The GSFC scientific data storage problem

Scientific data storage problems of telemetry tape

Globular Structures of a Helix-Coil Copolymer: Self-Consistent Treatment

A self-consistent field theory was developed in the grand-canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths correspondingly. The resulting field-theory takes, in addition to the conventional Zimm-Bragg (B.H. Zimm, I.K. Bragg, J. Chem. Phys. 31, 526 (1959)) parameters, also three-dimensional interaction terms into account. The appropriate differential equations which determine the self-consistent fields were solved numerically with finite element method. Three different phase states are found: open chain, amorphous globule and nematic liquid-crystalline (LC) globule. The LC-globule formation is driven by the interplay between the hydrophobic helical segments attraction and the anisotropic globule surface energy of an entropic nature. The full phase diagram of the helix-coil copolymer was calculated and thoroughly discussed. The suggested theory shows a clear interplay between secondary and tertiary structures in globular homopolypeptides.Comment: 26 pages, 30 figures, corrected some typo

The self-assembly of DNA Holliday junctions studied with a minimal model

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the phosphate-sugar backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately, and allows strand displacement to occur.Comment: 13 pages, 14 figure

DNA bubble dynamics as a quantum Coulomb problem

We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the bubble lifetime is associated with the continuum of scattering states of the repulsive Coulomb potential, at the melting temperature the Coulomb potential vanishes and the underlying first exit dynamics exhibits a long time power law tail, above the melting temperature, corresponding to an attractive Coulomb potential, the long time dynamics is controlled by the lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte

Entropically driven transition to a liquid-crystalline polymer globule

A self-consistent-field theory (SCFT) in the grand canonical ensemble formulation is used to study transitions in a helix-coil multiblock copolymer globule. The helices are modeled as stiff rods. In addition to the established coil-globule transition we show for the first time that, even without explicit rod-rod alignment interaction, the system undergoes a transition to a nematic liquid-crystalline (LC) globular state. The LC-globule formation is driven by the hydrophobic helical segment attraction and the anisotropy of the globule surface energy. The full phase diagram of the copolymer was calculated. It discriminates between an open chain, amorphous globule and LC-globule. This model provides a relatively simple example of the interplay between secondary and tertiary structures in homopolypeptides. Moreover, it gives a simple explanation for the formation of helix bundles in certain globular proteins.Comment: 5 pages, 5 figures, submitted to Europhys. Let

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4\nu-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure

Naturally processed measles virus peptide eluted from class II HLA-DRB1*03 recognized by T lymphocytes from human blood

AbstractThis is the first report of the direct identification of a HLA-DRB1*03 measles-derived peptide from measles virus infected EBV-transformed B cells. We purified HLA-DR3-peptide complexes from EBV-B cells infected with measles virus (Edmonston strain) and sequenced the HLA-DR3-peptides by mass spectrometry. A class II peptide, derived from a measles phosphoprotein, ASDVETAEGGEIHELLRLQ (P1, residues 179–197), exhibited the capacity to stimulate peripheral blood mononuclear cells to proliferate. Our data provides direct evidence that the antigenic peptide of measles virus was processed by antigen-presenting cells, presented in the context of HLA class II molecules, and was recognized by peripheral blood T cells from healthy individuals previously immunized with measles vaccine. The approach described herein provides a useful methodology for the future identification of HLA-presented pathogen-derived epitopes using mass spectrometry. The study of cell-mediated immune responses to the measles-derived peptide in immune persons should provide significant insight into the design and development of new vaccines

Experiences in effective communication on transgenic technology in Africa – the case of the insect resistant maize for Africa (IRMA) project

The Insect Resistant Maize for Africa (IRMA) Project, aimed to improve food security through developing and deploying locally adapted stem borer resistant maize varieties using both conventional and biotechnology mediated methods, especially Bt technology. This technology uses a gene from the soil bacterium Bacillus thuringiensis (Bt) to create transgenic maize varieties. Transgenic technologies have been a controversial and emotive topic in recent years, and the IRMA project was launched against this backdrop. To ensure widespread acceptance of the IRMA project and its Bt technology, the project carefully planned and implemented its communication and public awareness strategy. Following its public launch in March 2000, the project promoted an open communication environment and continuously engaged with stakeholders to update them on progress. The project achieved this through targeted and diverse communications products such as media articles and broadcast news pieces, newsletters, websites, videos and reports. To complement these, the project conducted annual stakeholders’ meetings, and specialized training for frontline project staff and collaborators, especially extension agents. This paper reviews the IRMA Project’s public awareness and communication strategy and analyzes its effectiveness.Key words: Transgenic technology, Bacillus thuringiensis (Bt) maize technology, communication, public awareness, insect resistant maize for Africa (IRMA) project

HLA homozygosity does not adversely affect measles vaccine-induced cytokine responses

AbstractThe association between HLA homozygosity and measles-specific Th1 (IFN-γ, IL-2 and IL-12p40) and Th2 (IL-4 and IL-10) cytokine responses were assessed in a group of 339 healthy schoolchildren 12–18 years of age previously immunized with two doses of live-attenuated measles virus vaccine. No associations were observed between class I HLA homozygosity and measles-specific cytokine levels. Children who were homozygous at the class II DRB1, DQA1, DPA1 and DPB1 loci had higher median IFN-γ secretion levels compared with children who were heterozygous for DRB1 (77.7 vs. 39.5 pg/ml, p=0.05), DQA1 (60.9 vs. 36.6 pg/ml, p=0.03), DPA1 (46.1 vs. 27.1 pg/ml, p=0.01) and DPB1 (61.5 vs. 36.0 pg/ml, p=0.01) loci, respectively. Homozygosity at increasing numbers of HLA loci ( >=4) was associated with increased IFN-γ secretion levels (test for trend p-value=0.01). Our results suggest that HLA homozygosity showed no disadvantage for measles-specific cytokine responses and instead was associated with increased IFN-γ levels