Optical Kerr Effect In Supercooled Water.

We present molecular dynamics simulations of the optical Kerr effect in liquid and supercooled water and compare with recent time-resolved Kerr spectroscopy measurements [R. Torre, Nature (London) 428, 296 (2004)]. The short time features of the Kerr response, characterized by peaks near 15, 60, and 160 fs, are weakly temperature dependent. The long-time decay is well described by a stretched exponential with a nearly constant stretch parameter and relaxation times that follow a power law approximately (T-T(S))(-gamma), with T(S)=198.3 K and gamma=2.35. Our findings are discussed in the light of the spectroscopy data and previous simulation analyzes of the structural relaxation in supercooled water.9413780

Collision-Induced Effects on the Dielectric Properties of Liquid Dimethylsulfoxide

We present a molecular dynamics (MD) simulation study of the dielectric properties of liquid dimethyl sulfoxide that includes interaction-induced effects due to molecular polarizability using a perturbative scheme in which the induced dipoles are computed a posteriori from the MD trajectories generated without explicit inductive forces. Static and dynamical quantities of relevance to the dielectric characterization of the liquid are reported for both polarizable and nonpolarizable versions of the system's collective dipolar densities. Our analysis within this scheme indicates that the role of the interaction induced contributions is predominantly to renormalize the magnitude of the permanent dipole fluctuations, with marginal effects upon the system's dielectric relaxation in the rotational-diffusion, microwave region of the spectrum. At higher frequencies, however, where the dielectric absorption is dominated by fast intermolecular librational motions, the dynamical effects of the molecular polarizability are more pronounced. In the presence of interaction induced contributions, the location of the peak in the MD far infrared absorption coefficient is in much better agreement with recent spectroscopic measurements of the intermolecular dynamics of this liquid.É apresentado um estudo por simulação de dinâmica molecular das propriedades dielétricas do dimetil sulfóxido líquido, onde são incluídos efeitos de indução devido à polarizabilidade molecular através de perturbação em primeira ordem. Neste formalismo, os dipolos induzidos são computados a partir de trajetórias geradas pelos potenciais intermoleculares isentos de forças indutivas. Propriedades dielétricas estáticas e dinâmicas são computadas para as versões polarizável e não-polarizável da densidade dipolar. As análises indicam que o principal papel das componentes de indução nesta abordagem é o de renormalizar o valor das flutuações estáticas dos dipolos permanentes, sendo apenas marginal a influência sobre as propriedades de relaxação no regime de difusão rotacional que caracteriza o espectro na região de micro-ondas. Entretanto, para maiores frequências, onde a absorção dielétrica é predominantemente determinada por movimentos intermoleculares libracionais, os efeitos dinâmicos da polarizabilidade molecular são mais aparentes. Na presença de contribuições indutivas, o máximo do espectro infravermelho obtido das simulações está em melhor concordância com recentes medidas espectroscópicas da dinâmica intermolecular deste líquido.583591Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOThe natural ligand 17β-estradiol (E2) is so far believed to induce a unique agonist-bound active conformation in the ligand binding domain (LBD) of the estrogen receptors (ERs). Both subtypes, ERα and ERβ, are transcriptionally activated in the presence o7FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2014/22007-02013/08293-72012/24750-6301981/2011-6This work was supported by the São Paulo Research Foundation FAPESP (grants 2014/22007-0, 2013/08293-7, 2012/24750-6) and by CNPq (grant 301981/2011-6

Subaru Coronagraphic Extreme-AO (SCExAO) wavefront control: current status and ongoing developments

Exoplanet imaging requires excellent wavefront correction and calibration. At the Subaru telescope this is achieved us- ing the 188-element facility adaptive optics system(AO188) feeding the Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) instrument; a multipurpose instrument built to deliver high contrast images of planets and disks around nearby stars. AO188 offers coarse correction while SCExAO performs fine correction and calibration of 1000 modes. The full system achieves 90%Strehl Ratio in H-band and diffraction limited images. A new Real Time Computer allowing higher performance between SCExAO and AO188 is currently implemented. Future upgrades will include a new Pyramid Wavefront Sensor and (64x64) DM to achieve extreme AO correction inside AO188. We are progressing in the development of predictive control and sensor fusion algorithms across the system to improve performance and calibration. With the new upgrades, SCExAO will be able to image giant planets in reflected light with Subaru and validate technologies necessary to image habitable Earth-like planets with the Thirty Meter Telescope (TMT)

The patterned structure of galactoglucomannan suggests it may bind to cellulose in seed mucilage

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOThe interaction between mannan polysaccharides and cellulose microfibrils contributes to cell wall properties in some vascular plants, but the molecular arrangement of mannan in the cell wall and the nature of the molecular bonding between mannan and cell178310111026FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO2013/08293-7The authors would like to acknowledge Prof. George Lomonossoff (John Innes Centre, UK), who developed the pEAQ-HyperTrans expression system used in this study. Plant Bioscience Limited supplied the pEAQ-HT vector that was used in this wor

Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose.

