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  • 51.
    Hu, Yue O. O.
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Karlson, Bengt
    Charvet, Sophie
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea2016Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, artikkel-id 679Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Erniliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

  • 52.
    Hu, Yue O. O.
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ndegwa, Nelson
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden..
    Alneberg, Johannes
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Johansson, Sebastian
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Logue, Jurg Brendan
    Huss, Mikael
    Käller, Max
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Jens
    Stockholm Vatten Och Avfall AB, Stockholm, Sweden..
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 11907Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.

  • 53.
    Hugerth, Luisa
    KTH, Skolan för bioteknologi (BIO), Genteknologi. Science for Life Laboratory.
    High-throughput DNA Sequencingin Microbial Ecology: Methods and Applications2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Microorganisms play central roles in planet Earth’s geochemical cycles, in food production, and in health and disease of humans and livestock. In spite of this, most microbial life forms remain unknown and unnamed, their ecological importance and potential technological applications beyond the realm of speculation. This is due both to the magnitude of microbial diversity and to technological limitations. Of the many advances that have enabled microbiology to reach new depth and breadth in the past decade, one of the most important is affordable high-throughput DNA sequencing. This technology plays a central role in each paper in this thesis.

    Papers I and II are focused on developing methods to survey microbial diversity based on marker gene amplification and sequencing. In Paper I we proposed a computational strategy to design primers with the highest coverage among a given set of sequences and applied it to drastically improve one of the most commonly used primer pairs for ecological surveys of prokaryotes. In Paper II this strategy was applied to an eukaryotic marker gene. Despite their importance in the food chain, eukaryotic microbes are much more seldom surveyed than bacteria. Paper II aimed at making this domain of life more amenable to high-throughput surveys.

    In Paper III, the primers designed in papers I and II were applied to water samples collected up to twice weekly from 2011 to 2013 at an offshore station in the Baltic proper, the Linnaeus Microbial Observatory. In addition to tracking microbial communities over these three years, we created predictive models for hundreds of microbial populations, based on their co-occurrence with other populations and environmental factors.

    In paper IV we explored the entire metagenomic diversity in the Linnaeus Microbial Observatory. We used computational tools developed in our group to construct draft genomes of abundant bacteria and archaea and described their phylogeny, seasonal dynamics and potential physiology. We were also able to establish that, rather than being a mixture of genomes from fresh and saline water, the Baltic Sea plankton community is composed of brackish specialists which diverged from other aquatic microorganisms thousands of years before the formation of the Baltic itself.

  • 54.
    Hugerth, Luisa
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. Science for Life Laboratory.
    Lindh, Markus
    Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
    Sjöqvist, Conny
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Carina, Bunse
    Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
    Legrand, Catherine
    Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial model Systems - Linnaeus University.
    Andersson, Anders
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Seasonal dynamics and interactions among Baltic Sea prokaryoticand eukaryotic plankton assemblagesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    One of the main goals of microbial ecology is to identify the mechanismsthat regulate patterns in community structure at temporal scalescompatible with populations’ turnover times across complete seasonalcycles. Here, we examined high-frequency temporal dynamics of marineplankton from a sampling effort covering 2011-2013, roughly twice weekly,comprising 144 samples. Bacterial and eukaryotic communities wereprofiled by 16S and 18S high-throughput sequencing, respectively.Interestingly, we found that no combination of the measured environmentalparameters could predict a significant proportion of the variation inpopulation dynamics of bacterioplankton, and even less so for eukaryoticplankton. Large differences in physicochemical conditions and communitycomposition typical of temperate climates mean that different regimes canquickly succeed each other over the year, with the relative importance ofdifferent drivers changing equally rapidly. Nevertheless, our approachrevealed interesting recurrent co-occurrence patterns across distinctenvironmental changes. Hence, we could make abundance predictions formore than half of the most frequent OTUs based on interactions with otherOTUs. These results suggests that a complex set of biotic interactions arecontributing to temporal patterns among planktonic assemblages despiterapid changes in environmental conditions.

  • 55.
    Hugerth, Luisa W.
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. Karolinska Institutet, Sweden.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 1561Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data inmicrobial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

  • 56.
    Hugerth, Luisa W.
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Larsson, John
    Alneberg, Johannes
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Lindh, Markus V.
    Legrand, Catherine
    Pinhassi, Jarone
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Metagenome-assembled genomes uncover a global brackish microbiome2015Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, artikkel-id 279Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Results: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. Conclusions: We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.

  • 57.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Data Analysis and Next Generation Sequencing : Applications in Microbiology.2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.

    The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.

    Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions.

    Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field.

  • 58.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Golumbeanu, Monica
    Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland.
    Fouquier d'Hérouël, Aymeric
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
    Lacoux, Caroline
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Bonnin, Rémy A.
    Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
    Kennedy, Sean P.
    INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
    Wessner, Francoise
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Serror, Pascale
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Bouloc, Philippe
    Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France.
    Repoila, Francis
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis2015Inngår i: RNA, ISSN 1355-8382Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA-and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small-and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

  • 59.
    Innocenti, Nicolas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Repoila, Francis
    INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France}\affiliation{AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bateria using tagRNA-seq2015Inngår i: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tag is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.

  • 60. Jarvis, Å.
    et al.
    Sundberg, Cecilia
    Swedish University of Agricultural Sciences, Sweden.
    Milenkovski, S.
    Pell, M.
    Smårs, S.
    Lindgren, P. -E
    Hallin, S.
    Activity and composition of ammonia oxidizing bacterial communities and emission dynamics of NH3 and N2O in a compost reactor treating organic household waste2009Inngår i: Journal of Applied Microbiology, ISSN 1364-5072, E-ISSN 1365-2672, Vol. 106, nr 5, s. 1502-1511Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aims: To monitor emissions of NH3 and N2O during composting and link these to ammonia oxidation rates and the community structure of ammonia oxidizing bacteria (AOB). Methods and Results: A laboratory-scale compost reactor treating organic household waste was run for 2 months. NH 3 emissions peaked when pH started to increase. Small amounts of N2O and CH4 were also produced. In total, 16% and less than 1% of the initial N was lost as NH3-N and N2O-N respectively. The potential ammonia oxidation rate, determined by a chlorate inhibition assay, increased fourfold during the first 9 days and then remained high. Initially, both Nitrosospira and Nitrosomonas populations were detected using DGGE analysis of AOB specific 16S rRNA fragments. Only Nitrosomonas europaea was detected under thermophilic conditions, but Nitrosospira populations re-established during the cooling phase. Conclusions: Thermophilic conditions favoured high potential ammonia oxidation rates, suggesting that ammonia oxidation contributed to reduced NH3 emissions. Small but significant amounts of N2O were emitted during the thermophilic phase. The significance of different AOBs detected in the compost for ammonia oxidation is not clear. Significance and Impact of Study: This study shows that ammonia oxidation occurs at high temperature composting and therefore most likely reduces NH3 emissions.

  • 61.
    Kroll, Jens
    et al.
    Westfälische Wilhelms-Universität Münster, Germany.
    Klinter, Stefan
    Westfälische Wilhelms-Universität Münster, Germany.
    Schneider, Cornelia
    Westfälische Wilhelms-Universität Münster, Germany.
    Voß, Isabella
    Westfälische Wilhelms-Universität Münster, Germany.
    Steinbüchel, Alexander
    Westfälische Wilhelms-Universität Münster, Germany.
    Plasmid addiction systems: Perspectives and applications in biotechnology2010Inngår i: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 3, nr 6, s. 634-657Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Biotechnical production processes often operate with plasmid-based expression systems in well-established prokaryotic and eukaryotic hosts such as Escherichia coli or Saccharomyces cerevisiae, respectively. Genetically engineered organisms produce important chemicals, biopolymers, biofuels and high-value proteins like insulin. In those bioprocesses plasmids in recombinant hosts have an essential impact on productivity. Plasmid-free cells lead to losses in the entire product recovery and decrease the profitability of the whole process. Use of antibiotics in industrial fermentations is not an applicable option to maintain plasmid stability. Especially in pharmaceutical or GMP-based fermentation processes, deployed antibiotics must be inactivated and removed. Several plasmid addiction systems (PAS) were described in the literature. However, not every system has reached a full applicable state. This review compares most known addiction systems and is focusing on biotechnical applications.

