A new tool based on faecal stanols can distinguish specific mammalian species in modern and past environments

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Holocene atmospheric dust deposition in NW Spain

This is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this record.Atmospheric dust plays an important role in terrestrial and marine ecosystems, particularly those that are nutrient limited. Despite that most dust originates from arid and semi-arid regions, recent research has shown that past dust events may have been involved in boosting productivity in nutrient-poor peatlands. We investigated dust deposition in a mid-latitude, raised bog, which is surrounded by a complex geology (paragneiss/schist, granite, quartzite and granodiorite). As proxies for dust fluxes, we used accumulation rates of trace (Ti, Zr, Rb, Sr and Y) as well as major (K and Ca) lithogenic elements. The oldest, largest dust deposition event occurred between ~8.6 and ~7.4 ka BP, peaking at ~8.1 ka BP (most probably the 8.2 ka BP event). The event had a large impact on the evolution of the mire, which subsequently transitioned from a fen into a raised bog in ~1500 years. From ~6.7 to ~4.0 ka BP, fluxes were very low, coeval with mid-Holocene forest stability and maximum extent. In the late Holocene, after ~4.0 ka BP, dust events became more prevalent with relatively major deposition at ~3.2–2.5, ~1.4 ka BP and ~0.35–0.05 ka BP, and minor peaks at ~4.0–3.7, ~1.7, ~1.10–0.95 ka BP and ~0.74–0.58 ka BP. Strontium fluxes display a similar pattern between ~11 and ~6.7 ka BP but then became decoupled from the other elements from the mid Holocene onwards. This seems to be a specific signal of the granodiorite batholith, which has an Sr anomaly. The reconstructed variations in dust fluxes bear a strong climatic imprint, probably related to storminess controlled by North Atlantic Oscillation conditions. Complex interactions also arise because of increased pressure from human activities.Natural Environment Research Council (NERC)Consiliencia networkFunding for Consolidation and Structuration of Research Unit

An application of kernel methods to variety identification based on SSR markers genetic fingerprinting

<p>Abstract</p> <p>Background</p> <p>In crop production systems, genetic markers are increasingly used to distinguish individuals within a larger population based on their genetic make-up. Supervised approaches cannot be applied directly to genotyping data due to the specific nature of those data which are neither continuous, nor nominal, nor ordinal but only partially ordered. Therefore, a strategy is needed to encode the polymorphism between samples such that known supervised approaches can be applied. Moreover, finding a minimal set of molecular markers that have optimal ability to discriminate, for example, between given groups of varieties, is important as the genotyping process can be costly in terms of laboratory consumables, labor, and time. This feature selection problem also needs special care due to the specific nature of the data used.</p> <p>Results</p> <p>An approach encoding SSR polymorphisms in a positive definite kernel is presented, which then allows the usage of any kernel supervised method. The polymorphism between the samples is encoded through the Nei-Li genetic distance, which is shown to define a positive definite kernel between the genotyped samples. Additionally, a greedy feature selection algorithm for selecting SSR marker kits is presented to build economical and efficient prediction models for discrimination. The algorithm is a filter method and outperforms other filter methods adapted to this setting. When combined with kernel linear discriminant analysis or kernel principal component analysis followed by linear discriminant analysis, the approach leads to very satisfactory prediction models.</p> <p>Conclusions</p> <p>The main advantage of the approach is to benefit from a flexible way to encode polymorphisms in a kernel and when combined with a feature selection algorithm resulting in a few specific markers, it leads to accurate and economical identification models based on SSR genotyping.</p

Identification of Nicotiana tabacum Linkage Group Corresponding to the Q Chromosome Gene(s) Involved in Hybrid Lethality

BACKGROUND: A linkage map consisting of 24 linkage groups has been constructed using simple sequence repeat (SSR) markers in Nicotiana tabacum. However, chromosomal assignments of all linkage groups have not yet been made. The Q chromosome in N. tabacum encodes a gene or genes triggering hybrid lethality, a phenomenon that causes death of hybrids derived from some crosses. METHODOLOGY/PRINCIPAL FINDINGS: We identified a linkage group corresponding to the Q chromosome using an interspecific cross between an N. tabacum monosomic line lacking the Q chromosome and N. africana. N. ingulba yielded inviable hybrids after crossing with N. tabacum. SSR markers on the identified linkage group were used to analyze hybrid lethality in this cross. The results implied that one or more genes on the Q chromosome are responsible for hybrid lethality in this cross. Furthermore, the gene(s) responsible for hybrid lethality in the cross N. tabacum × N. africana appear to be on the region of the Q chromosome to which SSR markers PT30342 and PT30365 map. CONCLUSIONS/SIGNIFICANCE: Linkage group 11 corresponded to the Q chromosome. We propose a new method to correlate linkage groups with chromosomes in N. tabacum

A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development

Tobacco (Nicotiana tabacum L.) is a species in the large family of the Solanaceae and is important as an agronomic crop and as a model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available that can be used for genome analysis, genetic mapping and breeding. We report here on the development and characterization of 5,119 new and functional microsatellite markers and on the generation of a high-resolution genetic map for the tetraploid tobacco genome. The genetic map was generated using an F2 mapping population derived from the intervarietal cross of Hicks Broadleaf × Red Russian and merges the polymorphic markers from this new set with those from a smaller set previously used to produce a lower density map. The genetic map described here contains 2,317 microsatellite markers and 2,363 loci, resulting in an average distance between mapped microsatellite markers which is less than 2 million base pairs or 1.5 cM. With this new and expanded marker resource, a sufficient number of markers are now available for multiple applications ranging from tobacco breeding to comparative genome analysis. The genetic map of tobacco is now comparable in marker density and resolution with the best characterized genomes of the Solanaceae: tomato and potato

Simultaneous Determination of Various Isothiocyanates by RP-LC Following Precolumn Derivatization with Mercaptoethanol

Numerous isothiocyanates (ITCs) are poorly soluble in water which causes their precipitation in aqueous mobile phases used in reversed phase liquid chromatography (RP-LC), thus impacting the accuracy of the quantification. By comparing the amounts of ITCs injected and released from the column, losses could be estimated at 5–32% depending on polarities and concentrations. Results could be dramatically improved in terms of separation and quantification using RP-LC with a mercaptoethanol precolumn derivatization aimed at avoiding ITCs precipitation. The cancer chemoprotective allyl-ITC and sulforaphane were found in cabbage extracts at 1.2 and 2.7 μg g−1 fresh weight, respectively