| 1. |
- Bottacin-Busolin, Andrea, 1980-, et al.
(författare)
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Effects of Streambed Morphology and Biofilm Growth on the Transient Storage of Solutes
- 2009
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 43:19, s. 7337-7342
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Tidskriftsartikel (refereegranskat)abstract
- Microbial biofilms are the prime site of nutrient and contaminant removal in streams. It is therefore essential to understand how biofilms affect hydrodynamic exchange, solute transport and retention in systems where geomorphology and induced hydrodynamics shape their growth and structure. We experimented with large-scale streamside flumes with streambed landscapes constructed from graded bedforms of constant height and wavelength. Each flume had a different bedform height and was covered with a layer of gravel as substratum for benthic microbial biofilms. Biofilms developed different biomass and physical structures in response to the hydrodynamic conditions induced by the streambed morphology. Step injections of conservative tracers were performed at different biofilm growth stages. The experimental breakthrough curves were analyzed with the STIR model, using a residence time approach to characterize the retention effects associated with biofilms. The retained mass of the solute increased with biofilm biomass and the biofilm-associated retention was furthermore related to bedform height We tentatively relate this behavior to biofilm structural differentiation induced by bed morphology, which highlights the strong linkage between geomorphology, hydrodynamics, and biofilms in natural streams and provide important clues for stream restoration.
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| 2. |
- Burian, Alfred, 1984-, et al.
(författare)
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Benthic-pelagic coupling drives non-seasonal zooplankton blooms and restructures energy flows in shallow tropical lakes
- 2016
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 61:3, s. 795-805
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Tidskriftsartikel (refereegranskat)abstract
- Zooplankton blooms are a frequent phenomenon in tropical systems. However, drivers of bloom formation and the contribution of emerging resting eggs are largely unexplored. We investigated the dynamics and the triggers of rotifer blooms in African soda-lakes and assessed their impact on other trophic levels. A meta-analysis of rotifer peak densities including abundances of up to 6 × 105 individuals L−1 demonstrated that rotifer bloom formation was uncoupled from the food environment and the seasonality of climatic conditions. A time series with weekly sampling intervals from Lake Nakuru (Kenya) revealed that intrinsic growth factors (food quality and the physicochemical environment) significantly affected rotifer population fluctuations, but were of minor importance for bloom formation. Instead, rotifer bloom formation was linked to sediment resuspension, a prerequisite for hatching of resting-eggs. Population growth rates exceed pelagic birth rates and simulations of rotifer dynamics confirmed the quantitative importance of rotifer emergence from the sediment egg-bank and signifying a decoupling of bloom formation from pelagic reproduction. Rotifer blooms led to a top-down control of small-sized algae and facilitated a switch to more grazing-resistant, filamentous cyanobacteria. This shift in phytoplankton composition cascaded up the food chain and triggered the return of filter-feeding flamingos. Calculations of consequent changes in the lake's energy budget and export of aquatic primary production to terrestrial ecosystems demonstrated the large potential impact of nonseasonal disturbances on the functioning of shallow tropical lakes.
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
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| 5. |
- Hawkes, Jeffrey A., et al.
(författare)
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An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry : Are we getting the same answer?
- 2020
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Ingår i: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 18:6, s. 235-258
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive-ion and negative-ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified similar to 1000 common ions in both negative- and positive-ion modes over a wide range of m/z values and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance-weighted average indices (H/C, O/C, aromaticity and m/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments.
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| 6. |
- Hoedl, Iris, et al.
(författare)
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Voronoi Tessellation Captures Very Early Clustering of Single Primary Cells as Induced by Interactions in Nascent Biofilms
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10, s. e26368-
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Tidskriftsartikel (refereegranskat)abstract
- Biofilms dominate microbial life in numerous aquatic ecosystems, and in engineered and medical systems, as well. The formation of biofilms is initiated by single primary cells colonizing surfaces from the bulk liquid. The next steps from primary cells towards the first cell clusters as the initial step of biofilm formation remain relatively poorly studied. Clonal growth and random migration of primary cells are traditionally considered as the dominant processes leading to organized microcolonies in laboratory grown monocultures. Using Voronoi tessellation, we show that the spatial distribution of primary cells colonizing initially sterile surfaces from natural streamwater community deviates from uniform randomness already during the very early colonisation. The deviation from uniform randomness increased with colonisation - despite the absence of cell reproduction - and was even more pronounced when the flow of water above biofilms was multidirectional and shear stress elevated. We propose a simple mechanistic model that captures interactions, such as cell-to-cell signalling or chemical surface conditioning, to simulate the observed distribution patterns. Model predictions match empirical observations reasonably well, highlighting the role of biotic interactions even already during very early biofilm formation despite few and distant cells. The transition from single primary cells to clustering accelerated by biotic interactions rather than by reproduction may be particularly advantageous in harsh environments - the rule rather than the exception outside the laboratory.
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| 7. |
- Marcé, Rafael, et al.