  • 62.
    Kroll, Jens
    et al.
    Westfälische Wilhelms-Universität Münster, Germany.
    Klinter, Stefan
    Westfälische Wilhelms-Universität Münster, Germany.
    Steinbüchel, Alexander
    Westfälische Wilhelms-Universität Münster, Germany.
    A novel plasmid addiction system for large-scale production of cyanophycin in Escherichia coli using mineral salts medium2011Inngår i: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 89, nr 3, s. 593-604Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Introduction: Hitherto the production of the biopolymer cyanophycin (CGP) using recombinant Escherichia coli strains and cheap mineral salts medium yielded only trace amounts of CGP (<0.5%, w/w) of the cell dry matter (CDM). This was probably due to the instability of the plasmids encoding the cyanophycin synthetase. Material and methods: In this study, we developed an anabolism-based media-dependent plasmid addiction system (PAS) to enhance plasmid stability, and we established a process based on a modified mineral salts medium yielding a CGP content of 42% (w/w) at the maximum without the addition of amino acids to the medium for the first time. This PAS is based on different lysine biosynthesis pathways and consists of two components: (1) a knockout of the chromosomal dapE disrupts the native succinylase pathway in E. coli and (2) the complementation by the plasmid-encoded artificial aminotransferase pathway mediated by the dapL gene from Synechocystis sp. PCC 6308, which allows the synthesis of the essential lysine precursor L,L-2,6-diaminopimelate. In addition, this plasmid also harbors cphAC595S, an engineered cyanophycin synthetase gene responsible for CGP production. Results: Cultivation experiments in Erlenmeyer flask and also in bioreactors in mineral salts medium without antibiotics revealed an at least 4.5-fold enhanced production of CGP in comparison to control cultivations without PAS. Discussion: Fermentation experiments with culture volume of up to 400 l yielded a maximum of 18% CGP (w/w) and a final cell density of 15.2 g CDM/l. Lactose was used constantly as an effective inducer and carbon source. Thus, we present a convenient option to produce CGP with E. coli at a technical scale without the need to add antibiotics or amino acids using the mineral salts medium designed in this study.

  • 63. Kujawa, M
    et al.
    Leitner, C
    Halada, P
    Volc, J
    Hallberg, B M
    Divne, Christina
    Peterbauer, C K
    Haltrich, D
    Pyranose oxidase from Trametes multicolour: application in biocatalysis2005Inngår i: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 118, s. 89-89Artikkel i tidsskrift (Fagfellevurdert)
  • 64. Kutsenko, Alexey
    et al.
    Svensson, Thomas
    Nystedt, Bjorn
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bjork, Petra
    Sonnhammer, Erik
    Giacomello, Stefania
    Visa, Neus
    Wieslander, Lars
    The Chironomus tentans genome sequence and the organization of the Balbiani ring genes2014Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, s. 819-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes. Results: The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations. Conclusions: We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.

  • 65. Kämpfer, Peter
    et al.
    Lindh, Jenny M.
    Dept of genetics microbiology and toxicology, Stockholm University.
    Terenius, Olle
    Dept of genetics microbiology and toxicology, Stockholm University.
    Haghdoost, Siamak
    Dept of genetics microbiology and toxicology, Stockholm University.
    Falsen, Enevold
    Busse, Hans-Jürgen
    Faye, Ingrid
    Dept of genetics microbiology and toxicology, Stockholm University.
    Thorsellia anophelis gen. nov., sp. nov., a new member of the Gammaproteobacteria2006Inngår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 56, nr 2, s. 335-338Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A Gram-negative, rod-shaped organism (CCUG 49520T) was isolated from the midgut of the mosquito Anopheles arabiensis. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing <93% similarity to species of the families Enterobacteriaceae and Vibrionaceae. The quinone system consisted exclusively of ubiquinone Q-8; the polar lipid profile consisted of the major compounds phosphatidylethanolamine and phosphatidylglycerol, a moderate to minor amount of two unknown aminophospholipids, an unknown phospholipid and two unknown polar lipids; the polyamine pattern was characterized by the predominant compound 1,3-diaminopropane and showed some significant differences when compared with members of the Enterobacteriaceae and Vibrionaceae. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic data, strain CCUG 49520T is considered to represent a new genus and species, for which the name Thorsellia anophelis gen. nov., sp. nov. is proposed. The type strain is CCUG 49520T (=CIP 108754T).

  • 66.
    Kämpfer, Peter
    et al.
    Institute fur Angewandte Mikrobiologie Giessen, Germany.
    Terenius, Olle
    Dept of genetics microbiology and toxicology, Stockholm University.
    Lindh, Jenny M.
    Dept of genetics microbiology and toxicology, Stockholm University.
    Faye, Ingrid
    Dept of genetics microbiology and toxicology, Stockholm University.
    Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis2006Inngår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 56, nr 2, s. 389-392Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A Gram-positive, aerobic, non-motile strain, H2.16BT, isolated from the midgut of the mosquito Anopheles arabiensis was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strain H2.16BT was shown to belong to the genus Janibacter, being most closely related to Janibacter melonis (98.3%), Janibacter terrae (98.5%) and Janibacter limosus (98.5%). Chemotaxonomic data (meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall and major fatty acids of iso-C16:0, C17:1omega8c and C17:0)) supported the allocation of the strain to the genus Janibacter. The results of DNA-DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain H2.16BT from closely related species. Thus, H2.16BT represents a novel species of the genus Janibacter, for which the name Janibacter anophelis sp. nov. is proposed. The type strain is H2.16BT (=CCUG 49715T=CIP 108728T).

  • 67.
    Larsbrink, Johan
    et al.
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Tuveng, T. R.
    Pope, P. B.
    Bulone, V.
    Eijsink, V. G. H.
    Brumer, Harry
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    McKee, Lauren S.
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap. KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis2017Inngår i: Journal of Proteomics, ISSN 1874-3919, E-ISSN 1876-7737, Vol. 156, s. 63-74Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Together with fungi, saprophytic bacteria are central to the decomposition and recycling of biomass in forest environments. The Bacteroidetes phylum is abundant in diverse habitats, and several species have been shown to be able to deconstruct a wide variety of complex carbohydrates. The genus Chitinophaga is often enriched in hotspots of plant and microbial biomass degradation. We present a proteomic assessment of the ability of Chitinophaga pinensis to grow on and degrade mannan polysaccharides, using an agarose plate-based method of protein collection to minimise contamination with exopolysaccharides and proteins from lysed cells, and to reflect the realistic setting of growth on a solid surface. We show that select Polysaccharide Utilisation Loci (PULs) are expressed in different growth conditions, and identify enzymes that may be involved in mannan degradation. By comparing proteomic and enzymatic profiles, we show evidence for the induced expression of enzymes and PULs in cells grown on mannan polysaccharides compared with cells grown on glucose. In addition, we show that the secretion of putative biomass-degrading enzymes during growth on glucose comprises a system for nutrient scavenging, which employs constitutively produced enzymes. Significance of this study Chitinophaga pinensis belongs to a bacterial genus which is prominent in microbial communities in agricultural and forest environments, where plant and fungal biomass is intensively degraded. Such degradation is hugely significant in the recycling of carbon in the natural environment, and the enzymes responsible are of biotechnological relevance in emerging technologies involving the deconstruction of plant cell wall material. The bacterium has a comparatively large genome, which includes many uncharacterised carbohydrate-active enzymes. We present the first proteomic assessment of the biomass-degrading machinery of this species, focusing on mannan, an abundant plant cell wall hemicellulose. Our findings include the identification of several novel enzymes, which are promising targets for future biochemical characterisation. In addition, the data indicate the expression of specific Polysaccharide Utilisation Loci, induced in the presence of different growth substrates. We also highlight how a constitutive secretion of enzymes which deconstruct microbial biomass likely forms part of a nutrient scavenging process.

