bluuebunny/crossref_metadata_2025_split huggingface dataset:
A developmental stretch-and-fill process that optimises dendritic wiring
Authors: Baltruschat Lothar , Tavosanis Gaia , Cuntz Hermann 
Published: July 2020

AbstractThe way in which dendrites spread within neural tissue determines the resulting circuit connectivity and computation. However, a general theory describing the dynamics of this growth process does not exist. Here we obtain the first time-lapse reconstructions of neurons in living fly larvae over the entirety of their developmental stages. We show that these neurons expand in a remarkably regular stretching process that conserves their shape. Newly available space is filled optimally, a direct consequence of constraining the total amount of dendritic cable. We derive a mathematical model that predicts one time point from the previous and use this model to predict dendrite morphology of other cell types and species. In summary, we formulate a novel theory of dendrite growth based on detailed developmental experimental data that optimises wiring and space filling and serves as a basis to better understand aspects of coverage and connectivity for neural circuit formation.In briefWe derive a detailed mathematical model that describes long-term time-lapse data of growing dendrites; it optimises total wiring and space-filling.HighlightsDendrite growth iterations guarantee optimal wiring at each iteration.Optimal wiring guarantees optimal space filling.The growth rule from fly predicts dendrites of other cell types and species.Fly neurons stretch-and-fill target area with precise scaling relations.Phase transition of growth process between fly embryo and larval stages.
Glycolytic pyruvate kinase moonlighting activities in DNA replication initiation and elongation
Authors: Horemans Steff , Pitoulias Matthaios , Holland Alexandria , Soultanas Panos , Janniere Laurent 
Published: July 2020

SUMMARYCells have evolved a metabolic control of DNA replication to respond to a wide range of nutritional conditions. Accumulating data suggest that this poorly understood control depends, at least in part, on Central Carbon Metabolism (CCM). InBacillus subtilis, the glycolytic pyruvate kinase (PykA) is intricately linked to replication. This 585 amino-acid-long enzyme comprises a catalytic (Cat) domain that binds to phosphoenolpyruvate (PEP) and ADP to produce pyruvate and ATP, and a C-terminal domain of unknown function. Interestingly, the C-terminal domain termed PEPut interacts with Cat and is homologous a domain that, in other metabolic enzymes, are phosphorylated at a conserved TSH motif at the expense of PEP and ATP to drive sugar import and catalytic or regulatory activities. To gain insights into the role of PykA in replication, DNA synthesis was analyzed in various Cat and PEPut mutants grown in a medium where the metabolic activity of PykA is dispensable for growth. Measurements of replication parameters (ori/terratio, C period and fork speed) and of the pyruvate kinase activity showed that PykA mutants exhibit replication defects resulting from side chain modifications in the PykA protein rather than from a reduction of its metabolic activity. Interestingly, Cat and PEPut have distinct commitments in replication: while Cat impacts positively and negatively replication fork speed, PEPut stimulates initiation through a process depending on Cat-PEPut interaction and growth conditions. Residues binding to PEP and ADP in Cat, stabilizing the Cat-PEPut interaction and belonging to the TSH motif of PEPut were found important for the commitment of PykA in replication.In vitro, PykA affects the activities of replication enzymes (the polymerase DnaE, helicase DnaC and primase DnaG) essential for initiation and elongation and genetically linked topykA. Our results thus connect replication initiation and elongation to CCM metabolites (PEP, ATP and ADP), critical Cat and PEPut residues and to multiple links between PykA and the replication enzymes DnaE, DnaC and DnaG. We propose that PykA is endowed with a moonlighting activity that senses the concentration of signaling metabolites and interacts with replication enzymes to convey information on the cellular metabolic state to the replication machinery and adjust replication initiation and elongation to metabolism. This defines a new type of replication regulator proposed to be part of the metabolic control that gates replication in the cell cycle.
FIP200 organizes the autophagy machinery at p62-ubiquitin condensates beyond activation of the ULK1 kinase
Authors: Turco Eleonora , Fischer Irmgard , Martens Sascha 
Published: July 2020

