Candidate genes for stress response in silver fir (Abies alba Mill.)

The aim of this thesis was the identification and analysis of candidate genes for stress response in silver fir (Abies alba Mill.). This ecologically and economically important forest tree species is native to many mountainous regions of Europe but little is known about its ecological characteristics. Silver fir populations were heavily transformed by human activity, which results in a mismatch between past and current distribution. Recent studies suggest that silver fir can occupy warmer and dryer climates than it currently does. However, the species also suffered considerably during the 1970s and 1980s, including foliar damage, radial growth depression and local diebacks in Germany. This is attributed mainly to the peak in air pollution during this period, especially sulfur dioxide (SO2), which seems to heavily increase drought sensitivity in silver fir. The combination of both stressors, SO2 and drought events, negatively affected silver fir even in regions where drought is usually not a problem. In the context of anthropogenic global climate change that will very likely lead to an increase in temperature in Europe and to more extreme events such as severe drought periods, the question arises, how silver fir will cope with these environmental changes. Given the speed of the predicted changes and the increasing landscape fragmentation, silver fir might not be able to evade it via seed dispersal. As a sessile organism, the only other option is adaptation, which will likely draw from standing genetic variation. To successfully predict the fate of silver fir, especially in the face of global climate change, and to potentially manage populations based on such predictions, the genetic architecture of silver fir in the context of such important stressors as drought and air pollution has to be understood. There exist, however, little genomic resources for silver fir and conifers in general. This is due to their large and complex genomes and the long generational cycle, which makes conifers typical nonmodel species. As such, methods for the identification of the genetic basis of stress response are effectively limited to a candidate gene approach. The candidate gene approach includes the identification of functional candidate genes by measuring differential gene expression between a stressed and a control group. In the context of this thesis, the water content of silver fir seedlings was monitored in a laboratory using a novel terahertz spectroscopy setup. One group of seedlings was regularly irrigated while the other group was drought stressed. Continually measuring the water content allowed to harvest needles from both groups at a time when the water status was comparable between the individuals within each group. A differential expression analysis between the needles from both groups then revealed 296 genes that were significantly up- or down-regulated in response to drought stress. Of those genes, approximately 45% have not been previously described in any organism and are potentially unique to silver fir or conifers in general. However, since only needles of seedlings were analyzed at a specific level of drought stress, the results are limited in scope to the source material and stress intensity and cannot be directly applied to silver fir or drought stress in general. Also, this approach implies a cause-effect relationship between gene expression and a specific level of drought stress. Thus, it is very important that confounding factors are excluded from the experiment. Chlorophyll content in the needles, for example, might change over the course of the monitoring period due to the drought treatment. To test if the chlorophyll content could potentially influence the terahertz signal, chlorophyll was extracted from silver fir needles, in the course of this thesis, and different concentrations were measured using terahertz spectroscopy, showing that chlorophyll content does not influence terahertz monitoring. Another aspect of the candidate gene approach involves the variation within a polymorphic gene and its potential association with the variation in a phenotypic trait. Since the growth depression period of silver fir in the 1970s and 1980s was mostly influenced by the combination of air pollution and drought, in the context of this thesis, genetic variation, in the form of single nucleotide polymorphims (SNPs) in pre-selected genes, was associated with tree-ring derived phenotypes for individual trees in the Bavarian Forest National Park. These so called ’dendrophenotypes’ were measures for resistance, resilience and recovery during the depression period, as well as the drought year 1976. Using general linear models and feature selection techniques based on the machine learning algorithm random forest, 15 out of 103 polymorphic candidate genes for trait variation could be identified. Since the associated dendrophenotyes are potentially adaptively relevant, the variation in this candidate genes could influence the stress coping capability of individual trees. However, this approach is of an observational nature and thus, cause-effect relationships cannot be derived from this type of experiment. The identified SNPs might be the causal variant or physically close to the true causal variant or it might just be a spurious correlation. Further, reliance on advanced statistical techniques can be troublesome, as could be demonstrated in the course of this thesis for a random forest based feature selection technique, developed for genetic association studies in conifers. Replicating this study and evaluating the algorithm, non-uniqueness of the results could be demonstrated, which not only hinders biological interpretation but can severely negatively influence downstream analyses, such as tests for interaction between SNPs. In conclusion, this thesis presents new techniques to add to the current methodology for candidate gene selection and analysis in the stress response of the non-model organism silver fir and other conifer species. Both approaches should be combined, for example by drawing polymorphic candidate genes for trait variation from the pool of functional candidate genes to ensure the involvement of the studied genes in the variation of the trait of interest. Further, the results of this thesis add to the growing molecular resources in silver fir and thereby, hopefully, contribute to the successful prediction and management of this important forest tree species in the face of rapidly changing environmental conditions

On computing the absolute geostrophic velocity spiral

Recently, Stommel and Schott (1977) have proposed a method for computing absolute geostrophic current spirals from observations of the density field alone . Some applications of the method have led to ambiguous results in which the computed spirals have depended on the depth range of the data used...

Thermal feedback on wind-stress as a contributing cause of the Gulf Stream

A simple model is used to explore a feedback mechanism which may be significant in the formation of the Gulf Stream. The feedback operates through the drag coefficient which is a function of the sea-air temperature difference. The model is divided into interior and western boundary regions which are overlaid by an atmosphere with a constant meridional temperature gradient...

How do uncertainties in NCEP R2 and CFSR surface fluxes impact tropical ocean simulations?

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Climate Dynamics 49 (2017): 3327–3344, doi:10.1007/s00382-016-3516-6.NCEP/DOE reanalysis (R2) and Climate Forecast System Reanalysis (CFSR) surface fluxes are widely used by the research community to understand surface flux climate variability, and to drive ocean models as surface forcings. However, large discrepancies exist between these two products, including (1) stronger trade winds in CFSR than in R2 over the tropical Pacific prior 2000; (2) excessive net surface heat fluxes into ocean in CFSR than in R2 with an increase in difference after 2000. The goals of this study are to examine the sensitivity of ocean simulations to discrepancies between CFSR and R2 surface fluxes, and to assess the fidelity of the two products. A set of experiments, where an ocean model was driven by a combination of surface flux component from R2 and CFSR, were carried out. The model simulations were contrasted to identify sensitivity to different component of the surface fluxes in R2 and CFSR. The accuracy of the model simulations was validated against the tropical moorings data, altimetry SSH and SST reanalysis products. Sensitivity of ocean simulations showed that temperature bias difference in the upper 100m is mostly sensitive to the differences in surface heat fluxes, while depth of 20°C (D20) bias difference is mainly determined by the discrepancies in momentum fluxes. D20 simulations with CFSR winds agree with observation well in the western equatorial Pacific prior 2000, but have large negative bias similar to those with R2 winds after 2000, partly because easterly winds over the central Pacific were underestimated in both CFSR and R2. On the other hand, the observed temperature variability is well reproduced in the tropical Pacific by simulations with both R2 and CFSR fluxes. Relative to the R2 fluxes, the CFSR fluxes improve simulation of interannual variability in all three tropical oceans to a varying degree. The improvement in the tropical Atlantic is most significant and is largely attributed to differences in surface winds

Survey of e-learning implementation and faculty support strategies in a cluster of mid-European medical schools

Background The use of electronic learning formats (e-learning) in medical education is reported mainly from individual specialty perspectives. In this study, we analyzed the implementation level of e-learning formats and the institutional support structures and strategies at an institutional level in a cluster of mid-European medical schools. Methods A 49-item online questionnaire was send to 48 medical schools in Austria, Germany and Switzerland using SurveyMonkey®. Data were collected between February and September of 2013 and analyzed using quantities, statistical and qualitative means. Results The response rate was 71 %. All schools had implemented e-learning, but mainly as an optional supplement to the curriculum. E-learning involved a wide range of formats across all disciplines. Online learning platforms were used by 97 % of the schools. Full-time e-learning staff was employed by 50 %, and these had a positive and significant effect on the presence of e-learning in the corresponding medical schools. In addition, 81 % offered training programs and qualifications for their teachers and 76 % awarded performance-oriented benefits, with 17 % giving these for e-learning tasks. Realization of e-learning offers was rewarded by 33 %, with 27 % recognizing this as part of the teaching load. 97 % would use curriculum- compatible e-learning tools produced by other faculties. Conclusions While all participating medical schools used e-learning concepts, this survey revealed also a reasonable support by institutional infrastructure and the importance of staff for the implementation level of e-learning offerings. However, data showed some potential for increasing tangible incentives to motivate teachers to engage in further use of e-learning. Furthermore, the use of individual tools and the distribution of e-learning presentations in various disciplines were quite inhomogeneous. The willingness of the medical schools to cooperate should be capitalized for the future, especially concerning the provision of e-learning tools and concepts

Multiple elements in human β-globin locus control region 5′ HS 2 are involved in enhancer activity and position independent, transgene expression

