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
  • 2014  (40)
Type of Medium
Language
Year
  • 2014  (40)
  • 1
    Other
    Other
    Figshare
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Language: English
    In: Nucleic acids research, August 2014, Vol.42(14), pp.8845-60
    Description: Phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. Single-cell transcriptomics using next-generation transcript sequencing (RNA-seq) is now emerging as a powerful tool to profile cell-to-cell variability on a genomic scale. Its application has already greatly impacted our conceptual understanding of diverse biological processes with broad implications for both basic and clinical research. Different single-cell RNA-seq protocols have been introduced and are reviewed here-each one with its own strengths and current limitations. We further provide an overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field.
    Keywords: Gene Expression Profiling -- Methods ; High-Throughput Nucleotide Sequencing -- Methods ; Sequence Analysis, RNA -- Methods ; Single-Cell Analysis -- Methods
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Science (New York, N.Y.), 30 May 2014, Vol.344(6187), pp.972-3
    Description: Argonaute proteins have emerged as the key effectors in virtually all eukaryotic small RNA-mediated gene silencing pathways . Central to all their activities is their association with the small guide RNAs that allow them to recognize through sequence complementarity, and in some cases also cleave, cellular transcripts. [PUBLICATION ]
    Keywords: DNA Cleavage ; Gene Silencing ; Argonaute Proteins -- Metabolism ; DNA -- Metabolism ; DNA, Bacterial -- Genetics ; Plasmids -- Genetics ; Prokaryotic Cells -- Metabolism ; Rhodobacter Sphaeroides -- Genetics ; Thermus Thermophilus -- Genetics
    ISSN: 00368075
    E-ISSN: 1095-9203
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Language: English
    In: Frontiers in cellular and infection microbiology, 2014, Vol.4, pp.91
    Description: Enteric pathogens often cycle between virulent and saprophytic lifestyles. To endure these frequent changes in nutrient availability and composition bacteria possess an arsenal of regulatory and metabolic genes allowing rapid adaptation and high flexibility. While numerous proteins have been characterized with regard to metabolic control in pathogenic bacteria, small non-coding RNAs have emerged as additional regulators of metabolism. Recent advances in sequencing technology have vastly increased the number of candidate regulatory RNAs and several of them have been found to act at the interface of bacterial metabolism and virulence factor expression. Importantly, studying these riboregulators has not only provided insight into their metabolic control functions but also revealed new mechanisms of post-transcriptional gene control. This review will focus on the recent advances in this area of host-microbe interaction and discuss how regulatory small RNAs may help coordinate metabolism and virulence of enteric pathogens.
    Keywords: Csra ; Hfq ; Carbon Metabolism ; Srna ; Virulence ; Energy Metabolism ; Carbon -- Metabolism ; Intestines -- Microbiology ; RNA, Small Untranslated -- Genetics
    E-ISSN: 2235-2988
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    In: RNA biology, 2014, Vol.11(5), pp.403-12
    Description: On June 4-8, 2013, the 3rd Conference on Regulation with RNA in Bacteria took place in Würzburg, Germany. Following two earlier meetings in Berlin and San Juan, this conference has established itself as the primary bi-annual meeting for everyone interested in RNA-based regulations in prokaryotes. The 2013 meeting was organized by Joel Belasco, Susan Gottesman, Franz Narberhaus, and Jörg Vogel. Close to 300 participants from more than 27 countries in Europe, North America, and Asia enjoyed four days of talks and posters on many experimental and biocomputational aspects of prokaryotic RNA biology.
    Keywords: Cascade ; Hfq ; RNA Stability ; RNA-Seq Crispr ; Bioinformatics ; Ribonucleoprotein Complex ; Small RNA ; Gene Expression Regulation, Bacterial ; Bacteria -- Genetics ; RNA, Bacterial -- Genetics
    E-ISSN: 1555-8584
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: Current Opinion in Microbiology, June 2014, Vol.19, pp.97-105
    Description: •RNA-seq has become the method of choice for bacterial transcriptomics.•Differential RNA-seq (dRNA-seq) distinguishes primary and processed transcripts.•dRNA-seq provides global TSS maps and other transcriptome information.•dRNA-seq is generic and has been applied to many different species. RNA-sequencing has revolutionized the quantitative and qualitative analysis of transcriptomes in both prokaryotes and eukaryotes. It provides a generic approach for gene expression profiling, annotation of transcript boundaries and operons, as well as identifying novel transcripts including small noncoding RNA molecules and antisense RNAs. We recently developed a differential RNA-seq (dRNA-seq) method which in addition to the above, yields information as to whether a given RNA is a primary or processed transcript. Originally applied to describe the primary transcriptome of the gastric pathogen Helicobacter pylori, dRNA-seq has since provided global maps of transcriptional start sites in diverse species, informed new biology in the CRISPR-Cas9 system, advanced to a tool for comparative transcriptomics, and inspired simultaneous RNA-seq of pathogen and host.
    Keywords: Chromosomes – Analysis ; Molecular Biology – Analysis ; Antisense RNA – Analysis ; Animal Behavior – Analysis ; Gene Expression – Analysis;
    ISSN: 1369-5274
    E-ISSN: 18790364
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    In: Bioinformatics, 2014, Vol. 30(23), pp.3421-3423
    Description: Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. To draw biological conclusions based on RNA-Seq data, several steps, some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea. Availability and implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849). Contact: cynthia.sharma@uni-wuerzburg.de and konrad.foerstner@uni-wuerzburg.de
    Keywords: Bacteria ; Computation ; Source Code ; Ribonucleic Acids ; Biological ; Licenses ; Tools ; Line Interfaces ; Life and Medical Sciences (Ci);
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: mBio, 08/29/2014, Vol.5(4)
    Description: Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function. Importance: The first step of gene expression is the initiation of transcription from promoters, which have been traditionally thought to be located upstream of genes. Recently, studies showed that in diverse bacteria, promoters are often located inside genes. It has not been clear if these unexpected promoters are important to the organism or if they result from transcriptional noise. Here, we identify and examine promoters in eight related bacterial species. Promoters that lie within genes on the sense strand are often conserved as locations and in their sequences. Furthermore, these promoters often affect the bacterium's growth. Thus, many of these unexpected promoters are likely functional. Fewer promoters that lie within genes on the antisense strand are conserved, but the conserved ones seem to drive the expression of nearby genes.
    Keywords: Biology;
    ISSN: mBio
    E-ISSN: 2150-7511
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: eLife, 31 December 2014, Vol.3
    Description: Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.
    Keywords: E. Coli ; Hfq ; RNA–Protein Interactions ; Rydc ; Biophysics ; Gene Regulation ; Natively Unstructured Protein ; Srna ; Structural Biology ; Host Factor 1 Protein -- Metabolism ; RNA, Bacterial -- Metabolism
    E-ISSN: 2050-084X
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    Other
    Other
    Figshare
    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