Kooperativer Bibliotheksverbund

Berlin Brandenburg

and
and

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Type of Medium
Language
Year
  • 1
    Language: English
    In: Nature, November 2018, Vol.563(7729), pp.121-125
    Description: Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
    Keywords: Antigenic Variation -- Genetics ; Chromatin -- Genetics ; DNA, Protozoan -- Metabolism ; Genome -- Genetics ; Trypanosoma Brucei Brucei -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Language: English
    In: Nucleic acids research, 12 October 2018, Vol.46(18), pp.e106
    Description: Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination. By establishing an episome-based CRISPR-Cas9 system for T. brucei, we have edited wild type cells without inserting selectable markers, inserted a GFP tag between an ORF and its 3'UTR, deleted both alleles of a gene in a single transfection, and performed precise editing of genes that exist in multicopy arrays, replacing histone H4K4 with H4R4 in the absence of detectable off-target effects. The newly established genome editing toolbox allows for the generation of precise mutants without needing to change other regions of the genome, opening up opportunities to study the role of individual histone modifications, catalytic sites of enzymes or the regulatory potential of UTRs in their endogenous environments.
    Keywords: Crispr-Cas Systems ; Gene Editing -- Methods ; Histone Code -- Genetics ; Histones -- Metabolism
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Experimental Parasitology, September 2017, Vol.180, pp.2-12
    Description: Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about the precise genomic locations of DNA-protein interactions is important because it provides insight into the regulation of these processes. Recently, we have adapted an approach that combines micrococcal nuclease (MNase) digestion of chromatin with chromatin immunoprecipitation in . Here, we describe in detail how this method can be used to map the genome-wide distribution of nucleosomes or other DNA-binding proteins at high resolution in .
    Keywords: Chromatin ; Nucleosome ; Chip ; Micrococcal Nuclease ; Biology ; Zoology
    ISSN: 0014-4894
    E-ISSN: 1090-2449
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    In: EMBO Journal, 01 September 2017, Vol.36(17), pp.2581-2594
    Description: Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well‐defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite in which polymerase transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site‐specific and genome‐wide assays, we identified ‐rich promoters that can drive transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context‐dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with pol enrichment and gene expression, pointing to a role in maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes. Our findings show that even highly dispersed, unregulated promoters contain specific elements that are able to induce transcription and changes in chromatin structure. The lack of recognisable promoters in trypanosomes has limited our understanding of transcriptional control in this important pathogen. Via genome‐wide assays this study shows that transcription initiates broadly on ‐rich elements that control incorporation of activating histone variants. RNA pol II transcription initiates across a 2 kb‐wide region upstream of polycistronic transcription units. GT‐rich sequence elements enriched at transcription start sites can induce transcription and recruit the histone variant H2A.Z. Sites enriched in H2A.Z show increased sensitivity to MNase. Nucleosome occupancy upstream of genes correlates with RNA pol II enrichment and transcript levels. Composition of polyY tract affects nucleosome positioning and transcript levels. While trypanosomes lack classical promoter elements, they initiate transcription broadly over ‐rich sequences that control incorporation of activating histone variants.
    Keywords: Core Promoter ; Histone Variant ; Nucleosome Occupancy ; Trypanosoma Brucei
    ISSN: 0261-4189
    E-ISSN: 1460-2075
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    Description: For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation. Die Transkription ist ein entscheidender Prozess in der Zelle und die DNA-Sequenz nimmt hierbei eine elementare Rolle ein. Promotoren beinhalten spezifische und konservierte DNASequenzen und vermitteln den Start der Transkription durch die Rekrutierung spezifischer Proteine. Jedoch haben Forschungen im vergangenen Jahrzehnt gezeigt, dass die Mehrzahl der Promotoren in eukaryotischen Genomen keine konservierten Promotormotive aufweisen und häufig konstitutiv exprimierte Gene transkribieren. Obgleich der Prozess der Transkriptionsinitiation im Allgemeinen gut erforscht ist, konnte bisher nicht nachgewiesen werden, ob ein definiertes DNA-Motiv während der Transkription von konstitutiv exprimierten Genes erforderlich ist. In dem eukaryotischen und einzelligen Parasiten Trypanosoma brucei ist die Mehrzahl der proteinkodierenden Gene in lange polycistronische Transkriptionseinheiten arrangiert. Diese werden von einem gemeinsamen Transkriptionsstart durch die RNA Polymerase II transkribiert, allerdings konnten hier bisher keine Promotormotive identifiziert werden. Aus diesem Grund besteht die Annahme, dass Transkription keiner Regulation unterliegt. Allgemein ist der Prozess der Transkriptionsinitiation in T. brucei bisher nur wenig verstanden. Um den Zusammenhang zwischen DNA-Motiven und konstitutiver Genexpression näher zu untersuchen und Schlussfolgerungen über die DNA-Sequenz-Abhängigkeit der Transkriptionsinitiation zu ziehen, habe ich eine systematische Analyse in T. brucei durchgeführt. Ich konnte GT-reiche Promotorelemente innerhalb dieser Regionen identifizieren, die sowohl eine gerichtete Transkriptionsinitiation, als auch den gezielten Einbau der Histonvariante H2A.Z in Nukleosomen nahe der Transkriptionsstartstelle vermittelt haben. Des Weiteren zeigten Nukleosomenpositionierungsdaten, dass in Trypanosomen die Transkripitonsstartstellen nicht die charakteristische, nukleosomendepletierte Region, wie für andere Organismen beschrieben, sondern eine offene Chromatinstruktur enthalten. Zusätzlich konnte ich zeigen, dass die Chromatinstruktur eine wichtige Rolle während der mRNAProzessierung spielt. In T. brucei wird die polycistronische pre-mRNA durch das Anfügen eines Miniexons während des sogenannten trans-Splicens in individuelle mRNAs aufgetrennt. Die Daten dieser Arbeit belegen, dass die Anreicherung von Nukleosomen eine Verlangsamung der transkribierenden Polymerase bewirken und sie somit die richtige Wahl der Splicestelle gewährleisten. Zusammenfassend wurde in dieser Arbeit die Rolle der DNA Sequenz während der Transkriptionsinitiation und Nukleosomenpositionierung in einem divergenten Eukaryoten untersucht. Die Erkenntnisse bringen mehr Licht in die Konservierung der Notwendigkeit eines DNA-Motivs während der Transkriptionsinitiation und das regulatorische Potential der Chromatinstruktur während der RNA-Reifung. Zudem verbessern sie das Verständnis der Genexpressionsregulation in T. brucei, einem eukaryotischen Parasiten, der ohne transkriptionelle Regulation überlebt.
