Species-selective killing of bacteria by antimicrobial peptide-PNAs

This is an open-access article distributed under the terms of the Creative Commons Attribution License, CC BY 4.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Broad-spectrum antimicrobials kill indiscriminately, a property that can lead to negative clinical consequences and an increase in the incidence of resistance. Species-specific antimicrobials that could selectively kill pathogenic bacteria without targeting other species in the microbiome could limit these problems. The pathogen genome presents an excellent target for the development of such antimicrobials. In this study we report the design and evaluation of species-selective peptide nucleic acid (PNA) antibacterials. Selective growth inhibition of B. subtilis, E. coli, K. pnuemoniae and S. enterica serovar Typhimurium in axenic or mixed culture could be achieved with PNAs that exploit species differences in the translation initiation region of essential genes. An S. Typhimurium-specific PNA targeting ftsZ resulted in elongated cells that were not observed in E. coli, providing phenotypic evidence of the selectivity of PNA-based antimicrobials. Analysis of the genomes of E. coli and S. Typhimurium gave a conservative estimate of >150 PNA targets that could potentially discriminate between these two closely related species. This work provides a basis for the development of a new class of antimicrobial with a tuneable spectrum of activity.Peer reviewedFinal Published versio

A high-throughput and sensitive method to measure Global DNA Methylation: Application in Lung Cancer

<p>Abstract</p> <p>Background</p> <p>Genome-wide changes in DNA methylation are an epigenetic phenomenon that can lead to the development of disease. The study of global DNA methylation utilizes technology that requires both expensive equipment and highly specialized skill sets.</p> <p>Methods</p> <p>We have designed and developed an assay, <it>CpG</it>lobal, which is easy-to-use, does not utilize PCR, radioactivity and expensive equipment. <it>CpG</it>lobal utilizes methyl-sensitive restriction enzymes, HRP Neutravidin to detect the biotinylated nucleotides incorporated in an end-fill reaction and a luminometer to measure the chemiluminescence. The assay shows high accuracy and reproducibility in measuring global DNA methylation. Furthermore, <it>CpG</it>lobal correlates significantly with High Performance Capillary Electrophoresis (HPCE), a gold standard technology. We have applied the technology to understand the role of global DNA methylation in the natural history of lung cancer. World-wide, it is the leading cause of death attributed to any cancer. The survival rate is 15% over 5 years due to the lack of any clinical symptoms until the disease has progressed to a stage where cure is limited.</p> <p>Results</p> <p>Through the use of cell lines and paired normal/tumor samples from patients with non-small cell lung cancer (NSCLC) we show that global DNA hypomethylation is highly associated with the progression of the tumor. In addition, the results provide the first indication that the normal part of the lung from a cancer patient has already experienced a loss of methylation compared to a normal individual.</p> <p>Conclusion</p> <p>By detecting these changes in global DNA methylation, <it>CpG</it>lobal may have a role as a barometer for the onset and development of lung cancer.</p

Azacytidine and Decitabine Induce Gene-Specific and Non-Random DNA Demethylation in Human Cancer Cell Lines

The DNA methyltransferase inhibitors azacytidine and decitabine represent archetypal drugs for epigenetic cancer therapy. To characterize the demethylating activity of azacytidine and decitabine we treated colon cancer and leukemic cells with both drugs and used array-based DNA methylation analysis of more than 14,000 gene promoters. Additionally, drug-induced demethylation was compared to methylation patterns of isogenic colon cancer cells lacking both DNA methyltransferase 1 (DNMT1) and DNMT3B. We show that drug-induced demethylation patterns are highly specific, non-random and reproducible, indicating targeted remethylation of specific loci after replication. Correspondingly, we found that CG dinucleotides within CG islands became preferentially remethylated, indicating a role for DNA sequence context. We also identified a subset of genes that were never demethylated by drug treatment, either in colon cancer or in leukemic cell lines. These demethylation-resistant genes were enriched for Polycomb Repressive Complex 2 components in embryonic stem cells and for transcription factor binding motifs not present in demethylated genes. Our results provide detailed insights into the DNA methylation patterns induced by azacytidine and decitabine and suggest the involvement of complex regulatory mechanisms in drug-induced DNA demethylation

Mechanisms, functions and ecology of colour vision in the honeybee.

notes: PMCID: PMC4035557types: Journal Article© The Author(s) 2014.This is an open access article that is freely available in ORE or from Springerlink.com. Please cite the published version available at: http://link.springer.com/article/10.1007%2Fs00359-014-0915-1Research in the honeybee has laid the foundations for our understanding of insect colour vision. The trichromatic colour vision of honeybees shares fundamental properties with primate and human colour perception, such as colour constancy, colour opponency, segregation of colour and brightness coding. Laborious efforts to reconstruct the colour vision pathway in the honeybee have provided detailed descriptions of neural connectivity and the properties of photoreceptors and interneurons in the optic lobes of the bee brain. The modelling of colour perception advanced with the establishment of colour discrimination models that were based on experimental data, the Colour-Opponent Coding and Receptor Noise-Limited models, which are important tools for the quantitative assessment of bee colour vision and colour-guided behaviours. Major insights into the visual ecology of bees have been gained combining behavioural experiments and quantitative modelling, and asking how bee vision has influenced the evolution of flower colours and patterns. Recently research has focussed on the discrimination and categorisation of coloured patterns, colourful scenes and various other groupings of coloured stimuli, highlighting the bees' behavioural flexibility. The identification of perceptual mechanisms remains of fundamental importance for the interpretation of their learning strategies and performance in diverse experimental tasks.Biotechnology and Biological Sciences Research Council (BBSRC

