Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.This work was supported in part by grant “Progetto di Ateneo PRAT CPDA154841/15” from the University of Padova

Draft genome sequence of the nitrogen-fixing Rhizobium sullae type strain IS123^T focusing on the key genes for symbiosis with its host Hedysarum coronarium L.

© 2017 Sablok, Rosselli, Seeman, van Velzen, Polone, Giacomini, La Porta, Geurts, Muresu and Squartini. The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli) and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments

Metabarcoding analysis of the bacterial and fungal communities during the maturation of preparation 500, used in biodynamic agriculture, suggests a rational link between horn and manure

Horn manure (Preparation 500) is a product used in the practice of biodynamic agriculture. It is obtained by an underground fermentation of cow fecal material incubated in cow horns for several months. The product is used as spray treatment meant to increase soil fertility. In the present report, we analyzed the successional changes in bacterial and fungal communities throughout the process of horn manure maturation by high throughput sequencing of ribosomal 16S (bacterial) and ITS (fungal) gene markers. Marked shifts in the microbial community were seen involving a general decrease from a Firmicutes dominated material to a product transiently enriched in Proteobacteria and later in Actinobacteria, mostly within the Nocardioidaceae family. In the fungal community evolution, the most abundant taxon in the starting fecal material resulted a member of the Onygenales order, known to specifically degrade keratin. Its abundance in the intestine is explained by the fact that keratin, which is also the structural component of hairs and horns, is found in all epithelial layers, including gut mucosae. This occurrence suggests a link of enzymatic/catabolic nature between manure and horn

Ecology and conservation of the Mediterranean trout in the central Apennines (Italy)

The Mediterranean brown trout (Salmo trutta complex) is one of the freshwater fish species complex at greater risk of extinction in the Mediterranean area. The introduction of alien invasive species and their interaction with the native fauna represent some of the major threats to the survival of this species. Currently, the genetic variability of the Mediterranean trout (Salmo trutta complex) is being compromised by the introgressive hybridization with the Atlantic trout (Salmo trutta Linnaeus, 1758). Therefore, it is necessary to gain further knowledge on genetic and demographic characteristics of Mediterranean trout populations, that, combined with environmental and angling data, will allow to undertake sound conservation strategies. The aims of the present study were to analyze: i) the demographic characteristics of the Mediterranean trout in seven central Apennine river basins where native populations are threatened by stocking with the domestic trout of north Atlantic origin; ii) the influence of both environmental parameters and different fishery management strategies on the status of native trout populations. The project focuses on 14 sites included in the Natura 2000 EU wide network of nature protection areas, established under the 1992 Habitat Directive. A total of 25 watercourses were investigated for a total of 32 sampling sites. A census of the fish fauna was carried out by electrofishing at each sampling location. Fish and environmental data were collected in spring and autumn 2014. The results obtained in the present research allowed us to detect the presence of three residual Mediterranean trout populations with a high degree of genetic integrity in the study area. The native trout populations were characterized by higher abundances and higher adult density values. Well-structured native populations with higher legal-size specimens density and poor body conditions in terms of relative weight were observed in the no-fishing areas, probably due to the presence of intraspecific competition phenomena. The environmental analysis confirmed the key role played by the geological characteristics of the central Apennines in shaping the introgression levels observed in the wild trout populations, while the recovery of the water quality appears decisive in the development of management strategies aimed at their conservation

Surface Functionalization of Grown-on-Tip ZnO Nanopyramids: From Fabrication to Light-Triggered Applications

We report on a combined chemical vapor deposition (CVD)/radio frequency (RF) sputtering synthetic strategy for the controlled surface modification of ZnO nanostructures by Ti-containing species. Specifically, the proposed approach consists in the CVD of grown-on-tip ZnO nanopyramids, followed by titanium RF sputtering under mild conditions. The results obtained by a thorough characterization demonstrate the successful ZnO surface functionalization with dispersed Ti-containing species in low amounts. This phenomenon, in turn, yields a remarkable enhancement of photoactivated superhydrophilic behavior, self-cleaning ability, and photocatalytic performances in comparison to bare ZnO. The reasons accounting for such an improvement are unravelled by a multitechnique analysis, elucidating the interplay between material chemico-physical properties and the corresponding functional behavior. Overall, the proposed strategy stands as an amenable tool for the mastering of semiconductor-based functional nanoarchitectures through <i>ad hoc</i> engineering of the system surface

Celebrating wildlife population recovery through education

Large mammal populations are rapidly recovering across Europe, yet people have not readapted to living with wild animals, resulting in human–wildlife conflict. We believe that society should unite to make the most of the instances of nature recovery, and propose science and education as the key to succes

Receptor Activator of NF-kB (RANK) Expression in Primary Tumors Associates with Bone Metastasis Occurrence in Breast Cancer Patients

Background: Receptor activator of NFkB (RANK), its ligand (RANKL) and the decoy receptor of RANKL (osteoprotegerin, OPG) play a pivotal role in bone remodeling by regulating osteoclasts formation and activity. RANKL stimulates migration of RANK-expressing tumor cells in vitro, conversely inhibited by OPG. Materials and Methods: We examined mRNA expression levels of RANKL/RANK/OPG in a publicly available microarray dataset of 295 primary breast cancer patients. We next analyzed RANK expression by immunohistochemistry in an independent series of 93 primary breast cancer specimens and investigated a possible association with clinicopathological parameters, bone recurrence and survival. Results: Microarray analysis showed that lower RANK and high OPG mRNA levels correlate with longer overall survival (P = 0.0078 and 0.0335, respectively) and disease-free survival (P = 0.059 and 0.0402, respectively). Immunohistochemical analysis of RANK showed a positive correlation with the development of bone metastases (P = 0.023) and a shorter skeletal disease-free survival (SDFS, P = 0.037). Specifically, univariate analysis of survival showed that "RANK-negative" and "RANK-positive" patients had a SDFS of 105.7 months (95% CI: 73.9-124.4) and 58.9 months (95% CI: 34.7-68.5), respectively. RANK protein expression was also associated with accelerated bone metastasis formation in a multivariate analysis (P = 0.029). Conclusions: This is the first demonstration of the role of RANK expression in primary tumors as a predictive marker of bone metastasis occurrence and SDFS in a large population of breast cancer patients

Análisis de los rayos registrados en Canarias en el periodo 2006-2015

En zonas dominadas por centros de altas presiones semipermanentes, como Canarias, el aire descendente, los bajos niveles de humedad por encima de la inversión térmica y la estratificación estable, inhiben las tormentas, pero no completamente. A partir de los rayos registrados en una amplia zona geográfica que engloba las islas Canarias y Madeira y el área oceánica circundante, se analiza la distribución espacial y temporal de los mismos, estimando su densidad y el número de días de tormenta en rejillas de resolución 0,1°, y comparando sus características con las de otras zonas geográficas similares. Seguidamente, se evalúa el comportamiento de algunos parámetros eléctricos de los rayos, como la intensidad, la polaridad y la multiplicidad. A continuación, se trazan algunos rasgos que, con una serie más dilatada, pueden llegar a adquirir rango climatológico. Finalmente, se conjeturan algunas de las claves del peculiar episodio de agosto de 2015

Colonial Heritage and Economic Development

While the importance of institutions for explaining cross-country income differences is widely recognized, comparatively little is known about the origins of economic institutions. One strand of the literature emphasizes cultural differences while another points at exogenous environmental factors such as mortality and climate. Both are supported by some empirical evidence. I reconcile the two schools of institutional origins by proposing a theory of self-selection of colonists to different geographic destinations. Exogenous characteristics such as climate, mortality and factor differences determine which type of settler decides to move to a particular colony. Settler type, in turn, shapes the institutional quality of the new country. The model is used to confirm observed regularities reported by previous researchers. Furthermore, robust new evidence is presented in support of this selection process. The results suggest that any theory of colonial development that does not take selection into account will be incomplete

Psychological and Brain Connectivity Changes Following Trauma-Focused CBT and EMDR Treatment in Single-Episode PTSD Patients

Among the different therapeutic alternatives for post-traumatic stress disorder (PTSD), Trauma-Focused Cognitive-Behavioral Therapy (TF-CBT) and Eye Movement Desensitization and Reprocessing (EMDR) Therapy have shown promising results in helping patients cope with PTSD symptoms. However, given the different theoretical and methodological substrate of TF-CBT and EMDR, a potentially different impact on the brain for the two interventions could be hypothesized, as well as an interaction between trauma-specific PTSD symptomatology and response to a given psychotherapy. In this study, we monitored psychological and spontaneous functional connectivity fMRI patterns in two groups of PTSD patients who suffered by the same traumatic event (i.e., natural disaster), before and after a cycle of psychotherapy sessions based on TF-CBT and EMDR. Thirty-seven (37) PTSD patients were enrolled from a larger sample of people exposed to a single, acute psychological stress (i.e., 2002 earthquake in San Giuliano di Puglia, Italy). Patients were randomly assigned to TF-CBT (n = 14) or EMDR (n = 17) psychotherapy. Clinical assessment was performed using the Clinician-Administered PTSD Scale (CAPS), the Davidson Trauma Scale (DTS) and the Work and Social Adjustment Scale (WSAS), both at baseline and after treatment. All patients underwent a fMRI data acquisition session before and after treatment, aimed at characterizing their functional connectivity (FC) profile at rest, as well as potential connectivity changes associated with the clinical impact of psychotherapy. Both EMDR and TF-CBT induced statistically significant changes in clinical scores, with no difference in the clinical impact of the two treatments. Specific changes in FC correlated with the improvement at the different clinical scores, and differently for EMDR and TF-CBT. However, a similarity in the connectivity changes associated with changes in CAPS in both groups was also observed. Specifically, changes at CAPS in the entire sample correlated with an (i) increase in connectivity between the bilateral superior medial frontal gyrus and right temporal pole, and a (ii) decrease in connectivity between left cuneus and left temporal pole. Results point to a similar, beneficial psychological impact of EMDR and TF-CBT for treatment of natural-disaster PTSD patients. Neuroimaging data suggest a similar neurophysiological substrate for clinical improvement following EMDR and TF-CBT, involving changes affecting bilateral temporal pole connectivity