Screening of sugar beet pre-breeding populations and breeding lines for resistance to Ditylenchus dipsaci penetration and reproduction

Ditylenchus dipsaci is an economically important plant-parasitic nematode affecting European sugar beets. To date, no sugar beet cultivars carrying resistance against D. dipsaci are available to farmers. To find potentially resistant sugar beet lines restricting reproduction and penetration of D. dipsaci, three consecutive in vivo bioassays were carried out. The first experiment determined the penetration rate of D. dipsaci in 79 breeding lines and 14 pre-breeding populations. Based on these results, D. dipsaci penetration and reproduction resistance of eight genotypes was intensively investigated. It could be demonstrated that none of the genotypes showed resistance towards D. dipsaci. However, a high variation of the penetration rate by D. dipsaci was observed among the genotypes. The breeding line ‘DIT_119’ effectively reduced D. dipsaci penetration (34.4 ± 8.8 nematodes/plant at 22 days post-planting) compared to the susceptible control (109.0 ± 16.9) while ensuring a yield comparable to non-inoculated plants. However, the breeding line ‘DIT_119’ did not reduce D. dipsaci reproduction. The paternal line of the cultivar BERETTA KWS, demonstrating a high tolerance to D. dipsaci crown rot symptoms, did not reduce penetration and reproduction. Thus, no correlation can be established between reduced penetration rates, reproduction, and tolerance to D. dipsaci. This study provides an essential basis for the development of resistant sugar beet cultivars to D. dipsaci. The variations observed among genotypes now need to be confirmed with larger-scale screenings

150 years Heterodera schachtii: A historical review of the early work

Mitte des 19. Jahrhunderts kam der Rübenanbau im damaligen Mitteldeutschland nahezu zum Erliegen. Die Suche nach den Ursachen der sogenannten Rübenmüdigkeit führte im Jahr 1859 zur Entdeckung des Rübenzystennematoden Heterodera schachtii durch den Botaniker Hermann Schacht. Obwohl sich Schacht recht intensiv mit der Morphologie und Biologie des Tieres befasste und ihm vermutlich bewusst war, dass es sich hierbei um eine neue Art handelte, vermied er es, dem Tier einen Namen zu geben. Dies holte Adolf Schmidt aus Aschersleben nach, indem er das Tier zu Ehren seines Entdeckers Heterodera schachtii nannte. Heterodera schachtii war der erste pflanzenparasitäre Nematode, der als Schaderreger unterirdischer Pflanzenorgane beschrieben wurde. Aufgrund seiner wirtschaftlichen Bedeutung für den Rübenanbau stand von Beginn an neben der Biologie vor allem die Entwicklung von Bekämpfungsmaßnahmen im Vordergrund des Forschungsinteresses. Hier ist es vor allem dem unermüdlichen Engagement und der intensiven Versuchstätigkeit von Prof. Julius Kühn aus Halle zu verdanken, dass innerhalb weniger Jahre Verfahren zur Vermeidung und Bekämpfung des Rübenzystennematoden erfolgreich in der Praxis etabliert wurden. Kühn zeigte, dass die Rübenmüdigkeit mit recht einfachen Mitteln verhindert werden konnte, dass solchen Methoden aber arbeits- und betriebswirtschaftliche Anforderungen entgegenstanden. Somit tragen intensive Rübenfruchtfolgen bis heute dazu bei, dass H. schachtii in gemäßigten Klimaregionen weltweit einer der wirtschaftlich bedeutendsten Schadnematoden ist. Anlässlich des 150jährigen Jubiläums der Entdeckung von H. schachtii sollen in diesem historischen Überblick die frühen Arbeiten zu diesem Nematoden vorgestellt werden, die in vielen Aspekten auch heute noch von hoher Aktualität sind.In the middle of the 1900 s, the production of sugarbeets severely declined in Central Germany. In 1859, the botanist Hermann Schacht discovered the sugar beet cyst nematode, Heterodera schachtii while searching for the cause of the observed “beet weariness”. Schacht intensively studied the morphology and biology of this animal; he probably was aware that he dealt with a new species but he avoided naming it. Adolf Schmidt (1871) of Aschersleben corrected this neglect and named the animal Heterodera schachtii in honor of its discoverer. Heterodera schachtii was the first plant-parasitic nematode described as feeding on below-ground plant parts. From the beginning and because of the nematode’s economic importance, the primary objectives of studies were focused on the development of management strategies in addition to investigations of its biology. Foremost due to the tireless efforts and intensive experimentation of Professor Julius Kühn of Halle, methods of avoidance and management strategies for the sugar beet cyst nematode were implemented in practical agriculture. Kühn demonstrated that fairly simple methods mitigated beet weariness but these were not always economically and logistically feasible. Therefore, H. schachtii remains among the most damaging plant-parasitic nematodes in moderate climates worldwide. In recognition of the 150-year anniversary of the discovery of H. schachtii, early works on this nematode are presented in this historical review to outline the implications of these for dealing with the sugar beet cyst nematode

