Iterative fragmentation improves the detection of ChIP-seq peaks for inactive histone marks

As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication –- sending the fragmented DNA after ChIP through additional round(s) of shearing –- to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pipeline that utilizes our unique, enrichment-type specific approach to peak calling. With the help of this pipeline, we managed to accurately describe the advantages and disadvantages of the iterative refragmentation technique, and we successfully identified possible fields for its applications, where it enhances the results greatly. In addition to the resonication protocol description, we provide guidelines for peak calling optimization and a freely implementable pipeline for data analysis

Wavefront shaping optics for laser-generated plasma heating

The use of pupil plane phase masks provides a useful and efficient method of manipulating focal région light distributions. Such masks have found application in the telecommunication sector, including the use of Fourier plane replicating holograms for weighted beamlet array generation for the addressing of optoelectronic devices. Rather than modifying the focal pattern at the focal plane, the through focus intensity distribution may also be controlled with an appropriately designed phase mask. In a high numerical aperture optical System, as is used for laser generated plasma X-ray sources, such phase mask can extend the depth of focus of the irradiating laser beam, to achieve more uniform plasma heating and consequently, a better shot-to-shot repeatability from the X-ray source

Noninvasive Perioperative Monitoring of Arterial Function in Patients With Kidney Transplantation

ABSTRACTDevelopment of atherosclerosis is accelerated in kidney transplant recipients. Impairedmetabolic pathways have a complex effect on the arterial wall, which can be measured bynoninvasive techniques. Few data are available on the change of stiffness parameters in thepostoperative course, so in this study we analyzed the stiffness parameters of kidneytransplant recipients during the perioperative period. Seventeen successful primary kidneytransplant patients with uneventful postoperative period (7 woman, 10 men; 46.16 12.19years) were involved in our short-term prospective longitudinal study. We analyzed thecorrelation between noninvasively assessed stiffness parameters (pulse wave velocity[PWV], augmentation index [AIx], pulse pressure [PP], systolic area index, diastolic areaindex, diastolic reflection area), ankle-brachial index (ABI), and laboratory parameters(creatinine, glomerular filtration rate, urea, haemoglobin, C-reactive protein). Stiffnessparameters were measured with a Tensiomed Arteriograph. These parameters wereassessed before the transplantation, and 24 hours, and 1 and 2 weeks after surgery understandard conditions. We found that creatinine (P ¼ .0008) and C-reactive protein(P ¼ .006) serum levels decreased, and glomerular filtration rate increased significantly(P ¼ .0005). We revealed that PWV (P ¼ .0075) and AIx (P ¼ .013) improved significantly.There was no significant change in ABI, PP, and the other monitored parameters. Alongwith the available data in the literature, our findings suggest that kidney transplantation hasa positive effect on the arterial function

Dynamic manipulation of Bose-Einstein condensates with a spatial light modulator

We manipulate a Bose-Einstein condensate using the optical trap created by the diffraction of a laser beam on a fast ferro-electric liquid crystal spatial light modulator. The modulator acts as a phase grating which can generate arbitrary diffraction patterns and be rapidly reconfigured at rates up to 1 kHz to create smooth, time-varying optical potentials. The flexibility of the device is demonstrated with our experimental results for splitting a Bose-Einstein condensate and independently transporting the separate parts of the atomic cloud.Comment: 4 pages, 4 figure