bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of cell cycle signals by multi-PAS domain kinases
Authors: Mann Thomas H. , Shapiro Lucy 
Published: May 2018

AbstractSpatial control of intracellular signaling relies on signaling proteins sensing their subcellular environment. In many cases, a large number of upstream signals are funneled to a master regulator of cellular behavior, but it remains unclear how individual proteins can rapidly integrate a complex array of signals within the appropriate spatial niche within the cell. As a model for how subcellular spatial information can control signaling activity, we have reconstituted the cell pole-specific control of the master regulator kinase/phosphatase CckA from the asymmetrically dividing bacterium Caulobacter crescentus. CckA is active as a kinase only when it accumulates within a microdomain at the new cell pole, where it co-localizes with the pseudokinase DivL. Both proteins contain multiple PAS domains, a multifunctional class of sensory domains present across the kingdoms of life. Here, we show that CckA uses its PAS domains to integrate information from DivL and on its own oligomerization state to control the balance of its kinase and phosphatase activities. We reconstituted the DivL-CckA complex on liposomes in vitro and found that DivL directly controls the CckA kinase-phosphatase switch, and that stimulation of either CckA catalytic activity depends on the second of its two PAS domains. We further show that CckA oligomerizes through a multi-domain interaction that is critical for stimulation of kinase activity by DivL, while DivL stimulation of CckA phosphatase activity is independent of CckA homo-oligomerization. Our results broadly demonstrate how signaling factors can leverage information from their subcellular niche to drive spatiotemporal control of cell signaling.SignificanceCells must constantly make decisions involving many pieces of information at a molecular level. Kinases containing multiple PAS sensory domains detect multiple signals to determine their signaling outputs. In the asymmetrically dividing bacterium Caulobacter crescentus, the multi-sensor proteins DivL and CckA promote different cell types depending upon their subcellular location. We reconstituted the DivL-CckA interaction in vitro and showed that specific PAS domains of each protein function to switch CckA between kinase and phosphatase activities, which reflects their functions in vivo. Within the context of the cell, our reconstitution illustrates how multi-sensor proteins can use their subcellular location to regulate their signaling functions.
Cryptsim: Modeling the evolutionary dynamics of the progression of Barrett’s esophagus to esophageal adenocarcinoma
Authors: Mallo Diego , Kostadinov Rumen , Cisneros Luis , Kuhner Mary K. , Maley Carlo C. 
Published: May 2018

AbstractTo alleviate the over-diagnosis and overtreatment of premalignant conditions we need to predict their progression to cancer, and therefore, the dynamics of an evolutionary process. However, monitoring evolutionary processes in vivo is extremely challenging. Computer simulations constitute an attractive alternative, allowing us to study these dynamics based on a set of evolutionary parameters.We introduce CryptSim, a simulator of crypt evolution inspired by Barrett’s esophagus. We detail the most relevant computational strategies it implements, and perform a simulation study showing that the interaction between neighboring crypts may play a crucial role in carcinogenesis.
In vitro neural networks minimise variational free energy
Authors: Isomura Takuya , Friston Karl 
Published: May 2018

AbstractIn this work, we address the neuronal encoding problem from a Bayesian perspective. Specifically, we ask whether neuronal responses in anin vitroneuronal network are consistent with ideal Bayesian observer responses under the free energy principle. In brief, we stimulated anin vitrocortical cell culture with stimulus trains that had a known statistical structure. We then asked whether recorded neuronal responses were consistent with variational message passing (i.e., belief propagation) based upon free energy minimisation (i.e., evidence maximisation). Effectively, this required us to solve two problems: first, we had to formulate the Bayes-optimal encoding of the causes or sources of sensory stimulation, and then show that these idealised responses could account for observed electrophysiological responses. We describe a simulation of an optimal neural network (i.e., the ideal Bayesian neural code) and then consider the mapping from idealisedin silicoresponses to recordedin vitroresponses. Our objective was to find evidence for functional specialisation and segregation in thein vitroneural network that reproducedin silicolearning via free energy minimisation. Finally, we combined thein vitroandin silicoresults to characterise learning in terms of trajectories in a variational information plane of accuracy and complexity.
Cooperative changes in solvent exposure identify cryptic pockets, conformational switches, and allosteric coupling
Authors: Porter Justin R. , Moeder Katelyn E. , Sibbald Carrie A. , Zimmerman Maxwell I. , Hart Kathryn M. , Greenberg Michael J. , Bowman Gregory R. 
Published: May 2018

AbstractProteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally-relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation datasets. We reasoned that many functionally-relevant conformational changes are likely to involve large, cooperative changes to the surfaces that are available to interact with potential binding partners. To examine this hypothesis, we introduce a method that returns a prioritized list of potentially functional conformational changes by segmenting protein structures into clusters of residues that undergo cooperative changes in their solvent exposure, along with the hierarchy of interactions between these groups. We term these groups exposons to distinguish them from other types of clusters that arise in this analysis and others. We demonstrate, using three different model systems, that this method identifies experimentally-validated and functionally-relevant conformational changes, including conformational switches, allosteric coupling, and cryptic pockets. Our results suggest that key functional sites are hubs in the network of exposons. As a further test of the predictive power of this approach, we apply it to discover cryptic allosteric sites in two different β-lactamase enzymes that are widespread sources of antibiotic resistance. Experimental tests confirm our predictions for both systems. Importantly, we provide the first evidence for a cryptic allosteric site in CTX-M-9 β-lactamase. Experimentally testing this prediction did not require any mutations, and revealed that this site exerts the most potent allosteric control over activity of any pockets found in β-lactamases to date. Discovery of a similar pocket that was previously overlooked in the well-studied TEM-1 β-lactamase demonstrates the utility of exposons.
An Atomistic view of Short-chain Antimicrobial Biomimetic peptides in Action
Authors: Mondal Jagannath , Ghosh Pushpita , Zhu Xiao 
Published: May 2018

AbstractAmphiphilicβ-peptides, which are rationally designed synthetic oligomers, are established biomimetic alternatives of natural antimicrobial peptides. The ability of these biomimetic peptides to form helical amphiphilic conformation using small number of residues provides a greater synthetic advantage over the naturally occurring antimicrobial peptides, which is reflected in more potent antimicrobial activity ofβ-peptides than its naturally occurring counterparts. Here we address whether the distinct molecular architecture of short-chain and rigid synthetic peptides compared to relatively long and flexible natural antimicrobial peptides translates to a distinct mechanistic action with membrane. By simulating the interaction of membrane with antimicrobial 10-residueβ-peptides at diverse range of concentrations we reveal spontaneous insertion ofβ-peptides in the membrane interface at a low concentration and occurrence of partial water leakage in the membrane at a high concentration. Intriguingly, unlike prototypical natural antimicrobial peptides, the water molecules leaked inside the membrane by these biomimetic peptides do not span entire membrane, as supported by free energy analysis. As a major advancement, this work brings into lights the key distinction in the membrane-activity of short synthetic biomimetic oligomers relative to the natural long-chain antimicrobial peptides.
Effects on cell viability, growth and morphology ofC. albicansSC5314 biofilms after kINPen®09 plasma treatment
Authors: Handorf O. , Weihe T. , Bekeschus S. , Graf A. C. , Schnabel U. , Riedel K. , Ehlbeck J. 
Published: May 2018

AbstractMicroorganisms are predominantly organized in biofilms, where cells live in dense communities and are more resistant to external stresses compared to their planktonic counterparts. Within vitroexperiments, the susceptibility ofCandida albicansbiofilms to a non-thermal plasma treatment (plasma source kINP®09), in terms of growth, survival, and cell viability was investigated. Behind that background, theC. albicansstrain SC5314 (ATCC® MYA-2876™) was plasma treated for different time periods (30 s, 60 s, 120 s, 180 s, 300 s). The results of experiments embracing colony forming units, fluorescence LIVE/DEAD assays, and XTT assays revealed a negative influence of the plasma treatment on the proliferation ability, vitality, and the metabolism ofC. albicansbiofilms, respectively. Morphological analysis of plasma-treated biofilms using atomic force microscopy supported the indications for lethal plasma effects concomitant with membrane disruptions and the loss of intracellular fluid. Controversial to other publications, fluorescence- and confocal laser scanning-microscopic inspection of plasma-treated biofilms indicated, that an inactivation of cells mainly appeared on the bottom side of the biofilms. If this inactivation leads to a detachment of the biofilms from the overgrown surface, it might offer completely new approaches in the plasma treatment of biofilms. Because of its biochemical-mechanical mode of action, resistances of microbial cells against plasma are unknown at this state of research.
Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities
Authors: Murray Aimee K. , Zhang Lihong , Yin Xiaole , Zhang Tong , Buckling Angus , Snape Jason , Gaze William H. 
Published: May 2018

