industry and of in vitro enzymatically-synthesized α-1,3-glucan in bio-plastics have been developed. This review focuses on the recent progress in our understanding of the biological functions and biosynthetic mechanism of cell wall α-1,3-glucan in fungi. We briefly consider the history of studies on α-1,3-glucan, overview its biological functions and biosynthesis, and finally consider the industrial applications of fungi deficient in α-1,3-glucan. PMID:29371579

Biotransformation of dianabol with the filamentous fungi and β-glucuronidase inhibitory activity of resulting metabolites.

PubMed

Khan, Naik T; Zafar, Salman; Noreen, Shagufta; Al Majid, Abdullah M; Al Othman, Zeid A; Al-Resayes, Saud Ibrahim; Atta-ur-Rahman; Choudhary, M Iqbal

2014-07-01

Biotransformation of the anabolic steroid dianabol (1) by suspended-cell cultures of the filamentous fungi Cunninghamella elegans and Macrophomina phaseolina was studied. Incubation of 1 with C. elegans yielded five hydroxylated metabolites 2-6, while M. phaseolina transformed compound 1 into polar metabolites 7-11. These metabolites were identified as 6β,17β-dihydroxy-17α-methylandrost-1,4-dien-3-one (2), 15α,17β-dihydroxy-17α-methylandrost-1,4-dien-3-one (3), 11α,17β-dihydroxy-17α-methylandrost-1,4-dien-3-one (4), 6β,12β,17β-trihydroxy-17α-methylandrost-1,4-dien-3-one (5), 6β,15α,17β-trihydroxy-17α-methylandrost-1,4-dien-3-one (6), 17β-hydroxy-17α-methylandrost-1,4-dien-3,6-dione (7), 7β,17β,-dihydroxy-17α-methylandrost-1,4-dien-3-one (8), 15β,17β-dihydroxy-17α-methylandrost-1,4-dien-3-one (9), 17β-hydroxy-17α-methylandrost-1,4-dien-3,11-dione (10), and 11β,17β-dihydroxy-17α-methylandrost-1,4-dien-3-one (11). Metabolite 3 was also transformed chemically into diketone 12 and oximes 13, and 14. Compounds 6 and 12-14 were identified as new derivatives of dianabol (1). The structures of all transformed products were deduced on the basis of spectral analyses. Compounds 1-14 were evaluated for β-glucuronidase enzyme inhibitory activity. Compounds 7, 13, and 14 showed a strong inhibition of β-glucuronidase enzyme, with IC50 values between 49.0 and 84.9 μM. Copyright © 2014 Elsevier Inc. All rights reserved.

Biodiversity of fungi in hot desert sands.

PubMed

Murgia, Manuela; Fiamma, Maura; Barac, Aleksandra; Deligios, Massimo; Mazzarello, Vittorio; Paglietti, Bianca; Cappuccinelli, Pietro; Al-Qahtani, Ahmed; Squartini, Andrea; Rubino, Salvatore; Al-Ahdal, Mohammed N

2018-03-05

The fungal community of six sand samples from Saudi Arabia and Jordan deserts was characterized by culture-independent analysis via next generation sequencing of the 18S rRNA genes and by culture-dependent methods followed by sequencing of internal transcribed spacer (ITS) region. By 18S sequencing were identified from 163 to 507 OTUs per sample, with a percentage of fungi ranging from 3.5% to 82.7%. The identified fungal Phyla were Ascomycota, Basal fungi, and Basidiomycota and the most abundant detected classes were Dothideomycetes, Pezizomycetes, and Sordariomycetes. A total of 11 colonies of filamentous fungi were isolated and cultured from six samples, and the ITS sequencing pointed toward five different species of the class Sordariomycetes, belonging to genera Fusarium (F. redolens, F. solani, F. equiseti), Chaetomium (C. madrasense), and Albifimbria (A. terrestris). The results of this study show an unexpectedly large fungal biodiversity in the Middle East desert sand and their possible role and implications on human health. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Cellular responses to the expression of unstable secretory proteins in the filamentous fungus Aspergillus oryzae.

PubMed

Yokota, Jun-Ichi; Shiro, Daisuke; Tanaka, Mizuki; Onozaki, Yasumichi; Mizutani, Osamu; Kakizono, Dararat; Ichinose, Sakurako; Shintani, Tomoko; Gomi, Katsuya; Shintani, Takahiro

2017-03-01

Filamentous fungi are often used as cell factories for recombinant protein production because of their ability to secrete large quantities of hydrolytic enzymes. However, even using strong transcriptional promoters, yields of nonfungal proteins are generally much lower than those of fungal proteins. Recent analyses revealed that expression of certain nonfungal secretory proteins induced the unfolded protein response (UPR), suggesting that they are recognized as proteins with folding defects in filamentous fungi. More recently, however, even highly expressed endogenous secretory proteins were found to evoke the UPR. These findings raise the question of whether the unfolded or misfolded state of proteins is selectively recognized by quality control mechanisms in filamentous fungi. In this study, a fungal secretory protein (1,2-α-D-mannosidase; MsdS) with a mutation that decreases its thermostability was expressed at different levels in Aspergillus oryzae. We found that, at moderate expression levels, wild-type MsdS was secreted to the medium, while the mutant was not. In the strain with a deletion for the hrdA gene, which is involved in the endoplasmic reticulum-associated degradation pathway, mutant MsdS had specifically increased levels in the intracellular fraction but was not secreted. When overexpressed, the mutant protein was secreted to the medium to a similar extent as the wild-type protein; however, the mutant underwent hyperglycosylation and induced the UPR. Deletion of α-amylase (the most abundant secretory protein in A. oryzae) alleviated the UPR induction by mutant MsdS overexpression. These findings suggest that misfolded MsdS and unfolded species of α-amylase might act synergistically for UPR induction.

Visualization of the endocytic pathway in the filamentous fungus Aspergillus oryzae using an EGFP-fused plasma membrane protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higuchi, Yujiro; Nakahama, Tomoyuki; Shoji, Jun-ya

2006-02-17

Endocytosis is an important process for cellular activities. However, in filamentous fungi, the existence of endocytosis has been so far elusive. In this study, we used AoUapC-EGFP, the fusion protein of a putative uric acid-xanthine permease with enhanced green fluorescent protein (EGFP) in Aspergillus oryzae, to examine whether the endocytic process occurs or not. Upon the addition of ammonium into the medium the fusion protein was internalized from the plasma membrane. The internalization of AoUapC-EGFP was completely blocked by sodium azide, cold, and cytochalasin A treatments, suggesting that the internalization possesses the general features of endocytosis. These results demonstrate themore » occurrence of endocytosis in filamentous fungi. Moreover, we discovered that the endosomal compartments appeared upon the induction of endocytosis and moved in a microtubule-dependent manner.« less

Self-assembly of nematic liquid crystal elastomer filaments

NASA Astrophysics Data System (ADS)

Wei, Wei-Shao; Xia, Yu; Yang, Shu; Yodh, A. G.

In this work we investigate the self-assembly of nematic liquid crystal polymer (NLCP) filaments and their corresponding cross-linked elastomer structures. Specifically, by fine-tuning surfactant concentration, prepolymer chain length, and temperature within a background aqueous phase we can generate filaments composed of oligomerized LC monomers. Filaments with narrowly dispersed diameters ranging from one hundred nanometers to a few micrometers can be obtained. Using polarization optical microscopy, we show that the nematic LCs within the filaments have an escaped radial structure. After photo-cross-linking, nematic liquid crystal elastomer filaments are obtained with well-maintained directors and smooth surface structure. Since these materials are elastomers, the size and mechanical and optical response of the filaments can be ''tuned'' near the nematic to isotropic phase transition temperature. This work is supported by NSF DMR16-07378, PENN MRSEC Grant DMR11-20901, and NASA Grant NNX08AO0G.

Biodegradation of pesticides using fungi species found in the aquatic environment.

PubMed

Oliveira, B R; Penetra, A; Cardoso, V V; Benoliel, M J; Barreto Crespo, M T; Samson, R A; Pereira, V J

2015-08-01

Relatively limited attention has been given to the presence of fungi in the aquatic environment compared to their occurrence in other matrices. Taking advantage and recognizing the biodegradable capabilities of fungi is important, since these organisms may produce many potent enzymes capable of degrading toxic pollutants. Therefore, the aim of this study was to evaluate the potential ability of some species of filamentous fungi that occur in the aquatic environment to degrade pesticides in untreated surface water. Several laboratory-scale experiments were performed using the natural microbial population present in the aquatic environment as well as spiked fungi isolates that were found to occur in different water matrices, to test the ability of fungi to degrade several pesticides of current concern (atrazine, diuron, isoproturon and chlorfenvinphos). The results obtained in this study showed that, when spiked in sterile natural water, fungi were able to degrade chlorfenvinphos to levels below detection and unable to degrade atrazine, diuron and isoproturon. Penicillium citrinum, Aspergillus fumigatus, Aspergillus terreus and Trichoderma harzianum were found to be able to resist and degrade chlorfenvinphos. These fungi are therefore expected to play an important role in the degradation of this and other pollutants present in the aquatic environment.

Sea salts as a potential source of food spoilage fungi.

PubMed

Biango-Daniels, Megan N; Hodge, Kathie T

2018-02-01

Production of sea salt begins with evaporation of sea water in shallow pools called salterns, and ends with the harvest and packing of salts. This process provides many opportunities for fungal contamination. This study aimed to determine whether finished salts contain viable fungi that have the potential to cause spoilage when sea salt is used as a food ingredient by isolating fungi on a medium that simulated salted food with a lowered water activity (0.95 a w ). The viable filamentous fungi from seven commercial salts were quantified and identified by DNA sequencing, and the fungal communities in different salts were compared. Every sea salt tested contained viable fungi, in concentrations ranging from 0.07 to 1.71 colony-forming units per gram of salt. In total, 85 fungi were isolated representing seven genera. One or more species of the most abundant genera, Aspergillus, Cladosporium, and Penicillium was found in every salt. Many species found in this study have been previously isolated from low water activity environments, including salterns and foods. We conclude that sea salts contain many fungi that have potential to cause food spoilage as well as some that may be mycotoxigenic. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Galactic cold cores. VII. Filament formation and evolution: Methods and observational constraints

NASA Astrophysics Data System (ADS)

Rivera-Ingraham, A.; Ristorcelli, I.; Juvela, M.; Montillaud, J.; Men'shchikov, A.; Malinen, J.; Pelkonen, V.-M.; Marston, A.; Martin, P. G.; Pagani, L.; Paladini, R.; Paradis, D.; Ysard, N.; Ward-Thompson, D.; Bernard, J.-P.; Marshall, D. J.; Montier, L.; Tóth, L. V.

2016-06-01

Context. The association of filaments with protostellar objects has made these structures a priority target in star formation studies. However, little is known about the link between filament properties and their local environment. Aims: The datasets from the Herschel Galactic Cold cores key programme allow for a statistical study of filaments with a wide range of intrinsic and environmental characteristics. Characterisation of this sample can therefore be used to identify key physical parameters and quantify the role of the environment in the formation of supercritical filaments. These results are necessary to constrain theoretical models of filament formation and evolution. Methods: Filaments were extracted from fields at distance D< 500 pc with the getfilaments algorithm and characterised according to their column density profiles and intrinsic properties. Each profile was fitted with a beam-convolved Plummer-like function, and the filament structure was quantified based on the relative contributions from the filament "core", represented by a Gaussian, and "wing" component, dominated by the power-law behaviour of the Plummer-like function. These filament parameters were examined for populations associated with different background levels. Results: Filaments increase their core (Mline,core) and wing (Mline,wing) contributions while increasing their total linear mass density (Mline,tot). Both components appear to be linked to the local environment, with filaments in higher backgrounds having systematically more massive Mline,core and Mline,wing. This dependence on the environment supports an accretion-based model of filament evolution in the local neighbourhood (D ≤ 500 pc). Structures located in the highest backgrounds develop the highest central AV, Mline,core, and Mline,wing as Mline,tot increases with time, favoured by the local availability of material and the enhanced gravitational potential. Our results indicate that filaments acquiring a significantly

AoAtg26, a putative sterol glucosyltransferase, is required for autophagic degradation of peroxisomes, mitochondria, and nuclei in the filamentous fungus Aspergillus oryzae.

PubMed

Kikuma, Takashi; Tadokoro, Takayuki; Maruyama, Jun-Ichi; Kitamoto, Katsuhiko

2017-02-01

Autophagy is a conserved process in eukaryotic cells for degradation of cellular proteins and organelles. In filamentous fungi, autophagic degradation of organelles such as peroxisomes, mitochondria, and nuclei occurs in basal cells after the prolonged culture, but its mechanism is not well understood. Here, we functionally analyzed the filamentous fungus Aspergillus oryzae AoAtg26, an ortholog of the sterol glucosyltransferase PpAtg26 involved in pexophagy in the yeast Pichia pastoris. Deletion of Aoatg26 caused a severe decrease in conidiation and aerial hyphae formation, which is typically observed in the autophagy-deficient A. oryzae strains. In addition, cup-shaped AoAtg8-positive membrane structures were accumulated in the Aoatg26 deletion strain, indicating that autophagic process is impaired. Indeed, the Aoatg26 deletion strain was defective in the degradation of peroxisomes, mitochondria, and nuclei. Taken together, AoAtg26 plays an important role for autophagic degradation of organelles in A. oryzae, which may physiologically contribute to the differentiation in filamentous fungi.

Controlled rate cooling of fungi using a stirling cycle freezer.

PubMed

Ryan, Matthew J; Kasulyte-Creasey, Daiva; Kermode, Anthony; San, Shwe Phue; Buddie, Alan G

2014-01-01

The use of a Stirling cycle freezer for cryopreservation is considered to have significant advantages over traditional methodologies including N2 free operation, application of low cooling rates, reduction of sample contamination risks and control of ice nucleation. The study assesses the suitability of an 'N2-free' Stirling Cycle controlled rate freezer for fungi cryopreservation. In total, 77 fungi representing a broad taxonomic coverage were cooled using the N2 free cooler following a cooling rate of -1 degrees C min(-1). Of these, 15 strains were also cryopreserved using a traditional 'N2 gas chamber' controlled rate cooler and a comparison of culture morphology and genomic stability against non-cryopreserved starter cultures was undertaken. In total of 75 fungi survived cryopreservation, only a recalcitrant Basidiomycete and filamentous Chromist failed to survive. No changes were detected in genomic profile after preservation, suggesting that genomic function is not adversely compromised as a result of using 'N2 free' cooling. The results demonstrate the potential of 'N2-free' cooling for the routine cryopreservation of fungi in Biological Resource Centres.

Diversity of spoilage fungi associated with various French dairy products.

PubMed

Garnier, Lucille; Valence, Florence; Pawtowski, Audrey; Auhustsinava-Galerne, Lizaveta; Frotté, Nicolas; Baroncelli, Riccardo; Deniel, Franck; Coton, Emmanuel; Mounier, Jérôme

2017-01-16

Yeasts and molds are responsible for dairy product spoilage, resulting in significant food waste and economic losses. Yet, few studies have investigated the diversity of spoilage fungi encountered in dairy products. In the present study, 175 isolates corresponding to 105 from various spoiled dairy products and 70 originating from dairy production environments, were identified using sequencing of the ITS region, the partial β-tubulin, calmodulin and/or EFα genes, and the D1-D2 domain of the 26S rRNA gene for filamentous fungi and yeasts, respectively. Among the 41 species found in spoiled products, Penicillium commune and Penicillium bialowiezense were the most common filamentous fungi, representing around 10% each of total isolates while Meyerozyma guilliermondii and Trichosporon asahii were the most common yeasts (4.8% each of total isolates). Several species (e.g. Penicillium antarcticum, Penicillium salamii and Cladosporium phyllophilum) were identified for the first time in dairy products or their environment. In addition, numerous species were identified in both spoiled products and their corresponding dairy production environment suggesting that the latter acts as a primary source of contamination. Secondly, the resistance to chemical preservatives (sodium benzoate, calcium propionate, potassium sorbate and natamycin) of 10 fungal isolates representative of the observed biodiversity was also evaluated. Independently of the fungal species, natamycin had the lowest minimum inhibitory concentration (expressed in gram of preservative/l), followed by potassium sorbate, sodium benzoate and calcium propionate. In the tested conditions, Cladosporium halotolerans and Didymella pinodella were the most sensitive fungi while Yarrowia lipolytica and Candida parapsilosis were the most resistant towards the tested preservatives. This study provides interesting information on the occurrence of fungal contaminants in dairy products and environments that may help developing

Screening of thermotolerant and thermophilic fungi aiming β-xylosidase and arabinanase production.

PubMed

Benassi, Vivian Machado; de Lucas, Rosymar Coutinho; Jorge, João Atílio; Polizeli, Maria de Lourdes Teixeira de Moraes

2014-01-01

Plant cell wall is mainly composed by cellulose, hemicellulose and lignin. The heterogeneous structure and composition of the hemicellulose are key impediments to its depolymerization and subsequent use in fermentation processes. Thus, this study aimed to perform a screening of thermophilic and thermotolerant filamentous fungi collected from different regions of the São Paulo state, and analyze the production of β-xylosidase and arabinanase at different temperatures. These enzymes are important to cell wall degradation and synthesis of end products as xylose and arabinose, respectively, which are significant sugars to fermentation and ethanol production. A total of 12 fungal species were analyzed and 9 of them grew at 45 °C, suggesting a thermophilic or thermotolerant character. Additionally Aspergillus thermomutatus anamorph of Neosartorya and A. parasiticus grew at 50 °C. Aspergillus niger and Aspergillus thermomutatus were the filamentous fungi with the most expressive production of β-xylosidase and arabinanase, respectively. In general for most of the tested microorganisms, β-xylosidase and arabinanase activities from mycelial extract (intracellular form) were higher in cultures grown at high temperatures (35-40 °C), while the correspondent extracellular activities were favorably secreted from cultures at 30 °C. This study contributes to catalogue isolated fungi of the state of São Paulo, and these findings could be promising sources for thermophilic and thermotolerant microorganisms, which are industrially important due to their enzymes.

Performance of mycology and histopathology tests for the diagnosis of toenail onychomycosis due to filamentous fungi: Dermatophyte and non-dermatophyte moulds.

PubMed

Lavorato, Fernanda G; Guimarães, Dávson A; Premazzi, Mario G; Piñeiro-Maceira, Juan M; Bernardes-Engemann, Andréa R; Orofino-Costa, Rosane

2017-09-01

Improvement of laboratory diagnosis of onychomychosis is important so that adequate treatment can be safely implemented. To evaluate and compare the performance of mycological and histopathological examinations in onychomycoses caused by dermatophyte and non-dermatophyte moulds. Patients with lateral/distal subungual onychomycosis in at least one hallux were enrolled in the protocol and assessed via mycological and histopathological tests. The isolation of filamentous fungi was considered the gold standard. Test performance was evaluated through sensitivity, specificity and positive and negative predictive values. A total of 212 patients were enrolled in the study. Direct microscopy (DM) was positive in 57.5% patients, and cultures in 34.4%. Among these patients, 23.3% were positive for dermatophytes, with Trichophyton rubrum the most frequently isolated, and 86.3% were positive for non-dermatophytes, with Neoscytalidium dimidiatum predominance. Histopathology was positive in 41.0% samples. Direct microscopy showed better sensitivity for non-dermatophyte moulds (P=.000) and nail clipping was more specific for dermatophyte (P=.018). Histopathology of the distal nail plate is a valuable complementary tool for the diagnosis of onychomycosis caused by dermatophytes and direct microscopy is especially useful for non-dermatophyte molds. © 2017 Blackwell Verlag GmbH.

Insights into the phylogeny or arylamine N-acetyltransferases in fungi.

PubMed

Martins, Marta; Dairou, Julien; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Silar, Philippe

2010-08-01

Previous studies have shown that Eumycetes fungi can acylate arylamine thanks to arylamine N-acetyltransferases, xenobiotic-metabolizing enzymes also found in animals and bacteria. In this article, we present the results of mining 96 available fungal genome sequences for arylamine N-acetyltransferase genes and propose their phylogeny. The filamentous Pezizomycotina are shown to possess many putative N-acetyltransferases, whilst these are often lacking in other fungal groups. The evolution of the N-acetyltransferases is best explained by the presence of at least one gene in the opisthokont ancestor of the fungi and animal kingdoms, followed by recurrent gene losses and gene duplications. A possible horizontal gene transfer event may have occurred from bacteria to the basidiomycetous yeast Malassezia globosa.

Overview on the Biochemical Potential of Filamentous Fungi to Degrade Pharmaceutical Compounds

PubMed Central

Olicón-Hernández, Darío R.; González-López, Jesús; Aranda, Elisabet

2017-01-01

Pharmaceuticals represent an immense business with increased demand due to intensive livestock raising and an aging human population, which guarantee the quality of human life and well-being. However, the development of removal technologies for these compounds is not keeping pace with the swift increase in their use. Pharmaceuticals constitute a potential risk group of multiclass chemicals of increasing concern since they are extremely frequent in all environments and have started to exhibit negative effects on micro- and macro-fauna as well as on human health. In this context, fungi are known to be extremely diverse and poorly studied microorganisms despite being well suited for bioremediation processes, taking into account their metabolic and physiological characteristics for the transformation of even highly toxic xenobiotic compounds. Increasing studies indicate that fungi can transform many structures of pharmaceutical compounds, including anti-inflammatories, β-blockers, and antibiotics. This is possible due to different mechanisms in combination with the extracellular and intracellular enzymes, which have broad of biotechnological applications. Thus, fungi and their enzymes could represent a promising tool to deal with this environmental problem. Here, we review the studies performed on pharmaceutical compounds biodegradation by the great diversity of these eukaryotes. We examine the state of the art of the current application of the Basidiomycota division, best known in this field, as well as the assembly of novel biodegradation pathways within the Ascomycota division and the Mucoromycotina subdivision from the standpoint of shared enzymatic systems, particularly for the cytochrome P450 superfamily of enzymes, which appear to be the key enzymes in these catabolic processes. Finally, we discuss the latest advances in the field of genetic engineering for their further application. PMID:28979245

Dynamics of Actin Cables in Polarized Growth of the Filamentous Fungus Aspergillus nidulans

PubMed Central

Bergs, Anna; Ishitsuka, Yuji; Evangelinos, Minoas; Nienhaus, G. U.; Takeshita, Norio

2016-01-01

Highly polarized growth of filamentous fungi requires a continuous supply of proteins and lipids to the hyphal tip. This transport is managed by vesicle trafficking via the actin and microtubule cytoskeletons and their associated motor proteins. Particularly, actin cables originating from the hyphal tip are essential for hyphal growth. Although, specific marker proteins have been developed to visualize actin cables in filamentous fungi, the exact organization and dynamics of actin cables has remained elusive. Here, we observed actin cables using tropomyosin (TpmA) and Lifeact fused to fluorescent proteins in living Aspergillus nidulans hyphae and studied the dynamics and regulation. GFP tagged TpmA visualized dynamic actin cables formed from the hyphal tip with cycles of elongation and shrinkage. The elongation and shrinkage rates of actin cables were similar and approximately 0.6 μm/s. Comparison of actin markers revealed that high concentrations of Lifeact reduced actin dynamics. Simultaneous visualization of actin cables and microtubules suggests temporally and spatially coordinated polymerization and depolymerization between the two cytoskeletons. Our results provide new insights into the molecular mechanism of ordered polarized growth regulated by actin cables and microtubules. PMID:27242709

Isolation of autochthonous non-white rot fungi with potential for enzymatic upgrading of Venezuelan extra-heavy crude oil

PubMed Central

Naranjo, Leopoldo; Urbina, Hector; De Sisto, Angela; Leon, Vladimir

2007-01-01

The increasing world demand for fuels makes it necessary to exploit the largest reserve of extra-heavy crude oil (EHCO) of the Orinoco Oil Belt from Venezuela. We propose the use of extracellular oxidative enzymes, in particular, lignin-degrading enzyme systems (LDS) of fungi, for enzymatic improvement of EHCO. Autochthonous non-white rot fungal strains able to use EHCO, and several polycyclic aromatic hydrocarbons (PAHs) as sole carbon source and energy, were isolated from EHCO-polluted soils and identified as belonging to the genera Fusarium, Penicillium , Trichoderma , Aspergillus , Neosartorya, Pseudallescheria, Cladosporium, Pestalotiopsis , Phoma and Paecillomyces. Phenotypic and biochemical assays revealed the ability of these filamentous fungi to synthesize extracellular oxidative enzymes, and suggested a relationship between the LDS and EHCO bioconversion. This work reports, for the first time, the use of o-phenylenediamine dihydrochloride (OPD) as substrate to measure extracellular ligninolytic peroxidases (ELP) in culture broths of filamentous fungi (Fusarium solani HP-1), and constitutes the first formal study of the fungal community associated with the EHCO of the Orinoco Oil Belt. PMID:18833334

Planck intermediate results: XXXIII. Signature of the magnetic field geometry of interstellar filaments in dust polarization maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.

2016-02-09

Planck observations at 353 GHz provide the first fully sampled maps of the polarized dust emission towards interstellar filaments and their backgrounds (i.e., the emission observed in the surroundings of the filaments). The data allow us to determine the intrinsic polarization properties of the filaments and therefore to provide insight into the structure of their magnetic field (B). In this paper, we present the polarization maps of three nearby (several parsecs long) star-forming filaments of moderate column density (N H about 10 22 cm -2): Musca, B211, and L1506. These three filaments are detected above the background in dust totalmore » and polarized emission. We use the spatial information to separate Stokes I, Q, and U of the filaments from those of their backgrounds, an essential step in measuring the intrinsic polarization fraction (p) and angle (ψ) of each emission component. We find that the polarization angles in the three filaments (ψ fil) are coherent along their lengths and not the same as in their backgrounds (ψ bg). The differences between ψ fil and ψ bg are 12° and 54° for Musca and L1506, respectively, and only 6° in the case of B211. These differences forMusca and L1506 are larger than the dispersions of ψ, both along the filaments and in their backgrounds. The observed changes of ψ are direct evidence of variations of the orientation of the plane of the sky (POS) projection of the magnetic field. As in previous studies, we find a decrease of several per cent in p with N H from the backgrounds to the crest of the filaments. We show that the bulk of the drop in p within the filaments cannot be explained by random fluctuations of the orientation of the magnetic field because they are too small (σ ψ< 10°). We recognize the degeneracy between the dust alignment efficiency (by, e.g., radiative torques) and the structure of the B-field in causing variations in p, but we argue that the decrease in p from the backgrounds to the filaments

Trichoderma harzianum: Inhibition of mycotoxin producing fungi and toxin biosynthesis.

PubMed

Braun, H; Woitsch, L; Hetzer, B; Geisen, R; Zange, B; Schmidt-Heydt, M

2018-04-19

A quarter of the world-wide crop is spoiled by filamentous fungi and their mycotoxins and weather extremes associated with the climate change lead to further deterioration of the situation. The ingestion of mycotoxins causes several health issues leading in the worst case to cancer in humans and animals. Common intervention strategies against mycotoxin producing fungi, such as the application of fungicides, may result in undesirable residues and in some cases to a stress induction of mycotoxin biosynthesis. Moreover, development of fungicide resistances has greatly impacted pre- and postharvest fungal diseases. Hence there is the need to develop alternative strategies to reduce fungal infestation and thus mycotoxin contamination in the food chain. Such a strategy for natural competition of important plant-pathogenic and mycotoxin producing fungi could be Trichoderma harzianum, a mycoparasitic fungus. Especially in direct comparison to certain tested fungicides, the inhibition of different tested fungal species by T. harzianum was comparable, more sustainable and in some cases more effective, too. Besides substantially reduced growth rates, a transcriptional based inhibition of mycotoxin biosynthesis in the competed Aspergillus species could be shown. Furthermore it could be clearly observed by high-resolution Scanning Electron Microscopy (SEM) that T. harzianum actively attaches to the competitor species followed by subsequent enzymatic lysis of those mycelial filaments. The analyzed isolate of T. harzianum MRI349 is not known to produce mycotoxins. In this study it could be successfully proven that T. harzianum as a biological competitor is an effective complement to the use of fungicides. Copyright © 2018 Elsevier B.V. All rights reserved.

Exploring Virulence Determinants of Filamentous Fungal Pathogens through Interactions with Soil Amoebae.

PubMed

Novohradská, Silvia; Ferling, Iuliia; Hillmann, Falk

2017-01-01

Infections with filamentous fungi are common to all animals, but attention is rising especially due to the increasing incidence and high mortality rates observed in immunocompromised human individuals. Here, Aspergillus fumigatus and other members of its genus are the leading causative agents. Attributes like their saprophytic life-style in various ecological niches coupled with nutritional flexibility and a broad host range have fostered the hypothesis that environmental predators could have been the actual target for some of their virulence determinants. In this mini review, we have merged the recent findings focused on the potential dual-use of fungal defense strategies against innate immune cells and soil amoebae as natural phagocytes. Well-established virulence attributes like the melanized surface of fungal conidia or their capacity to produce toxic secondary metabolites have also been found to be protective against the model amoeba Dictyostelium discoideum . Some of the recent advances during interaction studies with human cells have further promoted the adaptation of other amoeba infection models, including the wide-spread generalist Acanthamoeba castellanii , or less prominent representatives like Vermamoeba vermiformis . We further highlight prospects and limits of these natural phagocyte models with regard to the infection biology of filamentous fungi and in comparison to the phagocytes of the innate immune system.

Genetically shaping morphology of the filamentous fungus Aspergillus glaucus for production of antitumor polyketide aspergiolide A

PubMed Central

2014-01-01

Background For filamentous fungi, the basic growth unit of hyphae usually makes it sensitive to shear stress which is generated from mechanical force and dynamic fluid in bioreactor, and it severely decreases microbial productions. The conventional strategies against shear-sensitive conundrum in fungal fermentation usually focus on adapting agitation, impeller type and bioreactor configuration, which brings high cost and tough work in industry. This study aims to genetically shape shear resistant morphology of shear-sensitive filamentous fungus Aspergillus glaucus to make it adapt to bioreactor so as to establish an efficient fermentation process. Results Hyphal morphology shaping by modifying polarized growth genes of A. glaucus was applied to reduce its shear-sensitivity and enhance aspergiolide A production. Degenerate PCR and genome walking were used to obtain polarized growth genes AgkipA and AgteaR, followed by construction of gene-deficient mutants by homologous integration of double crossover. Deletion of both genes caused meandering hyphae, for which, ΔAgkipA led to small but intense curves comparing with ΔAgteaR by morphology analysis. The germination of a second germ tube from conidiospore of the mutants became random while colony growth and development almost maintained the same. Morphology of ΔAgkipA and ΔAgteaR mutants turned to be compact pellet and loose clump in liquid culture, respectively. The curved hyphae of both mutants showed no remarkably resistant to glass bead grinding comparing with the wild type strain. However, they generated greatly different broth rheology which further caused growth and metabolism variations in bioreactor fermentations. By forming pellets, the ΔAgkipA mutant created a tank environment with low-viscosity, low shear stress and high dissolved oxygen tension, leading to high production of aspergiolide A (121.7 ± 2.3 mg/L), which was 82.2% higher than the wild type. Conclusions A new strategy for shaping fungal

[Multicenter Prospective Observational Study of Fungal Keratitis--Identification and Susceptibility Test of Fungi].

PubMed

Sunada, Atsuko; Asari, Seishi; Inoue, Yoshitsugu; Ohashi, Yuichi; Suzuki, Takashi; Shimomura, Yoshikazu; Fukuda, Masahiko; Sotozono, Chie; Hatano, Hiroshi; Eguchi, Hiroshi; Araki-Sasaki, Kaoru; Hoshi, Saichi; Yaguchi, Takashi; Makimura, Koichi; Yokokura, Shunji; Mochizuki, Kiyofumi; Monden, Yu; Nejima, Ryohei

2016-01-01

To investigate the causative fungi of fungal keratitis in Japan and their drug susceptibility. Identification and antifungal susceptibility test for 8 drugs (micafungin, amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, miconazole and pimaricin) were performed using isolated fungi from patients with fungal keratitis treated at 27 facilities in Japan between November 1, 2011 and October 31, 2013. Fungal strains were detected in 72 (50.7%) out of 142 samples. The major isolates were Fusarium spp. (18), Candida parapsilosis (12), C. albicans (11) and Alternaria spp. (6), in all, fungi of 31 species were identified by gene analysis. In the yeast-like fungi, susceptibility rates were evident for more than 80% in voriconazole, pimaricin, flucytosine, micafungin, amphotericin B and fluconazole. In filamentous fungi, the susceptibility rate was less than 50% except for PMR (90%). Fusarium spp., which were susceptible to amphotericin B and pimaricin, showed lower susceptibility rates compared with other genera. Although various genera and species of fungi cause fungal keratitis, the obtained drug susceptibility data in this study demonstrates the different susceptibility patterns among the major isolates (Fusarium spp., C. parapsilosis, C. albicans and other groups). This is important evidence useful for fungal keratitis treatment.

Heterologous expression of surface-active proteins from barley and filamentous fungi in Pichia pastoris and characterization of their contribution to beer gushing.

PubMed

Lutterschmid, Georg; Muranyi, Monika; Stübner, Matthias; Vogel, Rudi F; Niessen, Ludwig

2011-05-14

The spontaneous over-foaming of beer upon opening, i.e. beer gushing, is an unwanted phenomenon for the brewing industry. Currently, surface-active proteins from filamentous fungi and non-specific lipid transfer proteins (nsLTP1) from barley are discussed as gushing inducers. In our study the class I hydrophobin FcHyd3p from Fusarium culmorum, the class II hydrophobin Hfb2 from Trichoderma reesei, the alkaline foam protein A (AfpA) from F. graminearum and nsLTP1 from Hordeum vulgare cv. Marnie (barley) were heterologously expressed in Pichia pastoris and used in gushing tests. The class I hydrophobin FcHyd3p was unable to induce gushing in beer. The class II hydrophobin Hfb2 was able to induce gushing in beer, but proved to be inhibited by heat treatment as well as by the presence of enriched hop compounds. Both resulted in a reduced gushing potential. AfpA and nsLTP1 exhibited no gushing-inducing potential at the amounts added to beer. Addition of these proteins to beer or carbonated water previously treated with class II hydrophobins revealed a gushing reducing character. Copyright © 2011 Elsevier B.V. All rights reserved.

Disruption of ten protease genes in the filamentous fungus Aspergillus oryzae highly improves production of heterologous proteins.

PubMed

Yoon, Jaewoo; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

2011-02-01

Proteolytic degradation by secreted proteases into the culture medium is one of the significant problems to be solved in heterologous protein production by filamentous fungi including Aspergillus oryzae. Double (tppA, and pepE) and quintuple (tppA, pepE, nptB, dppIV, and dppV) disruption of protease genes enhanced human lysozyme (HLY) and bovine chymosin (CHY) production by A. oryzae. In this study, we used a quintuple protease gene disruptant and performed successive rounds of disruption for five additional protease genes (alpA, pepA, AopepAa, AopepAd, and cpI), which were previously investigated by DNA microarray analyses for their expression. Gene disruption was performed by pyrG marker recycling with a highly efficient gene-targeting background (∆ligD) as previously reported. As a result, the maximum yields of recombinant CHY and HLY produced by a decuple protease gene disruptant were approximately 30% and 35%, respectively, higher than those produced by a quintuple protease gene disruptant. Thus, we successfully constructed a decuple protease gene disruptant possessing highly improved capability of heterologous protein production. This is the first report on decuple protease gene disruption that improved the levels of heterologous protein production by the filamentous fungus A. oryzae.

Fungi and mycotoxins in cocoa: from farm to chocolate.

PubMed

Copetti, Marina V; Iamanaka, Beatriz T; Pitt, John I; Taniwaki, Marta H

2014-05-16

Cocoa is an important crop, as it is the raw material from which chocolate is manufactured. It is grown mainly in West Africa although significant quantities also come from Asia and Central and South America. Primary processing is carried out on the farm, and the flavour of chocolate starts to develop at that time. Freshly harvested pods are opened, the beans, piled in heaps or wooden boxes, are fermented naturally by yeasts and bacteria, then dried in the sun on wooden platforms or sometimes on cement or on the ground, where a gradual reduction in moisture content inhibits microbial growth. Beans are then bagged and marketed. In processing plants, the dried fermented beans are roasted, shelled and ground, then two distinct processes are used, to produce powdered cocoa or chocolate. Filamentous fungi may contaminate many stages in cocoa processing, and poor practices may have a strong influence on the quality of the beans. Apart from causing spoilage, filamentous fungi may also produce aflatoxins and ochratoxin A. This review deals with the growth of fungal species and formation of mycotoxins during the various steps in cocoa processing, as well as reduction of these contaminants by good processing practices. Methodologies for fungal and mycotoxin detection and quantification are discussed while current data about dietary exposure and regulation are also presented. Copyright © 2014 Elsevier B.V. All rights reserved.

ΛGR Centennial: Cosmic Web in Dark Energy Background

NASA Astrophysics Data System (ADS)

Chernin, A. D.

The basic building blocks of the Cosmic Web are groups and clusters of galaxies, super-clusters (pancakes) and filaments embedded in the universal dark energy background. The background produces antigravity, and the antigravity effect is strong in groups, clusters and superclusters. Antigravity is very weak in filaments where matter (dark matter and baryons) produces gravity dominating in the filament internal dynamics. Gravity-antigravity interplay on the large scales is a grandiose phenomenon predicted by ΛGR theory and seen in modern observations of the Cosmic Web.

The interaction of fungi with the environment orchestrated by RNAi.

PubMed

Villalobos-Escobedo, José Manuel; Herrera-Estrella, Alfredo; Carreras-Villaseñor, Nohemí

2016-01-01

The fungal kingdom has been key in the investigation of the biogenesis and function of small RNAs (sRNAs). The discovery of phenomena such as quelling in Neurospora crassa represents pioneering work in the identification of the main elements of the RNA interference (RNAi) machinery. Recent discoveries in the regulatory mechanisms in some yeast and filamentous fungi are helping us reach a deeper understanding of the transcriptional and post-transcriptional gene-silencing mechanisms involved in genome protection against viral infections, DNA damage and transposon activity. Although most of these mechanisms are reasonably well understood, their role in the physiology, response to the environment and interaction of fungi with other organisms had remained elusive. Nevertheless, studies in fungi such as Mucor circinelloides, Magnaporthe oryzae, Cryptococcus neoformans, Trichoderma atroviride, Botrytis cinerea and others have started to shed light on the relevance of the RNAi pathway. In these fungi gene regulation by RNAi is important for growth, reproduction, control of viral infections and transposon activity, as well as in the development of antibiotic resistance and interactions with their hosts. Moreover, the increasing number of reports of the discovery of microRNA-like RNAs in fungi under different conditions highlights the importance of fungi as models for understanding adaptation to the environment using regulation by sRNAs. The goal of this review is to provide the reader with an up-to-date overview of the importance of RNAi in the interaction of fungi with their environment. © 2016 by The Mycological Society of America.

Identification of novel and robust internal control genes from Volvariella volvacea that are suitable for RT-qPCR in filamentous fungi.

PubMed

Tao, Yongxin; van Peer, Arend Frans; Huang, Qianhui; Shao, Yanping; Zhang, Lei; Xie, Bin; Jiang, Yuji; Zhu, Jian; Xie, Baogui

2016-07-12

The selection of appropriate internal control genes (ICGs) is a crucial step in the normalization of real-time quantitative PCR (RT-qPCR) data. Housekeeping genes are habitually selected for this purpose, despite accumulating evidence on their instability. We screened for novel, robust ICGs in the mushroom forming fungus Volvariella volvacea. Nine commonly used and five newly selected ICGs were evaluated for expression stability using RT-qPCR data in eight different stages of the life cycle of V. volvacea. Three different algorithms consistently determined that three novel ICGs (SPRYp, Ras and Vps26) exhibited the highest expression stability in V. volvacea. Subsequent analysis of ICGs in twenty-four expression profiles from nine filamentous fungi revealed that Ras was the most stable ICG amongst the Basidiomycetous samples, followed by SPRYp, Vps26 and ACTB. Vps26 was expressed most stably within the analyzed data of Ascomycetes, followed by HH3 and β-TUB. No ICG was universally stable for all fungal species, or for all experimental conditions within a species. Ultimately, the choice of an ICG will depend on a specific set of experiments. This study provides novel, robust ICGs for Basidiomycetes and Ascomycetes. Together with the presented guiding principles, this enables the efficient selection of suitable ICGs for RT-qPCR.

