Characterization of the caleosin gene family in the Triticeae

Background The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. Some members of the gene family have been shown to be upregulated by environmental stresses including low water availability and high salinity. Caleosin 3 from wheat has been shown to interact with the α-subunit of the heterotrimeric G proteins, and to act as a GTPase activating protein (GAP). This study characterizes the size and diversity of the gene family in wheat and related species and characterizes the differential tissue-specific expression of members of the gene family. Results A total of 34 gene family members that belong to eleven paralogous groups of caleosins were identified in the hexaploid bread wheat, T. aestivum. Each group was represented by three homeologous copies of the gene located on corresponding homeologous chromosomes, except the caleosin 10, which has four gene copies. Ten gene family members were identified in diploid barley, Hordeum vulgare, and in rye, Secale cereale, seven in Brachypodium distachyon, and six in rice, Oryza sativa. The analysis of gene expression was assayed in triticale and rye by RNA-Seq analysis of 454 sequence sets and members of the gene family were found to have diverse patterns of gene expression in the different tissues that were sampled in rye and in triticale, the hybrid hexaploid species derived from wheat and rye. Expression of the gene family in wheat and barley was also previously determined by microarray analysis, and changes in expression during development and in response to environmental stresses are presented. Conclusions The caleosin gene family had a greater degree of expansion in the Triticeae than in the other monocot species, Brachypodium and rice. The prior implication of one member of the gene family in the stress response and heterotrimeric G protein signaling, points to the potential importance of the caleosin gene family. The complexity of the family and differential expression in various tissues and under conditions of abiotic stress suggests the possibility that caleosin family members may play diverse roles in signaling and development that warrants further investigation

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The Signaling Network of the Caleosins and the Heterotrimeric G Proteins in Arabidopsis thaliana and The Analysis of the Esi3/RCI2/PMP3 and Pirin Gene Families in Triticum aestivum

Plants have complex mechanisms of response to environmental stresses that contribute to stress tolerance. This work is directed at the characterization of four classes of genes that encode proteins involved in the response to environmental stresses: caleosins, the α subunit of heterotrimeric G proteins (GPA1), Pirins and Early-Salt-stress-Induced-3 (Esi3) genes. The work investigates these genes in the model species, Arabidopsis, or the crop specie, wheat. It also characterizes the physical and genetic interaction of members of the caleosins family, GPA1, and Pirin1, to decipher their potential role in signalling pathways related to stress response in plants. The gene families encoding the Pirins and Esi3s were also characterized in hexaploid wheat to investigate possible roles in stress responses. This work reports that the Arabidopsis caleosins RD20/CLO3 and CLO7 interact both physically and genetically with the Gα subunit, GPA1. The interactions were characterized by Bimolecular Fluorescence Complementation and yeast two-hybrid assays. Interactions were enhanced by both calcium and the GTP bound state of GPA1. RD20/CLO3 and GPA1 play a role in hypocotyl elongation in the dark and in leaf morphology. CLO7 and GPA1 play a role in seed germination in response to ABA treatment and osmotic stress. The clo7 gpa1 double mutant is embryo lethal and cannot be recovered. RD20/CLO3 affects root architecture in response to ABA treatment. Both RD20/CLO3 and CLO7 affect flowering time under long day conditions. Members of the Triticum aestivum Esi3 and Pirin gene families were implicated in stress response pathways by their differential expression in response to stress treatment. The Esi3 gene family is comprised of 29 family members with 10 paralogs each with a copy in the A, B and D genome except for Esi3-2 which is missing a B copy. All members of the Esi3 gene family have altered gene expression in response to abiotic and biotic stress conditions. The Pirin gene family is comprised of 18 genes with six paralogous gene copies, each having an A, B and D homeolog. The members of the Pirin gene family have specialized expression and play differing roles in response to abiotic and biotic stress

Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae

Abstract Background Members of the Early Salt Induced 3 (Esi3/RCI2/PMP3) gene family in plants have been shown to be induced in response to both biotic and abiotic stresses and to enhance stress tolerance in both transgenic plants and Saccharomyces cerevisiae. Esi3 was first identified as a salt stress induced gene in the salt tolerant wild wheat grass, Lophopyrum elongatum, and subsequently homologous genes in many other species were found to be members of the gene family. These include Arabidopsis thaliana and Oryza sativa where they are referred to as Rare Cold Inducible 2 (RCI2), and Zea mays where they are referred to as Plasma Membrane Protein 3 (PMP3). This study characterizes the Esi3 family members in Triticum aestivum and explores the tissue specific expression patterns of the gene family members as well as their response to a variety of environmental stresses. Results The Esi3 gene family was found to have a total of 29 family members comprised of ten paralogous groups in the hexaploid T. aestivum. Each paralogous group contains three homeologous copies, one in each of the A, B and D genomes with the exception of Esi3–2 which is missing the B copy. The genes of the Esi3 gene family were also identified in four other monocot species, Aegilops tauschii, Hordeum vulgare, Secale cereale and Sorghum bicolor, and were confirmed or corrected for Brachypodium distachyon, Oryza sativa and Zea mays, as well as the dicot Arabidopsis thaliana. Gene expression of the Esi3s was analyzed using tissue-specific, abiotic and biotic stress RNA-Seq 454 sequence libraries and Affymetrix microarray data for T. aestivum. Conclusions Members of nearly all paralogous groups of the Esi3 genes in T. aestivum have altered gene expression in response to abiotic or biotic stress conditions. In addition, there are modest differences in gene expression among homeologous members of the gene family. This suggests that the Esi3 gene family plays an important role in the plants response to the stresses presented in this study. The Esi3–9 in T. aestivum has a unique N terminal extension placing it into Group III, a new group for the Esi3/RCI2/PMP3 gene family

