HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Microstructural stability and nanoindentation of an electrodeposited nanocrystalline Ni-1.5wt.%P alloy

Microstructural stability of nanocrystalline Ni-1.5wt.%P alloy with an initial grain size of 3 nm processed by pulsed electrodeposition was studied using differential scanning calorimetry (DSC) and annealing. Microstructural characterization suggests that the observed exothermic peak during heating in DSC is related to both concurrent grain growth and Ni3P formation. Nanoindentation on samples with grain sizes from 3 to 50 nm revealed a breakdown in Hall-Petch strengthening in nano Ni-P alloy at grain sizes <= 10 nm, consistent with some previous observations. It is concluded that there is a grain boundary weakening regime for grain sizes < 10 nm, based on analysis which show that the data cannot be rationalized in terms of microstrain relaxation, variation in elastic modulus, texture evolution and duplex structure formation.

Nanoparticle agglomeration in an evaporating levitated droplet for different acoustic amplitudes

Radiatively heated levitated functional droplets with nanosilica suspensions exhibit three distinct stages namely pure evaporation, agglomeration, and finally structure formation. The temporal history of the droplet surface temperature shows two inflection points. One inflection point corresponds to a local maximum and demarcates the end of transient heating of the droplet and domination of vaporization. The second inflection point is a local minimum and indicates slowing down of the evaporation rate due to surface accumulation of nanoparticles. Morphology and final precipitation structures of levitated droplets are due to competing mechanisms of particle agglomeration, evaporation, and shape deformation. In this work, we provide a detailed analysis for each process and propose two important timescales for evaporation and agglomeration that determine the final diameter of the structure formed. It is seen that both agglomeration and evaporation timescales are similar functions of acoustic amplitude (sound pressure level), droplet size, viscosity, and density. However, we show that while the agglomeration timescale decreases with initial particle concentration, the evaporation timescale shows the opposite trend. The final normalized diameter can be shown to be dependent solely on the ratio of agglomeration to evaporation timescales for all concentrations and acoustic amplitudes. The structures also exhibit various aspect ratios (bowls, rings, spheroids) which depend on the ratio of the deformation timescale (t(def)) and the agglomeration timescale (t(g)). For t(def) < t(g), a sharp peak in aspect ratio is seen at low concentrations of nanosilica which separates high aspect ratio structures like rings from the low aspect ratio structures like bowls and spheroids. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4775791]

Diaminotriazine substituted diphenyl ether: reversible structural transformation and solvent dependent solid state fluorescence

The effect of molecular shape and position of hydrogen bonding functionality in the solid state structural self-assembly was investigated using diaminotriazine substituted diphenyl ether based positional isomers (1-5). The molecular shape was modulated by changing diaminotriazine position that produced channel supramolecular structures in 1, 3 and 5. There exists a direct correlation between the molecular shape and three dimensional structures; more linear molecules resulted in close-packing whereas molecules with a labyrinthine topology formed a channel structure. Supramolecular aspects pertaining to the influence of solvent of crystallization in structure formation and reversible structural transformation in solid state were also explored. 1-5 exhibited tunable solid state fluorescence (lambda(max) = 437-496 nm) depending on the diaminotriazine substitutional position and 3 showed solvent-dependent solid state fluorescence. The present study describes the generation of a supramolecular channel structure with functional properties such as tunable fluorescence by varying the position of hydrogen bond functionality and solvent of crystallization.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

INDUCTION OF FOLDED STRUCTURES IN DESIGNED PEPTIDES USING CONFORMATIONALLY CONSTRAINED RESIDUES

Folding into compact globular structures, with well-defined modules of secondary structure, appears to be a characteristic of long polypeptide chains, with a specific patterning of coded amino acid residues along the length of sequence. Cooperative hydrogen bond driven secondary structure formation and solvent forces, which contribute favorably to the entropy of folding, by promoting compaction of the polymeric chain, have long been discussed as major determinants of the folding process. First principles design approaches, which use non-coded amino acids, employ an alternative structure directing strategy, by using amino acid residues which exhibit a strong conformational bias for specific regions of the Ramachandran map. This overview of ongoing studies in the authors' laboratory, attempts to explore the use of conformationally restricted amino acid residues in the design of peptides with well-defined secondary structures. Short peptides composed of 20 genetically coded amino acids usually exist in solution as an ensemble of equilibrating conformations. Apolar peptide sequences, which are readily soluble in organic solvents like chloroform and methanol, facilitate formation of structures which are predominately driven by intramolecular hydrogen bond formation. The choice of sequences containing residues with a limited range of conformational choices strongly favors formation of local turn structures, stabilized by short range intramolecular hydrogen bonds. Two residue beta-turns can nucleate either helical or hairpin folding, depending on the precise conformation of the turn segment Restriction of the conformational space available to amino acid residues is easily achieved by introduction of an additional alkyl group at the C alpha carbon atom or by side chain backbone cyclization, as in proline. Studies of synthetic sequences incorporating two prototype residues alpha-aminoisobutyric acid (Aib) and D-proline (DPro) illustrate the utility of the strategy in construction of helices and hairpins. Extensions to the design of conformationally switchable sequences and structurally defined hybrid peptides containing backbone homologated residues are also surveyed.

Microstructural Features of Hot Deformed Nb-1Zr-0.1C Alloy

Niobium-based alloys are well-established refractory materials; as a result of their high melting temperature and good creep properties, these alloys find their applications in nuclear reactors. The present study deals with a microstructural response of these materials during hot working. The evolution of microstructure and texture during high-temperature deformation has been investigated in the temperature range 1500-1700A degrees C and strain rate range of 0.001-0.1 s(-1). For each deformed sample, the microstructure has been examined in detail. The microstructural features clearly revealed the formation of a substructure and the occurrence of dynamic recrystallization in a proper temperature-strain rate window. At low strain rates, the necklace structure formation was more prominent.

Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and beta-hairpin

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel beta-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel beta-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (beta-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

Cosmological consequences of dark matter interactions and vacuum fluctuations

This thesis is divided into two parts: interacting dark matter and fluctuations in cosmology. There is an incongruence between the properties that dark matter is expected to possess between the early universe and the late universe. Weakly-interacting dark matter yields the observed dark matter relic density and is consistent with large-scale structure formation; however, there is strong astrophysical evidence in favor of the idea that dark matter has large self-interactions. The first part of this thesis presents two models in which the nature of dark matter fundamentally changes as the universe evolves. In the first model, the dark matter mass and couplings depend on the value of a chameleonic scalar field that changes as the universe expands. In the second model, dark matter is charged under a hidden SU(N) gauge group and eventually undergoes confinement. These models introduce very different mechanisms to explain the separation between the physics relevant for freezeout and for small-scale dynamics.

As the universe continues to evolve, it will asymptote to a de Sitter vacuum phase. Since there is a finite temperature associated with de Sitter space, the universe is typically treated as a thermal system, subject to rare thermal fluctuations, such as Boltzmann brains. The second part of this thesis begins by attempting to escape this unacceptable situation within the context of known physics: vacuum instability induced by the Higgs field. The vacuum decay rate competes with the production rate of Boltzmann brains, and the cosmological measures that have a sufficiently low occurrence of Boltzmann brains are given more credence. Upon further investigation, however, there are certain situations in which de Sitter space settles into a quiescent vacuum with no fluctuations. This reasoning not only provides an escape from the Boltzmann brain problem, but it also implies that vacuum states do not uptunnel to higher-energy vacua and that perturbations do not decohere during slow-roll inflation, suggesting that eternal inflation is much less common than often supposed. Instead, decoherence occurs during reheating, so this analysis does not alter the conventional understanding of the origin of density fluctuations from primordial inflation.

