BUSCADOR RECOLECTA

Experimental Procedures for Supplemental Figure: Double-stranded Zic2 and Zic2 mutant decoy DNA were prepared by annealing complementary single strands with the follow sequences: 5′-TCTTGGGTGGTCTCCGGAGACCACCCAAGA (for Zic2 decoy) and 5′-TCTTGAGTGAACTCCGGAGTTCACTCAAGA (for Zic2M decoy) as a negative control (Mizugishi et al., 2001). We utilized unlabeled and also Texas-red-tagged oligonucleotides (Invitrogen) to monitor DNA entry into cells. The terminal four bases on either site of the molecule were linked by phosphorothioate esters for added stability. Retinal explants were exposed to serial concentrations (0, 10, 100, and 200 μM) of decoy DNA combined with serial concentrations of serum-free medium (SFM) plus Fungene 6 transfection reagent (Roche) and incubated for 1 hr 30 min at 37°C. The explants were then washed several times in SFM, plated on D-polylysine/laminin, and incubated at 37°C, and dissociated chiasm cells were added to the cultures 2 hr later. They were then immunolabeled with α-neurofilament and explant outgrowth quantified, as indicated in Experimental Procedures., Figure S1. Zic2 Is Necessary for Ventrotemproal (VT) RGCs to Respond Negatively to Cues from the Chiasm Midline In Vitro. (A) Retinal explants grown on dissociated chiasm cells and immunostained with α-neurofilament. Representative images of dorsotemporal (DT) (a–d) and VT (e–h) retinal explants that were untransfected (a and e) or incubated with lipofectamine (b and f), Zic2 decoy oligos (c and g), or Zic2-mutant-decoy oligos (d and h) and subsequently cocultured with dissociated chiasm cells. Scale bar: 100 μm. (B) Quantification of area occupied by axons of DT (black columns) or VT (white columns) retinal explants that were untransfected or incubated with lipofectamine, Zic2-decoy oligos, or mutant-Zic2-decoy oligos, and then cocultured with dissociated chiasm cells. Left panels and graph: transfection of Zic2-decoy oligos does not affect the outgrowth in DT neurites (p > 0.2). Right panels and graph: transfection of Zic2-decoy oligos leads to increased growth of VT neurites. (*p < 0.05 compared with VT explants incubated with the lipofection agent alone or transfected with Zic2M-decoy). Number above bars indicates number of explants., Peer reviewed

Analytical and spectral characterization data of all new compounds, NMR/NOESY interprotonic distances, and crystallographic data (CIF)., Peer reviewed

Peer reviewed

Table1: Galaxies from AMIGA sample listed as active in the literature, Table2: Radio-excess galaxies found using the radio-FIR correlation, Table4: Radio-excess galaxies in FIRST, Table5: Classified galaxies using the IRAS colour method, Table6: Catalogue of AGN-candidates for the total sample, This paper is part of a series involving the AMIGA project (Analysis of the Interstellar Medium of Isolated GAlaxies). This project provides a statistically-significant sample of the most isolated galaxies in the northern sky. We present a study of the nuclear activity in a well-defined sample of the most isolated galaxies (total sample: n=1050, complete subsample: n=719) in the local Universe traced by their far-infrared (FIR) and radio continuum emission. We use the well-known radio continuum-FIR correlation to select radio-excess galaxies that are candidates to host an active galactic nucleus (AGN), as well as the FIR colours to find obscured AGN-candidates. We also used the existing information on nuclear activity in the Veron-Cetty catalogue and in the NASA Extragalactic Database. A final catalogue of AGN-candidate galaxies has been produced that will provide a baseline for studies on the dependence of activity on the environment. Our sample is mostly radio quiet, consistent with its high content of late-type galaxies. At most ~1.5% of the galaxies show a radio excess with respect to the radio-FIR correlation, and this fraction even goes down to less than 0.8% after rejection of back/foreground sources using FIRST. We find that the fraction of FIR colour selected AGN-candidates is ~28% with a lower limit of ~7%. Our final catalogue contains 89 AGN candidates and is publicly available on the AMIGA web page (http://www.iaa.csic.es/AMIGA.html).

