High-throughput and low-latency sorting is a key requirement in many applications that deal with large amounts of data. This paper presents efficient techniques for designing high-throughput, ...low-latency sorting units. Our sorting architectures utilize modular design techniques that hierarchically construct large sorting units from smaller building blocks. The sorting units are optimized for situations in which only the M largest numbers from N inputs are needed, because this situation commonly occurs in many applications for scientific computing, data mining, network processing, digital signal processing, and high-energy physics. We utilize our proposed techniques to design parameterized, pipelined, and modular sorting units. A detailed analysis of these sorting units indicates that as the number of inputs increases their resource requirements scale linearly, their latencies scale logarithmically, and their frequencies remain almost constant. When synthesized to a 65-nm TSMC technology, a pipelined 256-to-4 sorting unit with 19 stages can perform more than 2.7 billion sorts per second with a latency of about 7 ns per sort. We also propose iterative sorting techniques, in which a small sorting unit is used several times to find the largest values.
After endocytosis, transmembrane cargo reaches endosomes, where it encounters complexes dedicated to opposing functions: recycling and degradation. Microdomains containing endosomal sorting complexes ...required for transport (ESCRT)-0 component Hrs hepatocyte growth factor-regulated tyrosine kinase substrate (HGRS-1) in Caenorhabditis elegans mediate cargo degradation, concentrating ubiquitinated cargo and organizing the activities of ESCRT. At the same time, retromer associated sorting nexin one (SNX-1) and its binding partner, J-domain protein RME-8, sort cargo away from degradation, promoting cargo recycling to the Golgi. Thus, we hypothesized that there could be important regulatory interactions between retromer and ESCRT that balance degradative and recycling functions. Taking advantage of the naturally large endosomes of the C. elegans coelomocyte, we visualized complementary ESCRT-0 and RME-8/SNX-1 microdomains in vivo and assayed the ability of retromer and ESCRT microdomains to regulate one another. We found in snx-1(0) and rme-8(ts) mutants increased endosomal coverage and intensity of HGRS-1–labeled microdomains, as well as increased total levels of HGRS-1 bound to membranes. These effects are specific to SNX-1 and RME-8, as loss of other retromer components SNX-3 and vacuolar protein sorting-associated protein 35 (VPS-35) did not affect HGRS-1 microdomains. Additionally, knockdown of hgrs-1 had little to no effect on SNX-1 and RME-8microdomains, suggesting directionality to the interaction. Separation of the functionally distinct ESCRT-0 and SNX-1/RME-8 microdomains was also compromised in the absence of RME-8 and SNX-1, a phenomenonwe observed to be conserved, as depletion of Snx1 and Snx2 in HeLa cells also led to greater overlap of Rme-8 and Hrs on endosomes.
Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and ...underlie some forms of Alzheimer’s disease and Parkinson’s disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.
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•SNX3 participates in both retromer recruitment to membranes and cargo recognition•Canonical recycling signals bind to a site at the interface between SNX3 and VPS26•Signal recognition involves a conformational change in VPS26 upon SNX3 binding•The results suggest a mechanism for assembly of retromer coats on recycling tubules
Elucidation of how the full-size retromer complex recognizes a specific cargo reveals a mechanism for coupling membrane recruitment with cargo selection.
Sensor-based sorting in waste management is a method to separate valuable material or contaminants from a waste stream. Depending on the separation property different types of sensors are used. ...Separation properties and their corresponding sensors are e.g. molecular composition with near-infrared sensors, colour with visual spectroscopy or colour line scan cameras, or electric conductivity with electromagnetic sensors.
The methods described in this paper deal with the development of sorting models for a specific near-infrared, a visual spectroscopy and an induction sensor. For near-infrared and visual spectroscopy software is required to create sorting models, while for induction only machine settings have to be adjusted and optimized for a specific sorting task. These sensors are installed in the experimental sensor-based sorting setup at the Chair of Waste Processing Technology and Waste Management located at the Montanuniversitaet Leoben. This sorting stand is a special designed machine for the university to make experiments on sensor-based sorting in lab scale. It can be used for a variety of waste streams depending on the grain size and the pre-conditioning for the sensor-based sorting machine. In detail the methods to create these sorting models are described and validated with plastic, glass and metal waste.•Near-infrared spectroscopy measures the molecular composition of near-infrared-active particles.•Visual spectroscopy measures the absorption of visible light by chemical compounds.•Induction sensors use induced currents to detect nearby metal objects.
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The evolutionarily conserved endosomal retromer complex rescues transmembrane proteins from the lysosomal degradative pathway and facilitates their recycling to other cellular compartments. Retromer ...functions in conjunction with numerous associated proteins, including select members of the sorting nexin (SNX) family. In the present article, we review the molecular architecture and cellular roles of retromer and its various functional partners. The endosomal network is a crucial hub in the trafficking of proteins through the cellular endomembrane system. Transmembrane proteins, here termed cargos, enter endosomes by endocytosis from the plasma membrane or by trafficking from the trans-Golgi network (TGN). Endosomal cargo proteins face one of the two fates: retention in the endosome, leading ultimately to lysosomal degradation or export from the endosome for reuse ('recycling'). The balance of protein degradation and recycling is crucial to cellular homoeostasis; inappropriate sorting of proteins to either fate leads to cellular dysfunction. Retromer is an endosome-membrane-associated protein complex central to the recycling of many cargo proteins from endosomes, both to the TGN and the plasma membrane (and other specialized compartments, e.g. lysosome-related organelles). Retromer function is reliant on a number of proteins from the SNX family. In the present article, we discuss this inter-relationship and how defects in retromer function are increasingly being linked with human disease.
The molecular events that determine the recycling versus degradation fates of internalized membrane proteins remain poorly understood. Two of the three members of the SNX-FERM family, SNX17 and ...SNX31, utilize their FERM domain to mediate endocytic trafficking of cargo proteins harboring the NPxY/NxxY motif. In contrast, SNX27 does not recycle NPxY/NxxY-containing cargo but instead recycles cargo containing PDZ-binding motifs via its PDZ domain. The underlying mechanism governing this divergence in FERM domain binding is poorly understood. Here, we report that the FERM domain of SNX27 is functionally distinct from SNX17 and interacts with a novel DLF motif localized within the N terminus of SNX1/2 instead of the NPxY/NxxY motif in cargo proteins. The SNX27-FERM-SNX1 complex structure reveals that the DLF motif of SNX1 binds to a hydrophobic cave surrounded by positively charged residues on the surface of SNX27. The interaction between SNX27 and SNX1/2 is critical for efficient SNX27 recruitment to endosomes and endocytic recycling of multiple cargoes. Finally, we show that the interaction between SNX27 and SNX1/2 is critical for brain development in zebrafish. Altogether, our study solves a long-standing puzzle in the field and suggests that SNX27 and SNX17 mediate endocytic recycling through fundamentally distinct mechanisms.
Isolation and Culture of Microglia Bohlen, Christopher J; Bennett, F Chris; Bennett, Mariko L
Current protocols in immunology,
June 2019, Volume:
125, Issue:
1
Journal Article
This paper proposes a novel hardware-based multidimensional sorting algorithm and its respective architecture, called real-time hardware sorter (RTHS), for emerging data intensive processing ...applications where performance and resource conservation are serious concerns. The basic idea behind RTHS is to reduce the hardware complexity of parallel hardware sorting architectures (PHSAs) through a high-performance scalable matrix-based sorting method. The proposed method can also be used for implementing Min/Max queues or finding the largest/smallest records exclusively in the big data application. Implementing the RTHS design on a Virtex-7 field-programmable gate array (FPGA) reveals that the number of lookup tables (LUTs) of the proposed method has decreased by 66.3% and 87.3% compared to the conventional Bitonic sorting network (CBSN) and the state-of-the-art PHSA, respectively. In addition, the number of required registers for the proposed method has decreased by 94.8% compared to the state-of-the-art PHSA.
Following endocytosis, receptors that are internalized to sorting endosomes are sorted to different pathways, in part by sorting nexin (SNX) proteins. Notably, SNX17 interacts with a multitude of ...receptors in a sequence-specific manner to regulate their recycling. However, the mechanisms by which SNX17-labeled vesicles that contain sorted receptors bud and undergo vesicular fission from the sorting endosomes remain elusive. Recent studies suggest that a dynamin-homolog, Eps15 homology domain protein 1, catalyzes fission and releases endosome-derived vesicles for recycling to the plasma membrane. However, the mechanism by which EHD1 is coupled to various receptors and regulates their recycling remains unknown. Here we sought to characterize the mechanism by which EHD1 couples with SNX17 to regulate recycling of SNX17-interacting receptors. We hypothesized that SNX17 couples receptors to the EHD1 fission machinery in mammalian cells. Coimmunoprecipitation experiments and in vitro assays provided evidence that EHD1 and SNX17 directly interact. We also found that inducing internalization of a SNX17 cargo receptor, low-density lipoprotein receptor–related protein 1 (LRP1), led to recruitment of cytoplasmic EHD1 to endosomal membranes. Moreover, surface rendering and quantification of overlap volumes indicated that SNX17 and EHD1 partially colocalize on endosomes and that this overlap further increases upon LRP1 internalization. Additionally, SNX17-containing endosomes were larger in EHD1-depleted cells than in WT cells, suggesting that EHD1 depletion impairs SNX17-mediated endosomal fission. Our findings help clarify our current understanding of endocytic trafficking, providing significant additional insight into the process of endosomal fission and connecting the sorting and fission machineries.
Protein sorting in the endomembrane system is responsible for the coordination of cellular functions. Plant intracellular trafficking has its own unique features, which include specific regulatory ...aspects of endosomal sorting and recycling of cargo proteins, mediated by the retromer complex. Recent work has led to significant progress in understanding the role of
retromer subunits in recycling vacuolar sorting receptors and plasma membrane proteins. As a consequence, members of the sorting nexin (SNX) protein family and their interaction partners have emerged as critical protein trafficking regulators, in particular with regard to adaptation to environmental change, such as temperature fluctuations and nutrient deficiency. In this Review, we discuss the known and proposed functions of the comparatively small
SNX protein family. We review the available information on the role of the three Bin-Amphiphysin-Rvs (BAR)-domain-containing
(At)SNX proteins and discuss their function in the context of their potential participation in the plant retromer complex. We also summarize the role of AtSNX1-interacting proteins in different aspects of SNX-dependent protein trafficking and comment on the potential function of three novel, as yet unexplored,
SNX proteins.
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