| 1. |
- Sagova-Mareckova, M., et al.
(författare)
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Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring
- 2021
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 191
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Forskningsöversikt (refereegranskat)abstract
- Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems. (c) 2020 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ )
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| 2. |
- Testa, D., et al.
(författare)
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LTCC magnetic sensors at EPFL and TCV: Lessons learnt for ITER
- 2019
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Ingår i: Fusion Engineering and Design. - : Elsevier BV. - 0920-3796. ; 146, s. 1553-1558
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Tidskriftsartikel (refereegranskat)abstract
- Innovative 3D high-frequency magnetic sensors have been designed and manufactured in-house for installation on the Tokamak a Configuration Variable (TCV), and are currently routinely operational. These sensors combine the Low Temperature Co-fired Ceramic (LTCC) and the thick-film technologies, and are in various aspects similar to the majority of the inductive magnetic sensors currently being procured for ITER (290 out of 505 are LTCC-1D). The TCV LTCC-3D magnetic sensors provide measurements in the frequency range up to 1MHz of the perturbations to the toroidal (quasi-parallel: delta B-TOR(similar to)delta B-PAR), vertical (quasi-poloidal: delta B-V(ER)similar to delta B-PO(L)), and radial (delta B-RAD) magnetic field components, the latter being generally different from the component normal to the Last Closed Flux-Surface (delta B-NOR). The LTCC-3D delta B-RAD measurements improve significantly on the corresponding data with the saddle loops, which are mounted onto the wall and have a bandwidth of (similar to)3 kHz (due to the wall penetration time). The LTCC-3D delta B-TOR measurements (not previously available in TCV) provide evidence that certain MHD modes have a finite delta B-P(AR) at the LCFS, as recently calculated for pressure-driven instabilities. The LTCC-3D delta B-PO(L) measurements allow to cross-check the data obtained with the Mirnov coils, and led to the identification of large EM noise pick-up for the Mirnov DAQ. The LTCC-3D data for delta B-POL agree with those obtained with the Mirnov sensors in the frequency range where the respective data acquisition overlap, routinely up to 125kHz, and up to 250kHz in some discharges, when the EM noise pick-up on the Mirnov DAQ is removed. Finally, we look at what lessons can be learnt from our work for the forthcoming procurement, installation and operation of the LTCC-1D sensors in ITER.
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| 3. |
- Feron, Romain, et al.
(författare)
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RADSex : A computational workflow to study sex determination using restriction site-associated DNA sequencing data
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:5, s. 1715-1731
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Tidskriftsartikel (refereegranskat)abstract
- The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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| 4. |
- Litvinchuk, Spartak N., et al.
(författare)
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Influence of environmental conditions on the distribution of Central Asian green toads with three ploidy levels
- 2011
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Ingår i: Journal of Zoological Systematics and Evolutionary Research. - : Hindawi Limited. - 0947-5745 .- 1439-0469. ; 49:3, s. 233-239
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Tidskriftsartikel (refereegranskat)abstract
- We studied the distribution of Palearctic green toads (Bufo viridis subgroup), an anuran species group with three ploidy levels, inhabiting the Central Asian Amudarya River drainage. Various approaches (one-way, multivariate, components variance analyses and maximum entropy modelling) were used to estimate the effect of altitude, precipitation, temperature and land vegetation covers on the distribution of toads. It is usually assumed that polyploid species occur in regions with harsher climatic conditions (higher latitudes, elevations, etc.), but for the green toads complex, we revealed a more intricate situation. The diploid species (Bufo shaartusiensis and Bufo turanensis) inhabit the arid lowlands (from 44 to 789 m a.s.l.), while tetraploid Bufo pewzowi were recorded in mountainous regions (340-3492 m a.s.l.) with usually lower temperatures and higher precipitation rates than in the region inhabited by diploid species. The triploid species Bufo baturae was found in the Pamirs (Tajikistan) at the highest altitudes (2503-3859 m a.s.l.) under the harshest climatic conditions.
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