Computational studies on DNA: insights into structure and dynamics

The best-characterized epigenetic modification is DNA methylation, which was found to shape significantly gene expression in mammalian cells, though bacteria and plants display less sequence specificity. The cytosine methylation of DNA sequence here was studied by the molecular dynamic (MD) method. We found that the optimized structures are not significantly altered between unmethylated, methylated sequences. However, sampling of the molecule dynamical landscape via long MD simulations showed that the altered sequences could adopt different conformations (revealed in the twist and roll angles) from the unmodified DNA, which are dependent on the §sequence environment. We propose that this conformational diversity may play a role on protein recognition. The G-rich sequences are studied with MD simulations to check the propensity of the sequence to adopt to A-form or B-form of DNA. The results showed that the DNA sequence adopts most of the time in A-form and also spend sometime in between A-form and B-form. The groove widths showed the conformation in B-form. By analyzing the DNA in different contexts using computational methods we were able to test limits that force field methods offer for these systems. We propose that this conformational diversity may play a role in protein recognition. Finally, we have studied the conformational changes of DNA sequence with uracil as a base. Sometimes in the replication process uracil can be formed and the mismatch base pair in the DNA sequence is removed by the enzyme UDG (Uracil-DNA sequence). In the present work MD simulations were used to study the structure, dynamics and base pair kinetics of DNA sequence. The opening and closing kinetics of the T-A base pair were studied. A fast base pair opening was observed and also additionally base flipping was spotted. A very fast opening of the bases may be responsible for the fast closing of the bases. In order to characterize the complete study of base pair kinetics in relation to T-A versus U-A base pairs is currently under way

Theoretical modelling of epigenetically modified DNA sequences

We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts

Market research in the Finnish food industry

This study introduces the important factors of market research and its significancewhen aiming at new foreign markets. Understanding the cultural differences, the consumers and the market itself with the competitors’ actions among other factors, the organization has a better chance to succeed in entering new markets. The case company is a Belgian food industry company which is interested in the Finnish market environment with its consumers and competitors. Currently they are operating in Central European countries with a little market share. An interview was conducted in order to better understand their current situation and expectations on new markets. The company’s products are sold in specialty stores and in bigger hypermarkets due to their higher image which they would like to obtain in Finland. As a small country Finland can not offer big markets but this is no obstacle for the case company since they are not looking to challenge the market leader or even the followers. Instead they are looking for a small market share as in other countries that they already operate in. By using selective distribution focused on the biggest city areas the product availability is guaranteed to the majority of the Finnish population. The thesis emphasizes the different business chains - the different types of stores and their product variety as well as competitors and their product pricing. Among this, the importance of product visibility will be shown as the case company wishes to enter the markets with as little marketing as possible. Regulations on labelling are studied as well as there are little differences from organizations’ home markets. The study also introduces a Finnish importing company that could possibly cooperate with the customer when aiming at the Finnish markets.Tutkimus esittelee markkinatutkimuksen tärkeimmät osa-alueet sekä sen merkityksen tavoiteltaessa uusia markkinoita. Kulttuurillisten eroavaisuuksien, kuluttajien sekä itse markkinoiden ymmärtäminen kilpailijoineen edesauttaa yrityksen menestymistä uudella markkina-alueella. Asiakasyritys on Belgialainen elintarvikeyritys joka kiinnostui Suomen markkinaympäristöstä, kuluttajista sekä kilpailijoista. Tällä hetkellä he toimivat Keski-Euroopan markkinoilla pienin markkinaosuuksin. Haastattelu suoritettiin jotta saataisiin selville heidän nykytilanteensa sekä tulevaisuuden näkymät uusista markkinoista. Yrityksen tuotteet ovat myynnissä erikoisliikkeissä sekä suurimmissa marketeissa korkean imagon vuoksi ja näin he toivoisivat myös tapahtuvan Suomessa. Suomessa ei ole tarjolla suuria markkinoita jo pelkästään maan koon vuoksi. Tämä ei ole kuitenkaan este asiakasyritykselle sillä he eivät lähde haastamaan markkinajohtajaa tai seuraajia, vaan tyytyvät pieneen markkinaosuuteen aivan kuten muillakin markkinoilla. Selektiivisellä tuotejakelulla, keskittyen Suomen suurimpiin kaupunkialueisiin, taataan tuotteiden saatavuus suurimmalle osalle väestöstä. Tutkimus painottuu eri liikeketjuihin, Suomen kauppatyyppeihin ja niiden tuotevalikoiman suuruuteen sekä kilpailijoihin ja heidän tuotehinnoitteluun. Tämän lisäksi tuotteiden näkyvyyden tärkeys osoitetaan, sillä asiakasyritys toivoisi markkinoille tuloa vähäisin markkinointitoiminnoin. Pakkausmerkintäsäännökset tulevat myös esille sillä ne eroavat hieman yrityksen kotimarkkinoiden säännöksistä. Tutkimus esittelee myös suomalaisen maahantuontiyrityksen, joka voisi mahdollisesti toimia asiakasyrityksen yhteistyökumppanina Suomen markkinoille pyrittäessä

