Solvation Properties of Persistent Organic Pollutants and the Relationship to the Bioconcentration Factor

Persistent organic pollutants (POPs) are a class of substances that can cause major health issues in humans and other animals alike. They are difficult to track through the environment and even more difficult to remove. One of the ways in which we can learn more about these compounds is through the bioconcentration factor (BCF). Little work has been done to differentiate the effects of POP stereoisomers and degradation products on human populations, flora, and fauna. For this work, the selected POPs included Aldrin and related compounds, Chlordane and related compounds, Endosulfan and related compounds, and Hexabromocyclododecane. To learn more about the BCF of the selected compounds, the SMD solvent model was used to find the octanol-water partition coefficient (Kow) and the olive oil-water partition coefficient (Kvow). The basis set used was 6-31G (d) and the B3LYP density functional. A linear regression was performed to investigate the potential relationship between the Kv/ow and BCF. Other molecules with known BCF values were also used to strengthen the regression. This regression showed a potential correlation between the Kv/ow and the BCF that would be strengthened by more information about the BCF of POPs

Magnetic circular dichroism in the 2p4d x-ray emission of EuO

Magnetic circular dichroism is observed for ferromagnetic EuO (T C 569 K) in the b2,15 fluorescence at incident photon energies resonant with the 2p 3/2 excitation. The dichroism is dominated by exchange interac-tion between the localized 4 f electrons and the final state 4d core hole. The spectral shapes obtained by atomic multiplet calculations for the 2p4d emission show good agreement with the experimental data

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing

Wittkop T, Baumbach J, Lobo FP, Rahmann S. Large scale clustering of protein sequences with FORCE - a layout based heuristic for weighted cluster editing. BMC Bioinformatics. 2007;8(1): 396.Background: Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different strategies, have been published to attack this problem. Today, new sequencing technologies provide huge amounts of sequence data that has to be efficiently clustered with constant or increased accuracy, at increased speed. Results: We advocate that the model of weighted cluster editing, also known as transitive graph projection is well-suited to protein clustering. We present the FORCE heuristic that is based on transitive graph projection and clusters arbitrary sets of objects, given pairwise similarity measures. In particular, we apply FORCE to the problem of protein clustering and show that it outperforms the most popular existing clustering tools ( Spectral clustering, TribeMCL, GeneRAGE, Hierarchical clustering, and Affinity Propagation). Furthermore, we show that FORCE is able to handle huge datasets by calculating clusters for all 192 187 prokaryotic protein sequences ( 66 organisms) obtained from the COG database. Finally, FORCE is integrated into the corynebacterial reference database CoryneRegNet. Conclusion: FORCE is an applicable alternative to existing clustering algorithms. Its theoretical foundation, weighted cluster editing, can outperform other clustering paradigms on protein homology clustering. FORCE is open source and implemented in Java. The software, including the source code, the clustering results for COG and CoryneRegNet, and all evaluation datasets are available at http://gi.cebitec.uni-bielefeld.de/comet/force/

Crop adaptation to climate change as a consequence of long-term breeding

Major global crops in high-yielding, temperate cropping regions are facing increasing threats from the impact of climate change, particularly from drought and heat at critical developmental timepoints during the crop lifecycle. Research to address this concern is frequently focused on attempts to identify exotic genetic diversity showing pronounced stress tolerance or avoidance, to elucidate and introgress the responsible genetic factors or to discover underlying genes as a basis for targeted genetic modification. Although such approaches are occasionally successful in imparting a positive effect on performance in specific stress environments, for example through modulation of root depth, major-gene modifications of plant architecture or function tend to be highly context-dependent. In contrast, long-term genetic gain through conventional breeding has incrementally increased yields of modern crops through accumulation of beneficial, small-effect variants which also confer yield stability via stress adaptation. Here we reflect on retrospective breeding progress in major crops and the impact of long-term, conventional breeding on climate adaptation and yield stability under abiotic stress constraints. Looking forward, we outline how new approaches might complement conventional breeding to maintain and accelerate breeding progress, despite the challenges of climate change, as a prerequisite to sustainable future crop productivity.Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347Justus-Liebig-Universität Gießen (3114)Peer Reviewe

The Economic Impact of Exchanging Breeding Material: Assessing Winter Wheat Production in Germany

Climate change impacts imply that the stabilization and improvement of agricultural production systems using technological innovations has become vital. Improvements in plant breeding are integral to such innovations. In the context of German crop breeding programs, the economic impact of exchanging genetic material has yet to be determined. To this end, we analyze in this impact assessment the economic effects on German winter wheat production that are attributable to exchanging parental material amongst breeders in the breeding process. This exchange is supported by the breeders’ exemption, which is an integral part of the German plant variety protection legislation. It ensures that breeders can freely use licensed varieties created by other breeders for their own breeding activities and aims to speed up the development of improved varieties. For our analysis, we created a unique data set that combines variety-specific grain yield, adoption, and pedigree information of 133 winter wheat varieties. We determined the parental pedigree of each variety to see if a variety was created by interbreeding varieties that are internal or external to its specific breeder. Our study is the first that analyzes the economic impact of exchanging genetic material in German breeding programs. We found that more than 90 % of the tested varieties were bred with exchanged parental material, whereby the majority had two external parents. Also, these varieties were planted on an 8.5 times larger area than the varieties that were bred with two internal parents. Due to lower adoption, these only contributed 11 % to the overall winter wheat production in Germany, even though they yielded more. We used an economic surplus model to measure the benefits of exchanging parental breeding material on German winter wheat production. This resulted in an overall estimated economic surplus of 19.2 to 22.0 billion EUR from production year 1972 to 2018. This implies tremendous returns to using the breeder’s exemption, which, from an economic perspective, is almost cost-free for the breeder. We conclude that the exchange of breeding material contributes to improving Germany’s agricultural production and fosters the development of climate-resilient production systems and global food security. © Copyright © 2020 Lüttringhaus, Gornott, Wittkop, Noleppa and Lotze-Campen

Early Stages of Homopolymer Collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages respectively scale as the zeroth, 1/5 and 6/5 power of the the degree of polymerization of the chain.Comment: 11 pages, 3 figure

The oxidative demethylation of certain N-methylhydrazines by microsomal liver enzymes

The presence in rat liver microsomes of an enzyme system which demethylates N-methylhydrazines and azo compounds to formaldehyde has been reported. Some of the compounds found to be substrates were monomethylhydrazine, N-isopropyl-α-(2-methylhydrazino)- p-toluamide and the azo derivative of the latter hydrazine. This enzyme can be classified as a mixed function oxidase as defined by Mason (Adv. in Enzymology 19:79,1957) since the N-demethylase was dependent upon the presence of a NADPH-regenerating system and molecular oxygen. The reaction was not inhibited by SKF 525-A (2-diethylaminoethyl diphenylpropyl acetate), a compound that has been found to inhibit many microsomal enzyme systems. The N-demethylase was inducible by both phenobarbital and 3-methylcholanthrene. Addition of carbon monoxide to microsomes and the treatment of microsomes with trypsin led to the conclusion that rat liver microsomes possess a phenobarbital-inducible N-demethylase dependent upon P-450 and a non-inducible N-demethylase independent of P-450. A mechanism was proposed for the demethylation of the Nmethylhydrazines. Since the azo derivatives of two of the hydrazines were oxidized at a greater rate than their parent compounds, it was postulated that the hydrazines are first oxidized to their azo derivatives which in turn are demethylated to formaldehyde by microsomes. The possible formation of an azoxy intermediate was discussed. An attempt was made to solubilize and purify the N-demethylase but without success

The Economic Impact of Exchanging Breeding Material: Assessing Winter Wheat Production in Germany

Climate change impacts imply that the stabilization and improvement of agricultural production systems using technological innovations has become vital. Improvements in plant breeding are integral to such innovations. In the context of German crop breeding programs, the economic impact of exchanging genetic material has yet to be determined. To this end, we analyze in this impact assessment the economic effects on German winter wheat production that are attributable to exchanging parental material amongst breeders in the breeding process. This exchange is supported by the breeders’ exemption, which is an integral part of the German plant variety protection legislation. It ensures that breeders can freely use licensed varieties created by other breeders for their own breeding activities and aims to speed up the development of improved varieties. For our analysis, we created a unique data set that combines variety-specific grain yield, adoption, and pedigree information of 133 winter wheat varieties. We determined the parental pedigree of each variety to see if a variety was created by interbreeding varieties that are internal or external to its specific breeder. Our study is the first that analyzes the economic impact of exchanging genetic material in German breeding programs. We found that more than 90 % of the tested varieties were bred with exchanged parental material, whereby the majority had two external parents. Also, these varieties were planted on an 8.5 times larger area than the varieties that were bred with two internal parents. Due to lower adoption, these only contributed 11 % to the overall winter wheat production in Germany, even though they yielded more. We used an economic surplus model to measure the benefits of exchanging parental breeding material on German winter wheat production. This resulted in an overall estimated economic surplus of 19.2 to 22.0 billion EUR from production year 1972 to 2018. This implies tremendous returns to using the breeder’s exemption, which, from an economic perspective, is almost cost-free for the breeder. We conclude that the exchange of breeding material contributes to improving Germany’s agricultural production and fosters the development of climate-resilient production systems and global food security.Peer Reviewe

Stretched Polymers in a Poor Solvent

Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first and last monomers. We show that both in $d=2$ and $d=3$ a phase transition occurs as this force is increased beyond a critical value, where the polymer changes from a collapsed globule to a stretched configuration. This transition is second order in $d=2$ and first order in $d=3$. For $d=2$ we predict the transition point quantitatively from properties of the unstretched polymer. This is not possible in $d=3$, but even there we can estimate the transition point precisely, and we can study the scaling at temperatures slightly below the collapse temperature of the unstretched polymer. We find very large finite size corrections which would make very difficult the estimate of the transition point from straightforward simulations.Comment: 10 pages, 16 figure