Biological Strata Research Articles

Merging Genomics and Transcriptomics for Predicting Fusarium Head Blight Resistance in Wheat.

Genomic selection with genome-wide distributed molecular markers has evolved into a well-implemented tool in many breeding programs during the last decade. The resistance against Fusarium head blight (FHB) in wheat is probably one of the most thoroughly studied systems within this framework. Aside from the genome, other biological strata like the transcriptome have likewise shown some potential in predictive breeding strategies but have not yet been investigated for the FHB-wheat pathosystem. The aims of this study were thus to compare the potential of genomic with transcriptomic prediction, and to assess the merit of blending incomplete transcriptomic with complete genomic data by the single-step method. A substantial advantage of gene expression data over molecular markers has been observed for the prediction of FHB resistance in the studied diversity panel of breeding lines and released cultivars. An increase in prediction ability was likewise found for the single-step predictions, although this can mostly be attributed to an increased accuracy among the RNA-sequenced genotypes. The usage of transcriptomics can thus be seen as a complement to already established predictive breeding pipelines with pedigree and genomic data, particularly when more cost-efficient multiplexing techniques for RNA-sequencing will become more accessible in the future.

The bones beneath the streets: drifting through London’s Quaternary

This article reflects on a Situationist dérive in Central London, which mobilised a creative engagement with the city’s Quaternary history (the last 2.6 million years). The aim was to animate paleoecological knowledge in the resistant, opaque and frenetic environment of a dense urban centre. This brief excursion into an alternative London is offered as a model for contemporary drifting that stretches out beyond our immediate situation to connect to successive geological and biological strata, reframing experiences of the urban environment through shifting scales and chronologies. The Situationists had declared ‘sous les pavés, la plage!’ (under the paving stones, there is a beach!), evoking the playful space of possibility behind the veneer of the city’s systems and structures. This drift aimed to search even deeper, encountering spectral inhabitations revealed by the bones beneath the streets. The article argues that uncovering these hidden ecologies has the potential to counter the urban prevalence of spectacular representations of wildlife and develop an eco-politics of co-existence.

Beyond Genomic Prediction: Combining Different Types of omics Data Can Improve Prediction of Hybrid Performance in Maize.

The ability to predict the agronomic performance of single-crosses with high precision is essential for selecting superior candidates for hybrid breeding. With recent technological advances, thousands of new parent lines, and, consequently, millions of new hybrid combinations are possible in each breeding cycle, yet only a few hundred can be produced and phenotyped in multi-environment yield trials. Well established prediction approaches such as best linear unbiased prediction (BLUP) using pedigree data and whole-genome prediction using genomic data are limited in capturing epistasis and interactions occurring within and among downstream biological strata such as transcriptome and metabolome. Because mRNA and small RNA (sRNA) sequences are involved in transcriptional, translational and post-translational processes, we expect them to provide information influencing several biological strata. However, using sRNA data of parent lines to predict hybrid performance has not yet been addressed. Here, we gathered genomic, transcriptomic (mRNA and sRNA) and metabolomic data of parent lines to evaluate the ability of the data to predict the performance of untested hybrids for important agronomic traits in grain maize. We found a considerable interaction for predictive ability between predictor and trait, with mRNA data being a superior predictor for grain yield and genomic data for grain dry matter content, while sRNA performed relatively poorly for both traits. Combining mRNA and genomic data as predictors resulted in high predictive abilities across both traits and combining other predictors improved prediction over that of the individual predictors alone. We conclude that downstream "omics" can complement genomics for hybrid prediction, and, thereby, contribute to more efficient selection of hybrid candidates.

Omics-based hybrid prediction in maize.

Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction. Yet, predicting traits from parents to progeny has not been addressed by a combination of "omics" data. Here, we evaluate several "omics" predictors-genomic, transcriptomic and metabolic data-measured on parent lines at early developmental stages and demonstrate that the integration of transcriptomic with genomic data leads to higher success rates in the correct prediction of untested hybrid combinations in maize. Despite the high predictive ability of genomic data, transcriptomic data alone outperformed them and other predictors for the most complex heterotic trait, dry matter yield. An eQTL analysis revealed that transcriptomic data integrate genomic information from both, adjacent and distant sites relative to the expressed genes. Together, these findings suggest that downstream predictors capture physiological epistasis that is transmitted from parents to their hybrid offspring. We conclude that the use of downstream "omics" data in prediction can exploit important information beyond structural genomics for leveraging the efficiency of hybrid breeding.

Interaction of Antidepressant Drug, Clomipramine, with Model and Biological Stratum Corneum Membrane as Studied by Electron Paramagnetic Resonance

The interactions of tricyclic antidepressant drug, clomipramine (CLO), with pig ear stratum corneum (SC) and model membranes were investigated by electron paramagnetic resonance (EPR) spin labeling to get some insight into the possible application of this drug in transdermal delivery. The changes in membrane characteristics caused by CLO in the regions that are close to the water-lipid interfaces and the central parts of the membranes were searched. The experimental results were supported by computer simulation of EPR spectra, which showed heterogeneity of the membranes composed of regions with different fluidity characteristics. CLO was effective in both parts of the layers, indicating intercalation of the drug into model membranes as well as into the pig ear SC. Introduction of various molar ratios of CLO caused a decrease in the order parameter and an increase in the rotational diffusion of nitroxide moiety in different membrane regions as well as an increase in the polarity of spin probe environment. It also changed the number of resolved spectral components, which reflects the heterogeneity of the membrane. The fluidizing effect of CLO on pig ear SC throughout the whole membrane layers indicates that CLO penetrates into the SC, which is important for its transdermal delivery.

Nietzsche's Genealogy of Morality and the changing boundaries of medicine, psychiatry and psychiatric and mental health nursing practice: a slave revolt?

The main constructions in Nietzsche's On the Genealogy of Morality (1994) are employed in order to explore the changes in mental health care that have been recently taking place. Characterized by boundaries that define the objectivity of scientific method, the biological stratum or the area of concern (disease and the disembodied being) and the professional distance that is maintained in the healthcare encounter, the noble morality of contemporary allopathic (Western) mental health care practice appears to be being challenged, in an act of ressentiment, by the slave morality of society, inverting values and beliefs that have previously been held. Mental health care paternalism may be in the process of giving way to consumer sovereignty, patient participation in decision making and the re-discovery of the embodied being at the centre of the healthcare encounter. Nietzsche warns that the dominance of slave morality and the inversion of moral values (what was a quality that was held by the nobles and regarded as good) - that is, objectivity and mental health care paternalism - becomes bad; and what was a quality held by the slaves and regarded as bad - subjectivity - becomes good, may ultimately be detrimental to the advancement of society.

Medicine’s Nature and Goals: Nietzsche’s Genealogy of Morality and the Changing Boundaries of Medical Practice

Nietzsch’s On the Genealogy of Morality (1994) is used to explore recent changes in medical practice. Characterized by boundaries that define scientific objectivity, the biological stratum or the area of focus and concern (disease and the disembodied being), and the professional distance that is maintained in the healthcare encounter, the noble morality of contemporary medicine is being challenged in an act of ressentiment by the society’s slave morality that is inverting values and beliefs currently or previously held. Medical paternalism is in the process of giving way to consumer sovereignty, participation in decision-making, and the rediscovery of the embodied being. Nietzsche warns that dominant slave morality and the inversion of moral values may ultimately be detrimental to the advancement of man.

FT-Raman spectroscopic analysis of an Antarctic endolith

The FT-Raman spectra of an Antarctic endolith from the LTER site at Lake Hoare are reported. The specimen provides an unusual occurrence of endolithic colonization of an igneous rock substratum, which analyses as microcline feldspar. The presence of aragonite in the red biological stratum and calcite in a fissure of the rock which has not been subjected to colonization can be attributed to the penetration of calcareous deposits from shallow ground water in an earlier environment in the Dry Valleys. The green biological layer is composed of chlorophyll and β-carotene. Comparison with previous Raman spectroscopic work on endoliths in sedimentary Beacon sandstone is effected.

Fine‐layer depth relationships of lakewater chemistry, planktonic algae and photosynthetic bacteria in meromictic Lake Fidler, Tasmania

SUMMARY. Use of a multi‐column thin‐layer pneumatic sampler and modified analytic procedures has enabled resolutions of chemical and biological strata at 2.5 or 5.0 cm depth intervals. Examination of meromictic Lake Fidler, Tasmania, indicates the presence of a thin, intense stratum of bacteriochlorohyll d in the upper monimolimnion, associated with a discrete stratum of Chlorobium cf. limicola at the microaerobic interface between the oxygenated and sulphide‐rich zones. Algae included small populations of Chlorophyceae, Chrysophyceae, Bacillariophyceae and Cryptophyceae. Bacteria included microaerophils and obligate anaerobes, pigmented and colourless, in well‐defined strata in the upper monimolimnion. A population of the microcrustacean Calamoecia tasmanica tasmanica was present in the mixolimnion. Chaoborus larvae were concentrated within the Chlorobium layer. The chemical profile of Lake Fidler was stable, with a chemocline constant in position relative to the lake bottom. The surface water levels rose and fell through a distance of 1m in conjunction with heavy rainfall in the rainforest, and with river level variation, but had no measurable effect on the absolute position of the chemocline. Marked heterogeneity of dissolved substances at depths in the vicinity of bacteria suggested endogenous influence on pH and gelbstoff (‘gilvin’ in Australia). Downwelling light attenuation was influenced primarily by gelbstoff (‘gilvin’) in the mixolimnion, with only red light (peak at 700 nm) measurable below 2 m. Light was absorbed mainly by Chlorobium in the monimolimnion, and was unmeasurable deeper than 3 m. The absorption spectrum of the bacteriochlorophyll d in vivo, with a maximum absorbance at 721 nm, corresponds with the available downwelling light penetrating the mixolimnion to the Chlorobium layer.