proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/

Jardins per a la salut

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia. Assignatura: Botànica farmacèutica. Curs: 2014-2015. Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són el recull de les fitxes botàniques de 128 espècies presents en el Jardí Ferran Soldevila de l’Edifici Històric de la UB. Els treballs han estat realitzats manera individual per part dels estudiants dels grups M-3 i T-1 de l’assignatura Botànica Farmacèutica durant els mesos de febrer a maig del curs 2014-15 com a resultat final del Projecte d’Innovació Docent «Jardins per a la salut: aprenentatge servei a Botànica farmacèutica» (codi 2014PID-UB/054). Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pels professors de l’assignatura. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica. També s’ha pretès motivar els estudiants a través del retorn de part del seu esforç a la societat a través d’una experiència d’Aprenentatge-Servei, deixant disponible finalment el treball dels estudiants per a poder ser consultable a través d’una Web pública amb la possibilitat de poder-ho fer in-situ en el propi jardí mitjançant codis QR amb un smartphone

The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome

Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive web-based survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features

Análisis funcional de proteínas de respuesta a estrés expresadas diferencialmente en bacterias endosimbióticas en asociación con distintos hospedadores

In the Rhizobium-legume symbiosis, sophisticated plant- and bacterial-dependent mechanisms lead to the establishment of the symbiotic form of bacteria (bacteroid) that fixes nitrogen within root nodules. Comparative proteomics between bacteroids induced by Rhizobium leguminosarum bv. viciae UPM791 (Rlv UPM791) in pea and lentil nodules allowed to identify a list of over 100 rhizobial proteins expressed with a host-dependent variation. One of the most relevant group of proteins potentially involved in the host adaptation were the small Heat Shock Proteins (sHsp), chaperones that stabilize unfolded proteins produced in the cell under stress conditions. In order to analyse the functional role of these proteins in the differential symbiosis adaptation, one sHsp over-expressed in pea (protein 252), and other over-expressed in lens (protein 851) were chosen for study. Mutants affected on each of the proteins showed a moderate decrease of symbiotic performance in pea plants. The structural modelization of both proteins was consistent with the information available about the structures, including their potential ability to form oligomers, wich is crucial for their potential chaperone activity. The regulation of the expression of these sHsps has been studied by the construction of promoter-lacZ fusions, performing assays with different stressors agents such as temperature, low oxygen, ethanol, high salinity, and hypochlorite. The results revealed a microaerobiosis-dependent expression of 252’s promoter. In contrast, relevant induction was not shown in the 851’s promoter. Symbiotic induction was also analysed by measuring ß-galactosidase activity in pea and lens bacteroids. Finally, plasmid-based tools to study the function of these proteins were developed by incorporating a taurine-dependent inducible promoter and a C-terminal affinity tag to the corresponding genes. The funtionality of the inducible promoter present in these plasmids was confirmed in free living cells and in bacteroids. Furthermore, the protein 851 was detected by inmunoblotting in free living strains induced by taurine, as well as in bacteroids

Análisis funcional de proteínas de respuesta a estrés expresadas diferencialmente en bacterias endosimbióticas en asociación con distintos hospedadores

In the Rhizobium-legume symbiosis, sophisticated plant- and bacterial-dependent mechanisms lead to the establishment of the symbiotic form of bacteria (bacteroid) that fixes nitrogen within root nodules. Comparative proteomics between bacteroids induced by Rhizobium leguminosarum bv. viciae UPM791 (Rlv UPM791) in pea and lentil nodules allowed to identify a list of over 100 rhizobial proteins expressed with a host-dependent variation. One of the most relevant group of proteins potentially involved in the host adaptation were the small Heat Shock Proteins (sHsp), chaperones that stabilize unfolded proteins produced in the cell under stress conditions. In order to analyse the functional role of these proteins in the differential symbiosis adaptation, one sHsp over-expressed in pea (protein 252), and other over-expressed in lens (protein 851) were chosen for study. Mutants affected on each of the proteins showed a moderate decrease of symbiotic performance in pea plants. The structural modelization of both proteins was consistent with the information available about the structures, including their potential ability to form oligomers, wich is crucial for their potential chaperone activity. The regulation of the expression of these sHsps has been studied by the construction of promoter-lacZ fusions, performing assays with different stressors agents such as temperature, low oxygen, ethanol, high salinity, and hypochlorite. The results revealed a microaerobiosis-dependent expression of 252’s promoter. In contrast, relevant induction was not shown in the 851’s promoter. Symbiotic induction was also analysed by measuring ß-galactosidase activity in pea and lens bacteroids. Finally, plasmid-based tools to study the function of these proteins were developed by incorporating a taurine-dependent inducible promoter and a C-terminal affinity tag to the corresponding genes. The funtionality of the inducible promoter present in these plasmids was confirmed in free living cells and in bacteroids. Furthermore, the protein 851 was detected by inmunoblotting in free living strains induced by taurine, as well as in bacteroids

Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria

Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs.This research has been supported by grants PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE (to J.H.-C.), BIO2016-76779-P (to T.K.), AGL2017-82492-C2-1-R (to C.R.), and RTI2018-095222-B-I00 (to E.L.-S.) from the Ministerio de Ciencia, Innovación y Universidades, Spain, as well as grant P18-FR-1621 (to T.K.) from the Junta de Andalucía. C.S.-L. was supported by the FPU program (FPU19/06635, MICINN-Spain), and J.P.C.-V. by the FPI program (BES-2016-076452, MINECO-Spain)

Supplemental Material, Suppl_Fig_2_RSc_300ppi - Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells

<p>Supplemental Material, Suppl_Fig_2_RSc_300ppi for Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells by Nuria López-Pérez, Claudia Gil-Sanchis, Hortensia Ferrero, Amparo Faus, Ana Díaz, Antonio Pellicer, Irene Cervelló, and Carlos Simón in Reproductive Sciences</p

Supplemental Material, Suppl_Fig1_25.01.18_300PPI - Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells

<p>Supplemental Material, Suppl_Fig1_25.01.18_300PPI for Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells by Nuria López-Pérez, Claudia Gil-Sanchis, Hortensia Ferrero, Amparo Faus, Ana Díaz, Antonio Pellicer, Irene Cervelló, and Carlos Simón in Reproductive Sciences</p

Supplemental Material, Suppl_Fig3_25.01.18_300PPI - Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells

<p>Supplemental Material, Suppl_Fig3_25.01.18_300PPI for Human Endometrial Reconstitution From Somatic Stem Cells: The Importance of Niche-Like Cells by Nuria López-Pérez, Claudia Gil-Sanchis, Hortensia Ferrero, Amparo Faus, Ana Díaz, Antonio Pellicer, Irene Cervelló, and Carlos Simón in Reproductive Sciences</p

Correction

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