Plankton DNA extraction from Sterivex filter units

The objective of this protocol is to provide a reliable and replicable method for the DNA extraction of lake micro-plankton to be used for downstream DNA analysis. This protocol is one of those proposed by the Eco-AlpsWater consortium to promote the implementation of High Throughput Sequencing (HT S) of environmental DNA (eDNA) in the biomonitoring and ecological assessment of water bodies. The extraction is performed from samples filtered through Sterivex cartridges (Sterivex™ GP 0.22μm) and stored at -20°C, as described in the protocol dx.doi.org/10.17504/protocols.io.xn6fmhe, and with the use of the DNeasy® PowerWater Sterivex Kit (QIAGEN) with specific modifications adapted to plankton DNA extraction. The application proposed here, in the context of EcoAlpsWater, aims at comparing DNA inventories to traditional phytoplanktonic inventories and at characterizing more broadly the micro-planktonic diversity through eDNA analysis (including bacteria). This protocol is part of the deliverables provided by the WP1 of the Eco-AlpsWater project. All members of the EcoAlpsWater consortium (http://www.alpine-space.eu/projects/eco-alpswater/en/home) contributed to the optimization of this protocol

Population-specific material properties of the implantation site for transcatheter aortic valve replacement finite element simulations

Patient-specific computational models are an established tool to support device development and test under clinically relevant boundary conditions. Potentially, such models could be used to aid the clinical decision-making process for percutaneous valve selection; however, their adoption in clinical practice is still limited to individual cases. To be fully informative, they should include patient-specific data on both anatomy and mechanics of the implantation site. In this work, fourteen patient-specific computational models for transcatheter aortic valve replacement (TAVR) with balloon-expandable Sapien XT devices were retrospectively developed to tune the material parameters of the implantation site mechanical model for the average TAVR population. Pre-procedural computed tomography (CT) images were post-processed to create the 3D patient-specific anatomy of the implantation site. Balloon valvuloplasty and device deployment were simulated with finite element (FE) analysis. Valve leaflets and aortic root were modelled as linear elastic materials, while calcification as elastoplastic. Material properties were initially selected from literature; then, a statistical analysis was designed to investigate the effect of each implantation site material parameter on the implanted stent diameter and thus identify the combination of material parameters for TAVR patients. These numerical models were validated against clinical data. The comparison between stent diameters measured from post-procedural fluoroscopy images and final computational results showed a mean difference of 2.5 ± 3.9%. Moreover, the numerical model detected the presence of paravalvular leakage (PVL) in 79% of cases, as assessed by post-TAVR echocardiographic examination. The final aim was to increase accuracy and reliability of such computational tools for prospective clinical applications

Effect of Carbon Support, Capping Agent Amount, and Pd NPs Size for Bio-Adipic Acid Production from Muconic Acid and Sodium Muconate

The effect of support, stabilizing agent, and Pd nanoparticles (NPs) size was studied for sodium muconate and t,t-muconic acid hydrogenation to bio-adipic acid. Three different activated carbons (AC) were used (Norit, KB, and G60) and carbon morphology did not affect the substrate conversion, but it greatly influenced the adipic acid yield. 1% Pd/KB Darco catalyst, which has the highest surface area and Pd surface exposure, and the smallest NPs size displayed the highest activity. Furthermore, the effect of the amount of the protective agent was studied varying metal/protective agent weight ratios in the range of 1/0.00-1/1.20, using KB as the chosen support. For sodium muconate reduction 1% Pd/KB_1.2 catalyst gave the best results in terms of activity (0.73 s-1), conversion, and adipic acid yield (94.8%), while for t,t-muconic acid hydrogenation the best activity result (0.85 s-1) was obtained with 1% Pd/KB_0.0 catalyst. Correlating the results obtained from XPS and TEM analyses with catalytic results, we found that the amount of PVA (polyvinyl alcohol) influences mean Pd NPs size, Pd(0)/Pd(II) ratio, and Pd surface exposure. Pd(0)/Pd(II) ratio and Pd NPs size affected adipic acid yield and activity during sodium muconate hydrogenation, respectively, while adipic acid yield was related by exposed Pd amount during t,t-muconic acid hydrogenation. The synthesized catalysts showed higher activity than commercial 5% Pd/AC

A comparative study of the metabolic profiles of common nuisance cyanobacteria in southern perialpine lakes