The interaction between cellulose and xylan is important for the load-bearing secondary cell wall of flowering plants. Based on the precise, evenly spaced pattern of acetyl and glucuronosyl (MeGlcA) xylan substitutions in eudicots, we recently proposed that an unsubstituted face of xylan in a 2-fold helical screw can hydrogen bond to the hydrophilic surfaces of cellulose microfibrils. In gymnosperm cell walls, any role for xylan is unclear, and glucomannan is thought to be the important cellulose-binding polysaccharide. Here, we analyzed xylan from the secondary cell walls of the four gymnosperm lineages (Conifer, Gingko, Cycad, and Gnetophyta). Conifer, Gingko, and Cycad xylan lacks acetylation but is modified by arabinose and MeGlcA. Interestingly, the arabinosyl substitutions are located two xylosyl residues from MeGlcA, which is itself placed precisely on every sixth xylosyl residue. Notably, the Gnetophyta xylan is more akin to early-branching angiosperms and eudicot xylan, lacking arabinose but possessing acetylation on alternate xylosyl residues. All these precise substitution patterns are compatible with gymnosperm xylan binding to hydrophilic surfaces of cellulose. Molecular dynamics simulations support the stable binding of 2-fold screw conifer xylan to the hydrophilic face of cellulose microfibrils. Moreover, the binding of multiple xylan chains to adjacent planes of the cellulose fibril stabilizes the interaction further. Our results show that the type of xylan substitution varies, but an even pattern of xylan substitution is maintained among vascular plants. This suggests that 2-fold screw xylan binds hydrophilic faces of cellulose in eudicots, early-branching angiosperm, and gymnosperm cell walls.This work was supported by the Leverhulme Trust Centre for Natural Material Innovation (MBW, PD), The Low Carbon Energy University Alliance (AL), BBSRC Grant: BB/G016240/1 BBSRC Sustainable Bioenergy Centre cell wall sugars (TT, PD) and the Sao Paulo Research Foundation (RLS, CSP, MSS, TCFG) (Grants 2013/08293-7, 2014/10448-1 and 2015/25031-1)

Effect of Age and Lordotic Angle on the Level of Lumbar Disc Herniation

It has been previously suggested in the literature that with aging, degenerative changes as well as disc herniation start at the lower lumbar segments, with higher disc involvement observed in an ascending fashion in older age groups. We conducted a study to investigate this correlation between age and level of disc herniation, and to associate it with the magnitude of the Lumbar Lordotic Angle (LLA), as measured by Cobb's method. We followed retrospectively lumbosacral spine MRI's of 1419 patients with symptomatic disc herniation. Pearson's correlation was used in order to investigate the relationship between LLA, age, and level of disc herniation. Student's t-test was applied to assess gender differences. Young patients were found to have higher LLA (R = 0.44, P < 0.0001) and lower levels of disc herniation (R = 0.302, P < 0.0001), whereas older patients had higher level herniation in lower LLA group (mean LLA 28.6° and 25.4°) and lower level herniation in high LLA group (mean LLA 33.2°). We concluded that Lumbar lordotic Cobb's angle and age can be predictors of the level of lumbar disc herniation. This did not differ among men and women (R = 0.341, P < 0.0001)

A review on the dynamics of water

We present a review on the intermolecular dynamics of liquid aqueous systems focusing mainly on Molecular Dynamics simulation work that has been carried out at the State University of Campinas in recent years. Emphasis is given on simulation results that are more directly related to modern experimental spectroscopic measurements.316Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Microrna profiling analysis of differences between the melanoma of young adults and older adults

<p>Abstract</p> <p>Background</p> <p>This study represents the first attempt to perform a profiling analysis of the intergenerational differences in the microRNAs (miRNAs) of primary cutaneous melanocytic neoplasms in young adult and older age groups. The data emphasize the importance of these master regulators in the transcriptional machinery of melanocytic neoplasms and suggest that differential levels of expressions of these miRs may contribute to differences in phenotypic and pathologic presentation of melanocytic neoplasms at different ages.</p> <p>Methods</p> <p>An exploratory miRNA analysis of 666 miRs by low density microRNA arrays was conducted on formalin fixed and paraffin embedded tissues (FFPE) from 10 older adults and 10 young adults including conventional melanoma and melanocytic neoplasms of uncertain biological significance. Age-matched benign melanocytic nevi were used as controls.</p> <p>Results</p> <p>Primary melanoma in patients greater than 60 years old was characterized by the increased expression of miRs regulating TLR-MyD88-NF-kappaB pathway (hsa-miR-199a), RAS/RAB22A pathway (hsa-miR-204); growth differentiation and migration (hsa-miR337), epithelial mesenchymal transition (EMT) (let-7b, hsa-miR-10b/10b*), invasion and metastasis (hsa-miR-10b/10b*), hsa-miR-30a/e*, hsa-miR-29c*; cellular matrix components (hsa-miR-29c*); invasion-cytokinesis (hsa-miR-99b*) compared to melanoma of younger patients. MiR-211 was dramatically downregulated compared to nevi controls, decreased with increasing age and was among the miRs linked to metastatic processes. Melanoma in young adult patients had increased expression of hsa-miR-449a and decreased expression of hsa-miR-146b, hsa-miR-214*. MiR-30a* in clinical stages I-II adult and pediatric melanoma could predict classification of melanoma tissue in the two extremes of age groups. Although the number of cases is small, positive lymph node status in the two age groups was characterized by the statistically significant expression of hsa-miR-30a* and hsa-miR-204 (F-test, p-value < 0.001).</p> <p>Conclusions</p> <p>Our findings, although preliminary, support the notion that the differential biology of melanoma at the extremes of age is driven, in part, by deregulation of microRNA expression and by fine tuning of miRs that are already known to regulate cell cycle, inflammation, Epithelial-Mesenchymal Transition (EMT)/stroma and more specifically genes known to be altered in melanoma. Our analysis reveals that miR expression differences create unique patterns of frequently affected biological processes that clearly distinguish old age from young age melanomas. This is a novel characterization of the miRnomes of melanocytic neoplasms at two extremes of age and identifies potential diagnostic and clinico-pathologic biomarkers that may serve as novel miR-based targeted modalities in melanoma diagnosis and treatment.</p

X-ray Structure And Molecular Dynamics Simulations Of Endoglucanase 3 From Trichoderma Harzianum: Structural Organization And Substrate Recognition By Endoglucanases That Lack Cellulose Binding Module.

Plant biomass holds a promise for the production of second-generation ethanol via enzymatic hydrolysis, but its utilization as a biofuel resource is currently limited to a large extent by the cost and low efficiency of the cellulolytic enzymes. Considerable efforts have been dedicated to elucidate the mechanisms of the enzymatic process. It is well known that most cellulases possess a catalytic core domain and a carbohydrate binding module (CBM), without which the enzymatic activity can be drastically reduced. However, Cel12A members of the glycosyl hydrolases family 12 (GHF12) do not bear a CBM and yet are able to hydrolyze amorphous cellulose quite efficiently. Here, we use X-ray crystallography and molecular dynamics simulations to unravel the molecular basis underlying the catalytic capability of endoglucanase 3 from Trichoderma harzianum (ThEG3), a member of the GHF12 enzymes that lacks a CBM. A comparative analysis with the Cellulomonas fimi CBM identifies important residues mediating interactions of EG3s with amorphous regions of the cellulose. For instance, three aromatic residues constitute a harboring wall of hydrophobic contacts with the substrate in both ThEG3 and CfCBM structures. Moreover, residues at the entrance of the active site cleft of ThEG3 are identified, which might hydrogen bond to the substrate. We advocate that the ThEG3 residues Asn152 and Glu201 interact with the substrate similarly to the corresponding CfCBM residues Asn81 and Arg75. Altogether, these results show that CBM motifs are incorporated within the ThEG3 catalytic domain and suggest that the enzymatic efficiency is associated with the length and position of the substrate chain, being higher when the substrate interact with the aromatic residues at the entrance of the cleft and the catalytic triad. Our results provide guidelines for rational protein engineering aiming to improve interactions of GHF12 enzymes with cellulosic substrates.8e5906