2,500 research outputs found
Investigating the Architecture and Vesicle Tethering Function of the Yeast Exocyst Complex: A Dissertation
The exocyst is an evolutionarily conserved, hetero-octameric protein complex proposed to serve as a multi-subunit tethering complex for exocytosis, although it remains poorly understood at the molecular level. The classification of the exocyst as a multisubunit tethering complex (MTC) stems from its known interacting partners, polarized localization at the plasma membrane, and structural homology to other putative MTCs. The presence of 8 subunits begs the questions: why are so many subunits required for vesicle tethering and what are the contributions of each of these subunits to the overall structure of the complex? Additionally, are subunit or subcomplex dynamics a required feature of exocyst function? We purified endogenous exocyst complexes from Saccharomyces cerevisiae, and showed that the purified complexes are stable and consist of all eight subunits with equal stoichiometry. This conclusion contrasts starkly with current models suggesting that the yeast exocyst tethers vesicles by transient assembly of subcomplexes at sites of exocytosis. Using a combination of biochemical and auxininduced degradation experiments in yeast, we mapped the subunit connectivity, identified two stable four-subunit modules within the octamer, and demonstrated that several known exocyst binding partners are not necessary for exocyst assembly and stability. Furthermore, we visualized the structure of the yeast complex using negative stain electron microscopy; our results indicate that exocyst exists predominantly as an octameric complex in yeast with a stably assembled, elongated structure. This is the first complete structure of a CATCHR family MTC and it differs greatly from the EM structures available for the partial COG and Dsl1 complexes. Future work will be necessary to determine whether exocyst conformational changes are a required feature of vesicle tethering and how such changes are regulated.
These architectural insights are now informing the design of the first in vitro functional assay for the exocyst complex. We developed methodology for attaching fluorescently-labeled exocyst complexes to glass slides and monitoring the capture of purified, endogenous secretory vesicles by single molecule TIRF microscopy. By this approach, we can monitor tethering events in real time and determine the required factors and kinetics of exocytic vesicle tethering
SNE: Signed Network Embedding
Several network embedding models have been developed for unsigned networks.
However, these models based on skip-gram cannot be applied to signed networks
because they can only deal with one type of link. In this paper, we present our
signed network embedding model called SNE. Our SNE adopts the log-bilinear
model, uses node representations of all nodes along a given path, and further
incorporates two signed-type vectors to capture the positive or negative
relationship of each edge along the path. We conduct two experiments, node
classification and link prediction, on both directed and undirected signed
networks and compare with four baselines including a matrix factorization
method and three state-of-the-art unsigned network embedding models. The
experimental results demonstrate the effectiveness of our signed network
embedding.Comment: To appear in PAKDD 201
Multirelational Organization of Large-scale Social Networks in an Online World
The capacity to collect fingerprints of individuals in online media has
revolutionized the way researchers explore human society. Social systems can be
seen as a non-linear superposition of a multitude of complex social networks,
where nodes represent individuals and links capture a variety of different
social relations. Much emphasis has been put on the network topology of social
interactions, however, the multi-dimensional nature of these interactions has
largely been ignored in empirical studies, mostly because of lack of data.
Here, for the first time, we analyze a complete, multi-relational, large social
network of a society consisting of the 300,000 odd players of a massive
multiplayer online game. We extract networks of six different types of
one-to-one interactions between the players. Three of them carry a positive
connotation (friendship, communication, trade), three a negative (enmity, armed
aggression, punishment). We first analyze these types of networks as separate
entities and find that negative interactions differ from positive interactions
by their lower reciprocity, weaker clustering and fatter-tail degree
distribution. We then proceed to explore how the inter-dependence of different
network types determines the organization of the social system. In particular
we study correlations and overlap between different types of links and
demonstrate the tendency of individuals to play different roles in different
networks. As a demonstration of the power of the approach we present the first
empirical large-scale verification of the long-standing structural balance
theory, by focusing on the specific multiplex network of friendship and enmity
relations.Comment: 7 pages, 5 figures, accepted for publication in PNA
Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli
The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex
Interpol: An R package for preprocessing of protein sequences
<p>Abstract</p> <p>Background</p> <p>Most machine learning techniques currently applied in the literature need a fixed dimensionality of input data. However, this requirement is frequently violated by real input data, such as DNA and protein sequences, that often differ in length due to insertions and deletions. It is also notable that performance in classification and regression is often improved by numerical encoding of amino acids, compared to the commonly used sparse encoding.</p> <p>Results</p> <p>The software "Interpol" encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms. Interpol is distributed with open source as platform independent R-package. It is typically used for preprocessing of amino acid sequences for classification or regression.</p> <p>Conclusions</p> <p>The functionality of Interpol widens the spectrum of machine learning methods that can be applied to biological sequences, and it will in many cases improve their performance in classification and regression.</p
Dynamics of Social Balance on Networks
We study the evolution of social networks that contain both friendly and
unfriendly pairwise links between individual nodes. The network is endowed with
dynamics in which the sense of a link in an imbalanced triad--a triangular loop
with 1 or 3 unfriendly links--is reversed to make the triad balanced. With this
dynamics, an infinite network undergoes a dynamic phase transition from a
steady state to "paradise"--all links are friendly--as the propensity p for
friendly links in an update event passes through 1/2. A finite network always
falls into a socially-balanced absorbing state where no imbalanced triads
remain. If the additional constraint that the number of imbalanced triads in
the network does not increase in an update is imposed, then the network quickly
reaches a balanced final state.Comment: 10 pages, 7 figures, 2-column revtex4 forma
Heavy Superheated Droplet Detectors as a Probe of Spin-independent WIMP Dark Matter Existence
At present, application of Superheated Droplet Detectors (SDDs) in WIMP dark
matter searches has been limited to the spin-dependent sector, owing to the
general use of fluorinated refrigerants which have high spin sensitivity. Given
their recent demonstration of a significant constraint capability with
relatively small exposures and the relative economy of the technique, we
consider the potential impact of heavy versions of such devices on the
spin-independent sector. Limits obtainable from a -loaded SDD
are estimated on the basis of the radiopurity levels and backgrounds already
achieved by the SIMPLE and PICASSO experiments. With 34 kgd exposure,
equivalent to the current CDMS, such a device may already probe to below
10 pb in the spin-independent cross section.Comment: 9 pages, 4 figures, accepted Phys. Rev.
A scalable forecasting framework to predict COVID-19 hospital bed occupancy
The coronavirus disease 2019 (COVID-19) pandemic has led to capacity problems in many hospitals around the world. During the peak of new infections in Germany in April 2020 and October to December 2020, most hospitals had to cancel elective procedures for patients because of capacity shortages. We present a scalable forecasting framework with a Monte Carlo simulation to forecast the short-term bed occupancy of patients with confirmed and suspected COVID-19 in intensive care units and regular wards. We apply the simulation to different granularity and geographical levels. Our forecasts were a central part of the official weekly reports of the Bavarian State Ministry of Health and Care, which were sent to key decision makers in the individual ambulance districts from May 2020 to March 2021. Our evaluation shows that the forecasting framework delivers accurate forecasts despite data availability and quality issues
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