DNALinux Virtual Desktop Edition

The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn't affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications

Structural and functional analysis of violaxanthin de-epoxidase

Non photochemical quenching (NPQ) is an important way for plants to protect themselves from photooxidative damage. In higher plants, the major and most rapid part of NPQ is qE, which is controlled by the Violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZE). VDE converts Violaxanthin (Vx) to Antheraxanthin (Ax), and then to Zeaxanthin (Zx). Several experiments were carried through to analyze functional and structural properties of VDE. All the 13 Cysteines(Cys) in VDE were mutated to Serine (Ser) to detect the Cys that contribute to VDE activity. 12 mutations were found with decreased VDE activity. The function of the region between the N-terminal domain and the lipocalin domain was investigated by expression of the peptide before and after the linker region in different lengths combination and followed activity measurement. The results showed that the two independent domains lost majority of activity and N-terminal part of linker region was more important for activity. An experiment was set up to analyze the function of C-terminal by measuring the activity of VDE after cleaving different length of C-terminal. The result showed different degrees of activity loss that was caused by removal of different lengths of the C-terminal. A number of experiments suggests that VDE acts as a dimer that is formed at low pH. These experiments will contribute to further research of the function and structure of VDE.Popular Science Summary There is a saying that the sun supports the life living on earth. In general, the sunlight supports plants living, and plants become the base of almost all forms of ecosystems. A reaction called photosynthesis exists in all kinds of plants and is the foundation of usage of sunlight energy. In the photosynthesis process, energy in the sunlight converted into the energy stored in plants, the latter is used in various kinds of biochemical reactions. And during photosynthesis, oxygen is released into the environment and supports the metabolism of all living things. In the photosynthesis process, sunlight energy is gathered by a complex called light harvesting system, and excites chlorophyll, a molecule absorbs light. The excited chlorophyll continues to transfer the energy to the following photochemical reactions. In nature, the intensity of the sunlight is changing all the time. Sometimes, plants receive more sunlight energy than they need for the biochemical reactions in photosynthesis, that means not all excited chlorophyll are in use. And excited chlorophyll will dissipate its energy and return to the ground-energy state. The release of energy can form reactive oxygen species, a molecule that is harmful to plants cells. To prevent the formation of oxidative species, plants have evolved some other ways to release the energy in the excited chlorophyll. One typical way of de-excitation of excited chlorophyll is called non-photochemical quenching; it dissipates the energy into heat. Our research is mainly about an enzyme which is important to the major component of the non-photochemical quenching in higher plants. The enzyme is called violaxanthin de-epoxidase (VDE). VDE converts violaxanthin (a chain-structure pigment which contains two epoxy groups) to zeaxanthin (a chain-structure pigment without the two epoxy groups). And zeaxanthin is believed to quench the excited chlorophyll. Our research of VDE is to investigate the structure and function of VDE by using molecular and biochemistry methods. We produce different parts of the VDE molecule and we change cysteines (one kind of amino acid which can form covalent bond to each other) in VDE into another amino acid. We measure the activity of the protein we produced. We found that cysteines are important for VDE activity. Another discovery of ours is that the VDE molecule gives its activity only when two VDE molecules contact to each other in low pH, and this contact is influenced by the end part of VDE. We also found that VDE consists of two independent functional parts; each part can form its own structure independently. We believe our discoveries may contribute to the further functional and structural research of VDE

Identification of Key Residues for pH Dependent Activation of Violaxanthin De-Epoxidase from Arabidopsis thaliana

Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pKa values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121–Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

The budding yeast genome contains regions where meiotic recombination initiates more frequently than in others. This pattern parallels enrichment for the meiotic chromosome axis proteins Hop1 and Red1. These proteins are important for Spo11-catalyzed double strand break formation; their contribution to crossover recombination remains undefined. Using the sequencespecific VMA1-derived endonuclease (VDE) to initiate recombination in meiosis, we show that chromosome structure influences the choice of proteins that resolve recombination intermediates to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers, like most Spo11- initiated crossovers, required the meiosis-specific MutLg resolvase. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLg-independent. In pch2 mutants, the two loci displayed similar Hop1 occupancy levels, and VDE-induced crossovers were similarly MutLg-dependent. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, and that features of meiotic chromosome structure determine whether one or the other predominates in different regions