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells

PROM1 is the gene encoding prominin-1 or CD133, an important cell surface marker for the isolation of both normal and cancer stem cells. PROM1 transcripts initiate at a range of transcription start sites (TSS) associated with distinct tissue and cancer expression profiles. Using high resolution Cap Analysis of Gene Expression (CAGE) sequencing we characterize TSS utilization across a broad range of normal and developmental tissues. We identify a novel proximal promoter (P6) within CD133+ melanoma cell lines and stem cells. Additional exon array sampling finds P6 to be active in populations enriched for mesenchyme, neural stem cells and within CD133+ enriched Ewing sarcomas. The P6 promoter is enriched with respect to previously characterized PROM1 promoters for a HMGI/Y (HMGA1) family transcription factor binding site motif and exhibits different epigenetic modifications relative to the canonical promoter region of PROM1

Co-exposure to urban particulate matter and aircraft noise adversely impacts the cerebro-pulmonary-cardiovascular axis in mice

Worldwide, up to 8.8 million excess deaths/year have been attributed to air pollution, mainly due to the exposure to fine particulate matter (PM). Traffic-related noise is an additional contributor to global mortality and morbidity. Both health risk factors substantially contribute to cardiovascular, metabolic and neuropsychiatric sequelae. Studies on the combined exposure are rare and urgently needed because of frequent co-occurrence of both risk factors in urban and industrial settings. To study the synergistic effects of PM and noise, we used an exposure system equipped with aerosol generator and loud-speakers, where C57BL/6 mice were acutely exposed for 3d to either ambient PM (NIST particles) and/or noise (aircraft landing and take-off events). The combination of both stressors caused endothelial dysfunction, increased blood pressure, oxidative stress and inflammation. An additive impairment of endothelial function was observed in isolated aortic rings and even more pronounced in cerebral and retinal arterioles. The increase in oxidative stress and inflammation markers together with RNA sequencing data indicate that noise particularly affects the brain and PM the lungs. The combination of both stressors has additive adverse effects on the cardiovascular system that are based on PM-induced systemic inflammation and noise-triggered stress hormone signaling. We demonstrate an additive upregulation of ACE-2 in the lung, suggesting that there may be an increased vulnerability to COVID-19 infection. The data warrant further mechanistic studies to characterize the propagation of primary target tissue damage (lung, brain) to remote organs such as aorta and heart by combined noise and PM exposure

Systematic Functional Analysis of Bicaudal-D Serine Phosphorylation and Intragenic Suppression of a Female Sterile Allele of BicD

Protein phosphorylation is involved in posttranslational control of essentially all biological processes. Using mass spectrometry, recent analyses of whole phosphoproteomes led to the identification of numerous new phosphorylation sites. However, the function of most of these sites remained unknown. We chose the Drosophila Bicaudal-D protein to estimate the importance of individual phosphorylation events. Being involved in different cellular processes, BicD is required for oocyte determination, for RNA transport during oogenesis and embryogenesis, and for photoreceptor nuclei migration in the developing eye. The numerous roles of BicD and the available evidence for functional importance of BicD phosphorylation led us to identify eight phosphorylation sites of BicD, and we tested a total of 14 identified and suspected phosphoserine residues for their functional importance in vivo in flies. Surprisingly, all these serines turned out to be dispensable for providing sufficient basal BicD activity for normal growth and development. However, in a genetically sensitized background where the BicDA40V protein variant provides only partial activity, serine 103 substitutions are not neutral anymore, but show surprising differences. The S103D substitution completely inactivates the protein, whereas S103A behaves neutral, and the S103F substitution, isolated in a genetic screen, restores BicDA40V function. Our results suggest that many BicD phosphorylation events may either be fortuitous or play a modulating function as shown for Ser103. Remarkably, amongst the Drosophila serines we found phosphorylated, Ser103 is the only one that is fully conserved in mammalian BicD

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

<p>Abstract</p> <p>Background</p> <p>The addition of an acetyl group to protein N-termini is a widespread co-translational modification. NatB is one of the main N-acetyltransferases that targets a subset of proteins possessing an N-terminal methionine, but so far only a handful of substrates have been reported. Using a yeast <it>nat3Δ </it>strain, deficient for the catalytic subunit of NatB, we employed a quantitative proteomics strategy to identify NatB substrates and to characterize downstream effects in <it>nat3Δ</it>.</p> <p>Results</p> <p>Comparing by proteomics WT and <it>nat3Δ </it>strains, using metabolic ¹⁵N isotope labeling, we confidently identified 59 NatB substrates, out of a total of 756 detected acetylated protein N-termini. We acquired in-depth proteome wide measurements of expression levels of about 2580 proteins. Most remarkably, NatB deletion led to a very significant change in protein phosphorylation.</p> <p>Conclusions</p> <p>Protein expression levels change only marginally in between WT and <it>nat3Δ</it>. A comparison of the detected NatB substrates with their orthologous revealed remarkably little conservation throughout the phylogenetic tree. We further present evidence of post-translational N-acetylation on protein variants at non-annotated N-termini. Moreover, analysis of downstream effects in <it>nat3Δ </it>revealed elevated protein phosphorylation levels whereby the kinase Snf1p is likely a key element in this process.</p

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Hydromechanical stress in aerated stirred tanks

Turbulence intensity, or hydromechanical stress, is a controlling parameter in manyindustrially relevant processes that are operated in aerated stirred tanks. These processes areoften characterized by intense aeration and agitation, particularly in the fermentationindustries. Measurement of hydromechanical stress under conditions of intense aeration andagitation is extremely difficult. Very few data on turbulence characteristics exist due to alack of measurement techniques. Therefore, this thesis focused on three main topics: (1) thedevelopment of a measurement technique for hydromechanical stress in aerated stirredtanks, (2) the investigation of the influence of aeration on hydromechanical stress and (3)the characterization of the influence of geometry and scale on hydromechanical stress inaerated stirred tanks.A new measurement method was developed that is based on the well established correlationof maximum stable drop size of a break-up controlled dispersion with hydromechanicalstress. The continuous and dispersed phase properties were selected to be able for the firsttime to apply this principle to aerated operating conditions. This was achieved mainly byapplying a dilute dispersion, a low ionic strength and by incorporating a dispersed phase,paraffin oil, with a negative spreading coefficient. The negative spreading coefficientprevents coalescence due to drop-bubble interactions for aerated operating conditions.This new method was applied to investigate the influence of aeration on hydromechanicalstress for a broad range of aerated and unaerated operating conditions in a 3 m3 reactor.Results from drop dispersion experiments with two different setups of 6-bladed Rushtonturbine impellers with diameters of d = 0.41 m (d/DR = 0.34, setup B-1) and d = 0.51 m(d/DR = 0.43, setup B-3) in a 3 impeller configuration were presented. The results fromexperiments without aeration were well in agreement with the existing literature on dropdispersion. The results from experiments with aeration indicated a strong attenuation ofturbulence intensity in stirred tank reactors by the presence of air. The ratio betweenmaximum and volume-averaged energy dissipation rate, φ, was reduced by aeration by 64 %for the d/DR = 0.34 impeller setup (B-1) and by 52 % for the d/DR = 0.43 impeller setup (B-3) when compared with unaerated operating conditions on the basis of equal volumetricpower input. The value of the aeration rate had no measurable effect in the range of aerationrates applied, which was between 0.1 vvm and 1 vvm.The method was then applied in a broad range of reactor scales (50 L, 3 m3 and 40 m3volume), impeller geometries (Rushton turbines and an Ekato Phasejet/Combijetcombination) and operating conditions to investigate the influence of geometry and scale onhydromechanical stress. Comparison of data between the different scales showed that thereis a scale effect that results in higher values for φ in larger reactors. This behaviour is notcovered by the classic theory of turbulent drop dispersion but is in good agreement with thetheory of turbulence intermittency. The data for all impeller configurations and all aerationrates for the three scales correlated very well when calculated values for φ based on themeasured values for dmax were used to calculate the maximum local energy dissipation rate.Most of the data was within 20 % around the theoretical prediction from the classic theoryof drop dispersion when these values for φ were used. A correlation of the data for all scalesand all impeller configurations in the form φ = 2.3·(φunaerated)0.34·(DR)0.543 was suggested thatsuccessfully models the influence of scale and impeller geometry on φ for aerated operatingconditions. Results for an Ekato Phasejet/Combijet impeller setup showed that thiscorrelation can also be applied successfully to estimate hydromechanical stress for impellergeometries other than Rushton impellers.The measurement method and the data presented in this thesis represent an important stepforward in the characterization of hydromechanical stress in stirred tanks under aeratedoperating conditions. The newly developed measurement method can be applied in thefuture to characterize further agitator and reactor designs under process relevant operatingconditions which was frequently not possible in the past due to a lack of measurementtechniques. The correlation for φ developed in this work can be beneficially used forapproximate calculations of hydromechanical stress for geometries for which experimentaldata is not available. In combination with further important process parameters like masstransfer characteristics and mixing characteristics of impeller setups, characteristics ofhydromechanical stress can be incorporated in reactor and process optimization in a morerelevant manner than possible before

Hydromechanical stress in aerated stirred tanks

Turbulence intensity, or hydromechanical stress, is a controlling parameter in manyindustrially relevant processes that are operated in aerated stirred tanks. These processes areoften characterized by intense aeration and agitation, particularly in the fermentationindustries. Measurement of hydromechanical stress under conditions of intense aeration andagitation is extremely difficult. Very few data on turbulence characteristics exist due to alack of measurement techniques. Therefore, this thesis focused on three main topics: (1) thedevelopment of a measurement technique for hydromechanical stress in aerated stirredtanks, (2) the investigation of the influence of aeration on hydromechanical stress and (3)the characterization of the influence of geometry and scale on hydromechanical stress inaerated stirred tanks.A new measurement method was developed that is based on the well established correlationof maximum stable drop size of a break-up controlled dispersion with hydromechanicalstress. The continuous and dispersed phase properties were selected to be able for the firsttime to apply this principle to aerated operating conditions. This was achieved mainly byapplying a dilute dispersion, a low ionic strength and by incorporating a dispersed phase,paraffin oil, with a negative spreading coefficient. The negative spreading coefficientprevents coalescence due to drop-bubble interactions for aerated operating conditions.This new method was applied to investigate the influence of aeration on hydromechanicalstress for a broad range of aerated and unaerated operating conditions in a 3 m3 reactor.Results from drop dispersion experiments with two different setups of 6-bladed Rushtonturbine impellers with diameters of d = 0.41 m (d/DR = 0.34, setup B-1) and d = 0.51 m(d/DR = 0.43, setup B-3) in a 3 impeller configuration were presented. The results fromexperiments without aeration were well in agreement with the existing literature on dropdispersion. The results from experiments with aeration indicated a strong attenuation ofturbulence intensity in stirred tank reactors by the presence of air. The ratio betweenmaximum and volume-averaged energy dissipation rate, φ, was reduced by aeration by 64 %for the d/DR = 0.34 impeller setup (B-1) and by 52 % for the d/DR = 0.43 impeller setup (B-3) when compared with unaerated operating conditions on the basis of equal volumetricpower input. The value of the aeration rate had no measurable effect in the range of aerationrates applied, which was between 0.1 vvm and 1 vvm.The method was then applied in a broad range of reactor scales (50 L, 3 m3 and 40 m3volume), impeller geometries (Rushton turbines and an Ekato Phasejet/Combijetcombination) and operating conditions to investigate the influence of geometry and scale onhydromechanical stress. Comparison of data between the different scales showed that thereis a scale effect that results in higher values for φ in larger reactors. This behaviour is notcovered by the classic theory of turbulent drop dispersion but is in good agreement with thetheory of turbulence intermittency. The data for all impeller configurations and all aerationrates for the three scales correlated very well when calculated values for φ based on themeasured values for dmax were used to calculate the maximum local energy dissipation rate.Most of the data was within 20 % around the theoretical prediction from the classic theoryof drop dispersion when these values for φ were used. A correlation of the data for all scalesand all impeller configurations in the form φ = 2.3·(φunaerated)0.34·(DR)0.543 was suggested thatsuccessfully models the influence of scale and impeller geometry on φ for aerated operatingconditions. Results for an Ekato Phasejet/Combijet impeller setup showed that thiscorrelation can also be applied successfully to estimate hydromechanical stress for impellergeometries other than Rushton impellers.The measurement method and the data presented in this thesis represent an important stepforward in the characterization of hydromechanical stress in stirred tanks under aeratedoperating conditions. The newly developed measurement method can be applied in thefuture to characterize further agitator and reactor designs under process relevant operatingconditions which was frequently not possible in the past due to a lack of measurementtechniques. The correlation for φ developed in this work can be beneficially used forapproximate calculations of hydromechanical stress for geometries for which experimentaldata is not available. In combination with further important process parameters like masstransfer characteristics and mixing characteristics of impeller setups, characteristics ofhydromechanical stress can be incorporated in reactor and process optimization in a morerelevant manner than possible before