Reliable LC3 and p62 autophagy marker detection in formalin fixed paraffin embedded human tissue by immunohistochemistry

Autophagy assures cellular homeostasis, and gains increasing importance in cancer, where it impacts on carcinogenesis, propagation of the malignant phenotype and development of resistance. To date, its tissue-based analysis by immunohistochemistry remains poorly standardized. Here we show the feasibility of specifically and reliably assessing the autophagy markers LC3B and p62 (SQSTM1) in formalin fixed and paraffin embedded human tissue by immunohistochemistry. Preceding functional experiments consisted of depleting LC3B and p62 in H1299 lung cancer cells with subsequent induction of autophagy. Western blot and immunofluorescence validated antibody specificity, knockdown efficiency and autophagy induction prior to fixation in formalin and embedding in paraffin. LC3B and p62 antibodies were validated on formalin fixed and paraffin embedded cell pellets of treated and control cells and finally applied on a tissue microarray with 80 human malignant and non-neoplastic lung and stomach formalin fixed and paraffin embedded tissue samples. Dot-like staining of various degrees was observed in cell pellets and 18/40 (LC3B) and 22/40 (p62) tumors, respectively. Seventeen tumors were double positive for LC3B and p62. P62 displayed additional significant cytoplasmic and nuclear staining of unknown significance. Interobserver-agreement for grading of staining intensities and patterns was substantial to excellent (kappa values 0.60 - 0.83). In summary, we present a specific and reliable IHC staining of LC3B and p62 on formalin fixed and paraffin embedded human tissue. Our presented protocol is designed to aid reliable investigation of dysregulated autophagy in solid tumors and may be used on large tissue collectives.

Resolving diffusion in clay minerals at different time scales: Combination of experimental and modeling approaches

Since no single experimental or modeling technique provides data that allow a description of transport processes in clays and clay minerals at all relevant scales, several complementary approaches have to be combined to understand and explain the interplay between transport relevant phenomena. In this paper molecular dynamics simulations (MD) were used to investigate the mobility of water in the interlayer of montmorillonite (Mt), and to estimate the influence of mineral surfaces and interlayer ions on the water diffusion. Random Walk (RW) simulations based on a simplified representation of pore space in Mt were used to estimate and understand the effect of the arrangement of Mt particles on the meso- to macroscopic diffusivity of water. These theoretical calculations were complemented with quasielastic neutron scattering (QENS) measurements of aqueous diffusion in Mt with two pseudo-layers of water performed at four significantly different energy resolutions (i.e. observation times). The size of the interlayer and the size of Mt particles are two characteristic dimensions which determine the time dependent behavior of water diffusion in Mt. MD simulations show that at very short time scales water dynamics has the characteristic features of an oscillatory motion in the cage formed by neighbors in the first coordination shell. At longer time scales, the interaction of water with the surface determines the water dynamics, and the effect of confinement on the overall water mobility within the interlayer becomes evident. At time scales corresponding to an average water displacement equivalent to the average size of Mt particles, the effects of tortuosity are observed in the meso- to macroscopic pore scale simulations. Consistent with the picture obtained in the simulations, the QENS data can be described using a (local) 3D diffusion at short observation times, whereas at sufficiently long observation times a 2D diffusive motion is clearly observed. The effects of tortuosity measured in macroscopic tracer diffusion experiments are in qualitative agreement with RW simulations. By using experimental data to calibrate molecular and mesoscopic theoretical models, a consistent description of water mobility in clay minerals from the molecular to the macroscopic scale can be achieved. In turn, simulations help in choosing optimal conditions for the experimental measurements and the data interpretation. (C) 2014 Elsevier B.V. All rights reserved.

Diffusion transport of water in basalts

Studying diffusive transport in porous rocks is of fundamental importance in understanding a variety of geochemical processes including: element transfer, primary mineral dissolution kinetics and precipitation of secondary phases. Here we report new findings on the relationship between diffusive transport and textural characteristics of the pore systems on the example of mid-oceanic ridge basalts having different degree of alteration but very similar bulk pore volume. Diffusion processes in porous basalts were studied in situ using H2O -> D2O exchange experiments. The effective diffusion coefficients of water molecules increase systematically from 5.05*10**-11 to 1.19*10**-10 m**2/s for fresh and moderately altered basalts and from 2.40*10**-11 to 6.72*10**-11 m**2/s for completely altered basalt as temperature increases from 5 to 50 °C. The activation energy of the diffusion process increases from 12.29 ± 0.71 kJ/mol for fresh and moderately altered basalts to 14.3 ± 1.33 kJ/mol for completely altered basalt. The results indicate that neither the bulk porosity nor the degree of alteration can be used as proxies for the efficiency of element transport during MORB-water interaction. The formation of secondary phases that replace primary minerals and fill the pore space in the rock leads to the formation of tiny pores and phases with large specific surface area. These factors might have a dominant control on the transport properties of altered basaltic rocks.