ABSTRACTRecent research has demonstrated selection for antibiotic resistance occurs at very low antibiotic concentrations in single species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low sub-inhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a two order magnitude concentration range. This is likely to be due to cross-protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses on sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment forblaCTX-Mgenes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.
TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
Authors: Waldl Maria , Thiel Bernhard C. , Ochsenreiter Roman , Holzenleiter Alexander , de Araujo Oliveira João Victor , Walter Maria Emília M. T. , Wolfinger Michael T. , Stadler Peter F. 
Published: May 2018

Abstract:The telomerase RNA in yeasts is large, usually > 1,000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina still remain without annotated telomerase RNA.
Speed of time-compressed forward replay flexibly changes in human episodic memory
Authors: Michelmann Sebastian , Staresina Bernhard P. , Bowman Howard , Hanslmayr Simon 
Published: May 2018

SummaryRemembering information from continuous past episodes is a complex task. On the one hand, we must be able to recall events in a highly accurate way that often includes exact timing; on the other hand, we can ignore irrelevant details and skip to events of interest. We here track continuous episodes, consisting of different sub-events, as they are recalled from memory. In behavioral and MEG data, we show that memory replay is temporally compressed and proceeds in a forward direction. Neural replay is characterized by the reinstatement of temporal patterns from encoding. These fragments of activity reappear on a compressed timescale. Herein, the replay of sub-events takes longer than the transition from one sub-event to another. This identifies episodic memory replay as a dynamic process in which participants replay fragments of fine-grained temporal patterns and are able to skip flexibly across sub-events.
Manganese acquisition is essential for virulence ofEnterococcus faecalis
Authors: Colomer-Winter C , Flores-Mireles AL , Baker SP , Frank KL , Lynch AJL , Hultgren SJ , Kitten T , Lemos JA 
Published: May 2018

AbstractManganese (Mn) is an essential micronutrient that is not readily available to pathogens during infection due to an active host defense mechanism known as nutritional immunity. To overcome this nutrient restriction, bacteria utilize high-affinity transporters that allow them to compete with host metal-binding proteins. Despite the established role of Mn in bacterial pathogenesis, little is known about the relevance of Mn in the pathophysiology ofE. faecalis. Here, we identified and characterized the major Mn acquisition systems ofE. faecalis. We discovered that the ABC-type permease EfaCBA and two Nramp-type transporters, named MntH1 and MntH2, work collectively to promote cell growth under Mn-restricted conditions. The simultaneous inactivation of EfaCBA, MntH1 and MntH2 (ΔefaΔmntH1ΔmntH2strain) led to drastic reductions (>95%) in intracellular Mn content, severe growth defects in body fluids (serum and urine)ex vivo, significant loss of virulence inGalleria mellonella, and virtually complete loss of virulence in rabbit endocarditis and murine catheter-associated urinary tract infection (CAUTI) models. Despite the functional redundancy ofEfaCBA,MntH1andMntH2underin vitroorex vivoconditions and in the invertebrate model, dual inactivation ofefaCBAandmntH2(ΔefaΔmntH2strain) was sufficient to prompt maximal sensitivity to calprotectin, a Mn- and Zn-chelating host antimicrobial protein, and for the loss of virulence in mammalian models. Interestingly, EfaCBA appears to play a prominent role during systemic infection, whereas MntH2 was more important during CAUTI. The different roles of EfaCBA and MntH2 in these sites could be attributed, at least in part, to the differential expression ofefaAandmntH2in cells isolated from hearts or from bladders. Collectively, this study demonstrates that Mn acquisition is essential for the pathogenesis ofE. faecalisand validates Mn uptake systems as promising targets for the development of new antimicrobials.
An insulin, AMPK, and steroid hormone-mediated metabolic switch regulates the transition between growth and diapause inC. elegans
Authors: Penkov Sider , Raghuraman Bharath Kumar , Erkut Cihan , Oertel Jana , Galli Roberta , Ackerman Eduardo Jacobo Miranda , Vorkel Daniela , Verbavatz Jean-Marc , Koch Edmund , Fahmy Karim , Shevchenko Andrej , Kurzchalia Teymuras V. 
Published: May 2018

AbstractThe balance between growth and quiescence depends on the global metabolic state. The dauer larva ofC. elegans,a developmentally arrested stage for survival under adverse environment, undergoes a major metabolic transition. Here, we show that this switch involves the concerted activity of several regulatory pathways. Whereas the steroid hormone receptor DAF-12 controls dauer morphogenesis, the insulin pathway maintains low energy expenditure through DAF-16/FoxO, which also requires AAK-2/AMPKα. DAF-12 and AAK-2 separately promote a shift in the molar ratios between competing enzymes at two key branch points within the central carbon metabolic pathway. This way, carbon atoms are diverted from the TCA cycle and directed to gluconeogenesis. When both AAK-2 and DAF-12 are suppressed, the TCA cycle is active and the developmental arrest is bypassed. Hence, the metabolic status of each developmental stage is defined by stoichiometric ratios within the constellation of metabolic enzymes and controls the transition between growth and quiescence.
CardiacProfileR: An R package for extraction and visualisation of heart rate profiles from wearable fitness trackers
Authors: Djordjevic Djordje , Cawood Beni K. , Rispin Sabrina K. , Shah Anushi , Yim Leo H. H. , Hayward Christopher S. , Ho Joshua W. K. 
Published: May 2018

AbstractA person’s heart rate profile, which consists of resting heart rate, increase of heart rate upon exercise and recovery of heart rate after exercise, is traditionally measured by electrocardiography during a controlled exercise stress test. A heart rate profile is a useful clinical tool to identify individuals at risk of sudden death and other cardiovascular conditions. Nonetheless, conducting such exercise stress tests routinely is often inconvenient and logistically challenging for patients. The widespread availability of affordable wearable fitness trackers, such as Fitbit and Apple Watch, provides an exciting new means to collect longitudinal heart rate and physical activity data. We reason that by combining the heart rate and physical activity data from these devices, we can construct a person’s heart rate profile. Here we present an open source R package CardiacProfileR for extraction, analysis and visualisation of heart rate dynamics during physical activities from data generated from common wearable heart rate monitors. This package represents a step towards quantitative deep phenotyping in humans. CardiacProfileR is available via an MIT license at https://github.com/VCCRI/CardiacProfileR.
Fusion surface structure, function, and dynamics of gamete fusogen HAP2
Authors: Feng Juan , Dong Xianchi , Pinello Jennifer F. , Zhang Jun , Lu Chafen , Iacob Roxana E. , Engen John R , Snell Wiliam J. , Springer Timothy A. 
Published: May 2018

AbstractHAP2 is a class II gamete fusogen in many eukaryotic kingdoms. A crystal structure ofChlamydomonasHAP2 shows a trimeric fusion state. Domains D1, D2.1 and D2.2 line the 3-fold axis; D3 and a stem pack against the outer surface. Surprisingly, hydrogen-deuterium exchange shows that surfaces of D1, D2.2 and D3 closest to the 3-fold axis are more dynamic than exposed surfaces. Three fusion helices in the fusion loop of each monomer expose hydrophobic residues at the trimer apex that are splayed from the 3-fold axis, leaving a solvent-filled cavity between the fusion loops in each monomer. At the base of the long fusion loop, Arg185 docks in a carbonyl cage. Comparisons to other structures, dynamics, and the greater effect onChlamydomonasgamete fusion of mutation of axis-proximal than axis-distal fusion helices suggest that the apical portion of each monomer could tilt toward the 3-fold axis with merger of the fusion helices into a common fusion surface.
K-Ras G-domain binding with signaling lipid phosphoinositides: PIP2 association, orientation, function
Authors: Cao Shufen , Chung Stacey , Kim SoonJeung , Li Zhenlu , Manor Danny , Buck Matthias 
Published: May 2018

ABSTRACTRas genes are potent drivers of human cancers, with mutated K-Ras4B being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the holy grail of present-day cancer therapy, and recent discoveries of small molecule inhibitors for K-Ras4B greatly benefited from a deeper understanding of the protein structure and dynamics of the GTPase. Since interactions with biological membranes are key for Ras function, the details of Ras - lipid interactions have become a major focus of study, especially since it is becoming clear that such interactions not only involve the Ras C-terminus for lipid anchoring, but also the G-protein domain. Here we investigated the interaction between K-Ras4B with the signaling lipid phosphatidyl inositol (4,5) phosphate (PIP2) using NMR spectroscopy and molecular dynamics simulations, complemented by biophysical and cell biology assays. We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2, and that these secondary structural elements employ specific residues for these interactions. These likely occur in two orientation states of the protein relative to the membrane. Importantly, we found that some of these residues, which are known to be oncogenic when mutated (D47K, D92N, K104M and D126N), are critical for K-Ras-mediated transformation of fibroblast cells, while not substantially affecting basal and assisted nucleotide hydrolysis and exchange. We further showed that mutation K104M can indeed abolish localization of mutant K-Ras to the plasma membrane. These findings suggest that specific G-domain residues play an important, previously-unknown role in regulating Ras function by mediating interactions with membrane PIP2 lipids. Thus, a detailed description of the novel K-Ras-PIP2 binding surfaces is likely to inform the future design of therapeutic reagents.