Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles

Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro disassembly of particles lacking protein V (Ad5-ΔV). Ad5-ΔV particles were softer and less brittle than the wild-type ones (Ad5-wt), but they were more prone to release pentons under mechanical fatigue. In Ad5-ΔV, core components did not readily diffuse out of partially disrupted capsids, and the core appeared more condensed than in Ad5-wt. These observations suggest that instead of condensing the genome, protein V antagonizes the condensing action of the other core proteins. Protein V provides mechanical reinforcement and facilitates genome release by keeping DNA connected to capsid fragments that detach during disruption. This scenario is in line with the location of protein V in the virion and its role in Ad5 cell entry

Detección de estrés hídrico en olivar mediante datos hiperespectrales y térmicos del sensor AHS

El sensor hiperespectral AHS (Airborrne Hyperspectal Scanner) fue utilizado para obtener imágenes de 2.5 m de resolución espacial en el espectro visible, infrarrojo cercano y térmico en una parcela de olivar en Córdoba (España) con el fin de estudiar la variabilidad espacial y temporal del estrés hídrico. Los datos térmicos del AHS permitieron obtener imágenes de temperatura de superficie de la parcela a las 7:30, 9:30 y 12:30 GMT el 25 de julio de 2004. EL diseño experimental en bloques aleatorios consistió en aplicar tres dosis diferentes de riego durante julio, agosto y septiembre, realizando medidas semanales de potencial hídrico, fotosíntesis y conductancia para estudiar los efectos del estrés hídrico en el cultivo. Los sensores de infrarrojo IRT permitieron la realización de medidas continuas de temperatura sobre las copas de los árboles, facilitando la validación de las imágenes térmicas. Los resultados de este estudio son presentados, destacando la aplicabilidad en la agricultura de precisión de la teledetección térmica e hiperespectral de alta resolución espacial para el estudio del suministro y la dosificación del riego.The Airborne Hyperspectral Scanner (AHS) was used to acquire images with 2.5 m spatiala resolution in the visible, near infrared and thermal spectral regions over an olive orchard in Cordoba (Spain) to study the spatial and temporal variability of water stress. The AHS thermal information enabled obtaining surface temperature images of the orchard at 7:30, 9:30 and 12:30 GMT in 25 july 2004. The experimental design consisted of applying three different irrigation treatments in randomly selected blocks during july, august and septemper, acquiring measurements of leaf water potential, stomatal conductance and photosynthesis to study the water stress effects on the trees. Infrared sensors IRT placed on top of the trees allowed to obtain continuously temperature measurements, providing validation data for the airborne thermal imagery. Results of this study are presented, suggesting that hyperspectral and high resolution remote sensing methods have important applicability in precision agriculture for management of controlled deficit irrigation method

Characterization of a clinical olfactory test with an artificial nose

Clinical olfactory tests are used to address hyposmia/anosmia levels in patients with different types of olfactory impairments. Typically, a given test is employed clinically and then replaced by a new one after a certain period of use which can range from days to several months. There is a need to assess control quality of these tests and also for a procedure to quantify their degradation over time. In this paper we propose a protocol to employ low-cost artificial noses for the quantitative characterization of olfactory tests used in clinical studies. In particular, we discuss a preliminary study on the Connecticut Chemosensorial Clinical Research Center Test kit which shows that some odorants, as sensed by an artificial nose, seem to degrade while others are potentiated as the test ages. We also discuss the need to establish a map of correspondence between human and machine olfaction when artificial noses are used to characterize or compare human smell performance in research and clinical studies

Automation Proposal for the Intermediate Steps in the 16S FFPE Samples Analysis Pipeline

Cursos e Congresos, C-155[Abstract] In the day-to-day work of bioinformatics, the use of integrated software packages, which encompass a wide range of tools, enables the development of pipelines for omics data analysis. Within the various existing pipelines, we focus on the analysis of the 16S rRNA gene as it allows for the study of diversity and taxonomy of prokaryotic microorganisms such as Bacteria and Archaea. However, these pipelines often involve a sequence of multiple tools that require intermediate steps before further processing can proceed, as in the case between Cutadapt and DADA2. In fact, in a typical pipeline, the values for DADA2 input arguments ’trunc-len-f’ and ’trunc-len-r’ are extracted from the output of Cutadapt. The best approach for selecting optimal values (aka the trimming positions) is graphically visualizing Cutadapt output and manually selecting the most accurate trimming position length. Therefore, we propose the automation of this specific intermediate step between Cutadapt and DADA2 tools, by selecting values displayed in the graphs that meet the filtering criteria. This automation has been incorporated into a custom pipeline for the analysis of the microbiome in 16S paired-end samples from colorectal cancer patients, and could potentially serve as a standardization approach in these processesThe authors of this paper extend their sincere appreciation to the collaborative efforts and contributions of the meiGAbiome Group, aswell as the entire team of medical and anatomopathologists. Finally, we are deeply grateful to the patients whose selfless donations have made this and numerous other studies possibl

Acidification induces condensation of the adenovirus core

The adenovirus (AdV) icosahedral capsid encloses a nucleoprotein core formed by the dsDNA genome bound to numerous copies of virus-encoded, positively charged proteins. For an efficient delivery of its genome, AdV must undergo a cascade of dismantling events from the plasma membrane to the nuclear pore. Throughout this uncoating process, the virion moves across potentially disruptive environments whose influence in particle stability is poorly understood. In this work we analyze the effect of acidic conditions on AdV particles by exploring their mechanical properties, genome accessibility and capsid disruption. Our results show that under short term acidification the AdV virion becomes softer and its genome less accessible to an intercalating dye, even in the presence of capsid openings. The AFM tip penetrates deeper in virions at neutral pH, and mechanical properties of genome-less particles are not altered upon acidification. Altogether, these results indicate that the main effect of acidification is the compaction of the nucleoproteic core, revealing a previously unknown role for chemical cues in AdV uncoating. Statement of significance: Studying the behavior of virus particles under changing environmental conditions is key to understand cell entry and propagation. One such change is the acidification undergone in certain cell compartments, which is thought to play a role in the programmed uncoating of virus genomes. Mild acidification in the early endosome has been proposed as a trigger signal for human AdV uncoating. However, the actual effect of low pH in AdV stability and entry is not well defined. Understanding the consequences of acidification in AdV structure and stability is also relevant to define storage conditions for therapeutic vectors, or design AdV variants resistant to intestinal conditions for oral administration of vaccinesWe thank M. G. Mateu (CBMSO-CSIC-UAM) for careful reading and insightful comments on early drafts, M. Castellanos and L. A. Campos (CNB-CSIC) for advice with fluorescence measurements and analyses, and M.I. Laguna (CNB-CSIC) for expert technical help. This work was supported by grants from the Spanish Ministry of Economy, Industry and Competitiveness (FIS2017- 89549- R; “Maria de Maeztu” Program for Units of Excellence in R&D MDM-2014-0377; and FIS2017-90701-REDT) and from the Human Frontiers Science Program (HFSPO RGP0012/2018) to P.J.P.; as well as grants PID2019-104098GB-I00/AEI/10.13039/501100011033 and BFU2016-74868-P, co-funded by the Spanish State Research Agency and the European Regional Development Fund, and 2019AEP045 from the Agencia Estatal CSIC to C.S.M. The CNB-CSIC is further supported by a Severo Ochoa Excellence grant (SEV 2017-0712). MM was funded by grant RTI2018-099985-B-I00, (MICINN/FEDER, UE) and the Ciber of Respiratory Diseases (CIBERES), an initiative from the Spanish Institute of Health Carlos III (ISCIII). M.H.-P. was a recipient of a Juan de la Cierva Incorporation postdoctoral contract funded by the Spanish State Research Agency. M.P.-I. held a predoctoral contract from La Caixa Foundation (ID 100010434, under agreement LCF/BQ/SO16/52270032). J. G. is a re cipient of a FPI predoctoral contract (BES-2017-079868) funded by the Spanish State Research Agenc

Monitoring dynamics of human adenovirus disassembly induced by mechanical fatigue

The standard pathway for virus infection of eukaryotic cells requires disassembly of the viral shell to facilitate release of the viral genome into the host cell. Here we use mechanical fatigue, well below rupture strength, to induce stepwise disruption of individual human adenovirus particles under physiological conditions, and simultaneously monitor disassembly in real time. Our data show the sequence of dismantling events in individual mature (infectious) and immature (noninfectious) virions, starting with consecutive release of vertex structures followed by capsid cracking and core exposure. Further, our experiments demonstrate that vertex resilience depends inextricably on maturation, and establish the relevance of penton vacancies as seeding loci for virus shell disruption. The mechanical fatigue disruption route recapitulates the adenovirus disassembly pathway in vivo, as well as the stability differences between mature and immature virionsWe acknowledge funding by grants from the Ministry of Science and Innovation of Spain, PIB2010US-00233, FIS2011-29493, Consolider CSD2010-00024 and CAM project and the Comunidad de Madrid No. S2009/MAT-1467 to P. J. P.; BFU2010-16382/BMC to C.S.M.; and FIS2011-16090-E to C.S.M. and P.J.P. S.J.F acknowledges funding from the National Institutes of Health, USA (GM037705 and AI1058172). A.J.P.-B. holds a Juan de la Cierva postdoctoral contract from the Ministry of Science and Innovation of Spain; A.O.-E. and R.M.-C. are recipients of predoctoral fellowships from the Ministry of Education and the Instituto de Salud Carlos III of Spain, respectivel

Quantitative nanoscale electrostatics of viruses

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed 29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.MINECO of Spain through project FIS2011-29493, FIS2014-59562-R, and the Spanish Interdisciplinary Network on the Biophysics of Viruses (Biofivinet, FIS2011-16090-E). CSM acknowledges funding from BFU2013- 41249-P, and Biofivinet. MGM acknowledges funding from the Spanish Government (BIO2012-37649), Comunidad de Madrid (S-505/MAT-0303), and by an institutional grant from Fundación Areces to the Centro de Biología MolecularPeer Reviewe

Metavolcanic rocks from schistose domain of Galicia-Tras-os-Montes: petrography, geochemistry and tectonic environment (Galice, NW. Spain)

[Resumen] Se estudia el vulcanismo intercalado en los grupos litoestratigráficos inferiores que integran el Dominio Esquistoso de Galicia Tras-os-Montes (DEGTM) denominados de muro a techo Santabaía, Nogueira y Paraño. El grupo de LalínForcarei que completa la secuencia no será tratado en este trabajo. La edad de estos grupos debe comprender desde el Precámbrico hasta el Devónico Inf. Los tres grupos tiene un cierto carácter vulcanosedimentario, más marcado en el grupo de Santabaía que en los dos grupos superiores. Se encuentran en ellos diferentes niveles volcánicos y vulcanosedimentarios de espesor y continuidad lateral variables, correspondientes a neises microporfídicos de dos micas y ortoneises biotíticos, además de algún nivel de riolitas y tranquitas presentes hacia la parte alta del grupo de Paraño. Geoquímicamente se caracteriza por ser un vulcanismo ácido de naturaleza calcoalcalina en el que predominan los términos riolíticos y iodacíticos de alto contenido en K, posiblemente originado en la zona externa de un margen continental pasivo existente durante el Ordovícico-Silúrico en el NO. de la Península, en el que tendrían lugar diferentes episodios o etapas de aportes volcánicos alternando con etapas más largas de sedimentación detrítica.[Abstract] The Vulcanism interbedded in the lower litostratigraphic groups of the DEGTM is studied. Those gruoups are known as Santabaia, Nogueira and Paraño from bo~tom to top; The sequence is completed with the Lalín-Forcarei group that is not studied in this paper. The age of the whole sequence is probably, from Precambrian to lower Devonian. The three groups show volcano-sedimentary features which are dominant in the Santabaia group. Several volcanic and volcano-sedimentary levels with different thickness and extension are found; these correspond to two mica microporfidic gneisses and biotitic ortogneisses and seldom ryolites and trachites in the uppermost pan of the Paraño group. Geochemically correspond to acid calcoalcaline vulcanites with ryolites and K rich ryodacites as main types. These rocks are possibily related to an external area of a continental margin which existed during Ordovician-Silurian time in the NW of the Iberian Peninsula. Several volcanic stages would alternate with sedimentation in this geotectonic environment