Inactivation of viruses in water by chlorination using bacteriophages as model organisms

Climate change will lead to more extreme rain events in parts of Sweden resulting in sewage overflows and thus more contamination of surface water, leading to an increased risk of waterborne infections. Swedish and Norwegian surface waters are rich in humic substances with high organic carbon content that interferes with disinfection, the most important barrier to viruses in the water treatment plant. Therefore the disinfection potential of free chlorine was evaluated for a number of viruses: canine adenovirus (CAdV), murine norovirus (MNV), mammalian orthoreovirus (MRV) and porcine enterovirus (PEV), and model viruses (MS2, 28B, ФX174 and Ф6 bacteriophages) on different water qualities (pH, turbidity and organic carbon content). Viruses were enumerated by end-point titration and bacteriophages with plaque assay. The inactivation studies were done by chlorination (The amount of sodium hypochlorite added was 30–60 ml/L based on the types of water) at 5°C and the chlorine values were in between 0.12–0.2 mg/l range. Virus inactivations were determined for the initial reduction (IR) when the chlorine is consumed and further during the contact time within the test tube. During the later part, the chlorine contact time (CT) for one log reduction was determined (CT-1). The initial reduction was in between 3.18–3.94 logs for viruses (Adenovirus > Orthoreovirus > Norovirus > Enterovirus) and for bacteriophages it was in between 0.34–4.89 (ΦX174 > Φ6 > 28B > MS2). Due to high initial reduction the number of results used for determination of CT for one log reduction were limited. The CT-1 were around 0.5 mg*min/L for all the viruses. For a certain CT-1 time was more important than the chlorine concentration for MNV, PEV and MRV. The CT-1 for the bacteriophages MS2, 28B and фX174 were 12.6, 3.44 and 0.79 mg*min/L respectively. The CT values for ф6 bacteriophage could not be calculated because of its fast inactivation. MS2 and 28B bacteriophages were persistent to free chlorine and can preferably be used in larger scale pilot studies to better determine the effect of water quality parameters. The ΦX174 had a similar CT-1 as viruses, however the high initial reduction requires that it is added after the initial consumption to be used as a model organism. The fact that time seems to be more important than chlorine concentration for virus inactivation indicates that the design of contact reactors are important to provide as long minimum contact time for the water to react with free chlorine

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding

Data of theoretical modelling of epigenetically modified DNA sequences

<p>Data file 1<br>Local base pair parameters for the central GC in d(GCG) and d(ACA) modifications. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚.</p> <p>Data file 2<br>Base pair step and local helical parameters for the central GC in d(GCG) and d(ACA) modifications. The slide and X-displacement parameters are measured in Å, and the roll, twist and inclination parameters are measured in ˚.</p> <p>Data file 3<br>Comparison between the obtained base pair parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚.</p> <p>Data file 4<br>Comparison between the obtained base step parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The slide, shift and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in ˚.</p> <p>Data file 5<br>Values of local base pair parameters of central GC pair of d(GCG) obtained after energy minimization. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚.</p> <p>Data file 6<br>Values of base pair step parameters of d(GCG), obtained after energy minimization. The shift, slide and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in °.</p> <p>Data file 7<br>Cartesian coordinates of key species.</p> <p> </p

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

<div><p>We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.</p></div