Design of a dedicated beamline for x-ray microfocusing- and coherence- based techniques at the Advanced Photon Source

A dedicated insertion-device beamline has been designed and is being constructed at the Advanced Photon Source (APS) for development of x- ray microfocusing- and coherence-based techniques and applications. Important parameters considered in this design include preservation of source brilliance and coherence, selectable transverse coherence length and energy bandwidth, high beam angular stability, high order harmonic suppression, quick x-ray energy scan, and accurate and stable x-ray energy. The overall design of this beamline layout and the major beamline components are described. The use of a horizontally deflecting mirror as the first optical component is one of the main features of this beamline design, and the resulting advantages are briefly discussed

11 nm hard X-ray focus from a large-aperture multilayer Laue lens

The focusing performance of a multilayer Laue lens (MLL) with 43.4 μm aperture, 4 nm finest zone width and 4.2 mm focal length at 12 keV was characterized with X-rays using ptychography method. The reconstructed probe shows a full-width-at-half-maximum (FWHM) peak size of 11.2 nm. The obtained X-ray wavefront shows excellent agreement with the dynamical calculations, exhibiting aberrations less than 0.3 wave period, which ensures the MLL capable of producing a diffraction-limited focus while offering a sufficient working distance. This achievement opens up opportunities of incorporating a variety of in-situ experiments into ultra high-resolution X-ray microscopy studies

A hard x-ray scanning microprobe for fluorescence imaging and microdiffraction at the Advanced Photon Source

A hard x-ray scanning microprobe based on zone plate optics and undulator radiation, in the energy region from 6 to 20 keV, has reached a focal spot size (FWHM) of 0.15 {micro}m (v) x 0.6 {micro}m (h), and a photon flux of 4 x 10{sup 9} photons/sec/0.01%BW. Using a slit 44 meters upstream to create a virtual source, a circular beam spot of 0.15 {micro}m in diameter can be obtained with a photon flux of one order of magnitude less. During fluorescence mapping of trace elements in a single human ovarian cell, the microprobe exhibited an imaging sensitivity for Pt (L{sub a} line) of 80 attograms/{micro}m{sup 2} for a count rate of 10 counts per second. The x-ray microprobe has been used to map crystallographic strain and multiquantum well thickness in micro-optoelectronic devices produced with the selective area growth technique

Quantitative X-ray wavefront measurements of Fresnel zone plate and K-B mirrors using phase retrieval

A scanning coherent diffraction imaging method was used to reconstruct the X-ray wavefronts produced by a Fresnel zone plate (FZP) and by Kirkpatrick-Baez (KB) focusing mirrors. The ptychographical measurement was conducted repeatedly by placing a lithographed test sample at different defocused planes. The wavefronts, recovered by phase-retrieval at well-separated planes, show good consistency with numerical propagation results, which provides a self-verification. The validity of the obtained FZP wavefront was further confirmed with theoretical predictions

A method for phase reconstruction from measurements obtained using a configured detector with a scanning transmission X-ray microscope

Abstract We developed a technique for performing quantitative phase reconstructions from differential phase contrast images obtained using a configured detector in a scanning transmission X-ray microscope geometry. The technique uses geometric optics to describe the interaction of the X-ray beam with the specimen, which allows interpretation of the measured intensities in terms of the derivative of the phase thickness. Integration of the resulting directional derivatives is performed using a Fourier integration technique. We demonstrate the approach by reconstructing simulated measurements of a 0:5Àmm-diameter gold sphere at 7-keV photon energy. Published by Elsevier B.V

Sites of transcription initiation drive mRNA isoform selection

The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3' end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify mRNA isoforms in Drosophila tissues, including the transcriptionally complex nervous system. We find that in Drosophila heads, as well as in human cerebral organoids, 3' end site choice is globally influenced by the site of transcription initiation (TSS). "Dominant promoters," characterized by specific epigenetic signatures including p300/CBP binding, impose a transcriptional constraint to define splice and polyadenylation variants. In vivo deletion or overexpression of dominant promoters as well as p300/CBP loss disrupted the 3' end expression landscape. Our study demonstrates the crucial impact of TSS choice on the regulation of transcript diversity and tissue identity

Approccio globale alle mucopolisaccaridosi: applicazione di metodi altamente specifici per la diagnosi neonatale: risultati preliminari su campione di urina

Scopo dello studio Le Mucopolisaccaridosi (MPS) sono patologie multisistemiche ed invalidanti ad alto grado di mortalit\ue0 e morbidit\ue0, spesso diagnosticate in ritardo quando si sono gi\ue0 verificati danni irreversibili agli organi. Una diagnosi precoce ed accurata risulta quindi importante per la consulenza genetica alla famiglia e per ottimizzare le terapie che risultano pi\uf9 efficaci se attuate sin dalle prime settimane di vita del neonato, anche in assenza di un\u2019evidente sintomatologia. Obiettivo dello studio \ue8 quello di individuare marker affidabili, in grado di identificare diverse forme di MPS in una singola analisi. Campioni di sangue su spot (DBS) saranno analizzati attraverso una tecnica HPLC per la determinazione quantitativa e qualitativa dei disaccaridi che compongono i GAG, dopo il trattamento con enzimi specifici. Come controllo, i campioni di urine degli stessi soggetti verranno analizzati attraverso metodi standard: il saggio al colorante DMB e l\u2019elettroforesi su acetato di cellulosa. Vengono qui presentati i risultati della valutazione quantitativa e qualitativa dei GAG urinari. Metodi utilizzati Sono stati raccolti campioni di urina da 450 neonati sani a termine, dal 3\ub0 al 5\ub0 giorno di vita. La determinazione quantitativa dei GAG urinari totali \ue8 stata condotta mediante DMB test ed elettroforesi su acetato di cellulosa per identificare il pattern dei GAG escreti. Risultati La valutazione quantitativa dei GAG totali, con un valore medio di 227 \ub1 91 \ub5g GAG/mg di creatinina, ha messo in evidenza quantit\ue0 di GAG superiori (>50%) rispetto al valore medio di riferimento (114 \ub1 57 \ub5g GAG/mg di creatinina nella fascia di et\ue0 0-1 anno). Tutti i soggetti finora analizzati hanno mostrato all\u2019elettroforesi un pattern qualitativo normale rispetto ai patologici utilizzati come controllo. Conclusioni Lo studio si inserisce nell\u2019ambito di un progetto multicentrico triennale e fornir\ue0 un\u2019analisi di distribuzione dei valori normali dei GAG urinari nei primi giorni di vita, una valutazione dell\u2019affidabilit\ue0 del nuovo metodo per la determinazione dei disaccaridi su DBS e una stima della sua applicabilit\ue0. Ricerca in parte finanziata con fondi Progetto PRIN 201

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