Avaliação da influência da interação polímero-solvente sobre a porosidade de copolímeros de acrilonitrila e divinilbenzeno obtidos por polimerização em suspensão

Neste trabalho, copolímeros à base de acrilonitrila e divinilbenzeno foram sintetizados, utilizando a técnica de polimerização em suspensão, na presença de três agentes porogênicos diferentes (álcool isoamílico, metil-etil-cetona e tolueno). Esses copolímeros foram caracterizados por meio da determinação da densidade aparente, do volume e diâmetro de poros, por microscopia ótica e microscopia eletrônica de varredura e foram avaliados quanto à capacidade de inchamento em heptano e tolueno. O principal intuito dessa pesquisa foi correlacionar a formação da estrutura porosa desses materiais com os principais parâmetros de síntese (grau de diluição dos monômeros, poder solvatante do diluente e teor do agente de reticulação). Desses parâmetros, o que mais influenciou na formação da estrutura porosa desses materiais foi o poder solvatante do diluente. A teoria dos parâmetros de solubilidade de Hansen e Hildebrand foi utilizada com o intuito de fazer uma previsão das características porosas dos copolímeros à base de acrilonitrila e divinilbenzeno sintetizados na presença de três diluentes diferentes. Dentre esses diluentes, o álcool isoamílico foi o pior solvente para os copolímeros de AN-DVB, em todos os teores de agente de reticulação e em todas as diluições utilizadas. O tolueno foi o melhor solvente para os copolímeros que contêm altos teores de agente de reticulação. Estas observações estão de acordo com as previsões dos parâmetros de solubilidade de Hansen e Hildebrand. A metil-etil-cetona foi o melhor solvente para os copolímeros que contêm teores intermediários de agente de reticulação. Esta observação só está condizente com o parâmetro de solubilidade de Hansen.

Análise do processo de implementação das Diretrizes Curriculares Nacionais do curso em Farmácia no Estado do Rio de Janeiro: um estudo exploratório

O estabelecimento das Diretrizes Curriculares Nacionais do curso de graduação em Farmácia (DCNF) ocasionou muitas discussões acerca da formação dos farmacêuticos, visto que demandam mudanças significativas nessa formação. Essas mudanças envolvem, entre outros aspectos, o componente humanístico e crítico da profissão, o que significa repensar a formação do farmacêutico e até mesmo sua própria identidade como profissional, que apresenta um perfil eminente técnico. Este trabalho tem por foco o processo de implementação das DCNF no Estado do Rio de Janeiro. Buscou-se verificar com esta vem se desenvolvendo e identificar alguns dos embates, entraves e avanços nesse processo. Para a análise, foram realizadas entrevistas semiestruturadas com os coordenadores de um conjunto de cursos selecionados, além do exame dos currículos e projetos pedagógicos dos mesmos, com base nas DCNF. Os resultados demonstram que a construção das novas propostas de formação dos cursos, ocorreu a partir do currículo anterior. Houve uma baixa participação dos alunos e docentes no processo e também ocorreram conflitos entre departamentos, além da inadequação da estrutura universitária. A diretriz da formação voltada para atenção à saúde com ênfase no SUS estimulou a abertura para discussões acerca do Sistema de Saúde e conduziu a inserção dos alunos no mesmo, também causou questionamentos e preocupação, por se considerar essa formação restritiva em relação ao mercado de trabalho. A implementação das propostas enfrentou dificuldade que envolveram a carga horária docente, dificuldade de inserção dos alunos em estágio em algumas áreas de atuação e a falta de investimentos no setor público, tanto de infraestrutura, como de pessoal, além das dificuldades inerentes ao processo de transição entre os currículos. Nenhum curso promoveu iniciativas sistemáticas de desenvolvimento docente e a diversificação dos cenários ensino-aprendizagem (e parcerias como serviços de saúde) ainda são muito incipientes. Foram apontados pelos próprios coordenadores alguns desafios a serem superados para mudança do perfil do farmacêutico: ruptura da concepção tecnicista na formação; inserção do farmacêutico nas equipes multiprofissionais de saúde (exercendo seu papel de forma eficiente e resolutiva); e a sensibilização dos docentes para melhor compreensão e comprometimento com as mudanças necessárias para se alcançar a formação desejada. Em relação a avaliação do MEC e cobrança da implementação das DC, os entrevistados sugerem que os cursos privados, são mais pressionados pelo Ministério. Paradoxalmente as universidade privadas podem acabar por implementar as DC em seus cursos com mais rapidez do que as universidades públicas, e portanto estarem mais voltadas para atender as demandas do SUS, por serem mais sensíveis a esta pressão. De acordo com os resultados dessa pesquisa, considera-se que já ocorreram, alguns avanços em decorrência do estabelecimento das DCNF, que se refletiram em mudanças nos cursos estudados. Entretanto, faz-se necessário e urgente o desenvolvimento de estratégias que garantam avanços mais sistemáticos nas mudanças na formação do farmacêutico.