Seawater carbonate chemistry, nutrients, growth rate and phytoplnkton community response to increasing CO2 concentration during experiments, 2011

This paper reports for the first time upon the effects of increasing CO2 concentrations on a natural phytoplankton assemblage in a tropical estuary (the Godavari River Estuary in India). Two short-term (5-day) bottle experiments were conducted (with and without nutrient addition) during the pre-monsoon season when the partial pressure of CO2 in the surface water is quite low. The results reveal that the concentrations of total chlorophyll, the phytoplankton growth rate, the concentrations of particulate organic matter, the photosynthetic oxygen evolution rates, and the total bacterial count were higher under elevated CO2 treatments, as compared to ambient conditions (control). delta13C of particulate organic matter (POM) varied inversely with respect to CO2, indicating a clear signature of higher CO2 influx under the elevated CO2 levels. Whereas, delta13CPOM in the controls indicated the existence of an active bicarbonate transport system under limited CO2 supply. A considerable change in phytoplankton community structure was noticed, with marker pigment analysis by HPLC revealing that cyanobacteria were dominant over diatoms as CO2 concentrations increased. A mass balance calculation indicated that insufficient nutrients (N, P and Si) might have inhibited diatomgrowth compared to cyanobacteria, regardless of increased CO2 supply. The present study suggests that CO2 concentration and nutrient supply could have significant effects on phytoplankton physiology and community composition for natural phytoplankton communities in this region. However, this work was conducted during a non-discharge period (nutrient-limited conditions) and the responses of phytoplankton to increasing CO2 might not necessarily be the same during other seasons with high physicochemical variability. Further investigation is therefore needed.

Experimental determination of barium isotope fractionation during diffusion and adsorption processes at low temperatures

Variations in barium (Ba) stable isotope abundances measured in low and high temperature environments have recently received increasing attention. The actual processes controlling Ba isotope fractionation, however, remain mostly elusive. In this study, we present the first experimental approach to quantify the contribution of diffusion and adsorption on mass- dependent Ba isotope fractionation during transport of aqueous Ba2+ ions through a porous medium. Experiments have been carried out in which a BaCl2 solution of known isotopic composition diffused through u-shaped glass tubes filled with silica hydrogel at 10 C and 25 C for up to 201 days. The diffused Ba was highly fractionated by up to -2.15‰ in d137/134Ba, despite the low relative difference in atomic mass. The time-dependent isotope fractionation can be successfully reproduced by a diffusive transport model accounting for mass-dependent differences in the effective diffusivities of the Ba isotope species (D137Ba/D134Ba = (m134/m137)^b). Values of b extracted from the transport model were in the range of 0.010–0.011. Independently conducted batch experiments revealed that adsorption of Ba onto the surface of silica hydrogel favoured the heavier Ba isotopes (a = 1.00015 ± 0.00008). The contribution of adsorption on the overall isotope fractionation in the diffusion experiments, however, was found to be small. Our results contribute to the understanding of Ba isotope fractionation pro- cesses, which is crucial for interpreting natural isotope variations and the assessment of Ba isotope ratios as geochemical proxies.

Diffusion Issues of Heat and Light Species in Laser Fusion Devices

There are several heat and mass diffusion problems which affect to the IFC chamber design. New simulation models and experiments are needed to take into account the extreme conditions due to ignition pulses and neutron flux

A subgrid viscosity Lagrance-Galerkin method for convection-diffusion problems

We present and analyze a subgrid viscosity Lagrange-Galerk in method that combines the subgrid eddy viscosity method proposed in W. Layton, A connection between subgrid scale eddy viscosity and mixed methods. Appl. Math. Comp., 133: 14 7-157, 2002, and a conventional Lagrange-Galerkin method in the framework of P1⊕ cubic bubble finite elements. This results in an efficient and easy to implement stabilized method for convection dominated convection diffusion reaction problems. Numerical experiments support the numerical analysis results and show that the new method is more accurate than the conventional Lagrange-Galerkin one.

Coilin Shuttles between the Nucleus and Cytoplasm In Xenopus Oocytes

Coiled bodies are discrete nuclear organelles often identified by the marker protein p80-coilin. Because coilin is not detected in the cytoplasm by immunofluorescence and Western blotting, it has been considered an exclusively nuclear protein. In the Xenopus germinal vesicle (GV), most coilin actually resides in the nucleoplasm, although it is highly concentrated in 50–100 coiled bodies. When affinity-purified anti-coilin antibodies were injected into the cytoplasm of oocytes, they could be detected in coiled bodies within 2–3 h. Coiled bodies were intensely labeled after 18 h, whereas other nuclear organelles remained negative. Because the nuclear envelope does not allow passive diffusion of immunoglobulins, this observation suggests that anti-coilin antibodies are imported into the nucleus as an antigen–antibody complex with coilin. Newly synthesized coilin is not required, because cycloheximide had no effect on nuclear import and subsequent targeting of the antibodies. Additional experiments with myc-tagged coilin and myc-tagged pyruvate kinase confirmed that coilin is a shuttling protein. The shuttling of Nopp140, NO38/B23, and nucleolin was easily demonstrated by the targeting of their respective antibodies to the nucleoli, whereas anti-SC35 did not enter the germinal vesicle. We suggest that coilin, perhaps in association with Nopp140, may function as part of a transport system between the cytoplasm and the coiled bodies.

Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells

Fluorescein-labeled oligodeoxynucleotides (oligos) were introduced into cultured rat myoblasts, and their molecular movements inside the nucleus were studied by fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). FCS revealed that a large fraction of both intranuclear oligo(dT) (43%) and oligo(dA) (77%) moves rapidly with a diffusion coefficient of 4 × 10−7 cm2/s. Interestingly, this rate of intranuclear oligo movement is similar to their diffusion rates measured in aqueous solution. In addition, we detected a large fraction (45%) of the intranuclear oligo(dT), but not oligo(dA), diffusing at slower rates (≤1 × 10−7 cm2/s). The amount of this slower-moving oligo(dT) was greatly reduced if the oligo(dT) was prehybridized in solution with (unlabeled) oligo(dA) prior to introduction to cells, presumably because the oligo(dT) was then unavailable for subsequent hybridization to endogenous poly(A) RNA. The FCS-measured diffusion rate for much of the slower oligo(dT) population approximated the diffusion rate in aqueous solution of oligo(dT) hybridized to a large polyadenylated RNA (1.0 × 10−7 cm2/s). Moreover, this intranuclear movement rate falls within the range of calculated diffusion rates for an average-sized heterogeneous nuclear ribonucleoprotein particle in aqueous solution. A subfraction of oligo(dT) (15%) moved over 10-fold more slowly, suggesting it was bound to very large macromolecular complexes. Average diffusion coefficients obtained from FRAP experiments were in agreement with the FCS data. These results demonstrate that oligos can move about within the nucleus at rates comparable to those in aqueous solution and further suggest that this is true for large ribonucleoprotein complexes as well.

The Chlorella hexose/H+ symporter is a useful selectable marker and biochemical reagent when expressed in Volvox.

The multicellular obligately photoautotrophic alga Volvox is composed of only two types of cells, somatic and reproductive. Therefore, Volvox provides the simplest model system for the study of multicellularity. Metabolic labeling experiments using radioactive precursors are crucial for the detection of stage- and cell-type-specific proteins, glycoproteins, lipids, and carbohydrates. However, wild-type Volvox lacks import systems for sugars or amino acids. To circumvent this problem, the hexose/H+ symporter (HUP1) gene from the unicellular alga Chlorella was placed under the control of the constitutive Volvox beta-tubulin promoter. The corresponding transgenic Volvox strain synthesized the sugar transporter in a functional state and was able to efficiently incorporate 14C from labeled glucose or glucosamine. Sensitivity toward the toxic glucose/mannose analogue 2-deoxy-glucose increased by orders of magnitude in transformants. Thus we report the successful transformation of Volvox with a gene of heterologous origin. The chimeric gene may be selected for in either a positive or a negative manner, because transformants exhibit both prolonged survival in the dark in the presence of glucose and greatly increased sensitivity to the toxic sugar 2-deoxyglucose. The former trait may make the gene useful as a dominant selectable marker for use in transformation studies, whereas the latter trait may make it useful in development of a gene-targeting system.

μ-MAR: Multiplane 3D Marker based Registration for depth-sensing cameras

Many applications including object reconstruction, robot guidance, and. scene mapping require the registration of multiple views from a scene to generate a complete geometric and appearance model of it. In real situations, transformations between views are unknown and it is necessary to apply expert inference to estimate them. In the last few years, the emergence of low-cost depth-sensing cameras has strengthened the research on this topic, motivating a plethora of new applications. Although they have enough resolution and accuracy for many applications, some situations may not be solved with general state-of-the-art registration methods due to the signal-to-noise ratio (SNR) and the resolution of the data provided. The problem of working with low SNR data, in general terms, may appear in any 3D system, then it is necessary to propose novel solutions in this aspect. In this paper, we propose a method, μ-MAR, able to both coarse and fine register sets of 3D points provided by low-cost depth-sensing cameras, despite it is not restricted to these sensors, into a common coordinate system. The method is able to overcome the noisy data problem by means of using a model-based solution of multiplane registration. Specifically, it iteratively registers 3D markers composed by multiple planes extracted from points of multiple views of the scene. As the markers and the object of interest are static in the scenario, the transformations obtained for the markers are applied to the object in order to reconstruct it. Experiments have been performed using synthetic and real data. The synthetic data allows a qualitative and quantitative evaluation by means of visual inspection and Hausdorff distance respectively. The real data experiments show the performance of the proposal using data acquired by a Primesense Carmine RGB-D sensor. The method has been compared to several state-of-the-art methods. The results show the good performance of the μ-MAR to register objects with high accuracy in presence of noisy data outperforming the existing methods.

Diffusion modeling of percutaneous absorption kinetics: 3. Variable diffusion and partition coefficients, consequences for stratum corneum depth profiles and desorption kinetics

Stratum corneum (SC) desorption experiments have yielded higher calculated steady-state fluxes than those obtained by epidermal penetration studies. A possible explanation of this result is a variable diffusion or partition coefficient across the SC. We therefore developed the diffusion model for percutaneous penetration and desorption to study the effects of either a variable diffusion coefficient or variable partition coefficient in the SC over the diffusion path length. Steady-state flux, lag time, and mean desorption time were obtained from Laplace domain solutions. Numerical inversion of the Laplace domain solutions was used for simulations of solute concentration-distance and amount penetrated (desorbed)-time profiles. Diffusion and partition coefficients heterogeneity were examined using six different models. The effect of heterogeneity on predicted flux from desorption studies was compared with that obtained in permeation studies. Partition coefficient heterogeneity had a more profound effect on predicted fluxes than diffusion coefficient heterogeneity. Concentration-distance profiles show even larger dependence on heterogeneity, which is consistent with experimental tape-stripping data reported for clobetasol propionate and other solutes. The clobetasol propionate tape-stripping data were most consistent with the partition coefficient decreasing exponentially for half the SC and then becoming a constant for the remaining SC. (C) 2004 Wiley-Liss, Inc.

Quantum effects on adsorption and diffusion of hydrogen and deuterium in microporous materials

Monte Carlo and molecular dynamics simulations and neutron scattering experiments are used to study the adsorption and diffusion of hydrogen and deuterium in zeolite Rho in the temperature range of 30-150 K. In the molecular simulations, quantum effects are incorporated via the Feynman-Hibbs variational approach. We suggest a new set of potential parameters for hydrogen, which can be used when Feynman-Hibbs variational approach is used for quantum corrections. The dynamic properties obtained from molecular dynamics simulations are in excellent agreement with the experimental results and show significant quantum effects on the transport at very low temperature. The molecular dynamics simulation results show that the quantum effect is very sensitive to pore dimensions and under suitable conditions can lead to a reverse kinetic molecular sieving with deuterium diffusing faster than hydrogen.

Transport diffusion of gases is rapid in flexible carbon nanotu

Molecular dynamics simulations of rigid, defect-free single-walled carbon nanotubes have previously suggested that the transport diffusivity of gases adsorbed in these materials can be orders of magnitude higher than any other nanoporous material (A. I. Skoulidas et al., Phys. Rev. Lett. 2002, 89, 185901). These simulations must overestimate the molecular diffusion coefficients because they neglect energy exhange between the diffusing molecules and the nanotube. Recently, Jakobtorweihen et al. have reported careful simulations of molecular self-diffusion that allow nanotube flexibility (Phys. Rev. Lett. 2005, 95, 044501). We have used the efficient thermostat developed by Jakobtorweihen et al. to examine the influence of nanotube flexibility on the transport diffusion of CH4 in (20,0) and (15,0) nanotubes. The inclusion of nanotube flexibility reduces the transport diffusion relative to the rigid nanotube by roughly an order of magnitude close to zero pressure, but at pressures above about I bar the transport diffusivities for flexible and rigid nanotubes are very similar, differing by less than a factor or two on average. Hence, the transport diffusivities are still extremely large compared to other known materials when flexibility is taken into account.

8-Hydroxydeoxyguanosine. A marker of oxidative DNA damage in systemic lupus erythematosus

8-Hydroxydeoxyguanosine (80HDG) is a specific marker of oxidative damage to DNA. We have observed that patients with SLE (systemic lupus erythematosus), have undetectable levels of urinary 80HDG by HPLC. Further analysis by GC-MS confirmed that levels of 80HDG in SLE urine were 10(3)-fold lower than in an age- and sex-matched control group. Experiments utilising cultures of SLE and normal lymphocytes exposed to H2O2 confirmed the impaired ability of SLE lymphocytes to repair 80HDG. We subsequently observed in SLE patients that 80HDG had accumulated in low molecular weight DNA associated with circulating immune complexes. We suggest that oxygen radicals may induce pathology in SLE by maintaining the presence of an antigenic form of DNA in the circulation.