Publications by authors named "Josef Vlasák"

44 Publications

Molecular Phylogeny and Global Diversity of the Genus (Polyporales, Basidiomycota).

J Fungi (Basel) 2021 Jan 29;7(2). Epub 2021 Jan 29.

Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.

Phylogeny and taxonomy of the genus were carried out based on a larger number of samples covering a wider geographic range including East Asia, South Asia, Europe, and America, and the species diversity of the genus is updated. Four species, , , and , are described as new species based on morphology and molecular phylogenetic analyses inferred from the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), and the small subunit mitochondrial rRNA gene (mtSSU). is characterized by the distinctly different colors between the pore surface and the tubes, small pores measuring 5-7 per mm, and narrow basidiospores measuring 10.5-11.9 × 4.5-5 µm; differs from other species in the genus by its large pores measuring 2-3 per mm, hyphae at dissepiment edge with simple septum, and the long basidiospores (up to 22 µm); is distinguished by its cushion-shaped basidiocarps, wide fusiform cystidioles with a simple septum at the tips, the absence of dendrohyphidia and the cylindrical to slightly allantoid basidiospores measuring 9-10.8 × 3.8-5 µm; is characterized by its perennial habit, small pores measuring 4-5 per mm, dextrinoid skeletal hyphae, the presence of cystidioles and dendrohyphidia. An identification key to accepted species of is provided.
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http://dx.doi.org/10.3390/jof7020096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912676PMC
January 2021

Two new species, transference, notes, and new record in South American Acanthocinini (Coleoptera, Cerambycidae, Lamiinae).

Zootaxa 2020 May 20;4779(3):zootaxa.4779.3.4. Epub 2020 May 20.

207 Silverbrook Drive, Schwenksville, PA 19473, U.S.A..

Two new species are described from Ecuador: Anisopodus flavomarginatus, and Leptocometes brevicornis. Hyperplatys argus (Bates, 1872) is transferred to its original genus: Anisopodus White, 1855. Comments regarding the type locality of Hylettus eremita (Erichson, 1847) and variation of pronotal and elytral pubescence pattern in the species are provided. The species is reported from Colombia for the first time. The type locality, number of specimens in the original description, and institution depositary of the syntypes of Astynomus sallei Candèze (1861 (= H. eremita) are discussed.
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http://dx.doi.org/10.11646/zootaxa.4779.3.4DOI Listing
May 2020

New species of Cerambycinae and Lamiinae from Ecuador and Honduras, with transference of a species of Rhinotragini (Coleoptera, Cerambycidae).

Zootaxa 2020 Mar 9;4748(3):zootaxa.4748.3.3. Epub 2020 Mar 9.

207 Silverbrook Drive, Schwenksville, PA 19473, U.S.A..

Three new species are described from Ecuador: Scythropopsis granitica (Lamiinae, Acanthoderini); Apeba danielvlasaki (Lamiinae, Hemilophini); and Giesberteclipta unicolor (Cerambycinae, Rhinotragini). Two new species are described from Honduras: Anelaphus rotundus (Cerambycinae, Elaphidiini); and Euderces hefferni (Cerambycinae, Tillomorphini). A key to species of Apeba Martins Galileo, 1991, and Giesberteclipta Santos-Silva et al., 2012 are provided. Euderces hefferni sp. nov. is included in a previous key. Rashelapso morrisoni Bezark Santos-Silva, 2016 is transferred to Giesberteclipta. The holotype of Anelaphus subinermis Linsley, 1957 is illustrated for the first time.
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http://dx.doi.org/10.11646/zootaxa.4748.3.3DOI Listing
March 2020

A new species of Elaphidion Audinet-Serville, 1834, from Antigua and comparison with E. excelsum Gahan, 1895, from Guadeloupe (Coleoptera: Cerambycidae: Elaphidiini).

Authors:
Josef Vlasak

Zootaxa 2019 Oct 23;4688(3):zootaxa.4688.3.10. Epub 2019 Oct 23.

207 Silverbrook Drive, Schwenksville, PA 19473, U.S.A..

A new species of Elaphidion, E. antiguensis sp. nov. is described from Antigua (West Indies). The host plants and larval biology of E. antiguensis are described and compared to those of E. excelsum, Gahan.
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http://dx.doi.org/10.11646/zootaxa.4688.3.10DOI Listing
October 2019

Morphological plasticity in brown-rot fungi: is redefined to encompass both poroid and corticioid species.

Mycologia 2019 Sep-Oct;111(5):871-883. Epub 2019 Aug 21.

Natural History Museum, University of Oslo , P.O. Box 1172, NO-0318 Oslo , Norway.

