Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583

Small RNA molecules (sRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. We characterized 11 sRNAs by tiling microarray analysis, 5′ and 3′ RACE-PCR, and Northern blot analysis. Six sRNAs were specifically expressed at exponential phase, two sRNAs were observed at stationary phase, and three were detected during both phases. Searches of putative functions revealed that three of them (EFA0080_EFA0081 and EFB0062_EFB0063 on pTF1 and pTF2 plasmids, respectively, and EF0408_EF04092 located on the chromosome) are similar to antisense RNA involved in plasmid addiction modules. Moreover, EF1097_EF1098 shares strong homologies with tmRNA (bi-functional RNA acting as both a tRNA and an mRNA) and EF2205_EF2206 appears homologous to 4.5S RNA member of the Signal Recognition Particle (SRP) ribonucleoprotein complex. In addition, proteomic analysis of the ΔEF3314_EF3315 sRNA mutant suggests that it may be involved in the turnover of some abundant proteins. The expression patterns of these transcripts were evaluated by tiling array hybridizations performed with samples from cells grown under eleven different conditions some of which may be encountered during infection. Finally, distribution of these sRNAs among genome sequences of 54 E. faecalis strains was assessed. This is the first experimental genome-wide identification of sRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen

Application of the GIS methods for identification, to catalog and assessment of hazard to the environment caused by uranium mine facilities

Dziedzictwem zlikwidowanego górnictwa uranowego i powierzchniowej działalności zakładów górniczych są szkody górnicze i porzucone obiekty, które stwarzają zagrożenie dla środowiska. Dotychczas, zasadniczą przeszkodą wykonania remediacji terenu pogórniczego w Polsce był brak kompleksowej charakterystyki poszczególnych obiektów i zagrożeń z nimi związanych. W niniejszym artykule omówiono metodykę parametrycznej identyfikacji, katalogowania i oceny obiektów i szkód górniczych oraz zagrożeń z nimi związanych. Zastosowano ją praktycznie na terenie pięciu miejscowości, w trzech gminach SW Polski. Do tego celu wykorzystano narzędzia GIS i doświadczenia niemieckie. Ponadto, zwrócono uwagę na przydatność tych danych do przygotowania interwencji geotechnicznej, jako ważnej fazy remediacji terenu.The legacy of the liquidated uranium mine industry and its surface activity are mining damage and abandoned objects, hazardous to the environment. To date, the basic obstacle, which prevented remediation of such mine grounds, was lack of complex profile of particular objects and risks related. The paper presents methods for application of the Geographic Information Systems (GIS) for identification, to catalog and for assessment of hazard to the environment caused by uranium mine facilities and mining damage. The methods were implemented in five place, in three districts of SW Poland. Apart from the tools specific for GIS, there were utilized German experience. Moreover, it was pointed out that the data may be effectively used for geotechnical intervention, being an important part of the terrain remediation process

Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA Modifying Enzyme TGT

Fragment based lead discovery was applied to tRNA guanine transglycosylase, an enzyme modifying post transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella s virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1 recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1 recognition pocket. We synthesized 6 carboxamido , 6 hydrazido , and 4 guanidino benzimidazoles to target the opened pocket, including a dihydro imidazoquinazoline with a propyn 1 yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGT

Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery

This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration