Multivariate analysis of Vitis subgenus Vitis seed morphology

We studied 142 grapevine seed samples belonging to 5 Vitis species, 92 cultivars of Vitis vinifera, 12 feral/wild populations and 4 hybrid rootstock cultivars. Eleven different characters from the seed and one allometric index have been used. Seeds show a wide range of variation in body dimensions, and in other parameters. Two largely differentiated clusters were obtained. Coincidences with previous seed classifications are discussed. Wild extra-European species have smaller seeds. The index breadth/length (STUMMER’s index) doesn’t allow to separate wild grapevines and cultivars. It defines, however, the “wild syndrome” values above 0.8 corresponding to wild extra-European Vitis species, occasionally used as rootstocks. Ferals/wild individuals tend to display smaller berries and plumper pips than their cultivated relatives therefore “looking wild”. The multivariate analysis place together ferals/wild and related cultivars in their respective clusters and does not discriminate a cluster of wild European grapevine.

Anatomical and genetic study of an ancient animal tooth showing brachyodont and hypsodont mixed taxonomical characteristics

A non-human dental piece was found in a Roman Empire tomb dated the 3rd century A.C. in Zaragoza (Spain). The morphology of this piece showed mixed brachyodont (carnivores) and hypsodont (herbivores) characteristics. As a result, the taxonomical assignation of the piece was impossible. Therefore, a protocolbased on the DNA sequence of the cytochrome c oxidase subunit 1 mitochondrial region (COI) was applied. For this purpose, a pair of primers able to amplify thisregion in a large variety of animals was designed. The results point to a species of the Genus Bos (Family Bovidae). This assignation was later confirmed by these quencing of a short fragment of the mitochondrial D-loop region. A complete morphological description of the tooth is presented together with the DNA sequence study and comparison protocol

Identifying environmental risk factors for inflammatory bowel diseases: a Mendelian randomization study

Several studies have examined environmental factors and inflammatory bowel diseases (IBD) using traditional approaches; however, provided results are still conflicting. Our aim was to determine whether lifestyle and nutrient exposures, related to IBD in observational meta-analyses, influence IBD risk using a Mendelian randomization (MR) approach. A two-sample MR approach was applied on summary-level genome-wide association results. Genetic variants strongly associated with measures of tobacco smoking, obesity and fat distribution, physical activity, and blood levels of vitamins and fatty acids were evaluated on genetic data from international IBD consortia including a total of 25,042 IBD cases (12,194 cases of Crohn's disease (CD) and 12,366 cases of ulcerative colitis (UC)) and 34,915 controls. Our results indicated that, among lifestyle exposures, being a smoker was positively associated with CD (OR 1.13, P=0.02), but it was not associated with UC risk (OR 0.99, P=0.88). Body-mass index (BMI) and body fat percentage were positively associated with CD (OR 1.11, P=0.02, per standard deviation (SD) of 4.6 kg/m(2); and OR 1.50, P=3x10(-10), per SD of 6.6%; respectively); while for UC, BMI was inversely associated (OR 0.85, P=5x10(-5); per SD) and body fat percentage showed a OR of 1.11 (P=0.11; per SD). Additionally, among nutrient exposures, omega-3 fatty acids levels were inversely associated with CD (OR 0.67, P=2x10(-6)). Our MR results did not support a protective effect for being a smoker on UC risk; however, they are compatible with a risk effect for higher body fat proportion and a protective role for higher levels of omega-3 fatty acids on CD etiology

An innovative quick solidifying technique for the forensic investigation of brain circulation using addition silicones

Post-mortem study of the brain is extremely relevant to medico-legal autopsies. However, it can be difficult to handle due to its fragility. This article presents a study on the development of an arterial solidifying technique that can be applied to analyze arterial circulation, consequently easing the handling and later diagnosis of diseases in this anatomical site. Vinylpolysiloxane silicone is introduced into the internal carotid arteries until it completely fills the arterial tree, creating a detailed model of the arterial's internal anatomy. This technique is fast, easy to apply and requires no previous tissue fixation. In addition, it allows for further toxicological and pathological tests. In conclusion, this technique represents a simple, sensitive and efficient method to employ in conventional autopsies, which can help in the diagnosis of death

Caracterización genética y de caracteres reproductivos en variedades de vid sin semilla de Armenia

