Gene Network Holography of the Soil Bacterium Bacillus subtilis

Roth, Dalit; Madi, Asaf; Kenett, Dror Y.; Ben‐Jacob, Eshel

doi:10.1007/978-3-642-14512-4_10

Cited by 2 publications

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References 67 publications

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“…First, we tested the expression of flagellin and motility-related genes by real-time PCR (polymerase chain reaction) using primers amplifying the following genes: flagellin ( hag ) , flgK, fliI, motA and sigD (hypothetical annotations of flagella genes presented in Table S4). These genes were selected based on the outcome of the Genome Holography bioinformatics analysis of microarray chip results (Madi et al ., 2008 ; Roth et al ., 2011 ). For more details, see Figs S5 and S6, and Table S2.…”

Section: Resultsmentioning

confidence: 99%

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex

Roth

Finkelshtein

Ingham

et al. 2013

Environmental Microbiology

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SummaryBacteria often use sophisticated cooperative behaviours, such as the development of complex colonies, elaborate biofilms and advanced dispersal strategies, to cope with the harsh and variable conditions of natural habitats, including the presence of antibiotics. Paenibacillus vortex uses swarming motility and cell-to-cell communication to form complex, structured colonies. The modular organization of P. vortex colony has been found to facilitate its dispersal on agar surfaces. The current study reveals that the complex structure of the colony is generated by the coexistence and transition between two morphotypes – ‘builders’ and ‘explorers’ – with distinct functions in colony formation. Here, we focused on the explorers, which are highly motile and spearhead colonial expansion. Explorers are characterized by high expression levels of flagellar genes, such as flagellin (hag), motA, fliI, flgK and sigD, hyperflagellation, decrease in ATP (adenosine-5′-triphosphate) levels, and increased resistance to antibiotics. Their tolerance to many antibiotics gives them the advantage of translocation through antibiotics-containing areas. This work gives new insights on the importance of cell differentiation and task distribution in colony morphogenesis and adaptation to antibiotics.

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Section: Resultsmentioning

confidence: 99%

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex

Roth

Finkelshtein

Ingham

et al. 2013

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

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Link Clustering Reveals Structural Characteristics and Biological Contexts in Signed Molecular Networks

et al. 2013

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Many biological networks are signed molecular networks which consist of positive and negative links. To reveal the distinct features between links with different signs, we proposed signed link-clustering coefficients that assess the similarity of inter-action profiles between linked molecules. We found that positive links tended to cluster together, while negative links usually behaved like bridges between positive clusters. Positive links with higher adhesiveness tended to share protein domains, be associated with protein-protein interactions and make intra-connections within protein complexes. Negative links that were more bridge-like tended to make interconnections between protein complexes. Utilizing the proposed measures to group positive links, we observed hierarchical modules that could be well characterized by functional annotations or known protein complexes. Our results imply that the proposed sign-specific measures can help reveal the network structural characteristics and the embedded biological contexts of signed links, as well as the functional organization of signed molecular networks.

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Gene Network Holography of the Soil Bacterium Bacillus subtilis

Cited by 2 publications

References 67 publications

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex

Link Clustering Reveals Structural Characteristics and Biological Contexts in Signed Molecular Networks

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