| 1. |
- Hibbett, David S., et al.
(författare)
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Agaricomycetes
- 2014
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Ingår i: The Mycota. - Berlin : Springer. - 9783642553172 ; , s. 373-429
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Agaricomycetes includes ca. 21,000 described species of mushroom-forming fungi that function as decayers, pathogens, and mutualists in both terrestrial and aquatic habitats. The morphological diversity of Agaricomycete fruiting bodies is unparalleled in any other group of fungi, ranging from simple corticioid forms to complex, developmentally integrated forms (e.g., stinkhorns). In recent years, understanding of the phylogenetic relationships and biodiversity of Agaricomycetes has advanced dramatically, through a combination of polymerase chain reaction-based multilocus phylogenetics, phylogenomics, and molecular environmental surveys. Agaricomycetes is strongly supported as a clade and includes several groups formerly regarded as Heterobasidiomycetes, namely the Auriculariales, Sebacinales, and certain Cantharellales (Tulasnellaceae and Ceratobasidiaceae). The Agaricomycetes can be divided into 20 mutually exclusive clades that have been treated as orders. This chapter presents an overview of the phylogenetic diversity of Agaricomycetes, emphasizing recent molecular phylogenetic studies.
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| 2. |
- Wang, Zheng, 1980, et al.
(författare)
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Future perspectives and challenges of fungal systematics in the age of big data
- 2016
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Ingår i: Biology of Microfungi. - Switzerland : Springer International Publishing. - 9783319291352 ; , s. 25-46
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Bokkapitel (refereegranskat)abstract
- Mycological research, especially research on fungal evolution and ecology, requires a robust and detailed fungal classification and phylogeny to facilitate efficient and informative communication among mycologists as well as for comparative biology relevant to the larger bioscience community. The field of fungal systematics has undergone numerous revisions recently, from early morphological classifications to an integrative taxonomy that is increasingly reliant on molecular phylogeny. These revisions have taken place at a range of taxonomic ranks, fueled by advances surmounting two major challenges, namely, adequate and balanced sampling of genetic markers and taxa and reinterpretation of phylogenetic informativeness of numerous morphological and ecological characters. The Assembling the Fungal Tree of Life (AFTOL) projects reflected a corresponding surge of collaborative effort in fungal molecular phylogeny using PCR and Sanger sequencing. Here we review recent progress in fungal systematics after AFTOL, in the post-Sanger age, and discuss the future fungal systematics that is emerging as a result of the extraordinary volume of data being gathered by high-throughput sequencing. We examine how environmental DNA surveys, sequence-based classification, and phylogenomics and phylotranscriptomics can impact fungal systematics and point out that sequenced fungal genomes could significantly improve multi-marker phylogenetic inference at a range of levels of fungal systematics by facilitating application of phylogenetically informative experimental design. We argue that it is time to integrate fungal systematics, genome-enabled mycology, and other dimensions of fungal research within the framework of evolutionary biology.
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| 3. |
- De Wit, Pierre, 1978
(författare)
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SNP Discovery Using Next Generation Transcriptomic Sequencing
- 2016
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Ingår i: Marine Genomics - Methods and Protocols. - New York : Springer Science + Business Media. - 9781493937721
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Bokkapitel (refereegranskat)abstract
- In this chapter, I will guide the user through methods to find new SNP markers from expressed sequence (RNA-Seq) data, focusing on the sample preparation and also on the bioinformatic analyses needed to sort through the immense flood of data from high-throughput sequencing machines. The general steps included are as follows: sample preparation, sequencing, quality control of data, assembly, mapping, SNP discovery, filtering, validation. The first few steps are traditional laboratory protocols, whereas steps following the sequencing are of bioinformatic nature. The bioinformatics described herein are by no means exhaustive, rather they serve as one example of a simple way of analyzing high-throughput sequence data to find SNP markers. Ideally, one would like to run through this protocol several times with a new dataset, while varying software parameters slightly, in order to determine the robustness of the results. The final validation step, although not described in much detail here, is also quite critical as that will be the final test of the accuracy of the assumptions made in silico. There is a plethora of downstream applications of a SNP dataset, not covered in this chapter. For an example of a more thorough protocol also including differential gene expression and functional enrichment analyses, BLAST annotation and downstream applications of SNP markers, a good starting point could be the “Simple Fool’s Guide to population genomics via RNA-Seq,” which is available at http://sfg.stanford.edu.
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| 4. |
- Axelson-Fisk, Marina, 1972, et al.
(författare)
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Gene finding in fungal genomes
- 2005
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Ingår i: Topics in Current Genetics: Comparative genomics using fungi as models. - 9783540314806 ; , s. 1-28
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa, overview
- 2013
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Ingår i: Encyclopedia of Metagenomics. - Berlin : Springer.
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Bokkapitel (refereegranskat)abstract
- Metaxa is a software tool for extracting full-length and partial ribosomal small subunit (SSU; 16S/18S/12S) sequences from metagenomic datasets, and for classifying the extracted sequences to taxonomic domains and organelle of origin. Metaxa is freely available from http://microbiology.se/software/metaxa
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| 6. |
- Fjeldså, Jon, et al.
(författare)
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How new species evolve
- 2020
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Ingår i: The Largest Avian Radiation. - Barcelona : Lynx Edicions. - 9788416728336
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 7. |
- Liljenström, Hans
(författare)
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Multi-scale Causation in Brain Dynamics
- 2016
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Ingår i: Cognitive Phase Transitions in the Cerebral Cortex - Enhancing the Neuron Doctrine by Modeling Neural Fields. - Cham : Springer International Publishing. - 9783319244044 ; 39:39, s. 177-186
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- For any complex system, consisting of several organizational levels, the problem of causation is profound. Usually, science considers upward causation as funda-mental, paying less or no attention to any downward causation. This is also true for the nervous system, where cortical neurodynamics, or even higher mental functions of the brain are normally considered causally dependent on the nerve cell activity, or even the activity at the ion channel level. This study presents both upward and downward causation in cortical neural systems, using computational methods with focus on cortical fluctuations. We have developed models of paleo- and neocortical structures, in order to study their mesoscopic neurodynamics, as a link between the microscopic neuronal and macroscopic mental events and pro-cesses. We demonstrate how both noise and chaos may play a role for the func-tions of cortical structures. While microscopic random noise may trigger meso- or macroscopic states, the nonlinear dynamics at these levels may also affect the ac-tivity at the microscopic level.
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| 8. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Molecular techniques in mycological studies and sequence data curating: quality control and challenges
- 2016
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Ingår i: Biology of Microfungi. - Switzerland : Springer International Publishing. - 9783319291352 ; , s. 47-64
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Bokkapitel (refereegranskat)abstract
- Molecular (DNA sequence) data are a routine source of information in mycology. Environmental sequencing efforts of substrates, such as soil, wood, and air, have revealed vast numbers of previously unknown or poorly understood species, and their integration in the classification system of fungi and the fungal tree of life represent significant challenges. Underpinning such efforts are reference datasets of reliable sequences to which newly generated sequences can be compared for taxonomic affiliation and perhaps hints of species traits and ecological roles. The public sequence databases are however accumulating countless sequences that are compromised in terms of taxonomic annotation or technical quality. Metadata on, e.g., country or host of collection and any specimen/culture association are similarly lacking for the majority of entries. This invites further mistakes and reduces scientific explanatory power. This chapter discusses how to spot compromised sequences and what to do when they are found. These curation principles are implemented in the fungal nuclear ribosomal internal transcribed spacer (ITS) sequence database UNITE (http://unite.ut.ee) for molecular identification of fungi. UNITE supports web-based third-party sequence annotation, and the reader is invited to take part in the annotation effort.
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| 9. |
- Patil, K. R., et al.
(författare)
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Structure and flux analysis of metabolic networks
- 2009
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Ingår i: The Metabolic Pathway Engineering Handbook: Fundamentals. - 9781439802977 ; , s. 17 1-17 18
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Conceptual understanding of complex cellular organization can be facilitated through a perspective based on the central dogma of biology1 (Figure 17.1). Accordingly, information coded in a genome is translated into proteins via mRNA. Proteins play a variety of roles in a cell, including that of enzymes, which selectively catalyze chemical transformation between metabolites. Ensemble of all nongenetically encoded compounds (thus, excluding mRNA, proteins, etc.) and enzymes operating on them is generally referred to as a metabolic network.2 In essence, metabolic networks convert nutrients available from environment into fundamental building blocks for the synthesis of proteins, DNA, and other cellular components. By providing energy and building blocks for growth and maintenance of cells, metabolic networks play a central role in sustaining life. is key role of metabolic networks in cellular operations is evident by two facts. Firstly, the basic architecture of metabolic networks is largely conserved across several dierent species ranging from microscopic bacteria to humans.3 Second, cellular response and adaptation to genetic/environmental perturbations is oen mediated through or reected in the operation of metabolic networks.4 Although the structure of metabolic networks dier signicantly at local levels (e.g., specic pathway structures),3,5 their large-scale conservancy across dierent species implies common biochemical and evolutionary principles underlying their operation.6,7 Understanding such general principles has great implications for: (i) correlating and extrapolating knowledge across dierent species, especially from model organisms (such as yeast) to humans, (ii) devising rational strategies for metabolic engineering, iii) nding remedies for metabolism related diseases, and (iv) synthetic biology.
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| 10. |
- Ahrné, Karin, et al.
(författare)
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Rödlista över fjärilar Lepidoptera
- 2015
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Ingår i: Rödlistade arter i Sverige 2015. - Uppsala : ArtDatabanken SLU. - 9789187853104 ; , s. 98-112
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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