Patterning of crystalline organic materials by electro-hydrodynamic lithography.

The control of semi-crystalline polymers in thin films and in micrometer-sized patterns is attractive for (opto-)electronic applications. Electro-hydrodynamic lithography (EHL) enables the structure formation of organic crystalline materials on the micrometer length scale while at the same time exerting control over crystal orientation. This gives rise to well-defined micro-patterned arrays of uniaxially aligned polymer crystals. This study explores the interplay of EHL structure formation with crystal alignment and studies the mechanisms that give rise to crystal orientation in EHL-generated structures.

Oxygen vacancy defects in Ta2O5 showing long-range atomic re-arrangements

The structure, formation energy, and energy levels of the various oxygen vacancies in Ta2O5 have been calculated using the λ phase model. The intra-layer vacancies give rise to unusual, long-range bonding rearrangements, which are different for each defect charge state. The 2-fold coordinated intra-layer vacancy is the lowest cost vacancy and forms a deep level 1.5 eV below the conduction band edge. The 3-fold intra-layer vacancy and the 2-fold inter-layer vacancy are higher cost defects, and form shallower levels. The unusual bonding rearrangements lead to low oxygen migration barriers, which are useful for resistive random access memory applications. © 2014 AIP Publishing LLC.

Molecular cloning and characterization of the copper/zinc and manganese superoxide dismutase genes from the human parasite Clonorchis sinensis

A copper/zinc superoxide dismutase (Cu/ZnSOD) gene and a manganese superoxide dismutase (MnSOD) gene of the human parasite Clonorchis sinensis have been cloned and their gene products functionally characterized. Genes Cu/ZnSOD and MnSOD encode proteins of 16 kDa and 25.4 kDa, respectively. The deduced amino acid sequences of the two genes contained highly conserved residues required for activity and secondary structure formation of Cu/ZnSOD and MnSOD, respectively, and show up to 73.7% and 75.4% identities with their counterparts in other animals. The genomic DNA sequence analysis of Cu/ZnSOD gene revealed this as an intronless gene. Inhibitor studies with purified recombinant Cu/ ZnSOD and MnSOD, both of which were functionally expressed in Escherichia coli, confirmed that they are copper/zinc and manganese-containing SOD, respectively. Immunoblots showed that both C. sinensis Cu/ZnSOD and MnSOD should be antigenic for humans, and both, especially the C. sinensis MnSOD, exhibit extensive cross-reactions with sera of patients infected by other trematodes or cestodes. RT-PCR and SOD activity staining of parasite lysates indicate that there are no significant differences in mRNA level or SOD activity for both species of SOD, indicating cytosolic Cu/ZnSOD and MnSOD might play a comparatively important role in the C. sinensis antioxidant system.

Indium sulfide microflowers: Fabrication and optical properties

With the assistance of urea, uniform 2D nanoflakes assembled 3D In2S3 microflowers were synthesized via a facile hydrothermal method at relative low temperature. The properties of the as-obtained In2S3 flowers were characterized by various techniques. In this work, the utilization of urea and L-cysteine, as well as the amount of them played important roles in the formation of In2S3 with different nanostructures. Inferred from their morphology evolution, a urea induced precursor-decomposition associated with the Ostwald-ripening mechanism was proposed to interpret these hierarchical structure formation.