Endocytosed nanogold fiducials for improved in-situ cryo-electron tomography tilt-series alignment

Cryo-electron tomography (CET) on cryo-focused ion beam (FIB)-milled lamellae is becoming a powerful technique for determining the structure of macromolecular complexes in their native cellular environment. Prior to tomogram reconstruction, CET tilt-series recorded on FIB lamellae need to be aligned. Traditionally, CET tiltseries alignment is performed with 5-20 nm gold fiducials, but it has thus far proven difficult to apply this to FIB lamellae of eukaryotic cells. In here, we describe a simple method to allow uptake of bovine serum albumin (BSA)-gold fiducials into mammalian cells via endocytosis, which can subsequently be used as fiducials for tiltseries alignment of cryo-FIB lamellae. We compare the alignment of tilt-series with BSA-gold fiducials to fiducialless patch-tracking, and find better alignment results with BSA-gold. This technique can contribute to understand cells at a structural and ultrastructural level with both cryo- and room-temperature electron tomography. Furthermore, fluorescently labeled BSA-gold has the potential to be used as fiducials for correlative light and electron microscopy studies

Is juvenile anchovy a feeding resource for the demersal community in the Bay of Biscay? On the availability of pelagic prey to demersal predators

The role that juvenile anchovy (Engraulis encrasicolus) play as a food resource for the demersal community in the southern Bay of Biscay is assessed using 21 years of anchovy abundance data and demersal predator diets. During the study period, a total of 26 fish and elasmobranch species preyed on anchovy either frequently or occasionally. Predators with a crustacean-based diet targeted the smaller anchovy individuals. The size range of anchovy juveniles (centred at 7.5–8.9 cm) was comparable to that of the largest nektonic–benthic crustaceans, but generally smaller than other demersal and pelagic fish prey. Hake (Merluccius merluccius) and megrim (Lepidorhombus whiffiagonis) were the predators that consumed the highest number of anchovy, one of the main prey items driving the variability of their diets. Anchovy consumption conformed only partially to the abundance of anchovy in the southern Bay of Biscay, suggesting that factors other than abundance might condition its availability to demersal predators. Prey size could be one of them, as the size of the anchovy preyed on proved to be significantly smaller than the individuals collected with bottom trawls. However, other factors, such as the vertical position of the shoals of anchovy juveniles, could also constrain anchovy availability to demersal predators

The effects of spatial resolution on Integral Field Spectrograph surveys at different redshifts. The CALIFA perspective

Over the past decade, 3D optical spectroscopy has become the preferred tool for understanding the properties of galaxies and is now increasingly used to carry out galaxy surveys. Low redshift surveys include SAURON, DiskMass, ATLAS3D, PINGS and VENGA. At redshifts above 0.7, surveys such as MASSIV, SINS, GLACE, and IMAGES have targeted the most luminous galaxies to study mainly their kinematic properties. The on-going CALIFA survey ($z\sim0.02$) is the first of a series of upcoming Integral Field Spectroscopy (IFS) surveys with large samples representative of the entire population of galaxies. Others include SAMI and MaNGA at lower redshift and the upcoming KMOS surveys at higher redshift. Given the importance of spatial scales in IFS surveys, the study of the effects of spatial resolution on the recovered parameters becomes important. We explore the capability of the CALIFA survey and a hypothetical higher redshift survey to reproduce the properties of a sample of objects observed with better spatial resolution at lower redshift. Using a sample of PINGS galaxies, we simulate observations at different redshifts. We then study the behaviour of different parameters as the spatial resolution degrades with increasing redshift.Comment: 20 pages, 16 figures. Accepted for publication in A&

Ionized gas kinematics of galaxies in the CALIFA survey I: Velocity fields, kinematic parameters of the dominant component, and presence of kinematically distinct gaseous systems

