Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Live cell imaging of meiosis in Arabidopsis thaliana
Prusicki, Maria A. ; Keizer, Emma M. ; Rosmalen, Rik P. van; Komaki, Shinichiro ; Seifert, Felix ; Müller, Katja ; Wijnker, Erik ; Fleck, Christian ; Schnittger, Arp - \ 2019
eLife 8 (2019). - ISSN 2050-084X
A. thaliana - cell biology - cyclin - development - meiosis - phragmoplast - plant biology - reproduction - spindle

To follow the dynamics of meiosis in the model plant Arabidopsis, we have established a live cell imaging setup to observe male meiocytes. Our method is based on the concomitant visualization of microtubules (MTs) and a meiotic cohesin subunit that allows following five cellular parameters: cell shape, MT array, nucleus position, nucleolus position, and chromatin condensation. We find that the states of these parameters are not randomly associated and identify 11 cellular states, referred to as landmarks, which occur much more frequently than closely related ones, indicating that they are convergence points during meiotic progression. As a first application of our system, we revisited a previously identified mutant in the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM). Our imaging system enabled us to reveal both qualitatively and quantitatively altered landmarks in tam, foremost the formation of previously not recognized ectopic spindle- or phragmoplast-like structures that arise without attachment to chromosomes.

The Role and Need for Space-Based Forest Biomass-Related Measurements in Environmental Management and Policy
Herold, Martin ; Carter, Sarah ; Avitabile, Valerio ; Espejo, Andrés B. ; Jonckheere, Inge ; Lucas, Richard ; McRoberts, Ronald E. ; Næsset, Erik ; Nightingale, Joanne ; Petersen, Rachael ; Reiche, Johannes ; Romijn, Erika ; Rosenqvist, Ake ; Rozendaal, Danaë M.A. ; Seifert, Frank Martin ; Sanz, María J. ; Sy, V. de - \ 2019
Surveys in Geophysics 40 (2019)4. - ISSN 0169-3298 - p. 757 - 778.
The achievement of international goals and national commitments related to forest conservation and management, climate change, and sustainable development requires credible, accurate, and reliable monitoring of stocks and changes in forest biomass and carbon. Most prominently, the Paris Agreement on Climate Change and the United Nations’ Sustainable Development Goals in particular require data on biomass to monitor progress. Unprecedented opportunities to provide forest biomass data are created by a series of upcoming space-based missions, many of which provide open data targeted at large areas and better spatial resolution biomass monitoring than has previously been achieved. We assess various policy needs for biomass data and recommend a long-term collaborative effort among forest biomass data producers and users to meet these needs. A gap remains, however, between what can be achieved in the research domain and what is required to support policy making and meet reporting requirements. There is no single biomass dataset that serves all users in terms of definition and type of biomass measurement, geographic area, and uncertainty requirements, and whether there is need for the most recent up-to-date biomass estimate or a long-term biomass trend. The research and user communities should embrace the potential strength of the multitude of upcoming missions in combination to provide for these varying needs and to ensure continuity for long-term data provision which one-off research missions cannot provide. International coordination bodies such as Global Forest Observations Initiative (GFOI), Committee on Earth Observation Satellites (CEOS), and Global Observation of Forest Cover and Land Dynamics (GOFC‐GOLD) will be integral in addressing these issues in a way that fulfils these needs in a timely fashion. Further coordination work should particularly look into how space-based data can be better linked with field reference data sources such as forest plot networks, and there is also a need to ensure that reference data cover a range of forest types, management regimes, and disturbance regimes worldwide.
Forest biomass retrieval approaches from earth observation in different biomes
Rodríguez-Veiga, Pedro ; Quegan, Shaun ; Carreiras, Joao ; Persson, Henrik J. ; Fransson, Johan E.S. ; Hoscilo, Agata ; Ziółkowski, Dariusz ; Stereńczak, Krzysztof ; Lohberger, Sandra ; Stängel, Matthias ; Berninger, Anna ; Siegert, Florian ; Avitabile, Valerio ; Herold, Martin ; Mermoz, Stéphane ; Bouvet, Alexandre ; Toan, Thuy Le; Carvalhais, Nuno ; Santoro, Maurizio ; Cartus, Oliver ; Rauste, Yrjö ; Mathieu, Renaud ; Asner, Gregory P. ; Thiel, Christian ; Pathe, Carsten ; Schmullius, Chris ; Seifert, Frank Martin ; Tansey, Kevin ; Balzter, Heiko - \ 2019
International Journal of applied Earth Observation and Geoinformation 77 (2019). - ISSN 0303-2434 - p. 53 - 68.
