Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene

Background DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). Results We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Conclusions Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover ~200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach.

Gray matter network differences between behavioral variant frontotemporal dementia and Alzheimer's disease

We set out to study whether single-subject gray matter (GM) networks show disturbances that are specific for Alzheimer's disease (AD; n = 90) or behavioral variant frontotemporal dementia (bvFTD; n = 59), and whether such disturbances would be related to cognitive deficits measured with mini-mental state examination and a neuropsychological battery, using subjective cognitive decline subjects as reference. AD and bvFTD patients had a lower degree, connectivity density, clustering, path length, betweenness centrality, and small world values compared with subjective cognitive decline. AD patients had a lower connectivity density than bvFTD patients (F = 5.79, p = 0.02; mean ± standard deviation bvFTD 16.10 ± 1.19%; mean ± standard deviation AD 15.64 ± 1.02%). Lasso logistic regression showed that connectivity differences between bvFTD and AD were specific to 23 anatomical areas, in terms of local GM volume, degree, and clustering. Lower clustering values and lower degree values were specifically associated with worse mini-mental state examination scores and lower performance on the neuropsychological tests. GM showed disease-specific alterations, when comparing bvFTD with AD patients, and these alterations were associated with cognitive deficits

Exhaled metabolite patterns to identify recent asthma exacerbations

Asthma is a chronic respiratory disease that can lead to exacerbations, defined as acute episodes of worsening respiratory symptoms and lung function. Predicting the occurrence of these exacerbations is an important goal in asthma management. The measurement of exhaled breath by electronic nose (eNose) may allow for the monitoring of clinically unstable asthma and exacerbations. However, data on its ability to perform this is lacking. We aimed to evaluate whether eNose could identify patients that recently had asthma exacerbations. We performed a cross-sectional study, measuring exhaled breath using the SpiroNose in adults with a physician-reported diagnosis of asthma. Patients were randomly divided into a training (n = 252) and validation (n = 109) set. For the analysis of eNose signals, principal component (PC) and linear discriminant analysis (LDA) were performed. LDA, based on PC1-4, reliably discriminated between patients who had a recent exacerbation from those who had not (training receiver operating characteristic (ROC)–area under the curve (AUC) = 0.76,95% CI 0.69–0.82), (validation AUC = 0.76, 95% CI 0.64–0.87). Our study showed that, exhaled breath analysis using eNose could accurately identify asthma patients who recently had an exacerbation, and could indicate that asthma exacerbations have a specific exhaled breath pattern detectable by eNose

Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs)

Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration – leading to Endogenous ParaRetroViruses, EPRVs – by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21–24 nt and 18–30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs

Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments

Persistence of parental-reported asthma at early ages:A longitudinal twin study

Background: Currently, we cannot predict whether a pre-school child with asthma-like symptoms will have asthma at school age. Whether genetic information can help in this prediction depends on the role of genetic factors in persistence of pre-school to school-age asthma. We examined to what extent genetic and environmental factors contribute to persistence of asthma-like symptoms at ages 3 to asthma at age 7 using a bivariate genetic model for longitudinal twin data. Methods: We performed a cohort study in monozygotic and dizygotic twins from the Netherlands Twin Register (NTR, n = 21,541 twin pairs). Bivariate genetic models were fitted to longitudinal data on asthma-like symptoms reported by parents at age 3 and 7 years to estimate the contribution of genetic and environmental factors. Results: Bivariate genetic modeling showed a correlation on the liability scale between asthma-like symptoms at age 3 and asthma at age 7 of 0.746 and the contribution of genetics was estimated to be 0.917. The genetic analyses indicated a substantial influence of genetic factors on asthma-like symptoms at ages 3 and 7 (heritability 80% and 90%, respectively); hence, contribution of environmental factors was low. Persistence was explained by a high (rg = 0.807) genetic correlation. Conclusion: Parental-reported asthma-like symptoms at age 3 and asthma at age 7 are highly heritably. The phenotype of asthma-like symptoms at age 3 and 7 was highly correlated and mainly due to heritable factors, indicating high persistence of asthma development over ages 3 and 7

Early life antibiotic exposure is associated with an increased risk of atopic eczema and hay fever

Background: Several studies suggested that early life exposure to antibiotics is associated with an increased risk of developing allergies later in life, but results are inconsistent. In this study we aimed to systematically review and quantify the relationship between early life exposure to antibiotics and the risk of atopic eczema (dermatitis) or hay fever (allergic rhinitis). Method: PubMed and Web of Science databases were searched for observational studies published from January 1966 through November 11, 2015. Studies were included that assessed the association between antibiotic consumption during the first 2 years of life and the risk of eczema or hay fever later in life. Separate metaanalyses were performed to assess the risk estimates for cohort studies, cross sectional studies and case control studies. Furthermore, in subgroup analyses the effect of child's age at the time of antibiotic use/diagnosis of allergies, and the number of courses of antibiotic treatments have been analyzed. Overall pooled estimates of the odds ratios (ORs) were obtained using fixed or random-effects models. Results: Twenty-two studies (including 394 517 patients) were selected to study the risk of eczema and 23 studies (including 256 609 patients) to study the risk of hay fever. In all separate meta-analyses of the distinct study designs, those who were exposed to antibiotics early in life were found to have a statistically significantly increased risk of eczema and hay fever. The summary OR for risk of eczema were 1.24 (95% CI, 1.09-1.41; I2: 60.0%) in the meta-analyses of the cohort studies (n = 50 824); 1.41 (95% CI, 1.33-1.49; I2: 0.0%) in the cross sectional studies (n = 217 752), and 1.15 (95% CI, 1.01- 1.42; I2: 79.5%) in the case control studies (n = 125 941). The summary OR for risk of hay fever were 1.18 (95% CI, 1.01-1.37; I2: 74.3%) in the cohort studies (n = 46 540); 1.56 (95% CI, 1.29-1.90; I2: 63.6%) in cross sectional studies (n = 27 608), and 1.14 (95% CI, 1.04-1.26; I2: 64.8%) in the case control studies (n = 182 461). In subgroup analyses, there was no statistically significant effect of the child's age at time of antibiotic use as well as the time of allergy diagnosis on these associations. The association was stronger if patients had been treated with ≥2 courses compared with one course of antibiotics both for eczema and for hay fever. Conclusion: Early life exposure to antibiotics is related to an increased risk of both atopic eczema and hay fever later in life