Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.     

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.     

Protein degradation sets the fraction of active ribosomes at vanishing growth

Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data from E. coli and S. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms.     

Population Structure of Osmunda regalis in Relation to Environment and Vegetation: An Example in the Mediterranean Area

The structure of 42 natural populations of the endangered fern Osmunda regalis was studied at the southern limit of its European distribution. The aims were to i) investigate the population structures and status of the species; ii) test which local habitat and population characteristics correlate with the different population structures in the Mediterranean area; iii) evaluate which habitat types are suitable to support viable populations. The structure of populations is determined by the attribution of different stages of development of the sporophyte. This study documented the life-stage structure of O. regalis using an original classification of life stages that may be applicable to other fern populations with similar morphology. Using statistical analyses we distinguished: i) dynamic populations, which are characterized by a large proportion of sporelings and vegetative adults and are associated with streams and nemoral species; ii) stable populations, with a higher proportion of generative adults, growing prevalently in habitats rich in hygrophilous grasses and shrubs, with lower tree cover; iii) senile populations, with a relatively higher proportion of senescent individuals and with marked rejuvenation dominated by vegetative adults, which are prevalently located in spring swamps. The proportion of senescent stage individuals is positively correlated with the mean geographic distance between populations. Spring swamps, with populations that provide a clear example of remnant dynamics, are the habitat with the most stable conditions for O. regalis in the Mediterranean area.     

A wavelet-based ECG delineation algorithm for 32-bit integer online processing

Background  

Since the first well-known electrocardiogram (ECG) delineator based on Wavelet Transform (WT) presented by Li et al. in 1995, a significant research effort has been devoted to the exploitation of this promising method. Its ability to reliably delineate the major waveform components (mono- or bi-phasic P wave, QRS, and mono- or bi-phasic T wave) would make it a suitable candidate for efficient online processing of ambulatory ECG signals. Unfortunately, previous implementations of this method adopt non-linear operators such as root mean square (RMS) or floating point algebra, which are computationally demanding.     

Recent outbreaks of downy mildew on grape ivy (Parthenocissus tricuspidata, Vitaceae) in Germany are caused by a new species of Plasmopara

Plasmopara viticola is one of the most destructive pathogens in grape production and was introduced from North America to Europe more than a century ago. The pathogen is thought to affect a broad range of hosts in the Vitaceae, including the genera Vitis and Parthenocissus. However, the latter has not previously been reported as a host in Germany. Here, it is shown on the basis of phylogenetic and morphological data that recent outbreaks of downy mildew on Parthenocissus tricuspidata in the Stuttgart area of Southern Germany are not caused by Plasmopara viticola, but by an undescribed species introduced here as Plasmopara muralis. The new species has rapidly spread in the Stuttgart area throughout the past 2 years and poses a potential threat to ornamental vines grown as wall cover should its spread not be controlled.     

Performance prediction of deep learning applications training in GPU as a service systems

Cluster Computing - Data analysts predict that the GPU as a service (GPUaaS) market will grow to support 3D models, animated video processing, gaming, and deep learning model training. The main...