BUSCADOR RECOLECTA

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory., Peer reviewed

Ellis van Creveld syndrome and Weyers acrofacial dysostosis are two rare genetic diseases affecting skeletal development. They are both ciliopathies, as they are due to malfunction of primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae and are required for Hedgehog signaling, a key pathway during skeletal morphogenesis. These ciliopathies are caused by mutations affecting the EVC-EVC2 complex, a transmembrane protein heterodimer that regulates Hedgehog signaling from inside primary cilia. Despite the importance of this complex, the mechanisms underlying its stability, targeting and function are poorly understood. To address this, we characterized the endogenous EVC protein interactome in control and Evc-null cells. This proteomic screen confirmed EVC’s main known interactors (EVC2, IQCE, EFCAB7), while revealing new ones, including USP7, a deubiquitinating enzyme involved in Hedgehog signaling. We therefore looked at EVC-EVC2 complex ubiquitination. Such ubiquitination exists but is independent of USP7 (and of USP48, also involved in Hh signaling). We did find, however, that monoubiquitination of EVC-EVC2 cytosolic tails greatly reduces their protein levels. On the other hand, modification of EVC-EVC2 cytosolic tails with the small ubiquitin-related modifier SUMO3 has a different effect, enhancing complex accumulation at the EvC zone, immediately distal to the ciliary transition zone, possibly via increased binding to the EFCAB7-IQCE complex. Lastly, we find that EvC zone targeting of EVC-EVC2 depends on two separate EFCAB7-binding motifs within EVC2’s Weyers-deleted peptide. Only one of these motifs had been characterized previously, so we have mapped the second herein. Altogether, our data shed light on EVC-EVC2 complex regulatory mechanisms, with implications for ciliopathies., Peer reviewed

Additional structural (XRD and STEM) and chemical x-ray microanalysis, a detailed description of the STEM image analysis and calculation of polarization images, including the LSAT substrate, and further details on the experimental conditions are provided in the supplementary material., Peer reviewed

File 1 (.doc): 1Table - Mean (±SD) δ13C and δ15N values (‰) of the prey species used to analyze the diet of the common bottlenose dolphin in Madeiran waters, per season; 1 figure - Simulated mixing region calculated for each season (‘summer/autumn’- top; ‘winter/spring’- bottom) with the most likely prey (white crosses) based on bi-plot interpretation.-- File 2 (.xls), Supplementary material of the article Trophic ecology of common bottlenose dolphins in a pelagic insular environment inferred by stable isotopes, https://doi.org/10.1007/s10750-023-05294-4, Peer reviewed

The dataset includes: Microstructure profiles collected with a MSS Sea&Sun profiler during the three intensive samplings of the cruise (I01, I02, I03), Ocean currents measured with a bottom moored RD Instruments acoustic Doppler profiler (ADCP, 300Khz) for the duration of the cruise, Acoustic backscatter from a ship-borne echosounder Simrad EK80 for the frequencies 18, 38, 70, 120 and 200 KHz and the three intensive samplings of the cruise (I01, I02, I03), European anchovy (Engraulis encrasicolus) egg counts from plankton hauls samplings, This dataset includes data collected during the cruise REMEDIOS-TL in the Ría de Pontevedra (NW Iberia) at station P2 (42.357°N, 8.773°W) from 29 June to 18 July 2018 onboard of the Research Vessel Ramón Margalef belonging to the Spanish Institude of Oceanography. The archived data are described in a manuscript entitled "Intense upper ocean mixing due to large aggregations of spawning fish" by Fernández Castro et al. published in Nature Geoscience: Fernández Castro, B., Peña, M., Nogueira, E. et al. Intense upper ocean mixing due to large aggregations of spawning fish. Nat. Geosci. 15, 287–292 (2022). https://doi.org/10.1038/s41561-022-00916-3. The manuscript presents evidence that night-time aggregations of anchovies produce intense ocean turbulence and mixing. All the data needed to support the conclusions of the article are included in this dataset, The REMEDIOS project is funded by the Spanish Ministry of Economy and Innovation under the research project REMEDIOS (CTM2016-75451-C2-1-R), acoustic_backscatter_EK80_REMEDIOS_TL_I01.nc.-- acoustic_backscatter_EK80_REMEDIOS_TL_I02.nc.-- acoustic_backscatter_EK80_REMEDIOS_TL_I03.nc.-- bottom_moored_ADCP_REMEDIOS_TL.nc.-- egg_counts.xls.-- MSS_microstructure_REMEDIOS_TL_I01.nc.-- MSS_microstructure_REMEDIOS_TL_I02.nc.-- MSS_microstructure_REMEDIOS_TL_I03.nc, Peer reviewed