This work provides an overall characterization of the kinematic behavior of the ionized gas of the galaxies included in the Calar Alto Legacy Integral field Area (CALIFA), offering kinematic clues to potential users of this survey for including kinematical criteria for specific studies. From the first 200 galaxies observed by CALIFA, we present the 2D kinematic view of the 177 galaxies satisfying a gas detection threshold. After removing the stellar contribution, we used the cross-correlation technique to obtain the radial velocity of the dominant gaseous component. The main kinematic parameters were directly derived from the radial velocities with no assumptions on the internal motions. Evidence of the presence of several gaseous components with different kinematics were detected by using [OIII] profiles. Most objects in the sample show regular velocity fields, although the ionized-gas kinematics are rarely consistent with simple coplanar circular motions. 35% of the objects present evidence of a displacement between the photometric and kinematic centers larger than the original spaxel radii. Only 17% of the objects in the sample exhibit kinematic lopsidedness when comparing receding and approaching sides of the velocity fields, but most of them are interacting galaxies exhibiting nuclear activity. Early-type galaxies in the sample present clear photometric-kinematic misaligments. There is evidence of asymmetries in the emission line profiles suggesting the presence of kinematically distinct gaseous components at different distances from the nucleus. This work constitutes the first determination of the ionized gas kinematics of the galaxies observed in the CALIFA survey. The derived velocity fields, the reported kinematic peculiarities and the identification of the presence of several gaseous components might be used as additional criteria for selecting galaxies for specific studies.Comment: 38 pages, 16 figures, 4 tables. Paper accepted for publication in A&

Imprints of galaxy evolution on H ii regions Memory of the past uncovered by the CALIFA survey

H ii regions in galaxies are the sites of star formation and thus particular places to understand the build-up of stellar mass in the universe. The line ratios of this ionized gas are frequently used to characterize the ionization conditions. We use the Hii regions catalogue from the CALIFA survey (~5000 H ii regions), to explore their distribution across the classical [OIII]/Hbeta vs. [NII]/Halpha diagnostic diagram, and how it depends on the oxygen abundance, ionization parameter, electron density, and dust attenuation. We compared the line ratios with predictions from photoionization models. Finally, we explore the dependences on the properties of the host galaxies, the location within those galaxies and the properties of the underlying stellar population. We found that the location within the BPT diagrams is not totally predicted by photoionization models. Indeed, it depends on the properties of the host galaxies, their galactocentric distances and the properties of the underlying stellar population. These results indicate that although H ii regions are short lived events, they are affected by the total underlying stellar population. One may say that H ii regions keep a memory of the stellar evolution and chemical enrichment that have left an imprint on the both the ionizing stellar population and the ionized gasComment: 18 pages, 8 figures, accepted for publishing in A&

The Mass-Metallicity relation explored with CALIFA: I. Is there a dependence on the star formation rate?

We present the results on the study of the global and local M-Z relation based on the first data available from the CALIFA survey (150 galaxies). This survey provides integral field spectroscopy of the complete optical extent of each galaxy (up to 2-3 effective radii), with enough resolution to separate individual HII regions and/or aggregations. Nearly $\sim$3000 individual HII regions have been detected. The spectra cover the wavelength range between [OII]3727 and [SII]6731, with a sufficient signal-to-noise to derive the oxygen abundance and star-formation rate associated with each region. In addition, we have computed the integrated and spatially resolved stellar masses (and surface densities), based on SDSS photometric data. We explore the relations between the stellar mass, oxygen abundance and star-formation rate using this dataset. We derive a tight relation between the integrated stellar mass and the gas-phase abundance, with a dispersion smaller than the one already reported in the literature ($\sigma_{\Delta{\rm log(O/H)}}=$0.07 dex). Indeed, this dispersion is only slightly larger than the typical error derived for our oxygen abundances. However, we do not find any secondary relation with the star-formation rate, other than the one induced due to the primary relation of this quantity with the stellar mass. We confirm the result using the $\sim$3000 individual HII regions, for the corresponding local relations. Our results agree with the scenario in which gas recycling in galaxies, both locally and globally, is much faster than other typical timescales, like that of gas accretion by inflow and/or metal loss due to outflows. In essence, late-type/disk dominated galaxies seem to be in a quasi-steady situation, with a behavior similar to the one expected from an instantaneous recycling/closed-box model.Comment: 19 Pages, 8 figures, Accepted for Publishing in Astronomy and Astrophysics (A&A

Mixed Th2 and non-Th2 inflammatory pattern in the asthma-COPD overlap : a network approach