  • 68. Lin, H. Y.
    et al.
    Hoffmann, F.
    Rozkov, Aleksei
    KTH, Tidigare Institutioner, Bioteknologi.
    Enfors, Sven-Olof
    KTH, Tidigare Institutioner, Bioteknologi.
    Rinas, U.
    Neubauer, P.
    Change of extracellular cAMP concentration is a sensitive reporter for bacterial fitness in high-cell-density cultures of Escherichia coli2004Inngår i: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 87, nr 5, s. 602-613Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Guanosine-3'5'-tetraphosphate (ppGpp) and as, two regulators of the starvation response of Escherichia coli, have received increasing attention for monitoring cell physiological changes in production processes, although both are difficult to quantify. The kinetics of cAMP formation and degradation were not yet investigated in such processes, although the complex regulation of cAMP by synthesis, release, and degradation in connection with straightforward methods for analysis renders it a highly informative target. Therefore, we followed the cAMP concentration in various nonrecombinant and in four different recombinant glucose-limited fed-batch processes in different production scales. The intracellular cAMP concentration increases strongly at the end of the batch phase. Most cAMP is released to the cultivation medium. The rates of accumulation and degradation of extracellular cAMP are growth-rate-dependent and show a distinct maximum at a growth rate of about 0.35 h(-1). At very low growth rates, below 0.05 h(-1), extracellular cAMP is not produced but rather degraded, independent of whether this low growth rate is caused by glucose limitation or by the high metabolic load of recombinant protein production. In contrast to intracellular cAMP, which is highly unstable, analysis of extracellular cAMP is simpler and the kinetics of accumulation and degradation reflect well the physiological situation, including unlimited growth, limitation, and severe starvation of a production host.

  • 69.
    Lindh, Jenny M.
    et al.
    Dept of Genetics, Microbiology and Toxicology, Stockholm University.
    Terenius, Olle
    Dept of genetics microbiology and toxicology, Stockholm University.
    Eriksson-Gonzales, Karolina
    Dept of Genetics, Microbiology and Toxicology, Stockholm University.
    Knols, Bart G. J.
    Faye, Ingrid
    Dept of genetics microbiology and toxicology, Stockholm University.
    Re-introducing bacteria in mosquitoes - A method for determination of mosquito feeding preferences based on coloured sugar solutions2006Inngår i: Acta Tropica, ISSN 0001-706X, E-ISSN 1873-6254, Vol. 99, nr 2-3, s. 173-183Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study, sugar-feeding was investigated as a possible means of re-introducing bacteria into mosquito midguts with the aim of identifying bacteria that are suitable for creating paratransgenic mosquitoes. In a paratransgenic approach, bacteria are utilised to deliver effector molecules capable of inhibiting pathogen development in the midgut of the vector. To determine if mosquitoes discriminate between sterile sugar solutions and sugar solutions with bacteria, a method for screening mosquito feeding preferences was developed. This method was tested for Aedes aegypti, Anopheles arabiensis and An. gambiae s.s. mosquitoes and is based on a dual-choice test of solutions labelled with food dyes. Three different tests (dye/colour detection, sugar detection and sugar-concentration detection) were performed to evaluate the method, after which bacteria previously isolated from mosquitoes were used in the experiments. It was shown that mosquitoes do not discriminate between sugar solutions with or without these bacteria indicating that sugar-feeding is a possible means to introduce bacteria into mosquitoes. Furthermore, two different setups of the method were used, enabling us to differentiate between tactile/taste and olfactory responses. The method described in this paper is easy to use, cost-effective and allows broad screening of mosquito sugar-feeding preferences.

  • 70.
    Lindh, Jenny
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Borg-Karlson, Anna-Karin
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Faye, I.
    Transstadial and horizontal transfer of bacteria within a colony of Anopheles gambiae (Diptera: Culicidae) and oviposition response to bacteria-containing water2008Inngår i: Acta Tropica, ISSN 0001-706X, E-ISSN 1873-6254, Vol. 107, nr 3, s. 242-250Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In a paratransgenic approach, genetically modified bacteria are utilized to kill the parasite in the vector gut. A critical component for paratransgenics against malaria is how transgenic bacteria can be introduced and then kept in a mosquito population. Here, we investigated transstadial and horizontal transfer of bacteria within an Anopheles gambiae mosquito colony with the focus on spiked breeding sites as a possible means of introducing bacteria to mosquitoes. A Pantoea stewartii strain, previously isolated from An. gambiae, marked with a green fluorescent protein (GFP), was introduced to mosquitoes in different life stages. The following life stages or older mosquitoes in the case of adults were screened for bacteria in their guts. In addition to P. stewartii other bacteria were isolated from the guts: these were identified by 16S rRNA sequence analysis and temporal temperature gradient gel electrophoresis (TTGE). Bacteria were transferred from larvae to pupae but not from pupae to adults. The mosquitoes were able to take up bacteria from the water they emerged from and transfer the same bacteria to the water they laid eggs in. Eliza-bethkingia meningoseptica was more often isolated from adult mosquitoes than P. stewartii. A bioassay was used to examine An. gambiae oviposition responses towards bacteria-containing solutions. The volatiles emitted from the solutions were sampled by headspace-solid phase microextraction (SPME) and identified by gas chromatography and mass spectrometry (GC-MS) analysis. P. stewartii but not E. meningoseptica mediated a positive oviposition response. The volatiles emitted by P stewartii include indole and 3-methyl-1 -butanol, which previously have been shown to affect An. gambiae mosquito behaviour. E. meningoseptica emitted indole but not 3-methyl-1 -butanol, when suspended in saline. Taken together, this indicates that it may be possible to create attractive breeding sites for distribution of genetically modified bacteria in the field in a paratransgenic approach against malaria. Further research is needed to determine if the bacteria are also transferred in the same way in nature.

  • 71.
    Lindh, Jenny
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Kännaste, Astrid
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Knols, B. G. J.
    Faye, Ingrid
    Borg-Karlson, Anna-Karin
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Oviposition Responses of Anopheles gambiae s.s. (Diptera: Culicidae) and Identification of Volatiles from Bacteria-Containing Solutions2008Inngår i: Journal of medical entomology, ISSN 0022-2585, E-ISSN 1938-2928, Vol. 45, nr 6, s. 1039-1049Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study, a dual-choice oviposition bioassay was used to screen responses of gravid An. gambiae toward 17 bacterial species, previously isolated from Anopheles gambiae s.l. (Diptera: Culicidae) midguts or oviposition sites. The 10 isolates from oviposition sites have been identified by phylogenetic analyses of their 16S rRNA genes. Eight of the 10 isolates were gram-positive, out of which six belonged to the Bacilli class. Solid phase microextraction and gas chromatography coupled to mass spectrometry (GC-MS) were used to identify the volatiles emitted From the bacterial isolates, Aromatic and aliphatic alcohols, aliphatic ketones, alkylpyrazines, dimethyl oligosulfides, and indole were among the chemical compounds identified from the headspace above bacteria-containing saline. The mosquitoes laid significantly more eggs in six of the bacteria-containing solutions compared with the sterile solution. These six bacteria did not emit any compounds in common that could explain the positive oviposition response. Instead. the bacteria were grouped according to principal component analysis (PCA) based on the relative amouts of volatile emitted. The PCA-plots facilitated the identification of 13 putative oviposition attractants for An. gambiae mosquitoes.

  • 72.
    Lindh, Jenny M.
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Organisk kemi.
    Lehane, Michael J.
    The tsetse fly Glossina fuscipes fuscipes (Diptera: Glossina) harbours a surprising diversity of bacteria other than symbionts2011Inngår i: Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology, ISSN 0003-6072, E-ISSN 1572-9699, Vol. 99, nr 3, s. 711-720Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three different bacterial species are regularly described from tsetse flies. However, no broad screens have been performed to investigate the existence of other bacteria in this medically and agriculturally important vector insect. Utilising both culture dependent and independent methods we show that Kenyan populations of Glossina fuscipes fuscipes harbour a surprising diversity of bacteria. Bacteria were isolated from 72% of flies with 23 different bacterial species identified. The Firmicutes phylum dominated with 16 species of which seven belong to the genus Bacillus. The tsetse fly primary symbiont, Wigglesworthia glossinidia, was identified by the culture independent pathway. However, neither the secondary symbiont Sodalis nor Wolbachia was detected with either of the methods used. Two other bacterial species were identified with the DNA based method, Bacillus subtilis and Serratia marcescens. Further studies are needed to determine how tsetse flies, which only ever feed on vertebrate blood, pick up bacteria and to investigate the possible impact of these bacteria on Glossina longevity and vector competence.

  • 73.
    Lindh, Jenny M.
    et al.
    Dept of genetics microbiology and toxicology, Stockholm University.
    Terenius, Olle
    Dept of genetics microbiology and toxicology, Stockholm University.
    Faye, Ingrid
    Dept of genetics microbiology and toxicology, Stockholm University.
    16S rRNA gene-based identification of midgut bacteria from field-caught Anopheles gambiae sensu lato and A. funestus mosquitoes reveals new species related to known insect symbionts2005Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, nr 11, s. 7217-7223Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Field-collected mosquitoes of the two main malaria vectors in Africa, Anopheles gambiae sensu lato and Anopheles funestus, were screened for their midgut bacterial contents. The midgut from each blood-fed mosquito was screened with two different detection pathways, one culture independent and one culture dependent. Bacterial species determination was achieved by sequence analysis of 16S rRNA genes. Altogether, 16 species from 14 genera were identified, 8 by each method. Interestingly, several of the bacteria identified are related to bacteria known to be symbionts in other insects. One isolate, Nocardia corynebacterioides, is a relative of the symbiont found in the vector for Chagas' disease that has been proven useful as a paratransgenic bacterium. Another isolate is a novel species within the gamma-proteobacteria that could not be phylogenetically placed within any of the known orders in the class but is close to a group of insect symbionts. Bacteria representing three intracellular genera were identified, among them the first identifications of Anaplasma species from mosquitoes and a new mosquito-Spiroplasma association. The isolates will be further investigated for their suitability for a paratransgenic Anopheles mosquito.

  • 74. Lindh, Markus V.
    et al.
    Sjostedt, Johanna
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Baltar, Federico
    Hugerth, Luisa W.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundin, Daniel
    Muthusamy, Saraladevi
    Legrand, Catherine
    Pinhassi, Jarone
    Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling2015Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, nr 7, s. 2459-2476Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1). Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.

  • 75. Liu, Zihe
    et al.
    Liu, Lifang
    Osterlund, Tobias
    Hou, Jin
    Huang, Mingtao
    Fagerberg, Linn
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Petranovic, Dina
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Skolan för bioteknologi (BIO), Centra, Albanova VinnExcellence Center for Protein Technology, ProNova. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark .
    Nielsen, Jens
    Improved Production of a Heterologous Amylase in Saccharomyces cerevisiae by Inverse Metabolic Engineering2014Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, nr 17, s. 5542-5550Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The increasing demand for industrial enzymes and biopharmaceutical proteins relies on robust production hosts with high protein yield and productivity. Being one of the best-studied model organisms and capable of performing posttranslational modifications, the yeast Saccharomyces cerevisiae is widely used as a cell factory for recombinant protein production. However, many recombinant proteins are produced at only 1% (or less) of the theoretical capacity due to the complexity of the secretory pathway, which has not been fully exploited. In this study, we applied the concept of inverse metabolic engineering to identify novel targets for improving protein secretion. Screening that combined UV-random mutagenesis and selection for growth on starch was performed to find mutant strains producing heterologous amylase 5-fold above the level produced by the reference strain. Genomic mutations that could be associated with higher amylase secretion were identified through whole-genome sequencing. Several single-point mutations, including an S196I point mutation in the VTA1 gene coding for a protein involved in vacuolar sorting, were evaluated by introducing these to the starting strain. By applying this modification alone, the amylase secretion could be improved by 35%. As a complement to the identification of genomic variants, transcriptome analysis was also performed in order to understand on a global level the transcriptional changes associated with the improved amylase production caused by UV mutagenesis.

  • 76. Logue, Jurg B.
    et al.
    Stedmon, Colin A.
    Kellerman, Anne M.
    Nielsen, Nikoline J.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Laudon, Hjalmar
    Lindstrom, Eva S.
    Kritzberg, Emma S.
    Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter2016Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 3, s. 533-545Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low-or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

  • 77. Lourbakos, A.
    et al.
    Hiller, M.
    Kozaczynska, K.
    Baptiste, R. Jean
    Reza, M.
    Niks, E.
    Koeks, Z.
    de Klerk, D.
    Wolterbeek, R.
    Campion, G.
    Nadarajah, V. D.
    Szigyarto, Cristina Al-Khalili
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Calissano, M.
    Muntoni, F.
    Lochmueller, H.
    Verschuuren, J. J. G. M.
    Goemans, N.
    Tulinius, M.
    de Kimpe, S.
    Aartsma-Rus, A.
    't Hoen, P. A. C.
    Spitali, P.
    MMP-9 serum levels increase over time in Duchenne muscular dystrophy patients and decrease upon treatment with drisapersen2014Inngår i: Human Gene Therapy, ISSN 1043-0342, E-ISSN 1557-7422, Vol. 25, nr 11, s. A27-A28Artikkel i tidsskrift (Annet vitenskapelig)
  • 78.
    Lundin, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Severin, I.
    Logue, J. B.
    Östman, O.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lindström, E. S.
    Which sequencing depth is sufficient to describe patterns in bacterial alpha- and beta-diversity?2012Inngår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, nr 3, s. 367-372Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 615 communities from which 15 00020 000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in beta-diversity (Bray-Curtis index) among samples observed for 15 00020 000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in a-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.

  • 79.
    Långmark, Jonas
    KTH, Tidigare Institutioner, Mark- och vattenteknik.
    Biofilms and microbial barriers in drinking water treatment and distribution2004Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The primary objective of conventional drinking water treatment and distribution is to deliver to the consumer water that is both aesthetically pleasing and does not constitute a human health risk. To achieve this, water utilities employ a range of physical (i.e. sand and membrane filtration) and chemical (i.e. flocculation and disinfection) barriers in order to reduce the numbers of microorganisms as well as the nutrients that may support their growth within biofilms. In this thesis, biofilms and microbial barriers in water treatment and distribution were therefore examined. The development of biofilms within artificial recharge was investigated in pilot column at Norsborg waterworks in Stockholm. The proportion of active bacteria, measured as numbers of EUB338-positive cells relative to the total number of bacteria enumerated by total direct counts, decreased with time. Through the addition of nutrients however, two to three times more bacteria were able to be active (measured by increase in activity after activation with additional nutrients). By extracting the recalcitrant hydrophilic and hydrophobic fractions of humic substances it was possible to assess the microbiological response to those compounds. It was shown that bacteria more firmly attached to the sand grains preferred the hydrophobic fraction whilst more loosely-associated bacteria preferred the hydrophilic one. The amount of easily degradable matter in raw water (measured as assimilable organic carbon) was generally low. Biofilms were investigated by two different methods for extraction and analysis of microorganisms. Glass slides introduced into the sand material were dominated by α-Proteobacteria, and underestimated loosely-associated bacteria whilst extracts from sand were dominated by γ-Proteobacteria, and also caused variations due to the extraction method employed

    The barrier function of biofilms was investigated in biofilters, also fed with raw water from Gothenburg. The focus here was on particle removal in size-intervals of 1-15 µm (protozoa) and 0.4 - 1 µm (bacteria). In both size fractions, autofluorescent microalgae, which were naturally-occurring in raw water, were also enumerated in parallel. Their removal was 60-90%. In parallel, defined amounts of fluorescent hydrophilic and hydrophobic microspheres (1 µm) were added. They showed a reduction of hydrophobic spheres by 98% and hydrophilic ones by 86%. Removal of viruses was determined by adding a defined dose of bacteriophages and gave lower reduction values of 40 - 61%. Both naturally-occurring particles in defined size intervals and added particles or organisms were shown to provide a clearer picture of barrier function than usually performed measurements of turbidity.

    The efficiency of chemical treatment against viruses was also measured in a pilot-plant in Gothenburg. It was shown that commonly-used MS-2 bacteriophages were much more sensitive than φX174 bacteriophages. Reduction of MS-2 over the entire chemical step (when added after dosing of chemicals) was 5-log10 whilst φX174 was reduced by 1-log10. The latter was shown to be a more conservative model for virus removal. The effects of different steps in the chemical precipitation showed that the primary dosage of chemicals and the development of flocs had great importance for the assessment of removal efficacy. When added before the dosing of chemicals, reduction of φX174 and MS-2 was 3.8-log10 and 6.2-log10, respectively.