AbstractMacroautophagy is a conserved degradation pathway, which mediates cellular homeostasis by the delivery of harmful substances into lysosomes. This is achieved by the sequestration of these substances referred to as cargo within double membrane vesicles, the autophagosomes, which formde novo. Among the many cargoes that are targeted by autophagy are condensates containing p62 and ubiquitinated proteins. p62 recruits the FIP200 protein to initiate autophagosome formation at the condensates. How FIP200 in turn organizes the autophagy machinery is unclear. Here we show that FIP200 is dispensable for the recruitment of the upstream autophagy machinery to the condensates, but it is necessary for phosphatidylinositol 3-phosphate formation and WIPI2 recruitment. We further find that FIP200 is required for the activation of the ULK1 kinase. Surprisingly, ULK1 kinase activity is not strictly required for autophagosome formation at p62 condensates. Super-resolution microscopy of p62 condensates revealed that FIP200 surrounds the condensates where it spatially organizes ATG13 and ATG9A for productive autophagosome formation. Our data provide a mechanistic insight into how FIP200 orchestrates autophagosome initiation at the cargo.
CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites
Authors: Miura Michi , Chen Honglin 
Published: July 2020

AbstractCUT&RUN is a powerful tool to study protein-DNA interactionsin vivo. DNA fragments cleaved by the targeted micrococcal nuclease identify the footprints of DNA-binding proteins on the chromatin. We performed CUT&RUN on human lung carcinoma cell line A549 maintained in a multi-well cell culture plate to profile RNA polymerase II. Long (>270 bp) DNA fragments released by CUT&RUN corresponded to the bimodal peak around the transcription start sites, as previously seen with chromatin immunoprecipitation. However, we found that short (<120 bp) fragments identify a well-defined peak localised at the transcription start sites. This distinct DNA footprint of short fragments, which constituted only about 5% of the total reads, suggests the transient positioning of RNA polymerase II before promoter-proximal pausing, which has not been detected in the physiological settings by standard chromatin immunoprecipitation. We showed that the positioning of the large-size-class DNA footprints around the short-fragment peak was associated with the directionality of transcription, demonstrating the biological significance of distinct CUT&RUN footprints of RNA polymerase II.
Multiple dimensions of social motivation in adult female degus
Authors: Lidhar Navdeep K. , Thakur Ayushi , David Anna-Julia , Takehara-Nishiuchi Kaori , Insel Nathan 
Published: July 2020

AbstractMany animals become more motivated to interact after a period of isolation. This phenomenon may involve general drives, e.g. for social touch or companionship, as well as drives that are specific to particular peers, and which ultimately serve to reestablish relationships between the individuals. Female degus are known to be affiliative with multiple other individuals, including unrelated and unfamiliar conspecifics, offering an opportunity to study social motivation independent from exclusive pair-bonds or overt, same-sex competition. We attempted to disentangle factors driving peer interaction by examining reunion behavior across several social isolation and separation manipulations. High levels of interaction were observed between adult females who had been separated even without isolation, revealing a drive to re-establish relationships with specific peers. The content of separation-only reunions differed from isolation, with the latter involving more early-session interaction, higher levels of allogrooming before rear-sniffing, and a higher ratio of chitter vocalizations. To assess whether post-isolation behavior was related to stress, we examined reunions following a non-social (footshock) stressor. Like isolation, footshock increased early-session interactions, but did not increase allogrooming before rear-sniffing or chittering, as compared with controls. To test whether separation-only reunion behavior shared qualities with relationship formation, we also examined reunions of new (stranger) dyads. Strangers exhibited higher levels of interaction than cagemates, with particularly high levels of late-session rear-sniffing. Like separation-only reunions, strangers showed more non-chitter vocalizations and lower levels of allogrooming before rear-sniffing. Across experiments, an exploratory clustering method was used to identify vocalizations that differed between conditions. This yielded promising leads for future investigation, including a chaff-type syllable that may have been more common during relationship renewal. Overall, results are consistent with the hypothesis that female degu reunions are supported by both general and peer-stimulus specific drives, expressed through the structure of physical and vocal interactions over time.
Modulation of neural oscillations during working memory update, maintenance, and readout: an hdEEG study
Authors: Semprini Marianna , Bonassi Gaia , Barban Federico , Pelosin Elisa , Iandolo Riccardo , Chiappalone Michela , Mantini Dante , Avanzino Laura 
Published: July 2020

