| 1. |
- Buehligen, Franziska, et al.
(författare)
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Analysis of aging in lager brewing yeast during serial repitching
- 2014
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Ingår i: Journal of Biotechnology. - : Elsevier BV. - 0168-1656 .- 1873-4863. ; 187, s. 60-70
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Tidskriftsartikel (refereegranskat)abstract
- Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the same brewing yeast strain but different abiotic backgrounds and repitching regimes with varying numbers of reuses. Next to bud scar numbers the DNA content of the Saccharomyces pastorianus HEBRU cells was analyzed. Gene expression patterns were investigated using low-density microarrays with genes for aging, stress, storage compound metabolism and cell cycle. Two breweries showed a stable rejuvenation rate during serial repitching. In a third brewery the fraction of virgin cells varied, which could be explained with differing wort aeration rates. Furthermore, the number of bud scars per cell and cell size correlated in all 3 breweries throughout all runs. Transcriptome analyses revealed that from the 6th run on, mainly for the cells positive gene expression could be seen, for example up-regulation of trehalose and glycogen metabolism genes. Additionally, the cells' settling in the cone was dependent on cell size, with the lowest and the uppermost cone layers showing the highest amount of dead cells. In general, cells do not progressively age during extended serial repitching.
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| 2. |
- Buehligen, Franziska, et al.
(författare)
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Sustainability of industrial yeast serial repitching practice studied by gene expression and correlation analysis
- 2013
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Ingår i: Journal of Biotechnology. - : Elsevier BV. - 0168-1656 .- 1873-4863. ; 168:4, s. 718-728
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Tidskriftsartikel (refereegranskat)abstract
- Bottom-fermenting Saccharomyces pastorianus strains driving brewing fermentation processes are usually reused several times. It is still unclear, whether the number of successions may have an impact on cell physiology prompting consequences for brewing quality. In this study, fermentation performance of up to twenty consecutive runs in a brewery was investigated. For each run mRNA expression levels of cellular marker molecules, which are known to correlate with metabolism, hexose transport, aging processes, stress response mechanisms and flocculation capability was estimated to obtain information on changes in cell physiology over the successive runs. Low-density microarrays were used for this purpose and the resulting gene expression profiles were finally correlated with changes in the abiotic micro-environments. A surprising stability of the marker molecule expression profiles within each specific serial repitching was stated. Loss of flocculation or an advanced aging could not be detected during serial repitching in the analyzed brewery. However, certain runs of the serial repitchings showed high variation in stress response which was found to be caused by perturbations of the abiotic conditions. Regardless, the study showed that S. pastorianus can be used repeatedly in serial repitching processes without loss of prominent physiological characteristics.
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| 3. |
- Jahn, Michael, et al.
(författare)
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Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR
- 2016
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Ingår i: Microbial Cell Factories. - : BioMed Central. - 1475-2859. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). Results: In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. Conclusions: The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells.
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Koch, Christin, et al.
(författare)
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CHIC - An automated approach for the detection of dynamic variations in complex microbial communities
- 2013
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Ingår i: Cytometry Part A. - : Wiley. - 1552-4922 .- 1552-4930. ; 83A:6, s. 561-567
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Tidskriftsartikel (refereegranskat)abstract
- Altering environmental conditions change structures of microbial communities. These effects have an impact on the single-cell level and can be sensitively detected using community flow cytometry. However, although highly accurate, microbial monitoring campaigns are still rarely performed applying this technique. One reason is the limited access to pattern analysis approaches for the evaluation of microbial cytometric data. In this article, a new analyzing tool, Cytometric Histogram Image Comparison (CHIC), is presented, which realizes trend interpretation of variations in microbial community structures (i) without any previous definition of gates, by working (ii) person independent, and (iii) with low computational demand. Various factors influencing a sensitive determination of changes in community structures were tested. The sensitivity of this technique was found to discriminate down to 0.5% internal variation. The final protocol was exemplarily applied to a complex microbial community dataset, and correlations to experimental variation were successfully shown.
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| 6. |
- Majaneva, Markus, et al.
(författare)
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Sea-ice eukaryotes of the Gulf of Finland, Baltic Sea, and evidence for herbivory on weakly shade-adapted ice algae
- 2017
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Ingår i: European Journal of Protistology. - : Elsevier. - 0932-4739 .- 1618-0429. ; 57, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- To determine community composition and physiological status of early spring sea-ice organisms, we collected sea-ice, slush and under-ice water samples from the Baltic Sea. We combined light microscopy, HPLC pigment analysis and pyrosequencing, and related the biomass and physiological status of sea-ice algae with the protistan community composition in a new way in the area. In terms of biomass, centric diatoms including a distinct Melosira arctica bloom in the upper intermediate section of the fast ice, dinoflagellates, euglenoids and the cyanobacterium Aphanizomenon sp. predominated in the sea-ice sections and unidentified flagellates in the slush. Based on pigment analyses, the ice-algal communities showed no adjusted photosynthetic pigment pools throughout the sea ice, and the bottom-ice communities were not shade-adapted. The sea ice included more characteristic phototrophic taxa (49%) than did slush (18%) and under-ice water (37%). Cercozoans and ciliates were the richest taxon groups, and the differences among the communities arose mainly from the various phagotrophic protistan taxa inhabiting the communities. The presence of pheophytin a coincided with an elevated ciliate biomass and read abundance in the drift ice and with a high Eurytemora affinis read abundance in the pack ice, indicating that ciliates and Eurytemora affinis were grazing on algae. (C) 2016 Elsevier GmbH. All rights reserved.
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| 7. |
- Schwartzkopf, Matthias, et al.
(författare)
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In Situ Monitoring of Scale Effects on Phase Selection and Plasmonic Shifts during the Growth of AgCu Alloy Nanostructures for Anticounterfeiting Applications
- 2022
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Ingår i: ACS Applied Nano Materials. - : American Chemical Society (ACS). - 2574-0970. ; 5:3, s. 3832-3842
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Tidskriftsartikel (refereegranskat)abstract
- Tailoring of plasmon resonances is essential for applications in anticounterfeiting. This is readily achieved by tuning the composition of alloyed metal clusters; in the simplest case, binary alloys are used. Yet, one challenge is the correlation of cluster morphology and composition with the changing optoelectronic properties. Hitherto, the early stages of metal alloy nanocluster formation in immiscible binary systems such as silver and copper have been accessible by molecular dynamics (MD) simulations and transmission electron microscopy (TEM). Here, we investigate in real time the formation of supported silver, copper, and silver-copper-alloy nanoclusters during sputter deposition on poly(methyl methacrylate) by combining in situ surface-sensitive X-ray scattering with optical spectroscopy. While following the transient growth morphologies, we quantify the early stages of phase separation at the nanoscale, follow the shifts of surface plasmon resonances, and quantify the growth kinetics of the nanogranular layers at different thresholds. We are able to extract the influence of scaling effects on the nucleation and phase selection. The internal structure of the alloy cluster shows a copper-rich core/silver-rich shell structure because the copper core yields a lower mobility and higher crystallization tendency than the silver fraction. We compare our results to MD simulation and TEM data. This demonstrates a route to tailor accurately the plasmon resonances of nanosized, polymer-supported clusters which is a crucial prerequisite for anticounterfeiting.
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