Most known brown rot-producing species of Polyporales belong to the so-called "Antrodia clade" that largely consists of poroid species. In this study, we use three genetic markers to revise s. str., the core group of this clade. We show that a corticioid species with a smooth hymenophore, , belongs to s. str. Accordingly, we revise the generic concept of s. str. to accommodate this species and two recently described poroid taxa, and . In addition, we describe two new poroid species within s. str., from Africa and from East Asia, and provide new documentation for the Southeast Asian species based on recent collections from the type location.
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http://dx.doi.org/10.1080/00275514.2019.1640532DOI Listing
March 2020

Phylogeny and diversity of (Polyporaceae, Basidiomycota).

MycoKeys 2019 12;54:77-98. Epub 2019 Jun 12.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.

Four species of , , , and are described as new and is proposed as a new combination, based on morphological characteristics and molecular phylogenetic analyses inferred from internal transcribed spacer (ITS) and large subunit nuclear ribosomal RNA gene (nLSU) sequences. , and occur in China, occurs in the USA, and the distribution of is extended from New Zealand to Australia. is characterized by the distinct narrow oblong basidiospores measuring 10.5-13.5 × 3.9-5 µm. is characterized by the presence of ventricose cystidioles occasionally with a simple septum, dissepimental hyphae usually with a simple septum, unique thick-walled basidia and distinctly wide oblong basidiospores measuring 13.5-16.5 × 7.5-9.5 µm. is characterized by its large pores (2-3 per mm), a dimitic hyphal structure with non-dextrinoid skeletal hyphae and wide oblong basidiospores measuring 12-15 × 6-8 µm. is characterized by distinctly small pores (7-9 per mm), the presence of dendrohyphidia, and distinctly small ellipsoid basidiospores measuring 5.3-6.7 × 3-4.1 µm. is proposed as a new combination. is shown to be a synonym of and is considered a synonym of .
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http://dx.doi.org/10.3897/mycokeys.54.34362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584150PMC
June 2019

Phylogeny of the genus and taxonomic assessment of the group.

Mycologia 2019 May-Jun;111(3):423-444. Epub 2019 Apr 9.

a Beijing Advanced Innovation Center for Tree Breeding by Molecular Design , Beijing Forestry University , Beijing 100083 , China.

The genus of the Hymenochaetaceae is characterized by resupinate to pileate basidiocarps, a dimitic hyphal system with fine crystal aggregates and encrusted generative hyphae in dissepiment edge and tube trama, the presence of hymenial setae, and hyaline, thin-walled, smooth basidiospores. Members of the group are easy to distinguish from other species of because of the moderately large pores, presence of mycelial setae, and large hymenial setae. Here, we explore phylogenetic relationships among 20 species of based on examination of some 90 collections sampled worldwide. Seven new species are recognized in the group-, and -described from China, Costa Rica, Mexico, and the United States. Phylogenetic analyses inferred from DNA sequences of the nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), D1-D2 domains of nuc 28S rDNA (28S), and translation elongation factor EF-1 alpha () support the group as one of two major clades within comprising nine species worldwide.
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http://dx.doi.org/10.1080/00275514.2019.1570749DOI Listing
April 2020

Phylogeny and global diversity of Porodaedalea, a genus of gymnosperm pathogens in the Hymenochaetales.

Mycologia 2019 Jan-Feb;111(1):40-53. Epub 2019 Jan 14.

a Beijing Advanced Innovation Center for Tree Breeding by Molecular Design , Beijing Forestry University , Beijing 100083, China.

Porodaedalea is a polypore genus of the Hymenochaetales that encompasses pathogens of conifer trees. In this study, we conduct a comprehensive study of the phylogeny and diversity of Porodaedalea based on collections and isolates from Europe, North America, North Africa, and Asia. Phylogenetic analysis of a two-gene data set, nuc ribosomal DNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) and translation elongation factor 1-alpha (tef1), shows that 20 terminal clades that correspond to phylogenetic species well supported within Porodaedalea. Based on morphological evidence, five new species, P. alpicola, P. indica, P. kesiyae, P. microsperma, and P. yunnanensis, are described and illustrated. In addition, four still unnamed lineages are detected in North America and East Asia.
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http://dx.doi.org/10.1080/00275514.2018.1526618DOI Listing
May 2019

New genus, species, redescription, and new rank in Cerambycinae (Coleoptera, Cerambycidae).

Zootaxa 2018 Jul 18;4446(3):384-396. Epub 2018 Jul 18.

207 Silverbrook Drive, Schwenksville, PA 19473, U.S.A..

Two new species of Cerambycidae are described from Costa Rica: Cosmisoma luteoviridis sp. nov. (Rhopalophorini) and Katerinaella costaricensis gen. nov. and sp. nov. (Rhinotragini). Trachyderes (Dendrobias) Dupont, 1834 is restored to genus level. Male specimens of Dendrobias steinhauseni (Hüdepohl, 1987) from Nicaragua and Costa Rica are described and illustrated. The relationship of D. steinhauseni with other Dendrobias species is discussed.
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http://dx.doi.org/10.11646/zootaxa.4446.3.5DOI Listing
July 2018

Taxonomy and phylogeny of Pyrrhoderma: a redefinition, the segregation of Fulvoderma, gen. nov., and identifying four new species.

Mycologia 2018 Sep-Oct;110(5):872-889. Epub 2018 Sep 21.

c Institute of Microbiology, PO Box 61 , Beijing Forestry University , Beijing 100083 , China.

Previously, Pyrrhoderma accommodated two polypore species, P. adamantinum and P. scaurum; however, phylogenetic studies indicated that these two species were not congeneric within the Hymenochaetaceae and that P. adamantinum formed a clade with Phellinidium noxium. To resolve the relationships among the two species of Pyrrhoderma and other related taxa, specimens from China, Costa Rica, Singapore, and Thailand were studied from both morphological and phylogenetic perspectives. A new genus, Fulvoderma, is erected to accommodate F. scaurum comb. nov., and a new species, F. australe (the generic type). Pyrrhoderma is delimited to include the generic type, P. sendaiense (a later synonym of P. adamantinum); two new combinations, P. lamaënse comb. nov., and P. noxium comb. nov.; and three new species, P. hainanense, P. thailandicum, and P. yunnanense. In addition, an undescribed lineage including several specimens from subtropical and tropical forests in China, Costa Rica, Singapore, and Thailand also nested within the Pyrrhoderma clade. However, as the voucher specimens are sterile or almost so, they are not described. The concept of Pyrrhoderma was emended to also accommodate species bearing resupinate, effuse-reflexed basidiocarps, hymenial or hyphoid setae, and non-subglobose basidiospores. Keys to Fulvoderma and Pyrrhoderma are provided.
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http://dx.doi.org/10.1080/00275514.2018.1474326DOI Listing
March 2019

Three new species of (Hymenochaetales, Basidiomycota) based on the evidence from morphology and DNA sequence data.

MycoKeys 2018 8(30):73-89. Epub 2018 Mar 8.

Beijing advanced innovation center for tree breeding by molecular design, Beijing Forestry University, Beijing 100083, PR China.

, and are described and illustrated as new species based on morphological characters and molecular evidence. They have annual to perennial, mostly resupinate basidiomata with grayish fresh pores, an indistinct subiculum, lack any kind of setae, have brownish, thick-walled basidiospores, and cause a white rot. The distinctive morphological characters of the new species and their related species are discussed. Phylogenies based on the nuclear ribosomal large subunit (28S) and the nuclear ribosomal ITS region show that these three new species form three distinct lineages in the clade. A key to known species of is given.
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http://dx.doi.org/10.3897/mycokeys.30.23109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904509PMC
March 2018

Resolution of phylogenetic position of Nigrofomitaceae within Hymenochaetales (Basidiomycota) and sp. nov. (Nigrofomitaceae) from China.

MycoKeys 2018 12(29):1-13. Epub 2018 Jan 12.

Institute of Microbiology, Beijing Forestry University, Beijing 100083, China.

The family Nigrofomitaceae has been considered to be a member of Polyporales and a synonym of Polyporaceae for a long time. However, no molecular evidence supports this taxonomic opinion. For the first time, Nigrofomitaceae is included in a phylogenetic analysis, which shows that this family is separated from Polyporales and nested within Hymenochaetales as a distinct lineage from four well-known families, viz. Hymenochaetaceae, Neoantrodiellaceae, Oxyporaceae and Schizoporaceae. Therefore, Nigrofomitaceae is treated as the fifth family of Hymenochaetales. , the type species of Nigrofomitaceae, was considered to have a pantropical distribution. However, from both morphological and phylogenetic perspectives, the Chinese specimens labelled as are found not to be conspecific with the specimens of from Costa Rica, close to the type locality in Cuba. These Chinese specimens are thus described as a new species . The species diversity of in pantropical region is discussed.
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http://dx.doi.org/10.3897/mycokeys.29.21250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804300PMC
January 2018

Aphyllophoroid fungi in insular woodlands of eastern Ukraine.

Biodivers Data J 2017 22(5):e22426. Epub 2017 Dec 22.

Department of Ecology, University of Kassel, Kassel, Germany.

Background: Fungi play crucial roles in ecosystems and are among the species-richest organism groups on Earth. However, knowledge on their occurrence lags behind the data for animals and plants. Recent analyses of fungal occurrence data from Western, Central and Northern Europe provided important insights into response of fungi to global warming. The consequences of the global changes for biodiversity on a larger geographical scale are not yet understood. Landscapes of Eastern Europe and particularly of eastern Ukraine, with their specific geological history, vegetation and climate, can add substantially new information about fungal diversity in Europe.

