Metabolomic changes in lactating multiparous naturally MAP-infected Holstein-Friesian dairy cows suggest changes in mitochondrial energy pathways

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative organism of Johne's Disease, a chronic intestinal infection of ruminants. Infected cows begin shedding MAP within the asymptomatic, subclinical stage of infection before clinical signs, such as weight loss, diarrhoea and reduced milk yields develop within the clinical stages of disease. Herein, we examine the milk metabolomic profiles of naturally MAP-infected Holstein-Friesian cows. The study used biobanked milk samples which were collected 73.4 ± 3.79 (early lactation) and 143 ± 3.79 (mean ± SE) (mid-lactation) days post-calving from 5 MAP-infected and 5 control multiparous cows. The milk metabolome was assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) for sensitive, non-targeted metabolite fingerprinting. Metabolite fingerprinting assessments using partial least squares discriminate analyses (PLS-DA) indicated that lactation stage was a larger source of variation than MAP status. Examining each lactation stage separately for changes associated to MAP-infection status identified 45 metabolites, 33 in early lactation and 12 in mid-lactation, but only 6 metabolites were targeted in both stages of lactation. Pathway enrichment analysis suggested that MAP affected the malate-aspartate shuffle during early lactation. Pearson's correlation analysis indicated relationships between milk lactose concentrations in mid-lactation and 6 metabolites that were tentatively linked to MAP-infection status. The targeted metabolites were suggestive of wider changes in the bioenergetic metabolism that appear to be an acceleration of the effects of progressing lactation in healthy cows. Additionally, milk lactose concentrations suggest that MAP reduces the availability of lactose derivatives

Icescape-scale metabolomics reveals cyanobacterial and topographic control of the core metabolism of the cryoconite ecosystem of an Arctic ice cap

DATA AVAILABILITY STATEMENT : All data publicly available at DOI: 10.5281/zenodo.7669756.Glaciers host ecosystems comprised of biodiverse and active microbiota. Among glacial ecosystems, less is known about the ecology of ice caps since most studies focus on valley glaciers or ice sheet margins. Previously we detailed the microbiota of one such high Arctic ice cap, focusing on cryoconite as a microbe-mineral aggregate formed by cyanobacteria. Here, we employ metabolomics at the scale of an entire ice cap to reveal the major metabolic pathways prevailing in the cryoconite of Foxfonna, central Svalbard. We reveal how geophysical and biotic processes influence the metabolomes of its resident cryoconite microbiota. We observed differences in amino acid, fatty acid, and nucleotide synthesis across the cap reflecting the influence of ice topography and the cyanobacteria within cryoconite. Ice topography influences central carbohydrate metabolism and nitrogen assimilation, whereas bacterial community structure governs lipid, nucleotide, and carotenoid biosynthesis processes. The prominence of polyamine metabolism and nitrogen assimilation highlights the importance of recycling nitrogenous nutrients. To our knowledge, this study represents the first application of metabolomics across an entire ice mass, demonstrating its utility as a tool for revealing the fundamental metabolic processes essential for sustaining life in supraglacial ecosystems experiencing profound change due to Arctic climate change-driven mass loss.Great Britain Sasakawa Foundation; Natural Environment Research Council; Norges Forskningsråd; South Africa National Research Foundation.http://wileyonlinelibrary.com/journal/emiam2024Plant Production and Soil ScienceSDG-13:Climate actionSDG-15:Life on lan

The ALHAMBRA survey: Estimation of the clustering signal encoded in the cosmic variance

[Aims]: The relative cosmic variance (σv) is a fundamental source of uncertainty in pencil-beam surveys and, as a particular case of count-in-cell statistics, can be used to estimate the bias between galaxies and their underlying dark-matter distribution. Our goal is to test the significance of the clustering information encoded in the σv measured in the ALHAMBRA survey. [Methods]: We measure the cosmic variance of several galaxy populations selected with B-band luminosity at 0.35 ≤ z< 1.05 as the intrinsic dispersion in the number density distribution derived from the 48 ALHAMBRA subfields. We compare the observational σv with the cosmic variance of the dark matter expected from the theory, σv,dm. This provides an estimation of the galaxy bias b. [Results]: The galaxy bias from the cosmic variance is in excellent agreement with the bias estimated by two-point correlation function analysis in ALHAMBRA. This holds for different redshift bins, for red and blue subsamples, and for several B-band luminosity selections. We find that b increases with the B-band luminosity and the redshift, as expected from previous work. Moreover, red galaxies have a larger bias than blue galaxies, with a relative bias of brel = 1.4 ± 0.2. [Conclusions]: Our results demonstrate that the cosmic variance measured in ALHAMBRA is due to the clustering of galaxies and can be used to characterise the σv affecting pencil-beam surveys. In addition, it can also be used to estimate the galaxy bias b from a method independent of correlation functions.This work has been mainly funded by the FITE (Fondos de Inversiones de Teruel) and the projects AYA2012-30789, AYA2006-14056, and CSD2007-00060. We also acknowledge support from the Spanish Ministry for Economy and Competitiveness and FEDER funds through grants AYA2010-15081, AYA2010-15169, AYA2010-22111-C03-01, AYA2010-22111-C03-02, AYA2011-29517-C03-01, AYA2012-39620, AYA2013-40611-P, AYA2013-42227-P, AYA2013-43188-P, AYA2013-48623-C2-1, AYA2013-48623-C2-2, ESP2013-48274, AYA2014-58861-C3-1, Aragon Government Research Group E103, Generalitat Valenciana projects Prometeo 2009/064 and PROMETEOII/2014/060, Junta de Andalucia grants TIC114, JA2828, P10-FQM-6444, and Generalitat de Catalunya project SGR-1398. A.J.C. and C.H.-M. are Ramon y Cajal fellows of the Spanish government. A. M. acknowledges the financial support of the Brazilian funding agency FAPESP (Post-doc fellowship - process number 2014/11806-9). M.P. acknowledges financial support from JAE-Doc program of the Spanish National Research Council (CSIC), co-funded by the European Social Fund.Peer Reviewe

I. MUFFIT: A multi-filter fitting code for stellar population diagnostics

Numerical methods and codes.-- et al.[Aims]: We present MUFFIT, a new generic code optimized to retrieve the main stellar population parameters of galaxies in photometric multi-filter surveys, and check its reliability and feasibility with real galaxy data from the ALHAMBRA survey. [Methods]: Making use of an error-weighted X2-test, we compare the multi-filter fluxes of galaxies with the synthetic photometry of mixtures of two single stellar populations at different redshifts and extinctions, to provide the most likely range of stellar population parameters (mainly ages and metallicities), extinctions, redshifts, and stellar masses. To improve the diagnostic reliability, MUFFIT identifies and removes from the analysis those bands that are significantly affected by emission lines. The final parameters and their uncertainties are derived by a Monte Carlo method, using the individual photometric uncertainties in each band. Finally, we discuss the accuracies, degeneracies, and reliability of MUFFIT using both simulated and real galaxies from ALHAMBRA, comparing with results from the literature. [Results]: MUFFIT is a precise and reliable code to derive stellar population parameters of galaxies in ALHAMBRA. Using the results from photometric-redshift codes as input, MUFFIT improves the photometric-redshift accuracy by ∼10-20%. MUFFIT also detects nebular emissions in galaxies, providing physical information about their strengths. The stellar masses derived from MUFFIT show excellent agreement with the COSMOS and SDSS values. In addition, the retrieved age-metallicity locus for a sample of z ≤ 0.22 early-type galaxies in ALHAMBRA at different stellar mass bins are in very good agreement with the ones from SDSS spectroscopic diagnostics. Moreover, a one-to-one comparison between the redshifts, ages, metallicities, and stellar masses derived spectroscopically for SDSS and by MUFFIT for ALHAMBRA reveals good qualitative agreements in all the parameters, hence reinforcing the strengths of multi-filter galaxy data and optimized analysis techniques, like MUFFIT, to conduct reliable stellar population studies.L.A.D.G. acknowledges support from the "Caja Rural de Teruel" for developing this research. A.J.C. is a Ramon y Cajal Fellow of the Spanish Ministry of Science and Innovation. This work has been supported by the "Programa Nacional de Astronomia y Astrofisica" of the Spanish Ministry of Economy and Competitiveness (MINECO) under grant AYA2012-30789, as well as by FEDER funds and the Government of Aragon, through the Research Group E103. L.A.D.G. also thanks the Mullard Space Science Laboratory (MSSL) and Royal Astronomical Society (RAS) for offering the opportunity to support and develop part of this research in collaboration with I.F. MINECO grants AYA2010-15081, AYA2010-15169, AYA2010-22111-C03-01, AYA2010-22111-C03-02, AYA2011-29517-C03-01, AYA2013-40611-P, AYA2013-42227-P, AYA2013-43188-P, AYA2013-48623-C2-1, AYA2013-48623-C2-2, and AYA2014-58861-C3-1 are also acknowledged, together with Generalitat Valenciana projects Prometeo 2009/064 and PROMETEOII/2014/060, and Junta de Andalucia grants TIC114, JA2828, and P10-FQM-6444. MP acknowledges financial support from the JAE-Doc programme of the Spanish National Research Council (CSIC), co-funded by the European Social Fund.Peer Reviewe

The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

[Aims]: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. [Methods]: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections.We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. [Results]: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20 - 1:1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2:7 0:5) than for red galaxies (n = 1:3 0:4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nm red = 0:57 0:05 for red galaxies and Nm blue = 0:26 0:02 for blue galaxies. [Conclusions]: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology.This work has been mainly funded by the FITE (Fondos de Inversiones de Teruel) and the projects AYA2012-30789, AYA2006-14056, and CSD2007-00060. We also acknowledge financial support from the Spanish Government grants AYA2010-15169, AYA2010-22111-C03-01, AYA2010-22111-C03-02, and AYA2013-48623-C2-2, from the Aragón Government through the Research Group E103, from the Junta de Andalucía through TIC-114 and the Excellence Project P08-TIC-03531, and from the Generalitat Valenciana through the projects Prometeo/2009/064 and PrometeoII/2014/060. A.J.C. is Ramón y Cajal fellow of the Spanish government. M.P. acknowledges the financial support from JAE-Doc program of the Spanish National Research Council (CSIC), co-funded by the European Social Fund.Peer Reviewe