Trabajo presentado en las IV Jornadas del Grupo de Viticultura de la SECH (Sociedad Española de Ciencias Hortícolas), celebrada en Pamplona (España), los días 26 y 28 de octubre de 2022La apirenia de la mayoría de las variedades comerciales de la vid (Vitis vinifera L.) procede de 'Sultanina', una variedad con origen en Asia Menor. El principal objetivo de este trabajo ha sido la caracterización de posibles fuentes alternativas de apirenia en el germoplasma armenio. Se han estudiado 40 accesiones apirenas de las colecciones armenias de vid en Echmiadzin (ARM006) y en Nalbandyan (ARM011), así como de explotaciones privadas de la región de Armavir (Armenia). El análisis fenotípico de bayas se realizó de acuerdo con los descriptores de la OIV, y el análisis genético mediante el estudio de la mutación causal de apirenia en Sultanina en el gen VviAGL11 y del marcador VviAPT3 ligado al locus del sexo. El análisis de viabilidad y morfología de los granos de polen se visualizó por microscopía óptica y electrónica de barrido. El análisis fenotípico de bayas reveló una amplia variación en el peso de las mismas, así como en la formación de rudimentos seminales. Las flores de nueve cultivares son hermafroditas con un alto nivel de viabilidad del polen. La accesión 'Karmir kishmish' se caracterizó por tener flores funcionalmente femeninas con baja viabilidad de polen y se confirmó genéticamente con VviAPT3. El análisis de microscopía mostró que los granos de polen de las flores hermafroditas tienen forma esferoidal con 3 colporaciones y numerosas perforaciones, mientras que el de la variedad 'Karmir kishmish' es también esferoidal, pero acolporado y con menos perforaciones. El análisis genético reveló que todas las accesiones portan la mutación puntual dominante en VviAGL11 que causa la estenospermocarpia en 'Sultanina'. De hecho, el análisis de 7 marcadores SSR y 48 SNPs demostró que todas son descendientes de la misma. Este estudio confirma que las variedades apirenas armenias descienden de 'Sultanina', y motiva la búsqueda de otros determinantes genéticos que causen variación en el contenido de semillas de las uvas para utilizar como fuentes alternativas en programas de mejora de uva de mesa

GCAT|Genomes for life: a prospective cohort study of the genomes of Catalonia

PURPOSE: The prevalence of chronic non-communicable diseases (NCDs) is increasing worldwide. NCDs are the leading cause of both morbidity and mortality, and it is estimated that by 2030, they will be responsible for 80% of deaths across the world. The Genomes for Life (GCAT) project is a long-term prospective cohort study that was designed to integrate and assess the role of epidemiological, genomic and epigenomic factors in the development of major chronic diseases in Catalonia, a north-east region of Spain. PARTICIPANTS: At the end of 2017, the GCAT Study will have recruited 20 000 participants aged 40-65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. The GCAT Study has access to the electronic health records of the Catalan Public Healthcare System. Participants will be followed biannually at least 20 years after recruitment. FINDINGS TO DATE: Among all GCAT participants, 59.2% are women and 83.3% of the cohort identified themselves as Caucasian/white. More than half of the participants have higher education levels, 72.2% are current workers and 42.1% are classified as overweight (body mass index ≥25 and <30 kg/m2). We have genotyped 5459 participants, of which 5000 have metabolome data. Further, the whole genome of 808 participants will be sequenced by the end of 2017. FUTURE PLANS: The first follow-up study started in December 2017 and will end by March 2018. Residences of all subjects will be geocoded during the following year. Several genomic analyses are ongoing, and metabolomic and genomic integrations will be performed to identify underlying genetic variants, as well as environmental factors that influence metabolites

Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

BackgroundDiabetes is an established risk factor for colorectal cancer. However, the mechanisms underlying this relationship still require investigation and it is not known if the association is modified by genetic variants. To address these questions, we undertook a genome-wide gene-environment interaction analysis.MethodsWe used data from 3 genetic consortia (CCFR, CORECT, GECCO; 31,318 colorectal cancer cases/41,499 controls) and undertook genome-wide gene-environment interaction analyses with colorectal cancer risk, including interaction tests of genetics(G)xdiabetes (1-degree of freedom; d.f.) and joint testing of Gxdiabetes, G-colorectal cancer association (2-d.f. joint test) and G-diabetes correlation (3-d.f. joint test).ResultsBased on the joint tests, we found that the association of diabetes with colorectal cancer risk is modified by loci on chromosomes 8q24.11 (rs3802177, SLC30A8 - ORAA: 1.62, 95% CI: 1.34-1.96; ORAG: 1.41, 95% CI: 1.30-1.54; ORGG: 1.22, 95% CI: 1.13-1.31; p-value(3-d.f.): 5.46 x 10(-11)) and 13q14.13 (rs9526201, LRCH1 - ORGG: 2.11, 95% CI: 1.56-2.83; ORGA: 1.52, 95% CI: 1.38-1.68; ORAA: 1.13, 95% CI: 1.06-1.21; p-value(2-d.f.): 7.84 x 10(-09)).DiscussionThese results suggest that variation in genes related to insulin signaling (SLC30A8) and immune function (LRCH1) may modify the association of diabetes with colorectal cancer risk and provide novel insights into the biology underlying the diabetes and colorectal cancer relationship

GCAT|Genomes for life : A prospective cohort study of the genomes of Catalonia

The prevalence of chronic non-communicable diseases (NCDs) is increasing worldwide. NCDs are the leading cause of both morbidity and mortality, and it is estimated that by 2030, they will be responsible for 80% of deaths across the world. The Genomes for Life (GCAT) project is a long-term prospective cohort study that was designed to integrate and assess the role of epidemiological, genomic and epigenomic factors in the development of major chronic diseases in Catalonia, a north-east region of Spain. Participants At the end of 2017, the GCAT Study will have recruited 20 000 participants aged 40-65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. The GCAT Study has access to the electronic health records of the Catalan Public Healthcare System. Participants will be followed biannually at least 20 years after recruitment. Findings to date Among all GCAT participants, 59.2% are women and 83.3% of the cohort identified themselves as Caucasian/white. More than half of the participants have higher education levels, 72.2% are current workers and 42.1% are classified as overweight (body mass index ≥25 and <30 kg/m 2). We have genotyped 5459 participants, of which 5000 have metabolome data. Further, the whole genome of 808 participants will be sequenced by the end of 2017. Future plans The first follow-up study started in December 2017 and will end by March 2018. Residences of all subjects will be geocoded during the following year. Several genomic analyses are ongoing, and metabolomic and genomic integrations will be performed to identify underlying genetic variants, as well as environmental factors that influence metabolites

Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci

Background & aims: The association of genetic variation with tissue-specific gene expression and alternative splicing guides functional characterization of complex trait-associated loci and may suggest novel genes implicated in disease. Here, our aims were as follows: (1) to generate reference profiles of colon mucosa gene expression and alternative splicing and compare them across colon subsites (ascending, transverse, and descending), (2) to identify expression and splicing quantitative trait loci (QTLs), (3) to find traits for which identified QTLs contribute to single-nucleotide polymorphism (SNP)-based heritability, (4) to propose candidate effector genes, and (5) to provide a web-based visualization resource. Methods: We collected colonic mucosal biopsy specimens from 485 healthy adults and performed bulk RNA sequencing. We performed genome-wide SNP genotyping from blood leukocytes. Statistical approaches and bioinformatics software were used for QTL identification and downstream analyses. Results: We provided a complete quantification of gene expression and alternative splicing across colon subsites and described their differences. We identified thousands of expression and splicing QTLs and defined their enrichment at genome-wide regulatory regions. We found that part of the SNP-based heritability of diseases affecting colon tissue, such as colorectal cancer and inflammatory bowel disease, but also of diseases affecting other tissues, such as psychiatric conditions, can be explained by the identified QTLs. We provided candidate effector genes for multiple phenotypes. Finally, we provided the Colon Transcriptome Explorer web application. Conclusions: We provide a large characterization of gene expression and splicing across colon subsites. Our findings provide greater etiologic insight into complex traits and diseases influenced by transcriptomic changes in colon tissue

Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes

Simple Summary Colorectal cancer (CRC) is the third most common cancer in the world. The gut microbiome, which includes a collection of microbes, is a potential modifiable risk factor. The study of the microbiome is complex and many issues remain unsolved despite the scientific efforts that have been recently made. The present study aimed to build a CRC predictive model performing a meta-analyses of previously published shotgun metagenomics data, and to validate it in a new study. For that purpose, 156 participants of a CRC screening program were recruited, with an even distribution of CRCs, high-risk colonic precancerous lesions, and a control group with normal colonic mucosa. We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions. This suggests that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78-0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66-0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41-0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs