ρ-MtreeRing: A graphical user interface for X-ray microdensity analysis

Producción CientíficaWood microdensitometry provides an integrated measurement of inter and intra-annual changes in wood anatomy and lignification. Although it can be acquired through a wide array of techniques, X-ray-based techniques are still the standard. Conversion of a grayscale X-ray image to density and annual ring boundaries delimitation is performed through image analysis software. Proprietary software has dominated these applications, albeit Free Open Source Software (FOSS) has been developed recently. We present ρ-MtreeRing, a user-friendly FOSS that streamlines the entire microdensitometry analysis process through a graphical user interface based on Shiny R Software without any programming knowledge. We compared the results of this program with the most widely used commercial software (WinDendro), showing the validity of the results. ρ-MtreeRing can be personalized and developed by the microdensitometry research community.Junta de Castilla y León (VA171P20)Ministerio de Ciencia e Innovación y Ministerio de Universidades grant number CGL2017-87309-P (MGH PRE2018-084106) and project PROWARM (PID2020-118444GA-I00)Universidad Politécnica de Madrid (through Project RP200060107)Centro de Recursos Hídricos para la Agricultura y la Minería (ANID/FONDAP/15130015

Immune and spermatogenesis-related loci are involved in the development of extreme patterns of male infertility

We conducted a genome-wide association study in a large population of infertile men due to unexplained spermatogenic failure (SPGF). More than seven million genetic variants were analysed in 1,274 SPGF cases and 1,951 unaffected controls from two independent European cohorts. Two genomic regions were associated with the most severe histological pattern of SPGF, defined by Sertoli cell-only (SCO) phenotype, namely the MHC class II gene HLA-DRB1 (rs1136759, P = 1.32E-08, OR = 1.80) and an upstream locus of VRK1 (rs115054029, P = 4.24E-08, OR = 3.14), which encodes a protein kinase involved in the regulation of spermatogenesis. The SCO-associated rs1136759 allele (G) determines a serine in the position 13 of the HLA-DR beta 1 molecule located in the antigen-binding pocket. Overall, our data support the notion of unexplained SPGF as a complex trait influenced by common variation in the genome, with the SCO phenotype likely representing an immune-mediated condition. A GWAS in a large case-control cohort of European ancestry identifies two genomic regions, the MHC class II gene HLA-DRB1 and an upstream locus of VRK1, that are associated with the most severe phenotype of spermatogenic failure

Hongos. Ecología y biodiversidad en ecosistemas litorales de Huelva

Los hongos son un grupo biológico muy diversificado y con gran importancia en el funcionamiento de los ecosistemas: descomposición de la materia orgánica, establecimiento de relaciones de tipo mutualista con la vegetación (micorrizas), hábitat necesario para la reproducción de muchos insectos, alimento para la fauna o incidencia, cada vez mayor, de los hongos parásitos en relación con la conservación del arbolado en el bosque mediterráneo, entre otros. Este capítulo se centra en la biodiversidad fúngica y su importancia en el funcionamiento de los ecosistemas terrestres onubenses, aspecto que ha permanecido hasta la fecha sumido en una importante laguna de conocimiento, usando como ejemplo 70 especies diferentes de hongos (aunque se citan un total de 292 especies distribuidas por los diferentes órdenes y las principales familias de este reino), seleccionadas entre las más representativas y/o singulares de la comarca del litoral onubense

ρ-MtreeRing: A Graphical User Interface for X-ray Microdensity Analysis

Wood microdensitometry provides an integrated measurement of inter and intra-annual changes in wood anatomy and lignification. Although it can be acquired through a wide array of techniques, X-ray-based techniques are still the standard. Conversion of a grayscale X-ray image to density and annual ring boundaries delimitation is performed through image analysis software. Proprietary software has dominated these applications, albeit Free Open Source Software (FOSS) has been developed recently. We present ρ-MtreeRing, a user-friendly FOSS that streamlines the entire microdensitometry analysis process through a graphical user interface based on Shiny R Software without any programming knowledge. We compared the results of this program with the most widely used commercial software (WinDendro), showing the validity of the results. ρ-MtreeRing can be personalized and developed by the microdensitometry research community

Peptone from casein, an antagonist of nonribosomal peptide synthesis: a case study of pedopeptins produced by Pedobacter lusitanus NL19

