Practical guide to single-protein AFM nanomechanical spectroscopy mapping: insights and pitfalls as unraveled by all-atom MD simulations on immunoglobulin G

Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive - a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime - where the mechanical response is linked to the presence of the water environment - followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potentialJ.G.V. acknowledges funding from a Marie Sklodowska-Curie Fellowship within the Horizon 2020 framework (Grant No. DLV-795286) and the Swiss National Science Foundation (Grant No. CRSK-2 190731/1). R.P. acknowledges support from the Spanish MINECO (Grant No. MAT2017-83273-R) and from the Ministerio de Ciencia e Innovación (MICINN) through the “María de Maeztu” Programme for Units of Excellence in R&D (Grant No. CEX2018-000805-M). R.G. acknowledges funding from the MICINN (Grant No. PID2019-106801GB-I00) and Comunidad de Madrid Grant No. S2018/NMT-4443 (Tec4Bio-CM). We thankfully acknowledge the computer resources, technical expertise, and assistance provided by the Red Española de Supercomputación (RES) at the Minotauro and CTE-Power9 supercomputers (BSC, Barcelona). We thank Dr. Alejandro Martín-González for fruitful discussion

Infra-Red thermal image analysis for grapevines

Trabajo presentado en el 18th International Symposium of the Group of International Experts of vitivinicultural Systems for CoOperation (GIESCO 2013), celebrado en Oporto del 7 al 11 de julio de 2013.-- Número fuera de serie.Infrared thermal images (IRTI) have been used for grapevine research since the early 90’s. Even though its promising results in the assessment of canopy stomatal conductance and plant water status, from the beginning and recent research publications, it has not been fully applied on a commercial scale yet. It is believed that the bottleneck for this technology is the lack of reliable automation tools for IRTI analysis. Accurate and reliable automation technique s will allow the use of this technique to assess the spatial variability of physiological processes within the canopy using infrared cameras mounted on moving vehicles, drones, octocopters or robots. Automated analysis systems are requirement of The Vineyard of The Future initiative, which is an international effort to establis h fully monitored vineyards in the most prominent viticultural and winemaking areas in the world. In this work, a semi-automated IRTI analyses performed using a code written in MATLAB® for estimate dry and wet references excluding non-leaf temperatures was compared with evaporimeter (EvapoSensor, Skye Instruments Ltd, Powys, UK) measurements used to provide dry and wet references from IRTIs. Results obtained from this research (grapevines cv. Tempranillo) showed good and statistically significant correlations between temperatur e references obtained from IRTI analysis and measured values. This work constitutes one additional step forward to the implementation of thermal imaging as an automated routine technique for physiological vineyard assess ment from proximal sensing and unmanned aerial vehicles (UAV) platforms.The research leading to this report was supported by the Spanish project “STRESSIMAGING HPRN-CT-2002-00254” and Chilean projects CONICYT (Nº 79090035) and Programa de Investigación sobre Adaptación de la Agricultura al Cambio Climático - PIEI (Universidad de Talca).Peer Reviewe

Cytotoxic activity induced by the alkaloid extract from Ipomoea carnea on primary murine mixed glial cultures