The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The role of these modifications in transcriptional regulation is well-documented. However, the extent to which the enzymatic processes of histone posttranslational modification might affect metabolic regulation is less clear. Here, we investigated how histone methylation might affect metabolism using metabolomics, proteomics, and RNA-seq data from cancer cell lines, primary tumour samples and healthy tissue samples. In cancer, the expression of histone methyltransferases (HMTs) was inversely correlated to the activity of NNMT, an enzyme previously characterised as a methyl sink that disposes of excess methyl groups carried by the universal methyl donor S-adenosyl methionine (SAM or AdoMet). In healthy tissues, histone methylation was inversely correlated to the levels of an alternative methyl sink, PEMT. These associations affected the levels of multiple histone marks on chromatin genome-wide but had no detectable impact on transcriptional regulation. We show that HMTs with a variety of different associations to transcription are co-regulated by the Retinoblastoma (Rb) tumour suppressor in human cells. Rb-mutant cancers show increased total HMT activity and down-regulation of NNMT. Together, our results suggest that the total activity of HMTs affects SAM metabolism, independent of transcriptional regulation., Peer reviewed

GTEx NNMT-HMT correlation all tissues full labelled plots., Peer reviewed

(A) Schematic drawings of an S9 egg chamber illustrating the mirrorGal4 pattern of expression (mirrGal4, pink) and the point of ablation in the basal side of FCs (blue bar). NCs are in gray, BCs in yellow, FCs in purple, and BM in blue. (B) Images of life S9 control mirrGal4 and mirr>AbiRNAi egg chambers expressing Resille-GFP before and after FCs bonds are ablated. Blue bars indicate points of ablation. (C) Quantification of initial velocity of vertex displacement of the indicated ablated bonds. (D) Schematic drawing of an S9 egg chamber illustrating the mirrGal4 pattern of expression (pink) and the point of ablation in the NCs (blue bar). (E) Images of life S9 egg chambers of the indicated genotypes before and after NC bonds are ablated. Blue bars indicate points of ablation. (F) Quantification of initial velocity of vertex displacement of the indicated ablated bonds. (G–H’) Stills taken from live imaging of migrating BCs from egg chambers of the indicated genotypes. Discontinuous yellow lines demarcate the region between the anterior border of the egg chamber and the oocyte anterior membrane. (I, J) Quantification of BC migration speed in the area anterior to (I) and at the (J) mirr expressing region. The statistical significance of differences was assessed with a t test, * P value < 0.05, ** P value < 0.01, and *** P value < 0.001. Horizontal and vertical lines indicate mean and SD, respectively. Scale bar in B, E, and G–H’, 5 μm, 10 μm, and 20 μm, respectively. The raw data underlying panels C, F, I, and J are available in S1 Data. BC, border cell; BM, basement membrane; FC, follicle cell; GFP, green fluorescent protein; NC, nurse cell., Peer reviewed

The basement membrane (BM) is a specialized extracellular matrix (ECM), which underlies or encases developing tissues. Mechanical properties of encasing BMs have been shown to profoundly influence the shaping of associated tissues. Here, we use the migration of the border cells (BCs) of the Drosophila egg chamber to unravel a new role of encasing BMs in cell migration. BCs move between a group of cells, the nurse cells (NCs), that are enclosed by a monolayer of follicle cells (FCs), which is, in turn, surrounded by a BM, the follicle BM. We show that increasing or reducing the stiffness of the follicle BM, by altering laminins or type IV collagen levels, conversely affects BC migration speed and alters migration mode and dynamics. Follicle BM stiffness also controls pairwise NC and FC cortical tension. We propose that constraints imposed by the follicle BM influence NC and FC cortical tension, which, in turn, regulate BC migration. Encasing BMs emerge as key players in the regulation of collective cell migration during morphogenesis., Peer reviewed