AbstractWorking memory (WM) performance is very often measured using the n-back task, in which the participant is presented with a sequence of stimuli, and required to indicate whether the current stimulus matches the one presented n steps earlier. In this study, we used high-density electroencephalography (hdEEG) coupled to source localization to obtain information on spatial distribution and temporal dynamics of neural oscillations associated with WM update, maintenance and readout. Specifically, we a priori selected regions from a large fronto-parietal network, including also the insula and the cerebellum, and we analyzed modulation of neural oscillations by event-related desynchronization and synchronization (ERD/ERS).During update and readout, we found larger θ ERS and smaller β ERS respect to maintenance in all the selected areas. γLOWand γHIGHbands oscillations decreased in the frontal and insular cortices of the left hemisphere. In the maintenance phase we observed focally decreased θ oscillations and increased β oscillations (ERS) in most of the selected posterior areas and focally increased oscillations in γLOWand γHIGHbands in the frontal and insular cortices of the left hemisphere. Finally, during WM readout, we also found a focal modulation of the γLOWband in the left fusiform cortex and cerebellum, depending on the response trial type (true positive vs. true negative).Overall, our study demonstrated specific spectral signatures associated with updating of memory information, WM maintenance and readout, with relatively high spatial resolution.
Disease associated mutations in mitochondrial precursor tRNAs affect binding, m1R9 methylation and tRNA processing by mtRNase P
Authors: Karasik Agnes , Fierke Carol A. , Koutmos Markos 
Published: July 2020

ABSTRACTMitochondrial diseases linked to mutations in mitochondrial(mt) tRNA sequences are abundant. However, the contributions of these tRNA mutations to the development of diseases is mostly unknown. Mutations may affect interactions with (mt)tRNA maturation enzymes or protein synthesis machinery leading to mitochondrial dysfunction. In human mitochondria, the first step of tRNA processing is the removal of the 5’end of precursor tRNAs (pre-tRNA) catalyzed by the three-component enzyme, mtRNase P. Additionally, one sub-component of mtRNase P, mitochondrial RNase P protein 1 (MRPP1) catalyzes methylation of the R9 base in pre-tRNAs. Despite the central role of 5’ end processing in mitochondrial tRNA maturation, the link between mtRNase P and diseases is mostly unexplored. Here we investigate how 11 different human disease-linked mutations in (mt)pre-tRNAs affect the activities of mtRNase P. We find that several mutations weaken the pre-tRNA binding affinity, while the majority of mutations decrease 5’ end processing and methylation activity catalyzed by mtRNase P. Furthermore, all of the investigated mutations in (mt)pre-tRNALeu(UUR)alter the tRNA fold which contributes to the partial loss of function of mtRNase P. Overall, these results reveal an etiological link between early steps of (mt)tRNA-substrate processing and mitochondrial disease.
The developing relations between networks of cortical myelin and neurophysiological connectivity
Authors: Vandewouw Marlee M. , Hunt Benjamin A.E. , Ziolkowski Justine , Taylor Margot J. 
Published: July 2020

AbstractRecent work identified that patterns of distributed brain regions sharing similar myeloarchitecture are related to underlying functional connectivity, demonstrating cortical myelin’s plasticity to changes in functional demand. However, the changing relation between functional connectivity and structural architecture throughout child and adulthood is poorly understood. We show that structural covariance connectivity measured using T1-weighted/T2-weighted ratio and functional connectivity measured using magnetoencephalography exhibit nonlinear developmental changes. We then show significant relations between structural and functional connectivity, which have both shared and distinct characteristics dependent on the neural oscillatory frequency. Increases in structure-function coupling are visible during the protracted myelination observed throughout childhood and adolescence, and are followed by decreases near the onset of adulthood to potentially support increasing cognitive flexibility and functional specialization in adulthood. Our work lays the foundation for understanding the mechanisms by which myeloarchitecture supports brain function, enabling future investigations into how clinical populations may deviate from normative patterns.
Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity
Authors: Pal Debnath 
Published: July 2020

AbstractCompared to the other human coronaviruses, SARS-CoV-2 has a higher reproductive number that is driving the COVID-19 pandemic. The high transmission of SARS-CoV-2 has been attributed to environmental, immunological, and molecular factors. The Spike protein is the foremost molecular factor responsible for virus fusion, entry and spread in the host, and thus holds clues for the rapid viral spread. The dense glycosylation of Spike, its high affinity of binding to the human ACE2 receptor, and the efficient priming by cleavage have already been proposed for driving efficient virus-host entry, but these do not explain its unusually high transmission rate. I have investigated the Spike from six β-coronaviruses, including the SARS-CoV-2, and find that their surface-exposed fusion peptides constituting the defined fusion loop are spatially organized contiguous to each other to work synergistically for triggering the virus-host membrane fusion process. The architecture of the Spike quaternary structure ensures the participation of the fusion peptides in the initiation of the host membrane contact for the virus fusion process. The SARS-CoV-2 fusion peptides have unique physicochemical properties, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The specific contribution of these prolines shows significantly diminished fusogenicityin vitroand associated pathogenesisin vivo,inferred from comparative studies of their deletion-mutant in a fellow murine β-coronavirus MHV-A59. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread.Significance StatementThe three proximal fusion peptides constituting the fusion loop in Spike protein are the membranotropic segments most suitable for engaging the host membrane surface for its disruption. Spike’s unique quaternary structure architecture drives the fusion peptides to initiate the protein host membrane contact. The SARS-CoV-2 Spike trimer surface is relatively more hydrophobic among other human coronavirus Spikes, including the fusion peptides that are structurally more rigid owing to the presence of consecutive prolines, aromatic/hydrophobic clusters, a stretch of consecutive β-branched amino acids, and the hydrogen bonds. The synergy accrued from the location of the fusion peptides, their physicochemical features, and the fusogenic conformational transition appears to drive the virus fusion process and may explain the high spread of the SARS-CoV-2.
A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex
Authors: Eydoux Cecilia , Fattorini Veronique , Shannon Ashleigh , Le Thi-Tuyet-Nhung , Didier Bruno , Canard Bruno , Guillemot Jean-Claude 
Published: July 2020

