Calibrated Langevin dynamics simulations of intrinsically disordered proteins

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the inter-residue separations for 36 pairs of residues in five IDPs: $\alpha$-, $\beta$-, and $\gamma$-synuclein, the microtubule-associated protein $\tau$, and prothymosin $\alpha$. We find that our CG model is able to recapitulate the average inter-residue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.Comment: 16 pages, 10 figure

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp111073wDNA-directed assembly of gold nanoparticles (AuNPs) has been extensively studied because of its important applications in analytical chemistry, materials science, and nanomedicine. In a typical system, two DNA-functionalized AuNPs are assembled via a linker DNA to form large aggregates. In the majority of the previous reports, the linker DNA is fully base paired with no gaps or overhangs present. Introducing such nonbase-paired regions in the linker DNA has been recently shown to be important for making stimuli-responsive materials and in crystallization of such AuNPs. In this work, we systematically studied the effect of introducing gaps and overhangs in the linker DNA to understand the kinetics of assembly and the melting transition of these aggregates. We found that the assembly kinetics decreased with increasing linker DNA length. The melting temperature decreased with the loss of base stacking by introducing gaps as well as the steric effect of overhangs. Additional insights were obtained by measuring the melting curves of the free DNAs in the absence of AuNPs. For example, it appeared that DNA base stacking at the nick site was favored in assembled nanoparticles compared to that in free DNA. Our results indicate that, while it is possible to form AuNP assemblies with linker DNAs containing various types of unpaired regions, these kinetic and thermodynamic factors need to be considered when designing related sensors and materials.University of Waterloo || Natural Sciences and Engineering Research Council |

Dual pathways in social evolution: Population genetic structure of group-living and solitary species of kleptoparasitic spiders (Argyrodinae: Theridiidae)

Group-living behavior is taxonomically widespread but rare in spiders. The conventional view is that the main pathways to group-living in spiders are either sub-social, where extended maternal care leads to prolonged sibling association; or communal living, where individuals aggregate to exploit a common resource. Female egg-sac guarding behavior occurs throughout kleptoparasitic spiders in the subfamily Argyrodinae (Theridiidae), while individuals in group-living species cohabit in the resource rich webs of their host spiders. These attributes fit both sub-social and communal routes to group-living, which offers new insights to study the early stages of social evolution. We investigated whether members of kleptoparasitic groups in natural populations comprise related individuals by comparing the population structure of two group-living species, Argyrodes miniaceus and A. cf. fissifrons, and two solitary species, A. fasciatus and Neospintharus trigonum. We found that: (1) genetic-spatial autocorrelation in group-living species was highest among spiders sharing the same host web and declined steeply with increasing distance, but no significant autocorrelation at any scale for solitary species; (2) there was high relatedness among group members in two cases of group-living species, which indicated relatedness was not an adhesive agent in most of the groups, but no high relatedness in solitary species; and (3) the host web boundary was not the sole predictor of genetic structures in group-living species. These results suggest that population genetic structure in the group-living species is caused by limited dispersal of group members that is favored by ecological conditions, including the nature and size of resources. In contrast, the absence of genetic structuring in populations of solitary species indicates a high level of dispersal with individual interactions unlikely to have fitness benefits.2006353KMU-Q107006MOST107-2621- B-037-001-MY

Regenerable DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II) Detection and Removal in Water

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Dave, N., Chan, M. Y., Huang, P.-J. J., Smith, B. D., & Liu, J. (2010). Regenerable DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II) Detection and Removal in Water. Journal of the American Chemical Society, 132(36), 12668–12673. https://doi.org/10.1021/ja106098jMercury is a highly toxic environmental pollutant with bioaccumulative properties. Therefore, new materials are required to not only detect but also effectively remove mercury from environmental sources such as water. We herein describe a polyacrylamide hydrogel-based sensor functionalized with a thymine-rich DNA that can simultaneously detect and remove mercury from water. Detection is achieved by selective binding of Hg2+ between two thymine bases, inducing a hairpin structure where, upon addition of SYBR Green I dye, green fluorescence is observed. In the absence of Hg2+, however, addition of the dye results in yellow fluorescence. Using the naked eye, the detection limit in a 50 mL water sample is 10 nM Hg2+. This sensor can be regenerated using a simple acid treatment and can remove Hg2+ from water at a rate of ∼1 h−1. This sensor was also used to detect and remove Hg2+ from samples of Lake Ontario water spiked with mercury. In addition, these hydrogel-based sensors are resistant to nuclease and can be rehydrated from dried gels for storage and DNA protection. Similar methods can be used to functionalize hydrogels with other nucleic acids, proteins, and small molecules for environmental and biomedical applications.University of Waterloo || Natural Sciences and Engineering Research Council |

A controlled migration genetic algorithm operator for hardware-in-the-loop experimentation

In this paper, we describe the development of an extended migration operator, which combats the negative effects of noise on the effective search capabilities of genetic algorithms. The research is motivated by the need to minimize the num- ber of evaluations during hardware-in-the-loop experimentation, which can carry a significant cost penalty in terms of time or financial expense. The authors build on previous research, where convergence for search methods such as Simulated Annealing and Variable Neighbourhood search was accelerated by the implementation of an adaptive decision support operator. This methodology was found to be effective in searching noisy data surfaces. Providing that noise is not too significant, Genetic Al- gorithms can prove even more effective guiding experimentation. It will be shown that with the introduction of a Controlled Migration operator into the GA heuristic, data, which repre- sents a significant signal-to-noise ratio, can be searched with significant beneficial effects on the efficiency of hardware-in-the- loop experimentation, without a priori parameter tuning. The method is tested on an engine-in-the-loop experimental example, and shown to bring significant performance benefits

Contrasting Effects of Low-Dose IL-2 on Vaccine-Boosted Simian Immunodeficiency Virus (SIV)-Specific CD4+ and CD8+ T Cells in Macaques Chronically Infected with SIVmac251

Abstract IL-2, the first cytokine discovered with T cell growth factor activity, is now known to have pleiotropic effects on T cells. For example, it can promote growth, survival, and differentiation of Ag-selected cells, or facilitate Ag-induced cell death of T cells when Ag persists, and in vivo, it is thought to contribute to the regulation of the size of adaptive T cell response. IL-2 is deficient in HIV-1 infection and has been used in the management of HIV-1-infected individuals undergoing antiretroviral therapy. In this study, we investigated how continuous low-dose IL-2 affected the CD4+ and CD8+ T cell response induced by two inoculations of a canarypox recombinant SIV-based vaccine candidate in healthy macaques chronically infected with SIVmac251. These macaques had normal levels of CD4+ T cells at the beginning of antiretroviral therapy treatment. Vaccination in the presence of IL-2 significantly augmented Gag-specific CD8+ T cell responses, but actually reduced Gag-specific CD4+ T cell responses. Although IL-2 at low doses did not change the overall concentration of circulating CD4+ or CD8+ T cells, it expanded the frequency of CD4+CD25+ T cells. Depletion of the CD4+CD25+ T cells in vitro, however, did not result in a reconstitution of Gag-specific CD4+ responses or augmentation of SIV-specific CD8+ T cell responses. Thus, we conclude that the decrease in virus-specific CD4+ T cell response may be due to IL-2-promoted redistribution of cells from the circulation, or due to Ag-induced cell death, rather than suppression by a T regulatory population

Applying TADF Emitters in Bioimaging and Sensing—A Novel Approach Using Liposomes for Encapsulation and Cellular Uptake

A new method for facilitating the delivery, uptake and intracellular localisation of thermally activated delayed fluorescence (TADF) complexes was developed. First, confinement of TADF complexes in liposomes was demonstrated, which were subsequently used as the delivery vehicle for cellular uptake. Confocal fluorescence microscopy showed TADF complexes subsequently localise in the cytoplasm of HepG2 cells. The procedures developed in this work included the removal of molecular oxygen in the liposome preparation without disrupting the liposome structures. Time-resolved fluorescence microscopy (point scanning) showed initial prompt fluorescence followed by a weak, but detectable, delayed fluorescence component for liposomal TADF internalised in HepG2 cells. By demonstrating that it is possible to deliver un-functionalised and/or unshielded TADF complexes, a sensing function for TADFs, such as molecular oxygen, can be envisaged

Development of Single Nucleotide Polymorphism Markers for the Wheat Curl Mite Resistance Gene Cmc4

Wheat curl mite (Aceria tosichella Keifer) is an important wheat (Triticum aestivum L. em. Thell.) pest in many wheat-growing regions worldwide. Mite feeding damage not only directly affects wheat yield, but A. tosichella also transmits Wheat streak mosaic virus (WSMV). Wheat resistance to A. tosichella, therefore, helps control WSMV. OK05312 (PI 670019) is an advanced breeding line released from Oklahoma that shows a high level of A. tosichella resistance. To map the gene(s) conditioning wheat resistance to A. tosichella in OK05312, a genetic linkage map was constructed using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) and a population of 186 recombinant inbred lines (RILs) from the cross ‘Jerry’ (PI 632433)/OK05312. Seedlings of both parents and the RIL population were infested by A. tosichella Biotype 1 in greenhouse experiments. One major quantitative trait locus was identified on the short arm of chromosome 6D, which corresponds to the previously reported gene Cmc4 for A. tosichella resistance. This gene explained up to 71% of the phenotypic variation and was delimited in a 1.7-Mb (?3.3-cM) region by SNPs 370SNP7523 and 370SNP1639. We successfully converted 12 GBS-SNPs into Kompetitive allele specific polymerase chain reaction (KASP) markers. Two of them tightly linked to Cmc4 were validated to be highly diagnostic in a US winter wheat population and can be used for marker-assisted breeding for incorporation of Cmc4 into new wheat cultivars