| 1. |
- 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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| 2. |
- Leray, Matthieu, et al.
(författare)
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Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Adapter Ligation Method
- 2016
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Ingår i: Marine Genomics: Methods and Protocols. - New York : Springer. - 9781493937721 ; , s. 209-218
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Amplicon-based studies of marine microscopic eukaryotes, also referred to as metabarcoding studies, can be performed to analyze patterns of biodiversity or predator–prey interactions targeting the mitochondrial cytochrome oxidase 1 (CO1) or the small ribosomal subunit (SSU) markers. Because high-throughput sequencing (HTS) Illumina platforms provide millions of reads per run, hundreds of samples may be sequenced simultaneously. This protocol details the preparation of multiplexed amplicon libraries for Illumina MiSeq sequencing. We describe a strategy for sample multiplexing using a combination of tailed PCR primers and ligation of indexed adapters.
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| 3. |
- Doyle, Siamsa, et al.
(författare)
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Using a Reverse Genetics Approach to Investigate Small-Molecule Activity
- 2014
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Ingår i: Plant chemical genomics : methods and protocols. - Totowa, NJ : Humana Press. - 9781627035910 ; 1056:1056, s. 51-62
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Chemical genomics is a highly effective approach for understanding complex and dynamic biologicalprocesses in plants. A chemical activity can be investigated by a reverse genetics strategy, for which a hugeabundance and diversity of Arabidopsis thaliana mutants are readily available for exploitation. Here wepresent an approach to characterize a chemical of interest, as well as examples of studies demonstrating aneffective combination of chemical genomics with reverse genetics strategies, drawn from recent literatureon phytohormone signalling and auxin transport.
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| 4. |
- Engelbrecht Clemmensen, Karina, et al.
(författare)
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Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons
- 2016
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Ingår i: Microbial Environmental Genomics. - New York, NY : Springer New York. - 9781493933679 ; 1399, s. 61-88
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Bokkapitel (refereegranskat)abstract
- Fungal species participate in vast numbers of processes in the landscape around us. However, their often cryptic growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Recent technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enable identification and relative quantification of fungal community members across well-replicated experimental settings.Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, that is, the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon mix to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.
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| 5. |
- Hanson, Niklas, 1976, et al.
(författare)
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Bottendjuren påverkar fiskens hälsa
- 2016
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Ingår i: HAVET. ; , s. 86-89
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Under 2000-talet har kustfiskens hälsostatus förändrats kraftigt. Det gäller framför allt en mycket tydlig uppgång i aktiviteten av ett avgiftningssystem i levern hos abborre, följt av en lika kraftig nedgång. Förändringen var så stor att den är svår att förklara med något annat än ett förändrat upptag av miljögifter. Djupare analyser visar ett starkt samband med förekomsten av bottenlevande djur. Det är möjligt att dessa bidrar till att återföra miljögifter från bottensediment till ekosystemet.
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| 6. |
- Humphrey, Madeleine, et al.
(författare)
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Tracking Global and Local Changes in Membrane Fluidity Through Fluorescence Spectroscopy and Microscopy
- 2023
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Ingår i: Methods in Molecular Biology. - New York, NY : Springer US. - 1940-6029 .- 1064-3745. ; 2601, s. 203-229
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Membrane fluidity is a critical parameter of cellular membranes, which cells continuously strive to maintain within a viable range. Interference with the correct membrane fluidity state can strongly inhibit cell function. Triggered changes in membrane fluidity and associated impacts on lipid domains have been postulated to contribute to the mechanism of action of membrane targeting antimicrobials, but the corresponding analyses have been hampered by the absence of readily available analytical tools. Here, we expand upon the protocols outlined in the first edition of this book, providing further and alternative protocols that can be used to measure changes in membrane fluidity. We provide detailed protocols, which allow straightforward in vivo and in vitro measurement of antibiotic compound-triggered changes in membrane fluidity and fluid membrane microdomains. Furthermore, we summarize useful strains constructed by us and others to characterize and confirm lipid specificity of membrane antimicrobials directly in vivo.
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| 7. |
- Larsbrink, Johan, 1982, et al.
(författare)
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Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility
- 2020
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Ingår i: Advances in Applied Microbiology. - : Elsevier. - 0065-2164. ; 110, s. 63-98
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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| 8. |
- Larsson, Åke, 1944, et al.
(författare)
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Kustfisk - hälsa
- 2016
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Ingår i: HAVET. ; , s. 90-91
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Övervakningen av kustfisk i Bottniska viken, Öster sjön och Västerhavet visar fortsatt tydliga hälsoeffekter hos abborre och tånglake. Signifikanta tidstrender för många biomarkörer tyder på att de exponeras för kemiska ämnen som påverkar deras hälsa. Vanliga symptom i alla referensområden är påverkan på köns körtlar, leverenzymer, immunförsvar, saltreglering och kolhydratomsättning. Uppföljande forskning tyder på att det är miljögifter som orsakar effekterna. Samtidigt kan även förändringar i ekosystemet, såsom förändrad sammansättning av bottenlevande djur och födoväven, påverka exponeringen för olika miljögifter och därmed kustfiskens hälsa.
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| 9. |
- Lindahl, Björn
(författare)
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Metagenomics for Study of Fungal Ecology
- 2013
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Ingår i: The Ecological Genomics of Fungi. - Hoboken, NJ : John Wiley & Sons, Inc. - 9781119946106 ; , s. 279-303
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Bokkapitel (refereegranskat)
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| 10. |
- Linder, Tomas
(författare)
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Nitrogen Assimilation Pathways in Budding Yeasts
- 2019
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Ingår i: Non-conventional Yeasts: from Basic Research to Application. - Cham : Springer International Publishing. - 9783030211097 ; , s. 197-236
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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