[Organism] Homo sapiens, [Experiment type] Expression profiling by array, [Overall design] Adipose tissue and blood samples were obtained from 27 children, 14 obese (BMI adjusted for age and sex z score > 2) and 13 non obese undergoing appendix surgery. About 400 mg of adipose tissue was taken and immediately immersed in RNAlater solution and stored at -80°C for gene expression analysis. Informed consent was obtained from all patients after the nature of the study was explained, and the experimental design was approved, from an ethical and scientific standpoint, by the Hospital’s Ethical Committee responsible for research., [Platforms (1)] GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, [Relations] BioProject PRJNA103477, 1. GSM243215 Adipose tissue_423_control_rep1. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: M age: 10 year z score bmi: -1.45, 2. GSM243216 Adipose tissue_425_control_rep2. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: M age: 7 year z score bmi: 0.49, 3. GSM243217 Adipose tissue_426_control_rep3. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: F age: 8 year z score bmi: 0.12, 4. GSM243218 Adipose tissue_427_control_rep4. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: M age: 10 year z score bmi: -1.81, 5. GSM243219 Adipose tissue_428_control_rep5. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: M age: 7 year z score bmi: -0.64, 6. GSM243220 Adipose tissue_429_control_rep6. [Source name] Omental adipose tissue, normal weight, child. [Characteristics] tissue: omental adipose group: normal weight gender: M age: 7 year z score bmi: -0.36, 7. GSM243225 Adipose tissue_418_obese_rep1. [Source name] Omental adipose tissue, obese, child. [Characteristics] tissue: omental adipose group: obese gender: M age: 11 years z score bmi: 2, 8. GSM243226 Adipose tissue_419_obese_rep2. [Source name] Omental adipose tissue, obese, child. [Characteristics] tissue: omental adipose group: obese gender: M age: 9 years z score bmi: 4.25, 9. GSM243227 Adipose tissue_420_obese_rep3. [Source name] Omental adipose tissue, obese, child. [Characteristics] tissue: omental adipose group: obese gender: M age: 12 years z score bmi: 2.36, 10. GSM243228 Adipose tissue_421_obese_rep4. [Source name] Omental adipose tissue, obese, child. [Characteristics] tissue: omental adipose group: obese gender: M age: 9 years z score bmi: 4.25, 11. GSM243275 Adipose tissue_422_obese_rep5. [Source name] Omental adipose tissue, obese, child. [Characteristics] tissue: omental adipose group: obese gender: M age: 10 years z score bmi: 2.72, Characterization of genes associated with adipose tissue is key to understanding the pathogenesis of obesity and developing treatments for this disorder. Differential gene expression in the adipose tissue has been described in adulthood but none studies have been developed on childhood. The purpose of this study was to compare gene expression in omental adipose tissue from obese prepubertal and normal weight children. We selected 5 obese (BMI adjusted for age and sex z score >2) and 6 normal weight children. RNA was extracted from omental adipose tissue biopsies and cRNA was hybridizated on the human genome U133 Plus 2.0 Arrays (Affymetrix®). Microarray experiments were performed for each sample, and selected group of gene expression values were confirmed with real-time RT-PCR in 10 obese and 10 normal weigth prepubertal children. 1276 genes were found to be differentially expressed at P<0.05. Of those differential genes, 201 were upregulated (Fc>2) and 42 were downregulated (Fc<-2). Genes involved in metabolic and signalling pathways were altered in childhood obesity. Keywords: disease state analysis

[Organism] Rattus norvegicus, [Experiment type] Expression profiling by array, [Overall design] A single enema of 10mg of TNBS in 50% ethanol was administered to rats at day 0. Samples were recovered at days 2, 5, 7 and 14. According to inflammatory markers (myeloperoxidase activity, body weigh loss, colonic weigh/length ratio) we selected three replicates at each time point for the genimoc analysis, and 6 healthy control rats that received a saline enema. RNA was extracted from homogenized full-thickness colonic tissues in Trizol® reagent (Invitrogen) and purified with RNeasy affinity columns (Qiagen), according to manufacturer´s protocol. The microarray analysis was performed by Progenika Biopharma (Bilbao, Spain) on GeneChip® Rat Genome 230 2.0 Array (Affymetrix). All sample labeling (biotin), hybridization, staining and scanning procedures were carried out using Affimetrix, standard protocols (www.affymetrix.com). Normalization was carried out using Bioconductor sofware (affyPLM package)., [Platforms] GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array, [Relations] BioProject PRJNA102933, 1. GSM235052 Healthy control, replicate 1. [Characteristics] Sprague-Dawley female rats Tissue: full-thickness colon Rat received water, 2. GSM235053 Healthy control, replicate 2. Characteristics Sprague-Dawley female rats Tissue:full-thickness colon Rat received water, 3. GSM235055 Helathy control, replicate 3. [Characteristics] Sprague-Dawley female rats Tissue: full-thickness colon Rat received water, 4.GSM235056 Healthy control, replicate 4. [Characteristics] Sprague-Dawley female rats Tissue: full-thickness colon Rat received water, 5. GSM235057 Healthy control, replicate 5. [Characteristics] Sprague-Dawley female rats Tissue: full-thickness colon Rat received water, 6. GSM235058 Healthy control, replicate 6. [Characteristics] Sprague-Dawley female rats Tissue: full-thickness colon Rat received water, 7. GSM235552 TNBS day 2, replicate 1. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 8. GSM235558 TNBS day 2, replicate 2. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 9. GSM235559 TNBS day 2, replicate 3. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 10. GSM235643 TNBS day 5, replicate 1. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 11. GSM235745 TNBS day 5, replicate 2. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 12. GSM235832 TNBS day 5, replicate 3. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 13. GSM235872 TNBS day 7, replicate 1. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 14. GSM235873 TNBS day 7, replicate 2. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 15. GSM236126 TNBS day 7, replicate 3.[Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 16. GSM236922 TNBS day 14, replicate 1. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 17. GSM236924 TNBS day 14, replicate 2. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, 18. GSM236925 TNBS day 14, replicate 3. [Characteristics] Sprague-Dawley female rat Tissue: full-thickness colon Rat received an enema of 10mg TNBS in 50% ethanol at day 0, Trinitrobenzenesulfonic acid (TNBS) rat colitis is one of the most widely used models of inflammatory bowel disease, a condition whose etiology and pathophysiology are incompletely understood. We have characterized the model at the genomic level following a longitudinal approach.