Oscillatory motions and parabolic manifolds at infinity in the planar circular restricted three body problem

Consider the Restricted Planar Circular 3 Body Problem. If the trajectory of the body of zero mass is defined for all time, it can have the following four types of asymptotic motion when time tends to infinity forward or backward in time: bounded, parabolic (goes to infinity with asymptotic zero velocity), hyperbolic (goes to infinity with asymptotic positive velocity) or oscillatory (the position of the body is unbounded but goes back to a compact region of phase space for a sequence of arbitrarily large times). We consider realistic mass ratio for the Sun-Jupiter pair and Jacobi constant which allows the massless body to cross Jupiter's orbit. This is a non-perturbative regime. We prove the existence of all possible combinations of past and future final motions. In particular, we obtain the existence of oscillatory motions. All the constructed trajectories cross the orbit of Jupiter but avoid close encounters with it. The proof relies on analyzing the stable and unstable invariant manifolds of infinity and their intersections. We construct orbits shadowing these invariant manifolds by the method of correctly aligned windows. The proof is computer assisted.M. C. has been partially supported by the NCN grant 2018/29/B/ST1/00109 2M. G. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 757802). M. G. is supported by the Catalan Institution for Research and Advanced Studies via an ICREA Academia Prize 2019. P. M. has been partially supported by the Spanish MINECO-FEDER Grant PGC2018-100928-B-I00 and the Catalan grant 2017SGR1049 T. S. has been also partly supported by the Spanish MINECO-FEDER Grant PGC2018-098676-B100 (AEI/FEDER/UE), the Catalan grant 2017SGR1049 and by the Catalan Institution for Research and Advanced Studies via an ICREA Academia Prize 2019. P. Z. has been partially supported by the NCN grant 2019/35/B/ST1/00655Peer ReviewedPostprint (author's final draft

Optimization of Amino Acid Sequence of Fmoc-Dipeptides for Interaction with Lipid Membranes

Fmoc-dipeptides appear as highly relevant building blocks in smart hydrogels and nanovehicles for biological applications. The interactions of the Fmocdipeptides with the cell membrane determine the efficiency of the nanomaterials based on the Fmoc-dipeptides’ internalization of nanovehicles for drug delivery. Here, we aim to understand the interplay of the interactions between the Fmoc-dipeptides and a phospholipid surface as a function of the amino acid sequence. The DMPA (1,2-dimyristoyl-snglycero- 3-phosphate) phospholipid in Langmuir monolayers was used as a model cell surface. A set of seven derivatives of Fmoc-dipeptides with a broad range of hydrophobicity were included. Mixed monolayers composed of DMPA/Fmoc-dipeptides in an equimolar ratio were built and characterized in situ at the air/water interface. Surface pressure−molecular area isotherms (π−A), Brewster angle microscopy (BAM), and UV−vis reflection spectroscopy (ΔR) were combined to provide a holistic picture of the interactions of the Fmoc-dipeptide with the phospholipid molecules. An increase in the hydrophobicity led to enhanced interaction of the Fmoc-dipeptide and DMPA molecules. The compression of the mixed monolayer could displace a significant fraction of the Fmoc-dipeptide from the monolayer. High hydrophobicity promoted self-assembly of the Fmoc-dipeptides over interaction with the phospholipid surface. The interplay of these two phenomena was analyzed as a function of the amino acid sequence of the Fmoc-dipeptides. The toxicity effect of Fmoc-FF could be observed and detailed at the molecular level. This study suggests that the adjustment of the hydrophobicity of the Fmoc-dipeptides within a defined range might optimize their efficiency for interaction with the lipid membranes. A semiquantitative guide for the chemical design of Fmoc-dipeptides for biological applications is proposed herein