    Keywords: Transkription ; Chromatin ; Trypanosoma Brucei ; Genexpression ; Epigenetik ; Ddc:576
    Source: Networked Digital Library of Theses and Dissertations
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: Food Research International, May 2018, Vol.107, pp.19-26
    Description: Endospores of thermophilic bacilli are a major concern for producers of dairy powders. In this study, we heat treated 10 different spore suspensions at 110 °C in skim milk and skim milk concentrate (36% dry matter) of the species (10 min) and (5 min) in a new shear-heating device. The highest log reduction in skim milk concentrate was 3.5. The death behavior of the spores was strain dependent. Particle formation and Maillard reaction were observed. By increasing the shear-rate up to 1500 s the particle size was reduced for both heating times (D90 reduction: 57.4 and 77.0%, respectively). The particle size was lessened by a reduction of dry matter of 27%, compared to 36%. This work emphasizes, that heat treatment of concentrated dairy products represents a technological option to reduce thermophilic spores in skim milk concentrate and powders produced thereof.
    Keywords: Thermal Processing ; Thermophilic Spore Formers ; Skim Milk Powder ; Milk Concentrates ; Anoxybacillus Flavithermus ; Engineering ; Economics
    ISSN: 0963-9969
    E-ISSN: 1873-7145
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Language: English
    In: Reference Module in Food Science
    Description: The aim of the sterilization process is to produce a long-life product by destruction of microorganisms capable of causing spoilage of the product during storage and also to destroy the microorganisms detrimental to public health. For the sterilization of milk and milk products, continuous sterilization, in-container sterilization in autoclaves, and ultra-high-temperature treatment (UHT) are used. Sterilization processes are characterized by the applied heating temperature and the holding time. To evaluate the effectiveness of a sterilization process regarding destruction of microorganisms and to quantify the chemical changes in the product, the temperature, treatment time, and the concentration of the product need to be considered. The heat treatment conditions, in terms of temperature and time, can be optimized, ensuring a sufficient destruction of pathogenic and spoilage microorganisms and at the same time limiting the heat load on the product to avoid undesirable chemical changes. Depending on the microorganisms responsible for restricting the shelflife and for important chemical or textural changes, and on other special demands or standards, process conditions can be determined using kinetic parameters such as the activation energy (EA), the rate constant (kT) of the reaction, and the order of the reaction (n).
    Keywords: Autoclaves ; Heat treatment ; Microorganisms ; Milk ; Spoilage
    ISBN: 978-0-08-100596-5
    Source: ScienceDirect (Elsevier B.V.)
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: Food Microbiology, October 2019, Vol.83, pp.150-158
    Description: The occurrence of thermophilic spore formers in dairy powders is a major concern for producers worldwide. This study aims to investigate the resistance of thermophilic endospores towards cleaning solutions typically used for cleaning-in-place in dairy manufacturing plants. From eleven tested strains, all were able to survive an alkaline treatment (NaOH) at 65 °C for 10 min (0.5%), whereas at concentrations of 2% eight strains withstood the treatment. Acid solutions were more sporicidal. At 0.5% of HNO only three strains survived the treatment. Milk impurities reduced the inactivation effect of the NaOH solutions towards thermophilic spore formers. For two selected strains, a detailed kinetic inactivation in NaOH and HNO solutions at different temperatures was performed and non-log-linear inactivation curves were observed. This study highlights the risk of reusing cleaning solutions in dairies.
    Keywords: Cleaning-in-Place ; Thermophilic Spore Formers ; Milk Powder Processing ; Anoxybacillus Flavithermus ; Biology ; Economics
    ISSN: 0740-0020
    E-ISSN: 1095-9998
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: International Dairy Journal, November 2019, Vol.98, pp.64-71
    Description: Internationally, there are no official guidelines for the quantification of thermophilic spores in dairy products, which leads to variations in applied methodology. In this study, we assess the heat sensitivity of thermophilic spores, vegetative cells grown under laboratory conditions and spores in German dairy powders to determine appropriate heating conditions for accurate quantification of total thermophilic spores. The heat inactivation effect (80–95 °C) is limited for spores of and grown under laboratory conditions. However, for spores originating from whey, whey powder and skimmed milk powder (mostly identified as ), a different trend was observed; spore counts continuously reduced when heating time and temperature increased (80–98 °C, 10–30 min). The results indicate that data obtained using laboratory cultures cannot be extrapolated to commercial powders, and in this case, applying temperatures above 80 °C leads to an underestimation of spore counts in dairy powders.
    Keywords: Agriculture
    ISSN: 0958-6946
    E-ISSN: 1879-0143
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages