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  • 1
    Language: English
    In: Molecular & Biochemical Parasitology, February 2012, Vol.181(2), pp.61-72
    Description: ► Kinetoplastids do not regulate transcription. ► Yet, gene expression changes severely during life cycle progression. ► At what levels does gene expression change during development? ► What are the likely primary and final targets of differentiation signals? ► Differentiation in is discussed as an example. Kinetoplastids, including the human pathogens , and , are the only known organisms that do not regulate the transcription of protein coding genes transcribed by RNA polymerase II. Yet, profound changes in gene expression are induced by many different external stimuli and stresses, the extreme example are cascades of changes in gene expression initiated by differentiation triggers that ultimately and irreversibly result in the massive morphological and metabolic changes observed during life-cycle progression. This review explores how kinetoplastids change gene expression by looking at life-cycle stage specific changes in chromatin, mRNA processing, mRNA stability, mRNA translation, protein stability and protein modifications.
    Keywords: Kinetoplastids ; Gene Expression ; Life Cycle ; Differentiation ; Trypanosome ; Leishmania ; Biology ; Chemistry ; Zoology
    ISSN: 0166-6851
    E-ISSN: 1872-9428
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, June, 2013, Vol.61, p.76(10)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2013.02.006 Byline: Susanne Kramer (a), Sven Marhan (a), Heike Haslwimmer (a), Liliane Ruess (b), Ellen Kandeler (a) Abstract: Many studies of the microbial ecology of agricultural ecosystems focus on surface soils, whereas the impacts of management practice and season on soil microbial community composition and function below the plough zone are largely neglected. Deep soils have a high potential to store carbon; therefore any management driven stimulation or repression of microorganisms in subsoil could impact biogeochemical cycling in agricultural sites. The aim of this study was to understand whether soil management affects microbial communities in the topsoil (0-10 cm), rooted zone beneath the plough layer (40-50 cm), and the unrooted zone (60-70 cm). In a field experiment with different crops [wheat (Triticum aestivum L.) and maize (Zea mays L.)] and agricultural management strategies (litter amendment) we analysed microbial biomass as phospholipid fatty acids (PLFAs) and enzyme activities involved in the C-cycle ([beta]-glucosidase, N-acetyl-[beta]-d-glucosaminidase, [beta]-xylosidase, phenol- and peroxidase) across a depth transect over a period of two years. Wheat cultivation resulted in higher bacterial and fungal biomass as well as higher enzyme activities at most sampling dates in comparison to maize cultivated plots, and this effect was visible to 50 cm depth. Litter application increased bacterial and fungal biomass as well as hydrolytic enzyme activities but effects were apparent only in the topsoil. In winter high microbial biomass and enzyme activities were measured in all soil layers, possibly due to increased mobilization and translocation of organic matter into deeper soil. Hydrolytic enzyme activities decreased with depth, whereas oxidative enzyme activities showed no decrease or even an increase with depth. This could have been due to differing sorption mechanisms of hydrolytic and oxidative enzymes. Specific enzyme activities (enzyme activity per microbial biomass) were higher in the deeper layers and possible reasons are discussed. Author Affiliation: (a) Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Emil-Wolff-Str. 27, 70599 Stuttgart, Germany (b) Institute of Biology, Ecology Group, Humboldt-Universitat zu Berlin, Philippstr. 13, 10115 Berlin, Germany Article History: Received 28 September 2012; Revised 20 December 2012; Accepted 12 February 2013
    Keywords: Agroecosystems -- Analysis ; Fatty Acids -- Analysis ; Soil Microbiology -- Analysis ; Soil Management (Agronomy) -- Analysis ; Nucleotidases -- Analysis ; Agricultural Ecology -- Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 3
    In: Nucleic Acids Research, 2017, Vol. 45(7), pp.e49-e49
    Description: The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.
    Keywords: Methods Online;
    ISSN: 0305-1048
    E-ISSN: 1362-4962
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  • 4
    Language: English
    In: Trends in Parasitology, 2011, Vol.27(1), pp.23-30
    Description: In trypanosomatids, alterations in gene expression in response to intrinsic or extrinsic signals are achieved through post-transcriptional mechanisms. In the last 20 years, research has concentrated on defining the responsible -elements in the untranslated regions of several regulated mRNAs. More recently, the focus has shifted towards the identification of RNA-binding proteins that act as -acting factors. Trypanosomatids have a large number of predicted RNA-binding proteins of which the vast majority have no orthologues in other eukaryotes. Several RNA-binding proteins have been shown to bind and/or regulate the expression of a group of mRNAs that code for functionally related proteins, indicating the possible presence of co-regulated mRNA cohorts.
    Keywords: Biology ; Veterinary Medicine
    ISSN: 1471-4922
    E-ISSN: 1471-5007
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  • 5
    Language: English
    In: PLoS Pathogens, 01 June 2017, Vol.13(6), p.e1006456
    Description: 5'-3' decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5'-3' exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5'-3' degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5'-3' exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5'-3' decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5' polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA's 5' end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap.
    Keywords: Biology
    ISSN: 1553-7366
    E-ISSN: 1553-7374
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  • 6
    Language: English
    In: Soil Biology and Biochemistry, January 2016, Vol.92, pp.119-132
    Description: Mycorrhizal fungi enhance plant phosphorus (P) acquisition via their extraradical hyphae (ERH) that scavenge nutrients outside root depletion zones. While soil P availability declines during ecosystem retrogression, how ERH biomass and scavenging vary during ecosystem retrogression remains unknown; it is expected to increase if plants allocate more carbon (C) to mycorrhizal fungi as P availability declines. We measured fungal and bacterial biomass using in-growth cores and lipid biomarkers along a 2-million-year dune chronosequence in an Australian biodiversity hotspot showing a ∼60-fold decline in total soil P concentration with increasing soil age. We compared the levels of key fungal biomarkers (ergosterol, NLFA 16:1ω5, and PLFA 18:2ω6,9) between closed, mesh, and open cores during five months (four sampling dates including the wet winter months), thus allowing us to also determine the dynamics of mycorrhizal fungal scavenging. We found strikingly low and declining biomass of ERH with declining P availability, with minimal long-distance scavenging by ERH. Biomass of ERH was highest in the younger ( . 1 ka) soils that were comparatively rich in P and other nutrients. By contrast, the oldest, most P-impoverished soils had the lowest biomass of ERH, despite high mycorrhizal root colonisation, and high abundance and diversity of potential plant hosts. We show that extremely low P availability constrains ERH biomass. Such low mycorrhizal fungal biomass highlights the need for a more ‘mycocentric’ view of plant–mycorrhizal relationships in old, severely P-impoverished ecosystems.
    Keywords: Arbuscular Mycorrhizal ; Ecosystem Development ; Ectomycorrhizal ; Extraradical Hyphae ; Ergosterol ; Neutral Lipid and Phospholipid Fatty Acid (Nlfa, Plfa) ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 7
    Language: English
    In: 2012, Vol.7(11), p.e48870
    Description: Regulation of RNA polymerase II transcription initiation is apparently absent in trypanosomes. Instead, these eukaryotes control gene expression mainly at the post-transcriptional level. Regulation is exerted through the action of numerous RNA-binding proteins that modulate mRNA processing, turnover, translation and localization. In this work we show that the RNA-binding protein DRBD3 resides in the cytoplasm, but localizes to the nucleus upon oxidative challenge and to stress granules under starvation conditions. DRBD3 associates with other proteins to form a complex, the composition of which is altered by cellular stress. Interestingly, target mRNAs remain bound to DRBD3 under stress conditions. Our results suggest that DRBD3 transports regulated mRNAs within the cell in the form of ribonucleoprotein complexes that are remodeled in response to environmental cues.
    Keywords: Research Article ; Biology ; Genetics And Genomics ; Microbiology ; Biochemistry
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: PLoS ONE, 01 January 2018, Vol.13(3), p.e0192633
    Description: The degree of conservation and evolution of cytoplasmic mRNA metabolism pathways across the eukaryotes remains incompletely resolved. In this study, we describe a comprehensive genome and transcriptome-wide analysis of proteins involved in mRNA maturation, translation, and mRNA decay across representative organisms from the six eukaryotic super-groups. We demonstrate that eukaryotes share common pathways for mRNA metabolism that were almost certainly present in the last eukaryotic common ancestor, and show for the first time a correlation between intron density and a selective absence of some Exon Junction Complex (EJC) components in eukaryotes. In addition, we identify pathways that have diversified in individual lineages, with a specific focus on the unique gene gains and losses in members of the Excavata and SAR groups that contribute to their unique gene expression pathways compared to other organisms.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: Soil biology & biochemistry, 2013, Vol.61, pp.76-85
    Description: Many studies of the microbial ecology of agricultural ecosystems focus on surface soils, whereas the impacts of management practice and season on soil microbial community composition and function below the plough zone are largely neglected. Deep soils have a high potential to store carbon; therefore any management driven stimulation or repression of microorganisms in subsoil could impact biogeochemical cycling in agricultural sites. The aim of this study was to understand whether soil management affects microbial communities in the topsoil (0–10 cm), rooted zone beneath the plough layer (40–50 cm), and the unrooted zone (60–70 cm). In a field experiment with different crops [wheat (Triticum aestivum L.) and maize (Zea mays L.)] and agricultural management strategies (litter amendment) we analysed microbial biomass as phospholipid fatty acids (PLFAs) and enzyme activities involved in the C-cycle (β-glucosidase, N-acetyl-β-d-glucosaminidase, β-xylosidase, phenol- and peroxidase) across a depth transect over a period of two years. Wheat cultivation resulted in higher bacterial and fungal biomass as well as higher enzyme activities at most sampling dates in comparison to maize cultivated plots, and this effect was visible to 50 cm depth. Litter application increased bacterial and fungal biomass as well as hydrolytic enzyme activities but effects were apparent only in the topsoil. In winter high microbial biomass and enzyme activities were measured in all soil layers, possibly due to increased mobilization and translocation of organic matter into deeper soil. Hydrolytic enzyme activities decreased with depth, whereas oxidative enzyme activities showed no decrease or even an increase with depth. This could have been due to differing sorption mechanisms of hydrolytic and oxidative enzymes. Specific enzyme activities (enzyme activity per microbial biomass) were higher in the deeper layers and possible reasons are discussed. ; p. 76-85.
    Keywords: Beta-N-Acetylhexosaminidase ; Sorption ; Topsoil ; Crop Production ; Field Experimentation ; Organic Matter ; Peroxidase ; Plows ; Corn ; Phospholipid Fatty Acids ; Biogeochemical Cycles ; Triticum Aestivum ; Soil Microorganisms ; Carbon Sinks ; Agricultural Management ; Zea Mays ; Microbial Communities ; Enzyme Activity ; Community Structure ; Wheat ; Agroecosystems ; Xylan 1,4-Beta-Xylosidase ; Microbial Biomass ; Temporal Variation ; Beta-Glucosidase ; Crops ; Arable Soils ; Soil Management
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 10
    Language: English
    In: Soil Biology and Biochemistry, June 2013, Vol.61, pp.76-85
    Description: Many studies of the microbial ecology of agricultural ecosystems focus on surface soils, whereas the impacts of management practice and season on soil microbial community composition and function below the plough zone are largely neglected. Deep soils have a high potential to store carbon; therefore any management driven stimulation or repression of microorganisms in subsoil could impact biogeochemical cycling in agricultural sites. The aim of this study was to understand whether soil management affects microbial communities in the topsoil (0–10 cm), rooted zone beneath the plough layer (40–50 cm), and the unrooted zone (60–70 cm). In a field experiment with different crops [wheat ( L.) and maize ( L.)] and agricultural management strategies (litter amendment) we analysed microbial biomass as phospholipid fatty acids (PLFAs) and enzyme activities involved in the C-cycle (β-glucosidase, N-acetyl-β- -glucosaminidase, β-xylosidase, phenol- and peroxidase) across a depth transect over a period of two years. Wheat cultivation resulted in higher bacterial and fungal biomass as well as higher enzyme activities at most sampling dates in comparison to maize cultivated plots, and this effect was visible to 50 cm depth. Litter application increased bacterial and fungal biomass as well as hydrolytic enzyme activities but effects were apparent only in the topsoil. In winter high microbial biomass and enzyme activities were measured in all soil layers, possibly due to increased mobilization and translocation of organic matter into deeper soil. Hydrolytic enzyme activities decreased with depth, whereas oxidative enzyme activities showed no decrease or even an increase with depth. This could have been due to differing sorption mechanisms of hydrolytic and oxidative enzymes. Specific enzyme activities (enzyme activity per microbial biomass) were higher in the deeper layers and possible reasons are discussed. ► Crop type affects bacteria, fungi and enzyme activities down to a depth of 50 cm. ► Maize litter affects PLFAs and hydrolytic enzyme activities only in the topsoil. ► In winter, high substrate availability raises bacteria, fungi and enzyme activities. ► Varying sorption of enzyme classes result in a different depth distribution. ► Specific enzyme activities are higher in subsoil in comparison to topsoil.
    Keywords: Plfa ; Enzyme Activity ; Specific Enzyme Activity ; Topsoil ; Subsoil ; Crop Effect ; Litter Amendment ; Agricultural Field ; Season ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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