Project description:This study analysed the temporal transcriptional response of L. lactis UC509.9 undergoing infection with either Tuc2009 or c2, representing phages of two different species (P335 and c2, respectively) of the family Siphoviridae. For the first time, to our knowledge, both DNA microarrays of the host and high resolution tiling arrays of each phage were used provide corresponding data sets of the entire transcriptome at various points post-infection. DNA microarrays containing oligonucleotide primers representing each of the 2066 annotated genes on the genome of L. lactis UC509.9 (Genbank accession number: CP003157), in addition to complete genome tiling arrays of bacteriophages Tuc2009 NC_002703) and C2 (NC_001706) at 4 bp resolution, were designed using eArray (https://earray.chem.agilent.com/earray/) and ChipD (http://www.ncbi.nlm.nih.gov/pubmed/20529880) and obtained from Agilent Technologies (Palo Alto, CA). For sample collection, pre-warmed GM17 (30 M-BM-0C) was inoculated with 2 % of an overnight culture of L. lactis UC509.9. This was grown at 30 M-BM-0C under static conditions to an OD600 of 0.13 at which point CaCl2 was added to a final concentration of 10 mM. The culture was further incubated for 10 min to allow equilibration. At this point, the culture was split into two equal volumes. To one, phage (either C2 or Tuc2009) in TBT buffer (100 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2), was added to a final multiplicity of infection (MOI) of 5. To the other, acting as control, a corresponding amount of TBT buffer without phage was added. Samples (60 ml) were collected at 2, 5, 10, 15, 25, 35 and, in the case of Tuc2009 only, 45 min post infection (p.i.) by centrifugation. Pellets were flash frozen in a -80 M-BM-0C EtOH bath. Samples were then maintained at -80 M-BM-0C until further processing and analysis.

2013-06-27 | E-GEOD-45655 | biostudies-arrayexpress

Cachexia - Non-Cachexia Metagenome Analysis

Project description:Cancer cachexia has been linked to gut bacterial alterations, but alterations of gut viruses, mostly bacteriophages, have not yet been explored. We performed shotgun metagenomic sequencing of DNA from stool samples of 78 cachectic and 42 non-cachectic cancer patients. K-mer-based matching to reference databases revealed abundance variations of bacteria and viruses. Beyond bacterial alterations, cachectic patients exhibited significantly lower bacteriophage abundance, predominantly affecting Caudovirales and Siphoviridae species (double-stranded DNA) but also Inoviridae and Microviridae families (single-stranded DNA).

| EGAS00001007156 | EGA

Characterization of Streptococcus pneumoniae phage-like element SpnCI reveals an enhanced virulent phenotype in the acute invertebrate infection model Galleria mellonella

Project description:Phage-like elements are found in a multitude of streptococcal species, including pneumococcal strain Hungary19A-6 (SpnCI). The aim of our research was to investigate the role of phage-like element SpnCI in enhanced virulence and phenotypic modulation within Streptococcus pneumoniae. SpnCI was found to significantly enhance virulence within the invertebrate infection model Galleria mellonella. Infections with SpnCI led to a lower mean health score (1.6) and survival percentage (20%) compared to SpnCI null TIGR4 infections (3.85 mean health score and 50% survival). SpnCI remained integrated throughout growth, conferring greater sensitivity to UV irradiation. Change in transcriptional patterns occurred, including downregulation of operons involved with cell surface modelling in the SpnCI containing strain of TIGR4. Kanamycin-tagged SpnCI strain in Hungary19A-6 was inducible and isolated from lysate along with both annotated prophages. No phages were identified by PCR nor electron microscopy (EM) following induction of TIGR4 SpnCI∆strA suggesting helper-phage dependence for dissemination. EM of lysate showed typical siphoviridae morphology with an average capsid size of 60 nm. Two of sixty capsids were found to be smaller, suggesting SpnCI disseminates using a similar mechanism described for Staphylococcus aureus phage-like element SaPI. SpnCI from lysate infected capsule null strain T4R but was incapable of infecting the encapsulated TIGR4 strain suggesting that capsule impedes phage infection. Our work demonstrates that SpnCI can modulate virulence, UV susceptibility, alter transcriptional patterns, and furthermore, can disseminate via infection within pneumococcus. Further research is necessary to elucidate how SpnCI modulates virulence and what genes are responsible for the enhanced virulence phenotype.

2019-06-12 | GSE132556 | GEO

Comparing the chromosome binding profiles of nucleoid structuring protein H-NS in the presence or absence of conditions eliciting the depletion of transcription termination protein NusG in Salmonella

Project description: Not available

2022-07-04 | E-MTAB-11386 | biostudies-arrayexpress