Fast Bayesian inference of optical trap stiffness and particle diffusion

Bayesian inference provides a principled way of estimating the parameters of a stochastic process that is observed discretely in time. The overdamped Brownian motion of a particle confined in an optical trap is generally modelled by the Ornstein-Uhlenbeck process and can be observed directly in experiment. Here we present Bayesian methods for inferring the parameters of this process, the trap stiffness and the particle diffusion coefficient, that use exact likelihoods and sufficient statistics to arrive at simple expressions for the maximum a posteriori estimates. This obviates the need for Monte Carlo sampling and yields methods that are both fast and accurate. We apply these to experimental data and demonstrate their advantage over commonly used non-Bayesian fitting methods.

Density of states in graphene with vacancies: midgap power law and frozen multifractality

The density of states ϱ(E) of graphene is investigated numerically and within the self-consistent T-matrix approximation in the presence of vacancies within the tight binding model. The focus is on compensated disorder, where the concentration of vacancies n(A) and n(B) in both sublattices is the same. Formally, this model belongs to the chiral symmetry class BDI. The onlinear sigma model predicts for BDI a Gade-type singularity ϱ(E)∼|E|(-1)exp[-|log(E)|(-1/x)]. Our numerical data are comparable to this result in a preasymptotic regime that gives way, however, at even lower energies to ϱ(E)∼E(-1)|log(E)|(-x̃), 1≤x̃<2. We take this finding as evidence that, similar to the case of dirty d-wave superconductors, generic bipartite random hopping models may also exhibit unconventional (strong-coupling) fixed points for certain kinds of randomly placed scatterers if these are strong enough. Our research suggests that graphene with (effective) vacancy disorder is a physical representative of such systems.

The effects of selenium and the GPx-1 selenoprotein on the phosphorylation of H2AX

BACKGROUND

Significant data supports the health benefits of selenium although supplementation trials have yielded mixed results. GPx-1, whose levels are responsive to selenium availability, is implicated in cancer etiology by human genetic data. Selenium's ability to alter the phosphorylation of the H2AX, a histone protein that functions in the reduction of DNA damage by recruiting repair proteins to the damage site, following exposure to ionizing radiation and bleomycin was investigated.

METHODS

Human cell lines that were either exposed to selenium or were transfected with a GPx-1 expression construct were exposed to ionizing radiation or bleomycin. Phosphorylation of histone H2AX was quantified by flow cytometry and survival by the MTT assay. Phosphorylation of the Chk1 and Chk2 checkpoint proteins was quantified by western blotting.

RESULTS

In colon-derived cells, selenium increases GPx-1 and attenuated H2AX phosphorylation following genotoxic exposures while the viability of these cells was unaffected. MCF-7 cells and transfectants that express high GPx-1 levels were exposed to ionizing radiation and bleomycin, and H2AX phosphorylation and cell viability were assessed. GPx-1 increased H2AX phosphorylation and viability following the induction of DNA damage while enhancing the levels of activated Chk1 and Chk2.

CONCLUSIONS

Exposure of mammalian cells to selenium can alter the DNA damage response and do so by mechanisms that are dependent and independent of its effect on GPx-1.

GENERAL SIGNIFICANCE

Selenium and GPx-1 may stimulate the repair of genotoxic DNA damage and this may account for some of the benefits attributed to selenium intake and elevated GPx-1 activity.

Diffusion and criticality in undoped graphene with resonant scatterers

A general theory is developed to describe graphene with an arbitrary number of isolated impurities. The theory provides a basis for an efficient numerical analysis of the charge transport and is applied to calculate the Dirac-point conductivity σ of graphene with resonant scatterers. In the case of smooth resonant impurities the symmetry class is identified as DIII and σ grows logarithmically with increasing impurity concentration. For vacancies (or strong on-site potential impurities, class BDI) σ saturates at a constant value that depends on the vacancy distribution among two sublattices.

Molecular characterization of tumor associated glyceraldehyde-3-phosphate dehydrogenase

Here we describe the purification of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from normal leukocytes of healthy subjects and leukocytes of chronic myeloid leukemia (CML) patients and from normal mouse muscle and sarcoma tissue. The data indicate that some properties of GAPDH of leukocytes of CML patients and sarcoma tissues are similar and also similar to those of EAC (Ehrlich ascites carcinoma) cellular GAPDH but distinctly different from those of the normal cellular GAPDH. Polyclonal antiserum raised against the 54 kDa subunit of EAC cell GAPDH strongly reacted with GAPDH of leukocytes of CML patients and sarcoma tissue GAPDH only and weakly reacted with GAPDH of normal leukocyte and normal muscle and a variety of other tissues of normal rats. Both the subunits of GAPDH of sarcoma tissues were partially sequenced from the N-terminus and compared with the known sequences of GAPDH. The altered properties of GAPDH of three different malignant sources might be common feature of all malignant cells, which is discussed in relation to glycolysis and malignant aberrations.

Optimization study of the femtosecond laser-induced forward-transfer process with thin aluminum films

The parameters for an effective laser-induced forward-transfer (LIFT) process of aluminum thin films using a femtosecond laser are studied. Deposited feature size as a function of laser fluence, donor film thickness, quality of focus, and the pulse duration are varied, providing a metric of the most desirable conditions for femtosecond LIFT with thin aluminum films.

Microstructures of a Pt/Ni/C multilayer system: an X-ray reflectivity and ion scattering study

Microstructural characterization of a synthetic periodic and graded Pt/Ni/C multilayer system by X-ray reflectivity and ion scattering techniques is presented. The experimental reflectivity data are fitted with a theoretical multi-trilayer model with graded periodicity which increases from substrate to film surface along the surface normal direction. The increase in periodicity is found to be due to a linear increase in C-layer thickness from the bottom to the top, with a change of slope nearly at the middle of the multilayer stack. The thicknesses of Pt and Ni layers, the variation of C-layer thickness with depth, interface roughness of Pt/Ni, Ni/C, C/Pt interfaces are determined from the analysis of the reflectivity data. Rutherford backscattering spectrometry measurements were also made on the same sample. Simulated Rutherford back scattering spectrometry data using the parameters obtained from the analysis of the X-ray reflectivity data agree well with the measured Rutherford backscattering spectrum.

Probing atomic migration in nanostructured multilayers: application of X-ray standing wave fields

X-ray standing wave fields, excited in periodic nanostructured multilayers during Bragg diffraction, have been used to probe atomic migration in multilayers. Ion beam induced migration of Fe impurity atoms from the C layers to the Pt layers in a Pt(Fe)/C(Fe) multilayer, where each layer is about 2 nm thick, has been detected. With a depth resolution better than 0.2 nm of this technique, the direction of Fe migration (here outward) and the change of Fe concentration in C (also Pt) layers have been determined. The results of such measurements are important for understanding the properties of multilayers, for example, the evolution of ferromagnetism in the present example [Dev, Microelectron. Eng. 83, 1721 (2006)10.1016/j.mee.2006.01.230].

Development of a femtosecond micromachining workstation by use of spectral interferometry

A workstation that permits real-time measurement of ablation depth while micromachining with femtosecond laser pulses is demonstrated. This method incorporates the unamplified pulse train that is available in a chirped-pulse amplification system as the probe in an arrangement that uses spectral interferometry to measure the ablation depth while cutting with the amplified pulse in thin metal films.

Substituted hydrophobic and hydrophilic residues at methionine-68 influence the chaperone-like function of alphaB-crystallin

Amino acid residues 57-69 in alphaB-crystallin have been implicated as a target protein binding site. Moreover, a direct correlation between the extent of alpha-crystallin hydrophobicity and chaperone-like activity has been demonstrated. The purpose of this study was to mutate a moderately hydrophobic residue Met-68 (M-68) in the above region to strongly hydrophobic and hydrophilic residues and show whether chaperoning ability is affected with or without structural changes. Mutation of M-68 to Val, Ile or Thr did not result in significant changes in molecular mass and secondary and tertiary structures. However, the Val and Ile mutants showed significant improvement and the Thr mutant showed substantial loss in chaperone activity. Differences in chaperone function in the absence of any structural changes confirmed that the hydrophobicity or hydrophilicity of the substituted amino acid in the putative target protein binding site was the only contributing factor.

Substituted hydrophobic and hydrophilic residues at methionine-68 influence the chaperone-like function of alphaB-crystallin

Amino acid residues 57-69 in alphaB-crystallin have been implicated as a target protein binding site. Moreover, a direct correlation between the extent of alpha-crystallin hydrophobicity and chaperone-like activity has been demonstrated. The purpose of this study was to mutate a moderately hydrophobic residue Met-68 (M-68) in the above region to strongly hydrophobic and hydrophilic residues and show whether chaperoning ability is affected with or without structural changes. Mutation of M-68 to Val, Ile or Thr did not result in significant changes in molecular mass and secondary and tertiary structures. However, the Val and Ile mutants showed significant improvement and the Thr mutant showed substantial loss in chaperone activity. Differences in chaperone function in the absence of any structural changes confirmed that the hydrophobicity or hydrophilicity of the substituted amino acid in the putative target protein binding site was the only contributing factor.

The effect of glutathione upon chaperone activity of alpha-crystallin is probably mediated through target modulation

We studied the effect of the presence of glutathione, both reduced (GSH) and oxidized (GSSG), on the chaperone activity of alpha-crystallin towards thermal aggregation of gamma 2-crystallin. Results showed that while GSH enhanced the chaperone activity of alpha-crystallin, GSSG appeared to diminish it to some extent. When, however, the effect of the presence of glutathione was studied in the absence of alpha-crystallin, the nature of their action was found to be almost similar to that observed in its presence. These results suggest that glutathiones probably modulate the target protein which ultimately influences the chaperone activity of alpha-crystallin.

Mutation of R116C results in highly oligomerized alpha A-crystallin with modified structure and defective chaperone-like function

An autosomal dominant congenital cataract in human is associated with mutation of Arg-116 to Cys (R116C) in alpha A-crystallin. To investigate the molecular basis of cataract formation, rat alpha A-crystallin cDNA was cloned into pET-23d(+), and the site-directed mutants S142C (similar to wild-type human alpha A) and R116C/S142C or R116C (similar to human R116C variant) were generated. These were expressed in E. coli and the recombinant alpha A-crystallins purified by Sephacryl size-exclusion chromatography. The chaperone-like function of mutant R116C determined at 37 degrees C with insulin and alcohol dehydrogenase as target proteins was about 40% lower than those of wild-type and mutant S142C. Based on size-exclusion chromatography data, the oligomeric size of the R116C mutant was about 2000 kDa at 25 degrees C, 1400 kDa at 37 degrees C, and 900 kDa at 45 degrees C. In comparison, alpha A-wild-type and alpha A-S142C ranged from 477 to 581 kDa. Heat stability studies corroborated the effect of temperature on the dynamic quaternary structure of the R116C mutant. Circular dichroism spectra showed secondary and tertiary structural changes, and ANS fluorescence spectra showed loss of surface hydrophobicity in the R116C mutant. These findings suggest that the molecular basis for the congenital cataract with the alpha A-R116C mutation is due to the generation of a highly oligomerized alpha A-crystallin having a modified structure and decreased chaperone-like function.

Synthesis and antiviral studies of unsaturated analogues of isomeric dideoxynucleosides

Novel isomeric dideoxynucleosides with unsaturation in the carbohydrate moiety have been synthesized. For example, isod4A was synthesized through a rearrangement reaction involving a cyclonucleoside. Support for the structures of both purine and pyrimidine d4 compounds came from UV, NMR, HRMS and single crystal X-ray data. Interestingly, the single crystal X-ray data for isod4C shows that the base is almost orthogonal to the carbon-carbon double bond of the sugar moiety. Consistent with this is the observation that the UV data of this compound does not show a bathochromic shift compared to the saturated compound implying that the pi-bond is not in conjugation with the pyrimidine base.

Synthesis of novel isomeric dideoxydidehydronucleosides

Methodologies for the synthesis of novel isomeric dideoxynucleosides with unsaturation in the carbohydrate moiety have been developed. An example of the synthesis (Isod4A) is presented. Antiviral studies are in progress.

Small-area analysis: targeting high-risk areas for adolescent pregnancy prevention programs

CONTEXT

Traditional methods of identifying areas in need of adolescent pregnancy prevention programs may miss small localities with high levels of adolescent childbearing.

METHODS

Birthrates for 15-17-year-olds were computed for all California zip codes, and the zip codes with birthrates in the 75th percentile were identified. Panels of local experts in adolescent pregnancy reviewed these "hot spots" for accuracy and grouped them into potential project areas, based on their demographics, geography and political infrastructure.

RESULTS

In all, 415 zip codes exceeded the 75th-percentile cut-off point of 62.8 births per 1,000, and 210 of them differed significantly from the state average of 44.5 per 1,000 for 15-17-year-olds. While all had high adolescent birthrates, they varied greatly in racial and ethnic mix, poverty and educational attainment, and certain perinatal measures such as inadequate prenatal care and repeat pregnancy.

CONCLUSIONS

The use of zip code-level data holds promise for more effective program planning and intervention.

Behavioral and experiential patterns of avoidantly and securely attached women across adulthood: a 31-year longitudinal perspective

Attachment patterns of women avoidantly or securely attached at age 52 were studied using a 31-year longitudinal design and multiple perspectives, including life outcomes, observer descriptions of behavioral and personality characteristics, and self-reports of working models collected at ages 21, 27, 43, and 52. Findings from these diverse data sources provide evidence for the continuity of the behavioral and experiential patterns associated with attachment styles across adulthood. Avoidant compared with secure participants (a) experienced diverging relationship trajectories that were less happy and less steady, (b) showed a consistent pattern of behavioral and personality characteristics, including interpersonal distance, defensiveness, and vulnerability, as assessed by observers, (c) reported distinct and longitudinal consistent internal working models characterized by distrustful self-reliance and interpersonal and emotional distance, and (d) had childhood environments that afforded fewer opportunities for developing close interpersonal ties.

Interaction of H(+)-ions with alpha-crystallin: solvent accessibility of ionizable side chains and surface charge

Interaction of H(+)-ions with alpha-crystallin from goat lens has been studied at three different ionic strengths using the potentiometric titration method. Titrations have also been carried out in the presence of 1.5 M and 6 M GuHCl (guanidine hydrochloride). The isoionic pH of the protein in water and the effect of KCl on it have been determined. Titration curves have been found to be reversible between pH 3 to 9.25 at all ionic strengths. To aid in the data analyses, the reactivities of alpha-crystallin lysine residues to trinitrobenzenesulfonic acid have been determined in this work. For alpha-crystallin aggregate, 130 +/- 2 histidine side chains out of a total of 300 and about 134 +/- 4 lysine side chains out of 310 have been found to be inaccessible to the solvent in the native condition. The remaining titratable side chains determine the surface charge of the native protein. In 1.5 M GuHC1, however, the nontitratable histidine side chains are found to be available for titration as are the nontitratable lysine and tyrosine side chains in 6M GuHC1. The theoretical titration curve computed on the basis of Linderstrøm-Lang model is found to fit quite comfortably with the experimental one between pH 4.6 and 9.25. The pKint value for beta gamma-carboxyl side chains has been found to be 5.18 which is somewhat higher than usual indicating that the carboxyl groups in the protein are probably in some constrained condition which is released in the presence of a denaturant. Below pH 4.6, there begins a conformational change in the alpha-crystallin aggregate as is corroborated from the circular dichroism studies. The value of electrostatic interaction factor w which remains more or less constant between pH 4.6 and 9.25 is also found to gradually fall off below pH 4.6.

Behavioral and experiential patterns of avoidantly and securely attached women across adulthood: a 31-year longitudinal perspective

Attachment patterns of women avoidantly or securely attached at age 52 were studied using a 31-year longitudinal design and multiple perspectives, including life outcomes, observer descriptions of behavioral and personality characteristics, and self-reports of working models collected at ages 21, 27, 43, and 52. Findings from these diverse data sources provide evidence for the continuity of the behavioral and experiential patterns associated with attachment styles across adulthood. Avoidant compared with secure participants (a) experienced diverging relationship trajectories that were less happy and less steady, (b) showed a consistent pattern of behavioral and personality characteristics, including interpersonal distance, defensiveness, and vulnerability, as assessed by observers, (c) reported distinct and longitudinal consistent internal working models characterized by distrustful self-reliance and interpersonal and emotional distance, and (d) had childhood environments that afforded fewer opportunities for developing close interpersonal ties.

Chemical modifications and dissociation characteristics of tyrosine and tryptophan residues in alpha-crystallin

A quantitative estimation of surface accessibility of aromatic residues in alpha-crystallin from goat lens has been accomplished by chemical modifications using different specific reagents having varying sizes. Results of modification of tyrosine residues with N-acetylimidazole and tetranitromethane when combined with those of ionization studies carried out with hydroxyl ions having the smallest size reveal different classes of tyrosine residues in the native protein: 78 +/- 2 residues have been found to be easily available for modification; among the rest, 94 +/- 2 residues appear to be comparatively less exposed to the reagents while 28 +/- 2 residues are found to be completely unavailable for modification in the native protein and are modified only when the protein is denatured. Modification of tryptophan residues with H2O2 also indicates different classes of these residues available for oxidation at different concentrations of the oxidant. 34 +/- 2 residues of tryptophan are found to be easily oxidized at a lower concentration of H2O2 during the first phase of the reaction. The remaining tryptophan residues appear to be less exposed to the reagent. This is also corroborated from the studies of reactivities of these residues towards another specific but bulkier reagent, 2-hydroxy-5-nitrobenzyl bromide. These surface exposed aromatic residues in alpha-crystallin may be considered to be vulnerable to in vivo oxidative modifications forming insoluble aggregates which may finally contribute to the formation of cataract.