This corresponds to a series of approximately 40,000 quantum chemical calculations on one single system, the model dipeptide HCO-L-Ala-NH2, with 16 atoms and no charge. The conformational space of this molecule is scanned by defining a regular 12x12 grid from -165º to 165º in 30º steps in the 2D space spanned by its Ramachandran angles phi and psi. The energy at each of these 144-points set is calculated using using the methods RHF and MP2, and a large number of Pople basis sets ranging from 3-21G to 6-311++G(2df,2pd). These methods are combined using the same one for the geometry optimization and the energy calculation (homolevel) or different ones (heterolevel). The dataset contains 274 grids, each one corresponding to a different homo- or heterolevel. This consists of a set of human-readable ASCII files in the output format of Gaussian 03, in folders with descriptive names and compressed using tar and gzip (i.e., you need the GNU applications tar and gzip to uncompress them). Created with Gaussian 03, Revision C.02. Readable with any text editor. This dataset is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/. Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/dbcl/1.0/, This dataset is the basis of an exhaustive published study (see https://digital.csic.es/handle/10261/35334) of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) investigated are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, wss the most accurate PES in the literature at the moment of its publication. The great number of MCs evaluated has allowed us to significantly explore this space and show that the correlation between accuracy and computational cost of the methods is imperfect, thus justifying a systematic search for the combination of features in a MC that is optimal to deal with peptides. Regarding the particular MCs studied, the most important conclusion is that the potentially very cost-saving heterolevel approximation is a very efficient one to describe the whole PES of HCO-L-Ala-NH2. Finally, we show that, although RHF may be used to calculate the geometry if a MP2 single-point energy calculation follows, pure RHF//RHF homolevels are not recommendable for this problem., This work has been supported by the research projects E24/3 and PM048 (Aragón Government), MEC (Spain) FIS2006-12781-C02-01 and MCyT (Spain) FIS2004-05073-C04-01. P. Echenique was supported by a BIFI research contract., Peer reviewed

The item is made of 2 files, of which 1 is the dataset and the other includes a small description of the measured variables.-- Dataset contributed to the Project Carbochange, This dataset gathers discrete measurements of CO2 (pH and alkalinity) and hydrographic variables (salinity, temperature, dissolved oxygen, nitrate, phosphate and silicate) obtained during the cruise P3A22008. carried out in the Strait of Gibraltar from 6 to 12 October 2008, pH was measured spectrophotometrically following the Clayton and Byrne (1993). This method consists on adding a dye solution to the seawater sample, so that the ratio between two absorbances at two different wavelengths is proportional to the sample pH. Alkalinity was measured using an automatic potentiometric titrator Titrando 794 Metrohm, with a Metrohm 6.0232.100 combination glass electrode and a Pt-1000 probe for temperature measurement following the methodology given by Pérez and Fraga (1987). Dissolved oxygen was analyzed following the widely applied Winkler method. Determinations of nitrate, phosphate and silicate were carried out following methods described by Hansen and Grassoff (1983) Salinity and Temperature were recorded with a CTD probe, Proyecto CARBOOCEAN (511176GOCE), y proyectos del Ministerio de Ciencia e Innovación (CTM2005/01091-MAR y CTM2008-05680-C02-01), No

The item is made of 2 files, of which 1 is the dataset and the other include a small description of the measured variables.-- Dataset contributed to the Project Carbochange, This dataset gathers discrete measurements of CO2 (pH and alkalinity) and hydrographic variables (salinity, temperature, dissolved oxygen, nitrate, phosphate and silicate) obtained during the cruise OVIDE 2008 carried out from 6 June to 11 July 2008. pH was measured spectrophotometrically following the Clayton and Byrne (1993). This method consists on adding a dye solution to the seawater sample, so that the ratio between two absorbances at two different wavelengths is proportional to the sample pH. Alkalinity was measured using an automatic potentiometric titrator Titrando 809 Metrohm, with a Metrohm 6.0232.100 combination glass electrode and a Pt-1000 probe for temperature measurement following the methodology given by Pérez and Fraga (1987). Dissolved oxygen was analyzed following the widely applied Winkler method. Determinations of nitrate, phosphate and silicate were carried out following methods described by Hansen and Grassoff (1983) Salinity and Temperature were recorded with a CTD probe, French OVIDE Project supported by CNRS, and CARBOOCEAN (511176GOCE), No

Complementary material, containing the raw data used in the Table and Figure included in this article., Peer reviewed