What types of powdery mildew can infect wheat-barley introgression lines?

Peer reviewe

Model requirements for Biobank Software Systems

Biobanks are essential tools in diagnostics and therapeutics research and development related to personalized medicine. Several international recommendations, standards and guidelines exist that discuss the legal, ethical, technological, and management requirements of biobanks. Today's biobanks are much more than just collections of biospecimens. They also store a huge amount of data related to biological samples which can be either clinical data or data coming from biochemical experiments. A well-designed biobank software system also provides the possibility of finding associations between stored elements. Modern research biobanks are able to manage multicenter sample collections while fulfilling all requirements of data protection and security. While developing several biobanks and analyzing the data stored in them, our research group recognized the need for a well-organized, easy-to-check requirements guideline that can be used to develop biobank software systems. International best practices along with relevant ICT standards were integrated into a comprehensive guideline: The Model Requirements for the Management of Biological Repositories (BioReq), which covers the full range of activities related to biobank development. The guideline is freely available on the Internet for the research community

Spatio-temporal evolution of intraplate strike-slip faulting: the Neogene-Quaternary Kuh-e-Faghan Fault, Central Iran

Central Iran provides an ideal region to study the long-term morphotectonic response to the nucleation and propagation of intraplate faulting. In this study, a multidisciplinary approach that integrates structural and stratigraphic field investigations with apatite (U+Th)/He (AHe) thermochronometry is used to reconstruct the spatio-temporal evolution of the Kuh-e-Faghan Fault (KFF) in northeastern Central Iran. The KFF is a narrow, ca. 80 km long, deformation zone that consists of three main broadly left stepping, E-W trending, dextral fault strands that cut through the Mesozoic-Paleozoic substratum and the Neogene-Quaternary sedimentary cover. The AHe thermochronometry results indicate that the intra-fault blocks along the KFF experienced two major episodes of fault-related exhumation at ~18 Ma and ~4 Ma. The ~18 Ma faulting/exhumation episode is chiefly recorded by the structure and depositional architecture of the Neogene deposits along the KFF. A source-to-sink scenario can be reconstructed for this time frame, where topographic growth caused the synchronous erosion/exhumation of the pre-Neogene units and deposition of the eroded material in the surrounding fault-bounded continental depocenters. Successively, the KFF gradually entered a period of relative tectonic quiescence and, probably, of regional subsidence during which a thick pile of fine-grained onlapping sediments were deposited. This may have caused resetting of the He ages of apatite in the pre-Neogene and the basal Neogene successions. The ~4 Ma faulting episode caused the final exhumation of the fault system, resulting in the current fault zone and topography. The two fault-related exhumation episodes fit with the regional early Miocene collision-enhanced uplift/exhumation, and the late Miocene–early Pliocene widespread tectonic reorganization of the Iranian plateau. The reconstructed long term, spatially and temporally punctuated fault system evolution in intraplate Central Iran during Neogene-Quaternary times may reflect states of far-field stress changes at the collisional boundaries

Association of symptoms of insomnia and sleep parameters among kidney transplant recipients

Objective: Insomnia complaints are frequent among kidney transplant (kTx) recipients and are associated with fatigue, depression, lower quality of life and increased morbidity. However, it is not known if subjective insomnia symptoms are associated with objective parameters of sleep architecture. Thus, we analyze the association between sleep macrostructure and EEG activity versus insomnia symptoms among kTx recipients. Methods: Participants (n1 = 100) were selected from prevalent adult transplant recipients (n0 = 1214) followed at a single institution. Insomnia symptoms were assessed by the Athens Insomnia Scale (AIS) and standard overnight polysomnography was performed. In a subgroup of patients (n2 = 56) sleep microstructure was also analyzed with power spectral analysis. Results: In univariable analysis AIS score was not associated with sleep macrostructure parameters (sleep latency, total sleep time, slow wave sleep, wake after sleep onset), nor with NREM and REM beta or delta activity in sleep microstructure. In multivariable analysis after controlling for covariables AIS score was independently associated with the proportion of slow wave sleep (β = 0.263; CI: 0.026–0.500) and REM beta activity (β = 0.323; CI = 0.041–0.606) (p < 0.05 for both associations). Conclusions: Among kTx recipients the severity of insomnia symptoms is independently associated with higher proportion of slow wave sleep and increased beta activity during REM sleep but not with other parameters sleep architecture. The results suggest a potential compensatory sleep protective mechanism and a sign of REM sleep instability associated with insomnia symptoms among this population

Depressive symptoms are associated with objectively measured sleep parameters in kidney transplant recipients

STUDY OBJECTIVES: Both depression and sleep complaints are very prevalent among kidney transplant (kTx) recipients. However, details of the complex relationship between sleep and depression in this population are not well documented. Thus, we investigated the association between depressive symptoms and sleep macrostructure parameters among prevalent kTx recipients.  METHODS: Ninety-five kTx recipients participated in the study (54 males, mean age 51 ± 13 y, body mass index 26 ± 4 kg/m2, estimated glomerular filtration rate 53 ± 19 ml/min/1.73 m2). Symptoms of depression were assessed by the Center for Epidemiologic Studies - Depression Scale (CES-D). After 1-night polysomnography each recording was visually scored and sleep macrostructure was analyzed.  RESULTS: The CES-D score was significantly associated with the amount of stage 2 sleep (r = 0.20, p 0.05). In multivariable linear regression models the CES-D score was independently associated with the amount of stage 2 sleep (β: 0.205; confidence interval: 0.001-0.409; p = 0.05) and REM latency (β: 0.234; confidence interval: 0.001-0.468; p = 0.05) after adjustment for potential confounders.  CONCLUSIONS: Depressive symptoms among kTx recipients are associated with increased amount of stage 2 sleep and prolonged REM latency. Further studies are needed to confirm our findings and understand potential clinical implications

Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop of barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including based on exomic haplotype states, for genotype-by-environment (G 7E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G 7E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally-adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G 7E effect directions, and the importance of latitudinally-based genic context in the expression of large effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses

pH Modulation of Efflux Pump Activity of Multi-Drug Resistant Escherichia coli: Protection During Its Passage and Eventual Colonization of the Colon

BACKGROUND:Resistance Nodulation Division (RND) efflux pumps of Escherichia coli extrude antibiotics and toxic substances before they reach their intended targets. Whereas these pumps obtain their energy directly from the proton motive force (PMF), ATP-Binding Cassette (ABC) transporters, which can also extrude antibiotics, obtain energy from the hydrolysis of ATP. Because E. coli must pass through two pH distinct environments of the gastrointestinal system of the host, it must be able to extrude toxic agents at very acidic and at near neutral pH (bile salts in duodenum and colon for example). The herein described study examines the effect of pH on the extrusion of ethidium bromide (EB). METHODOLOGY/PRINCIPAL FINDINGS:E. coli AG100 and its tetracycline induced progeny AG100(TET) that over-expresses the acrAB efflux pump were evaluated for their ability to extrude EB at pH 5 and 8, by our recently developed semi-automated fluorometric method. At pH 5 the organism extrudes EB without the need for metabolic energy (glucose), whereas at pH 8 extrusion of EB is dependent upon metabolic energy. Phe-Arg beta-naphtylamide (PAbetaN), a commonly assumed inhibitor of RND efflux pumps has no effect on the extrusion of EB as others claim. However, it does cause accumulation of EB. Competition between EB and PAbetaN was demonstrated and suggested that PAbetaN was preferentially extruded. A K(m) representing competition between PAbetaN and EB has been calculated. CONCLUSIONS/SIGNIFICANCE:The results suggest that E. coli has two general efflux systems (not to be confused with a distinct efflux pump) that are activated at low and high pH, respectively, and that the one at high pH is probably a putative ABC transporter coded by msbA, which has significant homology to the ABC transporter coded by efrAB of Enterococcus faecalis, an organism that faces similar challenges as it makes its way through the toxic intestinal system of the host

Tramtrack Is Genetically Upstream of Genes Controlling Tracheal Tube Size in Drosophila

The Drosophila transcription factor Tramtrack (Ttk) is involved in a wide range of developmental decisions, ranging from early embryonic patterning to differentiation processes in organogenesis. Given the wide spectrum of functions and pleiotropic effects that hinder a comprehensive characterisation, many of the tissue specific functions of this transcription factor are only poorly understood. We recently discovered multiple roles of Ttk in the development of the tracheal system on the morphogenetic level. Here, we sought to identify some of the underlying genetic components that are responsible for the tracheal phenotypes of Ttk mutants. We therefore profiled gene expression changes after Ttk loss- and gain-of-function in whole embryos and cell populations enriched for tracheal cells. The analysis of the transcriptomes revealed widespread changes in gene expression. Interestingly, one of the most prominent gene classes that showed significant opposing responses to loss- and gain-of-function was annotated with functions in chitin metabolism, along with additional genes that are linked to cellular responses, which are impaired in ttk mutants. The expression changes of these genes were validated by quantitative real-time PCR and further functional analysis of these candidate genes and other genes also expected to control tracheal tube size revealed at least a partial explanation of Ttk's role in tube size regulation. The computational analysis of our tissue-specific gene expression data highlighted the sensitivity of the approach and revealed an interesting set of novel putatively tracheal genes