[ES] El conjunto de datos está dividido en tres subcarpetas, dentro de las cuales los datos se encuentran agrupados por especies: Eggs: Proporciona más de 900 imágenes en formato RAW en el rango visual del espectro visible de puestas completas sobre fondo negro, correspondientes a 14 especies distintas. Nests: Proporciona más de 800 imágenes de nidos de 6 especies distintas, tomadas en su entorno desde 1 metro de distancia y a 70 cm de altura. En este segundo conjunto de imágenes, se incluyen imágenes de los nidos tanto en el rango visible como en ultravioleta cercano. Incubating Behavior: Proporciona más de 950,000 imágenes en formato jpg correspondientes a secuencias de vigilancia del comportamiento de incubación de 5 especies distintas, junto con información de las condiciones ambientales., [EN] The dataset is divided into three subfolders, within which the data is grouped by species: Eggs: Provides over 900 images in RAW format within the visible spectrum of complete clutches on a black background, corresponding to 14 different species. Nests: Provides over 800 images of nests from 6 different species, taken in their environment from 1 meter away and at a height of 70 cm. This set includes images of the nests in both the visible range and near-ultraviolet. Incubating Behavior: Provides over 950,000 jpg images corresponding to surveillance sequences of incubation behavior from 5 different species, along with information on environmental conditions., [ES] Este conjunto de datos, generado en el marco del proyecto CAMNID: CGL2017-83518-P, Plan Nacional I+D+i, contiene información visual sobre huevos, nidos y comportamiento durante la incubación de diferentes especies de aves limícolas (shorebirds). Permite la realización de análisis de coloración y moteado, entre otros, para las especies en estudio. Asimismo, se proporcionan secuencias de imágenes de monitorización de diversos nidos de estas especies a lo largo de 3 horas (entre las 12:00 y las 15:00) junto con las condiciones ambientales durante la vigilancia. Esto permite la realización de estudios de los comportamientos de estas aves durante la incubación, abriendo la posibilidad de estudiar diversos mecanismos de mitigación de estrés térmico o las alternancias parentales macho/hembra durante la incubación en función de las condiciones ambientales, [EN] This dataset, generated within the framework of the CAMNID project: CGL2017-83518-P, Plan Nacional I+D+i, contains visual information on eggs, nests, and incubation behavior of various shorebird species. It enables color and spotting pattern analyses, among other studies, for the species included. Additionally, it provides image sequences monitoring various nests of these species over a 3-hour period (from 12:00 to 15:00) along with the environmental conditions during the surveillance. This allows for studies of the birds' behavior during incubation, opening the possibility to study mechanisms of thermal stress mitigation and male/female parental alternation during incubation based on environmental conditions., CAMNID PROJECT: Grant: CGL2017-83518-P, Plan Nacional I+D+i: EFECTOS DE LAS INVASIONES GEOLOGICAS DE ORIGEN ANTROPICO SOBRE LAS ESTRATEGIAS DE CAMUFLAJE DE NIDOS EN EL CHORLITEJO PATINEGRO CHARADRIUS ALEXANDRINUS, The dataset is comprissed of three folders. Eggs, Nests, and BehavioralMonitoring. ** Folder: Eggs: Photographs of shorebird eggs from a zenital view in raw format. - INFORMATION_TABLE.xlsx: Excel file with information about each picture in the Eggs folder subset. Image name can be used as unique identifier. - Folders corresponding to eggs of 14 different species. Species name corresponding to folder name. - Inside each folder, a single RAW format image file for each egg is provided, ** Folder: Nests: Zenital pictures of shorebirds nests in natural environments both in the Vis and UV wavelength ranges. - INFORMATION_TABLE.xlsx: Excel file with information about each picture in the Nests folder subset. Image name can be used as unique identifier. - Folders corresponding to 6 different species. Species name corresponding to folder name. - Inside each folder, two images per nest are provided. One for the visible wavelength range ({ImageName}_VIS.ARW) and another one for the UV range ({ImageName}_UV.ARW), **Folder: BehavioralMonitoring: Pictures showing the incubating activity of shorebird species. Additionally, environmental conditions are also provided. - README.txt: Readme file providing the description of each folder in the dataset - Folders corresponding to 5 shorebirds species being monitored. - Inside each species folder: ---subfolder: DATE_OF_OBSERVATION: | |---subfolder: DATALOGGERCODE (DTXX (XX from 0 to 9)) | |____FRAME_XXX_STD.jpg: XXXth Picture taken under normal conditions | |____YYY_ACT.jpg: YYYth Picture corresponding to a special activitity condition | |____DATA_LOGGER.txt: csv file containing enviromental conditions during this experiment. Updated every 100s | |____DTXX.gpx: GPS position of this observation (gpx standard format) | |____DTXX_GPS.txt: GPS position for this observation in txt format (the gpx file is not always available), Peer reviewed