Reproducibility and validity ELSA-Brasil Food Frequency Questionnaire

Introduction: To investigate the association between diet and health effects in population surveys, it is necessary to have precise tools that allow estimating the habitual consumption of the population. Aim: To evaluate the reproducibility and validity of the ELSA-Brasil food frequency questionnaire (FFQ) to assess macro and micronutrients intake. Material and Methods: We collected dietary information of 281 participants which completed two ELSA-Brasil food frequency questionnaires over a year period and three records. To assess the reproducibility of the FFQ, we compared the macro and micronutrients intake from the two FFQ while to assess the validity, we compared the intakes of FFQ with the mean of three records. The intraclass correlation test (ICC) and agreement percentages of nutrient intake were calculated after categorization by tertiles. Results: ICC coefficients for reproducibility ranged from 0.51 (polyunsaturated fat) to 0.70 (magnesium) while the ICC coefficients for validity ranged from 0.14 to 0.61 for omega 3 and magnesium, respectively. The exact concordances between methods ranged from 37% for omega 3 to 50.2% for magnesium (mean=44.6%). An average disagreement of 13.4% was found. Conclusions: This study suggests that the ELSA-Brasil FFQ is suitable tool to assess dietary intake with a satisfactory reproducibility and relative validity.Introducción: Para investigar la asociación entre dieta y efectos en salud en encuestas poblacionales, es necesario disponer de herramientas precisas que permitan estimar el consumo habitual de la población. Objetivo: Evaluar la reproducibilidad y validez del cuestionario de frecuencia alimentaria (FFQ) del ELSA-Brasil para evaluar la ingesta de macro y micronutrientes. Material y Métodos: Recopilamos información dietética de 281 participantes que completaron dos cuestionarios de frecuencia alimentaria del ELSA-Brasil durante un período de un año y tres registros. Para evaluar la reproducibilidad del FFQ, comparamos la ingesta de macro y micronutrientes de los dos FFQ mientras que, para evaluar la validez, comparamos las ingestas de FFQ con la media de tres registros. La prueba de correlación intraclase (ICC) y los porcentajes de acuerdo de la ingesta de nutrientes se calcularon después de la categorización por tertiles. Resultados: En la evaluación de la reproducibilidad, los coeficientes ICC variaron de 0,51-0,70 para magnesio de grasas poliinsaturadas, respectivamente; en la evaluación de la validez, oscilaron entre 0,14 y 0,61 para omega 3 y magnesio, respectivamente. Las concordancias exactas entre los métodos oscilaron entre el 37% para omega 3 y el 50,2% para magnesio (media=44,6%). Se encontró un desacuerdo promedio del 13,4%. Conclusiones: Este estudio sugiere que ELSA-Brasil FFQ es una herramienta adecuada para evaluar la ingesta dietética con una reproducibilidad satisfactoria y validez relativa

Natural history of KBG syndrome in a large European cohort

Abstract KBG syndrome (KBGS) is characterized by distinctive facial gestalt, short stature and variable clinical findings. With ageing, some features become more recognizable, allowing a differential diagnosis. We aimed to better characterize natural history of KBGS. In the context of a European collaborative study, we collected the largest cohort of KBGS patients (49). A combined array- based Comparative Genomic Hybridization and next generation sequencing (NGS) approach investigated both genomic Copy Number Variants and SNVs. Intellectual disability (ID) (82%) ranged from mild to moderate with severe ID identified in two patients. Epilepsy was present in 26.5%. Short stature was consistent over time, while occipitofrontal circumference (median value: −0.88 SD at birth) normalized over years. Cerebral anomalies, were identified in 56% of patients and thus represented the second most relevant clinical feature reinforcing clinical suspicion in the paediatric age when short stature and vertebral/dental anomalies are vague. Macrodontia, oligodontia and dental agenesis (53%) were almost as frequent as skeletal anomalies, such as brachydactyly, short fifth finger, fifth finger clinodactyly, pectus excavatum/carinatum, delayed bone age. In 28.5% of individuals, prenatal ultrasound anomalies were reported. Except for three splicing variants, leading to a premature termination, variants were almost all frameshift. Our results, broadening the spectrum of KBGS phenotype progression, provide useful tools to facilitate differential diagnosis and improve clinical management. We suggest to consider a wider range of dental anomalies before excluding diagnosis and to perform a careful odontoiatric/ear-nose-throat (ENT) evaluation in order to look for even submucosal palate cleft given the high percentage of palate abnormalities. NGS approaches, following evidence of antenatal ultrasound anomalies, should include ANKRD11

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press