The amount and spatial distribution of forest aboveground biomass (AGB) were estimated using a range of regionally developed methods using Earth Observation data for Poland, Sweden and regions in Indonesia (Kalimantan), Mexico (Central Mexico and Yucatan peninsula), and South Africa (Eastern provinces) for the year 2010. These regions are representative of numerous forest biomes and biomass levels globally, from South African woodlands and savannas to the humid tropical forest of Kalimantan. AGB retrieval in each region relied on different sources of reference data, including forest inventory plot data and airborne LiDAR observations, and used a range of retrieval algorithms. This is the widest inter-comparison of regional-to-national AGB maps to date in terms of area, forest types, input datasets, and retrieval methods. The accuracy assessment of all regional maps using independent field data or LiDAR AGB maps resulted in an overall root mean square error (RMSE) ranging from 10 t ha−1 to 55 t ha−1 (37% to 67% relative RMSE), and an overall bias ranging from −1 t ha−1 to +5 t ha−1 at pixel level. The regional maps showed better agreement with field data than previously developed and widely used pan-tropical or northern hemisphere datasets. The comparison of accuracy assessments showed commonalities in error structures despite the variety of methods, input data, and forest biomes. All regional retrievals resulted in overestimation (up to 63 t ha−1) in the lower AGB classes, and underestimation (up to 85 t ha−1) in the higher AGB classes. Parametric model-based algorithms present advantages due to their low demand on in situ data compared to non-parametric algorithms, but there is a need for datasets and retrieval methods that can overcome the biases at both ends of the AGB range. The outcomes of this study should be considered when developing algorithms to estimate forest biomass at continental to global scale level.
First report of Neofabraea kienholzii causing bull’s eye rot on pear (Pyrus communis) in the Netherlands
Wenneker, M. ; Pham, K.T.K. ; Boekhoudt, L.C. ; Boer, F.A. de; Leeuwen, P.J. van; Hollinger, T.C. ; Thomma, B.P.H.J. - \ 2017
Plant Disease 101 (2017)4. - ISSN 0191-2917 - p. 634 - 634.

Pear (Pyrus communis L.) is an important fruit crop in the Netherlands, with a total production of 349,000 tons in 2014, and ‘Conference’ is the main cultivar. In the Netherlands, pears are kept in controlled atmosphere cold storage up to 11 months after harvest. Symptoms of bull’s eye rot were observed in 2015 on ‘Conference’ pears in storage in the Netherlands. Bull’s eye lesions on apple and pear fruits are generally caused by four Neofabraea species: N. alba Jacks, N. malicorticis Guthrie, N. perennans Kienholz, and N. kienholzii Seifert, Spotts & Lévesque (Gariepy et al. 2005). N. alba is the major pathogen causing bull’s eye rot on pear fruits in the Netherlands. Independent of the species, the symptoms appear as flat or slightly sunken lesions, which are brown, often lighter brown in the center (Spotts et al. 2009). To isolate the causal agent, fruit were rinsed with sterile water, lesions were sprayed with 70% ethanol until droplet runoff, the skin was removed aseptically with a scalpel, and tissue under the lesion was isolated and placed onto potato dextrose agar (PDA). PDA plates were incubated at 20°C in the dark, and single spores were transferred to fresh PDA plates. The isolates produced colonies with white-yellowish to brownish mycelium. Microconidia were produced on feathery fascicles of aerial mycelium, with a white, powdery, or sugary appearance on the surface of the agar colony. Microconidia were 2.5 to 6.5 × 1.5 to 2.5 µm, ellipsoidal, slightly asymmetrical to a curved form. The identity of a representative isolate (PPO 45010) was confirmed by means of multilocus gene sequencing. To this end, genomic DNA was extracted using the LGC Mag Plant Kit (Berlin) in combination with the Kingfisher method (Waltham, MA). Segments of the internal transcribed spacer region (ITS), 28S ribosomal RNA (28S rRNA) and beta-tubulin (TUB2) loci were amplified, sequenced with primers ITS1/ITS4, LR0R/LR5, and Btub2Fd/Btub4Rd (Chen et al. 2016), and deposited in GenBank under accession nos. KX424942 (ITS), KX424941 (28S rRNA), and KX424940 (TUB2). MegaBLAST analysis revealed that the ITS, 28S rRNA, and TUB2 sequences matched with 99 to 100% identity to N. kienholzii isolates in GenBank (KR859082 and KR859083 [ITS], KR858873 and KR858874 [28S rRNA], KR859288 and KR859289 [TUB2]). Alcohol surface sterilized fruits were inoculated in pathogenicity tests in two ways: (i) with an agar disk (10 mm diameter) with actively growing mycelium of N. kienholzii prepared from a 14-day-old culture grown on PDA; and (ii) with 20 μl of a spore suspension (105 conidia ml-1) prepared from a 21-day-old PDA culture after wounding with a needle. Both experiments were performed on 10 ‘Conference’ pears. Inoculated fruits were sealed in plastic bags and were incubated in darkness at 20°C. Typical symptoms appeared between 7 and 14 days. Mock-inoculated controls with water and PDA-only controls remained symptomless. Fungi isolated from the lesions had morphological characteristics that resembled the original isolates from infected pears. The identity of these isolates was confirmed as N. kienholzii by sequencing, thus completing Koch’s postulates. Bull’s eye rot of apple and pear is an important postharvest disease, occurring in major fruit growing areas of North America, Chile, Australia, and Europe (Henriquez et al. 2004; Spotts et al. 2009). N. kienholzii was reported twice on apple in Europe (Michalecka et al. 2016). To the best of our knowledge, this is the first report of N. kienholzii causing bull’s eye rot of pear in Europe.

Metabolic in Vivo Labeling Highlights Differences of Metabolically Active Microbes from the Mucosal Gastrointestinal Microbiome between High-Fat and Normal Chow Diet
Oberbach, Andreas ; Haange, Sven Bastiaan ; Schlichting, Nadine ; Heinrich, Marco ; Lehmann, Stefanie ; Till, Holger ; Hugenholtz, Floor ; Kullnick, Yvonne ; Smidt, Hauke ; Frank, Karin ; Seifert, Jana ; Jehmlich, Nico ; Bergen, Martin Von - \ 2017
Journal of Proteome Research 16 (2017)4. - ISSN 1535-3893 - p. 1593 - 1604.
16S rRNA gene sequencing - gut microbiota - metaproteomics - mucus layer - protein-based stable isotope probing
The gastrointestinal microbiota in the gut interacts metabolically and immunologically with the host tissue in the contact zone of the mucus layer. For understanding the details of these interactions and especially their dynamics it is crucial to identify the metabolically active subset of the microbiome. This became possible by the development of stable isotope probing techniques, which have only sparsely been applied to microbiome research. We applied the in vivo stable isotope approach using 15N-labeled diet with subsequent identification of metabolically active bacterial species. Four-week old male Sprague-Dawley rats were randomly assigned to chow diet (CD, n =15) and high-fat diet (HFD, n =15). After 11 weeks, three animals from each group were sacrificed for baseline characterization of anthropometric and metabolic obesity. The remaining animals were exposed to either a 15N-labeled (n =9) or a 14N-unlabeled experimental diet (n =3). Three rats from each cohort (HFD and CD) were sacrificed at 12, 24, and 72 h. The remaining three animals from each cohort, which received the 14N-unlabeled diet, were sacrificed after 72 h. The colon was harvested and divided into three equal sections (proximal, medial, and distal), and the mucus layer of each specimen was sampled by scraping. We identified the active subset in an HFD model of obesity in comparison with lean controls rats using metaproteomics. In addition, all samples were investigated by 16S rRNA amplicon gene sequencing. The active microbiome of the HFD group showed an increase in bacterial taxa for Verrucomicrobia and Desulfovibrionaceae. In contrast with no significant changes in alpha diversity, time- and localization-dependent effects in beta-diversity were clearly observed. In terms of enzymatic functions the HFD group showed strong affected metabolic pathways such as energy production and carbohydrate metabolism. In vivo isotope labeling combined with metaproteomics provides a valuable method to distinguish the active from the non-active bacterial phylogenetic groups that are relevant for microbiota-host interaction. For morbid obesity such analysis may provide potentially new strategies for targeted pre- or probiotic treatments.
Earth Observation for REDD+: Requirements and Progress in Supporting Developing Countries – GOFC-GOLD and GFOI
Seifert, Frank Martin ; Herold, M. ; Mora, B. ; Briggs, S. - \ 2016
The Contribution of GOFC-GOLD to Land Cover and Land Use Monitoring: Achievements and Current Challenges
Mora, B. ; Herold, M. ; Seifert, Frank Martin ; Arino, O. - \ 2016
Independent Monitoring and New Technologies Supporting REDD+ and Land Use Sector Mitigation
Herold, M. ; Martius, Christopher ; Avitabile, V. ; Seifert, Frank Martin ; Fritz, S. ; Schepaschenko, D. ; Boetcher, H. ; Roman Cuesta, Rosa Maria ; Bucki, Mika ; Gaveau, D. - \ 2016
Combining satellite data for better tropical forest monitoring
Reiche, Johannes ; Lucas, Richard ; Mitchell, A.L. ; Verbesselt, Jan ; Hoekman, D.H. ; Haarpaintner, Jörg ; Kellndorfer, J.M. ; Rosenqvist, Ake ; Lehmann, E.A. ; Woodcock, C.E. ; Seifert, Frank Martin ; Herold, Martin - \ 2016
Nature Climate Change 6 (2016)2. - ISSN 1758-678X - p. 120 - 122.
Implementation of policies to reduce forest loss challenges the Earth observation community to improve forest monitoring. An important avenue for progress is the use of new satellite missions and the combining of optical and synthetic aperture radar sensor data.
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi, and plants
Kirk, P.M. ; Stalpers, J.A. ; Braun, U. ; Crous, P.W. ; Hansen, K. ; Hawksworth, D.L. ; Hyde, K.D. ; Lücking, R. ; Lumbsch, T.H. ; Rossman, A.Y. ; Seifert, K.A. ; Stadler, M. - \ 2013
IMA fungus 4 (2013)2. - ISSN 2210-6340 - p. 381 - 443.
As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption. We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Code to provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10th International Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.
Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection
Rossman, A.Y. ; Seifert, K.A. ; Samuels, G.J. ; Minnis, A.M. ; Schroers, H.J. ; Lombard, L. ; Crous, P.W. ; Põldmaa, K. ; Cannon, P.F. ; Summerbell, R.C. ; Geiser, D.M. ; Zhuang, W. ; Hirooka, Y. ; Herrera, C. ; Salgado-Salazar, C. ; Chaverri, P. - \ 2013
IMA fungus 4 (2013)1. - ISSN 2210-6340 - p. 41 - 51.
With the recent changes concerning pleomorphic fungi in the new International Code of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae, Clonostachys is recommended over Bionectria; in Hypocreaceae, Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae, Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.
Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity
Hernandez, E. ; Bargiela, R. ; Suarez Diez, M. ; Friedrichs, A. ; Pérez-Cobas, A.E. ; Gosalbes, M.J. ; Knecht, H. ; Martinez-Martinez, M. ; Seifert, J. ; Bergen, M. von; Martins Dos Santos, V.A.P. - \ 2013
Gut Microbes 4 (2013)4. - ISSN 1949-0976 - p. 306 - 315.
The microbiomes in the gastrointestinal tract (GIT) of individuals receiving antibiotics and those in obese subjects undergo compositional shifts, the metabolic effects and linkages of which are not clearly understood. Herein, we set to gain insight into these effects, particularly with regard to carbohydrate metabolism, and to contribute to unravel the underlying mechanisms and consequences for health conditions. We measured the activity level of GIT carbohydrate-active enzymes toward 23 distinct sugars in adults patients (n = 2) receiving 14-d ß-lactam therapy and in obese (n = 7) and lean (n = 5) adolescents. We observed that both 14 d antibiotic-treated and obese subjects showed higher and less balanced sugar anabolic capacities, with 40% carbohydrates being preferentially processed as compared with non-treated and lean patients. Metaproteome-wide metabolic reconstructions confirmed that the impaired utilization of sugars propagated throughout the pentose phosphate metabolism, which had adverse consequences for the metabolic status of the GIT microbiota. The results point to an age-independent positive association between GIT glycosidase activity and the body mass index, fasting blood glucose and insulin resistance (r ( 2) = 0.95). Moreover, antibiotics altered the active fraction of enzymes controlling the thickness, composition and consistency of the mucin glycans. Our data and analyses provide biochemical insights into the effects of antibiotic usage on the dynamics of the GIT microbiota and pin-point presumptive links to obesity. The knowledge and the hypotheses generated herein lay a foundation for subsequent, systematic research that will be paramount for the design of "smart" dietary and therapeutic interventions to modulate host-microbe metabolic co-regulation in intestinal homeostasis
Auch eine Folge der neoliberalen Politik
Jongerden, Joost - \ 2013
Die Hintergründe für die aktuelle Protestbewegung in der Türkei sind vielfältig. Eine Ursache liegt in einer neoliberalen Wirtschaftspolitik, die vordergründig erfolgreich ist, aber auch ihre Schattenseiten hat. Über die neue städtische Armut in der Türkei befragte der Sozialwissenschaftler Franz Seifert seine Kollegen Joost Jongerden und Murat Öztürk.Die Hintergründe für die aktuelle Protestbewegung in der Türkei sind vielfältig. Eine Ursache liegt in einer neoliberalen Wirtschaftspolitik, die vordergründig erfolgreich ist, aber auch ihre Schattenseiten hat. Über die neue städtische Armut in der Türkei befragte der Sozialwissenschaftler Franz Seifert seine Kollegen Joost Jongerden und Murat Öztürk.
Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities
Haange, S.B. ; Oberbach, A. ; Schlichting, N. ; Hugenholtz, F. ; Smidt, H. ; Bergen, M. van; Till, H. ; Seifert, J. - \ 2012
Journal of Proteome Research 11 (2012)11. - ISSN 1535-3893 - p. 5406 - 5417.
gut microbiota - superoxide reductase - escherichia-coli - host metabolism - fecal samples - bacteria - community - diversity - proteins - carbon
The digestion of food ingredients depends on the action of the gut microbiota and has a significant influence on the health, especially in the case of metabolic diseases, of the host organism. Despite the relevance of the structure and functionalities in the microbiota for the metabolism of the host, the spatial resolution of microbial consortia and the functionalities in the different gut sections of the rat are mostly unknown. Since there are suitable rat models for human metabolic diseases, the microbiota of the rat is of special interest. Samples along the intestinal tract of rats were investigated using metaproteomics and 16S rRNA gene pyrosequencing. The procedures for harvesting bacteria from the mucus and the content of the gut sections and feces were optimized leading to 2802 nonredundant bacterial protein groups in total that were assigned to spectra measured by liquid chromatography-tandem mass spectrometry. The majority of 16S rRNA genes and protein groups belonged to members of Firmicutes, Bacteroidetes and Proteobacteria. The functionalities in the enzyme repertoire were compared between the mucus and the content of the large intestine sections and the feces samples. This spatial resolution allowed pinpointing changes in the community to specific metabolic capacities like carbohydrate transport and energy conservation. The results showed that the mere analysis of feces samples reflects the functions of the gut microbiota only to a minor extent and sheds light on the metabolic interchange between the microbiota and the host organism.
Fungal Planet description sheets: 128–153
Crous, P.W. ; Shivas, R.G. ; Wingfield, M.J. ; Summerell, B.A. ; Rossman, A.Y. ; Alves, J.L. ; Adams, G.C. ; Barreto, R.W. ; Bell, A. ; Coutinho, M.L. ; Flory, S.L. ; Gates, G.K.R. ; Hardy, G.E.St.J. ; Kleczewski, N.M. ; Lombard, L. ; Longa, C.M.O. ; Louis-Seize, G. ; Macedo, F. ; Mahoney, D.P. ; Maresi, G. ; Martin-Sanchez, P.M. ; Marvanova, L. ; Minnis, A.M. ; Morgado, L.N. ; Noordeloos, M.E. ; Phillips, A.J.L. ; Quaedvlieg, W. ; Ryan, P.G. ; Saiz-Jimenez, C. ; Seifert, K.A. ; Swart, W.J. ; Tan, Y.P. ; Tanney, J.B. ; Thu, P.Q. ; Videira, S.I.R. ; Walker, D.M. ; Groenewald, J.Z. - \ 2012
Persoonia 29 (2012). - ISSN 0031-5850 - p. 146 - 201.
grass microstegium-vimineum - leaf-blight disease - sooty blotch - bipolaris sp - phylogeny - mycosphaerella - genus - cochliobolus - microfungi - eucalyptus
Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliaefistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Schoch, C.L. ; Seifert, K.A. ; Huhndorf, S. ; Robert, V. ; Spouge, J.L. ; Levesque, C.A. ; Chen, W. ; Crous, P.W. ; Boekhout, T. ; Damm, U. ; Hoog, G.S. de; Eberhardt, U. ; Groenewald, J.Z. ; Groenewald, M. ; Hagen, F. ; Houbraken, J. ; Quaedvlieg, W. ; Stielow, B. ; Vu, T.D. ; Walther, G. - \ 2012
Proceedings of the National Academy of Sciences of the United States of America 109 (2012)16. - ISSN 0027-8424 - p. 6241 - 6246.
arbuscular mycorrhizal fungi - phylogenetic-relationships - basidiomycetous yeasts - intragenomic variation - ectomycorrhizal fungi - species recognition - sequence-analysis - rpb1 sequences - rdna - subunit
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
Low-cost small scale processing technologies for production applications in various environments-Mass produced factories
Bramsiepe, C. ; Sievers, S. ; Seifert, T. ; Stefanidis, G.D. ; Vlachos, D.G. ; Schnitzer, H. ; Muster, B. ; Brunner, C. ; Sanders, J.P.M. ; Bruins, M.E. ; Schembecker, G. - \ 2012
Chemical Engineering and Processing 51 (2012). - ISSN 0255-2701 - p. 32 - 52.
fischer-tropsch synthesis - microwave-assisted pyrolysis - hydrogen-production - bio-oil - oxygenated hydrocarbons - reactive distillation - transportation fuels - microchannel reactor - microreactor stacks - catalytic pyrolysis
The requirements for chemical and food production technologies will change in the future as a result of shorter time to market and increasing market volatility. Especially the rising use of renewable resources will require the implementation of flexible and fast to install small-scale production technologies. The increasing number of necessary apparatuses and their distributed operation, however, will constitute major challenges, both economically and procedurally. The proposed solution to face the economic challenge is modularization and standardization. For food production, dewatering represents a key issue. Thus, biomass processing should first be divided into small-scale water separation steps and then into further large-scale processing steps. As dewatering usually happens thermally and heat exchangers often benefit from the economies of scale, heat supply and energy consumption or heat transfer with little capital investment are further issues. Therefore, temperature levels should be decreased and the use of solar heat increased. For the production of biofuels and chemicals from biomass, process integration and process simplification are proposed to improve the efficacy of production equipment and processes. Choosing raw materials with molecular structures, similar to the desired chemical building block, will lower the need for heat exchange and make small-scale manufacturing of fuels and chemicals possible
Fungal Planet description sheets: 69–91
Crous, P.W. ; Groenewald, J.Z. ; Shivas, R.G. ; Edwards, J. ; Seifert, K.A. ; Alfenas, A.C. ; Alfenas, R.F. ; Burgess, T.I. ; Carnegie, A.J. ; Hardy, G.E.S.T.J. ; Hiscock, N. ; Hüberli, D. ; Jung, T. ; Louis-Seize, G. ; Okada, G. ; Pereira, O.L. ; Stukely, M.J.C. ; Wang, W. ; White, G.P. ; Young, A.J. ; McTaggart, A.R. ; Pascoe, I.G. ; Porter, I.J. ; Quaedvlieg, W. - \ 2011
Persoonia 26 (2011). - ISSN 0031-5850 - p. 108 - 156.
