Large-scale analysis of Drosophila core promoter function using synthetic promoters

The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it “computes” expression remains poorly understood. To dissect its function, we carried out a comprehensive structure–function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters’ activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans

Degeneracija aksona i esteraza povezana s neuropatskim djelovanjem organofosfornih spojeva - pregled

This brief review summarises recent observations which suggest a possible mechanism for organophosphateinduced delayed neuropathy (OPIDN). Neuropathy target esterase (NTE) has been shown to deacylate endoplasmic reticulum (ER) membrane phosphatidylcholine (PtdCho). Raised levels of PtdCho are present in the brains of swiss cheese/NTE mutant Drosophila together with abnormal membrane structures, axonal and dendritic degeneration and neural cell loss. Similar vacuolated pathology is found in the brains of mice with brain-specific deletion of the NTE gene and, in old age, these mice show clinical and histopathological features of neuropathy resembling those in wild-type mice chronically dosed with tri-ortho-cresylphosphate. It is suggested that OPIDN results from the loss of NTE’s phospholipase activity which in turn causes ER malfunction and perturbation of axonal transport and glial-axonal interactions.Ovim se kratkim pregledom razmatraju nedavna opažanja koja upućuju na mogući mehanizam odgođene neuropatije uzrokovane organofosfatima (engl. organophosphate-induced delayed neuropathy, krat. OPIDN). Za esterazu povezanu s neuropatskim djelovanjem organofosfornih spojeva (engl. neuropathy target esterase, krat. NTE) dokazano je da deacilira fosfatidilkolin (PtdCho) membrane endoplazmatskog retikuluma (ER). Povišene razine PtdCho prisutne su u mozgu swiss cheese/NTE mutanta mušice Drosophila uz abnormalne membranske strukture, degeneraciju aksona i dendrita te gubitak neurona. Slična je vakuolarna patologija zamijećena u mozgu miševa u kojih je obrisan NTE gen u mozgu te koji u starijoj dobi pokazuju kliničke i histopatološke znakove neuropatije koja je slična onoj u običnih miševa kronično tretiranih tri-ortho-krezilfosfatom. Odgođena neuropatija uzrokovana organofosfatima mogla bi biti posljedicom prestanka djelovanja fosfolipaze NTE, što potom uzrokuje zatajenje endoplazmatskog retikuluma i smetnje u prijenosu signala putem aksona te interakcije između glija i aksona

Accumulation of α-synuclein mediates podocyte injury in Fabry nephropathy

Current therapies for Fabry disease are based on reversing intracellular accumulation of globotriaosylceramide (Gb3) by enzyme replacement therapy (ERT) or chaperone-mediated stabilization of the defective enzyme, thereby alleviating lysosomal dysfunction. However, their effect in the reversal of end-organ damage, like kidney injury and chronic kidney disease, remains unclear. In this study, ultrastructural analysis of serial human kidney biopsies showed that long-term use of ERT reduced Gb3 accumulation in podocytes but did not reverse podocyte injury. Then, a CRISPR/Cas9–mediated α-galactosidase knockout podocyte cell line confirmed ERT-mediated reversal of Gb3 accumulation without resolution of lysosomal dysfunction. Transcriptome-based connectivity mapping and SILAC-based quantitative proteomics identified α-synuclein (SNCA) accumulation as a key event mediating podocyte injury. Genetic and pharmacological inhibition of SNCA improved lysosomal structure and function in Fabry podocytes, exceeding the benefits of ERT. Together, this work reconceptualizes Fabry-associated cell injury beyond Gb3 accumulation, and introduces SNCA modulation as a potential intervention, especially for patients with Fabry nephropathy.publishedVersio

A data set from flash X-ray imaging of carboxysomes

Citation: Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. N. C. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3. doi:10.1038/sdata.2016.61Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere

Review of the techniques used in motor‐cognitive human‐robot skill transfer

Abstract A conventional robot programming method extensively limits the reusability of skills in the developmental aspect. Engineers programme a robot in a targeted manner for the realisation of predefined skills. The low reusability of general‐purpose robot skills is mainly reflected in inability in novel and complex scenarios. Skill transfer aims to transfer human skills to general‐purpose manipulators or mobile robots to replicate human‐like behaviours. Skill transfer methods that are commonly used at present, such as learning from demonstrated (LfD) or imitation learning, endow the robot with the expert's low‐level motor and high‐level decision‐making ability, so that skills can be reproduced and generalised according to perceived context. The improvement of robot cognition usually relates to an improvement in the autonomous high‐level decision‐making ability. Based on the idea of establishing a generic or specialised robot skill library, robots are expected to autonomously reason about the needs for using skills and plan compound movements according to sensory input. In recent years, in this area, many successful studies have demonstrated their effectiveness. Herein, a detailed review is provided on the transferring techniques of skills, applications, advancements, and limitations, especially in the LfD. Future research directions are also suggested

Automated tool for measuring nanotopography of 300 mm wafers at early stages of wafer production

Leading edge lithography processes require silicon wafers of nearly perfect flatness. In order to improve wafer manufacturing processes as well as the wafer quality, already early manufacturing processes like grinding and lapping have to be monitored. Assessment of nanotopography (NT) is an established approach to analyze surface features in a spatial wavelength range of 0.2 to 20 mm on silicon wafers end of line. This paper presents a fully automated measurement tool to measure NT on wafers with low reflectivity and wafer sizes up to 300 mm, based on the FRT MicroProf® MFE series. The system features a newly developed white-light interferometry sensor with a field of view of approximately 85 × 85 mm2. 16 single measurements are stitched to cover the entire surface of a 300 mm wafer. An NT analysis optimized stitching algorithm was developed in order to combine the individual images to a complete wafer map. The stitched map of the non-polished wafer is subsequently high pass filtered and analyzed to quantify NT. Measurement system analysis studies provided repeatability values below 1 nm at a throughput of > 20 wafer/h