The prolonged consumption of Ipomoea carnea produces neurologic symptoms in animals and a typical histological lesion, cytoplasmic vacuolization, especially in neurons. The toxic principles of I. carnea are the alkaloids swainsonine and calystegines B1, B2, B3 and C1. In this study, primary brain cultures from newborn mouse containing mixed glial cells were utilized. These cells were exposed to Ipomoea extracts containing between 0 and 250 μM swainsonine for 48 h. Morphological changes were investigated through Phase Contrast microscopy and Rosenfeld's staining. The extract induced cytoplasmic vacuolization in astrocytes and microglia in a dose dependent manner, being more evident when cultures were exposed to 250 μM of swainsonine. In addition, acridine orange staining evidenced an increase in the number of lysosomes in both microglia and astrocytes cells. Consistent with this, scanning electron microscopy also showed that both types of cells presented morphological characteristics of cell activation. Ultrastructurally, cells showed vacuoles filled with amorphous material and surrounded by a single membrane and also multilayer membranes. Taken together, these findings suggest that swainsonine along with calystegines, are probably responsible for the activation of glial cells due to a possible lysosomal dysfunction and therefore intracellular storage. Our results demonstrate that this in vitro glial cell model is a very good alternative to in vivo studies that require several weeks of animal intoxication to observe similar neurotoxic effects.Fil: Cholich, Luciana Andrea. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; ArgentinaFil: Pistan, Maria Elena. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Torres, Ana María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Química Básica y Aplicada del Nordeste Argentino. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas Naturales y Agrimensura. Instituto de Química Básica y Aplicada del Nordeste Argentino; ArgentinaFil: Ortega, Hugo Hector. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Ciencias Veterinarias del Litoral. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias. Instituto de Ciencias Veterinarias del Litoral; ArgentinaFil: Gardner, Dale R.. Poisonous Plant Research Laboratory; Estados UnidosFil: Bustillo, Soledad. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Química Básica y Aplicada del Nordeste Argentino. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas Naturales y Agrimensura. Instituto de Química Básica y Aplicada del Nordeste Argentino; Argentin

Mediterranean-type diet and brain structural change from 73 to 76 years in a Scottish cohort

STUDY FUNDING The data were collected by a Research into Ageing programme grant; research continues as part of the Age UK–funded Disconnected Mind project. The work was undertaken by The University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, part of the cross-council Lifelong Health and Wellbeing Initiative (MR/K026992/1), with funding from the BBSRC and Medical Research Council. Imaging and image analysis was performed at the Brain Research Imaging Centre (sbirc.ed.ac.uk/), Edinburgh, supported by the Scottish Funding Council SINAPSE Collaboration. Derivation of mean cortical thickness measures was funded by the Scottish Funding Council’s Postdoctoral and Early Career Researchers Exchange Fund awarded by SINAPSE to David Alexander Dickie. L.C.A.C. acknowledges funding from the Scottish Government's Rural and Environment Science and Analytical Services (RESAS) division.Peer reviewedPublisher PD

Can PRAME immunohistochemistry be used to differentiate sebaceous carcinoma from basal cell carcinoma?

The histopathology of sebaceous carcinoma (SBC) can mimic other skin neoplasms, including basal cell carcinoma (BCC).Therefore, diagnostic biomarkers are needed for a subset of cases. Normal sebaceous glands express PRAME (PRAME nuclearreceptor transcriptional regulator), a melanoma-associated biomarker.Donell et al. showed that PRAME has strong immunoreactivity with basaloid sebocytes in SBC. Ng et al. reported patchy cytoplasmic staining in the germinative sebocytes only.Sebaceous glands (H&E stain and PRAME stain)Objective: to evaluate the utility of PRAME immunohistochemistry as a diagnostic biomarker for SBC and its usefulness in the distinction of SBC from BCC

Influence of laser wavelength on Laser-Fired contacts for crystalline silicon solar cells

In the Laser-Fired Contact (LFC) process, a laser beam fires a metallic layer through a dielectric passivating layer into the silicon wafer to form an electrical contact with the silicon bulk [1]. This laser technique is an interesting alternative for the fabrication of both laboratory and industrial scale high efficiency passivated emitter and rear cell (PERC). One of the principal characteristics of this promising technique is the capability to reduce the recombination losses at the rear surface in crystalline silicon solar cells. Therefore, it is crucial to optimize LFC because this process is one of the most promising concepts to produce rear side point contacts at process speeds compatible with the final industrial application. In that sense, this work investigates the optimization of LFC processing to improve the back contact in silicon solar cells using fully commercial solid state lasers with pulse width in the ns range, thus studying the influence of the wavelength using the three first harmonics (corresponding to wavelengths of 1064 nm, 532 nm and 355 nm). Previous studies of our group focused their attention in other processing parameters as laser fluence, number of pulses, passivating material [2, 3] thickness of the rear metallic contact [4], etc. In addition, the present work completes the parametric optimization by assessing the influence of the laser wavelength on the contact property. In particular we report results on the morphology and electrical behaviour of samples specifically designed to assess the quality of the process. In order to study the influence of the laser wavelength on the contact feature we used as figure of merit the specific contact resistance. In all processes the best results have been obtained using green (532 nm) and UV (355 nm), with excellent values for this magnitude far below 1 mΩcm2