ribosomal dna - eucalyptus - genera - dictyosporium - microfungi - phylogeny - china - genus - spot - nov
Novel species of microfungi described in the present study include the following from Australia: Bagadiella victoriae and Bagadiella koalae on Eucalyptus spp., Catenulostroma eucalyptorum on Eucalyptus laevopinea, Cercospora eremochloae on Eremochloa bimaculata, Devriesia queenslandica on Scaevola taccada, Diaporthe musigena on Musa sp., Diaporthe acaciigena on Acacia retinodes, Leptoxyphium kurandae on Eucalyptus sp., Neofusicoccum grevilleae on Grevillea aurea, Phytophthora fluvialis from water in native bushland, Pseudocercospora cyathicola on Cyathea australis, and Teratosphaeria mareebensis on Eucalyptus sp. Other species include Passalora leptophlebiae on Eucalyptus leptophlebia (Brazil), Exophiala tremulae on Populus tremuloides and Dictyosporium stellatum from submerged wood (Canada), Mycosphaerella valgourgensis on Yucca sp. (France), Sclerostagonospora cycadis on Cycas revoluta (Japan), Rachicladosporium pini on Pinus monophylla (Netherlands), Mycosphaerella wachendorfiae on Wachendorfia thyrsifolia and Diaporthe rhusicola on Rhus pendulina (South Africa). Novel genera of hyphomycetes include Noosia banksiae on Banksia aemula (Australia), Utrechtiana cibiessia on Phragmites australis (Netherlands), and Funbolia dimorpha on blackened stem bark of an unidentified tree (USA). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
The Amsterdam Declaration on Fungal Nomenclature
Hawksworth, D.L. ; Crous, P.W. ; Redhead, S.A. ; Reynolds, D.R. ; Samson, R.A. ; Seifert, K.A. ; Taylor, J.W. ; Wingfield, M.J. ; Abaci, Ö. ; Aime, C. ; Asan, A. ; Bai, F.Y. ; Beer, W. de; Begerow, D. ; Berikten, D. ; Boekhout, T. ; Buchanan, P.K. ; Burgess, T. ; Buzina, W. ; Cai, L. ; Cannon, P.F. ; Crane, J.L. ; Damm, U. ; Daniel, H.M. ; Diepeningen, A.D. van; Druzhinina, I. ; Dyer, P.S. ; Eberhardt, U. ; Fell, J.W. ; Frisvad, J.C. ; Geiser, D.M. ; Geml, J. ; Glienke, C. ; Gräfenhan, T. ; Groenewald, J.Z. ; Groenewald, M. ; Gruyter, J. de; Guého-Kellemann, E. ; Guo, L.D. ; Hibbett, D.S. ; Hong, S.B. ; Hoog, G.S. de; Houbraken, J. ; Huhndorf, S.M. ; Hyde, K.D. ; Ismail, A. ; Johnston, P.R. ; Kadaifciler, D.G. ; Kirk, P.M. ; Köljalg, U. ; Kurtzman, C.P. ; Lagneau, P.E. ; Lévesque, C.A. ; Liu, X. ; Lombard, L. ; Meyer, W. ; Miller, A. ; Minter, D.W. ; Najafzadeh, M.J. ; Norvell, L. ; Ozerskaya, S.M. ; Öziç, R. ; Pennycook, S.R. ; Peterson, S.W. ; Pettersson, O.V. ; Quaedvlieg, W. ; Robert, V.A. ; Ruibal, C. ; Schnürer, J. ; Schroers, H.J. ; Shivas, R. ; Slippers, B. ; Spierenburg, H. ; Takashima, M. ; Taskin, E. ; Thines, M. ; Thrane, U. ; Uztan, A.H. ; Raak, M. van; Varga, J. ; Vasco, A. ; Verkley, G. ; Videira, S.I.R. ; Vries, R.P. de; Weir, B.S. ; Yilmaz, N. ; Yurkov, A. ; Zhang, N. - \ 2011
IMA fungus 2 (2011)1. - ISSN 2210-6340 - p. 105 - 112.
The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature offungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
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