    The establishment of biofilm within a distribution system was followed in a 1000 metre long pilot-plant (with parallel lines) at Lovö waterworks as well as in two of Stockholm's main distribution systems (Nockeby and Hässelby). The pilot-plant was shown to satisfactorily represent processes within the distribution systems. The development of biofilms was slow, producing thin biofilms over a one to two month periods. Numbers of bacteria were generally in the range of 104 - 105 per cm2, which is lower than shown in other earlier investigations. The implementation of primary ultra viloet (UV)-treatment in place of chlorination (both being chloraminated prior to distribution) did not considerably change the numbers of bacteria in biofilms. No significant difference could be seen between the system that had UV-treatment as a primary treatment step, and the system that was chlorinated over the whole period. Chlorine residuals were generally low at the distal parts of the distribution systems. Naturally-occurring protozoa were present in distribution systems in numbers ranging from 280 - 3500 protozoa per cm-2. Protozoa may play a significant role as predators of biofilm bacteria, however they can also act as protection for bacteria against external influences i.e. disinfection. Should sudden contamination of a distribution system occur, biofilm can provide protection and act as a site for potential regrowth of introduced microorganisms. Biofilms developed in the pilot-scale that represented water from different distances from waterworks were exposed to fluorescent microspheres, (hydrophobic and hydrophilic, 1 µm) legionellae (as a model for opportunistic bacterial pathogens) and bacteriophages (human enteric virus model) in order to determine their accumulation and persistence within the biofilm, and release to the bulk water. It was shown that introduced model organisms were released continuously, primarily through desorption, and additionally through the influence of disinfection and activity of protozoa.

    Desorption was also assessed in a laboratory experiment under laminar and turbulent flow. Laminar flow conditions that were representative of a distribution system gave a slow and continual release of individual cells, whilst turbulent conditions detached larger aggregates. In conclusion, based on this work an increased understanding was gained both of barrier functions at the different steps of water treatment, their effects on overall biofilm dynamics and structure and the role that biofilm plays within the drinking water system itself.

  • 80. Maes, Alexandre
    et al.
    Céline, Gracia
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Zhang, Kaiyang
    Aalto University, Finland .
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hajnsdorf, Eliane
    Landscape of RNA polyadenylation in E. coli2016Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.

    Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.

  • 81. Margeridon-Thermet, Severine
    et al.
    Svarovskaia, Evguenia S.
    Babrzadeh, Farbod
    Stanford Genome Technology Center, Stanford University, Stanford, CA, United States .
    Martin, Ross
    Liu, Tommy F.
    Pacold, Mary
    Reuman, Elizabeth C.
    Holmes, Susan P.
    Borroto-Esoda, Katyna
    Shafer, Robert W.
    Low-Level Persistence of Drug Resistance Mutations in Hepatitis B Virus-Infected Subjects with a Past History of Lamivudine Treatment2013Inngår i: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 57, nr 1, s. 343-349Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We sought to determine the prevalence of hepatitis B virus (HBV) lamivudine (LAM)-resistant minority variants in subjects who once received LAM but had discontinued it prior to virus sampling. We performed direct PCR Sanger sequencing and ultradeep pyrosequencing (UDPS) of HBV reverse transcriptase (RT) of plasma viruses from 45 LAM-naive subjects and 46 LAM-experienced subjects who had discontinued LAM a median of 24 months earlier. UDPS was performed to a depth of similar to 3,000 reads per nucleotide. Minority variants were defined as differences from the Sanger sequence present in >= 0.5% of UDPS reads in a sample. Sanger sequencing identified >= 1 LAM resistance mutations (rtL80I/V, rtM204I, and rtA181T) in samples from 5 (11%) of 46 LAM-experienced and none of 45 LAM-naive subjects (0%; P = 0.06). UDPS detected >= 1 LAM resistance mutations (rtL80I/V, rtV173L, rtL180M, rtA181T, and rtM204I/V) in 10 (22%) of the 46 LAM-experienced subjects, including 5 in whom LAM resistance mutations were not identified by Sanger sequencing. Overall, LAM resistance mutations were more likely to be present in LAM-experienced (10/46, 22%) than LAM-naive subjects (0/45, 0%; P = 0.001). The median time since LAM discontinuation was 12.8 months in the 10 subjects with a LAM resistance mutation compared to 30.5 months in the 36 LAM-experienced subjects without a LAM resistance mutation (P < 0.001). The likelihood of detecting a LAM resistance mutation was significantly increased using UDPS compared to Sanger sequencing and was inversely associated with the time since LAM discontinuation.

  • 82. Mattsson, Cecilia
    et al.
    Andersson, Sven-Ingvar
    Belkheiri, Tallal
    Amand, Lars-Erik
    Olausson, Lars
    Vamling, Lennart
    Theliander, Hans
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center. Chalmers, Sweden.
    Using 2D NMR to characterize the structure of the low and high molecular weight fractions of bio-oil obtained from LignoBoost (TM) kraft lignin depolymerized in subcritical water2016Inngår i: Biomass and Bioenergy, ISSN 0961-9534, E-ISSN 1873-2909, Vol. 95, s. 364-377Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work a multilevel analysis approach have been used for characterization of LignoBoostTM kraft lignin and bio-oil produced from LignoBoostTM kraft lignin using a process based on subcritical water (350 degrees C, 25 MPa). LignoBoostTM kraft lignin and the different fractions of the bio-oil (light oil, heavy oil and suspended solids) was characterized with high field NMR (18.8 T, 2D(13)C, H-1-HSQC NMR and C-13-NMR), GPC, GC-MS and elemental composition to improve understanding of the subcritical process. By using high resolution 2D HSQC NMR it was possible determine the chemical structures both on low and high molecular weight fractions of the bio-oil. It was confirmed that the signals from the aliphatic lignin inter-unit linkages, i.e. beta-O-4', beta-beta', beta-1' and beta-5', had disappeared from all of the bio-oil fractions studied. This means that both the aliphatic carbon-oxygen (C-O) and to some extent carbon-carbon (C-C) bonds in LignoBoostTM kraft lignin have been cleaved and an effective depolymerization has occurred. However, re-polymerization into higher molecular weight (Mw) fractions takes place simultaneously. These higher Mw fractions (heavy oil and suspended solids) were found to be re-polymerized macromolecules, with new structural networks based on guaiacol/disubstituted aromatic ethers and polyaromatic hydrocarbon structures bound tightly together.

  • 83.
    Melin, Jessica
    KTH, Tidigare Institutioner, Signaler, sensorer och system.
    Novel Microsystem Techniques for Liquid Manipulation and Pressure Sensing2004Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Scaling down operations and functions into the fascinating micro world not only improve performance, lower costs, and enable easier integration, but also opens the door to new functionalities. This truly multidisciplinary thesis presents novel solutions to current and relevant challenges in the areas of 1) on-chip liquid manipulation which has applications in micro total analysis systems, medical diagnostics, and drug discovery and 2) pressure sensing which has an established market in the automotive and industrial processes industry. Especially in the area of liquid manipulation, the aim was to take advantage of forces and properties dominating on the micro scale whenever possible, rather than compensating for these effects, and to create solutions with universal appeal and application areas.

    In the area of liquid manipulation, this thesis discusses a novel method of passively synchronizing liquid movement on-chip based on liquid surface tension and device geometry. This technique has potential applications in timing independent processes, liquid-liquid interactions, and digitizing liquid movement. A fast and passive discrete sample micromixer is also presented based on the same principles. A unique way of direct access, bubble tolerant sample interfacing with flow-through microfluidics using a closed-open-closed channel is also introduced. This method can be used to regulate flow on-chip without the need for any moving parts or electrical contact. Moreover, work is presented on two types of out-of-plane electrospray ionization mass spectrometry (ESI-MS) emitter tips which mimic ideal mass spectrometry tips. Fabrication of these tips is uncomplicated and results in robust structures with good performance.

    In the field of pressure sensing, this thesis investigates a form based resonating principle. The Q factor of the sensor is improved by low pressure encapsulation and structure design. A novel technique for excitation and detection of resonant microsensors using 'burst' technology is also demonstrated. This method involves temporally separating excitation and detection, thereby eliminating crosstalk and the need for electrical feedthroughs. It also allows high voltages to be used with sensitive circuitry and a single electrode to be used for both excitation and detection.

  • 84. Mellroth, Peter
    et al.
    Sandalova, Tatyana
    Kikhney, Alexey
    Vilaplana, Francisco
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Hesek, Dusan
    Lee, Mijoon
    Mobashery, Shahriar
    Normark, Staffan
    Svergun, Dmitri
    Henriques-Normark, Birgitta
    Achour, Adnane
    Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae2014Inngår i: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 5, nr 1, s. e01120-13-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The cytosolic N-acetylmuramoyl-L-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or beta-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-angstrom crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.