This work allowed the comparison of the metabolic profiles of the most important cyanobacteria species in southern perialpine lakes, namely Aphanizomenon flos-aquae, Dolichospermum lemmermannii, Microcystis aeruginosa, Planktothrix rubescens, and Tychonema bourrellyi. Monospecific cultures were obtained from samples of 3 different natural lakes (Garda, Idro, and Caldonazzo). LC-MS/MS analyses were conducted on strains. A first set of experiments was aimed at assessing the presence of the best known toxins (microcystins, nodularins, (homo)anatoxin-a, cylindrospermopsins, paralytic shellfish poisons) in the cultures. Results of this screening study revealed that M. aeruginosa and P. rubescens produced toxic peptides (microcystins), T. bourrellyi produced toxic alkaloids (anatoxin-a and possibly some paralytic shellfish toxins), Aph. flos-aquae and D. lemmermannii did not produce any of the analyzed toxins. M. aeruginosa and P. rubescens showed typical microcystin production with LR form dominant in the former, and RRdm form dominant in the latter. A second set of experiments was aimed at comparing the capability of the 5 cyanobacterial species to produce peptidic secondary metabolites. For this purpose, an untargeted peptidomic analysis was conducted on the strains. The analysis allowed revealing globally 328 metabolites, spanning in a mass range between 400 and 2000 Da. The majority of compounds with masses in the 500-1200 Da range (corresponding to the majority of peptidic secondary metabolites) resulted to be produced by M. aeruginosa and P. rubescens strains, thus indicating a higher ability of these species to produce non-ribosomal peptides compared to the others. 27 metabolites out of 328 could be putatively assigned to specific classes of compounds: microcystins, aeruginosins and anabaenopeptins were the most represented classes of compounds, and were mostly found in M. aeruginosa and P. rubescens strains

Neutralization of nerve growth factor impairs proliferation and differentiation of adult neural progenitors in the subventricular zone

Adult neurogenesis is a multistep process regulated by several extrinsic factors, including neurotrophins. Among them, little is known about the role of nerve growth factor (NGF) in the neurogenic niches of the mouse. Here we analyzed the biology of adult neural stem cells (NSCs) from the subventricular zone (SVZ) of AD11 anti-NGF transgenic mice, in which the expression of the recombinant antibody aD11 leads to a chronic postnatal neutralization of endogenous NGF. We showed that AD11-NSCs proliferate 10-fold less, with respect to their control counterparts, and display a significant impairment in their ability to differentiate into \u3b2-tubulin positive neurons. We found a considerable reduction in the number of SVZ progenitors and neuroblasts also in vivo, which correlates with a lower number of newborn neurons in the olfactory bulbs of AD11 mice and a severe deficit in the ability of these mice to discriminate between different odors. We also demonstrated that, in AD11 mice, the morphology of both SVZ-resident and neurosphere-derived astrocytes is significantly altered. We were able to reproduce the AD11 phenotype in vitro, by acutely treating wild type NSCs with the anti-NGF antibody, further demonstrating that both the proliferation and the differentiation defects are due to the NGF deprivation. Consistently, the proliferative impairment of AD11 progenitors, as well as the atrophic morphology of AD11 astrocytes, can be partly rescued in vitro and in vivo by exogenous NGF addition. Altogether, our results demonstrate a causal link between NGF signaling and proper proliferation and differentiation of neural stem cells from the SVZ.Adult neurogenesis is a multistep process regulated by several extrinsic factors, including neurotrophins. Among them, little is known about the role of nerve growth factor (NGF) in the neurogenic niches of the mouse. Here we analyzed the biology of adult neural stem cells (NSCs) from the subventricular zone (SVZ) of AD11 anti-NGF transgenic mice, in which the expression of the recombinant antibody aD11 leads to a chronic postnatal neutralization of endogenous NGF. We showed that AD11-NSCs proliferate 10-fold less, with respect to their control counterparts, and display a significant impairment in their ability to differentiate into \u3b2-tubulin positive neurons. We found a considerable reduction in the number of SVZ progenitors and neuroblasts also in vivo, which correlates with a lower number of newborn neurons in the olfactory bulbs of AD11 mice and a severe deficit in the ability of these mice to discriminate between different odors. We also demonstrated that, in AD11 mice, the morphology of both SVZ-resident and neurosphere-derived astrocytes is significantly altered. We were able to reproduce the AD11 phenotype in vitro, by acutely treating wild type NSCs with the anti-NGF antibody, further demonstrating that both the proliferation and the differentiation defects are due to the NGF deprivation. Consistently, the proliferative impairment of AD11 progenitors, as well as the atrophic morphology of AD11 astrocytes, can be partly rescued in vitro and in vivo by exogenous NGF addition. Altogether, our results demonstrate a causal link between NGF signaling and proper proliferation and differentiation of neural stem cells from the SVZ

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis

Alterations of K-ras, p53, p16 and DPC4/Smad4 characterize pancreatic ductal cancer (PDC). Reports of inactivation of these latter two genes in pancreatic endocrine tumours (PET) suggest that common molecular pathways are involved in the tumorigenesis of pancreatic exocrine and endocrine epithelia. We characterized 112 primary pancreatic tumours for alterations in p16 and DPC4 and immunohistochemical expression of DPC4. The cases included 34 PDC, 10 intraductal papillary-mucinous tumours (IPMT), 6 acinar carcinomas (PAC), 5 solid-pseudopapillary tumours (SPT), 16 ampulla of Vater cancers (AVC) and 41 PET. All tumours were also presently or previously analysed for K- ras and p53 mutations and allelic loss at 9p, 17p and 18q. Alterations in K- ras, p53, p16 and DPC4 were found in 82%, 53%, 38% and 9% of PDC, respectively and in 47%, 60%, 25% and 6% of AVC. Alterations in these genes were virtually absent in PET, PAC or SPT, while in IPMT only K-ras mutations were present (30%). Positive immunostaining confirmed the absence of DPC4 alterations in all IPMT, SPT, PAC and PET, while 47% of PDC and 38% of AVC were immunonegative. These data suggest that pancreatic exocrine and endocrine tumourigenesis involves different genetic targets and that among exocrine pancreatic neoplasms, only ductal and ampullary cancers share common molecular events. © 2001 Cancer Research Campaign http://www.bjcancer.co

Searches for axioelectric effect of solar axions with BGO-scintillator and BGO-bolometer detectors

A search for axioelectric absorption of 5.5 MeV solar axions produced in the $p + d \rightarrow {^3\rm{He}}+\gamma~(5.5~ \rm{MeV})$ reaction has been performed with a BGO detectors. A model-independent limit on the product of axion-nucleon $g_{AN}^3$ and axion-electron $g_{Ae}$ coupling constants has been obtained: $| g_{Ae}\times g_{AN}^3|< 1.9\times 10^{-10}$ for 90\% C.L..Comment: 5 pages, 3 figures, Proceedings of the 10th Patras Workshop on Axions, WIMPs and WISP 29 June - 4 July 2014, CERN, Geneva, Switzerlan

Laughlin Wave Function and One-Dimensional Free Fermions

Making use of the well-known phase space reduction in the lowest Landau level(LLL), we show that the Laughlin wave function for the $\nu = {1\over m}$ case can be obtained exactly as a coherent state representation of an one dimensional $(1D)$ wave function. The $1D$ system consists of $m$ copies of free fermions associated with each of the $N$ electrons, confined in a common harmonic well potential. Interestingly, the condition for this exact correspondence is found to incorporate Jain's parton picture. We argue that, this correspondence between the free fermions and quantum Hall effect is due to the mapping of the $1D$ system under consideration, to the Gaussian unitary ensemble in the random matrix theory.Comment: 7 pages, Latex , no figure

The effect of lower body negative pressure on phase 1 cardiovascular responses at exercise onset in healthy humans

We tested the hypothesis that vagal withdrawal and increased venous return interact in determining the rapid cardiac output response (Phase I) at exercise onset. We used lower body negative pressure (LBNP) to increase blood dislocation to the heart by muscle pump action and simultaneously reduce resting vagal activity. At exercise start, we expected larger response amplitude for stroke volume and smaller for heart rate at progressively stronger LBNP levels, so that the cardiac output response would remain unchanged. Ten subjects performed 50 W exercise supine in Control condition and during -45 mmHg LBNP exposure. On single beat basis, we measured heart rate (HR), stroke volume (SV), and we calculated cardiac output (CO). We computed Phase I response amplitudes (A1) using an exponential model. SV A1 was higher under LBNP than in Control (p &lt; 0.05). Conversely, the A1 of HR, was 23 ± 56 % lower under LBNP than in Control (although NS). Since these changes tended to compensate each other, the A1 for CO was unaffected by LBNP. The rapid SV kinetics at exercise onset is compatible with an effect of increased venous return, whereas the vagal withdrawal conjecture cannot be dismissed for HR kinetics. The rapid CO response may indeed be the result of two independent yet parallel mechanisms, as hypothesized, one acting on SV, the other on H