New Information: We describe the dataset and provide a checklist of aphyllophoroid fungi (non-gilled macroscopic ) from eastern Ukraine sampled in 16 areas between 2007 and 2011. The dataset was managed on the PlutoF biodiversity workbench (http://dx.doi.org/10.15156/BIO/587471) and can also be accessed via Global Biodiversity Information Facility (GBIF, parts of datasets https://doi.org/10.15468/kuspj6 and https://doi.org/10.15468/h7qtfd). This dataset includes 3418 occurences, namely 2727 specimens and 691 observations of fructifications belonging to 349 species of fungi. With these data, the digitised CWU herbarium (V. N. Karazin Kharkiv National University, Ukraine) doubled in size A most detailed description of the substrate's properties and habitat for each record is provided. The specimen records are supplemented by 26 nuclear ribosomal DNA ITS sequences and six 28S sequences. Additionally, 287 photographs depicting diagnostic macro- and microscopic features of fungal fruitbodies as well as studied habitats are linked to the dataset. Most of the specimens have at least one mention in literature and relevant references are displayed as associated with specimen data. In total, 16 publication references are linked to the dataset. The dataset sheds new light on the fungal diversity of Eastern Europe. It is expected to complement other public sources of fungal occurrence information on continental and global levels in addressing macroecological and biogeographical questions.
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http://dx.doi.org/10.3897/BDJ.5.e22426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769729PMC
December 2017

Phylogeny and diversity of the morphologically similar polypore genera Rigidoporus, Physisporinus, Oxyporus, and Leucophellinus.

Mycologia 2017 16;109(5):749-765. Epub 2018 Jan 16.

a Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University , Beijing 100083 , China.

Rigidoporus and its morphologically similar genera Physisporinus, Oxyporus, and Leucophellinus, which include some forest pathogens and medicinal species, are very important groups of wood-decaying fungi. Species of these genera have not only ecological functions, but also economic importance. Phylogenetic and taxonomic studies on taxa in these genera were carried out. Inferred from phylogenies based on DNA sequences of the nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) and D1-D2 domains of nuc 28S rDNA, 36 species sampled that traditionally belong to Physisporinus, Rigidoporus, Leucophellinus, and Oxyporus are nested mostly in eight lineages. Of these lineages, five (including four genera of Physisporinus, Emmia, Flaviporus, and Flavodon and one taxon "R. hypobrunneus") belong to Polyporales and three (including the genera Rigidoporus, Bridgeoporus, and Leucophellinus) belong to Hymenochaetales. Rigidoporus and Oxyporus are merged because the type species of both genera are nested in a single lineage within Hymenochaetales. Some taxon previously placed in Ceriporia and Oxyporus are transferred to Emmia and Flavodon, respectively, on the basis of current phylogeny. Utilizing a combination of the morphological and phylogenetic evidence, 16 new combinations in Bridgeoporus, Emmia, Flaviporus, Flavodon, Rigidoporus, and Physisporinus are proposed. Five new species, Physisporinus crataegi, P. lavendulus, P. subcrocatus, P. tibeticus, and Rigidoporus submicroporus, are recognized from China. Illustrated descriptions of these novel species are provided. Three taxa are treated at the generic level of Physisporinus because of limited samples.
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http://dx.doi.org/10.1080/00275514.2017.1405215DOI Listing
November 2018

Phylogeny and diversity of Fomitiporella (Hymenochaetales, Basidiomycota).

Mycologia 2017 15;109(2):308-322. Epub 2017 Mar 15.

a Institute of Microbiology, PO Box 61, Beijing Forestry University , Beijing 100083 , People's Republic of China.

Fomitiporella accommodates polypores producing annual to perennial basidiocarps with an indistinct subiculum (very thin to almost lacking), mostly a dimitic hyphal structure, lacking any kind of setae, with brownish, thick-walled basidiospores, and causing a white rot. Previously, only a few samples of Fomitiporella were studied on the basis of morphological and nuc 28S rDNA (28S)-based phylogenetic analyses. In this study, we made a comprehensive study on Fomitiporella on the basis of collections from Central America, USA, Europe, and China. The phylogenetic analysis, including 28 nuc 28S rDNA and 29 nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) sequences newly generated, discovered 14 new lineages. Combined with morphological evidence, 4 new lineages are described and illustrated as new species, viz., Fomitiporella americana, F. micropora, F. sinica, and F. subinermis; 10 other new lineages, each with a single collection, are still treated as unidentified taxa; three new combinations, viz., Fomitiporella tenuissima, F. chinensis, and F. resupinata, are proposed. In addition, F. inermis is redescribed. A key to the 12 known species of Fomitiporella is provided.
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http://dx.doi.org/10.1080/00275514.2017.1305943DOI Listing
October 2018

Studies in the Antrodia serialis group (Polyporales, Basidiomycota).

Mycologia 2017 1;109(2):217-230. Epub 2017 Mar 1.

a Botany Unit (Mycology), Finnish Museum of Natural History , P.O. Box 7 , FI-00014 University of Helsinki, Helsinki , Finland.

