Gametic configuration and inheritance of SSR markers in tetraploid interspecific and intergeneric citrus somatic hybrids : S02P20

Citrus somatic hybridization has become an integral part of citrus improvement programs worldwide. More than 100 somatic hybrids have been created by Cirad. Intra and interspecific somatic hybrids will be used mostly for the triploid scion breeding. Intergeneric somatic hybrids can have a direct application as rootstocks or be used as parents for sexual 'tetrazyg' breeding. To optimize the design of such breeding schemes, it is essential to have knowledge of the inheritance mode in such allotetraploid hybrids. The aim of the present study was to investigate the inheritance (disomic, tetrasomic or intermediate) in a citrus interspecific hybrid (Citrus reticulata x Citrus limon) and an intergeneric somatic hybrid (C. reticulata x Poncirus trifoliata). Two triploid populations were generated using the somatic hybrids as pollinators in crosses with the diploid 'Chandler' pummelo. The triploid progenies were genotyped with SSRs to infer the allelic constitution of the somatic hybrid gametes. A likelihood-based approach was used to estimate for each locus the proportion of disomic versus tetrasomic segregations. For the two somatic hybrids, intermediate inheritance was observed with a major tendency for tetrasomic segregation in the interspecific hybrid, but a tendency for disomic inheritance in the intergeneric hybrid. The implications of the observed inheritance mode for citrus breeding are discussed with special focus on heterozygosity restitution. (Texte intégral

Somatic, but not cognitive-affective, symptoms are associated with reduced heart rate variability in individuals with dysphoria

Background: Somatic, but not cognitive-affective, symptoms of depression have been associated with reduced heart rate variability (HRV), and with poor prognosis in cardiovascular patients. However, factors concomitant with cardiovascular diseases may confound the relationship between somatic symptoms of depression and reduced HRV. Therefore, this study examined whether reduced HRV was differentially associated with cognitive-affective and somatic symptoms of depression in medically healthy individuals with and without dysphoria. Methods: Self-reported cognitive-affective and somatic symptoms as measured with the Beck Depression Inventory-II (BDI-II) questionnaire and time and frequency domain parameters of HRV were collected in 62 medically healthy individuals, of whom 25 with and 37 without dysphoria. Results: Somatic, but not cognitive-affective, symptoms of depression were inversely associated with standard deviation of NN intervals (SDNN) (beta = -0.476, p .24). Conclusions: By showing that the relationship between somatic depressive symptoms and reduced HRV extends to medically healthy individuals with dysphoria, the present findings suggest that this association is independent of factors concomitant with cardiovascular diseases. The present study also suggests that individuals with somatic rather than cognitive-affective subsets of depressive symptoms may be at greater risk for developing cardiovascular diseases

Subtyping somatic tinnitus: a cross-sectional UK cohort study of demographic, clinical and audiological characteristics

Somatic tinnitus is the ability to modulate the psychoacoustic features of tinnitus by somatic manoeuvres. The condition is still not fully understood and further identification of this subtype is essential, particularly for the purpose of establishing protocols for both its diagnosis and treatment. This study aimed to investigate the characteristics of somatic tinnitus within a large UK cohort using a largely unselected sample. We believe this to be relatively unique in comparison to current literature on the topic. This was investigated by using a total of 608 participant assessments from a set of recognised tinnitus and audiology measures. Results from a set of chi-square tests of association found that amongst the individuals with somatic tinnitus, a higher proportion had pulsatile tinnitus (different from heartbeat), were under the age of 40, reported variation in the loudness of their tinnitus and reported temporomandibular joint (TMJ) disorder. The same pattern of results was confirmed using a multivariate analysis of the data based on logistic regression. These findings have strong implications towards the profiling of somatic tinnitus as a distinct subtype of general tinnitus

Somatosensory tinnitus: current evidence and future perspectives

In some individuals, tinnitus can be modulated by specific maneuvers of the temporomandibular joint, head and neck, eyes, and limbs. Neuroplasticity seems to play a central role in this capacity for modulation, suggesting that abnormal interactions between the sensory modalities, sensorimotor systems, and neurocognitive and neuroemotional networks may contribute to the development of somatosensory tinnitus. Current evidence supports a link between somatic disorders and higher modulation of tinnitus, especially in patients with a normal hearing threshold. Patients with tinnitus who have somatic disorders seems to have a higher chance of modulating their tinnitus with somatic maneuvers; consistent improvements in tinnitus symptoms have been observed in patients with temporomandibular joint disease following targeted therapy for temporomandibular disorders. Somatosensory tinnitus is often overlooked by otolaryngologists and not fully investigated during the diagnostic process. Somatic disorders, when identified and treated, can be a valid therapeutic target for tinnitus; however, somatic screening of subjects for somatosensory tinnitus is imperative for correct selection of patients who would benefit from a multidisciplinary somatic approach

Current applications of coffee (Coffea arabica) somatic embryogenesis for industrial propagation of elite heterozygous materials in Central America and Mexico

Of ail the possible micropropagation techniques, it is widely accepted that vegetative propagation by somatic embryogenesis is by far the most promising for rapid, large-scale dissemination of elite individuals. Yet, to date, examples of somatic embryogenesis processes applied on an industrial scale are very few and far between. There are many complications. They usually involve a major genotypic effect, particularly for obtaining embryogenic tissues, or are related to the quality of regenerated somatic embryos, the incidence of somaclonal variation and, more generally, a lack of reproducibility and efficiency at certain stages of the process, leading to production costs that are prohibitive. Research on coffee somatic embryogenesis began at the end of the 1970s at various institutes, including CIRAD. Between 1995 and 2001, CIRAD moved the technique forward from a research laboratory scale to a technique enabling industrial dissemination of extremely promising Coffea arabica F1 hybrids. Over that period, two technological innovations made technology transfer economically feasible: mass production of somatic embryos in temporary immersion bioreactors and the possibility of sowing them directly in the nursery. At the same time, reassuring data were obtained on the genetic conformity of regenerated plants (somaclonal variation frequency < 3%). In 2002, in partnership with the ECOM group, CIRAD decided to transfer the somatic embryogenesis method on an industrial scale to Central America so that four Arabica hybrid clones, that were selected for agroforestry-based farming systems, could be disseminated throughout that part of the world. This article describes the different stages and the difficulties we had to overcome before successful technology transfer could occur in 2010. . It describes one of the first examples of somatic embryogenesis technology applied on a commercial scale. Keywords: Somatic embryogenesis, micropropagation, technological transfer, coffee tree, production costs, clonai conformity, somaclonal variations, in vitro plantlet, nursery (Résumé d'auteur

Tissue culture of oil palm : finding the balance between mass propagation and somaclonal variation

The oil palm (Elaeis guineensis Jacq.) is typically propagated in vitro by indirect somatic embryogenesis, a process in which somatic cells of an explant of choice are, via an intermediate phase of callus growth, induced to differentiate into somatic embryos. The architecture of the oil palm, lacking axillary shoots, does not allow for vegetative propagation. Therefore, somatic embryogenesis is the only alternative to seed propagation, which is hampered by long germination times and low germination rates, for the production of planting material. The current oil palm somatic embryogenesis procedure is associated with several difficulties, which are described in this review. The limited availability of explants, combined with low somatic embryo initiation and regeneration rates, necessitate the proliferation of embryogenic structures, increasing the risk for somaclonal variants such as the mantled phenotype. Several ways to improve the efficiency of the tissue culture method and to reduce the risk of somaclonal variation are described. These include the use of alternative explants and propagation techniques, the introduction of specific embryo maturation treatments and the detection of the mantled abnormality in an early stage. These methods have not yet been fully explored and provide interesting research field for the future. The development of an efficient oil palm micropropagation protocol is needed to keep up with the increasing demand for palm oil in a sustainable way. Mass production of selected, high-yielding palms by tissue culture could raise yields on existing plantations, reducing the need for further expansion of the cultivated area, which is often associated with negative environmental impacts

Internal sensations as a source of fear: exploring a link between hypoxia and flight phobia

Although flight phobia is very common in the general population, knowledge of the underlying mechanisms is limited. The aim of the current study is to determine whether hypoxia is selectively associated with flight anxiety. We wanted to explore levels of oxygen saturation (SpO2) and the associated subjective somatic sensations in flight phobics and controls. The data collected in this study were obtained from 103 participants: 54 had flight phobia, 49 were controls. SpO2 as well as a subjective report of somatic sensations and anxiety were measured during short haul flights, both at ground level and at cruising altitude. Results indicated that both flight phobics and controls showed a comparable clinical significant decrease in SpO2 from sea level to cruising altitude. Next, at ground level the flight phobic group reported more somatic sensations, most likely due to the elevated levels of anxiety at that point. However, at cruising altitude the flight phobic group still reported more somatic sensations while the level of anxiety was no longer significantly different from controls. This finding points to altered symptom perception in flight phobia and stresses the importance of somatic sensations in this particular phobia

ISOWN: accurate somatic mutation identification in the absence of normal tissue controls.

BackgroundA key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison.ResultsIn this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded tissues; we tested our algorithm with both deep targeted and whole-exome sequencing data. Our algorithm correctly classified between 95 and 98% of somatic mutations with F1-measure ranges from 75.9 to 98.6% depending on the tumor type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues).ConclusionsIn this work, we describe the development, implementation, and validation of ISOWN, an accurate algorithm for predicting somatic mutations in cancer tissues in the absence of matching normal tissues. ISOWN is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN

Fast and scalable inference of multi-sample cancer lineages.

Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee