The data-exchange chase under the microscope

In this paper we take closer look at recent developments for the chase procedure, and provide additional results. Our analysis allows us create a taxonomy of the chase variations and the properties they satisfy. Two of the most central problems regarding the chase is termination, and discovery of restricted classes of sets of dependencies that guarantee termination of the chase. The search for the restricted classes has been motivated by a fairly recent result that shows that it is undecidable to determine whether the chase with a given dependency set will terminate on a given instance. There is a small dissonance here, since the quest has been for classes of sets of dependencies guaranteeing termination of the chase on all instances, even though the latter problem was not known to be undecidable. We resolve the dissonance in this paper by showing that determining whether the chase with a given set of dependencies terminates on all instances is coRE-complete. For the hardness proof we use a reduction from word rewriting systems, thereby also showing the close connection between the chase and word rewriting. The same reduction also gives us the aforementioned instance-dependent RE-completeness result as a byproduct. For one of the restricted classes guaranteeing termination on all instances, the stratified sets dependencies, we provide new complexity results for the problem of testing whether a given set of dependencies belongs to it. These results rectify some previous claims that have occurred in the literature.Comment: arXiv admin note: substantial text overlap with arXiv:1303.668

Rab3D is critical for secretory granule maturation in PC12 cells.

Neuropeptide- and hormone-containing secretory granules (SGs) are synthesized at the trans-Golgi network (TGN) as immature secretory granules (ISGs) and complete their maturation in the F-actin-rich cell cortex. This maturation process is characterized by acidification-dependent processing of cargo proteins, condensation of the SG matrix and removal of membrane and proteins not destined to mature secretory granules (MSGs). Here we addressed a potential role of Rab3 isoforms in these maturation steps by expressing their nucleotide-binding deficient mutants in PC12 cells. Our data show that the presence of Rab3D(N135I) decreases the restriction of maturing SGs to the F-actin-rich cell cortex, blocks the removal of the endoprotease furin from SGs and impedes the processing of the luminal SG protein secretogranin II. This strongly suggests that Rab3D is implicated in the subcellular localization and maturation of ISGs

Functional Dependencies Unleashed for Scalable Data Exchange

We address the problem of efficiently evaluating target functional dependencies (fds) in the Data Exchange (DE) process. Target fds naturally occur in many DE scenarios, including the ones in Life Sciences in which multiple source relations need to be structured under a constrained target schema. However, despite their wide use, target fds' evaluation is still a bottleneck in the state-of-the-art DE engines. Systems relying on an all-SQL approach typically do not support target fds unless additional information is provided. Alternatively, DE engines that do include these dependencies typically pay the price of a significant drop in performance and scalability. In this paper, we present a novel chase-based algorithm that can efficiently handle arbitrary fds on the target. Our approach essentially relies on exploiting the interactions between source-to-target (s-t) tuple-generating dependencies (tgds) and target fds. This allows us to tame the size of the intermediate chase results, by playing on a careful ordering of chase steps interleaving fds and (chosen) tgds. As a direct consequence, we importantly diminish the fd application scope, often a central cause of the dramatic overhead induced by target fds. Moreover, reasoning on dependency interaction further leads us to interesting parallelization opportunities, yielding additional scalability gains. We provide a proof-of-concept implementation of our chase-based algorithm and an experimental study aiming at gauging its scalability with respect to a number of parameters, among which the size of source instances and the number of dependencies of each tested scenario. Finally, we empirically compare with the latest DE engines, and show that our algorithm outperforms them

Avian neural crest cell migration is diversely regulated by the two major hyaluronan-binding proteoglycans PG-M/versican and aggrecan

It has been proposed that hyaluronan-binding proteoglycans play an important role as guiding cues during neural crest (NC) cell migration, but their precise function has not been elucidated. In this study, we examine the distribution, structure and putative role of the two major hyaluronan-binding proteoglycans, PG-M/versicans and aggrecan, during the course of avian NC development. PG-M/versicans V0 and V1 are shown to be the prevalent isoforms at initial and advanced phases of NC cell movement, whereas the V2 and V3 transcripts are first detected following gangliogenesis. During NC cell dispersion, mRNAs for PG-M/versicans V0/V1 are transcribed by tissues lining the NC migratory pathways, as well as by tissues delimiting nonpermissive areas. Immunohistochemistry confirm the deposition of the macromolecules in these regions and highlight regional differences in the density of these proteoglycans. PG-M/versicans assembled within the sclerotome rearrange from an initially uniform distribution to a preferentially caudal localization, both at the mRNA and protein level. This reorganization is a direct consequence of the metameric NC cell migration through the rostral portion of the somites. As suggested by previous in situ hybridizations, aggrecan shows a virtually opposite distribution to PG-M/versicans being confined to the perinotochordal ECM and extending dorsolaterally in a segmentally organized manner eventually to the entire spinal cord at axial levels interspacing the ganglia. PG-M/versicans purified from the NC migratory routes are highly polydispersed, have an apparent M(r) of 1,200-2,000 kDa, are primarily substituted with chondroitin-6-sulfates and, upon chondroitinase ABC digestion, are found to be composed of core proteins with apparent M(r)of 360–530, 000. TEM/rotary shadowing analysis of the isolated PG-M/versicans confirmed that they exhibit the characteristic bi-globular shape, have core proteins with sizes predicted for the V0/V1 isoforms and carry relatively few extended glycosaminoglycan chains. Orthotopical implantation of PG-M/versicans immobilized onto transplantable micromembranes tend to ‘attract’ moving cells toward them, whereas similar implantations of a notochordal type-aggrecan retain both single and cohorts of moving NC cells in close proximity of the implant and thereby perturb their spatiotemporal migratory pattern. NC cells fail to migrate through three-dimensional collagen type I-aggrecan substrata in vitro, but locomote in a haptotactic manner through collagen type I-PG-M/versican V0 substrata via engagement of HNK-1 antigen-bearing cell surface components. The present data suggest that PG-M/versicans and notochordal aggrecan exert divergent guiding functions during NC cell dispersion, which are mediated by both their core proteins and glycosaminoglycan side chains and may involve ‘haptotactic-like’ motility phenomena. Whereas aggrecan defines strictly impenetrable embryonic areas, PG-M/versicans are central components of the NC migratory pathways favoring the directed movement of the cells

Effects of sedimentation and periphyton communities on embryonic rainbow smelt, Osmerus mordax

The decline of anadromous rainbow smelt (Osmerus mordax) populations has been suspected to be linked to anthropogenic causes. Increased runoff from agriculture and urbanization has led to additional sediment inputs and eutrophying compounds in rivers. The aim of this study was to assess the survival of embryonic rainbow smelt from fertilization through hatching under varying levels of sedimentation (0.00, 0.25, 1.00, and 6.00 g per 45.6 cm 2) and with periphyton communities of different biomass and algal composition. Additionally, embryo survival was assessed when cultured on periphyton in combination with sterilized sediment or eutrophying compounds (nitrates and phosphates). Oxygen consumption was monitored from embryos cultured alone, on periphyton layers, and under sediment. Survival was significantly reduced under the highest sediment treatment and attributed to low oxygen availability to the embryos. Embryonic survival was also significantly reduced on the highest periphyton biomass (251.5 g/m2 dry weight, 15.7 g/m 2 ash free dry weight), and periphyton containing a high cyanobacteria content (50%). These results suggest that embryonic survival could be reduced in rivers with heavy sedimentation or a high standing biomass of periphyton

ERdj5 is the ER reductase that catalyzes the removal of non-native disulfides and correct folding of the LDL receptor

ERdj5 is a member of the protein disulfide isomerase family of proteins localized to the endoplasmic reticulum (ER) of mammalian cells. To date, only a limited number of substrates for ERdj5 are known. Here we identify a number of endogenous substrates that form mixed disulfides with ERdj5, greatly expanding its client repertoire. ERdj5 previously had been thought to exclusively reduce disulfides in proteins destined for dislocation to the cytosol for degradation. However, we demonstrate here that for one of the identified substrates, the low-density lipoprotein receptor (LDLR), ERdj5 is required not for degradation, but rather for efficient folding. Our results demonstrate that the crucial role of ERdj5 is to reduce non-native disulfides formed during productive folding and that this requirement is dependent on its interaction with BiP. Hence, ERdj5 acts as the ER reductase, both preparing misfolded proteins for degradation and catalyzing the folding of proteins that form obligatory non-native disulfides

APPL endosomes are not obligatory endocytic intermediates but act as stable cargo-sorting compartments

Endocytosis allows cargo to enter a series of specialized endosomal compartments, beginning with early endosomes harboring Rab5 and its effector EEA1. There are, however, additional structures labeled by the Rab5 effector APPL1 whose role in endocytic transport remains unclear. It has been proposed that APPL1 vesicles are transport intermediates that convert into EEA1 endosomes. Here, we tested this model by analyzing the ultrastructural morphology, kinetics of cargo transport, and stability of the APPL1 compartment over time. We found that APPL1 resides on a tubulo-vesicular compartment that is capable of sorting cargo for recycling or degradation and that displays long lifetimes, all features typical of early endosomes. Fitting mathematical models to experimental data rules out maturation of APPL1 vesicles into EEA1 endosomes as a primary mechanism for cargo transport. Our data suggest instead that APPL1 endosomes represent a distinct population of Rab5-positive sorting endosomes, thus providing important insights into the compartmental organization of the early endocytic pathway

Phosphoinositide-mediated clathrin adaptor progression at the trans-Golgi network.

Clathrin-coated vesicles mediate endocytosis and transport between the trans-Golgi network (TGN) and endosomes in eukaryotic cells. Clathrin adaptors play central roles in coat assembly, interacting with clathrin, cargo and membranes. Two main types of clathrin adaptor act in TGN-endosome traffic: GGA proteins and the AP-1 complex. Here we characterize the relationship between GGA proteins, AP-1 and other TGN clathrin adaptors using live-cell and super-resolution microscopy in yeast. We present evidence that GGA proteins and AP-1 are recruited sequentially in two waves of coat assembly at the TGN. Mutations that decrease phosphatidylinositol 4-phosphate (PtdIns(4)P) levels at the TGN slow or uncouple AP-1 coat assembly from GGA coat assembly. Conversely, enhanced PtdIns(4)P synthesis shortens the time between adaptor waves. Gga2p binds directly to the TGN PtdIns(4)-kinase Pik1p and contributes to Pik1p recruitment. These results identify a PtdIns(4)P-based mechanism for regulating progressive assembly of adaptor-specific clathrin coats at the TGN

An ultra-compact low temperature scanning probe microscope for magnetic fields above 30 T

We present the design of a highly compact High Field Scanning Probe Microscope (HF-SPM) for operation at cryogenic temperatures in an extremely high magnetic field, provided by a water-cooled Bitter magnet able to reach 38 T. The HF-SPM is 14 mm in diameter: an Attocube nano-positioner controls the coarse approach of a piezo resistive AFM cantilever to a scanned sample. The Bitter magnet constitutes an extreme environment for SPM due to the high level of vibrational noise; the Bitter magnet noise at frequencies up to 300 kHz is characterized and noise mitigation methods are described. The performance of the HF-SPM is demonstrated by topographic imaging and noise measurements at up to 30 T. Additionally, the use of the SPM as a three-dimensional dilatometer for magnetostriction measurements is demonstrated via measurements on a magnetically frustrated spinel sample.Comment: 6 pages, 5 figure