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  1. Book: Entwicklung einer anti-listeriellen, frühen Oberflächenreifungskultur für geschmierte Käse

    Scherer, Siegfried

    Schlussbericht 2009 ; [Projekt der industriellen Gemeinschaftsforschung]

    (F & E Dokumentation)

    2009  

    Institution Zentralinstitut für Ernährungs- und Lebensmittelforschung Weihenstephan / Abteilung Mikrobiologie
    Author's details [Forschungsstelle I: Technische Universität München, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Abt. Mikrobiologie. Projektleiter: S. Scherer ...]
    Series title F & E Dokumentation
    Language German
    Size 166 S. : Ill., graph. Darst.
    Publisher Forschungskreis der Ernährungsindustrie
    Publishing place Bonn
    Publishing country Germany
    Document type Book
    HBZ-ID HT016287292
    Database Catalogue ZB MED Nutrition, Environment, Agriculture

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    In stock of ZB MED Bonn / Germany

    Shelf markLoan statusLocation
    094/459 available for loan (reading room) Freihandmagazin (U1)

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  2. Article ; Online: Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.

    Zehentner, Barbara / Scherer, Siegfried / Neuhaus, Klaus

    BMC microbiology

    2023  Volume 23, Issue 1, Page(s) 243

    Abstract: Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well ... ...

    Abstract Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.
    MeSH term(s) Escherichia coli O157/genetics ; Transcription Initiation Site ; Enterohemorrhagic Escherichia coli ; Cell Cycle ; Culture Media
    Chemical Substances Culture Media
    Language English
    Publishing date 2023-08-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041505-9
    ISSN 1471-2180 ; 1471-2180
    ISSN (online) 1471-2180
    ISSN 1471-2180
    DOI 10.1186/s12866-023-02988-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Differenzierung von probiotischen und ubiquitären Milchsäurebakterien und aeroben Sporenbildnern aus Futtermitteln mittels FTIR-Spektroskopie

    Wenning, Mareike / Scherer, Siegfried / Mietke-Hofmann, Henriette

    (Schriftenreihe des LfULG ; 2011,26)

    2011  

    Title variant Differenzierung probiotischer Bakterien
    Author's details Mareike Wenning ; Siegfried Scherer ; Henriette Mietke-Hofmann
    Series title Schriftenreihe des LfULG ; 2011,26
    Schriftenreihe des Landesamtes für Umwelt, Landwirtschaft und Geologie / Freistaat Sachsen
    Collection Schriftenreihe des Landesamtes für Umwelt, Landwirtschaft und Geologie / Freistaat Sachsen
    Subject code 630
    Language German
    Publisher Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie
    Publishing place Dresden
    Publishing country Germany
    Document type Book ; Online
    Remark Elektronischer Volltext
    HBZ-ID HT016954530
    DOI 10.4126/98-004282035
    Database Repository for Life Sciences

    Full text online

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  4. Book ; Online: Differenzierung von probiotischen und ubiquitären Milchsäurebakterien und aeroben Sporenbildnern aus Futtermitteln mittels FTIR-Spektroskopie

    Wenning, Mareike / Scherer, Siegfried / Mietke-Hofmann, Henriette

    (Schriftenreihe des LfULG ; 2011,26)

    2011  

    Title variant Differenzierung probiotischer Bakterien
    Author's details Mareike Wenning ; Siegfried Scherer ; Henriette Mietke-Hofmann
    Series title Schriftenreihe des LfULG ; 2011,26
    Schriftenreihe des Landesamtes für Umwelt, Landwirtschaft und Geologie / Freistaat Sachsen
    Collection Schriftenreihe des Landesamtes für Umwelt, Landwirtschaft und Geologie / Freistaat Sachsen
    Subject code 630
    Language German
    Publisher Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie
    Publishing place Dresden
    Publishing country Germany
    Document type Book ; Online
    Remark Elektronischer Volltext
    HBZ-ID HT016954530
    DOI 10.4126/98-004282035
    Database Repository for Life Sciences

    Full text online

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  5. Article ; Online: Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.

    Graf, Franziska / Zehentner, Barbara / Fellner, Lea / Scherer, Siegfried / Neuhaus, Klaus

    Microbiology spectrum

    2022  Volume 11, Issue 1, Page(s) e0235122

    Abstract: The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel ... ...

    Abstract The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes.
    MeSH term(s) Escherichia coli O157/genetics ; Escherichia coli O157/metabolism ; Escherichia coli Proteins/genetics ; Base Sequence ; Genes, Overlapping ; Ribosome Profiling
    Chemical Substances Escherichia coli Proteins
    Language English
    Publishing date 2022-12-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.02351-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Biological factors in the synthetic construction of overlapping genes.

    Wichmann, Stefan / Scherer, Siegfried / Ardern, Zachary

    BMC genomics

    2021  Volume 22, Issue 1, Page(s) 888

    Abstract: Background: Overlapping genes (OLGs) with long protein-coding overlapping sequences are disallowed by standard genome annotation programs, outside of viruses. Recently however they have been discovered in Archaea, diverse Bacteria, and Mammals. The ... ...

