HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.     

Oligotrophication of Lake Balaton over a 20-year period and its implications for the relationship between phytoplankton and zooplankton biomass

Hydrobiologia - Lake Balaton, the largest lake in Central Europe, underwent severe eutrophication from the 1960s to the 1990s, due to phosphorus loadings from external anthropogenic sources. The...     

Protoplast fusion of Schizosaccharomyces pombe auxotrophic mutants of identical mating-type

Summary Protoplasts of methionine-and lysine-requiring h^- mutants isolated from the L972 h^- strain of Schizosaccharomyces pombe were fused. The protoplasts were obtained from the cells with enzymes produced by Trichoderma viride. When a mixture of the protoplasts was treated with 30% PEG 4000 solution containing 10 mM CaCl₂, cell fusion and complementation was attained with a frequency of 0.17%. Both fusion partners were recovered among the spores after crossing of the fusion products with the strain M210 ade6 h⁺. Cytological and haploidization examinations showed that the fusion cells are not heterokaryons, and that the increased amount of genetic material is situated in one nucleus.     

Allocation of random amplified polymorphic DNA markers and enzyme activities toAspergillus nidulans andAspergillus tetrazonus chromosomes

Chromosome-substituted haploid segregants of anA. nidulans × A. tetrazonus somatic hybrid were used to allocate several random amplified polymorphic DNA and isoenzyme markers to parental chromosomes. Twenty-six amplified DNA fragments, and nine isoenzyme activities, including lactate dehydrogenase, superoxide dismutase, and arylesterase isoenzymes were assigned to chromosomes. Chromosome-specific markers were found for eachA. nidulans andA. tetrazonus chromosome. These markers could be used to saturate the genetic map ofA. nidulans. The formation of two secondary metabolites was also assigned to chromosomes III and VIII. Attempts were made to allocate extracellular enzyme activities to parental chromosomes, mostly without success, possibly because multiple enzyme forms located on different chromosomes could be responsible for the production of an enzyme activity.     

Kinetics of the fast electric signal from oriented purple membrane

The photoinduced electric response of oriented purple membranes associated with processes before the K-intermediate decay of bacteriorhodopsin was measured in the 180-300 K temperature range. These response signals consist of two kinetically distinct components (both temperature dependent). The experimental data show a correlation between the time constants of the rise of the signal and solution resistance. A model is proposed to assign these components to two diffusion-limited processes of charge displacement in the solution. The displacement is caused by the electric field of the photoinduced transient dipole which is formed in the primary act of the bacteriorhodopsin photocycle. The two processes are assigned as: (a) the conduction of electrical current through H-bonds (time resolved only in the temperature range 180-200 K) and (b) the diffusion of charges through the interfacial layer.     

Phenotypic plasticity of melanocytes derived from human adult skin

We previously described a novel in vitro culture technique for dedifferentiated human adult skin melanocytes. Melanocytes cultured in a defined, cholera toxin and PMA free medium became bipolar, unpigmented, and highly proliferative. Furthermore, TRP-1 and c-Kit expression disappeared and EGFR receptor and nestin expression were induced in the cells. Here, we further characterized the phenotype of these dedifferentiated cells and by comparing them to mature pigmented melanocytes we detected crucial steps in their phenotype change. Our data suggest that normal adult melanocytes easily dedifferentiate into pluripotent stem cells given the right environment. This dedifferentiation process described here for normal melanocyte is very similar to what has been described for melanoma cells, indicating that phenotype switching driven by environmental factors is a general characteristic of melanocytes that can occur independent of malignant transformation.     

Enantioseparation of citalopram enantiomers by capillary electrophoresis: Method development through experimental design and computational modeling

Citalopram (CIT) is a frequently used modern antidepressant that inhibits selectively serotonin reuptake in the brain. It has a chiral center in its structure and is used in therapy as both racemic mixture and pure enantiomer as its pharmacological effect is almost entirely associated with S-CIT. The aim of this study was the development of a simple and rapid capillary electrophoresis (CE) method for the separation and quantification of CIT enantiomers. To establish the optimum chiral selector, several native and derivatized, neutral, and ionized cyclodextrins (CDs) were examined at different pH levels. An experimental design strategy was adopted for method optimization; a fractional factorial design was applied for screening purposes to identify significant experimental factors followed by a face-centered central composite design used for optimization purposes. Computational modeling was used to obtain information on the interaction energy and the geometry of the complexes to aid in the understanding of chiral separation mechanism. The best results were obtained when using a 25-mM phosphate buffer at pH 7.0, 3-mM CM-β-CD as chiral selector, 17.5°C temperature, 15-kV voltage, and 50 mbar/s hydrodynamic injection. The separation time was fast, below 3 min, and the migration order was S-CIT followed by R-CIT. The analytical performance of the method was verified in terms of precision, linearity, accuracy, sensibility, and robustness, and the method was applied for the determination of CIT enantiomers from pharmaceutical preparations.     

A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase η

The ubiquitin binding zinc finger (UBZ) domain in the C-terminal portion of Polη has been found to interact with ubiquitin. However, the affinity between the Polη UBZ and ubiquitin was shown to be low with a previously reported K(d) of 73-81 μM. This low-affinity binding between Polη UBZ and ubiquitin has been difficult to reconcile with its presumed role in translesion synthesis as suggested by genetic and cell biology studies. In this work, we constructed a minimal S. cerevisiae Polη UBZ domain and probed the Polη UBZ-ubiquitin interaction using a surface plasmon resonance (SPR) technique. Our quantitative binding data between the wild-type or mutant Polη UBZ and ubiquitin revealed an interesting divergence between the Polη UBZ from S. cerevisiae and humans. Moreover, we found that the C-terminal portion of yeast Polη (amino acid 515-632) binds ubiquitin with a much higher affinity than the minimal UBZ domain. Further, distinct ubiquitin-binding kinetics were observed for the C-terminal portion of Polη and the isolated UBZ domain. This observation raised the interesting possibility that the Polη C-terminal portion binds ubiquitin in a novel mode that affords higher affinity. Our findings have broader implication in understanding the generally weak interaction between the known ubiquitin-binding domains and ubiquitin.     

Genome sequence of Propionibacterium acnes type II strain ATCC 11828

Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota and is occasionally associated with inflammatory diseases (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). Here we present the complete genome sequence for the commercially available P. acnes type II reference strain ATCC 11828 (I. Nagy et al., Microbes Infect. 8:2195-2205, 2006) recovered from a subcutaneous abscess.