  • 85.
    Mélida, Hugo
    et al.
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Sain, D.
    Stajich, J. E.
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches2015Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, nr 5, s. 1649-1662Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most fungi from the Mucoromycotina lineage occur in ecosystems as saprobes, although some species are phytopathogens or may induce human mycosis. Mucoromycotina represent early diverging models that are most valuable for understanding fungal evolution. Here we reveal the uniqueness of the cell wall structure of the Mucoromycotina Rhizopus oryzae and Phycomyces blakesleeanus compared with the better characterized cell wall of the ascomycete Neurospora crassa. We have analysed the corresponding polysaccharide biosynthetic and modifying pathways, and highlight their evolutionary features and higher complexity in terms of gene copy numbers compared with species from other lineages. This work uncovers the presence in Mucoromycotina of abundant fucose-based polysaccharides similar to algal fucoidans. These unexpected polymers are associated with unusually low amounts of glucans and a higher proportion of chitin compared with N.crassa. The specific structural features are supported by the identification of genes potentially involved in the corresponding metabolic pathways. Phylogenomic analyses of genes encoding carbohydrate synthases, polysaccharide modifying enzymes and enzymes involved in nucleotide-sugar formation provide evidence for duplication events during evolution of cell wall metabolism in fungi. Altogether, the data highlight the specificity of Mucoromycotina cell walls and pave the way for a finer understanding of their metabolism.

  • 86.
    Mélida, Hugo
    et al.
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Sandoval-Sierra, Jose V.
    Dieguez-Uribeondo, Javier
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types2013Inngår i: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 12, nr 2, s. 194-203Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of N-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-beta-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-beta-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes.

  • 87. Nguyen, Thu-Ha
    et al.
    Splechtna, Barbara
    Krasteva, Stanimira
    Kneifel, Wolfgang
    Kulbe, Klaus D.
    Divne, Christina
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Haltrich, Dietmar
    Characterization and molecular cloning of a heterodimeric beta-galactosidase from the probiotic strain Lactobacillus acidophilus R222007Inngår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 269, nr 1, s. 136-144Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    beta-Galactosidase from the probiotic strain Lactobacillus acidophilus R22 was purified to apparent homogeneity by ammonium sulphate fractionation, hydrophobic interaction, and affinity chromatography. The enzyme is a heterodimer consisting of two subunits of 35 and 72 kDa, as determined by gel electrophoresis. The optimum temperature of beta-galactosidase activity was 55 degrees C (10-min assay) and the range of pH 6.5-8, respectively, for both o-nitrophenyl-beta-D-galactopyranoside (oNPG) and lactose hydrolysis. The K-m and V-max values for lactose and oNPG were 4.04 +/- 0.26 mM, 28.8 +/- 0.2 mu mol D-glucose released per min per mg protein, and 0.73 +/- 0.07 mM, 361 +/- 12 mu mol o-nitrophenol released per min per mg protein, respectively. The enzyme was inhibited by high concentrations of oNPG with K-i,K-s=31.7 +/- 3.5 mM. The enzyme showed no specific requirements for metal ions, with the exception of Mg2+, which enhanced both activity and stability. The genes encoding this heterodimeric enzyme, lacL and lacM, were cloned, and compared with other beta-galactosidases from lactobacilli. beta-Galactosidase from L. acidophilus was used for the synthesis of prebiotic galacto-oligosaccharides (GOS) from lactose, with the maximum GOS yield of 38.5% of total sugars at about 75% lactose conversion.

  • 88.
    Norström, Anna
    KTH, Skolan för bioteknologi (BIO).
    Treatment of domestic wastewater using microbiological processes and hydroponics in Sweden2005Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Conventional end-of-pipe solutions for wastewater treatment have been criticized from a sustainable view-point, in particular regarding recycling of nutrients. The integration of hydroponic cultivation into a wastewater treatment system has been proposed as an ecological alternative, where nutrients can be removed from the wastewater through plant uptake; however, cultivation of plants in a temperate climate, such as Sweden, implies that additional energy is needed during the colder and darker period. Thus, treatment capacity, additional energy usage and potential value of products are important aspects considering the applicability of hydroponic wastewater treatment in Sweden.

    To enable the investigation of hydroponic wastewater treatment, a pilot plant was constructed in a greenhouse located at Överjärva gård, Solna, Sweden. The pilot plant consisted of several steps, including conventional biological processes, hydroponics, algal treatment and sand filters. The system treated around 0.56-0.85 m3 domestic wastewater from the Överjärva gård area per day. The experimental protocol, performed in an average of twice per week over a period of three years, included analysis and measurements of water quality and physical parameters. In addition, two studies were performed when daily samples were analysed during a period of two-three weeks. Furthermore, the removal of pathogens in the system, and the microbial composition in the first hydroponic tank were investigated.

    Inflow concentrations were in an average of around 475 mg COD/L, 100 mg Tot-N/L and 12 mg Tot-P/L. The results show that 85-90% of COD was removed in the system. Complete nitrification was achieved in the hydroponic tanks. Denitrification, by means of pre-denitrification, occurred in the first anoxic tank. With a recycle ratio of 2.26, the achieved nitrogen removal in the system was around 72%. Approximately 4% of the removed amount of nitrogen was credited to plant uptake during the active growth period. Phosphorus was removed by adsorption in the anoxic tank and sand filters, natural chemical precipitation in the algal step induced by the high pH, and assimilation in plants, bacteria and algae. The main removal occurred in the algal step. In total, 47% of the amount of phosphorus was removed. Significant recycling of nitrogen and phosphorus through harvested biomass has not been shown. The indicators analysed for pathogen removal showed an achieved effluent quality comparable to, or better than, for conventional secondary treatment. The microbial composition was comparable to other nitrifying biological systems. The most abundant phyla were Betaproteobacteria and Planctomycetes.

    In Sweden, a hydroponic system is restricted to greenhouse applications, and the necessary amount of additional energy is related to geographic location. In conclusion, hydroponic systems are not recommended too far north, unless products are identified that will justify the increased energy usage. The potential for hydroponic treatment systems in Sweden lies in small decentralized systems where the greenness of the system and the possible products are considered as advantages for the users.

  • 89.
    Norström, Anna
    et al.
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Larsdotter, Karin
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Dalhammar, Gunnel
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Theoretical energy requirements for maintenance of green plants in hydroponic wastewater treatment.2004Inngår i: Vatten, ISSN 0042-2886, nr 3, s. 187-191Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Hydroponic wastewater treatment takes advantage of the nutrient removing capacity of green plants. In addition to the nutrient assimilation, the roots provide a growth substrate for microorganisms involved in the biological treatment processes. However, to maintain year-round performance by the plants, additional energy muse be provided at higher latitudes, even if the hydroponics are situated in a greenhouse. To evaluate the energy demand by hydroponics in Sweden, two theoretical operational conditions have been compared. These conditions were based on A: requirements by winter resting plants, 10°C and 400 lux 16 h day-1, and B: good growth. 20°C and 2000 lux 16 h day-1. Further, five Swedish cities at different latitudes and their respective demands to reach the two conditions were compared. These cities were Lund (55°72' N), Visbv (57°38' N) Stockholm (59°35’ N), Ostersund (63°20’ N) and Kiruna (67°83’ N). The calculations showed that under Swedish conditions, the extra heat demand always exceeds the light demand on a yearlv basis except for the high temperature and light standard in Lund. The yearly light requirements are similar for the five cities, whereas the heat energy displays strong latitude dependence, e.g. the yearly heat demand in Kiruna is almost seven times higher than in Lund to reach an average indoor temperature of 10°C.

  • 90.
    Othoum, G.
    et al.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Prigent, S.
    Chalmers Univ Technol, Div Syst & Synthet Biol, Dept Biol & Biol Engn, Kemivaen 10, S-41296 Gothenburg, Sweden..
    Derouiche, A.
    Chalmers Univ Technol, Div Syst & Synthet Biol, Dept Biol & Biol Engn, Kemivaen 10, S-41296 Gothenburg, Sweden..
    Shi, L.
    Chalmers Univ Technol, Div Syst & Synthet Biol, Dept Biol & Biol Engn, Kemivaen 10, S-41296 Gothenburg, Sweden..
    Bokhari, A.
    KAUST, Biol & Environm Sci & Engn Div BESE, Thuwal 239556900, Saudi Arabia..
    Alamoudi, S.
    King Abdulaziz Univ, Dept Biol, Sci & Arts Coll, Rabigh 21589, Saudi Arabia..
    Bougouffa, S.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Gao, X.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Hoehndorf, R.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Arold, S. T.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Gojobori, T.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia.;KAUST, Biol & Environm Sci & Engn Div BESE, Thuwal 239556900, Saudi Arabia..
    Hirt, H.
    KAUST, Biol & Environm Sci & Engn Div BESE, Thuwal 239556900, Saudi Arabia..
    Lafi, F. F.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia.;Zayed Univ, Coll Nat & Hlth Sci, Abu Dhabi 144534, U Arab Emirates..
    Nielsen, Jens
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bajic, V. B.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Mijakovic, I
    Chalmers Univ Technol, Div Syst & Synthet Biol, Dept Biol & Biol Engn, Kemivaen 10, S-41296 Gothenburg, Sweden.;Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2800 Lyngby, Denmark..
    Essack, M.
    KAUST, CBRC, Thuwal 239556900, Saudi Arabia..
    Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 19254Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

  • 91.
    Ottenhall, Anna
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Träkemi och massateknologi.
    Antimicrobial materials from cellulose using environmentally friendly techniques2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The transition to a more biobased society introduces both new opportunities and new challenges as we replace nonrenewable materials with renewable alternatives. One important challenge will be to control microbial growth on materials, both to protect the materials from biological degradation and to prevent the spread of infections and toxins that can cause illness.

    In this thesis, both existing and new types of cellulose-based materials were treated with environmentally friendly alternatives to usual biocides to prevent microbial growth and remove bacteria from water. Two types of antimicrobial systems were studied, and the antimicrobial effects were evaluated for bacteria and fungi using both model organisms and wild-type cultures.

    The first antimicrobial approach employed was a nonleaching and contact-active layer-by-layer adsorption of polyelectrolytes to provide the cellulose fibers with a cationic surface charge, which attracts and captures bacteria onto the fiber surface. The study showed that paper filters with pores much larger than bacteria could remove more than 99.9 % of E. coli from water when used in filtration mode. The polyelectrolyte-modified materials showed a good antibacterial effect but did not prevent fungal growth.

    The second approach was to utilize biobased compounds with antimicrobial properties, which were applied to cellulose fiber foam materials. Chitosan and extractives from birch bark were selected as biobased options for antimicrobial agents. Two types of cellulose fiber foam materials were developed and evaluated for their antimicrobial properties.

    This thesis shows the importance of understanding both the application and the targeted microorganism when selecting an environmentally friendly antimicrobial system for treating biobased materials. It highlights that a good understanding of both material science and microbiology is important when designing new antimicrobial materials.

  • 92. Parameswaran, Poornima
    et al.
    Sklan, Ella
    Wilkins, Courtney
    Burgon, Trever
    Samuel, Melanie A.
    Lu, Rui
    Ansel, K. Mark
    Heissmeyer, Vigo
    Einav, Shirit
    Jackson, William
    Doukas, Tammy
    Paranjape, Suman
    Polacek, Charlotta
    dos Santos, Flavia Barreto
    Jalili, Roxana
    Babrzadeh, Farbod
    Stanford Genome Technology Center, Stanford University School of Medicine, United States .
    Gharizadeh, Baback
    Grimm, Dirk
    Kay, Mark
    Koike, Satoshi
    Sarnow, Peter
    Ronaghi, Mostafa
    Ding, Shou-Wei
    Harris, Eva
    Chow, Marie
    Diamond, Michael S.
    Kirkegaard, Karla
    Glenn, Jeffrey S.
    Fire, Andrew Z.
    Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems2010Inngår i: PLoS Pathogens, ISSN 1553-7366, E-ISSN 1553-7374, Vol. 6, nr 2, s. e1000764-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived small RNAs (vsRNAs) from all six viruses, with total abundance varying from "vanishingly rare'' (less than 0.1% of cellular small RNA) to highly abundant (comparable to abundant micro-RNAs "miRNAs''). In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host miRNA profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We also found evidence for populations of vsRNAs that exist as duplexed siRNAs with zero to three nucleotide 39 overhangs. Using populations of cells carrying a Hepatitis C replicon, we observed strand-selective loading of siRNAs onto Argonaute complexes. These experiments define vsRNAs as one possible component of the interplay between animal viruses and their hosts.

  • 93. Peciulyte, Ausra
    et al.
    Karlström, Katarina
    Larsson, Per Tomas
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Olsson, Lisbeth
    Impact of the supramolecular structure of cellulose on the efficiency of enzymatic hydrolysis2015Inngår i: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 8, artikkel-id 56Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The efficiency of enzymatic hydrolysis is reduced by the structural properties of cellulose. Although efforts have been made to explain the mechanism of enzymatic hydrolysis of cellulose by considering the interaction of cellulolytic enzymes with cellulose or the changes in the structure of cellulose during enzymatic hydrolysis, the process of cellulose hydrolysis is not yet fully understood. We have analysed the characteristics of the complex supramolecular structure of cellulose on the nanometre scale in terms of the spatial distribution of fibrils and fibril aggregates, the accessible surface area and the crystallinity during enzymatic hydrolysis. Influence of the porosity of the substrates and the hydrolysability was also investigated. All cellulosic substrates used in this study contained more than 96% cellulose. Results: Conversion yields of six cellulosic substrates were as follows, in descending order: nano-crystalline cellulose produced from never-dried soda pulp (NCC-OPHS-ND) > never-dried soda pulp (OPHS-ND) > dried soda pulp (OPHS-D) > Avicel > cotton treated with sodium hydroxide (cotton + NaOH) > cotton. Conclusions: No significant correlations were observed between the yield of conversion and supramolecular characteristics, such as specific surface area (SSA) and lateral fibril dimensions (LFD). A strong correlation was found between the average pore size of the starting material and the enzymatic conversion yield. The degree of crystallinity was maintained during enzymatic hydrolysis of the cellulosic substrates, contradicting previous explanations of the increasing crystallinity of cellulose during enzymatic hydrolysis. Both acid and enzymatic hydrolysis can increase the LFD, but no plausible mechanisms could be identified. The sample with the highest initial degree of crystallinity, NCC-OPHS-ND, exhibited the highest conversion yield, but this was not accompanied by any change in LFD, indicating that the hydrolysis mechanism is not based on lateral erosion.

  • 94.
    Persson, Frank
    et al.
    Chalmers, Div Water Environm Technol, Dept Civil & Environm Engn, SE-41296 Gothenburg, Sweden..
    Suarez, Carolina
    Univ Gothenburg, Dept Chem & Mol Biol, SE-40530 Gothenburg, Sweden..
    Hermansson, Malte
    Univ Gothenburg, Dept Chem & Mol Biol, SE-40530 Gothenburg, Sweden..
    Plaza, Elzbieta
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik.
    Sultana, Razia
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik.
    Wilen, Britt-Marie
    Chalmers, Div Water Environm Technol, Dept Civil & Environm Engn, SE-41296 Gothenburg, Sweden..
    Community structure of partial nitritation-anammox biofilms at decreasing substrate concentrations and low temperature2017Inngår i: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 10, nr 4, s. 761-772Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Partial nitritation-anammox (PNA) permits energy effective nitrogen removal. Today PNA is used for treatment of concentrated and warm side streams at wastewater treatment plants, but not the more diluted and colder main stream. To implement PNA in the main stream, better knowledge about microbial communities at the typical environmental conditions is necessary. In order to investigate the response of PNA microbial communities to decreasing substrate availability, we have operated a moving bed biofilm reactor (MBBR) at decreasing reactor concentrations (311-27mg-N l(-1) of ammonium) and low temperature (13 degrees C) for 302days and investigated the biofilm community using high throughput amplicon sequencing; quantitative PCR; and fluorescence insitu hybridization. The anammox bacteria (Ca. Brocadia) constituted a large fraction of the biomass with fewer aerobic ammonia oxidizing bacteria (AOB) and even less nitrite oxidizing bacteria (NOB; Nitrotoga, Nitrospira and Nitrobacter). Still, NOB had considerable impact on the process performance. The anammox bacteria, AOB and NOB all harboured more than one population, indicating some diversity, and the heterotrophic bacterial community was diverse (seven phyla). Despite the downshifts in substrate availability, changes in the relative abundance and composition of anammox bacteria, AOB and NOB were small and also the heterotrophic community showed little changes in composition. This indicates stability of PNA MBBR communities towards decreasing substrate availability and suggests that even heterotrophic bacteria are integral components of these communities.