Taxonomy and phylogeny of the Antrodia serialis group are revised with morphological, ecological, and geographic data, partial translation elongation factor 1-α (tef1) gene sequences, and nuc rDNA ITS1-5.8S-ITS2-28S sequences. The group contains 13 species found in boreal and temperate zones of the Northern Hemisphere. The species are limited to certain geographic areas within Eurasia and North America. The traditional morphology-based concept of A. serialis covers at least four closely related species: A. serialis s. str. in Eurasia, A. angusta, sp. nov., in East Asia, A. serrata, sp. nov., in the American Northeast, and A. calcitrosa, sp. nov., in the American Northwest. They all are associated mostly with Picea spp. and show small, but stable morphological differences from each other. In addition, A. morganii, comb. nov., inhabiting wood of Populus spp., occurs in North America, and Antrodia alaskana, comb. nov., a large-pored species, macroscopically similar to A. variiformis, is distributed along the Pacific coast of North America. The pine-dwelling A. flavimontis, sp. nov., similar to A. primaeva from Eurasia, is so far known only from the eastern part of the Rocky Mountains (Utah and Wyoming).
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http://dx.doi.org/10.1080/00275514.2017.1300087DOI Listing
October 2018

Global diversity and phylogeny of Onnia (Hymenochaetaceae) species on gymnosperms.

Mycologia 2017 4;109(1):27-34. Epub 2017 Jan 4.

a Institute of Microbiology, PO Box 61, Beijing Forestry University , Beijing , China.

Onnia includes white rotting polypores with annual basidiocarps, a duplex context, monomitic hyphal structure, hymenial setae, and hyaline, thin-walled, smooth basidiospores. Specimens of Onnia, originating mainly from East Asia, Europe, and North America, were studied using both morphology and phylogenetic analyses. Our concatenated data set was derived from 25 collections and included (i) 25 nuc rDNA internal transcribed spacer region sequences (ITS1-5.8S-ITS2 = ITS), 17 generated in this study; and (ii) 14 nuc rDNA 28S rDNA sequences, including the D1-D2 domains, 11 of them generated in this study. The resulting maximum likelihood and Bayesian phylogenies recovered all sampled collections of Onnia as a well-supported clade. In this clade, three previously accepted species, viz., Onnia leporina, O. tomentosa, and O. triquetra, received strong support, whereas three additional lineages with strong support represent the new species described in this paper, O. subtriquetra, O. microspora, and O. tibetica. Of the six Onnia species occurring on gymnosperms, O. tomentosa and O. leporina grow mainly on Picea and have circumboreal distribution in the Northern Hemisphere. In contrast, other species that mostly grow on Pinus are geographically restricted to limited regions, viz., O. triquetra in Europe, O. subtriquetra in North America, and O. microspora and O. tibetica in Asia.
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http://dx.doi.org/10.1080/00275514.2016.1274619DOI Listing
May 2018

Neutralization of Diverse Human Cytomegalovirus Strains Conferred by Antibodies Targeting Viral gH/gL/pUL128-131 Pentameric Complex.

J Virol 2017 04 13;91(7). Epub 2017 Mar 13.

Merck Research Laboratories, Merck and Co., Inc., Kenilworth, New Jersey, USA

Human cytomegalovirus (HCMV) is the leading cause of congenital viral infection, and developing a prophylactic vaccine is of high priority to public health. We recently reported a replication-defective human cytomegalovirus with restored pentameric complex glycoprotein H (gH)/gL/pUL128-131 for prevention of congenital HCMV infection. While the quantity of vaccine-induced antibody responses can be measured in a viral neutralization assay, assessing the quality of such responses, including the ability of vaccine-induced antibodies to cross-neutralize the field strains of HCMV, remains a challenge. In this study, with a panel of neutralizing antibodies from three healthy human donors with natural HCMV infection or a vaccinated animal, we mapped eight sites on the dominant virus-neutralizing antigen-the pentameric complex of glycoprotein H (gH), gL, and pUL128, pUL130, and pUL131. By evaluating the site-specific antibodies in vaccine immune sera, we demonstrated that vaccination elicited functional antiviral antibodies to multiple neutralizing sites in rhesus macaques, with quality attributes comparable to those of CMV hyperimmune globulin. Furthermore, these immune sera showed antiviral activities against a panel of genetically distinct HCMV clinical isolates. These results highlighted the importance of understanding the quality of vaccine-induced antibody responses, which includes not only the neutralizing potency in key cell types but also the ability to protect against the genetically diverse field strains. HCMV is the leading cause of congenital viral infection, and development of a preventive vaccine is a high public health priority. To understand the strain coverage of vaccine-induced immune responses in comparison with natural immunity, we used a panel of broadly neutralizing antibodies to identify the immunogenic sites of a dominant viral antigen-the pentameric complex. We further demonstrated that following vaccination of a replication-defective virus with the restored pentameric complex, rhesus macaques can develop broadly neutralizing antibodies targeting multiple immunogenic sites of the pentameric complex. Such analyses of site-specific antibody responses are imperative to our assessment of the quality of vaccine-induced immunity in clinical studies.
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http://dx.doi.org/10.1128/JVI.02033-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355600PMC
April 2017

Taxonomy and phylogeny of Phellinidium (Hymenochaetales, Basidiomycota): A redefinition and the segregation of Coniferiporia gen. nov. for forest pathogens.

Fungal Biol 2016 08 12;120(8):988-1001. Epub 2016 May 12.

Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China. Electronic address:

Phellinidium, including 13 accepted polypore species mostly with resupinate basidiocarps, is one of the most aggressive forest pathogenic genera. This genus is characterized by the combination of a monomitic hyphal structure, abundant hyphoid setae in the context and trama, and hyaline and thin-walled basidiospores. To explore the relationships among the species of Phellinidium, especially those between forest pathogens and saprophytes, we examined 29 specimens representing all 13 previously known species from Asia, Europe and America from morphological and phylogenetic perspectives. A new genus, Coniferiporia, was found to segregate from Phellinidium for three aggressive forest pathogens, and three new combinations, viz. Coniferiporia qilianensis (the generic type), Coniferiporia weirii and Coniferiporia sulphurascens, were proposed. Phellinidium cryptocystidiatum was treated as a synonym of C. sulphurascens. The circumscription of Phellinidium was delimited to accommodate Phellinidium asiaticum, Phellinidium ferrugineofuscum (the generic type), Phellinidium fragrans and Phellinidium pouzarii. Accordingly, the concept of Phellinidium was emended to accommodate resupinate species bearing cylindrical to oblong-ellipsoid or allantoid basidiospores. No species of Phellinidium under the new circumscription has been reported to be a forest pathogen. Phellinidium noxium and Phellinidium rufitinctum were excluded from Phellinidium, while the taxonomical positions of Phellinidium aciferum, Phellinidium lamaënse, and Phellinidium orientale are still uncertain.
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http://dx.doi.org/10.1016/j.funbio.2016.04.008DOI Listing
August 2016

Use of flow cytometry for characterization of human cytomegalovirus vaccine particles.

Vaccine 2016 Apr 25;34(20):2321-8. Epub 2016 Mar 25.

Vaccine Bioprocess Research and Development, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ 07033, United States. Electronic address:

Despite a 40-year effort, an effective vaccine against human cytomegalovirus (HCMV) remains an unmet medical need. The discovery of potent neutralizing epitopes on the pentameric gH complex (gH/gL/UL128/130/131) has reenergized HCMV vaccine development. Our whole-virus vaccine candidate, currently in a Phase I clinical trial, is based on the attenuated AD169 strain with restored expression of the pentameric gH complex. Given the complexity of a whole-virus vaccine, improved analytical methods have been developed to better characterize heterogeneous viral particles released from infected cells during vaccine production. Here we show the utility of a commercial flow cytometer for the detection of individual HCMV particles, either via light scattering or using fluorescence after labeling of specific antigens. Rapid measurements requiring minimal material provide near real-time information on particle concentration, distributions of different particle types, and product purity. Additionally, utilizing immunoreagents has allowed us to characterize the distribution of key antigens across individual particles and particle types.
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http://dx.doi.org/10.1016/j.vaccine.2016.03.067DOI Listing
April 2016

Species diversity in the Antrodia crassa group (Polyporales, Basidiomycota).

Fungal Biol 2015 Dec 9;119(12):1291-1310. Epub 2015 Oct 9.

Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51015 Tartu, Estonia.

Antrodia is a polyphyletic genus, comprising brown-rot polypores with annual or short-lived perennial resupinate, dimitic basidiocarps. Here we focus on species that are closely related to Antrodia crassa, and investigate their phylogeny and species delimitation using geographic, ecological, morphological and molecular data (ITS and LSU rDNA, tef1). Phylogenetic analyses distinguished four clades within the monophyletic group of eleven conifer-inhabiting species (five described herein): (1)A. crassa s. str. (boreal Eurasia), Antrodia cincta sp. nova (North America) and Antrodia cretacea sp. nova (holarctic), all three being characterized by inamyloid skeletal hyphae that dissolve quickly in KOH solution; (2) Antrodia ignobilis sp. nova, Antrodia sitchensis and Antrodia sordida from North America, and Antrodia piceata sp. nova (previously considered conspecific with A. sitchensis) from Eurasia, possessing amyloid skeletal hyphae; (3) Antrodia ladiana sp. nova from the southern part of the USA, Antrodia pinea from East Asia, and Antrodia ferox - so far known from subtropical North America, but here reported also from Eurasia. These three species have inamyloid hyphae and narrow basidiospores; (4) the North American Antrodia pini-cubensis, sharing similar morphological characters with A. pinea, forming a separate clade. The habitat data indicate that several species are threatened by intensive forestry.
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http://dx.doi.org/10.1016/j.funbio.2015.09.008DOI Listing
December 2015

Global diversity and phylogeny of the Phellinus igniarius complex (Hymenochaetales, Basidiomycota) with the description of five new species.

Mycologia 2016 Jan-Feb;108(1):192-204. Epub 2015 Nov 9.