Environment surveillance of filamentous fungi in two tertiary care hospitals in China.

PubMed

Hao, Zhen-feng; Ao, Jun-hong; Hao, Fei; Yang, Rong-ya; Zhu, He; Zhang, Jie

2011-07-05

Invasive fungal infections have constituted an increasingly important cause of morbidity and mortality in immunocompromised patients. In this study, a surveillance project was conducted in three different intensive care units of two large tertiary hospitals in China. A one-year surveillance project was conducted in two tertiary hospitals which located in northern China and southwest China respectively. Air, surfaces and tap water were sampled twice a month in a central intensive care unit, a bone marrow transplant unit, a neurosurgery intensive care unit and a live transplant department. Environmental conditions such as humidity, temperature and events taking place, for example the present of the visitors, healthcare staff and cleaning crew were also recorded at the time of sampling. The air fungal load was 91.94 cfu/m(3) and 71.02 cfu/m(3) in the southwest China hospital and the northern China hospital respectively. The five most prevalent fungi collected from air and surfaces were Penicillium spp., Cladospcrium spp., Alternaria spp., Aspergillus spp. and Saccharomyces spp. in the southwest China hospital, meanwhile Penicillium spp., Fusarium spp., Aspergillus spp., Alternaria spp. and Cladospcrium spp. in the northern China hospital. The least contaminated department was intensive care units, and the heaviest contaminated department was neurosurgery intensive care unit. Seventy-three percent of all surfaces examined in the northern China hospital and eighty-six percent in the southwest China hospital yielded fungi. Fifty-four percent of water samples from the northern China hospital and forty-nine percent from the southwest China hospital yielded fungi. These findings suggested that the fungus exist in the environment of the hospital including air, surface and water. Air and surface fungal load fluctuated over the year. Air fungal load was lower in winter and higher in summer and autumn, but seldom exceeded acceptable level. The higher values were created during

Major bioactive metabolites from marine fungi: A Review.

PubMed

Hasan, Saba; Ansari, Mohammad Israil; Ahmad, Anis; Mishra, Maitreyi

2015-01-01

Biologists and chemists of the world have been attracted towards marine natural products for the last five decades. Approximately 16,000 marine natural products have been isolated from marine organisms which have been reported in approximately 6,800 publications, proving marine microorganisms to be a invaluable source for the production of novel antibiotic, anti tumor, and anti inflammatory agents. The marine fungi particularly those associated with marine alga, sponge, invertebrates, and sediments appear to be a rich source for secondary metabolites, possessing Antibiotic, antiviral, antifungal and antiyeast activities. Besides, a few growth stimulant properties which may be useful in studies on wound healing, carcinogenic properties, and in the study of cancers are reported. Recent investigations on marine filamentous fungi looking for biologically active secondary metabolites indicate the tremendous potential of them as a source of new medicines. The present study reviews about some important bioactive metabolites reported from marine fungal strains which are anti bacterial, anti tumour and anti inflammatory in action. It highlights the chemistry and biological activity of the major bioactive alkaloids, polyketides, terpenoids, isoprenoid and non-isoprenoid compounds, quinones, isolated from marine fungi.

Screening of filamentous fungi for antimicrobial silver nanoparticles synthesis.

PubMed

Ottoni, Cristiane Angélica; Simões, Marta Filipa; Fernandes, Sara; Dos Santos, Jonas Gomes; da Silva, Elda Sabino; de Souza, Rodrigo Fernando Brambilla; Maiorano, Alfredo Eduardo

2017-12-01

The present work had the goal of screening a batch of 20 fungal strains, isolated from sugar cane plantation soil, in order to identify those capable of biosynthesis of silver nanoparticles. These nanoparticles are known to have a large and effective application in clinical microbiology. Four strains were found to be capable of biosynthesis of silver nanoparticles. The biosynthesised nanoparticles were characterised by UV-vis spectroscopy, scanning electron microscopy, EDX, and XRD. They were found to have an average size of 30-100 nm, a regular round shape, and potential antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The antimicrobial activity was found to be directly related to the nanoparticles concentration. Mycogenic synthesis of nanoparticles is a green biogenic process preferable to other alternatives. Because fungi are great producers of extracellular enzymes this process makes scaling-up an easier task with high importance for clinical microbiology on the fight against microbial resistance, as well as for other industrial applications.

Diversity of endophytic fungi in Glycine max.

PubMed

Fernandes, Elio Gomes; Pereira, Olinto Liparini; da Silva, Cynthia Cânedo; Bento, Claudia Braga Pereira; de Queiroz, Marisa Vieira

2015-12-01

Endophytic fungi are microorganisms that live within plant tissues without causing disease during part of their life cycle. With the isolation and identification of these fungi, new species are being discovered, and ecological relationships with their hosts have also been studied. In Glycine max, limited studies have investigated the isolation and distribution of endophytic fungi throughout leaves and roots. The distribution of these fungi in various plant organs differs in diversity and abundance, even when analyzed using molecular techniques that can evaluate fungal communities in different parts of the plants, such as denaturing gradient gel electrophoresis (DGGE). Our results show there is greater species richness of culturable endophytic filamentous fungi in the leaves G. max as compared to roots. Additionally, the leaves had high values for diversity indices, i.e. Simpsons, Shannon and Equitability. Conversely, dominance index was higher in roots as compared to leaves. The fungi Ampelomyces sp., Cladosporium cladosporioides, Colletotrichum gloeosporioides, Diaporthe helianthi, Guignardia mangiferae and Phoma sp. were more frequently isolated from the leaves, whereas the fungi Fusarium oxysporum, Fusarium solani and Fusarium sp. were prevalent in the roots. However, by evaluating the two communities by DGGE, we concluded that the species richness was higher in the roots than in the leaves. UPGMA analysis showed consistent clustering of isolates; however, the fungus Leptospora rubella, which belongs to the order Dothideales, was grouped among species of the order Pleosporales. The presence of endophytic Fusarium species in G. max roots is unsurprising, since Fusarium spp. isolates have been previously described as endophyte in other reports. However, it remains to be determined whether the G. max Fusarium endophytes are latent pathogens or non-pathogenic forms that benefit the plant. This study provides a broader knowledge of the distribution of the fungal

Of smuts, blasts, mildews, and blights: cAMP signaling in phytopathogenic fungi.

PubMed

Lee, Nancy; D'Souza, Cletus A; Kronstad, James W

2003-01-01

cAMP regulates morphogenesis and virulence in a wide variety of fungi including the plant pathogens. In saprophytic yeasts such as Saccharomyces cerevisiae, cAMP signaling plays an important role in nutrient sensing. In filamentous saprophytes, the cAMP pathway appears to play an integral role in vegetative growth and sporulation, with possible connections to mating. Infection-related morphogenesis includes sporulation (conidia and teliospores), formation of appressoria, infection hyphae, and sclerotia. Here, we review studies of cAMP signaling in a variety of plant fungal pathogens. The primary fungi to be considered include Ustilago maydis, Magnaporthe grisea, Cryphonectria parasitica, Colletotrichum and Fusarium species, and Erisyphe graminis. We also include related information on Trichoderma species that act as mycoparasites and biocontrol agents of phytopathogenic fungi. We point out similarities in infection mechanisms, conservation of signaling components, as well as instances of cross-talk with other signaling pathways.

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berka, Randy M.; Grigoriev, Igor V.; Otillar, Robert

2011-10-02

Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanismsmore » in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.« less

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berka, Randy M.; Grigoriev, Igor V.; Otillar, Robert

2011-05-16

Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanismsmore » in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.« less

Key Ecological Roles for Zoosporic True Fungi in Aquatic Habitats.

PubMed

Gleason, Frank H; Scholz, Bettina; Jephcott, Thomas G; van Ogtrop, Floris F; Henderson, Linda; Lilje, Osu; Kittelmann, Sandra; Macarthur, Deborah J

2017-03-01

The diversity and abundance of zoosporic true fungi have been analyzed recently using fungal sequence libraries and advances in molecular methods, such as high-throughput sequencing. This review focuses on four evolutionary primitive true fungal phyla: the Aphelidea, Chytridiomycota, Neocallimastigomycota, and Rosellida (Cryptomycota), most species of which are not polycentric or mycelial (filamentous), rather they tend to be primarily monocentric (unicellular). Zoosporic fungi appear to be both abundant and diverse in many aquatic habitats around the world, with abundance often exceeding other fungal phyla in these habitats, and numerous novel genetic sequences identified. Zoosporic fungi are able to survive extreme conditions, such as high and extremely low pH; however, more work remains to be done. They appear to have important ecological roles as saprobes in decomposition of particulate organic substrates, pollen, plant litter, and dead animals; as parasites of zooplankton and algae; as parasites of vertebrate animals (such as frogs); and as symbionts in the digestive tracts of mammals. Some chytrids cause economically important diseases of plants and animals. They regulate sizes of phytoplankton populations. Further metagenomics surveys of aquatic ecosystems are expected to enlarge our knowledge of the diversity of true zoosporic fungi. Coupled with studies on their functional ecology, we are moving closer to unraveling the role of zoosporic fungi in carbon cycling and the impact of climate change on zoosporic fungal populations.

Fungi in the cystic fibrosis lung: bystanders or pathogens?

PubMed

Chotirmall, Sanjay H; McElvaney, Noel G

2014-07-01

Improvement to the life expectancy of people with cystic fibrosis (PWCF) brings about novel challenges including the need for evaluation of the role of fungi in the cystic fibrosis (CF) lung. To determine if such organisms represent bystanders or pathogens affecting clinical outcomes we review the existing knowledge from a clinical, biochemical, inflammatory and immunological perspective. The prevalence and importance of fungi in the CF airway has likely been underestimated with the most frequently isolated filamentous fungi being Aspergillus fumigatus and Scedosporium apiospermum and the major yeast Candida albicans. Developing non-culture based microbiological methods for fungal detection has improved both our classification and understanding of their clinical consequences including localized, allergic and systemic infections. Cross-kingdom interaction between bacteria and fungi are discussed as is the role of biofilms further affecting clinical outcome. A combination of host and pathogen-derived factors determines if a particular fungus represents a commensal, colonizer or pathogen in the setting of CF. The underlying immune state, disease severity and treatment burden represent key host variables whilst fungal type, form, chronicity and virulence including the ability to evade immune recognition determines the pathogenic potential of a specific fungus at a particular point in time. Further research in this emerging field is warranted to fully elucidate the spectrum of disease conferred by the presence of fungi in the CF airway and the indications for therapeutic interventions. Copyright © 2014. Published by Elsevier Ltd.

Interspecific metabolic diversity of root-colonizing endophytic fungi revealed by enzyme activity tests.

PubMed

Knapp, Dániel G; Kovács, Gábor M

2016-12-01

Although dark septate endophytes (DSE) represent a worldwide dispersed form group of root-colonizing endophytic fungi, our knowledge on their role in ecosystem functioning is far limited. In this study, we aimed to test if functional diversity exists among DSE fungi representing different lineages of root endophytic fungal community of semiarid sandy grasslands. To address this question and to gain general information on function of DSE fungi, we adopted api-ZYM and BioLog FF assays to study those non-sporulating filamentous fungi and characterized the metabolic activity of 15 different DSE species. Although there were striking differences among the species, all of the substrates tested were utilized by the DSE fungi. When endophytes characteristic to grasses and non-grass host plants were separately considered, we found that the whole substrate repertoire was used by both groups. This might illustrate the complementary functional diversity of the communities root endophytic plant-associated fungi. The broad spectra of substrates utilized by these root endophytes illustrate the functional importance of their diversity, which can play role not only in nutrient mobilization and uptake of plants from with nutrient poor soils, but also in general plant performance and ecosystem functioning. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Prevalence of transcription factors in ascomycete and basidiomycete fungi

PubMed Central

2014-01-01

Background Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented. Results In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes. Conclusions This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla. PMID:24650355

Carbon utilization profile of the filamentous fungal species Fusarium fujikuroi, Penicillium decumbens, and Sarocladium strictum isolated from marine coastal environments.

PubMed

Fuentes, Marcelo E; Quiñones, Renato A

Facultative marine filamentous fungi have recently emerged as a functional component in coastal marine systems. However, little is known about their ecological role and functions in biogeochemical cycles. Penicillium decumbens, S. strictum, and F. fujikuroi were isolated from the coastal upwelling zone off south-central Chile. Their carbon profiles were characterized using Biolog FF MicroPlates. These species used a wide range of carbon sources, mainly carbohydrates, but also amino acids, suggesting the use of metabolic routes that include glycolysis/gluconeogenesis. Substrate richness revealed a great capacity for the utilization of nutritional sources, reflected by the following Shannon Indices of utilization of specific substrates: 4.02 for S. strictum, 4.01 for P. decumbes, and 3.91 for F. fujikuroi, which reveals a high physiological capacity for oxidizing different substrates. Significant differences were found between 18 substrates utilized by all three species. Results suggest that filamentous fungi should be considered an integral part of the marine microbial community and included in biogeochemical cycling models of upwelling ecosystems.

The Ustilago maydis Nit2 Homolog Regulates Nitrogen Utilization and Is Required for Efficient Induction of Filamentous Growth

PubMed Central

Horst, Robin J.; Zeh, Christine; Saur, Alexandra; Sonnewald, Sophia; Sonnewald, Uwe

2012-01-01

Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen Ustilago maydis and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2. nit2 deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of U. maydis. PMID:22247264

Safety assessment of continuous glass filaments used in eclipse.

PubMed

Swauger, J E; Foy, J W

2000-11-01

Eclipse is a cigarette that produces smoke by primarily heating, rather than burning, tobacco. The Eclipse heat source assembly employs a continuous filament glass mat jacket to insulate the heat source. The glass mat insulator is composed of continuous glass filaments and a binder. The purpose of this article is to address the potential toxicological significance of the continuous glass filaments under the conditions of intended use. Transfer data and the unique physical characteristics of the filaments demonstrate that significant exposure of the smoker will not occur. The available environmental survey data clearly demonstrate that Eclipse smokers are extremely unlikely to be exposed to continuous glass filaments at a level that represents a biologically significant increase over background exposure to glass fibers. The chemical composition of the continuous glass filaments used in Eclipse is generally similar to C-glass fiber compositions such as MMVF 11 that have failed to produce either tumors or fibrosis in chronic inhalation studies conducted in rats. In vitro dissolution data demonstrate that the continuous glass filaments used in Eclipse are more soluble than biologically active fibers such as rock wool (MMVF 21) or asbestos. However, the continuous glass filaments used in Eclipse were not as soluble in simulated extracellular lung fluid as representative C-glass fibers (MMVF 10 and MMVF 11). In brief, exposure of Eclipse smokers to continuous glass filaments is extremely unlikely to occur at a level that may be construed to be of biological significance.

Occurrence of fungi in combs of fungus-growing termites (Isoptera: Termitidae, Macrotermitinae).

PubMed

Guedegbe, Herbert J; Miambi, Edouard; Pando, Anne; Roman, Jocelyne; Houngnandan, Pascal; Rouland-Lefevre, Corinne

2009-10-01

Fungus-growing termites cultivate their mutualistic basidiomycete Termitomyces species on a substrate called a fungal comb. Here, the Suicide Polymerase Endonuclease Restriction (SuPER) method was adapted for the first time to a fungal study to determine the entire fungal community of fungal combs and to test whether fungi other than the symbiotic cultivar interact with termite hosts. Our molecular analyses show that although active combs are dominated by Termitomyces fungi isolated with direct Polymerase Endonuclease Restriction - Denaturing Gradient Gel Electrophoresis (PCR-DGGE), they can also harbor some filamentous fungi and yeasts only revealed by SuPER PCR-DGGE. This is the first molecular evidence of the presence of non-Termitomyces species in active combs. However, because there is no evidence for a species-specific relationship between these fungi and termites, they are mere transient guests with no specialization in the symbiosis. It is however surprising to notice that termite-associated Xylaria strains were not isolated from active combs even though they are frequently retrieved when nests are abandoned by termites. This finding highlights the implication of fungus-growing termites in the regulation of fungi occurring within the combs and also suggests that they might not have any particular evolutionary-based association with Xylaria species.

Interkingdom Gene Transfer of a Hybrid NPS/PKS from Bacteria to Filamentous Ascomycota

PubMed Central

Lawrence, Daniel P.; Kroken, Scott; Pryor, Barry M.; Arnold, A. Elizabeth

2011-01-01

Nonribosomal peptides (NRPs) and polyketides (PKs) are ecologically important secondary metabolites produced by bacteria and fungi using multidomain enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Previous phylogenetic analyses of fungal NRPSs and PKSs have suggested that a few of these genes were acquired by fungi via horizontal gene transfer (HGT) from bacteria, including a hybrid NPS/PKS found in Cochliobolus heterostrophus (Dothideomycetes, Ascomycota). Here, we identify this hybrid gene in fungi representing two additional classes of Ascomycota (Aspergillus spp., Microsporum canis, Arthroderma spp., and Trichophyton spp., Eurotiomycetes; Chaetomium spp. and Metarhizium spp., Sordariomycetes) and use phylogenetic analyses of the most highly conserved domains from NRPSs (adenylation (A) domain) and PKSs (ketoacyl synthase (KS) domain) to examine the hypothesis that the hybrid NPS7/PKS24 was acquired by fungi from bacteria via HGT relatively early in the evolution of the Pezizomycotina. Our results reveal a unique ancestry of the A domain and KS domain in the hybrid gene relative to known fungal NRPSs and PKSs, provide strong evidence for HGT of the hybrid gene from a putative bacterial donor in the Burkholderiales, and suggest the HGT event occurred early in the evolution of the filamentous Ascomycota. PMID:22140558

Mycoremediation of congo red dye by filamentous fungi.

PubMed

Bhattacharya, Sourav; Das, Arijit; G, Mangai; K, Vignesh; J, Sangeetha

2011-10-01

Azo, anthroquinone and triphenylmethane dyes are the major classes of synthetic colourants, which are difficult to degrade and have received considerable attention. Congo red, a diazo dye, is considered as a xenobiotic compound, and is recalcitrant to biodegradative processes. Nevertheless, during the last few years it has been demonstrated that several fungi, under certain environmental conditions, are able to transfer azo dyes to non toxic products using laccases. The aim of this work was to study the factors influencing mycoremediation of Congo red. Several basidiomycetes and deuteromycetes species were tested for the decolourisation of Congo red (0.05 g/l) in a semi synthetic broth at static and shaking conditions. Poor decolourisation was observed when the dye acted as the sole source of nitrogen, whereas semi synthetic broth supplemented with fertilizer resulted in better decolourisation. Decolourisation of Congo red was checked in the presence of salts of heavy metals such as mercuric chloride, lead acetate and zinc sulphate. Decolourisation parameters such as temperature, pH, and rpm were optimized and the decolourisation obtained at optimized conditions varied between 29.25- 97.28% at static condition and 82.1- 100% at shaking condition. Sodium dodecyl sulphate polyacrylamide gel electrophoretic analysis revealed bands with molecular weights ranging between 66.5 to 71 kDa, a characteristic of the fungal laccases. High efficiency decolourisation of Congo red makes these fungal forms a promising choice in biological treatment of waste water containing Congo red.

Insect symbiosis: derivation of yeast-like endosymbionts within an entomopathogenic filamentous lineage.

PubMed

Suh, S O; Noda, H; Blackwell, M

2001-06-01

Yeast-like endosymbionts (YLSs) of insects often are restricted to specific hosts and are essential to the host's survival. For example, in planthoppers (Homoptera: Delphacidae), endosymbionts function in sterol utilization and nitrogen recycling for the hosts. Our study, designed to investigate evolutionary changes in the YLS lineage involved in the planthopper association, strongly suggests an origin of the YLSs from within the filamentous ascomycetes (Euascomycetes), not the true yeasts (Saccharomycetes), as their morphology might indicate. During divergence of the planthopper YLSs, dramatic changes would have occurred in the insect-fungus interaction and the fungal morphology that have previously been undescribed in filamentous ascomycetes. Phylogenetic trees were based on individual and combined data sets of 2.6 kb of the nuclear small- and large-subunit ribosomal RNA genes for YLSs from three rice planthoppers (Laodelphax striatellus, Nilaparvata lugens, and Sogatella furcifera) compared with 56 other fungi. Parsimony analysis placed the planthopper YLSs within Cordyceps (Euascomycetes: Hypocreales: Clavicipitaceae), a genus of filamentous insects and a few fungal pathogenic ascomycetes. Another YLS species restricted to the aphid Hamiltonaphis styraci (Homoptera: Aphididae) was a sister taxon to the planthopper YLSS: Filamentous insect pathogens (Metarhizium and Beauveria) specific to the same species of insect hosts as the YLSs also formed lineages within the Clavicipitaceae, but these were distinct from the clade comprising YLS species. Trees constrained to include the YLSs in families of the Hypocreales other than the Clavicipitaceae were rejected by the Kishino-Hasegawa test. In addition, the results of this study support a hypothesis of two independent origins of insect-associated YLSs from among filamentous ascomycetes: the planthopper YLSs in the Clavicipitaceae and the YLSs associated with anobiid beetles (Symbiotaphrina species). Several lineages of

Fungi-based treatment of brewery wastewater-biomass production and nutrient reduction.

PubMed

Hultberg, M; Bodin, H

2017-06-01

The beer-brewing process produces high amounts of nutrient-rich wastewater, and the increasing number of microbreweries worldwide has created a need for innovative solutions to deal with this waste. In the present study, fungal biomass production and the removal of organic carbon, phosphorus and nitrogen from synthetic brewery wastewater were studied. Different filamentous fungi with a record of safe use were screened for growth, and Trametes versicolor, Pleurotus ostreatus and Trichoderma harzianum were selected for further work. The highest biomass production, 1.78 ± 0.31 g L -1 of dry weight, was observed when P. ostreatus was used for the treatment, while T. harzianum demonstrated the best capability for removing nutrients. The maximum reduction of chemical oxygen demand, 89% of the initial value, was observed with this species. In the removal of total nitrogen and phosphorus, no significant difference was observed between the species, while removal of ammonium varied between the strains. The maximum reduction of ammonium, 66.1% of the initial value, was also found in the T. harzianum treatment. It can be concluded that all treatments provided significant reductions in all water-quality parameters after 3 days of growth and that the utilisation of filamentous fungi to treat brewery wastewater, linked to a deliberate strategy to use the biomass produced, has future potential in a bio-based society.

Mutation-specific effects on thin filament length in thin filament myopathy.

PubMed

Winter, Josine M de; Joureau, Barbara; Lee, Eun-Jeong; Kiss, Balázs; Yuen, Michaela; Gupta, Vandana A; Pappas, Christopher T; Gregorio, Carol C; Stienen, Ger J M; Edvardson, Simon; Wallgren-Pettersson, Carina; Lehtokari, Vilma-Lotta; Pelin, Katarina; Malfatti, Edoardo; Romero, Norma B; Engelen, Baziel G van; Voermans, Nicol C; Donkervoort, Sandra; Bönnemann, C G; Clarke, Nigel F; Beggs, Alan H; Granzier, Henk; Ottenheijm, Coen A C

2016-06-01

Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force-sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin-thick filament overlap. These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. Ann Neurol 2016;79:959-969. © 2016 American Neurological Association.

Mutation-Specific Effects on Thin Filament Length in Thin Filament Myopathy

PubMed Central

de Winter, Josine M.; Joureau, Barbara; Lee, Eun-Jeong; Kiss, Balázs; Yuen, Michaela; Gupta, Vandana A.; Pappas, Christopher T.; Gregorio, Carol C.; Stienen, Ger J. M.; Edvardson, Simon; Wallgren-Pettersson, Carina; Lehtokari, Vilma-Lotta; Pelin, Katarina; Malfatti, Edoardo; Romero, Norma B.; van Engelen, Baziel G.; Voermans, Nicol C.; Donkervoort, Sandra; Bönnemann, C. G.; Clarke, Nigel F.; Beggs, Alan H.; Granzier, Henk; Ottenheijm, Coen A. C.

2016-01-01

Objective Thin filament myopathies are among the most common nondystrophic congenital muscular disorders, and are caused by mutations in genes encoding proteins that are associated with the skeletal muscle thin filament. Mechanisms underlying muscle weakness are poorly understood, but might involve the length of the thin filament, an important determinant of force generation. Methods We investigated the sarcomere length-dependence of force, a functional assay that provides insights into the contractile strength of muscle fibers as well as the length of the thin filaments, in muscle fibers from 51 patients with thin filament myopathy caused by mutations in NEB, ACTA1, TPM2, TPM3, TNNT1, KBTBD13, KLHL40, and KLHL41. Results Lower force generation was observed in muscle fibers from patients of all genotypes. In a subset of patients who harbor mutations in NEB and ACTA1, the lower force was associated with downward shifted force–sarcomere length relations, indicative of shorter thin filaments. Confocal microscopy confirmed shorter thin filaments in muscle fibers of these patients. A conditional Neb knockout mouse model, which recapitulates thin filament myopathy, revealed a compensatory mechanism; the lower force generation that was associated with shorter thin filaments was compensated for by increasing the number of sarcomeres in series. This allowed muscle fibers to operate at a shorter sarcomere length and maintain optimal thin–thick filament overlap. Interpretation These findings might provide a novel direction for the development of therapeutic strategies for thin filament myopathy patients with shortened thin filament lengths. PMID:27074222

Diagnosis of femtosecond plasma filament by channeling microwaves along the filament

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alshershby, Mostafa; Ren, Yu; Qin, Jiang

2013-05-20

We introduce a simple, fast, and non-intrusive experimental method to obtain the basic parameters of femtosecond laser-generated plasma filament. The method is based on the channeling of microwaves along both a plasma filament and a well-defined conducting wire. By comparing the detected microwaves that propagate along the plasma filament and a copper wire with known conductivity and spatial dimension, the basic parameters of the plasma filament can be easily obtained. As a result of the possibility of channeling microwave radiation along the plasma filament, we were then able to obtain the plasma density distribution along the filament length.

Single cell oil of oleaginous fungi from the tropical mangrove wetlands as a potential feedstock for biodiesel

PubMed Central

2012-01-01

Background Single cell oils (SCOs) accumulated by oleaginous fungi have emerged as a potential alternative feedstock for biodiesel production. Though fungi from mangrove ecosystem have been reported for production of several lignocellulolytic enzymes, they remain unexplored for their SCO producing ability. Thus, these oleaginous fungi from the mangrove ecosystem could be suitable candidates for production of SCOs from lignocellulosic biomass. The accumulation of lipids being species specific, strain selection is critical and therefore, it is of importance to evaluate the fungal diversity of mangrove wetlands. The whole cells of these fungi were investigated with respect to oleaginicity, cell mass, lipid content, fatty acid methyl ester profiles and physicochemical properties of transesterified SCOs in order to explore their potential for biodiesel production. Results In the present study, 14 yeasts and filamentous fungi were isolated from the detritus based mangrove wetlands along the Indian west coast. Nile red staining revealed that lipid bodies were present in 5 of the 14 fungal isolates. Lipid extraction showed that these fungi were able to accumulate > 20% (w/w) of their dry cell mass (4.14 - 6.44 g L-1) as lipids with neutral lipid as the major fraction. The profile of transesterified SCOs revealed a high content of saturated and monounsaturated fatty acids i.e., palmitic (C16:0), stearic (C18:0) and oleic (C18:1) acids similar to conventional vegetable oils used for biodiesel production. The experimentally determined and predicted biodiesel properties for 3 fungal isolates correlated well with the specified standards. Isolate IBB M1, with the highest SCO yield and containing high amounts of saturated and monounsaturated fatty acid was identified as Aspergillus terreus using morphotaxonomic study and 18 S rRNA gene sequencing. Batch flask cultures with varying initial glucose concentration revealed that maximal cell biomass and lipid content were

Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

PubMed Central

Parrent, Jeri Lynn; James, Timothy Y; Vasaitis, Rimvydas; Taylor, Andrew FS

2009-01-01

Background Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. Results We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. Conclusion We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability

Standoff Detection of Uranium and its Isotopes by Femtosecond Filament Laser Ablation Molecular Isotopic Spectrometry

DOE PAGES

Hartig, Kyle C.; Ghebregziabher, Isaac; Jovanovic, Igor

2017-03-08

The ability to perform not only elementally but also isotopically sensitive detection and analysis at standoff distances is important for remote sensing applications in diverse ares, such as nuclear nonproliferation, environmental monitoring, geophysics, and planetary science. We demonstrate isotopically sensitive real-time standoff detection of uranium by the use of femtosecond filament-induced laser ablation molecular isotopic spectrometry. A uranium oxide molecular emission isotope shift of 0.05 ± 0.007 nm is reported at 593.6 nm. We implement both spectroscopic and acoustic diagnostics to characterize the properties of uranium plasma generated at different filament- uranium interaction points. The resulting uranium oxide emission exhibitsmore » a nearly constant signal-to-background ratio over the length of the filament, unlike the uranium atomic and ionic emission, for which the signal-to-background ratio varies significantly along the filament propagation. This is explained by the different rates of increase of plasma density and uranium oxide density along the filament length resulting from spectral and temporal evolution of the filament along its propagation. Lastly, the results provide a basis for the optimal use of filaments for standoff detection and analysis of uranium isotopes and indicate the potential of the technique for a wider range of remote sensing applications that require isotopic sensitivity.« less

Standoff Detection of Uranium and its Isotopes by Femtosecond Filament Laser Ablation Molecular Isotopic Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartig, Kyle C.; Ghebregziabher, Isaac; Jovanovic, Igor

The ability to perform not only elementally but also isotopically sensitive detection and analysis at standoff distances is important for remote sensing applications in diverse ares, such as nuclear nonproliferation, environmental monitoring, geophysics, and planetary science. We demonstrate isotopically sensitive real-time standoff detection of uranium by the use of femtosecond filament-induced laser ablation molecular isotopic spectrometry. A uranium oxide molecular emission isotope shift of 0.05 ± 0.007 nm is reported at 593.6 nm. We implement both spectroscopic and acoustic diagnostics to characterize the properties of uranium plasma generated at different filament- uranium interaction points. The resulting uranium oxide emission exhibitsmore » a nearly constant signal-to-background ratio over the length of the filament, unlike the uranium atomic and ionic emission, for which the signal-to-background ratio varies significantly along the filament propagation. This is explained by the different rates of increase of plasma density and uranium oxide density along the filament length resulting from spectral and temporal evolution of the filament along its propagation. Lastly, the results provide a basis for the optimal use of filaments for standoff detection and analysis of uranium isotopes and indicate the potential of the technique for a wider range of remote sensing applications that require isotopic sensitivity.« less

Standoff Detection of Uranium and its Isotopes by Femtosecond Filament Laser Ablation Molecular Isotopic Spectrometry

NASA Astrophysics Data System (ADS)

Hartig, Kyle C.; Ghebregziabher, Isaac; Jovanovic, Igor

2017-03-01

The ability to perform not only elementally but also isotopically sensitive detection and analysis at standoff distances is impor-tant for remote sensing applications in diverse ares, such as nuclear nonproliferation, environmental monitoring, geophysics, and planetary science. We demonstrate isotopically sensitive real-time standoff detection of uranium by the use of femtosecond filament-induced laser ablation molecular isotopic spectrometry. A uranium oxide molecular emission isotope shift of 0.05 ± 0.007 nm is reported at 593.6 nm. We implement both spectroscopic and acoustic diagnostics to characterize the properties of uranium plasma generated at different filament-uranium interaction points. The resulting uranium oxide emis-sion exhibits a nearly constant signal-to-background ratio over the length of the filament, unlike the uranium atomic and ionic emission, for which the signal-to-background ratio varies significantly along the filament propagation. This is explained by the different rates of increase of plasma density and uranium oxide density along the filament length resulting from spectral and temporal evolution of the filament along its propagation. The results provide a basis for the optimal use of filaments for standoff detection and analysis of uranium isotopes and indicate the potential of the technique for a wider range of remote sensing applications that require isotopic sensitivity.

Structural elucidation of novel phosphocholine-containing glycosylinositol-phosphoceramides in filamentous fungi and their induction of cell death of cultured rice cells.

PubMed Central

Aoki, Kazuhiro; Uchiyama, Ryosuke; Itonori, Saki; Sugita, Mutsumi; Che, Fang-Sik; Isogai, Akira; Hada, Noriyasu; Hada, Junko; Takeda, Tadahiro; Kumagai, Hidehiko; Yamamoto, Kenji

2004-01-01

Novel ZGLs (zwitterionic glycosphingolipids) have been found in and extracted from the mycelia of filamentous fungi ( Acremonium sp.) isolated from soil. Five ZGLs (ZGL1-ZGL5) were structurally elucidated by sugar compositional analysis, methylation analysis, periodate oxidation, matrix-assisted laser-desorption ionization-time-of-flight MS, (1)H-NMR spectroscopy and fast-atom bombardment MS. Their chemical structures were as follows: GlcN(alpha1-2)Ins1-P-1Cer (ZGL1), Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL2), Man(alpha1-6)Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL3), PC-->6Man(alpha1-6)GlcN(alpha1-2)Ins1- P -1Cer (ZGL4), and PC-->6Man(alpha1-6)Man(alpha1-6)GlcN(alpha1-2)Ins1-P-1Cer (ZGL5) (where Cer is ceramide and PC is phosphocholine). In addition, one acidic glycosphingolipid, which was the precursor of ZGLs, was also characterized as inositol-phosphoceramide. The core structure of the ZGLs, GlcN(alpha1-2)Ins1- P, is rather different from those found in other fungi, such as Man(alpha1-2)Ins1- P and Man(alpha1-6)Ins1- P. Interestingly, the terminal mannose residue of ZGL4 and ZGL5 was modified further with a PC group. The presence of PC-containing glycosylinositol-phosphoceramides has not been reported previously in any organism. The ceramide constituents of both ZGLs and acidic glycosphingolipid were essentially the same, and consisted of a 4-hydroxyoctadecasphinganine (phytosphingosine) as the sole sphingoid base and 2-hydroxytetracosanoic acid (>90%) as the major fatty acid. ZGLs were found to cause cell death in suspensions of cultured rice cells. The cell death-inducing activity of ZGLs is probably due to the characteristic glycan moiety of Man(alpha1-6)GlcN, and PC-containing ZGLs had high activity. This study is the first to demonstrate that fungal glycosylinositol-phosphoceramides induce cell death in cultured rice cells. PMID:14583095

Diversity, Application, and Synthetic Biology of Industrially Important Aspergillus Fungi.

PubMed

Park, Hee-Soo; Jun, Sang-Cheol; Han, Kap-Hoon; Hong, Seung-Beom; Yu, Jae-Hyuk

2017-01-01

The filamentous fungal genus Aspergillus consists of over 340 officially recognized species. A handful of these Aspergillus fungi are predominantly used for food fermentation and large-scale production of enzymes, organic acids, and bioactive compounds. These industrially important Aspergilli primarily belong to the two major Aspergillus sections, Nigri and Flavi. Aspergillus oryzae (section Flavi) is the most commonly used mold for the fermentation of soybeans, rice, grains, and potatoes. Aspergillus niger (section Nigri) is used in the industrial production of various enzymes and organic acids, including 99% (1.4 million tons per year) of citric acid produced worldwide. Better understanding of the genomes and the signaling mechanisms of key Aspergillus species can help identify novel approaches to enhance these commercially significant strains. This review summarizes the diversity, current applications, key products, and synthetic biology of Aspergillus fungi commonly used in industry. Copyright © 2017 Elsevier Inc. All rights reserved.

Activity of Antarctic fungi extracts against phytopathogenic bacteria.

PubMed

Purić, J; Vieira, G; Cavalca, L B; Sette, L D; Ferreira, H; Vieira, M L C; Sass, D C

2018-06-01

This study aims to obtain secondary metabolites extracts from filamentous fungi isolated from soil and marine sediments from Antarctic ecosystems and to assess its potential antibacterial activity on Xanthomonas euvesicatoria and Xanthomonas axonopodis pv. passiflorae (phytopathogenic bacteria causing diseases in pepper and tomato and passionfruit, respectively). Among the 66 crude intracellular and extracellular extracts obtained from fungi recovered from soil and 79 obtained from marine sediment samples, 25 showed the ability to prevent the growth of X. euvesicatoria in vitro and 28 showed the ability to prevent the growth of X. axonopodis pv. passiflorae in vitro. Intracellular and extracellular extracts from soil fungi inhibited around 97% of X. euvesicatoria and 98% of X. axonopodis pv. passiflorae at 2·1 mg ml -1 . The average inhibition rates against X. euvesicatoria and X. axonopodis pv. passiflorae for intracellular and extracellular extracts from marine sediments fungi were around 96 and 97%, respectively, at 3·0 mg ml -1 . Extracts containing secondary metabolites with antimicrobial activity against X. euvesicatoria and X. axonopodis pv. passiflorae were obtained, containing possible substitutes for the products currently used to control these phytopathogens. Micro-organisms from extreme ecosystems, such as the Antarctic ecosystem, need to survive in harsh conditions with low temperatures, low nutrients and high UV radiation. Micro-organisms adapt to these conditions evolving diverse biochemical and physiological adaptations essential for survival. All this makes these micro-organisms a rich source of novel natural products based on unique chemical scaffolds. Discovering novel bioactive compounds is essential because of the rise in antibiotic-resistant micro-organisms and the emergence of new infections. Fungi from Antarctic environments have been proven to produce bioactive secondary metabolites against various micro-organisms, but few studies

Effect of nonylphenol surfactants on fungi following the application of sewage sludge on agricultural soils.

PubMed

Kollmann, Albert; Brault, Agathe; Touton, Isabelle; Dubroca, Jacqueline; Chaplain, Véronique; Mougin, Christian

2003-01-01

The effect of nonylphenol on fungi following the application of contaminated sewage sludge on agricultural soil was studied in laboratory experiments. Nonylphenol bioavailability and adsorption were determined in the soil alone and soil-sludge mixtures. Mixing the soil with sludge made it possible to measure the nonylphenol concentration in the soil solution, which comprised between 6.6 x 10(-6) and 3.8 x 10(-7) M, according to the sludge. We then examined the dose-response relationship between nonylphenol concentration in the culture medium and both biomass production and germination rate of the spores from several strains of filamentous fungi. When applied in this range of concentration, nonylphenol was without noticeable short-term effect on these endpoints. Long-term exposure of fungi to nonylphenol was also assessed. The most intensive effect was a strong stimulation of spore production and germination in Fusarium oxysporum Schlechtendahl. Biomass production by the Fusarium strains also increased. Finally, nonylphenol was shown to induce laccase production in Trametes versicolor. We conclude that the potential of nonylphenol to adversely affect several soil fungi remains low.

Suppression on the mutagenicity of 4-nitroquinoline-N-oxide by the methanol extracts of soybean koji prepared with various filamentous fungi.

PubMed

Lin, Chia-Hung; Chou, Cheng-Chun

2006-07-01

In this study, solid fermentation of soybean with various GRAS filamentous fungi including Aspergillus sojae BCRC 30103, Aspergillus oryzae BCRC 30222, Aspergillus awamori, Actinomucor taiwanesis and Rhizopus sp. was performed to prepare various soybean kojis. Toxicity, mutagenicity and suppression on the mutagenesis induced by a direct mutagen, 4-nitroquinoline-N-oxide (4-NQO) on Salmonella typhimurium TA 100, by the various methanol extracts of the prepared soybean koji and unfermented soybean were determined and compared. Results revealed that methanol extracts of unfermented soybean and kojis show no toxicity and mutagenic activity within the dose levels examined on test organism. On the other hand, antimutagenic activity against 4-NQO was observed with the extract of unfermented soybean. Furthermore, fermentation, regardless of the starter organism employed, resulted in an enhanced antimutagenic effect on the mutagenesis of 4-NQO by the extracts of the soybean koji. Across the dose range (0.625-5.0 mg/plate) tested, a dose-dependent antimutagenic activity was observed. Antimutagenic activities of the koji extracts varied with starter organism, with A. awamori-prepared koji extract exhibiting the highest rate of suppression on the mutagenicity of 4-NQO. Further study with A. awamori also revealed that fermentation temperature affected the antimutagenic activity of the prepared koji extract. In general, the extract of the A. awamori-soybean koji prepared at 30 degrees C showed a higher antimutagenic activity than those prepared at 25 or 35 degrees C.

Volatile organic compounds emitted by filamentous fungi isolated from flooded homes after Hurricane Sandy show toxicity in a Drosophila bioassay.

PubMed

Zhao, G; Yin, G; Inamdar, A A; Luo, J; Zhang, N; Yang, I; Buckley, B; Bennett, J W

2017-05-01

Superstorm Sandy provided an opportunity to study filamentous fungi (molds) associated with winter storm damage. We collected 36 morphologically distinct fungal isolates from flooded buildings. By combining traditional morphological and cultural characters with an analysis of ITS sequences (the fungal DNA barcode), we identified 24 fungal species that belong to eight genera: Penicillium (11 species), Fusarium (four species), Aspergillus (three species), Trichoderma (two species), and one species each of Metarhizium, Mucor, Pestalotiopsis, and Umbelopsis. Then, we used a Drosophila larval assay to assess possible toxicity of volatile organic compounds (VOCs) emitted by these molds. When cultured in a shared atmosphere with growing cultures of molds isolated after Hurricane Sandy, larval toxicity ranged from 15 to 80%. VOCs from Aspergillus niger 129B were the most toxic yielding 80% mortality to Drosophila after 12 days. The VOCs from Trichoderma longibrachiatum 117, Mucor racemosus 138a, and Metarhizium anisopliae 124 were relatively non-toxigenic. A preliminary analysis of VOCs was conducted using solid-phase microextraction-gas chromatography-mass spectrometry from two of the most toxic, two of the least toxic, and two species of intermediate toxicity. The more toxic molds produced higher concentrations of 1-octen-3-ol, 3-octanone, 3-octanol, 2-octen-1-ol, and 2-nonanone; while the less toxic molds produced more 3-methyl-1-butanol and 2-methyl-1-propanol, or an overall lower amount of volatiles. Our data support the hypothesis that at certain concentrations, some VOCs emitted by indoor molds are toxigenic. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Investigation of the corneal filament in filamentary keratitis.

PubMed

Tanioka, Hidetoshi; Yokoi, Norihiko; Komuro, Aoi; Shimamoto, Takasumi; Kawasaki, Satoshi; Matsuda, Akira; Kinoshita, Shigeru

2009-08-01

To date, no studies have elucidated the composition of the corneal filament in detail. In this study, an immunohistochemical technique was used to clarify the exact composition of the corneal filament in filamentary keratitis. In addition, the mechanisms responsible for filament formation were identified. Filaments were obtained from 13 patients with filamentary keratitis with a background of penetrating keratoplasty, aqueous tear deficiency, and severe ocular surface disorders, who were receiving treatment at an outpatient facility. From those tissues, transverse and longitudinal frozen sections were prepared and subjected to an indirect fluorescent immunohistochemical analysis with primary antibodies, including cytokeratins (CK1, -4, -6, -10, -12, and -13), mucins (MUC1, -4, -5AC, and -16), keratinization-related proteins (transglutaminase [TGase]-1 and filaggrin), cell proliferation marker Ki67, and markers of infiltration cells (HLA-DR and neutrophil-elastase). TUNEL staining was used for the detection of apoptosis. Fluorescent images of the sections were inspected with a fluorescence microscope. The filaments were composed of CK12-positive cells and had a roll-formed central core. They were covered with MUC5AC- and -16-positive mucins including CK4- and -13-positive cells and neutrophil-elastase-positive cells. The filaments also included broken cells and DNA fiber-form postlesional nuclei that were positive for TUNEL staining. However, those areas stained weakly for CK6 and HLA-DR; faintly for CK1, CK10, MUC1, and MUC4; and not at all for Ki67, TGase-1, and filaggrin. The results of this research have the potential to open new pathways toward understanding the mechanism that generates the filament in filamentary keratitis, as well as new treatments in the future.

Standoff Detection of Uranium and its Isotopes by Femtosecond Filament Laser Ablation Molecular Isotopic Spectrometry

PubMed Central

Hartig, Kyle C.; Ghebregziabher, Isaac; Jovanovic, Igor

2017-01-01

The ability to perform not only elementally but also isotopically sensitive detection and analysis at standoff distances is impor-tant for remote sensing applications in diverse ares, such as nuclear nonproliferation, environmental monitoring, geophysics, and planetary science. We demonstrate isotopically sensitive real-time standoff detection of uranium by the use of femtosecond filament-induced laser ablation molecular isotopic spectrometry. A uranium oxide molecular emission isotope shift of 0.05 ± 0.007 nm is reported at 593.6 nm. We implement both spectroscopic and acoustic diagnostics to characterize the properties of uranium plasma generated at different filament-uranium interaction points. The resulting uranium oxide emis-sion exhibits a nearly constant signal-to-background ratio over the length of the filament, unlike the uranium atomic and ionic emission, for which the signal-to-background ratio varies significantly along the filament propagation. This is explained by the different rates of increase of plasma density and uranium oxide density along the filament length resulting from spectral and temporal evolution of the filament along its propagation. The results provide a basis for the optimal use of filaments for standoff detection and analysis of uranium isotopes and indicate the potential of the technique for a wider range of remote sensing applications that require isotopic sensitivity. PMID:28272450

Effect of an Energy Reservoir on the Atmospheric Propagation of Laser-Plasma Filaments

NASA Astrophysics Data System (ADS)

Eisenmann, Shmuel; Peñano, Joseph; Sprangle, Phillip; Zigler, Arie

2008-04-01

The ability to select and stabilize a single filament during propagation of an ultrashort, high-intensity laser pulse in air makes it possible to examine the longitudinal structure of the plasma channel left in its wake. We present the first detailed measurements and numerical 3-D simulations of the longitudinal plasma density variation in a laser-plasma filament after it passes through an iris that blocks the surrounding energy reservoir. Since no compensation is available from the surrounding background energy, filament propagation is terminated after a few centimeters. For this experiment, simulations indicate that filament propagation is terminated by plasma defocusing and ionization loss, which reduces the pulse power below the effective self-focusing power. With no blockage, a plasma filament length of over a few meters was observed.

Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls?

PubMed

Guennoc, Cora Miquel; Rose, Christophe; Labbé, Jessy; Deveau, Aurélie

2018-05-17

Ectomycorrhizal (ECM) fungi establish symbiosis with roots of most trees of boreal and temperate ecosystems and are major drivers of nutrient fluxes between trees and the soil. ECM fungi constantly interact with bacteria all along their life cycle and the extended networks of hyphae provide a habitat for complex bacterial communities. Despite the important effects these bacteria can have on the growth and activities of ECM fungi, little is known about the mechanisms by which these microorganisms interact. Here we investigated the ability of bacteria to form biofilm on the hyphae of the ECM fungus Laccaria bicolor. We showed that the ability to form biofilms on the hyphae of the ECM fungus is widely shared among soil bacteria. Conversely, some fungi, belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also modulated by the presence of tree roots and ectomycorrhizae, suggesting that biofilm formation does not occur randomly in soil but that it is regulated by several biotic factors. In addition, our study demonstrated that the formation of bacterial biofilm on fungal hyphae relies on the production of networks of filaments made of extracellular DNA.

Black Yeasts and Their Filamentous Relatives: Principles of Pathogenesis and Host Defense

PubMed Central

Netea, Mihai G.; Mouton, Johan W.; Melchers, Willem J. G.; Verweij, Paul E.; de Hoog, G. Sybren

2014-01-01

SUMMARY Among the melanized fungi, the so-called “black yeasts” and their filamentous relatives are particularly significant as agents of severe phaeohyphomycosis, chromoblastomycosis, and mycetoma in humans and animals. The pathogenicity and virulence of these fungi may differ significantly between closely related species. The factors which probably are of significance for pathogenicity include the presence of melanin and carotene, formation of thick cell walls and meristematic growth, presence of yeast-like phases, thermo- and perhaps also osmotolerance, adhesion, hydrophobicity, assimilation of aromatic hydrocarbons, and production of siderophores. Host defense has been shown to rely mainly on the ingestion and elimination of fungal cells by cells of the innate immune system, especially neutrophils and macrophages. However, there is increasing evidence supporting a role of T-cell-mediated immune responses, with increased interleukin-10 (IL-10) and low levels of gamma interferon (IFN-γ) being deleterious during the infection. There are no standardized therapies for treatment. It is therefore important to obtain in vitro susceptibilities of individual patients' fungal isolates in order to provide useful information for selection of appropriate treatment protocols. This article discusses the pathogenesis and host defense factors for these fungi and their severity, chronicity, and subsequent impact on treatment and prevention of diseases in human or animal hosts. PMID:24982320

Cell-to-cell communication in plants, animals, and fungi: a comparative review.

PubMed

Bloemendal, Sandra; Kück, Ulrich

2013-01-01

Cell-to-cell communication is a prerequisite for differentiation and development in multicellular organisms. This communication has to be tightly regulated to ensure that cellular components such as organelles, macromolecules, hormones, or viruses leave the cell in a precisely organized way. During evolution, plants, animals, and fungi have developed similar ways of responding to this biological challenge. For example, in higher plants, plasmodesmata connect adjacent cells and allow communication to regulate differentiation and development. In animals, two main general structures that enable short- and long-range intercellular communication are known, namely gap junctions and tunneling nanotubes, respectively. Finally, filamentous fungi have also developed specialized structures called septal pores that allow intercellular communication via cytoplasmic flow. This review summarizes the underlying mechanisms for intercellular communication in these three eukaryotic groups and discusses its consequences for the regulation of differentiation and developmental processes.

Cell-to-cell communication in plants, animals, and fungi: a comparative review

NASA Astrophysics Data System (ADS)

Bloemendal, Sandra; Kück, Ulrich

2013-01-01

Cell-to-cell communication is a prerequisite for differentiation and development in multicellular organisms. This communication has to be tightly regulated to ensure that cellular components such as organelles, macromolecules, hormones, or viruses leave the cell in a precisely organized way. During evolution, plants, animals, and fungi have developed similar ways of responding to this biological challenge. For example, in higher plants, plasmodesmata connect adjacent cells and allow communication to regulate differentiation and development. In animals, two main general structures that enable short- and long-range intercellular communication are known, namely gap junctions and tunneling nanotubes, respectively. Finally, filamentous fungi have also developed specialized structures called septal pores that allow intercellular communication via cytoplasmic flow. This review summarizes the underlying mechanisms for intercellular communication in these three eukaryotic groups and discusses its consequences for the regulation of differentiation and developmental processes.

Neurons show the path: tip-to-nucleus communication in filamentous fungal development and pathogenesis.

PubMed

Etxebeste, Oier; Espeso, Eduardo A

2016-09-01

Multiple fungal species penetrate substrates and accomplish host invasion through the fast, permanent and unidirectional extension of filamentous cells known as hyphae. Polar growth of hyphae results, however, in a significant increase in the distance between the polarity site, which also receives the earliest information about ambient conditions, and nuclei, where adaptive responses are executed. Recent studies demonstrate that these long distances are overcome by signal transduction pathways which convey sensory information from the polarity site to nuclei, controlling development and pathogenesis. The present review compares the striking connections of the mechanisms for long-distance communication in hyphae with those from neurons, and discusses the importance of their study in order to understand invasion and dissemination processes of filamentous fungi, and design strategies for developmental control in the future. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mucoralean fungi for sustainable production of bioethanol and biologically active molecules.

PubMed

Satari, Behzad; Karimi, Keikhosro

2018-02-01

Mucoralean fungi are suitable microorganisms for the sustainable production of food, fodder, and fuels from inexpensive natural resources. Ethanol-producing Mucorales are particularly advantageous for second-generation ethanol production in comparison to the conventional ethanolic yeasts and bacteria. They are able to ferment a wide range of sugars to a range of valuable products, while they are typically resistance against the inhibitors available in different substrates, including untreated lignocellulosic hydrolysates. In addition to a high ethanol yield, the fungi produce several commercially valuable by-products, including chitosan, microbial oil (mainly polyunsaturated fatty acids), and protein. Moreover, the fungal extracts can replace the expensive nutrients required in fermentation. Besides, their morphologies can be altered from filamentous to yeast like and are adjustable based on the process requirement. The focus of this review is on applying Mucorales in producing ethanol and the biomass by-products thereof.

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.

PubMed

Wentzel, Lia Costa Pinto; Inforsato, Fábio José; Montoya, Quimi Vidaurre; Rossin, Bruna Gomes; Nascimento, Nadia Regina; Rodrigues, André; Sette, Lara Durães

2018-06-19

Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.

Biologically Active Secondary Metabolites from the Fungi.

PubMed

Bills, Gerald F; Gloer, James B

2016-11-01

Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops

RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes

PubMed Central

Teichert, Ines; Dahlmann, Tim A.; Kück, Ulrich

2017-01-01

RNA editing is a post-transcriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe. Like F. graminearum, S. macrospora is a member of the Sordariomycetes, whereas P. confluens belongs to the early-diverging group of Pezizomycetes. We found extensive A-to-I editing in RNA-seq data from sexual mycelium from both filamentous ascomycetes, but not in vegetative structures. A-to-I editing was not detected in different stages of meiosis of S. pombe. A comparison of A-to-I editing in S. macrospora with F. graminearum and P. confluens, respectively, revealed little conservation of individual editing sites. An analysis of RNA-seq data from two sterile developmental mutants of S. macrospora showed that A-to-I editing is strongly reduced in these strains. Sequencing of cDNA fragments containing more than one editing site from P. confluens showed that at the beginning of sexual development, transcripts were incompletely edited or unedited, whereas in later stages transcripts were more extensively edited. Taken together, these data suggest that A-to-I RNA editing is an evolutionary conserved feature during fruiting body development in filamentous ascomycetes. PMID:28338982

Susceptibility of 100 filamentous fungi: comparison of two diffusion methods, Neo-Sensitabs and E-test, for amphotericin B, caspofungin, itraconazole, voriconazole and posaconazole.

PubMed

Colosi, Ioana A; Faure, Odile; Dessaigne, Bérangére; Bourdon, Cécile; Lebeau, Bernadette; Colosi, Horaţiu A; Pelloux, Hervé

2012-05-01

We compared the E-test method to that of the Neo-Sensitabs tablet diffusion assay for evaluating the in vitro susceptibility of 100 clinical isolates of filamentous fungi (Aspergillus spp., Fusarium spp., Scedosporium spp., zygomycetes and other molds) to amphotericin B, itraconazole, voriconazole, caspofungin, and posaconazole. We determined the categorical agreement level between E-test minimum inhibitory concentrations (MIC) and tablet end-points, as opposed to the following disagreement parameters: very major error - resistant parameter (R) in E-test and susceptible (S) in tablet; major error - S by E-test and R by tablet; minor error - shifts between S and susceptible dose-dependent (S-DD) or S-DD and R. We also performed linear regression analyses and computed Pearson's correlation coefficients (R values) between the log transforms of MICs and the inhibition zone diameters of the five studied antifungal agents. For itraconazole we obtained 97% categorical agreement and R = -0.727. Categorical agreement for caspofungin and voriconazole was 96% and R =-0.821 and R = -0.789, respectively. For posaconazole the categorical agreement was 94% and R =-0.743. Amphotericin B exhibited a lower degree of agreement (76%, R = -0.672), especially in studies of Aspergillus spp. Our results suggest a potential value of the Neo-Sensitabs assay for in vitro susceptibility testing of molds to itraconazole, voriconazole, caspofungin and posaconazole, while amphotericin B exhibited an overall lower degree of agreement.

Integrated inference and evaluation of host–fungi interaction networks

PubMed Central

Remmele, Christian W.; Luther, Christian H.; Balkenhol, Johannes; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus T.

2015-01-01

Fungal microorganisms frequently lead to life-threatening infections. Within this group of pathogens, the commensal Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of invasive mycoses in Europe. A key capability for host invasion and immune response evasion are specific molecular interactions between the fungal pathogen and its human host. Experimentally validated knowledge about these crucial interactions is rare in literature and even specialized host–pathogen databases mainly focus on bacterial and viral interactions whereas information on fungi is still sparse. To establish large-scale host–fungi interaction networks on a systems biology scale, we develop an extended inference approach based on protein orthology and data on gene functions. Using human and yeast intraspecies networks as template, we derive a large network of pathogen–host interactions (PHI). Rigorous filtering and refinement steps based on cellular localization and pathogenicity information of predicted interactors yield a primary scaffold of fungi–human and fungi–mouse interaction networks. Specific enrichment of known pathogenicity-relevant genes indicates the biological relevance of the predicted PHI. A detailed inspection of functionally relevant subnetworks reveals novel host–fungal interaction candidates such as the Candida virulence factor PLB1 and the anti-fungal host protein APP. Our results demonstrate the applicability of interolog-based prediction methods for host–fungi interactions and underline the importance of filtering and refinement steps to attain biologically more relevant interactions. This integrated network framework can serve as a basis for future analyses of high-throughput host–fungi transcriptome and proteome data. PMID:26300851

Femtosecond laser filament induced condensation and precipitation in a cloud chamber

PubMed Central

Ju, Jingjing; Liu, Jiansheng; Liang, Hong; Chen, Yu; Sun, Haiyi; Liu, Yonghong; Wang, Jingwei; Wang, Cheng; Wang, Tiejun; Li, Ruxin; Xu, Zhizhan; Chin, See Leang

2016-01-01

A unified picture of femtosecond laser induced precipitation in a cloud chamber is proposed. Among the three principal consequences of filamentation from the point of view of thermodynamics, namely, generation of chemicals, shock waves and thermal air flow motion (due to convection), the last one turns out to be the principal cause. Much of the filament induced chemicals would stick onto the existing background CCN’s (Cloud Condensation Nuclei) through collision making the latter more active. Strong mixing of air having a large temperature gradient would result in supersaturation in which the background CCN’s would grow efficiently into water/ice/snow. This conclusion was supported by two independent experiments using pure heating or a fan to imitate the laser-induced thermal effect or the strong air flow motion, respectively. Without the assistance of any shock wave and chemical CCN’s arising from laser filament, condensation and precipitation occurred. Meanwhile we believe that latent heat release during condensation /precipitation would enhance the air flow for mixing. PMID:27143227

Biodiversity of Pigmented Fungi Isolated from Marine Environment in La Réunion Island, Indian Ocean: New Resources for Colored Metabolites

PubMed Central

Llorente, Melissa; Magalon, Helene

2017-01-01

Marine ecosystems cover about 70% of the planet surface and are still an underexploited source of useful metabolites. Among microbes, filamentous fungi are captivating organisms used for the production of many chemical classes of secondary metabolites bound to be used in various fields of industrial application. The present study was focused on the collection, isolation, screening and genotyping of pigmented filamentous fungi isolated from tropical marine environments around La Réunion Island, Indian Ocean. About 150 micromycetes were revived and isolated from 14 marine samples (sediments, living corals, coral rubble, sea water and hard substrates) collected in four different locations. Forty-two colored fungal isolates belonging to 16 families, 25 genera and 31 species were further studied depending on their ability to produce pigments and thus subjected to molecular identification. From gene sequence analysis, the most frequently identified colored fungi belong to the widespread Penicillium, Talaromyces and Aspergillus genera in the family Trichocomaceae (11 species), then followed by the family Hypocreaceae (three species). This study demonstrates that marine biotopes in La Réunion Island, Indian Ocean, from coral reefs to underwater slopes of this volcanic island, shelter numerous species of micromycetes, from common or uncommon genera. This unstudied biodiversity comes along with the ability for some fungal marine inhabitants, to produce a range of pigments and hues. PMID:29371553

A penny-shaped crack in a filament reinforced matrix. 1: The filament model

NASA Technical Reports Server (NTRS)

Erdogan, F.; Pacella, A. H.

1973-01-01

The electrostatic problem of a penny-shaped crack in an elastic matrix which reinforced by filaments or fibers perpendicular to the plane of the crack was studied. The elastic filament model was developed for application to evaluation studies of the stress intensity factor along the periphery of the crack, the stresses in the filaments or fibers, and the interface shear between the matrix and the filaments or fibers. The requirements expected of the model are a sufficiently accurate representation of the filament and applicability to the interaction problems involving a cracked elastic continuum with multi-filament reinforcements. The technique for developing the model and numerical examples of it are shown.

Fungi from a Groundwater-Fed Drinking Water Supply System in Brazil

PubMed Central

Oliveira, Helena M.B.; Santos, Cledir; Paterson, R. Russell M.; Gusmão, Norma B.; Lima, Nelson

2016-01-01

Filamentous fungi in drinking water distribution systems are known to (a) block water pipes; (b) cause organoleptic biodeterioration; (c) act as pathogens or allergens and (d) cause mycotoxin contamination. Yeasts might also cause problems. This study describes the occurrence of several fungal species in a water distribution system supplied by groundwater in Recife—Pernambuco, Brazil. Water samples were collected from four sampling sites from which fungi were recovered by membrane filtration. The numbers in all sampling sites ranged from 5 to 207 colony forming units (CFU)/100 mL with a mean value of 53 CFU/100 mL. In total, 859 isolates were identified morphologically, with Aspergillus and Penicillium the most representative genera (37% and 25% respectively), followed by Trichoderma and Fusarium (9% each), Curvularia (5%) and finally the species Pestalotiopsis karstenii (2%). Ramichloridium and Leptodontium were isolated and are black yeasts, a group that include emergent pathogens. The drinking water system in Recife may play a role in fungal dissemination, including opportunistic pathogens. PMID:27005653

Fungi from a Groundwater-Fed Drinking Water Supply System in Brazil.

PubMed

Oliveira, Helena M B; Santos, Cledir; Paterson, R Russell M; Gusmão, Norma B; Lima, Nelson

2016-03-09

Filamentous fungi in drinking water distribution systems are known to (a) block water pipes; (b) cause organoleptic biodeterioration; (c) act as pathogens or allergens and (d) cause mycotoxin contamination. Yeasts might also cause problems. This study describes the occurrence of several fungal species in a water distribution system supplied by groundwater in Recife-Pernambuco, Brazil. Water samples were collected from four sampling sites from which fungi were recovered by membrane filtration. The numbers in all sampling sites ranged from 5 to 207 colony forming units (CFU)/100 mL with a mean value of 53 CFU/100 mL. In total, 859 isolates were identified morphologically, with Aspergillus and Penicillium the most representative genera (37% and 25% respectively), followed by Trichoderma and Fusarium (9% each), Curvularia (5%) and finally the species Pestalotiopsis karstenii (2%). Ramichloridium and Leptodontium were isolated and are black yeasts, a group that include emergent pathogens. The drinking water system in Recife may play a role in fungal dissemination, including opportunistic pathogens.

Filamentary structures in dense plasma focus: Current filaments or vortex filaments?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soto, Leopoldo, E-mail: lsoto@cchen.cl; Pavez, Cristian; Moreno, José

2014-07-15

Recent observations of an azimuthally distributed array of sub-millimeter size sources of fusion protons and correlation between extreme ultraviolet (XUV) images of filaments with neutron yield in PF-1000 plasma focus have re-kindled interest in their significance. These filaments have been described variously in literature as current filaments and vortex filaments, with very little experimental evidence in support of either nomenclature. This paper provides, for the first time, experimental observations of filaments on a table-top plasma focus device using three techniques: framing photography of visible self-luminosity from the plasma, schlieren photography, and interferometry. Quantitative evaluation of density profile of filaments frommore » interferometry reveals that their radius closely agrees with the collision-less ion skin depth. This is a signature of relaxed state of a Hall fluid, which has significant mass flow with equipartition between kinetic and magnetic energy, supporting the “vortex filament” description. This interpretation is consistent with empirical evidence of an efficient energy concentration mechanism inferred from nuclear reaction yields.« less

An Antarctic hot spot for fungi at Shackleton's historic hut on Cape Royds.

PubMed

Blanchette, Robert A; Held, Benjamin W; Arenz, Brett E; Jurgens, Joel A; Baltes, Nicolas J; Duncan, Shona M; Farrell, Roberta L

2010-07-01

The historic expedition huts located in the Ross Sea Region of the Antarctic and the thousands of artifacts left behind by the early explorers represent important cultural heritage from the "Heroic Era" of Polar exploration. The hut at Cape Royds built by Ernest Shackleton and members of the 1907-1908 British Antarctic Expedition has survived the extreme Antarctic environment for over 100 years, but recent studies have shown many forms of deterioration are causing serious problems, and microbial degradation is evident in the historic wood. Conservation work to reduce moisture at the hut required removal of fodder, wood, and many different types of organic materials from the stables area on the north side of the structure allowing large numbers of samples to be obtained for these investigations. In addition, wood from historic food storage boxes exposed in a ravine adjacent to the hut were also sampled. Fungi were cultured on several different media, and pure cultures were obtained and identified by sequencing of the internal transcribed spacer region of rDNA. From the 69 cultures of filamentous fungi obtained, the most predominant genera were Cadophora (44%) followed by Thielavia (17%) and Geomyces (15%). Other fungi found included Cladosporium, Chaetomium, and isolates identified as being in Pezizomycotina, Onygenales, Nectriaceae, and others. No filamentous basidiomycetes were found. Phylogenetic analyses of the Cadophora species showed great species diversity present revealing Cadophora malorum, Cadophora luteo-olivacea, Cadophora fastigiata, as well as Cadophora sp. 4E71-1, a C. malorum-like species, and Cadophora sp. 7R16-1, a C. fastigiata-like species. Scanning electron microscopy showed extensive decay was present in the wood samples with type 1 and type 2 forms of soft rot evident in pine and birch wood, respectively. Fungi causing decay in the historic wooden structures and artifacts are of great concern, and this investigation provides insight into the

RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes.

PubMed

Teichert, Ines; Dahlmann, Tim A; Kück, Ulrich; Nowrousian, Minou

2017-04-01

RNA editing is a post-transcriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe. Like F. graminearum, S. macrospora is a member of the Sordariomycetes, whereas P. confluens belongs to the early-diverging group of Pezizomycetes. We found extensive A-to-I editing in RNA-seq data from sexual mycelium from both filamentous ascomycetes, but not in vegetative structures. A-to-I editing was not detected in different stages of meiosis of S. pombe. A comparison of A-to-I editing in S. macrospora with F. graminearum and P. confluens, respectively, revealed little conservation of individual editing sites. An analysis of RNA-seq data from two sterile developmental mutants of S. macrospora showed that A-to-I editing is strongly reduced in these strains. Sequencing of cDNA fragments containing more than one editing site from P. confluens showed that at the beginning of sexual development, transcripts were incompletely edited or unedited, whereas in later stages transcripts were more extensively edited. Taken together, these data suggest that A-to-I RNA editing is an evolutionary conserved feature during fruiting body development in filamentous ascomycetes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sliding movement of single actin filaments on one-headed myosin filaments

NASA Astrophysics Data System (ADS)

Harada, Yoshie; Noguchi, Akira; Kishino, Akiyoshi; Yanagida, Toshio

1987-04-01

The myosin molecule consists of two heads, each of which contains an enzymatic active site and an actin-binding site. The fundamental problem of whether the two heads function independently or cooperatively during muscle contraction has been studied by methods using an actomyosin thread1, superprecipitation2-4 and chemical modification of muscle fibres5. No clear conclusion has yet been reached. We have approached this question using an assay system in which sliding movements of fluorescently labelled single actin filaments along myosin filaments can be observed directly6,7. Here, we report direct measurement of the sliding of single actin filaments along one-headed myosin filaments in which the density of heads was varied over a wide range. Our results show that cooperative interaction between the two heads of myosin is not essential for inducing the sliding movement of actin filaments.

From Discovery to Production: Biotechnology of Marine Fungi for the Production of New Antibiotics

PubMed Central

Silber, Johanna; Kramer, Annemarie; Labes, Antje; Tasdemir, Deniz

2016-01-01

Filamentous fungi are well known for their capability of producing antibiotic natural products. Recent studies have demonstrated the potential of antimicrobials with vast chemodiversity from marine fungi. Development of such natural products into lead compounds requires sustainable supply. Marine biotechnology can significantly contribute to the production of new antibiotics at various levels of the process chain including discovery, production, downstream processing, and lead development. However, the number of biotechnological processes described for large-scale production from marine fungi is far from the sum of the newly-discovered natural antibiotics. Methods and technologies applied in marine fungal biotechnology largely derive from analogous terrestrial processes and rarely reflect the specific demands of the marine fungi. The current developments in metabolic engineering and marine microbiology are not yet transferred into processes, but offer numerous options for improvement of production processes and establishment of new process chains. This review summarises the current state in biotechnological production of marine fungal antibiotics and points out the enormous potential of biotechnology in all stages of the discovery-to-development pipeline. At the same time, the literature survey reveals that more biotechnology transfer and method developments are needed for a sustainable and innovative production of marine fungal antibiotics. PMID:27455283

From Discovery to Production: Biotechnology of Marine Fungi for the Production of New Antibiotics.

PubMed

Silber, Johanna; Kramer, Annemarie; Labes, Antje; Tasdemir, Deniz

2016-07-21

Filamentous fungi are well known for their capability of producing antibiotic natural products. Recent studies have demonstrated the potential of antimicrobials with vast chemodiversity from marine fungi. Development of such natural products into lead compounds requires sustainable supply. Marine biotechnology can significantly contribute to the production of new antibiotics at various levels of the process chain including discovery, production, downstream processing, and lead development. However, the number of biotechnological processes described for large-scale production from marine fungi is far from the sum of the newly-discovered natural antibiotics. Methods and technologies applied in marine fungal biotechnology largely derive from analogous terrestrial processes and rarely reflect the specific demands of the marine fungi. The current developments in metabolic engineering and marine microbiology are not yet transferred into processes, but offer numerous options for improvement of production processes and establishment of new process chains. This review summarises the current state in biotechnological production of marine fungal antibiotics and points out the enormous potential of biotechnology in all stages of the discovery-to-development pipeline. At the same time, the literature survey reveals that more biotechnology transfer and method developments are needed for a sustainable and innovative production of marine fungal antibiotics.

Transition of Femtosecond-Filament-Solid Interactions from Single to Multiple Filament Regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skrodzki, P. J.; Burger, M.; Jovanovic, I.

High-peak-power fs-laser filaments offer unique characteristics attractive to remote sensing via techniques such as remote laser-induced breakdown spectroscopy (R-LIBS). The dynamics of several ablation mechanisms following the interaction between a filament and a solid determines the emission strength and reproducibility of target plasma, which is of relevance for R-LIBS applications. Here, we investigate the space- and time-resolved dynamics of ionic and atomic emission from copper as well as the surrounding atmosphere in order to understand limitations of fs-filament-ablation for standoff energy delivery. Furthermore, we probe the shock front produced from filament-target interaction using time-resolved shadowgraphy and infer laser-material coupling efficienciesmore » for both single and multiple filament regimes through analysis of shock expansion with the Sedov model for point detonation. The results provide insight into plasma structure for the range of peak powers up to 30 times the critical power for filamentation P cr. Despite the stochastic nucleation of multiple filaments at peak-powers greater than 16 P cr, emission of ionic and neutral species increases with pump beam intensity, and short-lived nitrogen emission originating from the ambient is consistently observed. Ultimately, results suggest favorable scaling of emission intensity from target species on the laser pump energy, furthering the prospects for use of filament-solid interactions for remote sensing.« less

Transition of Femtosecond-Filament-Solid Interactions from Single to Multiple Filament Regime

DOE PAGES

Skrodzki, P. J.; Burger, M.; Jovanovic, I.

2017-10-06

High-peak-power fs-laser filaments offer unique characteristics attractive to remote sensing via techniques such as remote laser-induced breakdown spectroscopy (R-LIBS). The dynamics of several ablation mechanisms following the interaction between a filament and a solid determines the emission strength and reproducibility of target plasma, which is of relevance for R-LIBS applications. Here, we investigate the space- and time-resolved dynamics of ionic and atomic emission from copper as well as the surrounding atmosphere in order to understand limitations of fs-filament-ablation for standoff energy delivery. Furthermore, we probe the shock front produced from filament-target interaction using time-resolved shadowgraphy and infer laser-material coupling efficienciesmore » for both single and multiple filament regimes through analysis of shock expansion with the Sedov model for point detonation. The results provide insight into plasma structure for the range of peak powers up to 30 times the critical power for filamentation P cr. Despite the stochastic nucleation of multiple filaments at peak-powers greater than 16 P cr, emission of ionic and neutral species increases with pump beam intensity, and short-lived nitrogen emission originating from the ambient is consistently observed. Ultimately, results suggest favorable scaling of emission intensity from target species on the laser pump energy, furthering the prospects for use of filament-solid interactions for remote sensing.« less

Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.

PubMed

Navarri, Marion; Jégou, Camille; Meslet-Cladière, Laurence; Brillet, Benjamin; Barbier, Georges; Burgaud, Gaëtan; Fleury, Yannick

2016-03-10

The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

Redox metabolites signal polymicrobial biofilm development via the NapA oxidative stress cascade in Aspergillus

PubMed Central

Zheng, He; Kim, Jaekuk; Liew, Mathew; Yan, John K.; Herrera, Oscar; Bok, JinWoo; Kelleher, Neil L.; Keller, Nancy P.; Wang, Yun

2014-01-01

Summary Background Filamentous fungi and bacteria form mixed-species biofilms in nature and diverse clinical contexts. They secrete a wealth of redox-active small molecule secondary metabolites, which are traditionally viewed as toxins that inhibit growth of competing microbes. Results Here we report that these “toxins” can act as interspecies signals, affecting filamentous fungal development via oxidative stress regulation. Specifically, in co-culture biofilms, Pseudomonas aeruginosa phenazine-derived metabolites differentially modulated Aspergillus fumigatus development, shifting from weak vegetative growth to induced asexual sporulation (conidiation) along a decreasing phenazine gradient. The A. fumigatus morphological shift correlated with the production of phenazine radicals and concomitant reactive oxygen species (ROS) production generated by phenazine redox cycling. Phenazine conidiation signaling was conserved in the genetic model A. nidulans, and mediated by NapA, a homolog of AP-1-like bZIP transcription factor, which is essential for the response to oxidative stress in humans, yeast, and filamentous fungi. Expression profiling showed phenazine treatment induced a NapA-dependent response of the global oxidative stress metabolome including the thioredoxin, glutathione and NADPH-oxidase systems. Conidiation induction in A. nidulans by another microbial redox-active secondary metabolite, gliotoxin, also required NapA. Conclusions This work highlights that microbial redox metabolites are key signals for sporulation in filamentous fungi, which are communicated through an evolutionarily conserved eukaryotic stress response pathway. It provides a foundation for interspecies signaling in environmental and clinical biofilms involving bacteria and filamentous fungi. PMID:25532893

Dynamical ejections of stars due to an accelerating gas filament

NASA Astrophysics Data System (ADS)

Boekholt, T. C. N.; Stutz, A. M.; Fellhauer, M.; Schleicher, D. R. G.; Matus Carrillo, D. R.

2017-11-01

Observations of the Orion A integral shaped filament (ISF) have shown indications of an oscillatory motion of the gas filament. This evidence is based on both the wave-like morphology of the filament and the kinematics of the gas and stars, where the characteristic velocities of the stars require a dynamical heating mechanism. As proposed by Stutz & Gould, such a heating mechanism (the `Slingshot') may be the result of an oscillating gas filament in a gas-dominated (as opposed to stellar-mass dominated) system. Here we test this hypothesis with the first stellar-dynamical simulations in which the stars are subjected to the influence of an oscillating cylindrical potential. The accelerating, cylindrical background potential is populated with a narrow distribution of stars. By coupling the potential to N-body dynamics, we are able to measure the influence of the potential on the stellar distribution. The simulations provide evidence that the slingshot mechanism can successfully reproduce several stringent observational constraints. These include the stellar spread (both in projected position and in velocity) around the filament, the symmetry in these distributions, and a bulk motion of the stars with respect to the filament. Using simple considerations, we show that star-star interactions are incapable of reproducing these spreads on their own when properly accounting for the gas potential. Thus, properly accounting for the gas potential is essential for understanding the dynamical evolution of star-forming filamentary systems in the era of Gaia (Gaia Collaboration 2016).

AoRim15 is involved in conidial stress tolerance, conidiation and sclerotia formation in the filamentous fungus Aspergillus oryzae.

PubMed

Nakamura, Hidetoshi; Kikuma, Takashi; Jin, Feng Jie; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

2016-04-01

The serine-threonine kinase Rim15p is a master regulator of stress signaling and is required for stress tolerance and sexual sporulation in the yeast Saccharomyces cerevisiae. However, in filamentous fungi that reproduce asexually via conidiation, the physiological function of Rim15p homologs has not been extensively analyzed. Here, we functionally characterized the protein homolog of Rim15p in the filamentous fungus Aspergillus oryzae, by deleting and overexpressing the corresponding Aorim15 gene and examining the role of this protein in stress tolerance and development. Deletion of Aorim15 resulted in an increase in the sensitivity of conidia to oxidative and heat stresses, whereas conidia of the Aorim15 overexpressing strain were more resistant to these stresses. These results indicated that AoRim15 functions in stress tolerance, similar to S. cerevisiae Rim15p. Phenotypic analysis revealed that conidiation was markedly reduced by overexpression of Aorim15 in A. oryzae, and was completely abolished in the deletion strain. In addition, the formation of sclerotia, which is another type of developmental structure in filamentous fungi, was decreased by the deletion of Aorim15, whereas Aorim15 overexpression increased the number of sclerotia. These results indicated that AoRim15 is a positive regulator of sclerotia formation and that overexpression of AoRim15 shifts the developmental balance from conidiation towards sclerotia formation. Collectively, we demonstrated that AoRim15 is involved in the stress tolerance of conidia and differentially regulates between the two developmental fates of conidiation and sclerotia formation. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Fungi from industrial tannins: potential application in biotransformation and bioremediation of tannery wastewaters.

PubMed

Prigione, Valeria; Trocini, Bruno; Spina, Federica; Poli, Anna; Romanisio, Davide; Giovando, Samuele; Varese, Giovanna Cristina

2018-05-01

Tannins are a complex family of polyphenolic compounds, widely distributed in the plant kingdom where they act as growth inhibitors towards many microorganisms including bacteria, yeasts, and fungi. Tannins are one of the major components of tannery wastewaters and may cause serious environmental pollution. In the present study, four different tannins (the hydrolysable chestnut ellagitannin and tara gallotannin and the condensed quebracho and wattle tannins) were characterized from a mycological point of view with the aim of selecting fungal strains capable of growing in the presence of high tannin concentration and thus potentially useful in industrial biotransformations of these compounds or in the bioremediation of tannery wastewaters. A total of 125 isolates of filamentous fungi belonging to 10 species and four genera (Aspergillus, Paecilomyces, Penicillium, and Talaromyces) were isolated from the tannin industrial preparations. Miniaturized biotransformation tests were set up with 10 fungal strains and the high-performance liquid chromatography (HPLC) analysis pointed out a strong activity of all the tested fungi on both chestnut and tara tannins. Two strains (Aspergillus tubingensis MUT 990 and Paecilomyces variotii MUT 1125), tested against a real tannery wastewater, were particularly efficient in chemical oxygen demand (COD) and tannin removal (> 60%), with a detoxification above 74%. These results indicate that these fungi are potentially exploitable in the treatment of tannery wastewaters.

Multi-code analysis of scrape-off layer filament dynamics in MAST

NASA Astrophysics Data System (ADS)

Militello, F.; Walkden, N. R.; Farley, T.; Gracias, W. A.; Olsen, J.; Riva, F.; Easy, L.; Fedorczak, N.; Lupelli, I.; Madsen, J.; Nielsen, A. H.; Ricci, P.; Tamain, P.; Young, J.

2016-11-01

Four numerical codes are employed to investigate the dynamics of scrape-off layer filaments in tokamak relevant conditions. Experimental measurements were taken in the MAST device using visual camera imaging, which allows the evaluation of the perpendicular size and velocity of the filaments, as well as the combination of density and temperature associated with the perturbation. A new algorithm based on the light emission integrated along the field lines associated with the position of the filament is developed to ensure that it is properly detected and tracked. The filaments are found to have velocities of the order of 1~\\text{km}~{{\\text{s}}-1} , a perpendicular diameter of around 2-3 cm and a density amplitude 2-3.5 times the background plasma. 3D and 2D numerical codes (the STORM module of BOUT++, GBS, HESEL and TOKAM3X) are used to reproduce the motion of the observed filaments with the purpose of validating the codes and of better understanding the experimental data. Good agreement is found between the 3D codes. The seeded filament simulations are also able to reproduce the dynamics observed in experiments with accuracy up to the experimental errorbar levels. In addition, the numerical results showed that filaments characterised by similar size and light emission intensity can have quite different dynamics if the pressure perturbation is distributed differently between density and temperature components. As an additional benefit, several observations on the dynamics of the filaments in the presence of evolving temperature fields were made and led to a better understanding of the behaviour of these coherent structures.

Comparative genomic analysis identified a mutation related to enhanced heterologous protein production in the filamentous fungus Aspergillus oryzae.

PubMed

Jin, Feng-Jie; Katayama, Takuya; Maruyama, Jun-Ichi; Kitamoto, Katsuhiko

2016-11-01

Genomic mapping of mutations using next-generation sequencing technologies has facilitated the identification of genes contributing to fundamental biological processes, including human diseases. However, few studies have used this approach to identify mutations contributing to heterologous protein production in industrial strains of filamentous fungi, such as Aspergillus oryzae. In a screening of A. oryzae strains that hyper-produce human lysozyme (HLY), we previously isolated an AUT1 mutant that showed higher production of various heterologous proteins; however, the underlying factors contributing to the increased heterologous protein production remained unclear. Here, using a comparative genomic approach performed with whole-genome sequences, we attempted to identify the genes responsible for the high-level production of heterologous proteins in the AUT1 mutant. The comparative sequence analysis led to the detection of a gene (AO090120000003), designated autA, which was predicted to encode an unknown cytoplasmic protein containing an alpha/beta-hydrolase fold domain. Mutation or deletion of autA was associated with higher production levels of HLY. Specifically, the HLY yields of the autA mutant and deletion strains were twofold higher than that of the control strain during the early stages of cultivation. Taken together, these results indicate that combining classical mutagenesis approaches with comparative genomic analysis facilitates the identification of novel genes involved in heterologous protein production in filamentous fungi.

Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria

PubMed Central

2012-01-01

Background Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. Results Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. Conclusions The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All

Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

PubMed

Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

2013-01-02

Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

Interactions among filamentous fungi Aspergillus niger, Fusarium verticillioides and Clonostachys rosea: fungal biomass, diversity of secreted metabolites and fumonisin production.

PubMed

Chatterjee, Subhankar; Kuang, Yi; Splivallo, Richard; Chatterjee, Paramita; Karlovsky, Petr

2016-05-10

Interactions among fungi colonizing dead organic matter involve exploitation competition and interference competition. Major mechanism of interference competition is antibiosis caused by secreted secondary metabolites. The effect of competition on secondary metabolite production by fungi is however poorly understood. Fungal biomass was rarely monitored in interaction studies; it is not known whether dominance in pairwise interactions follows congruent patterns. Pairwise interactions of three fungal species with different life styles were studied. The saprophyte Aspergillus niger (A.n.), the plant pathogen Fusarium verticillioides (F.v.), and the mycoparasite Clonostachys rosea (C.r.) were grown in single and dual cultures in minimal medium with asparagine as nitrogen source. Competitive fitness shifted with time: in dual C.r./F.v. cultures after 10 d F.v. grew well while C.r. was suppressed; after 20 d C.r. recovered while F.v. became suppressed; and after 30 d most F.v. was destroyed. At certain time points fungal competitive fitness exhibited a rock-paper-scissors pattern: F.v. > A.n., A.n. > C.r., and C.r. > F.v. Most metabolites secreted to the medium at early stages in single and dual cultures were not found at later times. Many metabolites occurring in supernatants of single cultures were suppressed in dual cultures and many new metabolites not occurring in single cultures were found in dual cultures. A. niger showed the greatest ability to suppress the accumulation of metabolites produced by the other fungi. A. niger was also the species with the largest capacity of transforming metabolites produced by other fungi. Fumonisin production by F. verticillioides was suppressed in co-cultures with C. rosea but fumonisin B1 was not degraded by C. rosea nor did it affect the growth of C. rosea up to a concentration of 160 μg/ml. Competitive fitness in pairwise interactions among fungi is incongruent, indicating that species-specific factors and/or effects are

Calcium-containing phosphopeptides pave the secretory pathway for efficient protein traffic and secretion in fungi.

PubMed

Martín, Juan F

2014-09-10

Casein phosphopeptides (CPPs) containing chelated calcium drastically increase the secretion of extracellular homologous and heterologous proteins in filamentous fungi. Casein phosphopeptides released by digestion of alpha - and beta-casein are rich in phosphoserine residues (SerP). They stimulate enzyme secretion in the gastrointestinal tract and enhance the immune response in mammals, and are used as food supplements. It is well known that casein phosphopeptides transport Ca2+ across the membranes and play an important role in Ca2+ homeostasis in the cells. Addition of CPPs drastically increases the production of heterologous proteins in Aspergillus as host for industrial enzyme production. Recent proteomics studies showed that CPPs alter drastically the vesicle-mediated secretory pathway in filamentous fungi, apparently because they change the calcium concentration in organelles that act as calcium reservoirs. In the organelles calcium homeostasis a major role is played by the pmr1 gene, that encodes a Ca2+/Mn2+ transport ATPase, localized in the Golgi complex; this transporter controls the balance between intra-Golgi and cytoplasmic Ca2+ concentrations. A Golgi-located casein kinase (CkiA) governs the ER to Golgi directionality of the movement of secretory proteins by interacting with the COPII coat of secretory vesicles when they reach the Golgi. Mutants defective in the casein-2 kinase CkiA show abnormal targeting of some secretory proteins, including cytoplasmic membrane amino acid transporters that in ckiA mutants are miss-targeted to vacuolar membranes. Interestingly, addition of CPPs increases a glyceraldehyde-3-phpshate dehydrogenase protein that is known to associate with microtubules and act as a vesicle/membrane fusogenic agent. In summary, CPPs alter the protein secretory pathway in fungi adapting it to a deregulated protein traffic through the organelles and vesicles what results in a drastic increase in secretion of heterologous and also of

Filament Breakage Monitoring in Fused Deposition Modeling Using Acoustic Emission Technique

PubMed Central

Jin, Li; Yan, Youruiling; Mei, Yiming

2018-01-01

Polymers are being used in a wide range of Additive Manufacturing (AM) applications and have been shown to have tremendous potential for producing complex, individually customized parts. In order to improve part quality, it is essential to identify and monitor the process malfunctions of polymer-based AM. The present work endeavored to develop an alternative method for filament breakage identification in the Fused Deposition Modeling (FDM) AM process. The Acoustic Emission (AE) technique was applied due to the fact that it had the capability of detecting bursting and weak signals, especially from complex background noises. The mechanism of filament breakage was depicted thoroughly. The relationship between the process parameters and critical feed rate was obtained. In addition, the framework of filament breakage detection based on the instantaneous skewness and relative similarity of the AE raw waveform was illustrated. Afterwards, we conducted several filament breakage tests to validate their feasibility and effectiveness. Results revealed that the breakage could be successfully identified. Achievements of the present work could be further used to develop a comprehensive in situ FDM monitoring system with moderate cost. PMID:29494559

Penicillium ochrochloron MTCC 517 chitinase: An effective tool in commercial enzyme cocktail for production and regeneration of protoplasts from various fungi.

PubMed

Patil, Nilambari S; Jadhav, Jyoti P

2015-03-01

Penicillium ochrochloron MTCC 517 is a potent producer of chitinolytic enzymes. Novozyme 234, traditional enzyme cocktail for protoplast generation is not available in the market. So, new enzyme cocktail is prepared for protoplast formation from various filamentous fungi which consists of 5 mg ml(-1) lysing enzymes from Trichoderma harzianum, 0.06 mg ml(-1) β-glucuronidase from Helix pomatia and 1 mg ml(-1) P. ochrochloron chitinase. The greatest number of protoplasts could be produced from most of the fungi in 0.8 M sorbitol and by incubation for about 2 h at 37 °C, but the number was decreased by incubation for more than 3 h. About twice as many protoplasts were produced from different species of fungi by involvement of P. ochrochloron chitinase than with combined commercial enzymes.

CYTOPLASMIC FILAMENTS OF AMOEBA PROTEUS

PubMed Central

Pollard, Thomas D.; Ito, Susumu

1970-01-01

The role of filaments in consistency changes and movement in a motile cytoplasmic extract of Amoeba proteus was investigated by correlating light and electron microscopic observations with viscosity measurements. The extract is prepared by the method of Thompson and Wolpert (1963). At 0°C, this extract is nonmotile and similar in structure to ameba cytoplasm, consisting of groundplasm, vesicles, mitochondria, and a few 160 A filaments. The extract undergoes striking ATP-stimulated streaming when warmed to 22°C. Two phases of movement are distinguished. During the first phase, the apparent viscosity usually increases and numerous 50–70 A filaments appear in samples of the extract prepared for electron microscopy, suggesting that the increase in viscosity in caused, at least in part, by the formation of these thin filaments. During this initial phase of ATP-stimulated movement, these thin filaments are not detectable by phase-contrast or polarization microscopy, but later, in the second phase of movement, 70 A filaments aggregate to form birefringent microscopic fibrils. A preparation of pure groundplasm with no 160 A filaments or membranous organelles exhibits little or no ATP-stimulated movement, but 50–70 A filaments form and aggregate into birefringent fibrils. This observation and the structural relationship of the 70 A and the 160 A filaments in the motile extract suggest that both types of filaments may be required for movement. These two types of filaments, 50–70 A and 160 A, are also present in the cytoplasm of intact amebas. Fixed cells could not be used to study the distribution of these filaments during natural ameboid movement because of difficulties in preserving the normal structure of the ameba during preparation for electron microscopy. PMID:4915451

Plasmids for increased efficiency of vector construction and genetic engineering in filamentous fungi.

PubMed

Schoberle, Taylor J; Nguyen-Coleman, C Kim; May, Gregory S

2013-01-01

Fungal species are continuously being studied to not only understand disease in humans and plants but also to identify novel antibiotics and other metabolites of industrial importance. Genetic manipulations, such as gene deletion, gene complementation, and gene over-expression, are common techniques to investigate fungal gene functions. Although advances in transformation efficiency and promoter usage have improved genetic studies, some basic steps in vector construction are still laborious and time-consuming. Gateway cloning technology solves this problem by increasing the efficiency of vector construction through the use of λ phage integrase proteins and att recombination sites. We developed a series of Gateway-compatible vectors for use in genetic studies in a range of fungal species. They contain nutritional and drug-resistance markers and can be utilized to manipulate different filamentous fungal genomes. Copyright © 2013 Elsevier Inc. All rights reserved.

Cytoplasmic filaments of Amoeba proteus. I. The role of filaments in consistency changes and movement.

PubMed

Pollard, T D; Ito, S

1970-08-01

The role of filaments in consistency changes and movement in a motile cytoplasmic extract of Amoeba proteus was investigated by correlating light and electron microscopic observations with viscosity measurements. The extract is prepared by the method of Thompson and Wolpert (1963). At 0 degrees C, this extract is nonmotile and similar in structure to ameba cytoplasm, consisting of groundplasm, vesicles, mitochondria, and a few 160 A filaments. The extract undergoes striking ATP-stimulated streaming when warmed to 22 degrees C. Two phases of movement are distinguished. During the first phase, the apparent viscosity usually increases and numerous 50-70 A filaments appear in samples of the extract prepared for electron microscopy, suggesting that the increase in viscosity in caused, at least in part, by the formation of these thin filaments. During this initial phase of ATP-stimulated movement, these thin filaments are not detectable by phase-contrast or polarization microscopy, but later, in the second phase of movement, 70 A filaments aggregate to form birefringent microscopic fibrils. A preparation of pure groundplasm with no 160 A filaments or membranous organelles exhibits little or no ATP-stimulated movement, but 50-70 A filaments form and aggregate into birefringent fibrils. This observation and the structural relationship of the 70 A and the 160 A filaments in the motile extract suggest that both types of filaments may be required for movement. These two types of filaments, 50-70 A and 160 A, are also present in the cytoplasm of intact amebas. Fixed cells could not be used to study the distribution of these filaments during natural ameboid movement because of difficulties in preserving the normal structure of the ameba during preparation for electron microscopy.

Reverse genetics studies on the filamentous morphology of influenza A virus.

PubMed

Bourmakina, Svetlana V; García-Sastre, Adolfo

2003-03-01

We have investigated the genetic determinants responsible for the filamentous morphology of influenza A viruses, a property characteristic of primary virus isolates. A plasmid-based reverse genetics system was used to transfer the M segment of influenza A/Udorn/72 (H3N2) virus into influenza A/WSN/33 (H1N1) virus. While WSN virions display spherical morphology, recombinant WSN-Mud virus acquired the ability of the parental Udorn strain to form filamentous virus particles. This was determined by immunofluorescence studies in infected MDCK cells and by electron microscopy of purified virus particles. To determine the gene product within the M segment responsible for filamentous virus morphology, we generated four recombinant viruses carrying different sets of M1 and M2 genes from WSN or Udorn strains in a WSN background. These studies revealed that the M1 gene of Udorn, independently of the origin of the M2 gene, conferred filamentous budding properties and filamentous virus morphology to the recombinant viruses. We also constructed two WSN viruses encoding chimeric M1 proteins containing the amino-terminal 1-162 amino acids or the carboxy-terminal 163-252 amino acids of the Udorn M1 protein. Neither of these two viruses acquired filamentous phenotypes, indicating that both amino- and carboxy-terminal domains of the M1 protein contribute to filamentous virus morphology. We next rescued seven mutant WSN-M1ud viruses containing Udorn M1 proteins carrying single amino acid substitutions corresponding to the seven amino acid differences with the M1 protein of WSN virus. Characterization of these recombinant viruses revealed that amino acid residues 95 and 204 are critical in determining filamentous virus particle formation.

New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus.

PubMed

Strullu-Derrien, Christine; Spencer, Alan R T; Goral, Tomasz; Dee, Jaclyn; Honegger, Rosmarie; Kenrick, Paul; Longcore, Joyce E; Berbee, Mary L

2018-02-05

Zoosporic fungi are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems. They comprise at least three phyla, of which two, Chytridiomycota and Blastocladiomycota, developed a range of thallus morphologies including branching hyphae. Here we describe Retesporangicus lyonii gen. et sp. nov., an exceptionally well preserved fossil, which is the earliest known to produce multiple sporangia on an expanded hyphal network. To better characterize the fungus we develop a new method to render surfaces from image stacks generated by confocal laser scanning microscopy. Here, the method helps to reveal thallus structure. Comparisons with cultures of living species and character state reconstructions analysed against recent molecular phylogenies of 24 modern zoosporic fungi indicate an affinity with Blastocladiomycota. We argue that in zoosporic fungi, kinds of filaments such as hyphae, rhizoids and rhizomycelium are developmentally similar structures adapted for varied functions including nutrient absorption and anchorage. The fossil is the earliest known type to develop hyphae which likely served as a saprotrophic adaptation to patchy resource availability. Evidence from the Rhynie chert provides our earliest insights into the biology of fungi and their roles in the environment. It demonstrates that zoosporic fungi were already diverse in 407 million-year-old terrestrial ecosystems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'. © 2017 The Author(s).

Antimicrobial and enzymatic activity of anemophilous fungi of a public university in Brazil.

PubMed

Sobral, Laureana V; Melo, Kelly N; Souza, Cleciana M; Silva, Sílvio F; Silva, Gilvania L R; Silva, Andressa L F; Wanderley, Katharine A A; Oliveira, Idjane S; Cruz, Roberta

2017-01-01

To the fungal microbiota the UFPE and biotechnological potential enzymatic and antimicrobial production. Air conditioned environments were sampled using a passive sedimentation technique, the air I ratio and the presence of aflatoxigenic strains evaluated for ANVISA. Icelles were to determine the enzymatic activity of lipase, amylase and protease metabolic liquids to determine antimicrobial activity. Diversity was observed in all CAV environments, CFU/m3 ranged from 14 to 290 and I/E ratio from 0.1 to 1.5. The of the fungal genera were: Aspergillus (50%), Penicillium (21%), Talaromyces (14%), Curvularia and Paecilomyces (7% each). Aspergillus sydowii (Bainier & Sartory) Thom & Church presented enzymatic activity and the Talaromyces purpureogenus Samson, Yilmaz, Houbraken, Spierenb., Seifert, Peterson, Varga & Frisvad presented antibacterial activity against all bacteria that all environments present fungal species biodiversity no toxigenic or pathogenic fungi were found, according to ANVISA legislation for conditioned environments and airborne filamentous fungi present potential for enzymatic and antimicrobial activity.

Solid friction between soft filaments.

PubMed

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A W C; Vitelli, Vincenzo; Mahadevan, L; Dogic, Zvonimir

2015-06-01

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments' overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes's drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament's elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

Antimicrobial activity of broccoli (Brassica oleracea var. italica) cultivar Avenger against pathogenic bacteria, phytopathogenic filamentous fungi and yeast.

PubMed

Pacheco-Cano, R D; Salcedo-Hernández, R; López-Meza, J E; Bideshi, D K; Barboza-Corona, J E

2018-01-01

The objective of this study was to show whether the edible part of broccoli has antibacterial and antifungal activity against micro-organism of importance in human health and vegetable spoilage, and to test if this effect was partially due to antimicrobial peptides (AMPs). Crude extracts were obtained from florets and stems of broccoli cultivar Avenger and the inhibitory effect was demonstrated against pathogenic bacteria (Bacillus cereus, Staphylococcus xylosus, Staphylococcus aureus, Shigella flexneri, Shigella sonnei, Proteus vulgaris), phytopathogenic fungi (Colletotrichum gloeosporioides, Asperigillus niger) and yeasts (Candida albicans and Rhodotorula sp.). It was shown that samples treated with proteolytic enzymes had a reduction of approximately 60% in antibacterial activity against Staph. xylosus, suggesting that proteinaceous compounds might play a role in the inhibitory effect. Antimicrobial components in crude extracts were thermoresistant and the highest activity was observed under acidic conditions. It was shown that antifungal activity of broccoli's crude extracts might not be attributed to chitinases. Organic broccoli cultivar Avenger has antimicrobial activity against pathogenic bacteria, yeast and phytophatogenic fungi. Data suggest that this effect is partially due to AMPs. Broccoli's crude extracts have activity not only against pathogenic bacteria but also against phytophatogenic fungi of importance in agriculture. We suggest for first time that the inhibitory effect is probably due to AMPs. © 2017 The Society for Applied Microbiology.

Demolition of a hospital building by controlled explosion: the impact on filamentous fungal load in internal and external air.

PubMed

Bouza, E; Peláez, T; Pérez-Molina, J; Marín, M; Alcalá, L; Padilla, B; Muñoz, P; Adán, P; Bové, B; Bueno, M J; Grande, F; Puente, D; Rodríguez, M P; Rodríguez-Créixems, M; Vigil, D; Cuevas, O

2002-12-01

The demolition of a maternity building at our institution provided us with the opportunity to study the load of filamentous fungi in the air. External (nearby streets) and internal (within the hospital buildings) air was sampled with an automatic volumetric machine (MAS-100 Air Samplair) at least daily during the week before the demolition, at 10, 30, 60, 90,120, 180, 240, 420, 540 and 660 min post-demolition, daily during the week after the demolition and weekly during weeks 2, 3 and 4 after demolition. Samples were duplicated to analyse reproducibility. Three hundred and forty samples were obtained: 115 external air, 69 'non-protected' internal air and 156 protected internal air [high efficiency particulate air (HEPA) filtered air under positive pressure]. A significant increase in the colony count of filamentous fungi occurred after the demolition. Median colony counts of external air on demolition day were significantly higher than from internal air (70.2 cfu/m(3) vs 35.8 cfu/m(3)) (P < 0.001). Mechanical demolition on day +4 also produced a significant difference between external and internal air (74.5 cfu/m(3) vs 41.7 cfu/m(3)). The counts returned to baseline levels on day +11. Most areas with a protected air supply yielded no colonies before demolition day and remained negative on demolition day. The reproducibility of the count method was good (intra-assay variance: 2.4 cfu/m(3)). No episodes of invasive filamentous mycosis were detected during the three months following the demolition. Demolition work was associated with a significant increase in the fungal colony counts of hospital external and non-protected internal air. Effective protective measures may be taken to avoid the emergence of clinical infections. Copyright 2002 The Hospital Infection Society

Environmental Factors and Bioremediation of Xenobiotics Using White Rot Fungi

PubMed Central

Fragoeiro, Silvia; Bastos, Catarina

2010-01-01

This review provides background information on the importance of bioremediation approaches. It describes the roles of fungi, specifically white rot fungi, and their extracellular enzymes, laccases, ligninases, and peroxidises, in the degradation of xenobiotic compounds such as single and mixtures of pesticides. We discuss the importance of abiotic factors such as water potential, temperature, and pH stress when considering an environmental screening approach, and examples are provided of the differential effect of white rot fungi on the degradation of single and mixtures of pesticides using fungi such as Trametes versicolor and Phanerochaete chrysosporium. We also explore the formulation and delivery of fungal bioremedial inoculants to terrestrial ecosystems as well as the use of spent mushroom compost as an approach. Future areas for research and potential exploitation of new techniques are also considered. PMID:23956663

Tolerance to heavy metals in filamentous fungi isolated from contaminated mining soils in the Zanjan Province, Iran.

PubMed

Mohammadian, Elham; Babai Ahari, Asadollah; Arzanlou, Mahdi; Oustan, Shahin; Khazaei, Sayyed Hossein

2017-10-01

In the present study the population of fungi inhabiting metal contaminated soil samples from lead-zinc mining area was investigated, and their tolerance and biosorption capacity towards Cd, Pb, Zn and Cu were evaluated. Fungal species, including Acremonium persicinum, Penicillium simplicissimum, Seimatosporium pistaciae, Trichoderma harzianum, Alternaria chlamydosporigena and Fusarium verticillioides were isolated. Fungal tolerance was determined by measuring of the "Minimum Inhibitory Concentration", after exposure to increasing concentrations of heavy metal chlorides. Among the test fungi, Trichoderma harzianum was the most tolerant against Cd, Pb and Cu. The Heavy metal content in the fungal biomass was quantified after combustion. The calculated total sorption of heavy metals showed that Acremonium persicinum and Penicillium simplicissimum had the highest accumulation of Zn and Cu, respectively. The data presented in this study should help to use the accumulation potential of some of those fungal species examined for bioremediation of contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Penicillium ochrochloron MTCC 517 chitinase: An effective tool in commercial enzyme cocktail for production and regeneration of protoplasts from various fungi

PubMed Central

Patil, Nilambari S.; Jadhav, Jyoti P.

2014-01-01

Penicillium ochrochloron MTCC 517 is a potent producer of chitinolytic enzymes. Novozyme 234, traditional enzyme cocktail for protoplast generation is not available in the market. So, new enzyme cocktail is prepared for protoplast formation from various filamentous fungi which consists of 5 mg ml−1 lysing enzymes from Trichoderma harzianum, 0.06 mg ml−1 β-glucuronidase from Helix pomatia and 1 mg ml−1P. ochrochloron chitinase. The greatest number of protoplasts could be produced from most of the fungi in 0.8 M sorbitol and by incubation for about 2 h at 37 °C, but the number was decreased by incubation for more than 3 h. About twice as many protoplasts were produced from different species of fungi by involvement of P. ochrochloron chitinase than with combined commercial enzymes. PMID:25737658

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodwin, Stephen; McCorison, Cassandra B.; Cavaletto, Jessica R.

Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelial growth in cellars with high humidity, and its ability to metabolize volatile organic compounds including alcohols, esters and formaldehyde is thought to improve air quality. It grows slowly but appears to outcompete ordinarily faster-growing species under anaerobic conditions.Whether these abilities have affected its mitochondrial genome is not known.To fill this gap, its mitochondrial genome was assembled as part of a whole- genome shotgun-sequencing project.The circular-mapping mitochondrial genome of Z. cellare, at onlymore » 23,743 bp, is the smallest yet reported for a filamentous fungus.It contains the complete set of 14 protein-coding genes seen typically in other filamentous fungi, along with genes for large and small ribosomal RNA subunits, 25 predicted tRNA genes capable of decoding all 20 amino acids, and a single open reading frame potentially coding for a protein of unknown function.The Z. cellare mitochondrial genome had genes encoded on both strands with a single change of direction, different from most other fungi but consistent with the Dothideomycetes. The high synteny among mitochondrial genomes of fungi in the Eurotiomycetes broke down almost completely in the Dothideomycetes.Only a low level of microsynteny was observed among protein-coding and tRNA genes in comparison with Mycosphaerella graminicola (synonym Zymoseptoria tritici), the only other fungus in the order Capnodiales with a sequenced mitochondrial genome, involving the three gene pairs atp8-atp9, nad2-nad3, and nad4L-nad5.However, even this low level of microsynteny did not extend to other fungi in the Dothideomycetes and Eurotiomycetes. Phylogenetic analysis of concatenated protein-coding genes confirmed the relationship between Z. cellare and M. graminicola in the Capnodiales, although

Diversity of indoor fungi as revealed by DNA metabarcoding.

PubMed

Korpelainen, Helena; Pietiläinen, Maria

2017-01-01

In the present study, we conducted DNA metabarcoding (the nuclear ITS2 region) for indoor fungal samples originating from two nursery schools with a suspected mould problem (sampling before and after renovation), from two university buildings, and from an old farmhouse. Good-quality sequences were obtained, and the results showed that DNA metabarcoding provides high resolution in fungal identification. The pooled proportions of sequences representing filamentous ascomycetes, filamentous basidiomycetes, yeasts, and other fungi equalled 62.3%, 8.0%, 28.3%, and 1.4%, respectively, and the total number of fungal genera found during the study was 585. When comparing fungal diversities and taxonomic composition between different types of buildings, no obvious pattern was detected. The average pairwise values of Sørensen Chao indices that were used to compare similarities for taxon composition between samples among the samples from the two university buildings, two nurseries, and farmhouse equaled 0.693, 0.736, 0.852, 0.928, and 0.981, respectively, while the mean similarity index for all samples was 0.864. We discovered that making explicit conclusions on the relationship between the indoor air quality and mycoflora is complicated by the lack of appropriate indicators for air quality and by the occurrence of wide spatial and temporal changes in diversity and compositions among samples.

Actin filament curvature biases branching direction

NASA Astrophysics Data System (ADS)

Wang, Evan; Risca, Viviana; Chaudhuri, Ovijit; Chia, Jia-Jun; Geissler, Phillip; Fletcher, Daniel

2012-02-01

Actin filaments are key components of the cellular machinery, vital for a wide range of processes ranging from cell motility to endocytosis. Actin filaments can branch, and essential in this process is a protein complex known as the Arp2/3 complex, which nucleate new ``daughter'' filaments from pre-existing ``mother'' filaments by attaching itself to the mother filament. Though much progress has been made in understanding the Arp2/3-actin junction, some very interesting questions remain. In particular, F-actin is a dynamic polymer that undergoes a wide range of fluctuations. Prior studies of the Arp2/3-actin junction provides a very static notion of Arp2/3 binding. The question we ask is how differently does the Arp2/3 complex interact with a straight filament compared to a bent filament? In this study, we used Monte Carlo simulations of a surface-tethered worm-like chain to explore possible mechanisms underlying the experimental observation that there exists preferential branch formation by the Arp2/3 complex on the convex face of a curved filament. We show that a fluctuation gating model in which Arp2/3 binding to the actin filament is dependent upon a rare high-local-curvature shape fluctuation of the filament is consistent with the experimental data.

Modulating Endoplasmic Reticulum-Golgi Cargo Receptors for Improving Secretion of Carrier-Fused Heterologous Proteins in the Filamentous Fungus Aspergillus oryzae

PubMed Central

Hoang, Huy-Dung; Maruyama, Jun-ichi

2014-01-01

Filamentous fungi are excellent hosts for industrial protein production due to their superior secretory capacity; however, the yield of heterologous eukaryotic proteins is generally lower than that of fungal or endogenous proteins. Although activating protein folding machinery in the endoplasmic reticulum (ER) improves the yield, the importance of intracellular transport machinery for heterologous protein secretion is poorly understood. Here, using Aspergillus oryzae as a model filamentous fungus, we studied the involvement of two putative lectin-like cargo receptors, A. oryzae Vip36 (AoVip36) and AoEmp47, in the secretion of heterologous proteins expressed in fusion with the endogenous enzyme α-amylase as the carrier. Fluorescence microscopy revealed that mDsRed-tagged AoVip36 localized in the Golgi compartment, whereas AoEmp47 showed localization in both the ER and the Golgi compartment. Deletion of AoVip36 and AoEmp47 improved heterologous protein secretion, but only AoVip36 deletion had a negative effect on the secretion of α-amylase. Analysis of ER-enriched cell fractions revealed that AoVip36 and AoEmp47 were involved in the retention of heterologous proteins in the ER. However, the overexpression of each cargo receptor had a different effect on heterologous protein secretion: AoVip36 enhanced the secretion, whereas AoEmp47 promoted the intracellular retention. Taken together, our data suggest that AoVip36 and AoEmp47 hinder the secretion of heterologous proteins by promoting their retention in the ER but that AoVip36 also promotes the secretion of heterologous proteins. Moreover, we found that genetic deletion of these putative ER-Golgi cargo receptors significantly improves heterologous protein production. The present study is the first to propose that ER-Golgi transport is a bottleneck for heterologous protein production in filamentous fungi. PMID:25362068

Vita activa in biotechnology: what we do with fungi and what fungi do with us.

PubMed

Weinhold, Martin; Mast-Gerlach, Edeltraud; Meyer, Vera

2017-01-01

Filamentous fungi are fascinating microorganisms. One of the reasons why it is so worthwhile to take a closer look at them is their capacity to produce secondary metabolites. Some of these substances have the potential to be of great use for mankind, such as it was the case with penicillin and its discovery in 1928. Almost a century later, the situation in healthcare could possibly turn back to the state before the development of the first antibiotics. Due to an overuse of antibiotics we are facing a surge of multiresistant bacteria that are not inhibited by any of the currently known drugs. That was part of the background why a European research project was launched in October 2013, titled "Quantitative Biology for Fungal Secondary Metabolite Producers", or "QuantFung". Fifteen young scientists embarked on a new phase in their career, moving to new work environments within Europe and dedicating their work lives intensively to the quest for useful secondary metabolites. After 4 years, the QuantFung project concluded in October this year. In this commentary, we aim to convey what it means to work in this field of fungal biotechnology and how important it is to improve the efficiency of the research therein. We introduce five out of the fifteen fellows at length and let them have their say about the adventure of science, euphoric moments, prospects and doubts. We also raise questions about the current state of research in academia, something the QuantFung fellows experienced first-hand. Being a scientist often goes beyond earning money to make one's living. This is why we also reflect on aspects of the meaning of work in our western society, where production for profit's sake is a main driver. For that we refer to one of the most distinguished thinkers of the twentieth century, to Hannah Arendt.

A penny-shaped crack in a filament-reinforced matrix. I - The filament model. II - The crack problem

NASA Technical Reports Server (NTRS)

Erdogan, F.; Pacella, A. H.

1974-01-01

The study deals with the elastostatic problem of a penny-shaped crack in an elastic matrix which is reinforced by filaments or fibers perpendicular to the plane of the crack. An elastic filament model is first developed, followed by consideration of the application of the model to the penny-shaped crack problem in which the filaments of finite length are asymmetrically distributed around the crack. Since the primary interest is in the application of the results to studies relating to the fracture of fiber or filament-reinforced composites and reinforced concrete, the main emphasis of the study is on the evaluation of the stress intensity factor along the periphery of the crack, the stresses in the filaments or fibers, and the interface shear between the matrix and the filaments or fibers. Using the filament model developed, the elastostatic interaction problem between a penny-shaped crack and a slender inclusion or filament in an elastic matrix is formulated.

The identification of fungi collected from the ceca of commercial poultry.

PubMed

Byrd, J A; Caldwell, D Y; Nisbet, D J

2017-07-01

Under normal conditions, fungi are ignored unless a disease/syndrome clinical signs are reported. The scientific communities are largely unaware of the roles fungi play in normal production parameters. Numerous preharvest interventions have demonstrated that beneficial bacteria can play a role in improving productions parameters; however, most researchers have ignored the impact that fungi may have on production. The goal of the present study was to record fungi recovered from commercial broiler and layer houses during production. Over 3,000 cecal samples were isolated using conventional culture methodology and over 890 samples were further characterized using an automated repetitive sequence-based PCR (rep-PCR) methodology. Eighty-eight different fungal and yeast species were identified, including Aspergillus spp., Penicillium spp., and Sporidiobolus spp, and 18 unknown genera were separated using rep-PCR. The results from the present study will provide a normal fungi background genera under commercial conditions and will be a stepping stone for investigating the impact of fungi on the gastrointestinal tract and on the health of poultry. Published by Oxford University Press on behalf of Poultry Science Association 2017.

Tungsten Filament Fire

ERIC Educational Resources Information Center

Ruiz, Michael J.; Perkins, James

2016-01-01

We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent…

Background derivation and image flattening: getimages

NASA Astrophysics Data System (ADS)

Men'shchikov, A.

2017-11-01

Modern high-resolution images obtained with space observatories display extremely strong intensity variations across images on all spatial scales. Source extraction in such images with methods based on global thresholding may bring unacceptably large numbers of spurious sources in bright areas while failing to detect sources in low-background or low-noise areas. It would be highly beneficial to subtract background and equalize the levels of small-scale fluctuations in the images before extracting sources or filaments. This paper describes getimages, a new method of background derivation and image flattening. It is based on median filtering with sliding windows that correspond to a range of spatial scales from the observational beam size up to a maximum structure width Xλ. The latter is a single free parameter of getimages that can be evaluated manually from the observed image ℐλ. The median filtering algorithm provides a background image \\tilde{Bλ} for structures of all widths below Xλ. The same median filtering procedure applied to an image of standard deviations 𝓓λ derived from a background-subtracted image \\tilde{Sλ} results in a flattening image \\tilde{Fλ}. Finally, a flattened detection image I{λD} = \\tilde{Sλ}/\\tilde{Fλ} is computed, whose standard deviations are uniform outside sources and filaments. Detecting sources in such greatly simplified images results in much cleaner extractions that are more complete and reliable. As a bonus, getimages reduces various observational and map-making artifacts and equalizes noise levels between independent tiles of mosaicked images.

Electron emitting filaments for electron discharge devices

DOEpatents

Leung, Ka-Ngo; Pincosy, Philip A.; Ehlers, Kenneth W.

1988-01-01

Electrons are copiously emitted by a device comprising a loop-shaped filament made of lanthanum hexaboride. The filament is directly heated by an electrical current produced along the filament by a power supply connected to the terminal legs of the filament. To produce a filament, a diamond saw or the like is used to cut a slice from a bar made of lanthanum hexaboride. The diamond saw is then used to cut the slice into the shape of a loop which may be generally rectangular, U-shaped, hairpin-shaped, zigzag-shaped, or generally circular. The filaments provide high electron emission at a relatively low operating temperature, such as 1600.degree. C. To achieve uniform heating, the filament is formed with a cross section which is tapered between the opposite ends of the filament to compensate for non-uniform current distribution along the filament due to the emission of electrons from the filament.

Electron emitting filaments for electron discharge devices

DOEpatents

Leung, K.N.; Pincosy, P.A.; Ehlers, K.W.

1983-06-10

Electrons are copiously emitted by a device comprising a loop-shaped filament made of lanthanum hexaboride. The filament is directly heated by an electrical current produced along the filament by a power supply connected to the terminal legs of the filament. To produce a filament, a diamond saw or the like is used to cut a slice from a bar made of lanthanum hexaboride. The diamond saw is then used to cut the slice into the shape of a loop which may be generally rectangular, U-shaped, hairpin-shaped, zigzag-shaped, or generally circular. The filaments provide high electron emission at a relatively low operating temperature, such as 1600/sup 0/C. To achieve uniform heating, the filament is formed with a cross section which is tapered between the opposite ends of the filament to compensate for nonuniform current distribution along the filament due to the emission of electrons from the filament.

A review on the inhibitory potential of Nigella sativa against pathogenic and toxigenic fungi.

PubMed

Shokri, Hojjatollah

2016-01-01

Nigella sativa (N. sativa) grows in various parts of the world, particularly in Iran. It has been traditionally used as a folk remedy to treat a number of diseases. The seeds of this plant contain moisture, proteins, carbohydrates, crude fiber, alkaloids, saponins, ash, fixed oils and essential oil. The major components of the essential oil are thymoquinone, p-cymene, trans-anethole, 2-methyl-5(1-methyl ethyl)-Bicyclo[3.1.0]hex-2-en and γ-terpinene. So far, several pharmacological effects such as anti-oxidant, anti-inflammatory, anti-cancer and anti-microbial have been reported for N. sativa or its active compounds. Thymoquinone, thymohydroquinone and thymol are the most active constituents which have different beneficial properties. The oil, extracts and some of N. sativa active components possessed moderate in vitro and in vivo inhibitory activity against pathogenic yeasts, dermatophytes, non-dermatophytic filamentous fungi and aflatoxin-producing fungi. The main morphological changes of pathogenic and toxigenic fungi treated with N. sativa oil were observed in the cell wall, plasma membrane and membranous organelles, particularly in the nuclei and mitochondria. Although this review represents first step in the search for a new anti-fungal drug, the full potential of N. sativa as a fungitoxic agent has not been exploited and necessitates further investigations.

A MAGNETIC RIBBON MODEL FOR STAR-FORMING FILAMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Auddy, Sayantan; Basu, Shantanu; Kudoh, Takahiro, E-mail: sauddy3@uwo.ca, E-mail: basu@uwo.ca, E-mail: kudoh@nagasaki-u.ac.jp

2016-11-01

We develop a magnetic ribbon model for molecular cloud filaments. These result from turbulent compression in a molecular cloud in which the background magnetic field sets a preferred direction. We argue that this is a natural model for filaments and is based on the interplay between turbulence, strong magnetic fields, and gravitationally driven ambipolar diffusion, rather than pure gravity and thermal pressure. An analytic model for the formation of magnetic ribbons that is based on numerical simulations is used to derive a lateral width of a magnetic ribbon. This differs from the thickness along the magnetic field direction, which ismore » essentially the Jeans scale. We use our model to calculate a synthetic observed relation between apparent width in projection versus observed column density. The relationship is relatively flat, similar to observations, and unlike the simple expectation based on a Jeans length argument.« less

The interaction of fungi with dendritic cells: implications for Th immunity and vaccination.

PubMed

Claudia, Montagnoli; Bacci, Angela; Silvia, Bozza; Gaziano, Roberta; Spreca, Antonio; Romani, Luigina

2002-09-01

Human beings are continuously exposed to fungi, yet they rarely get fungal diseases. The delicate balance between the host and these otherwise harmless pathogens may turn into a parasitic relationship, resulting in the development of severe infections. The ability to reversibly switch between unicellular and filamentous forms, all of which can be found in infected tissues, is thought to be important for virulence. Efficient responses to the different forms of fungi require different mechanisms of immunity. Dendritic cells (DC) are uniquely able at decoding the fungus-associated information and translating it in qualitatively different T helper (Th) immune responses, in vitro and in vivo. Myeloid DC phagocytosed yeasts and hyphae of Candida albicans and conidia and hyphae of Aspergillus fumigatus, both in vitro and in vivo. Phagocytosis occurred through distinct phagocytic morphologies, involving the engagement and cooperativity of distinct recognition receptors. However, receptor engagement and cooperativity were greatly modified by opsonization. The engagement of distinct receptors translated into disparate downstream signaling events, ultimately affecting cytokine production and costimulation. In vivo studies confirmed that the choice of receptor and mode of entry of fungi into DC was responsible for Th polarization and patterns of susceptibility or resistance to infection. Adoptive transfer of different types of DC activated protective, nonprotective and regulatory T cells, ultimately affecting the outcome of infection. The conclusions are that the selective exploitation of receptors and mode of entry into DC may determine the full range of host's immune relationships with fungi and have important implications in the design of vaccine-based strategies.

Comparison of background levels of culturable fungal spore concentrations in indoor and outdoor air in southeastern Austria

NASA Astrophysics Data System (ADS)

Haas, D.; Habib, J.; Luxner, J.; Galler, H.; Zarfel, G.; Schlacher, R.; Friedl, H.; Reinthaler, F. F.

2014-12-01

Background concentrations of airborne fungi are indispensable criteria for an assessment of fungal concentrations indoors and in the ambient air. The goal of this study was to define the natural background values of culturable fungal spore concentrations as reference values for the assessment of moldy buildings. The concentrations of culturable fungi were determined outdoors as well as indoors in 185 dwellings without visible mold, obvious moisture problems or musty odor. Samples were collected using the MAS-100® microbiological air sampler. The study shows a characteristic seasonal influence on the background levels of Cladosporium, Penicillium and Aspergillus. Cladosporium sp. had a strong outdoor presence, whereas Aspergillus sp. and Penicillium sp. were typical indoor fungi. For the region of Styria, the median outdoor concentrations are between 100 and 940 cfu/m³ for culturable xerophilic fungi in the course of the year. Indoors, median background levels are between 180 and 420 cfu/m³ for xerophilic fungi. The I/O ratios of the airborne fungal spore concentrations were between 0.2 and 2.0. For the assessment of indoor and outdoor air samples the dominant genera Cladosporium, Penicillium and Aspergillus should receive special consideration.

The vacuole system is a significant intracellular pathway for longitudinal solute transport in basidiomycete fungi.

PubMed

Darrah, P R; Tlalka, M; Ashford, A; Watkinson, S C; Fricker, M D

2006-07-01

Mycelial fungi have a growth form which is unique among multicellular organisms. The data presented here suggest that they have developed a unique solution to internal solute translocation involving a complex, extended vacuole. In all filamentous fungi examined, this extended vacuole forms an interconnected network, dynamically linked by tubules, which has been hypothesized to act as an internal distribution system. We have tested this hypothesis directly by quantifying solute movement within the organelle by photobleaching a fluorescent vacuolar marker. Predictive simulation models were then used to determine the transport characteristics over extended length scales. This modeling showed that the vacuolar organelle forms a functionally important, bidirectional diffusive transport pathway over distances of millimeters to centimeters. Flux through the pathway is regulated by the dynamic tubular connections involving homotypic fusion and fission. There is also a strongly predicted interaction among vacuolar organization, predicted diffusion transport distances, and the architecture of the branching colony margin.

Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells

PubMed Central

Kampourakis, Thomas; Yan, Ziqian; Gautel, Mathias; Sun, Yin-Biao; Irving, Malcolm

2014-01-01

Myosin binding protein-C (MyBP-C) is a key regulatory protein in heart muscle, and mutations in the MYBPC3 gene are frequently associated with cardiomyopathy. However, the mechanism of action of MyBP-C remains poorly understood, and both activating and inhibitory effects of MyBP-C on contractility have been reported. To clarify the function of the regulatory N-terminal domains of MyBP-C, we determined their effects on the structure of thick (myosin-containing) and thin (actin-containing) filaments in intact sarcomeres of heart muscle. We used fluorescent probes on troponin C in the thin filaments and on myosin regulatory light chain in the thick filaments to monitor structural changes associated with activation of demembranated trabeculae from rat ventricle by the C1mC2 region of rat MyBP-C. C1mC2 induced larger structural changes in thin filaments than calcium activation, and these were still present when active force was blocked with blebbistatin, showing that C1mC2 directly activates the thin filaments. In contrast, structural changes in thick filaments induced by C1mC2 were smaller than those associated with calcium activation and were abolished or reversed by blebbistatin. Low concentrations of C1mC2 did not affect resting force but increased calcium sensitivity and reduced cooperativity of force and structural changes in both thin and thick filaments. These results show that the N-terminal region of MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments and lead to a novel hypothesis for the physiological role of MyBP-C in the regulation of cardiac contractility. PMID:25512492

Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells.

PubMed

Kampourakis, Thomas; Yan, Ziqian; Gautel, Mathias; Sun, Yin-Biao; Irving, Malcolm

2014-12-30

Myosin binding protein-C (MyBP-C) is a key regulatory protein in heart muscle, and mutations in the MYBPC3 gene are frequently associated with cardiomyopathy. However, the mechanism of action of MyBP-C remains poorly understood, and both activating and inhibitory effects of MyBP-C on contractility have been reported. To clarify the function of the regulatory N-terminal domains of MyBP-C, we determined their effects on the structure of thick (myosin-containing) and thin (actin-containing) filaments in intact sarcomeres of heart muscle. We used fluorescent probes on troponin C in the thin filaments and on myosin regulatory light chain in the thick filaments to monitor structural changes associated with activation of demembranated trabeculae from rat ventricle by the C1mC2 region of rat MyBP-C. C1mC2 induced larger structural changes in thin filaments than calcium activation, and these were still present when active force was blocked with blebbistatin, showing that C1mC2 directly activates the thin filaments. In contrast, structural changes in thick filaments induced by C1mC2 were smaller than those associated with calcium activation and were abolished or reversed by blebbistatin. Low concentrations of C1mC2 did not affect resting force but increased calcium sensitivity and reduced cooperativity of force and structural changes in both thin and thick filaments. These results show that the N-terminal region of MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments and lead to a novel hypothesis for the physiological role of MyBP-C in the regulation of cardiac contractility.

Nonsteroidal Anti-inflammatory Drugs (NSAIDS) Inhibit the Growth and Reproduction of Chaetomium globosum and Other Fungi Associated with Water-Damaged Buildings.

PubMed

Dalmont, Kelsey; Biles, Charles L; Konsure, Heather; Dahal, Sujita; Rowsey, Tyler; Broge, Matthew; Poudyal, Shubhra; Gurung, Tara; Shrestha, Sabina; Biles, Caleb L; Cluck, Terry; Howard, Alisha

2017-12-01

Indoor mold due to water damage causes serious human respiratory disorders, and the remediation to homes, schools, and businesses is a major expense. Prevention of mold infestation of building materials would reduce health problems and building remediation costs. Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit yeasts and a limited number of filamentous fungi. The purpose of this research was to determine the possible inhibitory activity of nonsteroidal anti-inflammatory drugs (NSAIDs) on germination, fungal growth, and reproduction of Chaetomium globosum and other important filamentous fungi that occur in water-damaged buildings. Several NSAIDs were found to inhibit C. globosum germination, growth, and reproduction. The most effective NSAIDs inhibiting C. globosum were ibuprofen, diflunisal, and diclofenac. Fusarium oxysporum, Fusarium solani, Aspergillus niger, and Stachybotrys atra were also tested on the various media with similar results obtained. However, F. oxysporum and A. niger exhibited a higher level of resistance to aspirin and NaSAL when compared to the C. globosum isolates. The inhibition exhibited by NSAIDs was variable depending on growth media and stage of fungal development. These compounds have a great potential of inhibiting fungal growth on building materials such as gypsum board. Formulations of sprays or building materials with NSAID-like chemical treatments may hold promise in reducing mold in homes and buildings.

Fabrication of Polylactide Nanocomposite Filament Using Melt Extrusion and Filament Characterization for 3D Printing

NASA Astrophysics Data System (ADS)

Jain, Shrenik Kumar

Fused deposition modeling (FDM) technology uses thermoplastic filament for layer by layer fabrication of objects. To make functional objects with desired properties, composite filaments are required in the FDM. In this thesis, less expensive mesoporous Nano carbon (NC) and carbon nanotube (CNT) infused in Polylactide (PLA) thermoplastic filaments were fabricated to improve the electrical properties and maintain sufficient strength for 3D printing. Solution blending was used for nanocomposite fabrication and melt extrusion was employed to make cylindrical filaments. Mechanical and electrical properties of 1 to 20 wt% of NC and 1 to 3 wt% of CNT filaments were investigated and significant improvement of conductivity (3.76 S/m) and sufficient yield strength (35MPa) were obtained. Scanning electron microscopy (SEM) images exhibited uniform dispersion of nanoparticles in polymer matrix and differential scanning calorimetry (DSC) results showed no significant changes in the glass transition temperature (Tg) for all the compositions. Perspective uses of this filament are for fabrication of electrical wires in 3D printed robots, drones, prosthetics, orthotics and others.

Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces

NASA Astrophysics Data System (ADS)

Möller, Jens; Emge, Philippe; Avalos Vizcarra, Ima; Kollmannsberger, Philip; Vogel, Viola

2013-12-01

Sessile bacteria adhere to engineered surfaces and host tissues and pose a substantial clinical and economical risk when growing into biofilms. Most engineered and biological interfaces are of chemically heterogeneous nature and provide adhesive islands for bacterial attachment and growth. To mimic either defects in a surface coating of biomedical implants or heterogeneities within mucosal layers (Peyer's patches), we embedded micrometre-sized adhesive islands in a poly(ethylene glycol) biopassive background. We show experimentally and computationally that filamentation of Escherichia coli can significantly accelerate the bacterial surface colonization under physiological flow conditions. Filamentation can thus provide an advantage to a bacterial population to bridge non-adhesive distances exceeding 5 μm. Bacterial filamentation, caused by blocking of bacterial division, is common among bacterial species and can be triggered by environmental conditions or antibiotic treatment. While great awareness exists that the build-up of antibiotic resistance serves as intrinsic survival strategy, we show here that antibiotic treatment can actually promote surface colonization by triggering filamentation, which in turn prevents daughter cells from being washed away. Our combined microfabrication and computational approaches provide quantitative insights into mechanisms that enable biofouling of biopassive surfaces with embedded adhesive spots, even for spot distances that are multiples of the bacterial length.

The Kinetics Underlying the Velocity of Smooth Muscle Myosin Filament Sliding on Actin Filaments in Vitro*

PubMed Central

Haldeman, Brian D.; Brizendine, Richard K.; Facemyer, Kevin C.; Baker, Josh E.; Cremo, Christine R.

2014-01-01

Actin-myosin interactions are well studied using soluble myosin fragments, but little is known about effects of myosin filament structure on mechanochemistry. We stabilized unphosphorylated smooth muscle myosin (SMM) and phosphorylated smooth muscle myosin (pSMM) filaments against ATP-induced depolymerization using a cross-linker and attached fluorescent rhodamine (XL-Rh-SMM). Electron micrographs showed that these side polar filaments are very similar to unmodified filaments. They are ∼0.63 μm long and contain ∼176 molecules. Rate constants for ATP-induced dissociation and ADP release from acto-myosin for filaments and S1 heads were similar. Actin-activated ATPases of SMM and XL-Rh-SMM were similarly regulated. XL-Rh-pSMM filaments moved processively on F-actin that was bound to a PEG brush surface. ATP dependence of filament velocities was similar to that for solution ATPases at high [actin], suggesting that both processes are limited by the same kinetic step (weak to strong transition) and therefore are attachment-limited. This differs from actin sliding over myosin monomers, which is primarily detachment-limited. Fitting filament data to an attachment-limited model showed that approximately half of the heads are available to move the filament, consistent with a side polar structure. We suggest the low stiffness subfragment 2 (S2) domain remains unhindered during filament motion in our assay. Actin-bound negatively displaced heads will impart minimal drag force because of S2 buckling. Given the ADP release rate, the velocity, and the length of S2, these heads will detach from actin before slack is taken up into a backwardly displaced high stiffness position. This mechanism explains the lack of detachment-limited kinetics at physiological [ATP]. These findings address how nonlinear elasticity in assemblies of motors leads to efficient collective force generation. PMID:24907276

Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

PubMed

Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

2016-04-01

Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

Ultrastructural characteristics of tau filaments in tauopathies: immuno-electron microscopic demonstration of tau filaments in tauopathies.

PubMed

Arima, Kunimasa

2006-10-01

The microtubule-associated protein tau aggregates into filaments in the form of neurofibrillary tangles, neuropil threads and argyrophilic grains in neurons, in the form of variable astrocytic tangles in astrocytes and in the form of coiled bodies and argyrophilic threads in oligodendrocytes. These tau filaments may be classified into two types, straight filaments or tubules with 9-18 nm diameters and "twisted ribbons" composed of two parallel aligned components. In the same disease, the fine structure of tau filaments in glial cells roughly resembles that in neurons. In sporadic tauopathies, individual tau filaments show characteristic sizes, shapes and arrangements, and therefore contribute to neuropathologic differential diagnosis. In frontotemporal dementias caused by tau gene mutations, variable filamentous profiles were observed in association with mutation sites and insoluble tau isoforms, including straight filaments or tubules, paired helical filament-like filaments, and twisted ribbons. Pre-embedding immunoelectron microscopic studies were carried out using anti-3-repeat tau and anti-4-repeat tau specific antibodies, RD3 and RD4. Straight tubules in neuronal and astrocytic Pick bodies were immunolabeled by the anti-3-repeat tau antibody. The anti-4-repeat tau antibody recognized abnormal tubules comprising neurofibrillary tangles, coiled bodies and argyrophilic threads in progressive supranuclear palsy (PSP) and corticobasal degeneration. In the pre-embedding immunoelectron microscopic study using the phosphorylated tau AT8 antibody, tuft-shaped astrocytes of PSP were found to be composed of bundles of abnormal tubules in processes and perikarya of protoplasmic astrocytes. In this study, the 3-repeat tau or 4-repeat tau epitope was detected in situ at the ultrastructural level in abnormal tubules in representative pathological lesions in Pick's disease, PSP and corticobasal degeneration.

Computational studies on scattering of radio frequency waves by density filaments in fusion plasmas

NASA Astrophysics Data System (ADS)

Ioannidis, Zisis C.; Ram, Abhay K.; Hizanidis, Kyriakos; Tigelis, Ioannis G.

2017-10-01

In modern magnetic fusion devices, such as tokamaks and stellarators, radio frequency (RF) waves are commonly used for plasma heating and current profile control, as well as for certain diagnostics. The frequencies of the RF waves range from ion cyclotron frequency to the electron cyclotron frequency. The RF waves are launched from structures, like waveguides and current straps, placed near the wall in a very low density, tenuous plasma region of a fusion device. The RF electromagnetic fields have to propagate through this scrape-off layer before coupling power to the core of the plasma. The scrape-off layer is characterized by turbulent plasmas fluctuations and by blobs and filaments. The variations in the edge density due to these fluctuations and filaments can affect the propagation characteristics of the RF waves—changes in density leading to regions with differing plasma permittivity. Analytical full-wave theories have shown that scattering by blobs and filaments can alter the RF power flow into the core of the plasma in a variety of ways, such as through reflection, refraction, diffraction, and shadowing [see, for example, Ram and Hizanidis, Phys. Plasmas 23, 022504 (2016), and references therein]. There are changes in the wave vectors and the distribution of power-scattering leading to coupling of the incident RF wave to other plasma waves, side-scattering, surface waves, and fragmentation of the Poynting flux in the direction towards the core. However, these theoretical models are somewhat idealized. In particular, it is assumed that there is step-function discontinuity in the density between the plasma inside the filament and the background plasma. In this paper, results from numerical simulations of RF scattering by filaments using a commercial full-wave code are described. The filaments are taken to be cylindrical with the axis of the cylinder aligned along the direction of the ambient magnetic field. The plasma inside and outside the filament is

Side-binding proteins modulate actin filament dynamics

PubMed Central

Crevenna, Alvaro H; Arciniega, Marcelino; Dupont, Aurélie; Mizuno, Naoko; Kowalska, Kaja; Lange, Oliver F; Wedlich-Söldner, Roland; Lamb, Don C

2015-01-01

Actin filament dynamics govern many key physiological processes from cell motility to tissue morphogenesis. A central feature of actin dynamics is the capacity of filaments to polymerize and depolymerize at their ends in response to cellular conditions. It is currently thought that filament kinetics can be described by a single rate constant for each end. In this study, using direct visualization of single actin filament elongation, we show that actin polymerization kinetics at both filament ends are strongly influenced by the binding of proteins to the lateral filament surface. We also show that the pointed-end has a non-elongating state that dominates the observed filament kinetic asymmetry. Estimates of flexibility as well as effects on fragmentation and growth suggest that the observed kinetic diversity arises from structural alteration. Tuning elongation kinetics by exploiting the malleability of the filament structure may be a ubiquitous mechanism to generate a rich variety of cellular actin dynamics. DOI: http://dx.doi.org/10.7554/eLife.04599.001 PMID:25706231

Role of Intermediate Filaments in Vesicular Traffic.

PubMed

Margiotta, Azzurra; Bucci, Cecilia

2016-04-25

Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

Boolean gates on actin filaments

NASA Astrophysics Data System (ADS)

Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

2016-01-01

Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.

Solid friction between soft filaments

NASA Astrophysics Data System (ADS)

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A. W. C.; Vitelli, Vincenzo; Mahadevan, L.; Dogic, Zvonimir

2015-06-01

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

Solid friction between soft filaments

DOE PAGES

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; ...

2015-03-02

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag,more » can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. In conclusion, our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.« less

Recent observations of the formation of filaments

NASA Technical Reports Server (NTRS)

Martin, Sara F.

1986-01-01

Two examples of the formation of small filaments in H alpha are described and illustrated. In both cases, the formation is seen to be the spontaneous appearance of strands of absorbing mass that evolve from no previous structure. The initial development of the filaments appears to consist of the accumulation of these absorptive strands along approximately parallel paths in a channel between large-scale, opposite polarity magnetic fields on either side of the filaments. The strands exhibit continuous changes in shape and degree of absorption which can be due to successive condensations resulting in new strands, mass motions within the strands, and outflow of the mass from the strands. For at least several hours before the formation of both filaments, small-scale fragments of opposite polarity, line-of-sight magnetic flux adjacent to or immediately below the filaments, and at the ends of the filaments, were cancelling. This type of magnetic flux disappearance continued during the development of the filaments and is commonly observed in association with established filaments. Cancellation is interpreted as an important evolutionary change in the magnetic field that can lead to configurations suitable for the formation of filaments.

Interaction of Two Filaments in a Long Filament Channel Associated with Twin Coronal Mass Ejections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Ruisheng; Chen, Yao; Wang, Bing

Using the high-quality observations of the Solar Dynamics Observatory , we present the interaction of two filaments (F1 and F2) in a long filament channel associated with twin coronal mass ejections (CMEs) on 2016 January 26. Before the eruption, a sequence of rapid cancellation and emergence of the magnetic flux has been observed, which likely triggered the ascending of the west filament (F1). The east footpoints of rising F1 moved toward the east far end of the filament channel, accompanied by post-eruption loops and flare ribbons. This likely indicated a large-scale eruption involving the long filament channel, which resulted frommore » the interaction between F1 and the east filament (F2). Some bright plasma flew over F2, and F2 stayed at rest during the eruption, likely due to the confinement of its overlying lower magnetic field. Interestingly, the impulsive F1 pushed its overlying magnetic arcades to form the first CME, and F1 finally evolved into the second CME after the collision with the nearby coronal hole. We suggest that the interaction of F1 and the overlying magnetic field of F2 led to the merging reconnection that forms a longer eruptive filament loop. Our results also provide a possible picture of the origin of twin CMEs and show that the large-scale magnetic topology of the coronal hole is important for the eventual propagation direction of CMEs.« less

Femtosecond Laser Filamentation for Atmospheric Sensing

PubMed Central

Xu, Huai Liang; Chin, See Leang

2011-01-01

Powerful femtosecond laser pulses propagating in transparent materials result in the formation of self-guided structures called filaments. Such filamentation in air can be controlled to occur at a distance as far as a few kilometers, making it ideally suited for remote sensing of pollutants in the atmosphere. On the one hand, the high intensity inside the filaments can induce the fragmentation of all matters in the path of filaments, resulting in the emission of characteristic fluorescence spectra (fingerprints) from the excited fragments, which can be used for the identification of various substances including chemical and biological species. On the other hand, along with the femtosecond laser filamentation, white-light supercontinuum emission in the infrared to UV range is generated, which can be used as an ideal light source for absorption Lidar. In this paper, we present an overview of recent progress concerning remote sensing of the atmosphere using femtosecond laser filamentation. PMID:22346566

Powering of Hα Filaments by Cosmic Rays

NASA Astrophysics Data System (ADS)

Ruszkowski, Mateusz; Yang, H.-Y. Karen; Reynolds, Christopher S.

2018-05-01

Cluster cool cores possess networks of line-emitting filaments. These filaments are thought to originate via uplift of cold gas from cluster centers by buoyant active galactic nuclei (AGNs) bubbles, or via local thermal instability in the hot intracluster medium (ICM). Therefore, the filaments are either the signatures of AGN feedback or feeding of supermassive black holes. Despite being characterized by very short cooling times, the filaments are significant Hα emitters, which suggests that some process continuously powers these structures. Many cool cores host diffuse radio mini halos and AGN injecting radio plasma, suggesting that cosmic rays (CRs) and magnetic fields are present in the ICM. We argue that the excitation of Alfvén waves by CR streaming, and the replenishment of CR energy via accretion onto the filaments of high-plasma-β ICM characterized by low CR pressure support, can provide the adequate amount of heating to power and sustain the emission from these filaments. This mechanism does not require the CRs to penetrate the filaments, even if the filaments are magnetically isolated from the ambient ICM, and it may operate irrespectively of whether the filaments are dredged up from the center or form in situ in the ICM. This picture is qualitatively consistent with non-thermal line ratios seen in the cold filaments. Future X-ray observations of the iron line complex with XARM, Lynx, or Athena could help to test this model by providing constraints on the amount of CRs in the hot plasma that is cooling and accreting onto the filaments.

Solar filament material oscillations and drainage before eruption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bi, Yi; Jiang, Yunchun; Yang, Jiayan

Both large-amplitude longitudinal (LAL) oscillations and material drainage in a solar filament are associated with the flow of material along the filament axis, often followed by an eruption. However, the relationship between these two motions and a subsequent eruption event is poorly understood. We analyze a filament eruption using EUV imaging data captured by the Atmospheric Imaging Array on board the Solar Dynamics Observatory and the Hα images from the Global Oscillation Network Group. Hours before the eruption, the filament was activated, with one of its legs undergoing a slow rising motion. The asymmetric activation inclined the filament relative tomore » the solar surface. After the active phase, LAL oscillations were observed in the inclined filament. The oscillation period increased slightly over time, which may suggest that the magnetic fields supporting the filament evolve to be flatter during the slow rising phase. After the oscillations, a significant amount of filament material was drained toward one filament endpoint, followed immediately by the violent eruption of the filament. The material drainage may further support the change in magnetic topology prior to the eruption. Moreover, we suggest that the filament material drainage could play a role in the transition from a slow to a fast rise of the erupting filament.« less

Deception Island, Antarctica, harbors a diverse assemblage of wood decay fungi.

PubMed

Held, Benjamin W; Blanchette, Robert A

2017-02-01

Very little is known about fungal diversity in Antarctica as compared to other biomes and how these important organisms function in this unusual ecosystem. Perhaps one of the most unusual ecosystems is that of Deception Island; an active volcanic island part of the South Shetland Islands of the Antarctic Peninsula. Here we describe the fungal diversity associated with historic wood from structures on the island, which reveals a diverse fungal assemblage of known wood decay fungi as well as the discovery of undescribed species. The major group of wood decay fungi identified were species of Cadophora and as shown in previous studies in other geographic regions of Antarctica, they caused a soft-rot type of decay in the introduced woods. Additionally, unlike other areas of Antarctica that have been studied, filamentous basidiomycetes (Hypochniciellum spp. and Pholiota spp.) were also identified that have different modes of degradation including brown and white rot. Matches of fungal sequences to known species in temperate regions likely introduced on building materials indicates human influences and volcanic activity have greatly impacted fungal diversity. Lahars (mudslides from volcanic activity) have partially buried many of the structures and the buried environment as well as the moist, warm soils provided conditions conducive for fungal growth that are not found in other regions of Antarctica. The diverse assemblage of decay fungi and different forms of wood decomposition add to the difficulty of conserving wooden structures at these important polar heritage sites. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Prediction of Solar Eruptions Using Filament Metadata

NASA Astrophysics Data System (ADS)

Aggarwal, Ashna; Schanche, Nicole; Reeves, Katharine K.; Kempton, Dustin; Angryk, Rafal

2018-05-01

We perform a statistical analysis of erupting and non-erupting solar filaments to determine the properties related to the eruption potential. In order to perform this study, we correlate filament eruptions documented in the Heliophysics Event Knowledgebase (HEK) with HEK filaments that have been grouped together using a spatiotemporal tracking algorithm. The HEK provides metadata about each filament instance, including values for length, area, tilt, and chirality. We add additional metadata properties such as the distance from the nearest active region and the magnetic field decay index. We compare trends in the metadata from erupting and non-erupting filament tracks to discover which properties present signs of an eruption. We find that a change in filament length over time is the most important factor in discriminating between erupting and non-erupting filament tracks, with erupting tracks being more likely to have decreasing length. We attempt to find an ensemble of predictive filament metadata using a Random Forest Classifier approach, but find the probability of correctly predicting an eruption with the current metadata is only slightly better than chance.

Harvesting of Chlorella sorokiniana by co-culture with the filamentous fungus Isaria fumosorosea: A potential sustainable feedstock for hydrothermal gasification.

PubMed

Mackay, Stephen; Gomes, Eduardo; Holliger, Christof; Bauer, Rolene; Schwitzguébel, Jean-Paul

2015-06-01

Despite recent advances in down-stream processing, production of microalgae remains substantially limited because of economical reasons. Harvesting and dewatering are the most energy-intensive processing steps in their production and contribute 20-30% of total operational cost. Bio-flocculation of microalgae by co-cultivation with filamentous fungi relies on the development of large structures that facilitate cost effective harvesting. A yet unknown filamentous fungus was isolated as a contaminant from a microalgal culture and identified as Isaria fumosorosea. Blastospores production was optimized in minimal medium and the development of pellets, possibly lichens, was followed when co-cultured with Chlorella sorokiniana under strict autotrophic conditions. Stable pellets (1-2mm) formed rapidly at pH 7-8, clearing the medium of free algal cells. Biomass was harvested with large inexpensive filters, generating wet slurry suitable for hydrothermal gasification. Nutrient rich brine from the aqueous phase of hydrothermal gasification supported growth of the fungus and may increase the process sustainability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Core filaments of the nuclear matrix

PubMed Central

1990-01-01

The nuclear matrix is concealed by a much larger mass of chromatin, which can be removed selectively by digesting nuclei with DNase I followed by elution of chromatin with 0.25 M ammonium sulfate. This mild procedure removes chromatin almost completely and preserves nuclear matrix morphology. The complete nuclear matrix consists of a nuclear lamina with an interior matrix composed of thick, polymorphic fibers and large masses that resemble remnant nucleoli. Further extraction of the nuclear matrices of HeLa or MCF-7 cells with 2 M sodium chloride uncovered a network of core filaments. A few dark masses remained enmeshed in the filament network and may be remnants of the nuclear matrix thick fibers and nucleoli. The highly branched core filaments had diameters of 9 and 13 nm measured relative to the intermediate filaments. They may serve as the core structure around which the matrix is constructed. The core filaments retained 70% of nuclear RNA. This RNA consisted both of ribosomal RNA precursors and of very high molecular weight hnRNA with a modal size of 20 kb. Treatment with RNase A removed the core filaments. When 2 M sodium chloride was used directly to remove chromatin after DNase I digestion without a preceding 0.25 M ammonium sulfate extraction, the core filaments were not revealed. Instead, the nuclear interior was filled with amorphous masses that may cover the filaments. This reflected a requirement for a stepwise increase in ionic strength because gradual addition of sodium chloride to a final concentration of 2 M without an 0.25 M ammonium sulfate extraction uncovered core filaments. PMID:2307700

Assemblage of filamentous fungi associated with aculeate hymenopteran brood in reed galls.

PubMed

Heneberg, Petr; Bizos, Jiří; Čmoková, Adéla; Kolařík, Miroslav; Astapenková, Alena; Bogusch, Petr

2016-01-01

Monotypic stands of common reed and the reed-gall-associated insect assemblages are distributed worldwide. However, fungi associated with these assemblages have not been characterized in detail. Here we examined 5200 individuals (12 species) of immature aculeate hymenopterans or their parasitoids collected at 34 sampling sites in Central Europe. We noticed fungal outgrowth on exoskeletons of 83 (1.60%) larvae and pupae. The most common host was eudominant Pemphredon fabricii. However, the less abundant aculeate hymenopteran reed gall inquilines were infected at higher prevalence, these included Trypoxylon deceptorium, Trypoxylon minus, Hoplitis leucomelana and Hylaeus moricei (all considered new host records). We identified three fungal species, Penicillium buchwaldii (72% of cases), Aspergillus pseudoglaucus (22%) and Penicillium quebecense (6%). When multibrooded nests were affected, only a part of individuals was infected in 62% of cases. The sampling site-specific infection rate reached up to 13%, thus fungal infections should be considered an important variable driving the abundance of gall inquilines. Infections of generalist host species were more frequent than those of reed gall specialists, suggesting that suboptimal conditions decreased the immunocompetence of non-specialized species, which only occasionally nest in reed galls and feed in reed beds. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiple Filamentation of Laser Pulses in a Glass

NASA Astrophysics Data System (ADS)

Apeksimov, D. V.; Bukin, O. A.; Golik, S. S.; Zemlyanov, A. A.; Iglakova, A. N.; Kabanov, A. M.; Kuchinskaya, O. I.; Matvienko, G. G.; Oshlakov, V. K.; Petrov, A. V.; Sokolova, E. B.

2016-03-01

Results are presented of experiments on investigation of the spatial characteristics of multi-filamentation region of giga- and terawatt pulses of a Ti:sapphire laser in a glass. Dependences are obtained of the coordinate of the beginning of filamentation region, number of filaments, their distribution along the laser beam axis, and length of filaments on the pulse power. It is shown that with increasing radiation power, the number of filaments in the multi-filamentation region decreases, whereas the filament diameter has a quasiconstant value for all powers realized in the experiments. It is shown that as a certain power of the laser pulse with Gauss energy density distribution is reached, the filamentation region acquires the shape of a hollow cone with apex directed toward the radiation source.

Chirality and Magnetic Configurations of Solar Filaments

NASA Astrophysics Data System (ADS)

Ouyang, Y.; Zhou, Y. H.; Chen, P. F.; Fang, C.

2017-01-01

It has been revealed that the magnetic topology in the solar atmosphere displays hemispheric preference, I.e., helicity is mainly negative/positive in the northern/southern hemispheres, respectively. However, the strength of the hemispheric rule and its cyclic variation are controversial. In this paper, we apply a new method based on the filament drainage to 571 erupting filaments from 2010 May to 2015 December in order to determine the filament chirality and its hemispheric preference. It is found that 91.6% of our sample of erupting filaments follows the hemispheric rule of helicity sign. It is also found that the strength of the hemispheric preference of the quiescent filaments decreases slightly from ˜97% in the rising phase to ˜85% in the declining phase of solar cycle 24, whereas the strength of the intermediate filaments keeps a high value around 96 ± 4% at all times. Only the active-region filaments show significant variations. Their strength of the hemispheric rule rises from ˜63% to ˜95% in the rising phase, and keeps a high value of 82% ± 5% during the declining phase. Furthermore, during a half-year period around the solar maximum, their hemispheric preference totally vanishes. Additionally, we also diagnose the magnetic configurations of the filaments based on our indirect method and find that in our sample of erupting events, 89% are inverse-polarity filaments with a flux rope magnetic configuration, whereas 11% are normal-polarity filaments with a sheared arcade configuration.

Fungi with multifunctional lifestyles: endophytic insect pathogenic fungi.

PubMed

Barelli, Larissa; Moonjely, Soumya; Behie, Scott W; Bidochka, Michael J

2016-04-01

This review examines the symbiotic, evolutionary, proteomic and genetic basis for a group of fungi that occupy a specialized niche as insect pathogens as well as endophytes. We focus primarily on species in the genera Metarhizium and Beauveria, traditionally recognized as insect pathogenic fungi but are also found as plant symbionts. Phylogenetic evidence suggests that these fungi are more closely related to grass endophytes and diverged from that lineage ca. 100 MYA. We explore how the dual life cycles of these fungi as insect pathogens and endophytes are coupled. We discuss the evolution of insect pathogenesis while maintaining an endophytic lifestyle and provide examples of genes that may be involved in the transition toward insect pathogenicity. That is, some genes for insect pathogenesis may have been co-opted from genes involved in endophytic colonization. Other genes may be multifunctional and serve in both lifestyle capacities. We suggest that their evolution as insect pathogens allowed them to effectively barter a specialized nitrogen source (i.e. insects) with host plants for photosynthate. These ubiquitous fungi may play an important role as plant growth promoters and have a potential reservoir of secondary metabolites.

Measuring Filament Orientation: A New Quantitative, Local Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, C.-E.; Cunningham, M. R.; Jones, P. A.

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitativelymore » on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”.« less

Measuring Filament Orientation: A New Quantitative, Local Approach

NASA Astrophysics Data System (ADS)

Green, C.-E.; Dawson, J. R.; Cunningham, M. R.; Jones, P. A.; Novak, G.; Fissel, L. M.

2017-09-01

The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”

Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell

PubMed Central

Ishii, Shun'ichi; Shimoyama, Takefumi; Hotta, Yasuaki; Watanabe, Kazuya

2008-01-01

Background Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood. Results A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population. Conclusion Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community. PMID:18186940

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

PubMed Central

Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.; Ohm, Robin A.; Li, Zhou; LaButti, Kurt; Lapidus, Alla; Lipzen, Anna; Chen, Cindy; Johnson, Jenifer; Lindquist, Erika A.; Pan, Chongle; Hettich, Robert L.; Grigoriev, Igor V.; Singer, Steven W.; Banfield, Jillian F.

2016-01-01

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches. PMID:26973616

Sensitivity and Specificity of Laser-Scanning In Vivo Confocal Microscopy for Filamentous Fungal Keratitis: Role of Observer Experience.

PubMed

Kheirkhah, Ahmad; Syed, Zeba A; Satitpitakul, Vannarut; Goyal, Sunali; Müller, Rodrigo; Tu, Elmer Y; Dana, Reza

2017-07-01

To determine sensitivity and specificity of laser-scanning in vivo confocal microscopy (LS-IVCM) for detection of filamentous fungi in patients with microbial keratitis and to evaluate the effect of observer's imaging experience on these parameters. Retrospective reliability study. This study included 21 patients with filamentous fungal keratitis and 24 patients with bacterial keratitis (as controls). The etiology of infection was confirmed based on the response to specific therapy regardless of culture results. All patients had undergone full-thickness corneal imaging by a LS-IVCM (Heidelberg Retina Tomograph 3 with Rostock Cornea Module; Heidelberg Engineering, Heidelberg, Germany). The images were evaluated for the presence of fungal filaments by 2 experienced observers and 2 inexperienced observers. All observers were masked to the clinical and microbiologic data. The mean number of images obtained per eye was 917 ± 353. The average sensitivity of LS-IVCM for detecting fungal filaments was 71.4% ± 0% for the experienced observers and 42.9% ± 6.7% for the inexperienced observers. The average specificity was 89.6% ± 3.0% and 87.5% ± 17.7% for these 2 groups of observers, respectively. Although there was a good agreement between the 2 experienced observers (κ = 0.77), the inexperienced observers showed only a moderate interobserver agreement (κ = 0.51). The LS-IVCM sensitivity was higher in patients with fungal infections who had positive culture or longer duration of the disease. Although LS-IVCM has a high specificity for diagnosing filamentous fungal keratitis, its sensitivity is moderate and highly dependent on the level of the observer's experience and training with this imaging modality. Copyright © 2017 Elsevier Inc. All rights reserved.

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.

PubMed

Goodwin, Stephen B; McCorison, Cassandra B; Cavaletto, Jessica R; Culley, David E; LaButti, Kurt; Baker, Scott E; Grigoriev, Igor V

2016-08-01

Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelia in cellars with high humidity, and its ability to metabolize volatile organic compounds is thought to improve air quality. Whether these abilities have affected its mitochondrial genome is not known. To fill this gap, the circular-mapping mitochondrial genome of Z. cellare was sequenced and, at only 23 743 bp, is the smallest reported for a filamentous fungus. Genes were encoded on both strands with a single change of direction, different from most other fungi but consistent with the Dothideomycetes. Other than its small size, the only unusual feature of the Z. cellare mitochondrial genome was two copies of a 110-bp sequence that were duplicated, inverted and separated by approximately 1 kb. This inverted-repeat sequence confused the assembly program but appears to have no functional significance. The small size of the Z. cellare mitochondrial genome was due to slightly smaller genes, lack of introns and non-essential genes, reduced intergenic spacers and very few ORFs relative to other fungi rather than a loss of essential genes. Whether this reduction facilitates its unusual biology remains unknown. Published by Elsevier Ltd.

Dynamics and mechanics of motor-filament systems

NASA Astrophysics Data System (ADS)

Kruse, K.; Jülicher, F.

2006-08-01

Motivated by the cytoskeleton of eukaryotic cells, we develop a general framework for describing the large-scale dynamics of an active filament network. In the cytoskeleton, active cross-links are formed by motor proteins that are able to induce relative motion between filaments. Starting from pair-wise interactions of filaments via such active processes, our framework is based on momentum conservation and an analysis of the momentum flux. This allows us to calculate the stresses in the filament network generated by the action of motor proteins. We derive effective theories for the filament dynamics which can be related to continuum theories of active polar gels. As an example, we discuss the stability of homogenous isotropic filament distributions in two spatial dimensions.

Laser femtoseconde, filamentation, nuage et orage

NASA Astrophysics Data System (ADS)

Courvoisier, F.; Boutou, V.; Kasparian, J.; Salmon, E.; Méjean, G.; Yu, J.; Wolf, J.-P.

2005-06-01

Les applications telles que le contrôle de foudre grâce aux filaments autoguidés générés par un laser femtoseconde nécessitent de propager un tel filament à travers des aérosols de gouttes d'eau. Nous montrons qu'un filament survit à son interaction avec une goutte de diamètre comparable au sien (95 μ m), ainsi qu'à des nuages d'épaisseur optique 3,2, soit 5% de transmission. Cette transmission est permise par la présence d'un “bain de photons” autour du filament. Ce bain forme un réservoir contenant une part importante de l'énergie du faisceau, en équilibre avec le filament, et favorisant son alimentation.

Chemical ecology of fungi.

PubMed

Spiteller, Peter

2015-07-01

Fungi are widespread in nature and have conquered nearly every ecological niche. Fungi occur not only in terrestrial but also in freshwater and marine environments. Moreover, fungi are known as a rich source of secondary metabolites. Despite these facts, the ecological role of many of these metabolites is still unknown and the chemical ecology of fungi has not been investigated systematically so far. This review intends to present examples of the various chemical interactions of fungi with other fungi, plants, bacteria and animals and to give an overview of the current knowledge of fungal chemical ecology.

Dimorphism in Histoplasma capsulatum: a model for the study of cell differentiation in pathogenic fungi.

PubMed Central

Maresca, B; Kobayashi, G S

1989-01-01

Several fungi can assume either a filamentous or a unicellular morphology in response to changes in environmental conditions. This process, known as dimorphism, is a characteristic of several pathogenic fungi, e.g., Histoplasma capsulatum, Blastomyces dermatitidis, and Paracoccidioides brasiliensis, and appears to be directly related to adaptation from a saprobic to a parasitic existence. H. capsulatum is the most extensively studied of the dimorphic fungi, with a parasitic phase consisting of yeast cells and a saprobic mycelial phase. In culture, the transition of H. capsulatum from one phase to the other can be triggered reversibly by shifting the temperature of incubation between 25 degrees C (mycelia) and 37 degrees C (yeast phase). Mycelia are found in soil and never in infected tissue, in contrast to the yeast phase, which is the only form present in patients. The temperature-induced phase transition and the events in establishment of the disease state are very likely to be intimately related. Furthermore, the temperature-induced phase transition implies that each growth phase is an adaptation to two critically different environments. A fundamental question concerning dimorphism is the nature of the signal(s) that responds to temperature shifts. So far, both the responding cell component(s) and the mechanism(s) remain unclear. This review describes the work done in the last several years at the biochemical and molecular levels on the mechanisms involved in the mycelium to yeast phase transition and speculates on possible models of regulation of morphogenesis in dimorphic pathogenic fungi. Images PMID:2666842

Oligonucleotide microarray for the identification of potential mycotoxigenic fungi

PubMed Central

2010-01-01

Background Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. Results A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotide probes directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The probes selected for fungal identification and the probes specific for toxin producing genes were spotted onto microarray slides. Conclusions The diagnostic microarray developed can be used to identify single pure strains or cultures of potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory samples and maize-derived foods offering an interesting potential for microbiological laboratories. PMID:20307326

CHIRALITY AND MAGNETIC CONFIGURATIONS OF SOLAR FILAMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Y.; Zhou, Y. H.; Chen, P. F.

It has been revealed that the magnetic topology in the solar atmosphere displays hemispheric preference, i.e., helicity is mainly negative/positive in the northern/southern hemispheres, respectively. However, the strength of the hemispheric rule and its cyclic variation are controversial. In this paper, we apply a new method based on the filament drainage to 571 erupting filaments from 2010 May to 2015 December in order to determine the filament chirality and its hemispheric preference. It is found that 91.6% of our sample of erupting filaments follows the hemispheric rule of helicity sign. It is also found that the strength of the hemisphericmore » preference of the quiescent filaments decreases slightly from ∼97% in the rising phase to ∼85% in the declining phase of solar cycle 24, whereas the strength of the intermediate filaments keeps a high value around 96 ± 4% at all times. Only the active-region filaments show significant variations. Their strength of the hemispheric rule rises from ∼63% to ∼95% in the rising phase, and keeps a high value of 82% ± 5% during the declining phase. Furthermore, during a half-year period around the solar maximum, their hemispheric preference totally vanishes. Additionally, we also diagnose the magnetic configurations of the filaments based on our indirect method and find that in our sample of erupting events, 89% are inverse-polarity filaments with a flux rope magnetic configuration, whereas 11% are normal-polarity filaments with a sheared arcade configuration.« less

A Comparison Study of an Active Region Eruptive Filament and a Neighboring Non-Eruptive Filament

NASA Astrophysics Data System (ADS)

Wu, S. T.; Jiang, C.; Feng, X. S.; Hu, Q.

2014-12-01

We perform a comparison study of an eruptive filament in the core region of AR 11283 and a nearby non-eruptive filament. The coronal magnetic field supporting these two filaments is extrapolated using our data-driven CESE-MHD-NLFFF code (Jiang et al. 2013, Jiang etal. 2014), which presents two magnetic flux ropes (FRs) in the same extrapolation box. The eruptive FR contains a bald-patch separatrix surface (BPSS) spatially co-aligned very well with a pre-eruption EUV sigmoid, which is consistent with the BPSS model for the coronal sigmoids. The numerically reproduced magnetic dips of the FRs match observations of the filaments strikingly well, which supports strongly the FR-dip model for filaments. The FR that supports the AR eruptive filament is much smaller (with a length of 3 Mm) compared with the large-scale FR holding the quiescent filament (with a length of 30 Mm). But the AR eruptive FR contains most of the magnetic free energy in the extrapolation box and holds a much higher magnetic energy density than the quiescent FR, because it resides along the main polarity inversion line (PIL) around sunspots with strong magnetic shear. Both the FRs are weakly twisted and cannot trigger kink instability. The AR eruptive FR is unstable because its axis reaches above a critical height for torus instability (TI), at which the overlying closed arcades can no longer confine the FR stably. To the contrary, the quiescent FR is firmly held down by its overlying field, as its axis apex is far below the TI threshold height. (This work is partially supported by NSF AGS-1153323 and 1062050)

Targeting the Oxidative Stress Response System of Fungi with Redox-Potent Chemosensitizing Agents

PubMed Central

Kim, Jong H.; Chan, Kathleen L.; Faria, Natália C. G.; Martins, M. de L.; Campbell, Bruce C.

2012-01-01

The cellular antioxidant system is a target in the antifungal action of amphotericin B (AMB) and itraconazole (ITZ), in filamentous fungi. The sakAΔ mutant of Aspergillus fumigatus, a mitogen-activated protein kinase (MAPK) gene deletion mutant in the antioxidant system, was found to be more sensitive to AMB or ITZ than other A. fumigatus strains, a wild type and a mpkCΔ mutant (a MAPK gene deletion mutant in the polyalcohol sugar utilization system). Complete fungal kill (≥99.9%) by ITZ or AMB was also achieved by much lower dosages for the sakAΔ mutant than for the other strains. It appears msnA, an Aspergillus ortholog to Saccharomyces cerevisiae MSN2 (encoding a stress-responsive C2H2-type zinc-finger regulator) and sakA and/or mpkC (upstream MAPKs) are in the same stress response network under tert-butyl hydroperoxide (t-BuOOH)-, hydrogen peroxide (H2O2)- or AMB-triggered toxicity. Of note is that ITZ-sensitive yeast pathogens were also sensitive to t-BuOOH, showing a connection between ITZ sensitivity and antioxidant capacity of fungi. Enhanced antifungal activity of AMB or ITZ was achieved when these drugs were co-applied with redox-potent natural compounds, 2,3-dihydroxybenzaldehyde, thymol or salicylaldehyde, as chemosensitizing agents. We concluded that redox-potent compounds, which target the antioxidant system in fungi, possess a chemosensitizing capacity to enhance efficacy of conventional drugs. PMID:22438852

High-resolution Observations of Sympathetic Filament Eruptions by NVST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shangwei; Su, Yingna; Zhou, Tuanhui

We investigate two sympathetic filament eruptions observed by the New Vacuum Solar Telescope on 2015 October 15. The full picture of the eruptions is obtained from the corresponding Solar Dynamics Observatory ( SDO )/Atmospheric Imaging Assembly (AIA) observations. The two filaments start from active region NOAA 12434 in the north and end in one large quiescent filament channel in the south. The left filament erupts first, followed by the right filament eruption about 10 minutes later. Clear twist structure and rotating motion are observed in both filaments during the eruption. Both eruptions failed, since the filaments first rise up, thenmore » flow toward the south and merge into the southern large quiescent filament. We also observe repeated activations of mini filaments below the right filament after its eruption. Using magnetic field models constructed based on SDO /HMI magnetograms via the flux rope insertion method, we find that the left filament eruption is likely to be triggered by kink instability, while the weakening of overlying magnetic fields due to magnetic reconnection at an X-point between the two filament systems might play an important role in the onset of the right filament eruption.« less

Generalized minimal principle for rotor filaments.

PubMed

Dierckx, Hans; Wellner, Marcel; Bernus, Olivier; Verschelde, Henri

2015-05-01

To a reaction-diffusion medium with an inhomogeneous anisotropic diffusion tensor D, we add a fourth spatial dimension such that the determinant of the diffusion tensor is constant in four dimensions. We propose a generalized minimal principle for rotor filaments, stating that the scroll wave filament strives to minimize its surface area in the higher-dimensional space. As a consequence, stationary scroll wave filaments in the original 3D medium are geodesic curves with respect to the metric tensor G=det(D)D(-1). The theory is confirmed by numerical simulations for positive and negative filament tension and a model with a non-stationary spiral core. We conclude that filaments in cardiac tissue with positive tension preferentially reside or anchor in regions where cardiac cells are less interconnected, such as portions of the cardiac wall with a large number of cleavage planes.

Striation and convection in penumbral filaments

NASA Astrophysics Data System (ADS)

Spruit, H. C.; Scharmer, G. B.; Löfdahl, M. G.

2010-10-01

Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward propagating striations with inclination angles suggesting that they are aligned with the local magnetic field. We interpret it as the equivalent of the striations seen in the walls of small isolated magnetic structures. Their origin is then a corrugation of the boundary between an overturning convective flow inside the filament and the magnetic field wrapping around it. The outward propagation is a combination of a pattern motion due to the downflow observed along the sides of bright filaments, and the Evershed flow. The observed short wavelength of the striation argues against the existence of a dynamically significant horizontal field inside the bright filaments. Its intensity contrast is explained by the same physical effect that causes the dark cores of filaments, light bridges and “canals”. In this way striation represents an important clue to the physics of penumbral structure and its relation with other magnetic structures on the solar surface. We put this in perspective with results from the recent 3-D radiative hydrodynamic simulations. 4 movies are only available in electronic form at http://www.aanda.org

The formation of massive molecular filaments and massive stars triggered by a magnetohydrodynamic shock wave

NASA Astrophysics Data System (ADS)

Inoue, Tsuyoshi; Hennebelle, Patrick; Fukui, Yasuo; Matsumoto, Tomoaki; Iwasaki, Kazunari; Inutsuka, Shu-ichiro

2018-05-01

Recent observations suggest an that intensive molecular cloud collision can trigger massive star/cluster formation. The most important physical process caused by the collision is a shock compression. In this paper, the influence of a shock wave on the evolution of a molecular cloud is studied numerically by using isothermal magnetohydrodynamics simulations with the effect of self-gravity. Adaptive mesh refinement and sink particle techniques are used to follow the long-time evolution of the shocked cloud. We find that the shock compression of a turbulent inhomogeneous molecular cloud creates massive filaments, which lie perpendicularly to the background magnetic field, as we have pointed out in a previous paper. The massive filament shows global collapse along the filament, which feeds a sink particle located at the collapse center. We observe a high accretion rate \\dot{M}_acc> 10^{-4} M_{⊙}yr-1 that is high enough to allow the formation of even O-type stars. The most massive sink particle achieves M > 50 M_{⊙} in a few times 105 yr after the onset of the filament collapse.

Incidence, populations and diversity of fungi from raw materials, final products and air of processing environment of multigrain whole meal bread.

PubMed

Santos, Juliana Lane Paixão Dos; Bernardi, Angélica Olivier; Pozza Morassi, Letícia L; Silva, Beatriz S; Copetti, Marina Venturini; S Sant'Ana, Anderson

2016-09-01

This study aimed to assess the incidence, to quantify and to assess the diversity of fungi in a multigrain whole meal bread processing plant. Two hundred and eight one (n=281) samples were analyzed, including raw materials (n=120), air samples (n=136) and multigrain breads (n=25). Among the raw materials, the whole corn flour showed the highest counts of fungi (4.8logCFU/g), followed by whole-wheat flour (3.1logCFU/g). The counts of fungi in the air of processing environment were higher in post-baking steps (oven output, cooling, slicing, packaging) than in pre-baking steps (weighing and mixer) (p<0.05). Species of fungi isolated from spoiled bread samples stored at 5, 20, 25 and 30, and 40°C corresponded mostly to Penicillium paneum and Penicillium polonicum isolated from 20 and 24% of samples, respectively. These species were also isolated from raw materials (P. paneum and P. polonicum) and air collected at different processing sampling points (P. polonicum). The high counts of filamentous fungi in raw materials and air samples in processing steps such as cooling, slicing, and packaging, suggest that contamination that may occur in these steps can be critical for the shelf life of breads. The results of this study highlight that the prevention of contamination of breads by fungal spores is still a challenge for bakery industries and that other strategies such as control of germination and growth of spoilage fungi through the development of more stable formulations have to be developed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Methods for modeling cytoskeletal and DNA filaments

NASA Astrophysics Data System (ADS)

Andrews, Steven S.

2014-02-01

This review summarizes the models that researchers use to represent the conformations and dynamics of cytoskeletal and DNA filaments. It focuses on models that address individual filaments in continuous space. Conformation models include the freely jointed, Gaussian, angle-biased chain (ABC), and wormlike chain (WLC) models, of which the first three bend at discrete joints and the last bends continuously. Predictions from the WLC model generally agree well with experiment. Dynamics models include the Rouse, Zimm, stiff rod, dynamic WLC, and reptation models, of which the first four apply to isolated filaments and the last to entangled filaments. Experiments show that the dynamic WLC and reptation models are most accurate. They also show that biological filaments typically experience strong hydrodynamic coupling and/or constrained motion. Computer simulation methods that address filament dynamics typically compute filament segment velocities from local forces using the Langevin equation and then integrate these velocities with explicit or implicit methods; the former are more versatile and the latter are more efficient. Much remains to be discovered in biological filament modeling. In particular, filament dynamics in living cells are not well understood, and current computational methods are too slow and not sufficiently versatile. Although primarily a review, this paper also presents new statistical calculations for the ABC and WLC models. Additionally, it corrects several discrepancies in the literature about bending and torsional persistence length definitions, and their relations to flexural and torsional rigidities.

The Regulation of Filamentous Growth in Yeast

PubMed Central

Cullen, Paul J.; Sprague, George F.

2012-01-01

Filamentous growth is a nutrient-regulated growth response that occurs in many fungal species. In pathogens, filamentous growth is critical for host–cell attachment, invasion into tissues, and virulence. The budding yeast Saccharomyces cerevisiae undergoes filamentous growth, which provides a genetically tractable system to study the molecular basis of the response. Filamentous growth is regulated by evolutionarily conserved signaling pathways. One of these pathways is a mitogen activated protein kinase (MAPK) pathway. A remarkable feature of the filamentous growth MAPK pathway is that it is composed of factors that also function in other pathways. An intriguing challenge therefore has been to understand how pathways that share components establish and maintain their identity. Other canonical signaling pathways—rat sarcoma/protein kinase A (RAS/PKA), sucrose nonfermentable (SNF), and target of rapamycin (TOR)—also regulate filamentous growth, which raises the question of how signals from multiple pathways become integrated into a coordinated response. Together, these pathways regulate cell differentiation to the filamentous type, which is characterized by changes in cell adhesion, cell polarity, and cell shape. How these changes are accomplished is also discussed. High-throughput genomics approaches have recently uncovered new connections to filamentous growth regulation. These connections suggest that filamentous growth is a more complex and globally regulated behavior than is currently appreciated, which may help to pave the way for future investigations into this eukaryotic cell differentiation behavior. PMID:22219507

The Stokesian hydrodynamics of flexing, stretching filaments

NASA Astrophysics Data System (ADS)

Shelley, Michael J.; Ueda, Tetsuji

2000-11-01

A central element of many fundamental problems in physics and biology lies in the interaction of a viscous fluid with slender, elastic filaments. Examples arise in the dynamics of biological fibers, the motility of microscopic organisms, and in phase transitions of liquid crystals. When considering the dynamics on the scale of a single filament, the surrounding fluid can often be assumed to be inertialess and hence governed by the Stokes’ equations. A typical simplification then is to assume a local relation, along the filament, between the force per unit length exerted by the filament upon the fluid and the velocity of the filament. While this assumption can be justified through slender-body theory as the leading-order effect, this approximation is only logarithmically separated (in aspect ratio) from the next-order contribution capturing the first effects of non-local interactions mediated by the surrounding fluid; non-local interactions become increasingly important as a filament comes within proximity to itself, or another filament. Motivated by a pattern forming system in isotropic to smectic-A phase transitions, we consider the non-local Stokesian dynamics of a growing elastica immersed in a fluid. The non-local interactions of the filament with itself are included using a modification of the slender-body theory of Keller and Rubinow. This modification is asymptotically equivalent, and removes an instability of their formulation at small, unphysical length-scales. Within this system, the filament lives on a marginal stability boundary, driven by a continual process of growth and buckling. Repeated bucklings result in filament flex, which, coupled to the non-local interactions and mediated by elastic response, leads to the development of space-filling patterns. We develop numerical methods to solve this system accurately and efficiently, even in the presence of temporal stiffness and the close self-approach of the filament. While we have ignored many of the

Mini-thin filaments regulated by troponin–tropomyosin

PubMed Central

Gong, Huiyu; Hatch, Victoria; Ali, Laith; Lehman, William; Craig, Roger; Tobacman, Larry S.

2005-01-01

Striated muscle thin filaments contain hundreds of actin monomers and scores of troponins and tropomyosins. To study the cooperative mechanism of thin filaments, “mini-thin filaments” were generated by isolating particles nearly matching the minimal structural repeat of thin filaments: a double helix of actin subunits with each strand approximately seven actins long and spanned by a troponin–tropomyosin complex. One end of the particles was capped by a gelsolin (segment 1–3)–TnT fusion protein (substituting for normal TnT), and the other end was capped by tropomodulin. EM showed that the particles were 46 ± 9 nm long, with a knob-like mass attributable to gelsolin at one end. Average actin, tropomyosin, and gelsolin–troponin composition indicated one troponin–tropomyosin attached to each strand of the two-stranded actin filament. The minifilaments thus nearly represent single regulatory units of thin filaments. The myosin S1 MgATPase rate stimulated by the minifilaments was Ca2+-sensitive, indicating that single regulatory length particles are sufficient for regulation. Ca2+ bound cooperatively to cardiac TnC in conventional thin filaments but noncooperatively to cardiac TnC in minifilaments in the absence of myosin. This suggests that thin filament Ca2+-binding cooperativity reflects indirect troponin–troponin interactions along the long axis of conventional filaments, which do not occur in minifilaments. Despite noncooperative Ca2+ binding to minifilaments in the absence of myosin, Ca2+ cooperatively activated the myosin S1-particle ATPase rate. Two-stranded single regulatory units therefore may be sufficient for myosin-mediated Ca2+-binding cooperativity. Functional mini-thin filaments are well suited for biochemical and structural analysis of thin-filament regulation. PMID:15644437

Colloidal transport by active filaments

NASA Astrophysics Data System (ADS)

Manna, Raj Kumar; Kumar, P. B. Sunil; Adhikari, R.

2017-01-01

Enhanced colloidal transport beyond the limit imposed by diffusion is usually achieved through external fields. Here, we demonstrate the ballistic transport of a colloidal sphere using internal sources of energy provided by an attached active filament. The latter is modeled as a chain of chemo-mechanically active beads connected by potentials that enforce semi-flexibility and self-avoidance. The fluid flow produced by the active beads and the forces they mediate are explicitly taken into account in the overdamped equations of motion describing the colloid-filament assembly. The speed and efficiency of transport depend on the dynamical conformational states of the filament. We characterize these states using filament writhe as an order parameter and identify ones yielding maxima in speed and efficiency of transport. The transport mechanism reported here has a remarkable resemblance to the flagellar propulsion of microorganisms which suggests its utility in biomimetic systems.

Novel mechanisms of biotransformation of p-tert-amylphenol by bacteria and fungi with special degradation abilities and simultaneous detoxification of the disinfectant.

PubMed

Schlueter, Rabea; Röder, Anja; Czekalski, Nadine; Gliesche, Daniel; Mikolasch, Annett; Schauer, Frieder

2014-01-01

The compound p-tert-amylphenol (p-(1,1-dimethylpropyl)phenol) is a widely used disinfectant belonging to the group of short branched-chain alkylphenols. It is produced in or imported into the USA with more than one million pounds per year and can be found in the environment in surface water, sediments, and soil. We have investigated for the first time the biotransformation of this disinfectant and the accumulation of metabolites by five bacterial strains, three yeast strains, and three filamentous fungi, selected because of their ability to transform either aromatic or branched-chain compounds. Of the 11 microorganisms tested, one yeast strain and three bacteria could not transform the disinfectant despite of a very low concentration applied (0.005%). None of the other seven organisms was able to degrade the short branched alkyl chain of p-tert-amylphenol. However, two yeast strains, two filamentous fungi, and two bacterial strains attacked the aromatic ring system of the disinfectant via the hydroxylated intermediate 4-(1,1-dimethyl-propyl)-benzene-1,2-diol resulting in two hitherto unknown ring fission products with pyran and furan structures, 4-(1,1-dimethyl-propyl)-6-oxo-6-H-pyran-2-carboxylic acid and 2-[3-(1,1-dimethyl-propyl)-5-oxo-2H-furan-2-yl]acetic acid. While the disinfectant was toxic to the organisms applied, one of the ring cleavage products was not. Thus, a detoxification of the disinfectant was achieved by ring cleavage. Furthermore, one filamentous fungus formed sugar conjugates with p-tert-amylphenol as another mechanism of detoxification of toxic environmental pollutants. With this work, we can also contribute to the allocation of unknown chemical compounds within environmental samples to their parent compounds.

Convergent-Filament Nonmechanical Pump

NASA Technical Reports Server (NTRS)

Collins, Earl R., Jr.

1989-01-01

Simple device induces small flow of liquid without help of moving parts, in presence or absence of gravity. Drops of liquid move on filaments from wide end of cone to narrow end. Gradually blend with drops on adjacent filaments to form large drops with menisci. Important use expected to be returning liquid condensate in heat pipes, and collection of samples from clouds or fog.

Ultraminiature broadband light source with spiral shaped filament

NASA Technical Reports Server (NTRS)

McConaghy, Charles F. (Inventor); Olsen, Barry L. (Inventor); Tuma, Margaret L. (Inventor); Collura, Joseph S. (Inventor); Pocha, Michael D. (Inventor); Helvajian, Henry (Inventor); Meyer, Glenn A. (Inventor); Hansen, William W (Inventor)

2012-01-01

An ultraminiature light source using a double-spiral shaped tungsten filament includes end contact portions which are separated to allow for radial and length-wise unwinding of the spiral. The double-spiral filament is spaced relatively far apart at the end portions thereof so that contact between portions of the filament upon expansion is avoided. The light source is made by fabricating a double-spiral ultraminiature tungsten filament from tungsten foil and housing the filament in a ceramic package having a reflective bottom and a well wherein the filament is suspended. A vacuum furnace brazing process attaches the filament to contacts of the ceramic package. Finally, a cover with a transparent window is attached onto the top of the ceramic package by solder reflow in a second vacuum furnace process to form a complete hermetically sealed package.

Graphene-based filament material for thermal ionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hewitt, J.; Shick, C.; Siegfried, M.

The use of graphene oxide materials for thermal ionization mass spectrometry analysis of plutonium and uranium has been investigated. Filament made from graphene oxide slurries have been 3-D printed. A method for attaching these filaments to commercial thermal ionization post assemblies has been devised. Resistive heating of the graphene based filaments under high vacuum showed stable operation in excess of 4 hours. Plutonium ion production has been observed in an initial set of filaments spiked with the Pu 128 Certified Reference Material.

Filament eruption connected to protospheric activity

NASA Technical Reports Server (NTRS)

Simon, G.; Gesztelyi, L.; Schmieder, B.; Mein, N

1986-01-01

Two cases of activation of filaments that occured in regions of intense magnetic activity was studied. The simultaneous observations from Debrecen Observatory (white light and H alpha filtergram), and from Meudon Observatory (magnetogram, MSDP dopplergram and intensity maps in H alpha) gave a complementary set of data from which can be produced evidence of the influence of the photospheric magnetic field on the destabilization process of the filaments. On June 22, 1980, the eruption of the filament is associated with the motion of pores, which are manifestations of emerging flux knots. On September 3, 1980, the twisting motions in the filament are associated to the birth of a pore in its neighborhood. These observations are discussed.

Production, characterization, and modeling of mineral filled polypropylene filaments

NASA Astrophysics Data System (ADS)

George, Brian Robert

1999-11-01

This research produced mineral filled polypropylene filaments using a variety of fillers, characterized these filaments, and attempted to model their mechanical properties with current composite models. Also, these filaments were compared with bone to determine if they are suitable for modeling the mechanical properties of bone. Fillers used consist of wollastonite, talc, calcium carbonate, titanium dioxide, and hydroxyapatite. Fillers and polypropylene chips were combined and extruded into rods with the use of a mixer. The rods were chipped up and then formed into filaments through melt extrusion utilizing a piston extruder. Filaments with volume fractions of filler of 0.05, 0.10, 0.15, and 0.20 were produced. Additionally, some methods of trying to improve the properties of these filaments were attempted, but did not result in any significant property improvements. The fillers and filaments were visually characterized with a scanning electron microscope. Cross-sections, filament outer surfaces, fracture surfaces, and longitudinal cut open surfaces were viewed in this manner. Those filaments with anisotropic filler had some oriented filler particles, while all filaments suffered from poor adhesion between the polypropylene and the filler as well as agglomerations of filler particles. Twenty specimens of each filament were tensile tested and the average tenacity, strain, and modulus were calculated. Filaments containing talc, talc and wollastonite, titanium dioxide, or hydroxyapatite suffered from a drastic transition from ductile to brittle with the addition of 0.05 volume fraction of filler. This is evidenced by the sharp decrease in strain at this volume fraction of filler when compared to the strain of the unfilled polypropylene filament. Additionally, these same filaments suffered a sharp decrease in tenacity at the same volume fraction. These instant decreases are attributed to the agglomerations of filler in the filament. Generally, the modulus of the

Thick Filament Protein Network, Functions, and Disease Association.

PubMed

Wang, Li; Geist, Janelle; Grogan, Alyssa; Hu, Li-Yen R; Kontrogianni-Konstantopoulos, Aikaterini

2018-03-13

Sarcomeres consist of highly ordered arrays of thick myosin and thin actin filaments along with accessory proteins. Thick filaments occupy the center of sarcomeres where they partially overlap with thin filaments. The sliding of thick filaments past thin filaments is a highly regulated process that occurs in an ATP-dependent manner driving muscle contraction. In addition to myosin that makes up the backbone of the thick filament, four other proteins which are intimately bound to the thick filament, myosin binding protein-C, titin, myomesin, and obscurin play important structural and regulatory roles. Consistent with this, mutations in the respective genes have been associated with idiopathic and congenital forms of skeletal and cardiac myopathies. In this review, we aim to summarize our current knowledge on the molecular structure, subcellular localization, interacting partners, function, modulation via posttranslational modifications, and disease involvement of these five major proteins that comprise the thick filament of striated muscle cells. © 2018 American Physiological Society. Compr Physiol 8:631-709, 2018. Copyright © 2018 American Physiological Society. All rights reserved.

Dynamics of contracting surfactant-covered filaments

NASA Astrophysics Data System (ADS)

Kamat, Pritish; Thete, Sumeet; Xu, Qi; Basaran, Osman

2013-11-01

When drops are produced from a nozzle, a thin liquid thread connects the primary drop that is about to form to the rest of the liquid in the nozzle. Often, the thread becomes disconnected from both the primary drop and the remnant liquid mass hanging from the nozzle and thereby gives rise to a free filament. Due to surface tension, the free filament then contracts or recoils. During recoil, the filament can either contract into a single satellite droplet or break up into several small satellites. Such satellite droplets are undesirable in applications where they can, for example, cause misting in a manufacturing environment and mar product quality in ink-jet printing. In many applications, the filaments are coated with a monolayer of surfactant. In this work, we study the dynamics of contraction of slender filaments of a Newtonian fluid that are covered with a monolayer of surfactant when the surrounding fluid is a passive gas. Taking advantage of the fact that the filaments are long and slender, we use a 1D-slender-jet approximation of the governing system of equations consisting of the Navier-Stokes system and the convection-diffusion equation for surfactant transport. We solve the 1D system of equations by a finite element based numerical method.

Identification and functional analysis of endogenous nitric oxide in a filamentous fungus.

PubMed

Pengkit, Anchalee; Jeon, Seong Sil; Son, Soo Ji; Shin, Jae Ho; Baik, Ku Yeon; Choi, Eun Ha; Park, Gyungsoon

2016-07-18

In spite of its prevalence in animals and plants, endogenous nitric oxide (NO) has been rarely reported in fungi. We present here our observations on production of intracellular NO and its possible roles during development of Neurospora crassa, a model filamentous fungus. Intracellular NO was detected in hypha 8-16 hours after incubation in Vogel's minimal liquid media and conidiophores during conidiation using a fluorescent indicator (DAF-FM diacetate). Treatment with cPTIO, an NO scavenger, significantly reduced fluorescence levels and hindered hyphal growth in liquid media and conidiation, whereas exogenous NO enhanced hyphal extension on VM agar media and conidia formation. NO scavenging also dramatically diminished transcription of con-10 and con-13, genes preferentially expressed during conidiation. Our results suggest that intracellular NO is generated in young hypha growing in submerged culture and during conidia development and regulate mycelial development and conidia formation.

Identification and functional analysis of endogenous nitric oxide in a filamentous fungus

PubMed Central

Pengkit, Anchalee; Jeon, Seong Sil; Son, Soo Ji; Shin, Jae Ho; Baik, Ku Yeon; Choi, Eun Ha; Park, Gyungsoon

2016-01-01

In spite of its prevalence in animals and plants, endogenous nitric oxide (NO) has been rarely reported in fungi. We present here our observations on production of intracellular NO and its possible roles during development of Neurospora crassa, a model filamentous fungus. Intracellular NO was detected in hypha 8–16 hours after incubation in Vogel’s minimal liquid media and conidiophores during conidiation using a fluorescent indicator (DAF-FM diacetate). Treatment with cPTIO, an NO scavenger, significantly reduced fluorescence levels and hindered hyphal growth in liquid media and conidiation, whereas exogenous NO enhanced hyphal extension on VM agar media and conidia formation. NO scavenging also dramatically diminished transcription of con-10 and con-13, genes preferentially expressed during conidiation. Our results suggest that intracellular NO is generated in young hypha growing in submerged culture and during conidia development and regulate mycelial development and conidia formation. PMID:27425220

INTERACTION OF TWO FILAMENT CHANNELS OF DIFFERENT CHIRALITIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joshi, Navin Chandra; Magara, Tetsuya; Moon, Yong-Jae

2016-07-10

We present observations of the interactions between the two filament channels of different chiralities and associated dynamics that occurred during 2014 April 18–20. While two flux ropes of different helicity with parallel axial magnetic fields can only undergo a bounce interaction when they are brought together, the observations at first glance show that the heated plasma is moving from one filament channel to the other. The SDO /AIA 171 Å observations and the potential-field source-surface magnetic field extrapolation reveal the presence of a fan-spine magnetic configuration over the filament channels with a null point located above them. Three different eventsmore » of filament activations, partial eruptions, and associated filament channel interactions have been observed. The activation initiated in one filament channel seems to propagate along the neighboring filament channel. We believe that the activation and partial eruption of the filaments brings the field lines of flux ropes containing them closer to the null point and triggers the magnetic reconnection between them and the fan-spine magnetic configuration. As a result, the hot plasma moves along the outer spine line toward the remote point. Utilizing the present observations, for the first time we have discussed how two different-chirality filament channels can interact and show interrelation.« less

Two-step solar filament eruptions

NASA Astrophysics Data System (ADS)

Filippov, B.

2018-04-01

Coronal mass ejections (CMEs) are closely related to eruptive filaments and usually are the continuation of the same eruptive process into the upper corona. There are failed filament eruptions when a filament decelerates and stops at some greater height in the corona. Sometimes the filament after several hours starts to rise again and develops into the successful eruption with a CME formation. We propose a simple model for the interpretation of such two-step eruptions in terms of equilibrium of a flux rope in a two-scale ambient magnetic field. The eruption is caused by a slow decrease of the holding magnetic field. The presence of two critical heights for the initiation of the flux-rope vertical instability allows the flux rope to stay after the first jump some time in a metastable equilibrium near the second critical height. If the decrease of the ambient field continues, the next eruption step follows.

METHOD OF MAKING TUNGSTEN FILAMENTS

DOEpatents

Frazer, J.W.

1962-12-18

A method of making tungsten filaments is described in which the tungsten is completely free of isotope impurities in the range of masses 234 to 245 for use in mass spectrometers. The filament comprises a tantalum core generally less than 1 mil in diameter having a coating of potassium-free tantalum-diffused tungsten molecularly bonded thereto. In the preferred process of manufacture a short, thin tantalum filament is first mounted between terminal posts mounted in insulated relation through a backing plate. The tungsten is most conveniently vapor plated onto the tantalum by a tungsten carbonyl vapor decomposition method having a critical step because of the tendency of the tantalum to volatilize at the temperature of operntion of the filament. The preferred recipe comprises volatilizing tantalum by resistance henting until the current drops by about 40%, cutting the voltage back to build up the tungsten, and then gradually building the temperature back up to balance the rate of tungsten deposition with the rate of tantalum volatilization. (AEC)

Proper horizontal photospheric flows in a filament channel

NASA Astrophysics Data System (ADS)

Schmieder, B.; Roudier, T.; Mein, N.; Mein, P.; Malherbe, J. M.; Chandra, R.

2014-04-01

Context. An extended filament in the central part of the active region NOAA 11106 crossed the central meridian on Sept. 17, 2010 in the southern hemisphere. It has been observed in Hα with the THEMIS telescope in the Canary Islands and in 304 Å with the EUV imager (AIA) onboard the Solar Dynamic Observatory (SDO). Counterstreaming along the Hα threads and bright moving blobs (jets) along the 304 Å filament channel were observed during 10 h before the filament erupted at 17:03 UT. Aims: The aim of the paper is to understand the coupling between magnetic field and convection in filament channels and relate the horizontal photospheric motions to the activity of the filament. Methods: An analysis of the proper photospheric motions using SDO/HMI continuum images with the new version of the coherent structure tracking (CST) algorithm developed to track granules, as well as the large scale photospheric flows, was performed for three hours. Using corks, we derived the passive scalar points and produced a map of the cork distribution in the filament channel. Averaging the velocity vectors in the southern hemisphere in each latitude in steps of 3.5 arcsec, we defined a profile of the differential rotation. Results: Supergranules are clearly identified in the filament channel. Diverging flows inside the supergranules are similar in and out of the filament channel. Converging flows corresponding to the accumulation of corks are identified well around the Hα filament feet and at the edges of the EUV filament channel. At these convergence points, the horizontal photospheric velocity may reach 1 km s-1, but with a mean velocity of 0.35 km s-1. In some locations, horizontal flows crossing the channel are detected, indicating eventually large scale vorticity. Conclusions: The coupling between convection and magnetic field in the photosphere is relatively strong. The filament experienced the convection motions through its anchorage points with the photosphere, which are

Degradation of slime extracellular polymeric substances and inhibited sludge flocs destruction contribute to sludge dewaterability enhancement during fungal treatment of sludge using filamentous fungus Mucor sp. GY-1.

PubMed

Wang, Zhenyu; Zheng, Guanyu; Zhou, Lixiang

2015-09-01

Mechanisms responsible for the sludge dewaterability enhanced by filamentous fungi during fungal treatment of sludge were investigated in the present study. The filamentous fungus Mucor sp. GY-1, isolated from waste activated sludge, enhanced sludge dewaterability by 82.1% to achieve the lowest value of normalized sludge specific resistance to filtration (SRF), 8.18 × 10(10) m · L/kg · g-TSS. During the fungal treatment of sludge, 57.8% of slime extracellular polymeric substances (EPS) and 51.1% of polysaccharide in slime EPS were degraded, respectively, by Mucor sp. GY-1, contributing to the improvement of sludge dewaterability. Slime EPS is much more available for Mucor sp. GY-1 than either LB-EPS or TB-EPS that bound with microbial cells. In addition, filamentous fungus Mucor sp. GY-1 entrapped small sludge particles and inhibited the destruction of sludge flocs larger than 100 μm, thus enhancing sludge dewaterability, during fungal treatment of sludge using Mucor sp. GY-1. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plasma Brightenings in a Failed Solar Filament Eruption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y.; Ding, M. D., E-mail: yingli@nju.edu.cn

Failed filament eruptions are solar eruptions that are not associated with coronal mass ejections. In a failed filament eruption, the filament materials usually show some ascending and falling motions as well as generating bright EUV emissions. Here we report a failed filament eruption (SOL2016-07-22) that occurred in a quiet-Sun region observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory . In this event, the filament spreads out but gets confined by the surrounding magnetic field. When interacting with the ambient magnetic field, the filament material brightens up and flows along the magnetic field lines through the coronamore » to the chromosphere. We find that some materials slide down along the lifting magnetic structure containing the filament and impact the chromosphere, and through kinetic energy dissipation, cause two ribbon-like brightenings in a wide temperature range. There is evidence suggesting that magnetic reconnection occurs between the filament magnetic structure and the surrounding magnetic fields where filament plasma is heated to coronal temperatures. In addition, thread-like brightenings show up on top of the erupting magnetic fields at low temperatures, which might be produced by an energy imbalance from a fast drop of radiative cooling due to plasma rarefaction. Thus, this single event of a failed filament eruption shows the existence of a variety of plasma brightenings that may be caused by completely different heating mechanisms.« less

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

PubMed Central

2011-01-01

Background Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. Results 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. Conclusions Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens. PMID:21247460

NADPH Oxidase-Driven Phagocyte Recruitment Controls Candida albicans Filamentous Growth and Prevents Mortality

PubMed Central

Brothers, Kimberly M.; Gratacap, Remi L.; Barker, Sarah E.; Newman, Zachary R.; Norum, Ashley; Wheeler, Robert T.

2013-01-01

Candida albicans is a human commensal and clinically important fungal pathogen that grows as both yeast and hyphal forms during human, mouse and zebrafish infection. Reactive oxygen species (ROS) produced by NADPH oxidases play diverse roles in immunity, including their long-appreciated function as microbicidal oxidants. Here we demonstrate a non-traditional mechanistic role of NADPH oxidase in promoting phagocyte chemotaxis and intracellular containment of fungi to limit filamentous growth. We exploit the transparent zebrafish model to show that failed NADPH oxidase-dependent phagocyte recruitment to C. albicans in the first four hours post-infection permits fungi to germinate extracellularly and kill the host. We combine chemical and genetic tools with high-resolution time-lapse microscopy to implicate both phagocyte oxidase and dual-specific oxidase in recruitment, suggesting that both myeloid and non-myeloid cells promote chemotaxis. We show that early non-invasive imaging provides a robust tool for prognosis, strongly connecting effective early immune response with survival. Finally, we demonstrate a new role of a key regulator of the yeast-to-hyphal switching program in phagocyte-mediated containment, suggesting that there are species-specific methods for modulation of NADPH oxidase-independent immune responses. These novel links between ROS-driven chemotaxis and fungal dimorphism expand our view of a key host defense mechanism and have important implications for pathogenesis. PMID:24098114

Fabrication of PLA Filaments and its Printable Performance

NASA Astrophysics Data System (ADS)

Liu, Wenjie; Zhou, Jianping; Ma, Yuming; Wang, Jie; Xu, Jie

2017-12-01

Fused deposition modeling (FDM) is a typical 3D printing technology and preparation of qualified filaments is the basis. In order to prepare polylactic acid (PLA) filaments suitable for personalized FDM 3D printing, this article investigated the effect of factors such as extrusion temperature and screw speed on the diameter, surface roughness and ultimate tensile stress of the obtained PLA filaments. The optimal process parameters for fabrication of qualified filaments were determined. Further, the printable performance of the obtained PLA filaments for 3D objects was preliminarily explored.

Terahertz waves radiated from two noncollinear femtosecond plasma filaments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Hai-Wei; Hoshina, Hiromichi; Otani, Chiko, E-mail: otani@riken.jp

2015-11-23

Terahertz (THz) waves radiated from two noncollinear femtosecond plasma filaments with a crossing angle of 25° are investigated. The irradiated THz waves from the crossing filaments show a small THz pulse after the main THz pulse, which was not observed in those from single-filament scheme. Since the position of the small THz pulse changes with the time-delay of two filaments, this phenomenon can be explained by a model in which the small THz pulse is from the second filament. The denser plasma in the overlap region of the filaments changes the movement of space charges in the plasma, thereby changingmore » the angular distribution of THz radiation. As a result, this schematic induces some THz wave from the second filament to propagate along the path of the THz wave from the first filament. Thus, this schematic alters the direction of the THz radiation from the filamentation, which can be used in THz wave remote sensing.« less

Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and inmore » the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. Finally, these findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.« less

Fungi contribute critical but spatially varying roles in nitrogen and carbon cycling in acid mine drainage

DOE PAGES

Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.; ...

2016-03-03

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and inmore » the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. Finally, these findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.« less

Do fungi need to be included within environmental radiation protection assessment models?

PubMed

Guillén, J; Baeza, A; Beresford, N A; Wood, M D

2017-09-01

Fungi are used as biomonitors of forest ecosystems, having comparatively high uptakes of anthropogenic and naturally occurring radionuclides. However, whilst they are known to accumulate radionuclides they are not typically considered in radiological assessment tools for environmental (non-human biota) assessment. In this paper the total dose rate to fungi is estimated using the ERICA Tool, assuming different fruiting body geometries, a single ellipsoid and more complex geometries considering the different components of the fruit body and their differing radionuclide contents based upon measurement data. Anthropogenic and naturally occurring radionuclide concentrations from the Mediterranean ecosystem (Spain) were used in this assessment. The total estimated weighted dose rate was in the range 0.31-3.4 μGy/h (5 th -95 th percentile), similar to natural exposure rates reported for other wild groups. The total estimated dose was dominated by internal exposure, especially from 226 Ra and 210 Po. Differences in dose rate between complex geometries and a simple ellipsoid model were negligible. Therefore, the simple ellipsoid model is recommended to assess dose rates to fungal fruiting bodies. Fungal mycelium was also modelled assuming a long filament. Using these geometries, assessments for fungal fruiting bodies and mycelium under different scenarios (post-accident, planned release and existing exposure) were conducted, each being based on available monitoring data. The estimated total dose rate in each case was below the ERICA screening benchmark dose, except for the example post-accident existing exposure scenario (the Chernobyl Exclusion Zone) for which a dose rate in excess of 35 μGy/h was estimated for the fruiting body. Estimated mycelium dose rate in this post-accident existing exposure scenario was close to the 400 μGy/h benchmark for plants, although fungi are generally considered to be less radiosensitive than plants. Further research on appropriate

Isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings

PubMed Central

Soltani, Maryam; Bayat, Mansour; Hashemi, Seyed J.; Zia, Mohammadali; Pestechian, Nader

2013-01-01

Background: Invasive fungal infections cause considerable morbidity and mortality in immunocompromised hosts. Pigeon droppings could especially be a potential carrier in the spread of pathogenic yeasts and mold fungi into the environment. The objective of this study was to isolation of Cryptococcus neoformans and other opportunistic fungi from pigeon droppings. Materials and Methods: One hundred twenty samples of pigeon droppings were suspended 1:10 in saline solution and then cultured. Identification of C. neoformans was performed on bird seed agar, presence of a capsule on India ink preparation, urease production on urea agar medium and RapID yeast plus system. The identification of candida species was based on micro-morphological analysis on corn meal-Tween 80 agar, RapID yeast plus system and growth in CHROMagar candida. The identification of other fungi was based on macromorphologic, microscopic, biochemical and physiological characteristics. Results: The highest frequency of yeasts and mold fungi were observed in Candida albicans 6.6% and Penicillium spp. 25%. The frequency rate of C. neoformans isolation was 2.5%. Conclusion: Several types of fungi are present in pigeon droppings that can spread in environment and transmit to children and elderly as well as immunocompromised patients who are at increased risk of contracting opportunistic diseases. PMID:23901339

Aerogel-supported filament

DOEpatents

Wuest, Craig R.; Tillotson, Thomas M.; Johnson, III, Coleman V.

1995-01-01

The present invention is a thin filament embedded in a low density aerogel for use in radiation detection instruments and incandescent lamps. The aerogel provides a supportive matrix that is thermally and electrically nonconductive, mechanically strong, highly porous, gas-permeable, and transparent to ionizing radiation over short distances. A low density, open-cell aerogel is cast around a fine filament or wire, which allows the wire to be positioned with little or no tension and keeps the wire in place in the event of breakage. The aerogel support reduces the stresses on the wire caused by vibrational, gravitational, electrical, and mechanical forces.

Lamp automatically switches to new filament on burnout

NASA Technical Reports Server (NTRS)

Ingle, W. B.

1966-01-01

Lamp with primary and secondary filaments has a means for automatic switching to the secondary filament at primary filament burnout. Lamp failures and resultant expenses during oscillograph printing are appreciably reduced.

Integrated economic and environmental analysis of agricultural straw reuse in edible fungi industry

PubMed Central

Lu, Wencong; Yu, Shuao; Huang, Hairong

2018-01-01

Background China currently faces severe environmental pollution caused by burning agricultural straw; thus, resource utilization of these straws has become an urgent policy and practical objective for the Chinese government. Methods This study develops a bio-economic model, namely, “straw resource utilization for fungi in China (SRUFIC),” on the basis of a field survey of an edible fungi plant in Zhejiang, China, to investigate an integrated economic and environmental performance of straw reuse in fungi production. Five scenarios, which cover changes in the production scale, wage level, and price fluctuations of the main product and inputs, are simulated. Results Results reveal that (1) the pilot plant potentially provides enhanced economic benefits and disposes added agricultural residues by adjusting its production strategy; (2) the economic performance is most sensitive to fungi price fluctuations, whereas the environmental performance is more sensitive to production scale and price of fungi than other factors; (3) expanding the production scale can be the most efficient means of improving the performance of a plant economically and environmentally. Discussion Overall, agricultural straw reuse in the edible fungi industry can not only reduce the environmental risk derived from burning abandoned straws but also introduce economic benefits. Thus, the straw reuse in the fungi industry should be practiced in China, and specific economic incentive policies, such as price support or subsidies, must be implemented to promote the utilization of agricultural straws in the fungi industry. PMID:29682417

A comparison study of a solar active-region eruptive filament and a neighboring non-eruptive filament

NASA Astrophysics Data System (ADS)

Jiang, Chao-Wei; Wu, Shi-Tsan; Feng, Xue-Shang; Hu, Qiang

2016-01-01

Solar active region (AR) 11283 is a very magnetically complex region and it has produced many eruptions. However, there exists a non-eruptive filament in the plage region just next to an eruptive one in the AR, which gives us an opportunity to perform a comparison analysis of these two filaments. The coronal magnetic field extrapolated using our CESE-MHD-NLFFF code reveals that two magnetic flux ropes (MFRs) exist in the same extrapolation box supporting these two filaments, respectively. Analysis of the magnetic field shows that the eruptive MFR contains a bald-patch separatrix surface (BPSS) cospatial very well with a pre-eruptive EUV sigmoid, which is consistent with the BPSS model for coronal sigmoids. The magnetic dips of the non-eruptive MFRs match Hα observation of the non-eruptive filament strikingly well, which strongly supports the MFR-dip model for filaments. Compared with the non-eruptive MFR/filament (with a length of about 200 Mm), the eruptive MFR/filament is much smaller (with a length of about 20 Mm), but it contains most of the magnetic free energy in the extrapolation box and holds a much higher free energy density than the non-eruptive one. Both the MFRs are weakly twisted and cannot trigger kink instability. The AR eruptive MFR is unstable because its axis reaches above a critical height for torus instability, at which the overlying closed arcades can no longer confine the MFR stably. On the contrary, the quiescent MFR is very firmly held by its overlying field, as its axis apex is far below the torus-instability threshold height. Overall, this comparison investigation supports that an MFR can exist prior to eruption and the ideal MHD instability can trigger an MFR eruption.

Efficient formation of heterokaryotic sclerotia in the filamentous fungus Aspergillus oryzae.

PubMed

Wada, Ryuta; Jin, Feng Jie; Koyama, Yasuji; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

2014-01-01

Heterokaryon formation by hyphal fusion occurs during a sexual/parasexual cycle in filamentous fungi, and therefore, it is biotechnologically important for crossbreeding. In the industrial filamentous fungus Aspergillus oryzae, a parasexual cycle has been reported, and it was recently suggested that sexual reproduction should be possible. However, as A. oryzae enters into hyphal fusion with a much lower frequency than Neurospora crassa, the process of heterokaryon formation has not been extensively characterized in A. oryzae. Here, we developed a detection system for heterokaryon formation by expressing red or green fluorescent proteins in nuclei and conferring uridine/uracil or adenine auxotrophy to MAT1-1 and MAT1-2 strains of A. oryzae. The heterokaryon formation of A. oryzae was investigated in paired culture using the genetically modified strains. No sclerotial formation was observed in the hyphal contact regions of the two strains with the same auxotrophy, whereas numerous sclerotia were formed between the strains with different auxotrophies. In most of the formed sclerotia, the uridine/uracil and adenine auxotrophies were complemented, and both red and green fluorescence were detected, indicating that heterokaryotic fusants were formed by hyphal fusion before or during sclerotial formation. Moreover, overexpressing the sclR gene, which encodes a transcription factor promoting sclerotial formation, increased the number of heterokaryotic sclerotia formed between the two auxotrophic strains. Notably, these effects in sclerotial formation of heterokaryotic fusants were observed independently of the mating type pairing combinations. Taken together, these findings demonstrated that paring of different auxotrophs and sclR overexpression promote the formation of heterokaryotic sclerotia in A. oryzae.

Paths and determinants for Penicillium janthinellum to resist low and high copper

PubMed Central

Xu, Jian; Chen, Guo-Li; Sun, Xue-Zhe; Fan, Xian-Wei; You-Zhi, Li

2015-01-01

Copper (Cu) tolerance was well understood in fungi yeasts but not in filamentous fungi. Filamentous fungi are eukaryotes but unlike eukaryotic fungi yeasts, which are a collection of various fungi that are maybe classified into different taxa but all characterized by growth as filamentous hyphae cells and with a complex morphology. The current knowledge of Cu resistance of filamentous fungi is still fragmental and therefore needs to be bridged. In this study, we characterized Cu resistance of Penicillium janthinellum strain GXCR and its Cu-resistance-decreasing mutants (EC-6 and UC-8), and conducted sequencing of a total of 6 transcriptomes from wild-type GXCR and mutant EC-6 grown under control and external Cu. Taken all the results together, Cu effects on the basal metabolism were directed to solute transport by two superfamilies of solute carrier and major facilitator, the buffering free CoA and Acyl-CoA pool in the peroxisome, F-type H+-transporting ATPases-based ATP production, V-type H+-transporting ATPases-based transmembrane transport, protein degradation, and alternative splicing of pre-mRNAs. Roles of enzymatic and non-enzymatic antioxidants in resistance to low and high Cu were defined. The backbone paths, signaling systems, and determinants that involve resistance of filamentous fungi to high Cu were determined, discussed and outlined in a model. PMID:26265593

The Connection Between Solar Coronal Cavities and Solar Filaments

NASA Astrophysics Data System (ADS)

Zawadzki, B.; Karna, N.; Prchlik, J.; Reeves, K.; Kempton, D.; Angryk, R.

2017-12-01

Filaments are structures in the solar corona made up of relatively cool, dense, partially ionized plasma. Coronal cavities, circular or elliptical regions of low plasma density, are observed above prominences on the solar limb when viewed in EUV and white light coronal images. Since most filament/cavity eruptions lead to a coronal mass ejection (CME), determining the likelihood of an eruption event will improve our ability to predict space weather. We examine SDO/AIA cavity metadata and HEK filament metadata to determine which cavities are associated with which filaments from 2012 to 2015. Our study involved 140 cavities and 368 filaments that appeared poleward of +-30 degrees. We categorized the cavities and filaments based on the stability of the structures, defined by whether or not the cavity and filament exist long enough to track fully across the solar disk. Using these categories we perform a statistical study on various filament qualities within the metadata. Our findings indicate that filaments with cavities are observed more often at high latitude in compared to filaments without cavities. Moreover, our study indicates that a statistically significant difference exists between the filament length and tilt distributions for certain categories. This work supported by the NSF-REU solar physics program at SAO, grant number AGS-1560313, and the NSF-DIBBS project, grant number ACI-1443061.

Suzaku observations of the outskirts of the galaxy cluster Abell 3395, including a filament toward Abell 3391

NASA Astrophysics Data System (ADS)

Sugawara, Yuuki; Takizawa, Motokazu; Itahana, Madoka; Akamatsu, Hiroki; Fujita, Yutaka; Ohashi, Takaya; Ishisaki, Yoshitaka

2017-12-01

The results of Suzaku observations of the outskirts of Abell 3395, including a large-scale structure filament toward Abell 3391, are presented. We measured temperature and abundance distributions from the southern outskirt of A 3395 to the north at the virial radius, where a filament structure has been found in the former X-ray and Sunyaev-Zel'dovich (SZ) effect observations between A 3391 and A 3395. The overall temperature structure is consistent with the universal profile proposed by Okabe, N., et al. 2014, PASJ, 66, 99 for relaxed clusters, except for the filament region. A hint of intracluster medium heating is found between the two clusters, which might be due to their interaction in the early phase of a cluster merger. Although we obtained a relatively low metal abundance of Z=0.169^{+0.164+0.009+0.018}_{-0.150-0.004-0.015} solar, where the first, second, and third errors are statistical, cosmic X-ray background systematic, and non-X-ray background systematic, respectively, at the virial radius in the filament, our results are still consistent with previous results for other clusters (Z ˜ 0.3 solar) within errors. Therefore, our results are also consistent with the early enrichment scenario. We estimated Compton y parameters only from X-ray results in the region between A 3391 and A 3395 assuming a simple geometry. They are smaller than the previous SZ results with the Planck satellite. The difference could be attributed to a more elaborate geometry such as a filament inclined to the line-of-sight direction, or underestimation of the X-ray temperature because of the unresolved multi-temperature structures or undetected hot X-ray emission of the shock-heated gas.

Mixed submerged fermentation with two filamentous fungi for cellulolytic and xylanolytic enzyme production.

PubMed

Garcia-Kirchner, O; Muñoz-Aguilar, M; Pérez-Villalva, R; Huitrón-Vargas, C

2002-01-01

The efficient saccharification of lignocellulosic materials requires the cooperative actions of different cellulase enzyme activities: exoglucanase, endoglucanase, beta-glucosidase, and xylanase. Previous studies with the fungi strains Aureobasidium sp. CHTE-18, Penicillium sp. CH-TE-001, and Aspergillus terreus CH-TE-013, selected mainly because of their different cellulolytic and xylanolytic activities, have demonstrated the capacity of culture filtrates of cross-synergistic action in the saccharification of native sugarcane bagasse pith. In an attempt to improve the enzymatic hydrolysis of different cellulosic materials, we investigated a coculture fermentation with two of these strains to enhance the production of cellulases and xylanases. The 48-h batch experimental results showed that the mixed culture of Penicillium sp. CH-TE-001 and A. terreus CH-TE-013 produced culture filtrates with high protein content, cellulase (mainly beta-glucosidase), and xylanase activities compared with the individual culture of each strain. The same culture conditions were used in a simple medium with mineral salts, corn syrup liquor, and sugarcane bagasse pith as the sole carbon source with moderate shaking at 29 degrees C. Finally, we compared the effect of the cell-free culture filtrates obtained from the mixed and single fermentations on the saccharification of different kinds of cellulosic materials.

Observations of the Growth of an Active Region Filament

NASA Astrophysics Data System (ADS)

Yang, Bo

2017-04-01

We present observations of the growth of an active region filament caused by magnetic interactions among the filament and its adjacent superpenumbral filament (SF) and dark thread-like structures (T). Multistep reconnections are identified during the whole growing process. Magnetic flux convergence and cancellation occurring at the positive footpoint region of the filament is the first step reconnection, which resulted in the filament bifurcating into two sets of intertwined threads. One set anchored in situ, while the other set moved toward and interacted with the SF and part of T. This indicates the second step reconnection, which gave rise to the disappearance of the SF and the formation of a long thread-like structure that connects the far ends of the filament and T. The long thread-like structure further interacted with the T and then separated into two parts, representing the third step reconnection. Finally, another similar long thread-like structure, which intertwined with the fixed filament threads, appeared. Hαobservations show that this twisted structure is a longer sinistral filament. Based on the observed photospheric vector magnetograms, we performed a non-linear force-free field extrapolation to reconstruct the magnetic fields above the photosphere and found that the coronal magnetic field lines associated with the filament consists of two twisted flux ropes winding around each other. These results suggest that magnetic interactions among filaments and their adjacent SFs and T could lead to the growth of the filaments, and the filament is probably supported in a flux rope.

OBSERVATIONS OF THE GROWTH OF AN ACTIVE REGION FILAMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Bo; Jiang, Yunchun; Yang, Jiayan

We present observations of the growth of an active region filament caused by magnetic interactions among the filament and its adjacent superpenumbral filament (SF) and dark thread-like structures (T). Multistep reconnections are identified during the whole growing process. Magnetic flux convergence and cancellation occurring at the positive footpoint region of the filament is the first step reconnection, which resulted in the filament bifurcating into two sets of intertwined threads. One set anchored in situ, while the other set moved toward and interacted with the SF and part of T. This indicates the second step reconnection, which gave rise to themore » disappearance of the SF and the formation of a long thread-like structure that connects the far ends of the filament and T. The long thread-like structure further interacted with the T and then separated into two parts, representing the third step reconnection. Finally, another similar long thread-like structure, which intertwined with the fixed filament threads, appeared. H {sub α} observations show that this twisted structure is a longer sinistral filament. Based on the observed photospheric vector magnetograms, we performed a non-linear force-free field extrapolation to reconstruct the magnetic fields above the photosphere and found that the coronal magnetic field lines associated with the filament consists of two twisted flux ropes winding around each other. These results suggest that magnetic interactions among filaments and their adjacent SFs and T could lead to the growth of the filaments, and the filament is probably supported in a flux rope.« less

Brownian microhydrodynamics of active filaments.

PubMed

Laskar, Abhrajit; Adhikari, R

2015-12-21

Slender bodies capable of spontaneous motion in the absence of external actuation in an otherwise quiescent fluid are common in biological, physical and technological contexts. The interplay between the spontaneous fluid flow, Brownian motion, and the elasticity of the body presents a challenging fluid-structure interaction problem. Here, we model this problem by approximating the slender body as an elastic filament that can impose non-equilibrium velocities or stresses at the fluid-structure interface. We derive equations of motion for such an active filament by enforcing momentum conservation in the fluid-structure interaction and assuming slow viscous flow in the fluid. The fluid-structure interaction is obtained, to any desired degree of accuracy, through the solution of an integral equation. A simplified form of the equations of motion, which allows for efficient numerical solutions, is obtained by applying the Kirkwood-Riseman superposition approximation to the integral equation. We use this form of equation of motion to study dynamical steady states in free and hinged minimally active filaments. Our model provides the foundation to study collective phenomena in momentum-conserving, Brownian, active filament suspensions.

Casein Kinase II Induced Polymerization of Soluble TDP-43 into Filaments Is Inhibited by Heat Shock Proteins

PubMed Central

Davis, Mary; Lin, Wen-Lang; Cook, Casey; Dunmore, Judy; Tay, William; Menkosky, Kyle; Cao, Xiangkun; Petrucelli, Leonard; DeTure, Michael

2014-01-01

Background Trans-activation Response DNA-binding Protein-43 (TDP-43) lesions are observed in Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Lobar Degeneration with ubiquitin inclusions (FTLD-TDP) and 25–50% of Alzheimer's Disease (AD) cases. These abnormal protein inclusions are composed of either amorphous TDP-43 aggregates or highly ordered filaments. The filamentous TDP-43 accumulations typically contain clean 10–12 nm filaments though wider 18–20 nm coated filaments may be observed. The TDP-43 present within these lesions is phosphorylated, truncated and ubiquitinated, and these modifications appear to be abnormal as they are linked to both a cellular heat shock response and microglial activation. The mechanisms associated with this abnormal TDP-43 accumulation are believed to result in a loss of TDP-43 function, perhaps due to the post-translational modifications or resulting from physical sequestration of the TDP-43. The formation of TDP-43 inclusions involves cellular translocation and conversion of TDP-43 into fibrillogenic forms, but the ability of these accumulations to sequester normal TDP-43 and propagate this behavior between neurons pathologically is mostly inferred. The lack of methodology to produce soluble full length TDP-43 and recapitulate this polymerization into filaments as observed in disease has limited our understanding of these pathogenic cascades. Results The protocols described here generate soluble, full-length and untagged TDP-43 allowing for a direct assessment of the impact of various posttranslational modifications on TDP-43 function. We demonstrate that Casein Kinase II (CKII) promotes the polymerization of this soluble TDP-43 into 10 nm diameter filaments that resemble the most common TDP-43 structures observed in disease. Furthermore, these filaments are recognized as abnormal by Heat Shock Proteins (HSPs) which can inhibit TDP-43 polymerization or directly promote TDP-43 filament depolymerization. Conclusion These

Remote electrical arc suppression by laser filamentation.

PubMed

Schubert, Elise; Mongin, Denis; Kasparian, Jérôme; Wolf, Jean-Pierre

2015-11-02

We investigate the interaction of narrow plasma channels formed in the filamentation of ultrashort laser pulses, with a DC high voltage. The laser filaments prevent electrical arcs by triggering corona that neutralize the high-voltage electrodes. This phenomenon, that relies on the electric field modulation and free electron release around the filament, opens new prospects to lightning and over-voltage mitigation.

Spontaneous beating and synchronization of extensile active filament

NASA Astrophysics Data System (ADS)

Sarkar, Debarati; Thakur, Snigdha

2017-04-01

We simulate a semi-flexible active filament that exhibits spontaneous oscillations on clamping and show self-propulsion when left free. The activity on the filament relies on the nano-dimers distributed at regular intervals along the chain. With an emphasis on the spontaneous beating of a clamped filament, we demonstrate that the two competing forces necessary for oscillation are the elastic forces due to polymer rigidity and the active forces due to chemical activity. In addition, we also study the synchronization of two extensile filaments and the role played by non-local hydrodynamic interactions. We observe a phase lock scenario between the filaments during their synchronous motion.

Hydrodynamic interaction induced spontaneous rotation of coupled active filaments.

PubMed

Jiang, Huijun; Hou, Zhonghuai

2014-12-14

We investigate the coupled dynamics of active filaments with long range hydrodynamic interactions (HI). Remarkably, we find that filaments can rotate spontaneously under the same conditions in which a single filament alone can only move in translation. Detailed analysis reveals that the emergence of coupled rotation originates from an asymmetric flow field associated with HI which breaks the symmetry of translational motion when filaments approach. The breaking is then further stabilized by HI to form self-sustained coupled rotation. Intensive simulations show that coupled rotation forms easily when one filament tends to collide with the front-half of the other. For head-to-tail approaching, we observe another interesting HI-induced coupled motion, where filaments move together in the form of one following the other. Moreover, the radius of coupled rotation increases exponentially as the rigidity of the filament increases, which suggests that HI are also important for the alignment of rigid-rod-like filaments which has been assumed to be solely a consequence of direct collisions.

Aerogel-supported filament

DOEpatents

Wuest, C.R.; Tillotson, T.M.; Johnson, C.V. III

1995-05-16

The present invention is a thin filament embedded in a low density aerogel for use in radiation detection instruments and incandescent lamps. The aerogel provides a supportive matrix that is thermally and electrically nonconductive, mechanically strong, highly porous, gas-permeable, and transparent to ionizing radiation over short distances. A low density, open-cell aerogel is cast around a fine filament or wire, which allows the wire to be positioned with little or no tension and keeps the wire in place in the event of breakage. The aerogel support reduces the stresses on the wire caused by vibrational, gravitational, electrical, and mechanical forces. 6 Figs.

Nematode-Trapping Fungi.

PubMed

Jiang, Xiangzhi; Xiang, Meichun; Liu, Xingzhong

2017-01-01

Nematode-trapping fungi are a unique and intriguing group of carnivorous microorganisms that can trap and digest nematodes by means of specialized trapping structures. They can develop diverse trapping devices, such as adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and nonconstricting rings. Nematode-trapping fungi have been found in all regions of the world, from the tropics to Antarctica, from terrestrial to aquatic ecosystems. They play an important ecological role in regulating nematode dynamics in soil. Molecular phylogenetic studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Nematode-trapping fungi serve as an excellent model system for understanding fungal evolution and interaction between fungi and nematodes. With the development of molecular techniques and genome sequencing, their evolutionary origins and divergence, and the mechanisms underlying fungus-nematode interactions have been well studied. In recent decades, an increasing concern about the environmental hazards of using chemical nematicides has led to the application of these biological control agents as a rapidly developing component of crop protection.

Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea during exponential growth in axenic cultures.

PubMed

Davanture, Marlène; Dumur, Jérôme; Bataillé-Simoneau, Nelly; Campion, Claire; Valot, Benoît; Zivy, Michel; Simoneau, Philippe; Fillinger, Sabine

2014-07-01

This study describes the gel-free phosphoproteomic analysis of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under nonlimiting conditions. Using a combination of strong cation exchange and IMAC prior to LC-MS, we identified over 1350 phosphopeptides per fungus representing over 800 phosphoproteins. The preferred phosphorylation sites were found on serine (>80%) and threonine (>15%), whereas phosphorylated tyrosine residues were found at less than 1% in A. brassicicola and at a slightly higher ratio in B. cinerea (1.5%). Biological processes represented principally among the phoshoproteins were those involved in response and transduction of stimuli as well as in regulation of cellular and metabolic processes. Most known elements of signal transduction were found in the datasets of both fungi. This study also revealed unexpected phosphorylation sites in histidine kinases, a category overrepresented in filamentous ascomycetes compared to yeast. The data have been deposited to the ProteomeXchange database with identifier PXD000817 (http://proteomecentral.proteomexchange.org/dataset/PXD000817). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Star-forming Filament Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myers, Philip C., E-mail: pmyers@cfa.harvard.edu

2017-03-20

New models of star-forming filamentary clouds are presented in order to quantify their properties and to predict their evolution. These 2D axisymmetric models describe filaments that have no core, one low-mass core, and one cluster-forming core. They are based on Plummer-like cylinders and spheroids that are bounded by a constant-density surface of finite extent. In contrast to 1D Plummer-like models, they have specific values of length and mass, they approximate observed column density maps, and their distributions of column density ( N -pdfs) are pole-free. Each model can estimate the star-forming potential of a core-filament system by identifying the zonemore » of gas dense enough to form low-mass stars and by counting the number of enclosed thermal Jeans masses. This analysis suggests that the Musca central filament may be near the start of its star-forming life, with enough dense gas to make its first ∼3 protostars, while the Coronet filament is near the midpoint of its star formation, with enough dense gas to add ∼8 protostars to its ∼20 known stars. In contrast, L43 appears to be near the end of its star-forming life, since it lacks enough dense gas to add any new protostars to the two young stellar objectsalready known.« less

Mid-infrared laser filaments in the atmosphere

PubMed Central

Mitrofanov, A. V.; Voronin, A. A.; Sidorov-Biryukov, D. A.; Pugžlys, A.; Stepanov, E. A.; Andriukaitis, G.; Flöry, T.; Ališauskas, S.; Fedotov, A. B.; Baltuška, A.; Zheltikov, A. M.

2015-01-01

Filamentation of ultrashort laser pulses in the atmosphere offers unique opportunities for long-range transmission of high-power laser radiation and standoff detection. With the critical power of self-focusing scaling as the laser wavelength squared, the quest for longer-wavelength drivers, which would radically increase the peak power and, hence, the laser energy in a single filament, has been ongoing over two decades, during which time the available laser sources limited filamentation experiments in the atmosphere to the near-infrared and visible ranges. Here, we demonstrate filamentation of ultrashort mid-infrared pulses in the atmosphere for the first time. We show that, with the spectrum of a femtosecond laser driver centered at 3.9 μm, right at the edge of the atmospheric transmission window, radiation energies above 20 mJ and peak powers in excess of 200 GW can be transmitted through the atmosphere in a single filament. Our studies reveal unique properties of mid-infrared filaments, where the generation of powerful mid-infrared supercontinuum is accompanied by unusual scenarios of optical harmonic generation, giving rise to remarkably broad radiation spectra, stretching from the visible to the mid-infrared. PMID:25687621

Prokaryotic cytoskeletons: protein filaments organizing small cells.

PubMed

Wagstaff, James; Löwe, Jan

2018-04-01

Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.

A Method for 3D-Reconstruction of a Muscle Thick Filament Using the Tilt Series Images of a Single Filament Electron Tomogram

PubMed Central

Márquez, G.; Pinto, A.; Alamo, L.; Baumann, B.; Ye, F.; Winkler, H.; Taylor, K.; Padrón, R.

2014-01-01

Summary Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament –calculated without any image averaging and/or imposition of helical symmetry- only reveals MIH motifs infrequently. This is –to our knowledge- the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. PMID:24727133

A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

PubMed

Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

2014-05-01

Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. Copyright © 2014 Elsevier Inc. All rights reserved.

Direct observation of subunit exchange along mature vimentin intermediate filaments.

PubMed

Nöding, Bernd; Herrmann, Harald; Köster, Sarah

2014-12-16

Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Fusarium and other opportunistic hyaline fungi

USDA-ARS?s Scientific Manuscript database

This chapter focuses on those fungi that grow in tissue in the form of hyaline or lightly colored septate hyphae. These fungi include Fusarium and other hyaline fungi. Disease caused by hyaline fungi is referred to as hyalohyphomycosis. Hyaline fungi described in this chapter include the anamorphic,...

Antifungal activity of synthetic naphthoquinones against dermatophytes and opportunistic fungi: preliminary mechanism-of-action tests.

PubMed

Ferreira, Maria do Perpetuo Socorro Borges Carriço; Cardoso, Mariana Filomena do Carmo; da Silva, Fernando de Carvalho; Ferreira, Vitor Francisco; Lima, Emerson Silva; Souza, João Vicente Braga

2014-07-06

This study evaluated the antifungal activities of synthetic naphthoquinones against opportunistic and dermatophytic fungi and their preliminary mechanisms of action. The minimum inhibitory concentrations (MICs) of four synthetic naphthoquinones for 89 microorganisms, including opportunistic yeast agents, dermatophytes and opportunistic filamentous fungi, were determined. The compound that exhibited the best activity was assessed for its action against the cell wall (sorbitol test), for interference associated with ergosterol interaction, for osmotic balance (K+ efflux) and for membrane leakage of substances that absorb at the wavelength of 260 nm. All tested naphthoquinones exhibited antifungal activity, and compound IVS320 (3a,10b-dihydro-1H-cyclopenta [b] naphtho [2,3-d] furan-5,10-dione)-dione) demonstrated the lowest MICs across the tested species. The MIC of IVS320 was particularly low for dermatophytes (values ranging from 5-28 μg/mL) and Cryptococcus spp. (3-5 μg/mL). In preliminary mechanism-of-action tests, IVS320 did not alter the fungal cell wall but did cause problems in terms of cell membrane permeability (efflux of K+ and leakage of substances that absorb at 260 nm). This last effect was unrelated to ergosterol interactions with the membrane.

Single cell oil of oleaginous fungi from the tropical mangrove wetlands as a potential feedstock for biodiesel.

PubMed

Khot, Mahesh; Kamat, Srijay; Zinjarde, Smita; Pant, Aditi; Chopade, Balu; Ravikumar, Ameeta

2012-05-30

Single cell oils (SCOs) accumulated by oleaginous fungi have emerged as a potential alternative feedstock for biodiesel production. Though fungi from mangrove ecosystem have been reported for production of several lignocellulolytic enzymes, they remain unexplored for their SCO producing ability. Thus, these oleaginous fungi from the mangrove ecosystem could be suitable candidates for production of SCOs from lignocellulosic biomass. The accumulation of lipids being species specific, strain selection is critical and therefore, it is of importance to evaluate the fungal diversity of mangrove wetlands. The whole cells of these fungi were investigated with respect to oleaginicity, cell mass, lipid content, fatty acid methyl ester profiles and physicochemical properties of transesterified SCOs in order to explore their potential for biodiesel production. In the present study, 14 yeasts and filamentous fungi were isolated from the detritus based mangrove wetlands along the Indian west coast. Nile red staining revealed that lipid bodies were present in 5 of the 14 fungal isolates. Lipid extraction showed that these fungi were able to accumulate > 20% (w/w) of their dry cell mass (4.14 - 6.44 g L-1) as lipids with neutral lipid as the major fraction. The profile of transesterified SCOs revealed a high content of saturated and monounsaturated fatty acids i.e., palmitic (C16:0), stearic (C18:0) and oleic (C18:1) acids similar to conventional vegetable oils used for biodiesel production. The experimentally determined and predicted biodiesel properties for 3 fungal isolates correlated well with the specified standards. Isolate IBB M1, with the highest SCO yield and containing high amounts of saturated and monounsaturated fatty acid was identified as Aspergillus terreus using morphotaxonomic study and 18 S rRNA gene sequencing. Batch flask cultures with varying initial glucose concentration revealed that maximal cell biomass and lipid content were obtained at 30gL-1

Topology of interaction between titin and myosin thick filaments.

PubMed

Kellermayer, Miklós; Sziklai, Dominik; Papp, Zsombor; Decker, Brennan; Lakatos, Eszter; Mártonfalvi, Zsolt

2018-05-05

Titin is a giant protein spanning between the Z- and M-lines of the sarcomere. In the A-band titin is associated with the myosin thick filament. It has been speculated that titin may serve as a blueprint for thick-filament formation due to the super-repeat structure of its A-band domains. Accordingly, titin might provide a template that determines the length and structural periodicity of the thick filament. Here we tested the titin ruler hypothesis by mixing titin and myosin at in situ stoichiometric ratios (300 myosins per 12 titins) in buffers of different ionic strength (KCl concentration range 100-300 mM). The topology of the filamentous complexes was investigated with atomic force microscopy. We found that the samples contained distinct, segregated populations of titin molecules and myosin thick filaments. We were unable to identify complexes in which myosin molecules were regularly associated to either mono- or oligomeric titin in either relaxed or stretched states of the titin filaments. Thus, the electrostatically driven self-association is stronger in both myosin and titin than their binding to each other, and it is unlikely that titin functions as a geometrical template for thick-filament formation. However, when allowed to equilibrate configurationally, long myosin thick filaments appeared with titin oligomers attached to their surface. The titin meshwork formed on the thick-filament surface may play a role in controlling thick-filament length by regulating the structural dynamics of myosin molecules and placing a mechanical limit on the filament length. Copyright © 2018 Elsevier Inc. All rights reserved.

Physical principles of filamentous protein self-assembly kinetics

NASA Astrophysics Data System (ADS)

Michaels, Thomas C. T.; Liu, Lucie X.; Meisl, Georg; Knowles, Tuomas P. J.

2017-04-01

The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.

New strategy for rapid diagnosis and characterization of fungal infections: the example of corneal scrapings.

PubMed

Goldschmidt, Pablo; Degorge, Sandrine; Che Sarria, Patricia; Benallaoua, Djida; Semoun, Oudy; Borderie, Vincent; Laroche, Laurent; Chaumeil, Christine

2012-01-01

The prognosis of people infected with Fungi especially immunocompromised depends on rapid and accurate diagnosis to capitalize on time administration of specific treatments. However, cultures produce false negative results and nucleic-acid amplification techniques require complex post-amplification procedures to differentiate relevant fungal types. The objective of this work was to develop a new diagnostic strategy based on real-time polymerase-chain reaction high-resolution melting analysis (PCR-HRM) that a) detects yeasts and filamentous Fungi, b) differentiates yeasts from filamentous Fungi, and c) discriminates among relevant species of yeasts. PCR-HRM detection limits and specificity were assessed with a) isolated strains; b) human blood samples experimentally infected with Fungi; c) blood experimentally infected with other infectious agents; d) corneal scrapings from patients with suspected fungal keratitis (culture positive and negative) and e) scrapings from patients with suspected bacterial, viral or Acanthamoeba infections. The DNAs were extracted and mixed with primers diluted in the MeltDoctor® HRM Master Mix in 2 tubes, the first for yeasts, containing the forward primer CandUn (5'CATGCCTGTTTGAGCGTC) and the reverse primer FungUn (5'TCCTCCGCTT ATTGATATGCT) and the second for filamentous Fungi, containing the forward primer FilamUn (5'TGCCTGTCCGAGCGTCAT) and FungUn. Molecular probes were not necessary. The yields of DNA extraction and the PCR inhibitors were systematically monitored. PCR-HRM detected 0.1 Colony Forming Units (CFU)/µl of yeasts and filamentous Fungi, differentiated filamentous Fungi from yeasts and discriminated among relevant species of yeasts. PCR-HRM performances were higher than haemoculture and sensitivity and specificity was 100% for culture positive samples, detecting and characterizing Fungi in 7 out 10 culture negative suspected fungal keratitis. PCR-HRM appears as a new, sensitive, specific and inexpensive test that detects

[New natural products from the marine-derived Aspergillus fungi-A review].

PubMed

Zhao, Chengying; Liu, Haishan; Zhu, Weiming

2016-03-04

Marine-derived fungi were the main source of marine microbial natural products (NPs) due to their complex genetic background, chemodiversity and high yield of NPs. According to our previous survey for marine microbial NPs from 2010 to 2013, Aspergillus fungi have received the most of attention among all the marine-derived fungi, which accounted for 31% NPs of the marine fungal origins. This paper reviewed the sources, chemical structures and bioactivites of all the 512 new marine NPs of Aspergillus fungal origins from 1992 to 2014. These marine NPs have diverse chemical structures including polyketides, fatty acids, sterols and terpenoids, alkaloids, peptides, and so on, 36% of which displayed bioactivities such as cytotoxicity, antimicrobial activity, antioxidant and insecticidal activity. Nitrogen compounds are the major secondary metabolites accounting for 52% NPs from the marine-derived Aspergillus fungi. Nitrogen compounds are also the class with the highest ratio of bioactive compounds, 40% of which are bioactive. Plinabulin, a dehydrodiketopiperazine derivative of halimide had been ended its phase II trial and has received its phase III study from the third quarter of 2015 for the treatment of advanced, metastatic non-small cell lung cancer.

Enhancement of clover growth by inoculation of P-solubilizing fungi and arbuscular mycorrhizal fungi.

PubMed

Souchie, Edson L; Azcón, Rosario; Barea, Jose M; Silva, Eliane M R; Saggin-Júnior, Orivaldo J

2010-09-01

This study evaluated the synergism between several P-solubilizing fungi isolates and arbuscular mycorrhizal fungi to improve clover ( Trifolium pratense) growth in the presence of Araxá apatite. Clover was sown directly in plastic pots with 300g of sterilized washed sand, vermiculite and sepiolite 1:1:1 (v:v:v) as substrate, and grown in a controlled environment chamber. The substrate was fertilized with 3 g L(-1) of Araxá apatite. A completely randomized design, in 8×2 factorial scheme (eight P-solubilizing fungi treatments with or without arbuscular mycorrhizal fungi)and four replicates were used. The P-solubilizing fungi treatments consisted of five Brazilian P-solubilizing fungi isolates (PSF 7, 9, 20, 21 and 22), two Spanish isolates ( Aspergillus niger and the yeast Yarowia lipolytica) and control (non-inoculated treatment). The greatest clover growth rate was recorded when Aspergillus niger and PSF 21 were co-inoculated with arbuscular mycorrhizal fungi. Aspergillus niger, PSF 7 and PSF 21 were the most effective isolates on increasing clover growth in the presence of arbuscular mycorrhizal fungi. Greater mycorrhizal colonization resulted in greater clover growth rate in most PSF treatments. PSF 7 was the best isolate to improve the establishment of mycorrhizal and rhizobia symbiosis.

On the fragmentation of filaments in a molecular cloud simulation

NASA Astrophysics Data System (ADS)

Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.

2018-03-01

Context. The fragmentation of filaments in molecular clouds has attracted a lot of attention recently as there seems to be a close relation between the evolution of filaments and star formation. The study of the fragmentation process has been motivated by simple analytical models. However, only a few comprehensive studies have analysed the evolution of filaments using numerical simulations where the filaments form self-consistently as part of large-scale molecular cloud evolution. Aim. We address the early evolution of parsec-scale filaments that form within individual clouds. In particular, we focus on three questions: How do the line masses of filaments evolve? How and when do the filaments fragment? How does the fragmentation relate to the line masses of the filaments? Methods: We examine three simulated molecular clouds formed in kiloparsec-scale numerical simulations performed with the FLASH adaptive mesh refinement magnetohydrodynamic code. The simulations model a self-gravitating, magnetised, stratified, supernova-driven interstellar medium, including photoelectric heating and radiative cooling. We follow the evolution of the clouds for 6 Myr from the time self-gravity starts to act. We identify filaments using the DisPerSe algorithm, and compare the results to other filament-finding algorithms. We determine the properties of the identified filaments and compare them with the predictions of analytic filament stability models. Results: The average line masses of the identified filaments, as well as the fraction of mass in filamentary structures, increases fairly continuously after the onset of self-gravity. The filaments show fragmentation starting relatively early: the first fragments appear when the line masses lie well below the critical line mass of Ostriker's isolated hydrostatic equilibrium solution ( 16 M⊙ pc-1), commonly used as a fragmentation criterion. The average line masses of filaments identified in three-dimensional volume density cubes

Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi

PubMed Central

Roy, Mélanie; Watthana, Santi; Stier, Anna; Richard, Franck; Vessabutr, Suyanee; Selosse, Marc-André

2009-01-01

Background Mycoheterotrophic plants are considered to associate very specifically with fungi. Mycoheterotrophic orchids are mostly associated with ectomycorrhizal fungi in temperate regions, or with saprobes or parasites in tropical regions. Although most mycoheterotrophic orchids occur in the tropics, few studies have been devoted to them, and the main conclusions about their specificity have hitherto been drawn from their association with ectomycorrhizal fungi in temperate regions. Results We investigated three Asiatic Neottieae species from ectomycorrhizal forests in Thailand. We found that all were associated with ectomycorrhizal fungi, such as Thelephoraceae, Russulaceae and Sebacinales. Based on 13C enrichment of their biomass, they probably received their organic carbon from these fungi, as do mycoheterotrophic Neottieae from temperate regions. Moreover, 13C enrichment suggested that some nearby green orchids received part of their carbon from fungi too. Nevertheless, two of the three orchids presented a unique feature for mycoheterotrophic plants: they were not specifically associated with a narrow clade of fungi. Some orchid individuals were even associated with up to nine different fungi. Conclusion Our results demonstrate that some green and mycoheterotrophic orchids in tropical regions can receive carbon from ectomycorrhizal fungi, and thus from trees. Our results reveal the absence of specificity in two mycoheterotrophic orchid-fungus associations in tropical regions, in contrast to most previous studies of mycoheterotrophic plants, which have been mainly focused on temperate orchids. PMID:19682351

In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

PubMed

Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

2016-01-01

Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

Flux Cancellation Leading to Solar Filament Eruptions

NASA Astrophysics Data System (ADS)

Popescu, R. M.; Panesar, N. K.; Sterling, A. C.; Moore, R. L.

2016-12-01

Solar filaments are strands of relatively cool, dense plasma magnetically suspended in the lower density hotter solar corona. They trace magnetic polarity inversion lines (PILs) in the photosphere below, and are supported against gravity at heights of up to 100 Mm above the chromosphere by the magnetic field in and around them. This field erupts when it is rendered unstable by either magnetic flux cancellation or emergence at or near the PIL. We have studied the evolution of photospheric magnetic flux leading to ten observed filament eruptions. Specifically, we look for gradual magnetic changes in the neighborhood of the PIL prior to and during eruption. We use Extreme Ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA), and magnetograms from the Helioseismic and Magnetic Imager (HMI), both onboard the Solar Dynamics Observatory (SDO), to study filament eruptions and their photospheric magnetic fields. We examine whether flux cancellation or/and emergence leads to filament eruptions and find that continuous flux cancellation was present at the PIL for many hours prior to each eruption. We present two events in detail and find the following: (a) the pre-eruption filament-holding core field is highly sheared and appears in the shape of a sigmoid above the PIL; (b) at the start of the eruption the opposite arms of the sigmoid reconnect in the middle above the site of (tether-cutting) flux cancellation at the PIL; (c) the filaments first show a slow-rise, followed by a fast-rise as they erupt. We conclude that these two filament eruptions result from flux cancellation in the middle of the sheared field and are in agreement with the standard model for a CME/flare filament eruption from a closed bipolar magnetic field [flux cancellation (van Ballegooijen and Martens 1989 and Moore and Roumelrotis 1992) and runaway tether-cutting (Moore et. al 2001)].

Flux Cancellation Leading to CME Filament Eruptions

NASA Technical Reports Server (NTRS)

Popescu, Roxana M.; Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L.

2016-01-01

Solar filaments are strands of relatively cool, dense plasma magnetically suspended in the lower density hotter solar corona. They trace magnetic polarity inversion lines (PILs) in the photosphere below, and are supported against gravity at heights of up to approx.100 Mm above the chromosphere by the magnetic field in and around them. This field erupts when it is rendered unstable, often by magnetic flux cancellation or emergence at or near the PIL. We have studied the evolution of photospheric magnetic flux leading to ten observed filament eruptions. Specifically, we look for gradual magnetic changes in the neighborhood of the PIL prior to and during eruption. We use Extreme Ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA), and magnetograms from the Helioseismic and Magnetic Imager (HMI), both on board the Solar Dynamics Observatory (SDO), to study filament eruptions and their photospheric magnetic fields. We examine whether flux cancellation or/and emergence leads to filament eruptions. We find that continuous flux cancellation was present at the PIL for many hours prior to each eruption. We present two CME-producing eruptions in detail and find the following: (a) the pre-eruption filament-holding core field is highly sheared and appears in the shape of a sigmoid above the PIL; (b) at the start of the eruption the opposite arms of the sigmoid reconnect in the middle above the site of (tether-cutting) flux cancellation at the PIL; (c) the filaments first show a slow-rise, followed by a fast-rise as they erupt. We conclude that these two filament eruptions result from flux cancellation in the middle of the sheared field, and thereafter evolve in agreement with the standard model for a CME/flare filament eruption from a closed bipolar magnetic field [flux cancellation (van Ballegooijen and Martens 1989 and Moore and Roumelrotis 1992) and runaway tether-cutting (Moore et. al 2001)].

Cofilin-Linked Changes in Actin Filament Flexibility Promote Severing

PubMed Central

McCullough, Brannon R.; Grintsevich, Elena E.; Chen, Christine K.; Kang, Hyeran; Hutchison, Alan L.; Henn, Arnon; Cao, Wenxiang; Suarez, Cristian; Martiel, Jean-Louis; Blanchoin, Laurent; Reisler, Emil; De La Cruz, Enrique M.

2011-01-01

The actin regulatory protein, cofilin, increases the bending and twisting elasticity of actin filaments and severs them. It has been proposed that filaments partially decorated with cofilin accumulate stress from thermally driven shape fluctuations at bare (stiff) and decorated (compliant) boundaries, thereby promoting severing. This mechanics-based severing model predicts that changes in actin filament compliance due to cofilin binding affect severing activity. Here, we test this prediction by evaluating how the severing activities of vertebrate and yeast cofilactin scale with the flexural rigidities determined from analysis of shape fluctuations. Yeast actin filaments are more compliant in bending than vertebrate actin filaments. Severing activities of cofilactin isoforms correlate with changes in filament flexibility. Vertebrate cofilin binds but does not increase the yeast actin filament flexibility, and does not sever them. Imaging of filament thermal fluctuations reveals that severing events are associated with local bending and fragmentation when deformations attain a critical angle. The critical severing angle at boundaries between bare and cofilin-decorated segments is smaller than in bare or fully decorated filaments. These measurements support a cofilin-severing mechanism in which mechanical asymmetry promotes local stress accumulation and fragmentation at boundaries of bare and cofilin-decorated segments, analogous to failure of some nonprotein materials. PMID:21723825

Optical spectroscopy using gas-phase femtosecond laser filamentation.

PubMed

Odhner, Johanan; Levis, Robert

2014-01-01

Femtosecond laser filamentation occurs as a dynamic balance between the self-focusing and plasma defocusing of a laser pulse to produce ultrashort radiation as brief as a few optical cycles. This unique source has many properties that make it attractive as a nonlinear optical tool for spectroscopy, such as propagation at high intensities over extended distances, self-shortening, white-light generation, and the formation of an underdense plasma. The plasma channel that constitutes a single filament and whose position in space can be controlled by its input parameters can span meters-long distances, whereas multifilamentation of a laser beam can be sustained up to hundreds of meters in the atmosphere. In this review, we briefly summarize the current understanding and use of laser filaments for spectroscopic investigations of molecules. A theoretical framework of filamentation is presented, along with recent experimental evidence supporting the established understanding of filamentation. Investigations carried out on vibrational and rotational spectroscopy, filament-induced breakdown, fluorescence spectroscopy, and backward lasing are discussed.

Formation of a solar Hα filament from orphan penumbrae

NASA Astrophysics Data System (ADS)

Buehler, D.; Lagg, A.; van Noort, M.; Solanki, S. K.

2016-05-01

Aims: The formation and evolution of an Hα filament in active region (AR) 10953 is described. Methods: Observations from the Solar Optical Telescope (SOT) aboard the Hinode satellite starting from UT 18:09 on 27th April 2007 until UT 06:08 on 1st May 2007 were analysed. 20 scans of the 6302 Å Fe I line pair recorded by SOT/SP were inverted using the spatially coupled version of the SPINOR code. The inversions were analysed together with co-spatial SOT/BFI G-band and Ca II H and SOT/NFI Hα observations. Results: Following the disappearance of an initial Hα filament aligned along the polarity inversion line (PIL) of the AR, a new Hα filament formed in its place some 20 h later, which remained stable for, at least, another 1.5 days. The creation of the new Hα filament was driven by the ascent of horizontal magnetic fields from the photosphere into the chromosphere at three separate locations along the PIL. The magnetic fields at two of these locations were situated directly underneath the initial Hα filament and formed orphan penumbrae already aligned along the Hα filament channel. The 700 G orphan penumbrae were stable and trapped in the photosphere until the disappearance of the overlying initial Hα filament, after which they started to ascend into the chromosphere at 10 ± 5 m/s. Each ascent was associated with a simultaneous magnetic flux reduction of up to 50% in the photosphere. The ascended orphan penumbrae formed dark seed structures in Hα in parallel with the PIL, which elongated and merged to form an Hα filament. The filament channel featured horizontal magnetic fields of on average 260 G at log (τ) = -2 suspended above the nearly field-free lower photosphere. The fields took on an overall inverse configuration at log (τ) = -2 suggesting a flux rope topology for the new Hα filament. The destruction of the initial Hα filament was likely caused by the flux emergence at the third location along the PIL. Conclusions: We present a new

Importance of filament diameter when using bass brushing technique.

PubMed

Vowles, A D; Wade, A B

1977-08-01

A comparative study using a crossover experimental construction was made of the effectiveness of brushes containing 6/10 nylon filaments of 0.132 mm mean diameter using a Bass technique with those containing filaments of the same type of nylon but 0.280 mm diameter. Each type of brush was used for a 2-week period. Even though the finer filament brushes contained more than three times as many filaments, they were inferior in cleaning achievement to the brushes with the broader filaments. The difference was particularly marked on the facial aspect, but was largely nullified lingually. The effectiveness of the Bass technique in the gingival zone demonstrated in a previous investigation when brushes containing filaments of 0.18 and 0.20 mm were used, was not found in this investigation. It is concluded that filament diameter is critical in achieving effective cleaning using the Bass technique.

Method for preparing metallated filament-wound structures

DOEpatents

Peterson, George R.

1979-01-01

Metallated graphite filament-wound structures are prepared by coating a continuous multi-filament carbon yarn with a metal carbide, impregnating the carbide coated yarn with a polymerizable carbon precursor, winding the resulting filament about a mandrel, partially curing the impregnation in air, subjecting the wound composite to heat and pressure to cure the carbon precursor, and thereafter heating the composite in a sizing die at a pressure loading of at least 1000 psi for graphitizing the carbonaceous material in the composite. The carbide in the composite coalesces into rod-like shapes which are disposed in an end-to-end relationship parallel with the filaments to provide resistance to erosion in abrasive laden atmospheres.

Beam wandering of femtosecond laser filament in air.

PubMed

Yang, Jing; Zeng, Tao; Lin, Lie; Liu, Weiwei

2015-10-05

The spatial wandering of a femtosecond laser filament caused by the filament heating effect in air has been studied. An empirical formula has also been derived from the classical Karman turbulence model, which determines quantitatively the displacement of the beam center as a function of the propagation distance and the effective turbulence structure constant. After fitting the experimental data with this formula, the effective turbulence structure constant has been estimated for a single filament generated in laboratory environment. With this result, one may be able to estimate quantitatively the displacement of a filament over long distance propagation and interpret the practical performance of the experiments assisted by femtosecond laser filamentation, such as remote air lasing, pulse compression, high order harmonic generation (HHG), etc.

Scroll wave filaments self-wrap around unexcitable heterogeneities.

PubMed

Jiménez, Zulma A; Steinbock, Oliver

2012-09-01

Scroll waves are three-dimensional excitation vortices rotating around one-dimensional phase singularities called filaments. In experiments with a chemical reaction-diffusion system and in numerical simulations, we study the pinning of closed filament loops to inert cylindrical heterogeneities. We show that the filament wraps itself around the heterogeneity and thus avoids contraction and annihilation. This entwining steadily increases the total length of the pinned filament and reshapes the entire rotation backbone of the vortex. Self-pinning is fastest for thin cylinders with radii not much larger than the core of the unpinned rotor. The process ends when the filament is attached to the entire length of the cylinder. The possible importance of self-pinning in cardiac systems is discussed.

Cleavage of beta,beta-carotene to flavor compounds by fungi.

PubMed

Zorn, H; Langhoff, S; Scheibner, M; Berger, R G

2003-09-01

More than 50 filamentous fungi and yeasts, known for de novo synthesis or biotransformation of mono-, sesqui-, tri-, or tetraterpenes, were screened for their ability to cleave beta,beta-carotene to flavor compounds. Ten strains discolored a beta,beta-carotene-containing growth agar, indicating efficient degradation of beta,beta-carotene. Dihydroactinidiolide was formed as the sole conversion product of beta,beta-carotene in submerged cultures of Ganoderma applanatum, Hypomyces odoratus, Kuehneromyces mutabilis, and Trametes suaveolens. When mycelium-free culture supernatants from five species were applied for the conversions, nearly complete degradation of beta,beta-carotene was observed after 12 h. Carotenoid-derived volatile products were detected in the media of Ischnoderma benzoinum, Marasmius scorodonius, and Trametes versicolor. beta-Ionone proved to be the main metabolite in each case, whereas beta-cyclocitral, dihydroactinidiolide, and 2-hydroxy-2,6,6-trimethylcyclohexanone were formed in minor quantities. Using a photometric bleaching test, the beta,beta-carotene cleaving enzyme activities of M. scorodonius were partially characterized.

Dimensional quantization effects in the thermodynamics of conductive filaments

NASA Astrophysics Data System (ADS)

Niraula, D.; Grice, C. R.; Karpov, V. G.

2018-06-01

We consider the physical effects of dimensional quantization in conductive filaments that underlie operations of some modern electronic devices. We show that, as a result of quantization, a sufficiently thin filament acquires a positive charge. Several applications of this finding include the host material polarization, the stability of filament constrictions, the equilibrium filament radius, polarity in device switching, and quantization of conductance.

Dimensional quantization effects in the thermodynamics of conductive filaments.

PubMed

Niraula, D; Grice, C R; Karpov, V G

2018-06-29

We consider the physical effects of dimensional quantization in conductive filaments that underlie operations of some modern electronic devices. We show that, as a result of quantization, a sufficiently thin filament acquires a positive charge. Several applications of this finding include the host material polarization, the stability of filament constrictions, the equilibrium filament radius, polarity in device switching, and quantization of conductance.

Functional Analysis of the Polyketide Synthase Genes in the Filamentous Fungus Gibberella zeae (Anamorph Fusarium graminearum)

PubMed Central

Gaffoor, Iffa; Brown, Daren W.; Plattner, Ron; Proctor, Robert H.; Qi, Weihong; Trail, Frances

2005-01-01

Polyketides are a class of secondary metabolites that exhibit a vast diversity of form and function. In fungi, these compounds are produced by large, multidomain enzymes classified as type I polyketide synthases (PKSs). In this study we identified and functionally disrupted 15 PKS genes from the genome of the filamentous fungus Gibberella zeae. Five of these genes are responsible for producing the mycotoxins zearalenone, aurofusarin, and fusarin C and the black perithecial pigment. A comprehensive expression analysis of the 15 genes revealed diverse expression patterns during grain colonization, plant colonization, sexual development, and mycelial growth. Expression of one of the PKS genes was not detected under any of 18 conditions tested. This is the first study to genetically characterize a complete set of PKS genes from a single organism. PMID:16278459

Propagation distance-resolved characteristics of filament-induced copper plasma

DOE PAGES

Ghebregziabher, Isaac; Hartig, Kyle C.; Jovanovic, Igor

2016-03-02

Copper plasma generated at different filament-copper interaction points was characterized by spectroscopic, acoustic, and imaging measurements. The longitudinal variation of the filament intensity was qualitatively determined by acoustic measurements in air. The maximum plasma temperature was measured at the location of peak filament intensity, corresponding to the maximum mean electron energy during plasma formation. The highest copper plasma density was measured past the location of the maximum electron density in the filament, where spectral broadening of the filament leads to enhanced ionization. Acoustic measurements in air and on solid target were correlated to reconstructed plasma properties. Lastly, optimal line emissionmore » is measured near the geometric focus of the lens used to produce the filament.« less

Immunocontraception: Filamentous Bacteriophage as a Platform for Vaccine Development

PubMed Central

Samoylova, Tatiana I.; Braden, Timothy D.; Spencer, Jennifer A.; Bartol, Frank F.

2017-01-01

Background: Population control of domestic, wild, invasive, and captive animal species is a global issue of importance to public health, animal welfare and the economy. There is pressing need for effective, safe, and inexpensive contraceptive technologies to ad-dress this problem. Contraceptive vaccines, designed to stimulate the immune system in order to block critical reproductive events and suppress fertility, may provide a solution. Fil-amentous bacteriophages can be used as platforms for development of such vaccines. Objective: In this review authors highlight structural and immunogenic properties of fila-mentous phages, and discuss applications of phage-peptide vaccines for advancement of immunocontraception technology in animals. Results: Phages can be engineered to display fusion (non-phage) peptides as coat proteins. Such modifications can be accomplished via genetic manipulation of phage DNA, or by chemical conjugation of synthetic peptides to phage surface proteins. Phage fusions with antigenic determinants induce humoral as well as cell-mediated immune responses in ani-mals, making them attractive as vaccines. Additional advantages of the phage platform include environmental stability, low cost, and safety for immunized animals and those ad-ministering the vaccines. Conclusion: Filamentous phages are viable platforms for vaccine development that can be engineered with molecular and organismal specificity. Phage-based vaccines can be pro-duced in abundance at low cost, are environmentally stable, and are immunogenic when administered via multiple routes. These features are essential for a contraceptive vaccine to be operationally practical in animal applications. Adaptability of the phage platform also makes it attractive for design of human immunocontraceptive agents. PMID:28901276

Fluorescence of fungi in superficial and deep fungal infections

PubMed Central

Elston, Dirk M

2001-01-01

Background Fluorescence of many fungi is noted when H&E stained sections are examined under a fluorescent microscope. In theory, this phenomenon could aid in the diagnosis of cutaneous and disseminated fungal infections without the delay associated with special stains. Seventy-six cases of superficial and deep fungal infections and 3 cases of protothecosis were studied to determine the clinical usefulness of this technique. Results In most cases, fluorescence was noted, but was not intense. Fluorescence of fungi did not correlate with the age of the specimen. In most cases, organisms in H&E stained sections were more easily identified with routine light microscopy than with fluorescent microscopy. Conclusion This report suggests that in H&E stained skin specimens, fluorescent microscopy is of little benefit in the identification of fungal organisms. PMID:11602016

Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.

PubMed

Fuchino, Katsuya; Bagchi, Sonchita; Cantlay, Stuart; Sandblad, Linda; Wu, Di; Bergman, Jessica; Kamali-Moghaddam, Masood; Flärdh, Klas; Ausmees, Nora

2013-05-21

Intermediate filament (IF)-like cytoskeleton emerges as a versatile tool for cellular organization in all kingdoms of life, underscoring the importance of mechanistically understanding its diverse manifestations. We showed previously that, in Streptomyces (a bacterium with a mycelial lifestyle similar to that of filamentous fungi, including extreme cell and growth polarity), the IF protein FilP confers rigidity to the hyphae by an unknown mechanism. Here, we provide a possible explanation for the IF-like function of FilP by demonstrating its ability to self-assemble into a cis-interconnected regular network in vitro and its localization into structures consistent with a cytoskeletal network in vivo. Furthermore, we reveal that a spatially restricted interaction between FilP and DivIVA, the main component of the Streptomyces polarisome complex, leads to formation of apical gradients of FilP in hyphae undergoing active tip extension. We propose that the coupling between the mechanism driving polar growth and the assembly of an IF cytoskeleton provides each new hypha with an additional stress-bearing structure at its tip, where the nascent cell wall is inevitably more flexible and compliant while it is being assembled and matured. Our data suggest that recruitment of cytoskeleton around a cell polarity landmark is a broadly conserved strategy in tip-growing cells.

Transition from linear- to nonlinear-focusing regime in filamentation

PubMed Central

Lim, Khan; Durand, Magali; Baudelet, Matthieu; Richardson, Martin

2014-01-01

Laser filamentation in gases is often carried out in the laboratory with focusing optics to better stabilize the filament, whereas real-world applications of filaments frequently involve collimated or near-collimated beams. It is well documented that geometrical focusing can alter the properties of laser filaments and, consequently, a transition between a collimated and a strongly focused filament is expected. Nevertheless, this transition point has not been identified. Here, we propose an analytical method to determine the transition, and show that it corresponds to an actual shift in the balance of physical mechanisms governing filamentation. In high-NA conditions, filamentation is primarily governed by geometrical focusing and plasma effects, while the Kerr nonlinearity plays a more significant role as NA decreases. We find the transition between the two regimes to be relatively insensitive to the intrinsic laser parameters, and our analysis agrees well with a wide range of parameters found in published literature. PMID:25434678

COMPLEX FLARE DYNAMICS INITIATED BY A FILAMENT–FILAMENT INTERACTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Chunming; McAteer, R. T. James; Liu, Rui

2015-11-01

We report on an eruption involving a relatively rare filament–filament interaction on 2013 June 21, observed by SDO and STEREO-B. The two filaments were separated in height with a “double-decker” configuration. The eruption of the lower filament began simultaneously with a descent of the upper filament, resulting in a convergence and direct interaction of the two filaments. The interaction was accompanied by the heating of surrounding plasma and an apparent crossing of a loop-like structure through the upper filament. The subsequent coalescence of the filaments drove a bright front ahead of the erupting structures. The whole process was associated withmore » a C3.0 flare followed immediately by an M2.9 flare. Shrinking loops and descending dark voids were observed during the M2.9 flare at different locations above a C-shaped flare arcade as part of the energy release, giving us unique insight into the flare dynamics.« less

Spatial evolution of laser filaments in turbulent air

NASA Astrophysics Data System (ADS)

Zeng, Tao; Zhu, Shiping; Zhou, Shengling; He, Yan

2018-04-01

In this study, the spatial evolution properties of laser filament clusters in turbulent air were evaluated using numerical simulations. Various statistical parameters were calculated, such as the percolation probability, filling factor, and average cluster size. The results indicate that turbulence-induced multi-filamentation can be described as a new phase transition universality class. In addition, during this process, the relationship between the average cluster size and filling factor could be fit by a power function. Our results are valuable for applications involving filamentation that can be influenced by the geometrical features of multiple filaments.

Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

PubMed

Wang, Q-M; Begerow, D; Groenewald, M; Liu, X-Z; Theelen, B; Bai, F-Y; Boekhout, T

2015-06-01

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Proper horizontal photospheric flows below an eruptive filament

NASA Astrophysics Data System (ADS)

Schmieder, Brigitte; Mein, Pierre; Mein, Nicole; Roudier, Thierry; Chandra, Ramseh

An analysis of the proper motions using SDO/HMI continuum images with the new version of the coherent structure tracking (CST) algorithm developed to track the granules as well as the large scale photospheric flows, was perfomed during three hours in a region containing a large filament channel on September 17, 2010. Supergranules were idenfied in the filament channel. Diverging flows inside the supergranules are similar in and out the filament channel. Using corks, we derived the passive scalar points and produced maps of cork distribution. The anchorage structures with the photosphere (feet) of the filament are located in the areas of converging flows with accumulations of corks. Averaging the velocity vectors for each latitude we defined a profile of the differential rotation. We conclude that the coupling between the convection and magnetic field in the photosphere is relatively strong. The filament experienced the convection motions through its feet. On a large scale point-of-view the differential rotation induced a shear of 0.1 km/s in the filament. On a small scale point-of-view convection motions favored the interaction/cancellation of the parasitic polarities at the base of the feet with the surrounding network explaining the brightenings,/jets and the eruption that were observed in the EUV filament.

Measuring the regulation of keratin filament network dynamics

PubMed Central

Moch, Marcin; Herberich, Gerlind; Aach, Til; Leube, Rudolf E.; Windoffer, Reinhard

2013-01-01

The organization of the keratin intermediate filament cytoskeleton is closely linked to epithelial function. To study keratin network plasticity and its regulation at different levels, tools are needed to localize and measure local network dynamics. In this paper, we present image analysis methods designed to determine the speed and direction of keratin filament motion and to identify locations of keratin filament polymerization and depolymerization at subcellular resolution. Using these methods, we have analyzed time-lapse fluorescence recordings of fluorescent keratin 13 in human vulva carcinoma-derived A431 cells. The fluorescent keratins integrated into the endogenous keratin cytoskeleton, and thereby served as reliable markers of keratin dynamics. We found that increased times after seeding correlated with down-regulation of inward-directed keratin filament movement. Bulk flow analyses further revealed that keratin filament polymerization in the cell periphery and keratin depolymerization in the more central cytoplasm were both reduced. Treating these cells and other human keratinocyte-derived cells with EGF reversed all these processes within a few minutes, coinciding with increased keratin phosphorylation. These results highlight the value of the newly developed tools for identifying modulators of keratin filament network dynamics and characterizing their mode of action, which, in turn, contributes to understanding the close link between keratin filament network plasticity and epithelial physiology. PMID:23757496

Bundling of elastic filaments induced by hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Man, Yi; Page, William; Poole, Robert J.; Lauga, Eric

2017-12-01

Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a tight helical bundle. When the bacterium changes its direction, the flagellar filaments unbundle and randomly reorient the cell for a short period of time before returning to their bundled state and resuming swimming. This rapid bundling and unbundling is, at its heart, a mechanical process whereby hydrodynamic interactions balance with elasticity to determine the time-varying deformation of the filaments. Inspired by this biophysical problem, we present in this paper what is perhaps the simplest model of bundling whereby two or more straight elastic filaments immersed in a viscous fluid rotate about their centerline, inducing rotational flows which tend to bend the filaments around each other. We derive an integrodifferential equation governing the shape of the filaments resulting from mechanical balance in a viscous fluid at low Reynolds number. We show that such equation may be evaluated asymptotically analytically in the long-wavelength limit, leading to a local partial differential equation governed by a single dimensionless bundling number. A numerical study of the dynamics predicted by the model reveals the presence of two configuration instabilities with increasing bundling numbers: first to a crossing state where filaments touch at one point and then to a bundled state where filaments wrap along each other in a helical fashion. We also consider the case of multiple filaments and the unbundling dynamics. We next provide an intuitive physical model for the crossing instability and show that it may be used to predict analytically its threshold and adapted to address the transition to a bundling state. We then use a macroscale experimental implementation of the two-filament configuration in order to validate our theoretical predictions and obtain excellent agreement. This long

Energetics and kinetics of cooperative cofilin-actin filament interactions.

PubMed

Cao, Wenxiang; Goodarzi, Jim P; De La Cruz, Enrique M

2006-08-11

We have evaluated the thermodynamic parameters associated with cooperative cofilin binding to actin filaments, accounting for contributions of ion-linked equilibria, and determined the kinetic basis of cooperative cofilin binding. Ions weaken non-contiguous (isolated, non-cooperative) cofilin binding to an actin filament without affecting cooperative filament interactions. Non-contiguous cofilin binding is coupled to the dissociation of approximately 1.7 thermodynamically bound counterions. Counterion dissociation contributes approximately 40% of the total cofilin binding free energy (in the presence of 50 mM KCl). The non-contiguous and cooperative binding free energies are driven entirely by large, positive entropy changes, consistent with a cofilin-mediated increase in actin filament structural dynamics. The rate constant for cofilin binding to an isolated site on an actin filament is slow and likely to be limited by filament breathing. Cooperative cofilin binding arises from an approximately tenfold more rapid association rate constant and an approximately twofold slower dissociation rate constant. The more rapid association rate constant is presumably a consequence of cofilin-dependent changes in the average orientation of subdomain 2, subunit angular disorder and filament twist, which increase the accessibility of a neighboring cofilin-binding site on an actin filament. Cooperative association is more rapid than binding to an isolated site, but still slow for a second-order reaction, suggesting that cooperative binding is limited also by binding site accessibility. We suggest that the dissociation of actin-associated ions weakens intersubunit interactions in the actin filament lattice that enhance cofilin-binding site accessibility, favor cooperative binding and promote filament severing.

Large scale filaments associated with Milky Way spiral arms

NASA Astrophysics Data System (ADS)

Wang, Ke; Testi, Leonardo; Ginsburg, Adam; Walmsley, Malcolm; Molinari, Sergio; Schisano, Eugenio

2015-08-01

The ubiquity of filamentary structure at various scales through out the Galaxy has triggered a renewed interest in their formation, evolution, and role in star formation. The largest filaments can reach up to Galactic scale as part of the spiral arm structure. However, such large scale filaments are hard to identify systematically due to limitations in identifying methodology (i.e., as extinction features). We present a new approach to directly search for the largest, coldest, and densest filaments in the Galaxy, making use of sensitive Herschel Hi-GAL data complemented by spectral line cubes. We present a sample of the 9 most prominent Herschel filaments from a pilot search field. These filaments measure 37-99 pc long and 0.6-3.0 pc wide with masses (0.5-8.3)×104 Msun, and beam-averaged (28", or 0.4-0.7 pc) peak H2 column densities of (1.7-9.3)x1022 cm-2. The bulk of the filaments are relatively cold (17-21 K), while some local clumps have a dust temperature up to 25-47 K due to local star formation activities. All the filaments are located within <~60 pc from the Galactic mid-plane. Comparing the filaments to a recent spiral arm model incorporating the latest parallax measurements, we find that 7/9 of them reside within arms, but most are close to arm edges. These filaments are comparable in length to the Galactic scale height and therefore are not simply part of a grander turbulent cascade. These giant filaments, which often contain regularly spaced pc-scale clumps, are much larger than the filaments found in the Herschel Gould's Belt Survey, and they form the upper ends in the filamentary hierarchy. Full operational ALMA and NOEMA will be able to resolve and characterize similar filaments in nearby spiral galaxies, allowing us to compare the star formation in a uniform context of spiral arms.

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

PubMed Central

2013-01-01

Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

Hanging Filament

NASA Image and Video Library

2014-06-16

The Sun sported a very long filament that stretched out over 500,000 miles (800,000 km) and was visible for several days (June 3-4, 2014). It broke apart and dissipated soon after the end of the video clip. Filaments are tenuous strands of plasma held above the Sun's surface by magnetic forces. They appear darker because their temperature is somewhat cooler than that of the Sun's surface. The still image, shown in a combination of two wavelengths of extreme ultraviolet light, was taken at 11:33 UT on June 4. Credit: NASA/Goddard/Solar Dynamics Observatory NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Geometrical and Mechanical Properties Control Actin Filament Organization

PubMed Central

Ennomani, Hajer; Théry, Manuel; Nedelec, Francois; Blanchoin, Laurent

2015-01-01

The different actin structures governing eukaryotic cell shape and movement are not only determined by the properties of the actin filaments and associated proteins, but also by geometrical constraints. We recently demonstrated that limiting nucleation to specific regions was sufficient to obtain actin networks with different organization. To further investigate how spatially constrained actin nucleation determines the emergent actin organization, we performed detailed simulations of the actin filament system using Cytosim. We first calibrated the steric interaction between filaments, by matching, in simulations and experiments, the bundled actin organization observed with a rectangular bar of nucleating factor. We then studied the overall organization of actin filaments generated by more complex pattern geometries used experimentally. We found that the fraction of parallel versus antiparallel bundles is determined by the mechanical properties of actin filament or bundles and the efficiency of nucleation. Thus nucleation geometry, actin filaments local interactions, bundle rigidity, and nucleation efficiency are the key parameters controlling the emergent actin architecture. We finally simulated more complex nucleation patterns and performed the corresponding experiments to confirm the predictive capabilities of the model. PMID:26016478

Recruitment Kinetics of Tropomyosin Tpm3.1 to Actin Filament Bundles in the Cytoskeleton Is Independent of Actin Filament Kinetics.

PubMed

Appaduray, Mark A; Masedunskas, Andrius; Bryce, Nicole S; Lucas, Christine A; Warren, Sean C; Timpson, Paul; Stear, Jeffrey H; Gunning, Peter W; Hardeman, Edna C

2016-01-01

The actin cytoskeleton is a dynamic network of filaments that is involved in virtually every cellular process. Most actin filaments in metazoa exist as a co-polymer of actin and tropomyosin (Tpm) and the function of an actin filament is primarily defined by the specific Tpm isoform associated with it. However, there is little information on the interdependence of these co-polymers during filament assembly and disassembly. We addressed this by investigating the recovery kinetics of fluorescently tagged isoform Tpm3.1 into actin filament bundles using FRAP analysis in cell culture and in vivo in rats using intracellular intravital microscopy, in the presence or absence of the actin-targeting drug jasplakinolide. The mobile fraction of Tpm3.1 is between 50% and 70% depending on whether the tag is at the C- or N-terminus and whether the analysis is in vivo or in cultured cells. We find that the continuous dynamic exchange of Tpm3.1 is not significantly impacted by jasplakinolide, unlike tagged actin. We conclude that tagged Tpm3.1 may be able to undergo exchange in actin filament bundles largely independent of the assembly and turnover of actin.

Terrestrial and marine Antarctic fungi extracts active against Xanthomonas citri subsp. citri.

PubMed

Vieira, G; Purić, J; Morão, L G; Dos Santos, J A; Inforsato, F J; Sette, L D; Ferreira, H; Sass, D C

2018-07-01

This study aims to obtain secondary metabolites extracts from filamentous fungi isolated from soil and marine sediments from Antarctica and assess its potential antibacterial activity on Xanthomonas citri subsp. citri, the agent of citrus canker. Metabolites production was conducted in Malt 2% broth at 15°C for 20 days after which intracellular and extracellular extracts were obtained. The extracts were evaluated by cell viability assays through Resazurin Microtitre Assay. From 158 fungal extracts, 33 hampered bacterial growth in vitro. The average inhibition of the extracts obtained from terrestrial (soil) and marine (sediments) fungi was 94 and 97% respectively. These inhibition values were close to the average of 90% cell death for the positive control. MIC90 and MBC for the bioactive extracts were established. Isolates that produced active metabolites against the phytopathogen were identified using molecular taxonomy (ITS-rRNA sequencing) as: Pseudogymnoascus, Penicillium, Cadophora, Paraconiothyrium and Toxicocladosporium. Antarctic fungal strains isolated from terrestrial and marine sediments were able to produce secondary metabolites with antimicrobial activity against X. citri subsp. citri, highlighting the importance of these microbial genetic resources. These metabolites have potential to be used as alternatives for the control of this plant pathogen. This manuscript makes an impact on the study of micro-organisms from extreme habitats and their possible contribution in discovering new active molecules against pathogens of agricultural interest. Studies on the Antarctic continent and its communities have attracted the scientific community due to the long period of isolation and low levels of disturbance that surrounds the region. Knowing the potential of fungi in this region to produce active secondary metabolites, we aim to contribute to the discovery of compounds with antibacterial action in Xanthomonas citri subsp. citri, a plant pathogen present in

Mechanical model for filament buckling and growth by phase ordering.

PubMed

Rey, Alejandro D; Abukhdeir, Nasser M

2008-02-05

A mechanical model of open filament shape and growth driven by phase ordering is formulated. For a given phase-ordering driving force, the model output is the filament shape evolution and the filament end-point kinematics. The linearized model for the slope of the filament is the Cahn-Hilliard model of spinodal decomposition, where the buckling corresponds to concentration fluctuations. Two modes are predicted: (i) sequential growth and buckling and (ii) simultaneous buckling and growth. The relation among the maximum buckling rate, filament tension, and matrix viscosity is given. These results contribute to ongoing work in smectic A filament buckling.

Fungi in space--literature survey on fungi used for space research.

PubMed

Kern, V D; Hock, B

1993-09-01

A complete review of the scientific literature on experiments involving fungi in space is presented. This review begins with balloon experiments around 1935 which carried fungal spores, rocket experiments in the 1950's and 60's, satellite and moon expeditions, long-time orbit experiments and Spacelab missions in the 1980's and 90's. All these missions were aimed at examining the influence of cosmic radiation and weightlessness on genetic, physiological, and morphogenetic processes. During the 2nd German Spacelab mission (D-2, April/May 1993), the experiment FUNGI provided the facilities to cultivate higher basidiomycetes over a period of 10 d in orbit, document gravimorphogenesis and chemically fix fruiting bodies under weightlessness for subsequent ultrastructural analysis. This review shows the necessity of space travel for research on the graviperception of higher fungi and demonstrates the novelty of the experiment FUNGI performed within the framework of the D-2 mission.

Kinetic analysis of F-actin depolymerization in polymorphonuclear leukocyte lysates indicates that chemoattractant stimulation increases actin filament number without altering the filament length distribution

PubMed Central

1991-01-01

The rate of filamentous actin (F-actin) depolymerization is proportional to the number of filaments depolarizing and changes in the rate are proportional to changes in filament number. To determine the number and length of actin filaments in polymorphonuclear leukocytes and the change in filament number and length that occurs during the increase in F-actin upon chemoattractant stimulation, the time course of cellular F-actin depolymerization in lysates of control and peptide- stimulated cells was examined. F-actin was quantified by the TRITC- labeled phalloidin staining of pelletable actin. Lysis in 1.2 M KCl and 10 microM DNase I minimized the effects of F-actin binding proteins and G-actin, respectively, on the kinetics of depolymerization. To determine filament number and length from a depolymerization time course, depolymerization kinetics must be limited by the actin monomer dissociation rate. Comparison of time courses of depolymerization in the presence (pointed ends free) or absence (barbed and pointed ends free) of cytochalasin suggested depolymerization occurred from both ends of the filament and that monomer dissociation was rate limiting. Control cells had 1.7 +/- 0.4 x 10(5) filaments with an average length of 0.29 +/- 0.09 microns. Chemo-attractant stimulation for 90 s at room temperature with 0.02 microM N-formylnorleucylleucylphenylalanine caused a twofold increase in F-actin and about a two-fold increase in the total number of actin filaments to 4.0 +/- 0.5 x 10(5) filaments with an average length of 0.27 +/- 0.07 microns. In both cases, most (approximately 80%) of the filaments were quite short (less than or equal to 0.18 micron). The length distributions of actin filaments in stimulated and control cells were similar. PMID:1918158

Fungi isolated from flue-cured tobacco inoculated in the field with storage fungi.

PubMed

Welty, R E

1971-03-01