  • 95. Pham, Trang A.T.
    et al.
    Schwerdt, Julian G.
    Shirley, Neil J.
    Xing, Xiaohui
    Hsieh, Yves S. Y.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Centra, Wallenberg Wood Science Center.
    Srivastava, Vaibhav
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Bulone, Vincent
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Little, Alan
    Analysis of cell wall synthesis and metabolism during early germination of Blumeria graminis f. sp. hordei conidial cells induced in vitro2019Inngår i: The Cell Surface, ISSN 2468-2330, Vol. 5, s. 100030-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As an obligate biotroph, Blumeria graminis f. sp. hordei (Bgh) cannot be grown in an axenic culture, and instead must be cultivated on its host species, Hordeum vulgare (barley). In this study an in vitro system utilizing n-hexacosanal, a constituent of the barley cuticle and known inducer of Bgh germination, was used to cultivate Bgh and differentiate conidia up to the appressorial germ tube stage for analysis. Transcriptomic and proteomic profiling of the appressorial germ tube stage revealed that there was a significant shift towards energy and protein production during the pre-penetrative phase of development, with an up-regulation of enzymes associated with cellular respiration and protein synthesis, modification and transport. Glycosidic linkage analysis of the cell wall polysaccharides demonstrated that during appressorial development an increase in 1,3- and 1,4-linked glucosyl residues and xylosyl residues was detected along with a significant decrease in galactosyl residues. The use of this in vitro cultivation method demonstrates that it is possible to analyse the pre-penetrative processes of Bgh development in the absence of a plant host.

  • 96.
    Rezinciuc, Svetlana
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Vladimir Sandoval-Sierra, Jose
    Ruiz-Leon, Yolanda
    van West, Pieter
    Dieguez-Uribeondo, Javier
    Specialized attachment structure of the fish pathogenic oomycete Saprolegnia parasitica2018Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, nr 1, artikkel-id e0190361Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The secondary cysts of the fish pathogen oomycete Saprolegnia parasitica possess bundles of long hooked hairs that are characteristic to this economically important pathogenic species. Few studies have been carried out on elucidating their specific role in the S. parasitica life cycle and the role they may have in the infection process. We show here their function by employing several strategies that focus on descriptive, developmental and predictive approaches. The strength of attachment of the secondary cysts of this pathogen was compared to other closely related species where bundles of long hooked hairs are absent. We found that the attachment of the S. parasitica cysts was around three times stronger than that of other species. The time sequence and influence of selected factors on morphology and the number of the bundles of long hooked hairs conducted by scanning electron microscopy study revealed that these are dynamic structures. They are deployed early after encystment, i.e., within 30 sec of zoospore encystment, and the length, but not the number, of the bundles steadily increased over the encystment period. We also observed that the number and length of the bundles was influenced by the type of substrate and encystment treatment applied, suggesting that these structures can adapt to different substrates (glass or fish scales) and can be modulated by different signals (i.e., protein media, 50 mM CaCl2 concentrations, carbon particles). Immunolocalization studies evidenced the presence of an adhesive extracellular matrix. The bioinformatic analyses of the S. parasitica secreted proteins showed that there is a high expression of genes encoding domains of putative proteins related to the attachment process and cell adhesion (fibronectin and thrombospondin) coinciding with the deployment stage of the bundles of long hooked hairs formation. This suggests that the bundles are structures that might contribute to the adhesion of the cysts to the host because they are composed of these adhesive proteins and/or by increasing the surface of attachment of this extracellular matrix.

  • 97.
    Rodriguez-Gomez, Raúl
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik. KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik, Mark- och vattenteknik.
    Renman, Gunno
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik, Mark- och vattenteknik.
    Moreno, Luis
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik.
    Liu, Longcheng
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik.
    A model to describe the performance of the UASB reactor2014Inngår i: Biodegradation, ISSN 0923-9820, E-ISSN 1572-9729, Vol. 25, nr 2, s. 239-251Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A dynamic model to describe the performance of the Upflow Anaerobic Sludge Blanket (UASB) reactor was developed. It includes dispersion, advection, and reaction terms, as well as the resistances through which the substrate passes before its biotransformation. The UASB reactor is viewed as several continuous stirred tank reactors connected in series. The good agreement between experimental and simulated results shows that the model is able to predict the performance of the UASB reactor (i.e. substrate concentration, biomass concentration, granule size, and height of the sludge bed).

  • 98. Samalova, Marketa
    et al.
    Melida, Hugo
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Vilaplana, Francisco
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Soanes, Darren M.
    Talbot, Nicholas J.
    Gurr, Sarah J.
    The beta-1,3-glucanosyltransferases (Gels) affect the structure of the rice blast fungal cell wall during appressorium-mediated plant infection2017Inngår i: Cellular Microbiology, ISSN 1462-5814, E-ISSN 1462-5822, Vol. 19, nr 3, artikkel-id UNSP e12659Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The fungal wall is pivotal for cell shape and function, and in interfacial protection during host infection and environmental challenge. Here, we provide the first description of the carbohydrate composition and structure of the cell wall of the rice blast fungus Magnaporthe oryzae. We focus on the family of glucan elongation proteins (Gels) and characterize five putative beta-1,3-glucan glucanosyltransferases that each carry the Glycoside Hydrolase 72 signature. We generated targeted deletion mutants of all Gel isoforms, that is, the GH72(+), which carry a putative carbohydrate-binding module, and the GH72(-)Gels, without this motif. We reveal that M. oryzae GH72(+) GELs are expressed in spores and during both infective and vegetative growth, but each individual Gel enzymes are dispensable for pathogenicity. Further, we demonstrated that Delta gel1 Delta gel3 Delta gel4 null mutant has a modified cell wall in which 1,3-glucans have a higher degree of polymerization and are less branched than the wild-type strain. The mutant showed significant differences in global patterns of gene expression, a hyper-branching phenotype and no sporulation, and thus was unable to cause rice blast lesions (except via wounded tissues). We conclude that Gel proteins play significant roles in structural modification of the fungal cell wall during appressorium-mediated plant infection.

  • 99. Song, Chunxu
    et al.
    Sundqvist, Gustav
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Malm, Erik
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    de Bruijn, Irene
    Kumar, Aundy
    van de Mortel, Judith
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Raaijmakers, Jos M.
    Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP2015Inngår i: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 15, artikkel-id 29Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Lipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. In Pseudomonas and other bacterial genera, LP biosynthesis is governed by large multimodular nonribosomal peptide synthetases (NRPS). To date, relatively little is known about the regulatory genetic network of LP biosynthesis. Results: This study provides evidence that the chaperone ClpA, together with the serine protease ClpP, regulates the biosynthesis of the LP massetolide in Pseudomonas fluorescens SS101. Whole-genome transcriptome analyses of clpA and clpP mutants showed their involvement in the transcription of the NRPS genes massABC and the transcriptional regulator massAR. In addition, transcription of genes associated with cell wall and membrane biogenesis, energy production and conversion, amino acid transport and metabolism, and pilus assembly were altered by mutations in clpA and clpP. Proteome analysis allowed the identification of additional cellular changes associated to clpA and clpP mutations. The expression of proteins of the citrate cycle and the heat shock proteins DnaK and DnaJ were particularly affected. Combined with previous findings, these results suggest that the ClpAP complex regulates massetolide biosynthesis via the pathway-specific, LuxR-type regulator MassAR, the heat shock proteins DnaK and DnaJ, and proteins of the TCA cycle. Conclusions: Combining transcriptome and proteome analyses provided new insights into the regulation of LP biosynthesis in P. fluorescens and led to the identification of specific missing links in the regulatory pathways.

  • 100. Song, Han
    et al.
    Dotzauer, Erik
    Thorin, Eva
    Yan, Jinyue
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Energiprocesser.
    Annual performance analysis and comparison of pellet production integrated with an existing combined heat and power plant2011Inngår i: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 102, nr 10, s. 6317-6325Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three optional pellet production processes integrated with an existing biomass-based CHP plant using different raw materials (wood chips and solid hydrolysis residues) are studied. The year is divided into 12 periods, and the integrated biorefinery systems are modeled and simulated for each period. The annual economic performance of three integrated biorefinery systems is analyzed based on the simulation results. The option of pellet production integrated with the existing CHP plant with the exhaust flue gas and superheated steam as drying mediums has the lowest specific pellet production cost of 105 epsilon/t(pellet), the shortest payback time of less than 2 years and the greatest CO2 reduction of the three options. An advantage in common among the three options is a dramatic increase of the total annual power production and significant CO2 reduction in spite of a small decrease of power efficiency.

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