State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China

The Phellinus igniarius complex corresponds to Phellinus s.s., a well supported clade in the polyphyletic Phellinus s.l. studied worldwide. Recently a molecular phylogeny of this complex was performed for the European and North American species. In this study we expand the taxon samplings of the P. igniarius complex to include 59, seven and 12 additional collections originating from China, Czech Republic and USA, respectively. We generated 78 nuc rDNA ITS1-5.8S-ITS2 (ITS) and 42 translation elongation factor 1-α gene (tef1α) sequences. Based on the morphological and phylogenetic (combined ITS and tef1α dataset) analyses, Phellinus monticola, P. orientoasiaticus, P. padicola, P. parmastoi and P. pomaceoides are newly described and illustrated from China and USA. Phellinus pseudoigniarius is treated as a later synonym of P. igniarius, whereas Phellinus betulinus subsp. betulinus is accepted as P. betulinus. A total of 15 species are accepted in the P. igniarius complex worldwide. Of them, 10 species are distributed in eastern Asia, eight in Europe and six in North America. The taxonomy, phylogeny, host associations and geographic distributions of these 15 species are briefly discussed.
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http://dx.doi.org/10.3852/15-099DOI Listing
May 2016

Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

Phytochemistry 2015 Jun 25;114:7-15. Epub 2014 Oct 25.

State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China. Electronic address:

Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected.
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http://dx.doi.org/10.1016/j.phytochem.2014.09.023DOI Listing
June 2015

What is Antrodia sensu stricto?

Mycologia 2013 Nov-Dec;105(6):1555-76

Botanical Museum, PO Box 7, 00014 University of Helsinki, Finland.

The polypore genus Antrodia (Polyporales, Basidiomycota) in the strict sense consists of a small number of species grouped around the type species A. serpens in phylogenetic analyses. This distinct clade (Antrodia sensu stricto in our view) contains species of the Antrodia heteromorpha complex, A. macra coll. and Antrodia mappa (formerly Postia mappa). Nuclear rDNA ITS and tef1 data show that the Antrodia heteromorpha species complex includes four species: A. heteromorpha sensu stricto (mostly on gymnosperms, large pores and spores), A. serpens (on angiosperms in Europe, resupinate, smaller pores but large spores), A. favescens (smaller pores and spores, pileate species in North America, formerly known as Trametes sepium), and A. tanakai (a close kin of A. favescens in Eurasia). Antrodia albida is a synonym of A. heteromorpha sensu stricto. We combine A. mappa, A. favescens and A. tanakai in Antrodia and designate neotypes for A. albida and A. heteromorpha, and an epitype for A. serpens. We also compare the morphologically similar but distantly related A. albidoides and A. mellita, and conclude that A. macrospora and A. subalbidoides are synonyms of A. albidoides.
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http://dx.doi.org/10.3852/13-039DOI Listing
January 2014

Norway spruce (Picea abies) genetic transformation with modified Cry3A gene of Bacillus thuringiensis.

Acta Biochim Pol 2013 25;60(3):395-400. Epub 2013 Jul 25.

Institute of Plant Molecular Biology, Biology Centre AS CR, and Faculty of Science, South Bohemia University, České Budějovice, Czech Republic.

Modified versions of the Cry3A gene of Bacillus thuringiensis (Bt) were transferred into Norway spruce (Picea abies). Both the biolistic approach and Agrobacterium tumefaciens mediated procedure were employed for transformation of embryogenic tissue (ET) cultures. The latter method proved to be more efficient yielding 70 transgenic embryogenic tissue lines compared with 18 lines obtained by biolistics. The modified Cry3A genes were driven by a 35S promoter and the nptII screenable selection marker gene was used in all vectors. The transgenic ETs were molecularly characterized and converted into mature somatic embryos. Germinating embryos formed plantlets which were finally planted into perlite and their Cry3A gene transcription activities were demonstrated by RT-PCR.
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April 2014

Fragmentation of monoclonal antibodies.

MAbs 2011 May-Jun;3(3):253-63. Epub 2011 May 1.

BioProcess Analytical and Formulation Sciences Department; Merck Research Laboratories; Merck Sharp and Dohme Corp., West Point, PA, USA.

Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5 to 6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149706PMC
http://dx.doi.org/10.4161/mabs.3.3.15608DOI Listing
December 2011

Isolation and characterization of IgG1 with asymmetrical Fc glycosylation.

Glycobiology 2011 Aug 5;21(8):1087-96. Epub 2011 Apr 5.

Merck Research Laboratories, West Point, PA 19486, USA.

