Role of the unstable directions in the equilibrium and aging dynamics of supercooled liquids

The connectivity of the potential energy landscape in supercooled atomic liquids is investigated through the calculation of the instantaneous normal modes spectrum and a detailed analysis of the unstable directions in configuration space. We confirm the hypothesis that the mode-coupling critical temperature is the $T$ at which the dynamics crosses over from free to activated exploration of configuration space. We also report the observed changes in the local connectivity of configuration space sampled during aging, following a temperature jump from a liquid to a glassy state.Comment: 5 pages, 3 figures. Phys. Rev. Lett., in pres

Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

2openInternationalMetagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.openAlbanese, Davide; Donati, ClaudioAlbanese, D.; Donati, C

Simultaneous Detection of H and D NMR Signals in a micro-Tesla Field

We present NMR spectra of remote-magnetized deuterated water, detected in an unshielded environment by means of a differential atomic magnetometer. The measurements are performed in a $\mu$T field, while pulsed techniques are applied -following the sample displacement- in a 100~$\mu$T field, to tip both D and H nuclei by controllable amounts. The broadband nature of the detection system enables simultaneous detection of the two signals and accurate evaluation of their decay times. The outcomes of the experiment demonstrate the potential of ultra-low-field NMR spectroscopy in important applications where the correlation between proton and deuteron spin-spin relaxation rates as a function of external parameters contains significant information.Comment: 7 pages (letter, 4 pages) plus supplemental material as an appendix. This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Journal of Phys. Chem. Lett., copyright American Chemical Society after peer review. To access the final edited and published work see: pubs.acs.org/doi/abs/10.1021/acs.jpclett.7b0285

Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.

Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes

Macular Edema and Silicone Oil Tamponade

Purpose: To analyze the risk factors for inflammatory macular edema (ME) in a series of patients undergoing vitreoretinal surgery using Silicone Oil (SO) as a long-term tamponade. Materials and methods: We examined 118 consecutive eyes of 115 patients, mean age 57.8 years (range 39-79), suffering from various types of severe retinal detachment. Surgical procedures were carried out on all patients, and SO 1000cs was injected into the eye at the end of surgery to permit stable retinal reattachment. ME was classified as initial, medium and severe. The characteristics of ME were compared with various preoperative, intra-surgical and postoperative parameters. Statistical analyses were carried out using the T test and the Pearson correlation coefficient. Results: Twenty-six eyes were excluded. Twenty out of 92 eyes (22%) presented various types of ME. No significant correlation was found between ME and age or complication and duration of surgery. Significant correlation was found between ME and macular status before surgery and time length of intraocular permanence of SO. Conclusion: SO should be removed as soon as possible, in particular when the preoperative macular status is compromised. Decreased molecular transport in the vitreous space, permanence of inflammatory substances between SO and the macula, mechanical floating of SO and dangerous light exposure might be involved in the pathogenesis of ME

PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes

PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD

Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy

Erwinia amylovora is a Gram-negative bacterium that colonizes a wide variety of plant species causing recurrent local outbreaks of fire blight in crops of the Rosaceae family. Recent genomic surveys have documented the limited genomic diversity of this species, possibly related to a recent evolutionary bottleneck and a strong correlation between geography and phylogenetic structure of the species. Despite its economic importance, little is known about the genetic variability of co-circulating strains during local outbreaks. Here, we report the genome sequences of 82 isolates of E. amylovora, collected from different host plants in a period of 16 years in Trentino, a small region in the Northeastern Italian Alps that has been characterized by recurrent outbreaks of fire blight in apple orchards. While the genome isolated before 2018 are closely related to other strains already present in Europe, we found a novel subclade composed only by isolates that were sampled starting from 2018 and demonstrate that the endemic population of this pathogen can be composed by mixture of strain

Intergenerational transfer of persistent bacterial communities in female Nile tilapia

5openInternationalInternational coauthor/editorResident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.openAbdelhafiz, Yousri; Fernandes, Jorge M. O.; Donati, Claudio; Pindo, Massimo; Kiron, ViswanathAbdelhafiz, Y.; Fernandes, J.M.O.; Donati, C.; Pindo, M.; Kiron, V