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Bioluminescent fungi from Peninsular Malaysia-a taxonomic and phylogenetic overview

Fungal Diversity 2015年第1期70卷 149-187页

作者： Audrey L.C.Chew dennis e.desjardin Yee-Shin Tan Md Yusoff Musa Vikineswary Sabaratnam Mushroom Research Centre University of Malaya50603 Kuala LumpurMalaysia Institute of Biological Sciences Faculty of ScienceUniversity of Malaya50603 Kuala LumpurMalaysia Department of Biology San Francisco State University1600 Holloway Ave.San FranciscoCA 94132USA

Fifteen bioluminescent fungi recently collected from Peninsular Malaysia are analysed *** phylogeny of the Malaysian bioluminescent fungi and closely related taxa were evaluated with molecular data from the nuclear ribosomal large subunit(LSU),RNA polymerase 2 second largest subunit(RPB2)and internal transcribed spacers(ITS)gene *** sequences data support the circumscription of species based on the morphological species concept,but was unable to fully support the current sectional delimitation of genus *** the 15 taxa analysed here,four are novel species described herein,*** gombakensis,***,*** and Panellus luxfilamentus;while four taxa of Mycena *** were recently described as *** species(***)represents a new distribution record to Peninsular Malaysia,and six species(Neonothopanus nambi,Filoboletus manipularis,***,Roridomyces pruinosoviscidus,*** and ***)have been previously *** pruinosoviscidus is accepted as a new combination based on morphological and phylogenetic *** morphology data indicate its potential for taxon delimitation as axenic cultures of each species produced unique and distinguishable *** descriptions,illustrations and photographs are provided on basidiome and culture morphology.A key to aid in species identification,comparisons with allied species and data on basidiome and mycelium luminescence are also *** study gives the first report on mycelial luminescence for ***,***,*** as well as all new species described *** reports in this study bring the total known luminescent fungi worldwide to 81 species.

关键词： Basidiomycete Biodiversity Culture morphology Filoboletus Mycena Neonothopanus Panellus Phylogeny Roridomyces Systematics Taxonomy

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A monograph of Micropsalliota in Northern Thailand based on morphological and molecular data

A monograph of Micropsalliota in Northern Thailand based on ...

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2012年中国菌物学会学术年会

作者： dennis e.desjardin Kasem Soytong Brian A.Perry Kevin D.Hyde Department of Biology San Francisco State UniversitySan FranciscoCalifornia 94132USA Faculty of Agricultural Technology King Mongkut's Institute of Technology Ladkrabang(KMITL)LadkrabangBangkok 10520Thailand School of Science Mae Fah Luang UniversityTasudChiang Rai 57100Thailand Visiting Professor Botany and Microbiology DepartmentCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia

＜正＞Using a combination of morphological and molecular data,the genus Micropsalliota is shown to represent a monophyletic lineage in the Agaricaceae sister to *** that distinguish the genus from Agaricus and allied genera include usually small,gracile basidiomes with a membranous partial veil, dextrinoid basidiospores with an apically thickened endosporium and lack of a germ pore,capitate or subcapitate, conspicuous cheilocystidia,and incrusted pileipellis hyphae that turn green in ammonia *** provide a monographic treatment of 23 taxa of Micropsalliota from Northern Thailand,of which 13 taxa represent new distribution reports for Thailand and 10 represent new taxa,including ***,***,***,M. lateritia ***,***,***,***,*** var. rubrobrunnescens,*** ***,and *** in this monograph are comprehensive descriptions,illustrations of micromorphological features,photographs of basidiomes,comparisons with allied species,phylogenetic trees inferring relationships amongst Thai species based on nrITS and nrLSU sequence datasets,and a key to aid in diagnosis.

关键词： Agaricaceae Agaricus Hymenagaricus phylogenetic analyses taxonomy tropics

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Major clades in tropical Agaricus

Major clades in tropical Agaricus

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中国菌物学会第五届会员代表大会暨2011年学术年会

作者： Samantha KARUNARATHNA Olivier.RASP Luis A.PARRA Jacque GUINBeRTeAU Magalie MOINARD Andre De KeSeL Grard.BARROSO Rgis COURTeCUISSe Kevin D.HYDe Atsu K.GUeLLY dennis e.desjardin Philippe CALLAC School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Botany and Microbiology Department College of ScienceKing Saud UniversityRiyadh 11442Saudi Arabia

＜正＞Agaricus（Basidiomycota） is a genus of saprobic fungi that includes edible cultivated species such as Agaricus bisporus,the button *** has been considerable ecological,nutritional and medicinal interest in the genus,yet its biodiversity remains poorly known,particularly in subtropical and tropical areas. Classification of the tropical taxa has for a large part followed the classification of temperate *** objective of our study was to examine to what extent this system of classification is appropriate for tropical Agaricus *** from temperate sections were therefore compared to the major clades of tropical taxa using a phylogenetic *** 1+2 sequence data from 128 taxa were used in the phylogenetic analysis. Specimens included four species of genera closely related to Agaricus,37 temperate species representing the eight classical sections of the genus,and 87 putative species of Agaricus from tropical areas of Africa,Asia and *** and maximum likelihood analyses produced relatively congruent trees and almost identical *** data showed that（i） only about one-third of tropical taxa belong to the classical sections;the systematics of the genus therefore needs to be reconsidered;（ii） basal clades and branches contain only African and Asian tropical taxa suggesting that the genus originated from these areas;（iii） among the remaining two-thirds of tropical taxa,those from America and those from Africa and/or Asia grouped in distinct clades,suggesting that secondary diversification occurred in these two areas and that direct migration between these areas has never or rarely occurred;（iv） in contrast,several clades of classical sections contain American and African+Asian species along with temperate *** two conclusions added to the fact that the distribution range of some temperate species extends to both europe and North America,suggest that the genus would have migrated from tropical Africa +Asia to tropical

关键词： Agaricus tropical biodiversity biogeography ITS phylogeny

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Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

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Fungal Diversity 2014年第1期64卷 1-99页

作者： D.Jean Lodge Mahajabeen Padamsee P.Brandon Matheny M.Catherine Aime Sharon A.Cantrell David Boertmann Alexander Kovalenko Alfredo Vizzini Bryn T.M.Dentinger Paul M.Kirk A.Martyn Ainsworth Jean-Marc Moncalvo Rytas Vilgalys ellen Larsson Robert Lücking Gareth W.Griffith Matthew e.Smith Lorelei L.Norvell dennis e.desjardin Scott A.Redhead Clark L.Ovrebo edgar B.Lickey enrico ercole Karen W.Hughes Régis Courtecuisse Anthony Young Manfred Binder Andrew M.Minnis Daniel L.Lindner Beatriz Ortiz-Santana John Haight Thomas Læssøe Timothy J.Baroni József Geml Tsutomu Hattori Center for Forest Mycology Research Northern Research StationUSDA-Forest ServiceLuquilloPR 00773-1377USA Systematics Team Landcare Research231 Morrin RoadAuckland 1072New Zealand ecology&evolutionary Biology University of TennesseeKnoxvilleTN 37996-1610USA Department of Botany&Plant Pathology Purdue UniversityWest LafayetteIN 47907USA Science and Technology Universidad del TuraboGuraboPR 00778-3030USA Department of Bioscience Aarhus UniversityFrederiksborgvej 399DK-4000 RoskildeDenmark Komarov Botanical Institute of the Russian Academy of Sciences 2 Prof.Popov Str.St.Petersburg 197376Russia Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale P.A.Mattioli 2510125 TorinoItaly Mycology Royal Botanic GardensKewRichmondSurrey TW93DSUK Royal Ontario Museum 100 Queen’s ParkTorontoONCanada Biology Department Duke UniversityDurhamNC 27708-0338USA Biological&environmental Sciences University of GothenburgGöteborgSweden Science&eduaction Integrative Research&Collections(Botany)The Field Museum of Natural History1400 Lake Shore Dr.ChicagoIL 60605-2496USA University of Wales AberystwythCeredigion SY233DDUK Department of Plant Pathology University of FloridaGainesvilleFL 32611-0680USA Pacific Northwest Mycology Service 6720 NW Skyline BvdPortlandOR 97229-1309USA Department of Biology San Francisco State University1600 Holloway Ave.San FranciscoCA 94132USA National Mycological Herbarium(DAOM) Science and Technology BranchAgriculture&Agri-FoodsCanada960 Carling AvenueOttawaOntarioCanada ONT K1A 0C6 Department of Biology University of Central OklahomaEdmondOK 73034USA Department of Biology Bridgewater College402 E.College St.BridgewaterVA 22812USA Department of Botany Faculty of Pharmaceutical&Biological SciencesLilleFrance 100 Langton Road BlackbuttQld 4306Australia CBS Fungal Biodiversity Centre Evolutionary PhytopathologyInst.of the Royal Netherlands Academy of Arts&Sciences(KNAW)Uppsalalaan 83584 CT UtrechtThe Netherlands

Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family *** phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are:Acantholichen,Ampulloclitocybe,Arrhenia,Cantharellula,Cantharocybe,Chromosera,Chrysomphalina,Cora,Corella,Cuphophyllus,Cyphellostereum,Dictyonema,eonema,Gliophorus,Haasiella,Humidicutis,Hygroaster,Hygrocybe,Hygrophorus,Lichenomphalia,Neohygrocybe,Porpolomopsis and Pseudoarmillariella.A new genus that is sister to Chromosera is described as *** were made at the ranks of subfamily,tribe,genus,subgenus,section and *** present three new subfamilies,eight tribes(five new),eight subgenera(one new,one new combination and one ***.),26 sections(five new and three new combinations and two ***.)and 14 subsections(two new,two ***.).Species of Chromosera,Gliophorus,Humidicutis,and Neohygrocybe are often treated within the genus Hygrocybe;we therefore provide valid names in both classification *** used a minimalist approach in transferring genera and creating new names and ***,we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus,Ampulloclitocybe andCantharocybe,despite weak phylogenetic *** include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are *** lower hygrophoroid clade is basal to Hygrophoraceae s.s.,comprising the genera Aphroditeola,Macrotyphula,Phyllotopsis,Pleurocybella,Sarcomyxa,Tricholomopsis and Typhula.

关键词： Hygrophoraceae Fungi Revisionary systematics Nomenclatural revision Phylogenetics Pigment chemistry Lamellar trama construction Hymenial morphology ecology

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Neural Regeneration Research 2025年第2期20卷 366-377页

作者： Samuel Abokyi dennis Yan-yin Tse School of Optometry The Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina Research Center for SHARP Vision The Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina Center for eye and Vision Research Sha TinHong Kong Special Administrative RegionChina

Retinal aging has been recognized as a significant risk factor for various retinal disorders,including diabetic retinopathy,age-related macular degeneration,and glaucoma,following a growing understanding of the molecular underpinnings of their *** comprehensive review explores the mechanisms of retinal aging and investigates potential neuroprotective approaches,focusing on the activation of transcription factor *** meta-analyses have demonstrated promising outcomes of transcription factor eB-targeted strategies,such as exercise,calorie restriction,rapamycin,and metformin,in patients and animal models of these common retinal *** review critically assesses the role of transcription factor eB in retinal biology during aging,its neuroprotective effects,and its therapeutic potential for retinal *** impact of transcription factor eB on retinal aging is cell-specific,influencing metabolic reprogramming and energy homeostasis in retinal neurons through the regulation of mitochondrial quality control and nutrient-sensing *** vascular endothelial cells,transcription factor eB controls important processes,including endothelial cell proliferation,endothelial tube formation,and nitric oxide levels,thereby influencing the inner blood-retinal barrier,angiogenesis,and retinal ***,transcription factor eB affects vascular smooth muscle cells,inhibiting vascular calcification and *** retinal pigment epithelial cells,transcription factor eB modulates functions such as autophagy,lysosomal dynamics,and clearance of the aging pigment lipofuscin,thereby promoting photoreceptor survival and regulating vascular endothelial growth factor A expression involved in *** cell-specific functions of transcription factor eB significantly impact retinal aging mechanisms encompassing proteostasis,neuronal synapse plasticity,energy metabolism,microvasculature,and inflammation,ultimately offering pro

关键词： age-related macular degeneration anti-aging interventions autophagy calorie restriction diabetic retinopathy exercise glaucoma neuromodulation phagocytosis photoreceptor outer segment degradation retinal aging transcription factor eB

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Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2008年第10期9卷 779-786页

作者： Rui-lin ZHAO dennis e. desjardin Kasem SOYTONG Kevin D. HYDe Faculty of Biology Conservation Southwest Forestry University Kunming 650224 China Department of Biology San Francisco State University San Francisco California 94132 USA Faculty of Agricultural Technology King Mongkut＇s Institute of Technology Ladkrabang （KMITL） Ladkrabang Bangkok 10520 Thailand International Fungal Resource and Development Centre the Research Institute of Resources Insects Chinese Academy of Forestry Kunming 650224 China Fungal Research Group School of Science Mae Fah Luang University Tasud Chiang Rai 57100 Thailand

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.

关键词： Gene Molecular Mushrooms Phylogeny

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Asymptotic false discovery control of the Benjamini-Hochberg procedure for pairwise comparisons

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Science China Mathematics 2025年第1期 223-252页

作者： Weidong Liu dennis Leung Qi-Man Shao School of Mathematical Sciences Shanghai Jiao Tong University School of Mathematics and Statistics University of Melbourne Department of Statistics and Data Science SICMSouthern University of Science and Technology

In a one-way analysis-of-variance(ANOVA) model,the number of pairwise comparisons can become large even with a moderate number of *** by this,we consider a regime with a growing number of groups and prove that,when testing pairwise comparisons,the Benjamini-Hochberg(BH) procedure can asymptotically control false discoveries,despite the fact that the involved t-statistics do not exhibit the wellknown positive dependence structure required for exact false discovery rate(FDR) *** Tukey's perspective that the difference between the means of any two groups cannot be exactly zero,our main result provides control over the directional false discovery rate and directional false discovery proportion.A key technical contribution of our work is demonstrating that the dependence among the t-statistics is sufficiently weak to establish the convergence result typically required for asymptotic FDR *** analysis does not rely on conventional assumptions such as normality,variance homogeneity,or a balanced design,thereby offering a theoretical foundation for applications in more general settings.

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Nuclear mechanics during constricted migration

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Acta Mechanica Sinica 2019年第2期35卷 299-308页

作者： Yuntao Xia Charlotte R. Pfeifer dennis e. Discher Physical Sciences Oncology Center at Pennsylvania (PSOC@Penn) University of Pennsylvania PhiladelphiaPA 19104USA Molecular and Cell Biophysics Lab University of PennsylvaniaPhiladelphiaPA 19104 USA Department of Physics and Astronomy University of Pennsylvania Philadelphia PA 19104USA

Cell migration through narrow interstitial space in tissues is commonly seen in both physiological and pathological conditions. For example, immune cells have to squeeze through vasculature and extracellular matrix to reach the wound or diseased sites, and similarly cancer cells need to crawl through porous space in tissues to invade surrounding tumor-free regions. Therefore, the bulky stiff nucleus in the cell becomes a barrier during constricted migration making such process pore-size dependent with smaller pores exponentially alleviate the passage capability. However, in some cases, cells can actively deform their nuclei to squeeze through constrictions although some price needs to be paid. In this review, we focus on:(1) nuclear structures and morphological regulations,(2) proposed mechanisms that drive constricted migration,(3) short-term consequences such as nuclear envelope (Ne) rupture and DNA damage during such process,(4) biophysical factors that facilitate Ne rupture, and (5) long term consequences such as genomic variation caused by repetitive Ne rupture. Both experimental results and modeling are provided with the intention to better understand the constricted migration.

关键词： Constricted migration Nuclear envelope rupture DNA damage

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Chemical biology: a toolbox to unlock neurochemical epigenetics?

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Neural Regeneration Research 2021年第2期16卷 298-299页

作者： dennis Ozcelik Center for Biopharmaceuticals Department of Drug Design and PharmacologyUniversity of CopenhagenCopenhagenDenmark Department of Chemistry and Biomolecular Sciences University of OttawaOttawaOntarioCanada

The complex challenges of studying neurochemistry: Neurochemistry comprises the molecular and biochemical roles of a vast variety of chemical compounds, including amino acids, peptides, gaseous molecules, and small mo... 详细信息

关键词： chemical chemistry gaseous

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Principles to Support Modular Software Construction

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Journal of Computer Science & Technology 2017年第1期32卷 3-10页

作者： Jack B. dennis Department of electrical engineering and Computer Science Massachusetts Institute of Technology Cambridge MA 02139 U.S.A.

The construction of large software systems is always achieved through assembly of independently written components -- program modules. For these software components to work together, they must share a common set of data types and principles for representing structured data such as arrays of values and files. This common set of tools for creating and operating on data objects is provided by the infrastructure of the computer system： the hardware, operating system and runtime code. Because the nature and properties of these tools are crucial for correct operation of software components and their inter-operation, it is essential to have a precise specification that may be used for verifying correctness of application software on one hand, and to verify correctness of system behavior on the other. We call such a specification a program execution model （PXM）. It is evident that the properties of the PXM implemented by a computer system can have serious impact on the ability of application programmers to practice modular software construction. This paper discusses the concept of program execution models and presents a set of principles that a PXM must satisfy to provide a sound basis for modular software construction. Because parallel program execution on computer systems with many processing units is an essential part of contemporary computing environments, the expression of parallelism and modular software construction using components involving parallel operations is included in this treatment. The conclusion is that it is possible to build computer systems that implement a PXM within which any parallel program may be used, unmodified, as a component for building more substantial parallel programs.

关键词： program execution model data flow model codelet abstract architecture parallel computing

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