Effects of galectin-1 on immunomodulatory properties of human monocyte-derived dendritic cells.

Our study aimed to evaluate the effects of Gal-1 in dose depending manner on maturation and immunomodulatory properties of monocyte-derived (Mo) DCs . The effects were analyzed by monitoring their phenotypic characteristics, cytokine profile, and the ability to direct the immune response in the co-culture with allogeneic CD4T cells. Gal-1 reduced the expression of CD80 and CD86 molecules on MoDCs compared to untreated MoDCs.

Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Efficiency of Prespacer Selection during Primed Adaptation.

CRISPR DNA arrays of unique spacers separated by identical repeats ensure prokaryotic immunity through specific targeting of foreign nucleic acids complementary to spacers. New spacers are acquired into a CRISPR array in a process of CRISPR adaptation. Selection of foreign DNA fragments to be integrated into CRISPR arrays relies on PAM (protospacer adjacent motif) recognition, as only those spacers will be functional against invaders.

Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence.

In addition to its well-established defense function, CRISPR/Cas can also exhibit crucial non-canonical activity through endogenous gene expression regulation, which was found to mainly affect bacterial virulence. These non-canonical functions depend on scaRNA, which is a small RNA encoded outside of CRISPR array, that is typically flanked by a transcription start site (TSS) and a terminator, and is in part complementary to another small CRISPR/Cas-associated RNA (tracrRNAs). Identification of scaRNAs is however largely complicated by the scarcity of RNA-Seq data across different bacteria, so that they were identified only in a relatively rare CRISPR/Cas subtype (IIB), and the possibility of finding them in other Type II systems is currently unclear.

Mix-and-matching as a promoter recognition mechanism by ECF σ factors.

Background: Transcription initiation is in bacteria exhibited by different σ factors, most of which fall within σ family. This family is diverse, ranging from the housekeeping Group I (RpoDs), to Group IV (ECF) σ factors, that transcribe smaller regulons under more stringent conditions. RpoDs employ a kinetic mix-and-match mechanism, where promoter elements complement each other binding strengths in achieving sufficient transcription activity.

Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs.

Unlabelled: Extracytoplasmic function (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both -35 and -10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups.

Inferring bacteriophage infection strategies from genome sequence: analysis of bacteriophage 7-11 and related phages.

Background: Analyzing regulation of bacteriophage gene expression historically lead to establishing major paradigms of molecular biology, and may provide important medical applications in the future. Temporal regulation of bacteriophage transcription is commonly analyzed through a labor-intensive combination of biochemical and bioinformatic approaches and macroarray measurements. We here investigate to what extent one can understand gene expression strategies of lytic phages, by directly analyzing their genomes through bioinformatic methods.