Epigenetics of human cutaneous melanoma: setting the stage for new therapeutic strategies

Cutaneous melanoma is a very aggressive neoplasia of melanocytic origin with constantly growing incidence and mortality rates world-wide. Epigenetic modifications (i.e., alterations of genomic DNA methylation patterns, of post-translational modifications of histones, and of microRNA profiles) have been recently identified as playing an important role in melanoma development and progression by affecting key cellular pathways such as cell cycle regulation, cell signalling, differentiation, DNA repair, apoptosis, invasion and immune recognition. In this scenario, pharmacologic inhibition of DNA methyltransferases and/or of histone deacetylases were demonstrated to efficiently restore the expression of aberrantly-silenced genes, thus re-establishing pathway functions. In light of the pleiotropic activities of epigenetic drugs, their use alone or in combination therapies is being strongly suggested, and a particular clinical benefit might be expected from their synergistic activities with chemo-, radio-, and immuno-therapeutic approaches in melanoma patients. On this path, an important improvement would possibly derive from the development of new generation epigenetic drugs characterized by much reduced systemic toxicities, higher bioavailability, and more specific epigenetic effects

Structure of bryozoan communities in an Antarctic glacial fjord (Admiralty Bay, South Shetlands)

Bryozoans are among the most important groups of the Southern Ocean benthic macrofauna, both in terms of species richness and abundance. However, there is a considerable lack of ecological research focused on their distribution patterns and species richness on smaller scale, especially in the soft bottom habitats of Antarctic glacial fjords. The aim of this study was to describe those patterns in the Admiralty Bay. Forty-nine Van Veen grab samples were collected at the depth range from 15 to 265 m, in the summer season of 1979/1980, at three sites distributed along the main axis of the fjord. Among 53 identified species of bryozoans, 32 were recorded in the Admiralty Bay for the first time. The most common and abundant species were Himantozoum antarcticum, Inversiula nutrix and Nematoflustra flagellata. Genera such as Arachnopusia, Cellarinella and Osthimosia were the most speciose taxa. It was demonstrated that depth was important for the distribution of the bryozoans. More than half of the recorded species were found only below 70 m. An influence of glacial disturbance was reflected in the dominance structure of colony growth-forms. The inner region of the fjord was dominated almost entirely by encrusting species, while the diversity of bryozoan growth-forms in less disturbed areas was much higher. In those sites the highest percentage of branched, tuft like species represented by buguliform and flustriform zoaria was observed.The study was supported by a grant of Polish Ministry of Science and Higher Education No. 51/N-IPY/2007/0 as well as Census of Antarctic Marine Life Project. Krzysztof Pabis was also partially supported by University of Lodz internal funds. This research was also supported by the Polish Geological Institute-National Research Institute during the realization of the project numbered 40.2900.0903.18.0 titled “Bryozoan assemblage of Admiralty Bay—richness, diversity and abundance.” Urszula Hara is deeply grateful to Leszek Giro (Micro-area Analyses Laboratory at the Polish Geological Institute-National Research Institute, Warsaw), for providing SEM assistance during the project. We also want to thank two anonymous reviewers for their suggestions that helped us improve this article. Thanks are also due to Magdalena Błażewicz-Paszkowycz for language correction and polishing the final version of the manuscript

KASHz: No evidence for ionised outflows instantaneously suppressing star formation in moderate luminosity AGN at z∼1.4–2.6

As part of our KMOS AGN Survey at High-redshift (KASHz), we present spatially-resolved VLT/KMOS and VLT/SINFONI spectroscopic data and ALMA 870μm continuum imaging of eight z=1.4–2.6 moderate AGN (⁠L 2−10kev L2−10kev = 1042 − 1045 ergs s−1). We map [O iii], Hα and rest-frame FIR emission to search for any spatial anti-correlation between ionised outflows (traced by the [O iii] line) and star formation (SF; traced by Hα and FIR), that has previously been claimed for some high-z AGN and used as evidence for negative and/or positive AGN feedback. Firstly, we conclude that Hα is unreliable to map SF inside our AGN host galaxies based on: (i) SF rates inferred from attenuation-corrected Hα can lie below those inferred from FIR; (ii) the FIR continuum is more compact than the Hα emission by a factor of ∼2 on average; (iii) in half of our sample, we observe significant spatial offsets between the FIR and Hα emission, with an average offset of 1.4 ± 0.6 kpc. Secondly, for the five targets with outflows we find no evidence for a spatial anti-correlation between outflows and SF using either Hα or FIR as a tracer. This holds for our re-analysis of a famous z=1.6 X-ray AGN (‘XID 2028’) where positive and negative feedback has been previously claimed. Based on our results, any impact on SF by ionised outflows must be subtle, either occurring on scales below our resolution, or on long timescales