Characterization and cytotoxic activity on glial cells of alkaloid-enriched extracts from pods of the plants prosopis flexuosa and prosopis Nigra (Fabaceae)

Introduction: Prosopis spp. pods have shown to be a potential source of protein and energy in livestock. However, prolonged ingestion of some of these species produces neurological symptoms in ruminants. Objective: In the present study, the alkaloid content and the in vitro neurotoxic activity of alkaloid enriched-extracts from P. flexuosa and P. nigra pods were determined in order to elucidate the mechanism of animal poisoning caused by these species. Methods: The main alkaloids present in both extracts were analysed by high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS). The cytotoxic activity of Prosopis alkaloid enriched-extracts in primary mixed glial cell culture was assessed by phase contrast microscopy and using neutral red, and lactate dehydrogenase (LDH) activity assays. Results: Juliprosine and juliprosopine were identified in P. flexuosa pods, while the absence of these alkaloids in P. nigra was confirmed. Both extracts (5-30 μg/mL) induced in a dose dependent manner, morphological alterations, such as swelling, enlargement and detachment from the culture surface. Consistent with this, decrease in cell viability and release of LDH 48 hours after exposure, revealed that P. flexuosa pods was significantly more cytotoxic than P. nigra. Conclusions: In P. flexuosa pods, juliprosine and juliprosopine alkaloids were identified for the first time. Moreover, the present study suggests that the cytotoxic effect displayed by both extracts is due to its alkaloid content. However, the presence of piperidine alkaloids in P. flexuosa could explain the greater cytotoxicity on glial cells with respect to P. nigra that was not shown to contain these alkaloids.Fil: Cholich, Luciana Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Pistan, Maria Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Torres, Ana Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Química Básica y Aplicada del Nordeste Argentino. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas Naturales y Agrimensura. Instituto de Química Básica y Aplicada del Nordeste Argentino; ArgentinaFil: Ortega, Hugo Hector. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Ciencias Veterinarias del Litoral. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias. Instituto de Ciencias Veterinarias del Litoral; ArgentinaFil: Gardner, Dale R.. No especifíca;Fil: Bustillo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Química Básica y Aplicada del Nordeste Argentino. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas Naturales y Agrimensura. Instituto de Química Básica y Aplicada del Nordeste Argentino; Argentin

Protective role of renal proximal tubular alpha-synuclein in the pathogenesis of kidney fibrosis

Kidney fibrosis is a highly deleterious process and a final manifestation of chronic kidney disease. Alpha-(α)-synuclein (SNCA) is an actin-binding neuronal protein with various functions within the brain; however, its role in other tissues is unknown. Here, we describe the expression of SNCA in renal epithelial cells and demonstrate its decrease in renal tubules of murine and human fibrotic kidneys, as well as its downregulation in renal proximal tubular epithelial cells (RPTECs) after TGF-β1 treatment. shRNA-mediated knockdown of SNCA in RPTECs results in de novo expression of vimentin and α-SMA, while SNCA overexpression represses TGF-β1-induced mesenchymal markers. Conditional gene silencing of SNCA in RPTECs leads to an exacerbated tubulointerstitial fibrosis (TIF) in two unrelated in vivo fibrotic models, which is associated with an increased activation of MAPK-p38 and PI3K-Akt pathways. Our study provides an evidence that disruption of SNCA signaling in RPTECs contributes to the pathogenesis of renal TIF by facilitating partial epithelial-to-mesenchymal transition and extracellular matrix accumulation.This work was supported by research grants PI15/00960 and PI17/00119 from the Instituto de Salud Carlos III (ISCII, Spanish Ministry of Economy and Competitiveness) and REDinREN (RD12/0021). The work on human kidney tissue samples was supported by the IRBLleida Biobank (B.0000682) and PLATAFORMA BIOBANCOS PT17/0015/ 0027. M.B. was supported by the REDinREN (RD12/0021/0026) and Department of Health, Government of Catalonia (PERIS 2016-2020, SLT002/16/00178). M.C. was supported by the studentship from the Catalan Government (AGAUR). R.R.R-D. was supported by a grant from the Comunidad Autonóma de Madrid (B2017/BMD-3751 NOVELREN-CM)

Branched-chain amino acids promote endothelial dysfunction through increased reactive oxygen species generation and inflammation

Branched‐chain amino acids (BCAA: leucine, isoleucine and valine) are essential amino acids implicated in glucose metabolism and maintenance of correct brain function. Elevated BCAA levels can promote an inflammatory response in peripheral blood mononuclear cells. However, there are no studies analysing the direct effects of BCAA on endothelial cells (ECs) and its possible modulation of vascular function. In vitro and ex vivo studies were performed in human ECs and aorta from male C57BL/6J mice, respectively. In ECs, BCAA (6 mmol/L) increased eNOS expression, reactive oxygen species production by mitochondria and NADPH oxidases, peroxynitrite formation and nitrotyrosine expression. Moreover, BCAA induced pro‐inflammatory responses through the transcription factor NF‐κB that resulted in the release of intracellular adhesion molecule‐1 and E‐selectin conferring endothelial activation and adhesion capacity to inflammatory cells. Pharmacological inhibition of mTORC1 intracellular signalling pathway decreased BCAA-induced pro‐oxidant and pro‐inflammatory effects in ECs. In isolated murine aorta, BCAA elicited vasoconstrictor responses, particularly in pre‐contracted vessels and after NO synthase blockade, and triggered endothelial dysfunction, effects that were inhibited by different antioxidants, further demonstrating the potential of BCAA to induce oxidative stress with functional impact. In summary, we demonstrate that elevated BCAA levels generate inflammation and oxidative stress in ECs, thereby facilitating inflammatory cells adhesion and endothelial dysfunction. This might contribute to the increased cardiovascular risk observed in patients with elevated BCAA blood levels.This study was supported by Ministerio de Economía y Competitividad (MINECO SAF2016‐80305‐P), Instituto de Salud Carlos III (ISCIII) Fondo Europeo de Desarrollo Regional (FEDER) a way to build Europe (PI14/00386, PI14/0041, PIE13/00051, PI13/01488; PI17‐01495, CiberCV, CiberDEM), FP7 grant e‐PREDICE, by the Fundación Renal Iñigo Álvarez de Toledo (FRIAT)/Instituto Reina Sofía de Investigación Nefrológica and from Roche‐IdiPa

Galantamine-memantine hybrids for Alzheimer's disease: The influence of linker rigidity in biological activity and pharmacokinetic properties

Neurodegenerative processes characterizing Alzheimer's disease (AD) are strictly related to the impairment of cholinergic and glutamatergic neurotransmitter systems which provoke synaptic loss. These experimental evidences still represent the foundation of the actual standard-of-care treatment for AD, albeit palliative, consisting on the coadministration of an acetylcholinesterase inhibitor and the NMDAR antagonist memantine. In looking for more effective treatments, we previously developed a series of galantamine-memantine hybrids where compound 1 (ARN14140) emerged with the best-balanced action toward the targets of interest paired to neuroprotective efficacy in a murine AD model. Unfortunately, it showed a suboptimal pharmacokinetic profile, which required intracerebroventricular administration for in vivo studies. In this work we designed and synthesized new hybrids with fewer rotatable bonds, which is related to higher brain exposure. Particularly, compound 2, bearing a double bond in the tether, ameliorated the biological profile of compound 1 in invitro studies, increasing cholinesterases inhibitory potencies and selective antagonism toward excitotoxic-related GluN1/2B NMDAR over beneficial GluN1/2A NMDAR. Furthermore, it showed increased plasma stability and comparable microsomal stability in vitro, paired with lower half-life and faster clearance in vivo. Remarkably, pharmacokinetic evaluations of compound 2 showed a promising increase in brain uptake in comparison to compound 1, representing the starting point for further chemical optimizations