Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics

Motivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera. Contact: [email protected] Supplementary informatio

Can Life develop in the expanded habitable zones around Red Giant Stars?

We present some new ideas about the possibility of life developing around sub-giant and red giant stars. Our study concerns the temporal evolution of the habitable zone. The distance between the star and the habitable zone, as well as its width, increases with time as a consequence of stellar evolution. The habitable zone moves outward after the star leaves the main sequence, sweeping a wider range of distances from the star until the star reaches the tip of the asymptotic giant branch. If life could form and evolve over time intervals from $5 \times 10^8$ to $10^9$ years, then there could be habitable planets with life around red giant stars. For a 1 M$_{\odot}$ star at the first stages of its post main-sequence evolution, the temporal transit of the habitable zone is estimated to be of several 10$^9$ years at 2 AU and around 10$^8$ years at 9 AU. Under these circumstances life could develop at distances in the range 2-9 AU in the environment of sub-giant or giant stars and in the far distant future in the environment of our own Solar System. After a star completes its first ascent along the Red Giant Branch and the He flash takes place, there is an additional stable period of quiescent He core burning during which there is another opportunity for life to develop. For a 1 M$_{\odot}$ star there is an additional $10^9$ years with a stable habitable zone in the region from 7 to 22 AU. Space astronomy missions, such as proposed for the Terrestrial Planet Finder (TPF) and Darwin should also consider the environments of sub-giants and red giant stars as potentially interesting sites for understanding the development of life

Catheter Ablation of Atrial Fibrillation in Patients with Previous Lobectomy or Partial Lung Resection: Long-Term Results of an International Multicenter Study

Introduction: Data regarding the efficacy of catheter ablation in patients with atrial fibrillation (AF) and patients' previous history of pulmonary lobectomy/pneumonectomy are scanty. We sought to evaluate the efficacy and long-term follow-up of catheter ablation in this highly selected group of patients. Material and Methods: Twenty consecutive patients (8 females, 40%; median age 65.2 years old) with a history of pneumonectomy/lobectomy and paroxysmal or persistent AF, treated by means of pulmonary vein isolation (PVI) at ten participating centers were included. Procedural success, intra-procedural complications, and AF recurrences were considered. Results: Fifteen patients had a previous lobectomy and five patients had a complete pneumonectomy. A large proportion (65%) of PV stumps were electrically active and represented a source of firing in 20% of cases. PVI was performed by radiofrequency ablation in 13 patients (65%) and by cryoablation in the remaining 7 cases. Over a median follow up of 29.7 months, a total of 7 (33%) AF recurrences were recorded with neither a difference between patients treated with cryoablation or radiofrequency ablation or between the two genders. Conclusions: Catheter ablation by radiofrequency ablation or cryoablation in patients with pulmonary stumps is feasible and safe. Long-term outcomes are favorable, and a similar efficacy of catheter ablation has been noticed in both males and females

Disaster Situation and Humanitarian Emergency – In-Between Responses to the Refugee Crisis in Germany

In 2015, the needs of hundreds of thousands of refugees who arrived in Germany could only be met by deploying all available civil protection units. This article presents procedures and practices of state and non-state formal actors in the field of civil protection and related crisis management structures implemented and established across the board in the municipalities, the Federal Government and mass shelters, in particular in Bavaria. From a disaster research and humanitarian studies perspective we use the concept of “patterns of interpretation” to analyse the application of the “humanitarian emergency” and the “disaster situation” procedures to discuss whether the situation can really be categorized as “either-or” or whether the coexistence of the two served a function in managing such a complex situation. Finally, we discuss some developments that occurred after 2015/16 and consider the extent to which these developments shift or expand the existing patterns of interpretation

Seismic site characterization of the Kastelli (Kissamos) Basin in northwest Crete (Greece): Assessments using ambient noise recordings

Crete is actively seismic and site response studies are needed for estimating local site conditions subjected to seismic activity. In order to collect basic data, we performed ambient noise recordings to estimate the site response of the surface and near subsurface structure of the small-scale Kastelli Basin in northwest Crete. The spatial horizontal to vertical spectral ratios (HVSR) resonance pattern of the investigated sites in the centre of the Basin consists of either one or two peaks divided into low to high frequency range in different sites as follows: (a) in some sites only one amplified peak at low frequencies (0.6–1.2 Hz), (b) in other sites only one amplified peak at medium frequencies (2.9–8.5 Hz) and (c) in yet other sites two amplified peaks in the low to high frequency range (0.6–15.5 Hz). The investigated sites are amplified in the frequency range 0.6–15.5 Hz, while the amplitude reaches to a factor of 4 in the spectral ratios. The one HVSR amplified peak at low frequencies is related to locally soft or thick Quaternary deposits. Microtremors were measured in the coastal northwest part of the Basin in a well—lithified Cretaceous limestone site characterized by fractures and faults striking predominantly in a sector NNE to NNW. Sites of one amplified peak at medium frequencies are extended from coastal northwest to southwest delineating a structure striking to NNW. The two amplified peaks are attributed to shallow subsurface heterogeneities/irregularities, locally induced by fault zones and to the overlying Quaternary deposits. Spatial HVSR variations in the frequency and HVSR shape delineate four structures striking NNE, NNW and in a sector NW to WNW, crosscutting the dense populated Basin suggesting that microtremors could be a valuable tool for providing a first approximation of fault zone delineation at least for the Kastelli-Kissamos Basin. The Basin is classified into the X soil category of the Greek Seismic Code 2000.This work was implemented through the project entitled “Interdisciplinary Multi-Scale Research of Earth-quake Physics and Seismotectonics at the Front of the Hellenic Arc (IMPACT-ARC)” in the framework of action “ARCHIMEDES III—Support of Research Teams at TEI of Crete” (MIS380353) of the Operational Program “Education and Lifelong Learning” and is co-financed by the European Union (European Social Fund) and Greek national fund

Physics-Based Earthquake Ground Shaking Scenarios in Large Urban Areas

With the ongoing progress of computing power made available not only by large supercomputer facilities but also by relatively common workstations and desktops, physics-based source-to-site 3D numerical simulations of seismic ground motion will likely become the leading and most reliable tool to construct ground shaking scenarios from future earthquakes. This paper aims at providing an overview of recent progress on this subject, by taking advantage of the experience gained during a recent research contract between Politecnico di Milano, Italy, and Munich RE, Germany, with the objective to construct ground shaking scenarios from hypothetical earthquakes in large urban areas worldwide. Within this contract, the SPEED computer code was developed, based on a spectral element formulation enhanced by the Discontinuous Galerkin approach to treat non-conforming meshes. After illustrating the SPEED code, different case studies are overviewed, while the construction of shaking scenarios in the Po river Plain, Italy, is considered in more detail. Referring, in fact, to this case study, the comparison with strong motion records allows one to derive some interesting considerations on the pros and on the present limitations of such approach

Uncoupled Embryonic and Extra-Embryonic Tissues Compromise Blastocyst Development after Somatic Cell Nuclear Transfer

Somatic cell nuclear transfer (SCNT) is the most efficient cell reprogramming technique available, especially when working with bovine species. Although SCNT blastocysts performed equally well or better than controls in the weeks following embryo transfer at Day 7, elongation and gastrulation defects were observed prior to implantation. To understand the developmental implications of embryonic/extra-embryonic interactions, the morphological and molecular features of elongating and gastrulating tissues were analysed. At Day 18, 30 SCNT conceptuses were compared to 20 controls (AI and IVP: 10 conceptuses each); one-half of the SCNT conceptuses appeared normal while the other half showed signs of atypical elongation and gastrulation. SCNT was also associated with a high incidence of discordance in embryonic and extra-embryonic patterns, as evidenced by morphological and molecular “uncoupling”. Elongation appeared to be secondarily affected; only 3 of 30 conceptuses had abnormally elongated shapes and there were very few differences in gene expression when they were compared to the controls. However, some of these differences could be linked to defects in microvilli formation or extracellular matrix composition and could thus impact extra-embryonic functions. In contrast to elongation, gastrulation stages included embryonic defects that likely affected the hypoblast, the epiblast, or the early stages of their differentiation. When taking into account SCNT conceptus somatic origin, i.e. the reprogramming efficiency of each bovine ear fibroblast (Low: 0029, Med: 7711, High: 5538), we found that embryonic abnormalities or severe embryonic/extra-embryonic uncoupling were more tightly correlated to embryo loss at implantation than were elongation defects. Alternatively, extra-embryonic differences between SCNT and control conceptuses at Day 18 were related to molecular plasticity (high efficiency/high plasticity) and subsequent pregnancy loss. Finally, because it alters re-differentiation processes in vivo, SCNT reprogramming highlights temporally and spatially restricted interactions among cells and tissues in a unique way

Prostate carcinoma metastatic to the skin as an extrammamary Paget's disease

Aim: The current paper describes a case of prostatic adenocarcinoma metastatic to the skin presenting as an extrammamary Paget's disease, a very rare and poorly characterised morphological entity. We report a case of prostatic carcinoma metastatic to skin showing a pattern of extramammary Paget's disease which has not been clearly illustrated in the literature Case presentation: A 63 year-old man with prostatic adenocarcinoma developed cutaneous metastases after 16 years. The inguinal metastases were sessile and 'keratotic.' The tumour displayed solid, glandular areas as well as a polypoid region suggestive of extramammary Paget's disease were identified.Discussion and conclusions: We review the diagnostic criteria that have led to the correct histopathological diagnosis in this case. A differential diagnosis of the pagetoid spread in the skin and various forms of cutaneous metastases determined by a prostatic adenocarcinoma as well as the role of immunohistochemistry in establishing the prostatic origin are presented in the context of this case. Although, morphologically the cells presented in the skin deposits were not characteristic for adenocarcinoma of prostate, immunohistochemistry for PSA and PSAP suggested a prostatic origin.Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1395450057455276. © 2012 Petcu et al.; licensee BioMed Central Ltd