    Abstract Background: Overlapping genes (OLGs) with long protein-coding overlapping sequences are disallowed by standard genome annotation programs, outside of viruses. Recently however they have been discovered in Archaea, diverse Bacteria, and Mammals. The biological factors underlying life's ability to create overlapping genes require more study, and may have important applications in understanding evolution and in biotechnology. A previous study claimed that protein domains from viruses were much better suited to forming overlaps than those from other cellular organisms - in this study we assessed this claim, in order to discover what might underlie taxonomic differences in the creation of gene overlaps.
    Results: After overlapping arbitrary Pfam domain pairs and evaluating them with Hidden Markov Models we find OLG construction to be much less constrained than expected. For instance, close to 10% of the constructed sequences cannot be distinguished from typical sequences in their protein family. Most are also indistinguishable from natural protein sequences regarding identity and secondary structure. Surprisingly, contrary to a previous study, virus domains were much less suitable for designing OLGs than bacterial or eukaryotic domains were. In general, the amount of amino acid change required to force a domain to overlap is approximately equal to the variation observed within a typical domain family. The resulting high similarity between natural sequences and those altered so as to overlap is mostly due to the combination of high redundancy in the genetic code and the evolutionary exchangeability of many amino acids.
    Conclusions: Synthetic overlapping genes which closely resemble natural gene sequences, as measured by HMM profiles, are remarkably easy to construct, and most arbitrary domain pairs can be altered so as to overlap while retaining high similarity to the original sequences. Future work however will need to assess important factors not considered such as intragenic interactions which affect protein folding. While the analysis here is not sufficient to guarantee functional folding proteins, further analysis of constructed OLGs will improve our understanding of the origin of these remarkable genetic elements across life and opens up exciting possibilities for synthetic biology.
    MeSH term(s) Amino Acid Sequence ; Animals ; Biological Factors ; Genes, Overlapping ; Genome ; Open Reading Frames
    Chemical Substances Biological Factors
    Language English
    Publishing date 2021-12-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-021-08181-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online ; Thesis: Thermophilic spore formers in powdered dairy products: Source tracking, population dynamics and genomic characterisation of persisting strains

    Dettling, Anna [Verfasser] / Scherer, Siegfried [Akademischer Betreuer] / Scherer, Siegfried (Prof. Dr.), Hinrichs, Jörg [Gutachter]

    2021  

    Author's details Anna Dettling ; Gutachter: Siegfried (Prof. Dr.), Hinrichs, Jörg Scherer ; Betreuer: Siegfried Scherer
    Keywords Landwirtschaft, Veterinärmedizin ; Agriculture, Veterinary Science
    Subject code sg630
    Language English
    Publisher Universitätsbibliothek der TU München
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  8. Book ; Online ; Thesis: Influence of the Standard Genetic Code on Overlapping Genes: A Study of Multiple Properties

    Wichmann, Stefan Werner Verfasser] / [Scherer, Siegfried [Akademischer Betreuer] / Frishman, Dmitrij Gutachter] / [Scherer, Siegfried [Gutachter]

    2022  

    Author's details Stefan Werner Wichmann ; Gutachter: Dmitrij Frishman, Siegfried Scherer ; Betreuer: Siegfried Scherer
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek der TU München
    Publishing place München
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  9. Article: Towards low-spore milk powders: A review on microbiological challenges of dairy powder production with focus on aerobic mesophilic and thermophilic spores

    Wedel, Carolin / Atamer, Zeynep / Dettling, Anna / Wenning, Mareike / Scherer, Siegfried / Hinrichs, Jörg

    Elsevier Ltd International dairy journal. 2022 Mar., v. 126

    2022  

    Abstract: Powdered milk products, such as skim milk powder or whey protein powder, represent a large fraction of the dairy sector, especially with respect to export. In the past years, the contamination with aerobic endospore-forming bacteria has become one of the ...

    Abstract Powdered milk products, such as skim milk powder or whey protein powder, represent a large fraction of the dairy sector, especially with respect to export. In the past years, the contamination with aerobic endospore-forming bacteria has become one of the main factors to evaluate microbial powder quality. Besides mesophilic spore formers, thermophilic and thermoresistant species have been isolated all over the world. During production of powdered commodities, milk or intermediate products go through several process steps. This review highlights and discusses individual production steps and their effect on the microbiota and the spore count. The plant cleaning and its influence on spore resistance are discussed in detail, since this is the most important step in controlling recontamination and persistence. Finally, future technologies to reduce spore counts during powder production are presented. The contribution on ‘non-thermal’ and novel technologies towards low-spore milk powders are discussed critically.
    Keywords dairy industry ; dried skim milk ; heat tolerance ; milk ; spores ; whey protein
    Language English
    Dates of publication 2022-03
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1076400-8
    ISSN 0958-6946
    ISSN 0958-6946
    DOI 10.1016/j.idairyj.2021.105252
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  10. Article: Are Antisense Proteins in Prokaryotes Functional?

    Ardern, Zachary / Neuhaus, Klaus / Scherer, Siegfried

    Frontiers in molecular biosciences

    2020  Volume 7, Page(s) 187

    Abstract: Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ... ...

    Abstract Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.
    Language English
    Publishing date 2020-08-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2020.00187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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