The human β-globin Locus Control Region (LCR) has two important activities. First, the LCR opens a 200 kb chromosomal domain containing the human ε-, γ- and β-giobin genes and, secondly, these sequences function as a powerful enhancer of ε-, γ- and β-globin gene expression. Erythrold-specific, DNase I hypersensitive sites (HS) mark sequences that are critical for LCR activity. Previous experiments demonstrated that a 1.9 kb fragment containing the 5′ HS 2 site confers position-independent expression in transgenic mice and enhances human β-giobin gene expression 100-fold. Further analysis of this region demonstrates that multiple sequences are required for maximal enhancer activity; deletion of SP1, NF-E2, GATA-1 or USF binding sites significantly decrease β-globin gene expression. In contrast, no single site is required for position- independent transgene expression; all mice with site- specific mutations in 5′ HS 2 express human β-globin mRNA regardless of the site of transgene integration. Apparently, multiple combinations of protein binding sites in 5′ HS 2 are sufficient to prevent chromosomal position effects that inhibit transgene expression. © 1994 Oxford University Press

The Spatio-Temporal Structure of Spiral-Defect Chaos

We present a study of the recently discovered spatially-extended chaotic state known as spiral-defect chaos, which occurs in low-Prandtl-number, large-aspect-ratio Rayleigh-Benard convection. We employ the modulus squared of the space-time Fourier transform of time series of two-dimensional shadowgraph images to construct the structure factor ${S}({\vec k},\omega )$. This analysis is used to characterize the average spatial and temporal scales of the chaotic state. We find that the correlation length and time can be described by power-law dependences on the reduced Rayleigh number ${\epsilon}$. These power laws have as yet no theoretical explanation.Comment: RevTex 38 pages with 13 figures. Due to their large size, some figures are stored as separate gif images. The paper with included hi-res eps figures (981kb compressed, 3.5Mb uncompressed) is available at ftp://mobydick.physics.utoronto.ca/pub/MBCA96.tar.gz An mpeg movie and samples of data are also available at ftp://mobydick.physics.utoronto.ca/pub/. Paper submitted to Physica

A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes

Recent genomic and metagenomic studies have led to a dramatic expansion of the known diversity of nucleocytoplasmic large DNA viruses (NCLDVs) of eukaryotes, which include giant viruses of protists and important pathogens of vertebrates, such as poxviruses. However, the characterization of viruses from nonmodel hosts still lags behind. We sequenced the complete genomes of three viruses infecting crustaceans, the Caribbean spiny lobster, demon shrimp, and European shore crab. These viruses have the smallest genomes among the known NCLDVs, with losses of many core genes, some of which are shared with iridoviruses. The deterioration of the transcription apparatus is compatible with microscopic and ultrastructural observations indicating that these viruses replicate in the nucleus of infected cells rather than in the cytoplasm. Phylogenomic analysis indicates that these viruses are sufficiently distinct from all other NCLDVs to justify the creation of a separate family, for which we propose the name “Mininucleoviridae” (i.e., small viruses reproducing in the cell nucleus).Panulirus argus virus 1 (PaV1) is the only known virus infecting the Caribbean spiny lobster (Panulirus argus) from the Caribbean Sea. Recently, related viruses, Dikerogammarus haemobaphes virus 1 (DhV1) and Carcinus maenas virus 1 (CmV1), have been detected in the demon shrimp (Dikerogammarus haemobaphes) and the European shore crab (Carcinus maenas), respectively, from sites in the United Kingdom. The virion morphology of these crustacean viruses is similar to that of iridoviruses. However, unlike iridoviruses and other nucleocytoplasmic large DNA viruses (NCLDVs), these viruses complete their morphogenesis in the host cell nucleus rather than in the cytoplasm. To date, these crustacean viruses have remained unclassified due to a lack of genomic data. Using an Illumina MiSeq sequencer, we sequenced the complete genomes of PaV1, CmV1, and DhV1. Comparative genome analysis shows that these crustacean virus genomes encode the 10 hallmark proteins previously described for the NCLDVs of eukaryotes, strongly suggesting that they are members of this group. With a size range of 70 to 74 kb, these are the smallest NCLDV genomes identified to date. Extensive gene loss, divergence of gene sequences, and the accumulation of low-complexity sequences reflect the extreme degradation of the genomes of these “minimal” NCLDVs rather than any direct relationship with the NCLDV ancestor. Phylogenomic analysis supports the classification of these crustacean viruses as a distinct family, “Mininucleoviridae,” within the pitho-irido-Marseille branch of the NCLDVs