bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusion and fission events regulate endosome maturation and viral escape
Authors: Castro Mario , Lythe Grant , Smit Jolanda M. , Molina-París Carmen 
Published: September 2020

AbstractMany intra-cellular processes rely on transport by endosomes. Recent experimental techniques have provided insights into organelle maturation and its specific role in, for instance, the ability of a virus to escape an endosome and release its genetic material in the cytoplasm. Endosome maturation and dynamics depend on GTPases called Rabs, found on their membrane. Here, we introduce a mathematical framework, combining coagulation and fragmentation of endosomes with two variables internal to each organelle, to model endosomes as intra-cellular compartments characterised by their levels of (active) Rab5 and Rab7. The key element in our framework is the “per-cell endosomal distribution” and its its dynamical equation or Boltzmann equation. The Boltzmann equation, then, allows one to deduce simple equations for the total number of endosomes in a cell, and for the mean and standard deviation of the Rab5 and Rab7 levels. We compare our solutions with experimental data sets of Dengue viral escape from endosomes. The relationship between endosomal Rab levels and pH suggests a mechanism which can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intra-cellular infection.Author summaryEndosomes are intra-cellular receptacle-like organelles, which transport endocytosed cargo upon internalisation from the plasma membrane. These early endosomes, also known as sorting endosomes, mature to late endosomes, with a lower pH than early ones, as a consequence of the intricate dynamics of a family of molecules called Rabs. Viruses exploit this endosomal pH drop to their advantage. Here we bring together experimental data on Dengue viral escape times from endosomes and a novel mathematical framework inspired by the theory of droplet coalescence, to improve our understanding of endosome maturation, and in turn to quantify the large variability of viral escape times. This mathematical framework can easily be generalised to model the dynamics of other intra-cellular organelles, such as mitochondria or the endoplasmic reticulum.
Memory specificity is linked to repetition effects in event-related potentials across the lifespan
Authors: Sommer Verena R. , Mount Luzie , Weigelt Sarah , Werkle-Bergner Markus , Sander Myriam C. 
Published: September 2020

AbstractThe specificity with which past experiences can be remembered varies across the lifespan, possibly due to differences in how precisely information is encoded. Memory formation can be investigated through repetition effects, the common finding that neural activity is altered when stimuli are repeated. However, whether differences in this indirect measure of memory formation relate to lifespan differences in memory specificity has not yet been established. In the present study, we examined repetition effects in event-related potentials and their relation to recognition. During incidental encoding, children (aged 7–9 years), young adults (18–30 years), and older adults (65–76 years) viewed repeated object images from different categories. During subsequent recognition, we distinguished memory for the specific items versus the general categories. We identified repetition suppression in all age groups, and repetition enhancement for adults. Furthermore, individual item recognition performance comprising lure discrimination was positively associated with the magnitude of the neural repetition effects, which did not differ between groups, indicating common neural mechanisms of memory formation. Our findings demonstrate that neural repetition effects reflect the formation of highly specific memory representations and highlight their significance as a neural indicator of individual differences in episodic memory encoding across the lifespan.
The kallikrein-kinin system is falling into pieces: bradykinin fragments are biological active peptides
Authors: Souza-Silva Igor Maciel , de Paula Cristiane Amorim , Santos Anderson Kenedy , de Oliveira Vívian Louise Soares , da Rocha Isabella Domingos , Antunes Maísa Mota , Barbosa Cordeiro Lídia Pereira , Teixeira Vanessa Pereira , Scalzo Júnior Sérgio Ricardo Aluotto , Amaral Flávio Almeida , Resende Jarbas Magalhães , Peliky Fontes Marco Antônio , Menezes Gustavo Batista , Guatimosim Silvia , Souza Santos Robson Augusto , Verano-Braga Thiago 
Published: September 2020

ABSTRACTBackground and purposeBradykinin [BK-(1-9)] is an endogenous peptide involved in many physiological and pathological processes, such as cardiovascular homeostasis and inflammation. The central dogma of the kallikrein-kinin system is that BK-(1-9) fragments are biologically inactive. In this manuscript, we proposed to test whether these fragments were indeed inactive.Experimental ApproachNitric oxide (NO) was quantified in human, mouse and rat cells loaded with DAF-FM after stimulation with BK-(1-9), BK-(1-7), BK-(1-5) and BK-(1-3). We used adult male rat aortic ring preparation to test vascular reactivity mediated by BK-(1-9) fragments. Changes in blood pressure and heart rate was measured in conscious adult male rats by intraarterial catheter method.Key resultsBK-(1-9) induced NO production in all cell types tested by B2 receptor activation. BK-(1-7), BK-(1-5) and BK-(1-3) also induced NO production in all tested cell types but this response was independent of the activation of B1 receptor and/or B2 receptor. BK-(1-7), BK-(1-5) or BK-(1-3) induced only vasorelaxant effect and in a concentration-dependent fashion. Vasorelaxant effects for BK-(1-7), BK-(1-5) or BK-(1-3) were independent of the kinin receptors. Different administration routes (i.e., intravenous or intra-arterial) did not affect the observed hypotension induced by BK-(1-7), BK-(1-5) or BK-(1-3). Importantly, these observations diverged from the BK-(1-9) results, highlighting that indeed the BK-(1-9) fragments do not seem to act via the classical kinin receptors.Conclusions and implicationsIn conclusion, BK-(1-7), BK-(1-5) and BK-(1-3) are biologically active components of the kallikrein-kinin system. Importantly, observed pathophysiological outcomes of these peptides are independent of B1R and/or B2R activation.
W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model
Authors: Janeček Michal , Kührová Petra , Mlýnský Vojtěch , Otyepka Michal , Šponer Jiří , Banáš Pavel 
Published: September 2020

ABSTRACTRepresentation of electrostatic interactions by a Coulombic pair-wise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules, and thus electrostatic interactions in the force field. In particular, we re-optimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme and included extra point charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model showed clear potential for improving the performance of the nucleic acid force fields, for which poor description of nonbonded interactions, such as underestimated base pairing, makes it difficult to describe the folding free energy landscape of small oligonucleotides.
Feeding recombinant Royalactin: Measures of improved lifespan and mitochondrial function inCaenorhabditis elegans
Authors: Li Xia , Ingram Thomas L. , Wang Ying , Derecka Kamila , Courtier Nathan , Piana Mattia , Hardy Ian C. W. , Chakrabarti Lisa , Stöger Reinhard 
Published: September 2020

AbstractAgeing, the decline of biological functions over time, is inherent to eukaryotes. Female honeybees attain a long-lived queen phenotype upon continuous consumption of royal jelly, whereas restricted supply of this nutritional substance promotes the development of worker bees, which are short-lived. An abundant protein found within royal jelly is major royal jelly protein 1 (MRJP1), also known as ‘Royalactin’. Health- and lifespan promoting effects have been attributed to Royalactin in species from diverse animal taxa, suggesting it acts on phylogenetically conserved physiological processes. Here, we explore the effects of feeding the nematodeCaenorhabditis eleganswithEscherichia colithat express a recombinant form of Royalactin (RArec). We confirm that consumption of RArecincreases body size, improves locomotion and extends lifespan. We discover a link between Royalactin and mitochondria, organelles which play a key part in the ageing process: both spare respiratory capacity and morphology indicate improved mitochondrial function in RArecfedC. elegans. These results demonstrate the feasibility of using recombinant Royalactin to gain further insight into processes of healthy ageing in many species.RArecproduction allows insight into potential beneficial effects across species.
Synchronous and Asynchronous Response in Dynamically Perturbed Proteins
Authors: Erkip Albert , Hacisuleyman Aysima , Erman Batu , Erman Burak 
Published: September 2020

AbstractWe developed a Dynamic Gaussian Network Model to study perturbation and response in proteins. The model is based on the solution of the Langevin equation in the presence of noise and perturbation. A residue is perturbed periodically with a given frequency and the response of other residues is determined in terms of a storage and loss modulus of the protein. The amount of work lost upon periodic perturbation and the residues that contribute significantly to the lost work is determined. The model shows that perturbation introduces new dynamic correlations into the system with time delayed synchronous and asynchronous components. Residues whose perturbation induces large correlations in the protein and those that do not lead to correlations may be identified. The model is used to investigate the dynamic modulation of nanobodies. Despite its simplicity, the model explains several features of perturbation and response such as the role of loops and linkers in perturbation, dispersion of work of perturbation, and information transfer through preexisting pathways, all shown to be important factors in allostery.
The mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress
Authors: Backes Sandra , Bykov Yury S. , Räschle Markus , Zhou Jialin , Lenhard Svenja , Krämer Lena , Mühlhaus Timo , Bibi Chen , Jann Cosimo , Smith Justin D. , Steinmetz Lars M. , Rapaport Doron , Storchová Zuzana , Schuldiner Maya , Boos Felix , Herrmann Johannes M. 
Published: September 2020

SummaryMost mitochondrial proteins are synthesized as precursors in the cytosol and post-translationally transported into mitochondria. The mitochondrial surface protein Tom70 acts at the interface of the cytosol and mitochondria.In vitroimport experiments identified Tom70 as targeting receptor, particularly for hydrophobic carriers. Usingin vivomethods and high content screens, we revisited the question of Tom70 function and considerably expanded the set of Tom70-dependent mitochondrial proteins. We demonstrate that the crucial activity of Tom70 is its ability to recruit cytosolic chaperones to the outer membrane. Indeed, tethering an unrelated chaperone-binding domain onto the mitochondrial surface complements most of the defects caused by Tom70 deletion. Tom70-mediated chaperone recruitment reduces the proteotoxicity of mitochondrial precursor proteins, in particular of hydrophobic inner membrane proteins. Thus, our work suggests that the predominant function of Tom70 is to tether cytosolic chaperones to the outer mitochondrial membrane, rather than to serve as a mitochondria-specifying targeting receptor.
Autophagy induced accumulation of lipids inpgrl1andpgr5ofChlamydomonas reinhardtiiunder high light
Authors: Chouhan Nisha , Devadasu Elsin Raju , Yadav Ranay Mohan , Subramanyam Rajagopal 
Published: September 2020

AbstractChlamydomonas (C) reinhardtiicells (wild-type CC125 and137AH, and cyclic electron transport dependant mutantspgrl1andpgr5) were grown in high light 500 µmol photons m−2s−1where the growth was significantly enhanced after three days. The starch and lipid contents were also increased; however, starch content was decreased inpgr5. Further, the Nile Red fluorescence shows that a significant amount of lipid bodies were observed inpgr5cells under high light. Similarly, the electron micrographs show that large vacuoles were formed in high light stress despite the change in stacks of grana structure. We also observed increased production of reactive oxygen species (ROS) that could lead to autophagy. Inline, a significant increase of ATG8 protein was noticed inpgr5, which is a hallmark characteristic for autophagy formation. Consequently, the triacylglycerol (TAG) content was increased due to DGAT and PDAT enzymes’ expression, especially inpgr5. Here, the TAG synthesis would have been obtained from degraded membrane lipids inpgr5. Additionally, mono, polyunsaturated, and saturated fatty acids were identified more in the high light condition. Our study shows that the high light induces ROS, leads to autophagy and TAGs accumulation, which is stored as an energy source to acclimatize the algae.
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data
Authors: Conard Ashley Mae , Goodman Nathaniel , Hu Yanhui , Perrimon Norbert , Singh Ritambhara , Lawrence Charles , Larschan Erica 
Published: September 2020

SummaryUncovering how transcription factors (TFs) regulate their targets at the DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) in normal and diseased states. RNA-seq has become a standard method to measure gene regulation using an established set of analysis steps. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Furthermore, methods which integrate ordered RNA-seq data with transcription factor binding data are urgently needed. Here, we present TIMEOR (Trajectory Inference and Mechanism Exploration with Omics data in R), the first web-based and adaptive time series multi-omics pipeline method which infers the relationship between gene regulatory events across time. TIMEOR addresses the critical need for methods to predict causal regulatory mechanism networks between TFs from time series multi-omics data. We used TIMEOR to identify a new link between insulin stimulation and the circadian rhythm cycle. TIMEOR is available athttps://github.com/ashleymaeconard/TIMEOR.git.
The adaptive value of tandem communication in ants: insights from an agent-based model
Authors: Goy Natascha , Glaser Simone M. , Grüter Christoph 
Published: September 2020

AbstractSocial animals often share information about the location of resources, such as a food source or a new nest-site. One well-studied communication strategy in ants is tandem running, whereby a leader guides a recruit to a resource. Tandem running is considered an example of animal teaching because a leader adjusts her behaviour and invests time to help another ant to learn the location of a resource more efficiently. Tandem running also has costs, such as waiting inside the nest for a leader and a reduced walking speed. Whether and when these costs outweigh the benefits of tandem running is not well understood. We developed an agent-based simulation model to investigate the conditions that favour communication by tandem running during foraging. We predicted that the spatio-temporal distribution of food sources, colony size and the ratio of scouts and recruits affect colony foraging success. Our results suggest that communication is favoured when food sources are hard to find, of variable quality and long lasting. These results mirror the findings of simulations of honeybee communication. Scouts locate food sources faster than tandem followers in some environments, suggesting that tandem running may fulfil the criteria of teaching only in some situations. Furthermore, tandem running was only beneficial above a critical colony size threshold. Taken together, our model suggests that there is a considerable parameter range that favours colonies that do not use communication, which could explain why many social insects with small colony sizes forage solitarily.
Heme oxygenase-1 affects cytochrome P450 function through the formation of heteromeric complexes: Interactions between CYP1A2 and heme oxygenase-1
Authors: Connick J. Patrick , Reed James R. , Cawley George F. , Backes Wayne L. 
Published: September 2020

AbstractHeme oxygenase 1 (HO-1) and the cytochromes P450 (P450s) are endoplasmic reticulum-bound enzymes that rely on the same protein, NADPH-cytochrome P450 reductase (POR), to provide the electrons necessary for substrate metabolism. Although the HO-1 and P450 systems are interconnected due to their common electron donor, they generally have been studied separately. As the expression of both HO-1 and P450s are affected by xenobiotic exposure, changes in HO-1 expression can potentially affect P450 function, and conversely, changes in P450 expression can influence HO-1. The goal of this study was to examine interactions between the P450 and HO-1 systems. Using bioluminescence resonance energy transfer (BRET), HO-1 formed HO-1•P450 complexes with CYP1A2, CYP1A1, and CYP2D6, but not all P450s. Studies then focused on the HO-1/CYP1A2 interaction. CYP1A2 formed a physical complex with HO-1 that was stable in the presence of POR. As expected, both HO-1 and CYP1A2 formed BRET-detectable complexes with POR. Whereas the POR•CYP1A2 complex was readily disrupted by the addition of HO-1, the POR•HO-1 complex was not significantly affected by the addition of CYP1A2. Interestingly, enzyme activities did not follow this pattern. Whereas BRET data suggested substantial inhibition of CYP1A2-mediated 7-ethoxyresorufin deethylation in the presence of HO-1, its activity was actually stimulated at subsaturating POR. In contrast, HO-1-mediated heme metabolism was inhibited at subsaturating POR. These results indicate that HO-1 and CYP1A2 form a stable complex and have mutual effects on the catalytic behavior of both proteins that cannot be explained by simple competition for POR.
Identification of Hyal2-expressing tumor-associated myeloid cells in cancer: implications for cancer-related inflammation through enhanced hyaluronan degradation
Authors: Dominguez Gutierrez Paul R. , Kwenda Elizabeth P. , Donelan William , O’Malley Padraic , Crispen Paul L. , Kusmartsev Sergei 
Published: September 2020

AbstractIncreased presence of myeloid derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) in tumor tissue has been extensively reported. These cells represent a major constituent of tumor infiltrate and exhibit a distinct phenotype with immunosuppressive and tolerogenic functions. However, their role in the regulation of hyaluronan (HA) metabolism in the tumor microenvironment has not been established. Here we describe a novel function of tumor-associated myeloid cells related to the enhanced breakdown of extracellular HA in human bladder cancer tissue leading to accumulation of small HA fragments with MW <20 kDa. Increased fragmentation of extracellular HA and accumulation of low molecular weight HA (LMW-HA) in tumor tissue was associated with elevated production of multiple inflammatory cytokines, chemokines, and angiogenic factors. The fragmentation of HA by myeloid cells was mediated by the membrane-bound enzyme hyaluronidase 2 (Hyal2). The increased numbers of Hyal2+CD11b+myeloid cells were detected in the tumor tissue as well as in the peripheral blood of bladder cancer patients. Co-expression of CD33 suggests that these cells belong to monocytic myeloid-derived suppressor cells. HA-degrading function of Hyal2-expressing MDSCs could be enhanced by exposure to tumor-conditioned medium, and IL-1β was identified as one of factors involved in the stimulation of Hyal2 activity. CD44-mediated signaling plays an important role in the regulation of HA-degrading activity of Hyal2-expressing myeloid cells, since engagement of CD44 receptor with specific monoclonal antibody triggered translocation of Hyal2 enzyme to the cellular surface and also stimulated secretion of IL-1β. Taken together, this work identifies the Hyal2-expressing tumor-associated myeloid cells, and links these cells to the accumulation of LMW-HA in the tumor microenvironment and cancer-related inflammation and angiogenesis.
Promoter-proximal elongation regulates transcription in archaea
Authors: Blombach Fabian , Fouqueau Thomas , Matelska Dorota , Smollett Katherine , Werner Finn 
Published: September 2020

AbstractRecruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeonSulfolobus solfataricus.We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.