Altres ajuts: The authors are grateful to all the patients who participated in the study. A number of investigators contributed to the study logistics and they are listed in the Supplementary materials. The project was endorsed by the COPD and Asthma Research Board (PII de EPOC y asma) of the Spanish Society of Pneumology and Thoracic Surgery (SEPAR).The asthma-chronic obstructive pulmonary disease (COPD) overlap (ACO) is a clinical condition that combines features of those two diseases, and that is difficult to define due to the lack of understanding of the underlying mechanisms. Determining systemic mediators may help clarify the nature of inflammation in patients with ACO. We aimed at investigating the role and interaction of common markers of systemic inflammation (IL-6, IL-8, and tumor necrosis factor-α), Th2-related markers (periostin, IL-5, and IL-13), and IL-17 in asthma, COPD, and ACO. This is a cross-sectional study of patients aged ≥40 years with a post-bronchodilator forced expiratory volume in the first second/forced vital capacity 10 pack-years in a patient with a previous diagnosis of asthma or by the presence of eosinophilia in a patient with a previous diagnosis of COPD. Clinical, functional, and inflammatory parameters were compared between categories using discriminant and network analysis. In total, 109 ACO, 89 COPD, and 94 asthma patients were included. Serum levels (median [interquartile range]) of IL-5 were higher in asthma patients than in COPD patients (2.09 [0.61-3.57] vs 1.11 [0.12-2.42] pg/mL, respectively; p =0.03), and IL-8 levels (median [interquartile range]) were higher in COPD patients than in asthma patients (9.45 [6.61-13.12] vs 7.03 [4.69-10.44] pg/mL, respectively; p <0.001). Their values in ACO were intermediate between those in asthma and in COPD. Principal component and network analysis showed a mixed inflammatory pattern in ACO in between asthma and COPD. IL-13 was the most connected node in the network, with different weights among the three conditions. Asthma and COPD are two different inflammatory conditions that may overlap in some patients, leading to a mixed inflammatory pattern. IL-13 could be central to the regulation of inflammation in these conditions

CALIFA, the Calar Alto Legacy Integral Field Area survey: I. Survey presentation

We present here the Calar Alto Legacy Integral Field Area (CALIFA) survey, which has been designed to provide a first step in this direction.We summarize the survey goals and design, including sample selection and observational strategy.We also showcase the data taken during the first observing runs (June/July 2010) and outline the reduction pipeline, quality control schemes and general characteristics of the reduced data. This survey is obtaining spatially resolved spectroscopic information of a diameter selected sample of $\sim600$ galaxies in the Local Universe (0.005< z <0.03). CALIFA has been designed to allow the building of two-dimensional maps of the following quantities: (a) stellar populations: ages and metallicities; (b) ionized gas: distribution, excitation mechanism and chemical abundances; and (c) kinematic properties: both from stellar and ionized gas components. CALIFA uses the PPAK Integral Field Unit (IFU), with a hexagonal field-of-view of \sim1.3\sq\arcmin', with a 100% covering factor by adopting a three-pointing dithering scheme. The optical wavelength range is covered from 3700 to 7000 {\AA}, using two overlapping setups (V500 and V1200), with different resolutions: R\sim850 and R\sim1650, respectively. CALIFA is a legacy survey, intended for the community. The reduced data will be released, once the quality has been guaranteed. The analyzed data fulfill the expectations of the original observing proposal, on the basis of a set of quality checks and exploratory analysis. We conclude from this first look at the data that CALIFA will be an important resource for archaeological studies of galaxies in the Local Universe.Comment: 32 pages, 29 figures, Accepted for publishing in Astronomy and Astrophysic

Coastal upwelling in the Rias Bajas, NW Spain: Contrasting the benthic regimes of the Rias de Arosa and de Muros

Nutrient-rich North Atlantic water upwells off the NW coast of Spain and intermittently intrudes into the rias, coastal embayments, by displacement during periods of offshore winds. High primary production associated with the upwelling supports an intensive raft culture of the edible mussel, Mytilus edulis. This culture is most intensive (ca. 2000 rafts) in the Ria de Arosa, and results in one of the highest protein yields per unit area on earth...