Combined X-ray microfluorescence and atomic force microscopy studies of Mg distribution in whole cells

We present in this paper a novel methodology that combines scanning x\u2010ray fluorescencee microscopy and atomic force microscopy. The combination of these two techniques allows the determination of a concentration map of Mg in whole (not sectioned) cells

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

High-resolution x-ray imaging for microbiology at the Advanced Photon Source

Exciting new applications of high-resolution x-ray imaging have emerged recently due to major advances in high-brilliance synchrotrons sources and high-performance zone plate optics. Imaging with submicron resolution is now routine with hard x-rays: the authors have demonstrated 150 run in the 6--10 keV range with x-ray microscopes at the Advanced Photon Source (APS), a third-generation synchrotrons radiation facility. This has fueled interest in using x-ray imaging in applications ranging from the biomedical, environmental, and materials science fields to the microelectronics industry. One important application they have pursued at the APS is a study of the microbiology of bacteria and their associated extracellular material (biofilms) using fluorescence microanalysis. No microscopy techniques were previously available with sufficient resolution to study live bacteria ({approx}1 {micro}m x 4 {micro}m in size) and biofilms in their natural hydrated state with better than part-per-million elemental sensitivity and the capability of determining g chemical speciation. In vivo x-ray imaging minimizes artifacts due to sample fixation, drying, and staining. This provides key insights into the transport of metal contaminants by bacteria in the environment and potential new designs for remediation and sequestration strategies

MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences.

Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres. Surprisingly, amplified genes (mainly PVT1) frequently participated in fusion transcripts lacking a corresponding DNA template. We also detected a significant overexpression of the circular RNA of PVT1 (circPVT1) in AML-amp cases versus AML with a normal karyotype. Our results show that 8q24 amplicons in AML are surprisingly plastic DNA structures with an unexpected association to novel fusion transcripts and circular RNAs

Electronic structure of disordered CuPd alloys by positron-annihilation 2D-ACAR

We report 2D-ACAR experiments and KKR CPA calculations on alpha-phase single-crystal Cu/sub 1-x/Pd/sub x/ in the range x less than or equal to 0.25. The flattening of the Fermi surface near (110) with increasing x predicted by theory is confirmed by our experimental results. 16 refs., 2 figs

Positron-annihilation measurements of vacancy formation in Ni and Ni(Ge)

Vacancy formation in Ni and in dilute Ni(Ge) alloys was studied under thermal equilibrium conditions using positron-annihilation Doppler broadening. A monovacancy formation enthalpy of 1.8 +- 0.1 eV was determined for pure Ni; combining this result with that from previous tracer self-diffusion measurements, a monovacancy migration enthalpy of 1.1 +- 0.1 eV was also deduced. Analysis of the vacancy formation measurements in Ni(0.3 at.% Ge) and Ni(1 at.% Ge) yielded a value for the vacancy-Ge binding enthalpy of 0.20 +- 0.04 eV

Low-temperature effects in metals as observed by positron annihilation

Recently published experimental positron annihilation data in metals have demonstrated exceptional temperature-dependent behavior in the prevacancy region. However, the magnitude of these effects seems at present to scatter widely among different observers. New lifetime and Doppler-broadening results for Au between 30 and 590/sup 0/K are presented and compared to results obtained in other laboratories. Doppler-broadening results obtained for Cu in the temperature region 300 to 1310/sup 0/K demonstrate that some temperature-dependent structure observed in the prevacancy region is related to the thermal history of the sample

Using x-ray microprobes for environmental research.

Understanding the fate of environmental contaminants is of fundamental importance in the development and evaluation of effective remediation strategies. Among the factors influencing the transport of these contaminants are the chemical speciation of the sample and the chemical and physical attributes of the surrounding medium. Characterization of the spatial distribution and chemical speciation at micron and submicron resolution is essential for studying the microscopic physical, geological, chemical, and biological interfaces that play a crucial role in determining contaminant fate and mobility. Hard X-ray spectroscopy and imaging are powerful techniques for the element-specific investigation of complex environmental samples at the needed micron and submicron resolution. An important advantage of these techniques results from the large penetration depth of hard X-rays in water. This minimizes the requirements for sample preparation and allows the detailed study of hydrated samples. This paper discusses some current problems in environmental science that can be addressed by using synchrotron-based X-ray imaging and spectroscopy. These concepts are illustrated by the results of recent X-ray microscopy studies at the Advanced Photon Source