Evidence that MEK1 positively promotes interhomologue double-strand break repair

During meiosis there is an imperative to create sufficient crossovers for homologue segregation. This can be achieved during repair of programmed DNA double-strand breaks (DSBs), which are biased towards using a homologue rather than sister chromatid as a repair template. Various proteins contribute to this bias, one of which is a meiosis specific kinase Mek1. It has been proposed that Mek1 establishes the bias by creating a barrier to sister chromatid repair, as distinct from enforcing strand invasion with the homologue. We looked for evidence that Mek1 positively stimulates strand invasion of the homologue. This was done by analysing repair of DSBs induced by the VMA1- derived endonuclease (VDE) and flanked by directly repeated sequences that can be used for intrachromatid single-strand annealing (SSA). SSA competes with interhomologue strand inva- sion significantly more successfully when Mek1 function is lost. We suggest the increase in intrachromosomal SSA reflects an opportunistic default repair pathway due to loss of a MEK1 stimulated bias for strand invasion of the homologous chromosome. Making use of an inhibitor sensitive mek1-as1 allele, we found that Mek1 function influences the repair pathway throughout the first 4-5 h of meiosis. Perhaps reflecting a particular need to create bias for successful interhomologue events before chromosome pairing is complete. © The Author(s) 2010. Published by Oxford University Pres

An algal enzyme required for biosynthesis of the most abundant marine carotenoids.

Fucoxanthin and its derivatives are the main light-harvesting pigments in the photosynthetic apparatus of many chromalveolate algae and represent the most abundant carotenoids in the world's oceans, thus being major facilitators of marine primary production. A central step in fucoxanthin biosynthesis that has been elusive so far is the conversion of violaxanthin to neoxanthin. Here, we show that in chromalveolates, this reaction is catalyzed by violaxanthin de-epoxidase-like (VDL) proteins and that VDL is also involved in the formation of other light-harvesting carotenoids such as peridinin or vaucheriaxanthin. VDL is closely related to the photoprotective enzyme violaxanthin de-epoxidase that operates in plants and most algae, revealing that in major phyla of marine algae, an ancient gene duplication triggered the evolution of carotenoid functions beyond photoprotection toward light harvesting

Transferable neural networks for enhanced sampling of protein dynamics

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable and is generally applicable to sets of related simulations, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure

Reactivity of hydrated hydroxide anion cluster OH(H2_{2}O)n−_{n}^{-} with H and Rb: an ab initio study

We present a theoretical investigation of the hydrated hydroxide anion clusters OH(H$_{2}$O)$_{n}^{-}$ and of the collisional complexes H-OH(H$_{2}$O)$_{n}^{-}$ and Rb-OH(H$_{2}$O)$_{n}^{-}$ (with n$=1-4$). The MP2 and CCSD(T) methods are used to calculate interaction energies, optimized geometries and vertical detachment energies. Part of the potential energy surfaces are explored with a focus on the autodetachment region. We point out the importance of diffuse functions to correctly describe the latter. We use our results to discuss the different water loss and electronic detachment channels which are the main reaction routes at room temperature. In particular, we have considered a direct and an indirect process for the electronic detachment, depending on whether water loss follows or precedes the detachment of the excess electron. We use our results to discuss the implication for astrochemistry and hybrid trap experiments in the context of cold chemistry

Out of equilibrium quantum field dynamics of an initial thermal state after a change in the external field

The effects of the initial temperature in the out of equilibrium quantum field dynamics in the presence of an homogeneous external field are investigated. We consider an initial thermal state of temperature T for a constant external field J. A subsequent sign flip of the external field, J to -J, gives rise to an out of equilibrium nonperturbative quantum field dynamics. The dynamics is studied here for the symmetry broken lambda(Phi^2)^2 scalar N component field theory in the large N limit. We find a dynamical effective potential for the expectation value that helps to understand the dynamics. The dynamics presents two regimes defined by the presence or absence of a temporal trapping close to the metastable equilibrium position of the potential. The two regimes are separated by a critical value of the external field that depends on the initial temperature. The temporal trapping is shorter for larger initial temperatures or larger external fields. Parametric resonances and spinodal instabilities amplify the quantum fluctuations in the field components transverse to the external field. When there is a temporal trapping this is the main mechanism that allows the system to escape from the metastable state for large N. Subsequently backreaction stops the growth of the quantum fluctuations and the system enters a quasiperiodic regime.Comment: LaTeX, 19 pages, 12 .eps figures, improved version to appear in Phys Rev