Arthrobots

This paper describes a class of robots—“arthrobots”— inspired, in part, by the musculoskeletal system of arthropods (spiders and insects, inter alia). An exoskeleton, constructed from thin organic polymeric tubes, provides lightweight structural support. Pneumatic joints modeled after the hydrostatic joints of spiders provide actuation and inherent mechanical compliance to external forces. An inflatable elastomeric tube (a “balloon”) enables active extension of a limb; an opposing elastic tendon enables passive retraction. A variety of robots constructed from these structural elements demonstrate i) crawling with one or two limbs, ii) walking with four or six limbs (including an insect-like triangular gait), iii) walking with eight limbs, or iv) floating and rowing on the surface of water. Arthrobots are simple to fabricate, inexpensive, light-weight, and able to operate safely in contact with humans.Chemistry and Chemical Biolog

Dissecting the molecular organization of the translocon-associated protein complex

In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation

Deep Learning Improves Macromolecule Identification in 3D Cellular Cryo-Electron Tomograms

International audienceCryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (~3.2 MDa), Rubisco (~560 kDa soluble complex), and photosystem II (~550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semi-automated analysis of a wide range of molecular targets in cellular tomograms

VIPP1 rods engulf membranes containing phosphatidylinositol phosphates

In cyanobacteria and plants, VIPP1 plays crucial roles in the biogenesis and repair of thylakoid membrane protein complexes and in coping with chloroplast membrane stress. In chloroplasts, VIPP1 localizes in distinct patterns at or close to envelope and thylakoid membranes. In vitro, VIPP1 forms higher-order oligomers of >1 MDa that organize into rings and rods. However, it remains unknown how VIPP1 oligomerization is related to function. Using time-resolved fluorescence anisotropy and sucrose density gradient centrifugation, we show here that Chlamydomonas reinhardtii VIPP1 binds strongly to liposomal membranes containing phosphatidylinositol-4-phosphate (PI4P). Cryo-electron tomography reveals that VIPP1 oligomerizes into rods that can engulf liposomal membranes containing PI4P. These findings place VIPP1 into a group of membrane-shaping proteins including epsin and BAR domain proteins. Moreover, they point to a potential role of phosphatidylinositols in directing the shaping of chloroplast membranes

Performance of scientific cameras with different sensor types in measuring dynamic processes in fluorescence microscopy

The plethora of available scientific cameras of different types challenges the biologically oriented experimenter when picking the appropriate camera for his experiment. In this study, we chose to investigate camera performances in a typical nonsingle molecule situation in life sciences, that is, quantitative measurements of fluorescence intensity changes from video data with typically skewed intensity distributions. Here, intensity profile dynamics of pH-sensors upon triggered changes of pH-environments in living cells served as a model system. The following camera types were tested: sCMOS, CCD (scientific and nonscientific) and EM-CCD (back-and front-illuminated). We found that although the EM-CCD cameras achieved the best absolute spatial SNR (signal-to-noise ratio) values, the sCMOS was at least of equal performance when the spatial SNR was related to the effective dynamic range, and it was superior in terms of temporal SNR. In the measurements of triggered intensity changes, the sCMOS camera had the advantage that it used the smallest fraction of its dynamic range when depicting intensity changes, and thus featured the best SNR at full usage of its dynamic range. (C) 2013 Wiley Periodicals, Inc