Microbiology Blog: The weblog for microbiologists
Microbiology news and views to help the busy scientist keep up-to-date on current research, forthcoming conferences, hot research topics, high impact publications, and much more.
E6 Oncoproteins
from Scott B. Vande Pol writing in Small DNA Tumour Viruses:
Papillomavirus E6 oncoproteins are small zinc-binding proteins with a bewildering array of biological activities, including modulation of apoptosis, cellular transcription, host cell differentiation, growth factor dependence, DNA damage responses, and cell cycle progression. How can such a tiny protein do so much? This review examines insights from studies of oncogenic human papillomavirus E6 and bovine papillomavirus E6 to illuminate the mechanism by which E6 proteins interact with cellular binding partners. The origins of E6 and the history of its investigation are presented with the discovery of the major interaction partners that mediate E6 effects on DNA damage responses, cellular transcription, and modulation of keratinocyte differentiation.
Further reading: Small DNA Tumour Viruses Related publications
Dynamics of DNA Double-strand Break Repair in Bacillus subtilis
from Begoña Carrasco, Paula P. Cardenas, Cristina Cañas, Tribuhwuan Yadav, Carolina E. César, Silvia Ayora and Juan C. Alonso writing in Bacillus: Cellular and Molecular Biology (Second edition):
All organisms have developed a variety of DNA repair mechanisms to cope with DNA lesions. Homologous recombination (HR), which uses a homologous template to restore lost information at the break site, is the ultimate step for repair of one- or two-ended double strands breaks (DSBs) and for promoting the re-establishment of replication forks. Genetic and cytological approaches were used to analyze the requirements of exponentially growing Bacillus subtilis cells to survive chemical or physical agents that generate one- or two-ended DSBs and the choreography of DSB repair. The damage-induced multi-protein complex (recombinosome), organised into focal assemblies, has been confirmed by biochemical approaches. HR is coordinated with other essential processes, such as DNA replication, transcription and chromosomal segregation. When DSB recognition or end resection is severely impaired or an intact homologous template is not available the DNA ends of two-ended DSBs are repaired via non-homologous end joining.
Further reading: Bacillus: Cellular and Molecular Biology (Second edition)
Dynamics and Robustness of Metabolic Networks: a Systems Biology Review of Escherichia coli Metabolism
from Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla writing in Systems Microbiology: Current Topics and Applications:
The functional repertoire of an organism's metabolic network is closely linked to its phenotype and potential for utility in metabolic engineering applications. In this chapter, we discuss a systems biology view of Escherichia coli metabolism by integrating current genome-scale computational modelling approaches with available molecular genetics tools, as well as the experimental framework for metabolite and metabolic flux determination.
Further reading: Systems Microbiology Related publications
DNA sequencing of uncultured microbes from single cells
from Roger S. Lasken, Mary-Jane Lombardo, Mark Novotny, Joyclyn Yee-Greenbaum and Rashel V. Grindberg writing in Metagenomics: Current Innovations and Future Trends:
Development of a method to sequence DNA from a single cell has enabled new strategies to investigate the microbial world. Only a few years ago, sequencing from one cell was not feasible. A bacterium only contains a few femtograms of DNA which is insufficient for current sequencing technologies. This limitation was overcome with the development of a method to amplify DNA called multiple displacement amplification (MDA) which can generate micrograms of genomic sequence from one cell. Improvements have also been made in our ability to isolate cells by flow cytometry, micromanipulation and microfluidics and to lyse the cells to release the single genome copy as a template for MDA. Large portions of the genome can be obtained from each cell and this has opened up a new front in the effort to sequence uncultivated species. Cells can be isolated from an environment or clinical specimen and directly sequenced with no need to develop culture methods. This chapter will review the current methodologies, the strengths and limitations of the single cell approach and its application to microbial genomics.
Further reading: Metagenomics: Current Innovations and Future Trends
DNA Sequence Contribution to Nucleosome Distribution
from Justin A. Fincher and Jonathan H. Dennis writing in Epigenetics: A Reference Manual:
DNA in eukaryotes is efficiently and compactly organized into chromatin, the fundamental subunit of which is the nucleosome: approximately 150 bp of DNA spooled 1.65 times around a histone octamer. The location and density of nucleosomes play a role in regulating nuclear processes including transcription, replication, recombination, and repair. Mechanisms acting in trans, like ATP-dependent remodelers and cellular memory complexes, as well as in cis features intrinsic to the DNA sequence itself regulate the location and density of nucleosomes. Here, we review the three cis acting DNA sequence features that affect the distribution of nucleosomes: (1) two frameworks defining the relationship between the histone octamer and the underlying DNA sequence (nucleosome occupancy and nucleosome position, then statistical positioning and a nucleosome positioning code), (2) the organization of DNA into the nucleosome core particle, and (3) specific DNA sequence features and DNA templates that promote or inhibit the formation of nucleosomes. We close by describing three computational algorithms trained on DNA sequence that have been used to predict nucleosome position and density. In summary, we hope to draw attention to multiple aspects of DNA sequence that specify organization of sequence into nucleosomes and influence the distribution of nucleosomes in eukaryotic genomes.
Further reading: Epigenetics: A Reference Manual
Environmental Microbiology review
"This volume provides a good overview of how newer techniques are being used to study environmental microbial populations, primarily in water. It is a very useful starting point for those who are looking for an introduction to some of the methods or need to come up to speed on developments over the last decade or so ... The chapters are very well referenced ... it provides quite a comprehensive and useful look at the applications of a range of methodologies to aquatic microbiology in recent years. " from Jean MacRae (University of Maine, Orono, USA) writing in The Quarterly Review of Biology (2011) 86: 354-355. read more ...
 | Edited by: Keya Sen and Nicholas J. Ashbolt "comprehensive and useful" (Quar. Rev. Biol.)ISBN: 978-1-904455-70-7 Publisher: Caister Academic Press Publication Date: January 2011 Cover: hardback |