A DNA Coarse-Grain Rigid Base Model and Parameter Estimation from Molecular Dynamics Simulations

Sequence dependent mechanics of DNA is believed to play a central role in the functioning of the cell through the expression of genetic information. Nucleosome positioning, gene regulation, DNA looping and packaging within the cell are only some of the processes that are believed to be at least partially governed by mechanical laws. Therefore it is important to understand how the sequence of DNA affects its mechanical properties. For exploring the mechanical properties of DNA, various discrete and continuum models have been, and continue to be, developed. A large family of these models, including the model considered in this work, assume that bases or base pairs of DNA are rigid bodies. The most standard are rigid base pair models, with parameters either obtained directly from experimental data or from Molecular Dynamics (MD) simulations. The drawback of current experimental data, such as crystal structures, is that only small ensembles of configurations are available for a small number of sequences. In contrast, MD simulations allow a much more detailed view of a larger number of DNA sequences. However, the drawback is that the results of these simulations depend on the choice of the simulation protocol and force field parameters. MD simulations also have sequence length limitations and are currently too intensive for (linear) molecules longer than a few tens of base pairs. The only way to simulate longer sequences is to construct a coarse-grain model. The goal of this work is to construct a small parameter set that can model a sequence- dependent equilibrium probability distribution for rigid base configurations of a DNA oligomer with any given sequence of any length. The model parameter sets previously available were for rigid base pair models ignoring all the couplings beyond nearest neighbour interactions. However it was shown in previous work, that this standard model of rigid base pair nearest neighbour interactions is inconsistent with a (then) large scale MD simulation of a single oligomer [36]. In contrast we here show that a rigid base nearest neighbour, dimer sequence dependent model is a quite good fit to many MD simulations of different duration and se- quence. In fact a hierarchy of rigid base models with different interaction range and length of sequence-dependence is discussed, and it is concluded that the nearest neighbour, dimer based model is a good compromise between accuracy and complexity of the model. A full parameter set for this model is estimated. An interesting feature is that despite the dimer dependence of the parameter set, due to the phenomenon of frustration, our model predicts non local changes in the oligomer shape as a function of local changes in the sequence, down to the level of a point mutation

Conformational analysis of nucleic acids revisited: Curves+

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamic

Effect of disinfectants on viability of Ascaris suum and Ascaridia galli eggs

Ascaris suum and Ascaridia galli, the large round worm of pigs and poultry, respectively, persist even in intensive management systems, where a high level of hygiene is practiced. It is necessary to control these helminths to minimize production losses and improve animal welfare. Commercial disinfectants are commonly used to clean pens in conventional pig and poultry farms but their efficacy against the thick-shelled nematode eggs has not been sufficiently documented. However, it might be difficult to control these parasites because of their complex thick-shelled eggs, which can resist harsh environmental conditions. Commonly used disinfectants such as Virkon S®, FL-des GA® typically claim efficacy against viruses, bacteria and some fungi, but very few disinfectants (FL-des Allround®) claim to also eliminate parasite eggs

Conformational analysis of nucleic acids revisited: Curves

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics

Environmental stress responses and experimental handling artifacts of a model organism, the copepod Acartia tonsa (Dana)

Handling animals during experiments potentially affects the differential expression of genes chosen as biomarkers of sub-lethal stress. RNA sequencing was used to examine whole-transcriptome responses caused by laboratory handling of the calanoid copepod, Acartia tonsa. Salinity shock (S = 35 to S = 5) was used as positive stress control; individuals not exposed to handling or other stressors served as negative stress control. All copepods were grown from eggs to adults without being handled or exposed to any stressors prior the experiment. Survival of nauplii and adults was estimated for up to 10 min of exposure to handling stress and salinity shock. Only adults exhibited decreased survival (44 ± 7% with 10 min of exposure) in response to handling stress and were selected for definitive experiments for RNA sequencing. After 10 min of experimental exposures to handling stress or salinity shock, adults were incubated for 15 min or 24 h at normal culture conditions. A small number of significantly differentially expressed genes (DEGs) were observed 15 min after exposure to handling stress (2 DEGs) or salinity shock (7 DEGs). However, 24 h after exposure, handling stress resulted in 276 DEGs and salinity shock resulted in 573 DEGs, of which 174 DEGs were overlapping between the treatments. Among the DEGs observed 24 h after exposure to handling stress or salinity shock, some commonly-used stress biomarkers appeared at low levels. This suggests that a stress-response was induced at the transcriptional level for these genes between 15 min and 24 h following exposure. Since handling stress clearly affects transcriptional patterns, it is important to consider handling when designing experiments, by either including additional controls or avoiding focus on impacted genes. Not considering handling in gene expression studies can lead to inaccurate conclusions. The present study provides a baseline for studying handling stress in future studies using this model organism and others

Population genomics of marine zooplankton

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Bucklin, Ann et al. "Population Genomics of Marine Zooplankton." Population Genomics: Marine Organisms. Ed. Om P. Rajora and Marjorie Oleksiak. Springer, 2018. doi:10.1007/13836_2017_9.The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.Support was provided by the US National Science Foundation to AB and RJO (PLR-1044982) and to RJO (MCB-1613856); support to IS and MC was provided by Nord University (Norway)

ESG Controversies: How Do They Affect Market Returns and Individual Asset Choices?

This paper examines how the financial markets and individual investors react to ESG controversies from 2003 to 2021. First, we use an event study methodology to analyze the market responses to 7,500 controversies affecting 2,826 companies, in returns and volumes. Second, we analyze how individual investors rebalance their portfolios after an ESG controversy. This second analysis relies on the trading records of 20,935 individual investors of a Belgian brokerage house. At the market level, abnormal returns are significantly negative during the week of the event (t) and this effect also continues to be visible the week after the event (t+1). However, we notice that the impact of ESG controversies on abnormal returns seems to be stronger regarding the events occurred during the second half of our sample period. We see no such difference between time periods when looking at the abnormal volume of traded shares during the event windows. At the individual level, retail investors significantly decrease their portfolio weights in stocks that experience an ESG controversy during the week of the event, this tendency again being stronger in the second sub-sample period. They also tend to decrease their portfolio weights in the whole industry that the company experiencing an ESG controversy belongs to. This paper is a work in progress

Gender and Sustainable Negotiation,

Nowadays women more often lead teams, make plans as well as important decisions. They also strive for good results when collaborating with partners and take part in negotiations. Most of them get rather general recommendations on how to act in negotiations but very little attention is paid to gender differences, especially not enough interest is paid to the impact of women and their behavior in negotiations. Success in sustainable negotiation in many cases depends on gender stereotypes prevailing in the society. The object in this paper is the importance of gender differences in sustainable negotiations. The aim of the paper is to discuss the main gender behavior differences in sustainable negotiations