(författare)
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Emissions from dry inland waters are a blind spot in the global carbon cycle
- 2019
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Ingår i: Earth-Science Reviews. - : Elsevier. - 0012-8252 .- 1872-6828. ; 188, s. 240-248
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Forskningsöversikt (refereegranskat)abstract
- A large part of the world's inland waters, including streams, rivers, ponds, lakes and reservoirs is subject to occasional, recurrent or even permanent drying. Moreover, the occurrence and intensity of drying events are increasing in many areas of the world because of climate change, water abstraction, and land use alteration. Yet, information on the gaseous carbon (C) fluxes from dry inland waters is scarce, thus precluding a comprehensive assessment of C emissions including all, also intermittently dry, inland waters. Here, we review current knowledge on gaseous C fluxes from lotic (streams and rivers) and lentic (ponds, lakes, and reservoirs) inland waters during dry phases and the response to rewetting, considering controls and sources as well as implications of including 'dry' fluxes for local and global scale estimates. Moreover, knowledge gaps and research needs are discussed. Our conservative estimates indicate that adding emissions from dry inland waters to current global estimates of CO2 emissions from inland waters could result in an increase of 0.22 Pg C year(-1), or similar to 10% of total fluxes. We outline the necessary conceptual understanding to successfully include dry phases in a more complete picture of inland water C emissions and identify potential implications for global C cycle feedbacks.
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| 8. |
- Merder, Julian, et al.
(författare)
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ICBM-OCEAN : Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures
- 2020
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 92:10, s. 6832-6838
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Tidskriftsartikel (refereegranskat)abstract
- Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg-complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.
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| 9. |
- Schaper, Jonas L., et al.
(författare)
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Fate of Trace Organic Compounds in the Hyporheic Zone : Influence of Retardation, the Benthic Biolayer, and Organic Carbon
- 2019
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:8, s. 4224-4234
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Tidskriftsartikel (refereegranskat)abstract
- The fate of 28 trace organic compounds (TrOCs) was investigated in the hyporheic zone (HZ) of an urban lowland river in Berlin, Germany. Water samples were collected hourly over 17 h in the river and in three depths in the HZ using minipoint samplers. The four relatively variable time series were subsequently used to calculate first order removal rates and retardation coefficients via a one-dimensional reactive transport model. Reversible sorption processes led to substantial retardation of many TrOCs along the investigated hyporheic flow path. Some TrOCs, such as dihydroxy-carbamazepine, O-desmethylvenlafaxine, and venlafaxine, were found to be stable in the HZ. Others were readily removed with half-lives in the first 10 cm of the HZ ranging from 0.1 +/- 0.01 h for iopromide to 3.3 +/- 0.3 h for tramadol. Removal rate constants of the majority of reactive TrOCs were highest in the first 10 cm of the HZ, where removal of biodegradable dissolved organic matter was also the highest. Because conditions were oxic along the top 30 cm of the investigated flow path, we attribute this finding to the high microbial activity typically associated with the shallow HZ. Frequent and short vertical hyporheic exchange flows could therefore be more important for reach-scale TrOC removal than long, lateral hyporheic flow paths.
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| 10. |
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| 11. |
- Shrine, N, et al.
(författare)
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Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk
- 2023
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 55:3, s. 410-
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Tidskriftsartikel (refereegranskat)abstract
- Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.
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| 12. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 13. |
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| 14. |
- Zhou, Qing, et al.
(författare)
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Persistence of ctDNA in breast cancer patients during neoadjuvant treatment is a significant predictor of poor tumour response.
- 2021
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Ingår i: Clinical cancer research : an official journal of the American Association for Cancer Research. - 1557-3265. ; 28:4, s. 697-707
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Tidskriftsartikel (refereegranskat)abstract
- Accurate response assessment during neoadjuvant systemic treatment (NST) poses a clinical challenge. Therefore, a minimally-invasive assessment of tumor response based on cell-free circulating tumor DNA (ctDNA) may be beneficial to guide treatment decisions.We profiled 93 genes in tissue from 193 early breast cancer patients. Patient-specific assays were designed for 145 patients to track ctDNA during NST in plasma. ctDNA presence and levels were correlated with complete pathological response (pCR), residual cancer burden (RCB) as well as clinicopathologic characteristics of the tumor to identify potential proxies for ctDNA release.At baseline, ctDNA could be detected in 63/145 (43.4%) patients and persisted in 25/63 (39.7%) patients at mid-therapy (MT) and 15/63 (23.8%) patients at the end of treatment. ctDNA detection at MT was significantly associated with higher RCB (OR 0.062, 95% CI 0.01-0.48, P=0.0077).Out of 31 patients with detectable ctDNA at MT, 30 patients (96.8%) were non-responders (RCB II, n=8; RCB III, n=22) and only one patient responded to the treatment (RCB I). Considering all 145 patients with baseline (BL) plasma, none of the patients with RCB 0 and only 6.7% of patients with RCB I had ctDNA detectable at MT, while 30.6% and 29.6% of patients with RCB II/III, respectively, had a positive ctDNA result.Overall, our results demonstrate that the detection and persistence of ctDNA at MT may have the potential to negatively predict response to neoadjuvant treatment and identify patients who will not achieve pCR or be classified with RCB II/III.
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| 15. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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