Novel natural products are urgently needed to address the worldwide incidence of bacterial resistance to antibiotics. Extreme environments are a major source of novel compounds with unusual chemical structures. Pedobacter lusitanus NL19 is a new bacterial species that was isolated from one such environment and which produces compounds with potent activity against relevant microorganisms in the clinical, food, veterinary and aquaculture areas. The production of antimicrobials by P. lusitanus NL19 was identified in tryptic soy agar (TSA), but not in its equivalent broth (TSB). It was observed that in TSB medium a high concentration of casein peptone (PC) repressed the production of antibacterial compounds. HPLC, MS and MS/MS spectra with de novo sequencing revealed that the bioactivity of P. lusitanus NL19 was due to the production of pedopeptins. Hence, biosynthesis of pedopeptins is inhibited by high concentrations of PC in the broth medium. Furthermore, a nonribosomal peptide synthetase (NRPS) gene cluster was identified in the genome of NL19 encoding the biosynthesis of the peptides. qPCR analysis confirmed that the transcription of these genes is repressed in cells cultivated in high concentrations of PC. It is shown that pedopeptins are nonribosomal peptides with a broad-spectrum activity, including against Gram-positive and Gram-negative bacteria and yeasts.publishe

Intronic variation of the SOHLH2 gene confers risk to male reproductive impairment

Objective: To evaluate whether SOHLH2 intronic variation contributes to the genetic predisposition to male infertility traits, including severe oligospermia (SO) and different nonobstructive azoospermia (NOA) clinical phenotypes. Design: Genetic association study. Setting: Not applicable. Patient(s): Five hundred five cases (455 infertile patients diagnosed with NOA and 50 with SO) and 1,050 healthy controls from Spain and Portugal. Intervention(s): None. Main outcome measure(s): Genomic DNA extraction from peripheral blood mononuclear cells, genotyping of the SOHLH2 polymorphisms rs1328626 and rs6563386 using the TaqMan allelic discrimination technology, case-control association analyses using logistic regression models, and exploration of functional annotations in publicly available databases. Result(s): Evidence of association was observed for both rs6563386 with SO and rs1328626 with unsuccessful sperm retrieval after testicular sperm extraction (TESE-) in the context of NOA. A dominant effect of the minor alleles was suggested in both associations, either when the subset of patients with the manifestation were compared against the control group (rs6563386/SO: P=.021, odds ratio [OR] = 0.51; rs1328626/TESE-: P=.066, OR = 1.46) or against the group of patients without the manifestation (rs6563386/SO: P=.014, OR = 0.46; rs1328626/TESE-: P=.012, OR = 2.43). The haplotype tests suggested a combined effect of both polymorphisms. In silico analyses evidenced that this effect could be due to alteration of the isoform population. Conclusion(s): Our data suggest that intronic variation of SOHLH2 is associated with spermatogenic failure. The genetic effect is likely caused by different haplotypes of rs6563386 and rs1328626, which may predispose to SO or TESE- depending on the specific allelic combination.info:eu-repo/semantics/publishedVersio

Next generation flow for highly sensitive and standardized detection of minimal residual disease in multiple myeloma

Flow cytometry has become a highly valuable method to monitor minimal residual disease (MRD) and evaluate the depth of complete response (CR) in bone marrow (BM) of multiple myeloma (MM) after therapy. However, current flow-MRD has lower sensitivity than molecular methods and lacks standardization. Here we report on a novel next generation flow (NGF) approach for highly sensitive and standardized MRD detection in MM. An optimized 2-tube 8-color antibody panel was constructed in five cycles of design-evaluation-redesign. In addition, a bulk-lysis procedure was established for acquisition of ⩾107 cells/sample, and novel software tools were constructed for automatic plasma cell gating. Multicenter evaluation of 110 follow-up BM from MM patients in very good partial response (VGPR) or CR showed a higher sensitivity for NGF-MRD vs conventional 8-color flow-MRD -MRD-positive rate of 47 vs 34% (P=0.003)-. Thus, 25% of patients classified as MRD-negative by conventional 8-color flow were MRD-positive by NGF, translating into a significantly longer progression-free survival for MRD-negative vs MRD-positive CR patients by NGF (75% progression-free survival not reached vs 7 months; P=0.02). This study establishes EuroFlow-based NGF as a highly sensitive, fully standardized approach for MRD detection in MM which overcomes the major limitations of conventional flow-MRD methods and is ready for implementation in routine diagnostics.This work has been supported by the International Myeloma Foundation-Black Swan Research Initiative, the Red Temática de Investigación Cooperativa en Cáncer (RTICC); grant SA079U14 from the Consejería de Educación, Junta de Castilla y León, Valladolid, Spain and; grant DTS15/00119 from Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Madrid, Spain.Peer Reviewe