N-glycosylation of immunoglobulin G (IgG) at asparigine residue 297 plays a critical role in antibody stability and immune cell-mediated Fc effector function. Current understanding pertaining to Fc glycosylation is based on studies with IgGs that are either fully glycosylated [both heavy chain (HC) glycosylated] or aglycosylated (neither HC glycosylated). No study has been reported on the properties of hemi-glycosylated IgGs, antibodies with asymmetrical glycosylation in the Fc region such that one HC is glycosylated and the other is aglycosylated. We report here for the first time a detailed study of how hemi-glycosylation affects the stability and functional activities of an IgG1 antibody, mAb-X, in comparison to its fully glycosylated counterpart. Our results show that hemi-glycosylation does not impact Fab-mediated antigen binding, nor does it impact neonatal Fc receptor binding. Hemi-glycosylated mAb-X has slightly decreased thermal stability in the CH2 domain and a moderate decrease (∼20%) in C1q binding. More importantly, the hemi-glycosylated form shows significantly decreased binding affinities toward all Fc gamma receptors (FcγRs) including the high-affinity FcγRI, and the low-affinity FcγRIIA, FcγRIIB, FcγRIIIA and FcγRIIIB. The decreased binding affinities to FcγRs result in a 3.5-fold decrease in antibody-dependent cell cytotoxicity (ADCC). As ADCC often plays an important role in therapeutic antibody efficacy, glycosylation status will not only affect the antibody quality but also may impact the biological function of the product.
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http://dx.doi.org/10.1093/glycob/cwr047DOI Listing
August 2011

Impact of methionine oxidation in human IgG1 Fc on serum half-life of monoclonal antibodies.

Mol Immunol 2011 Mar 21;48(6-7):860-6. Epub 2011 Jan 21.

Preclinical DMPK Department, Merck Research Laboratories, Merck Sharp and Dohme Corp., West Point, PA 19486, United States.

IgG monoclonal antibodies (mAbs) consist of two Fab fragments and one Fc fragment. The Fab fragments contain the variable regions and are responsible for drug specificity (via antigen binding); the Fc fragment contains constant regions and is responsible for effector functions (via interactions with Fcγ receptors) and extended serum half-life (via interaction with the neonatal Fc receptor, FcRn). There are two conserved methionine (Met) residues located in the FcRn binding site of the Fc fragment. It has been shown previously that oxidation of these two Met residues decreases the binding affinity to FcRn. We have further evaluated the impact of Met oxidation on serum half-lives of two humanized IgG1 mAbs in transgenic mice with human FcRn. Variable oxidation levels were obtained by several procedures: exposure to an oxidizing agent, accumulation during extended refrigerated storage, or chromatographic separation. Our results show that Met oxidation can result in a significant reduction of the serum circulation half-life and the magnitude of the change correlates well with the extent of Met oxidation and changes in FcRn binding affinities. The relatively low levels of Met oxidation accumulated during 3 years of refrigerated storage had minimal impact on FcRn binding and no detectable impact on the serum half-life.
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http://dx.doi.org/10.1016/j.molimm.2010.12.009DOI Listing
March 2011

Separation of post-translational modifications in monoclonal antibodies by exploiting subtle conformational changes under mildly acidic conditions.

J Chromatogr A 2010 Oct 21;1217(42):6496-502. Epub 2010 Aug 21.

Merck Research Laboratories, West Point, PA 19486, USA.

Chromatographic separation plays a key role in the identification, quantification, and characterization of protein variants. Here we describe separation of species containing two post-translational modifications (glycosylation and methionine oxidation) in the Fc fragment of a monoclonal antibody. The method is based on cation-exchange chromatography under mildly acidic conditions that destabilize mainly the CH2 domain. Our data suggest that the separation is not mediated by the chemical modification itself, but rather by subtle structural changes induced by the chemical modification in the domain-decoupled conformation that monoclonal antibodies adopt around pH 4. Compared to other procedures already described in the literature, this method demonstrates an improved separation and allows purification of species in the native fold for additional functional characterization. This approach of separation under conditions where the protein assumes an alternative conformation could find a more general utility for the separation of chemical modifications in proteins.
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http://dx.doi.org/10.1016/j.chroma.2010.08.044DOI Listing
October 2010

Kinetics of chemical degradation in monoclonal antibodies: relationship between rates at the molecular and peptide levels.

Anal Chem 2010 Apr;82(8):3198-206

Merck Research Laboratories, Merck & Co. Inc., West Point, Pennsylvania 19486, USA.

This article describes a method to analyze the kinetics of monoclonal antibody degradation and to determine the quantitative relationship between the degradation rates observed at the molecular and peptide levels. The proposed model can be applied to any degradation pathway that can be well approximated by a first order reaction; if several pathways exist, the model assumes that they are independent. Three examples are presented to illustrate the benefits of this approach. For each case, the calculated fractions of species were compared to one or more data sets to demonstrate the good agreement between experimental results and model prediction. This method can serve as a valuable tool in interpreting chromatograms of degraded samples and predicting the population of species present at the molecular level when only data from degradation observed at the peptide level is available. This method further demonstrates how deviations from predictions of simple models can be used to unravel additional, unforeseen reactions.
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http://dx.doi.org/10.1021/ac902752eDOI Listing
April 2010