AbstractThe Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) emergence in 2003 introduced the first serious human coronavirus pathogen to an unprepared world. To control emerging viruses, existing successful anti(retro)viral therapies can inspire antiviral strategies, as conserved viral enzymes (eg., viral proteases and RNA-dependent RNA polymerases) represent targets of choice. Since 2003, much effort has been expended in the characterization of the SARS-CoV replication/transcription machinery. Until recently, a pure and highly active preparation of SARS-CoV recombinant RNA synthesis machinery was not available, impeding target-based high throughput screening of drug candidates against this viral family. The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. This phylogenetic relatedness highlights the potential use of conserved replication enzymes to discover inhibitors against this significant pathogen, which in turn, contributes to scientific preparedness against emerging viruses. Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. The screening of a small (1,520 compounds) chemical library of FDA-approved drugs demonstrates the robustness of our assay and will allow to speed-up drug repositioning or novel drug discovery against the SARS-CoV-2.Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assayHighlights- A new SARS-CoV non radioactive RNA polymerase assay is described- The robotized assay is suitable to identify RdRp inhibitors based on HTS
Structural and molecular dynamics ofMycobacterium tuberculosismalic enzyme, a potential anti-TB drug target
Authors: Burley Kalistyn H. , Cuthbert Bonnie J. , Basu Piyali , Newcombe Jane , Irimpan Ervin M. , Quechol Robert , Foik Ilona P. , Mobley David L. , Beste Dany J.V. , Goulding Celia W. 
Published: July 2020

AbstractTuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent,Mycobacterium tuberculosis(Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ provides the required reducing power for lipid biosynthesis. Here, we present the X-ray crystal structure of MEZ to 3.6 Å resolution and compare it with known structures of prokaryotic and eukaryotic malic enzymes. We use biochemical assays to determine its oligomeric state and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually disordered, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that MEZ subunits alternate between open and closed states and that MEZ can stably bind its NAD(P)+cofactor in multiple conformations, including an inactive, compact NAD+form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb.
A rapidly adaptable biomaterial vaccine for SARS-CoV-2
Authors: Langellotto Fernanda , Seiler Benjamin T. , Yu Jingyou , Cartwright Mark J. , White Des , Yeager Chyenne , Super Michael , Doherty Edward J. , Barouch Dan H. , Mooney David J. 
Published: July 2020

ABSTRACTThe global COVID-19 pandemic motivates accelerated research to develop safe and efficacious vaccines. To address this need, we leveraged a biomaterial vaccine technology that consists of mesoporous silica rods (MSRs) that provide a sustained release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and adjuvants to concentrate and mature antigen-presenting cells at the vaccine site. Here we explored the humoral responses resulting from the use of monophosphoryl lipid A (MPLA) as the adjuvant and SARS-CoV-2 spike proteins S1, S2, the nucleocapsid (N) protein, and receptor binding domain (RBD) as the target antigens. The dose of antigen and impact of pre-manufacturing of vaccines as versus loading antigen just-in-time was explored in these studies. Single shot MSR vaccines induced rapid and robust antibody titers to the presented antigens, even without the use of a boost, and sera from vaccinated animals demonstrated neutralizing activity against a SARS-CoV-2 pseudovirus. Overall, these results suggest the MSR vaccine system may provide potent protective immunity when utilized to present SARS-CoV-2 antigens.
Genome-wide assessment of REST binding profiles reveals distinctions between human and mouse hippocampus
Authors: McGann James C. , Spinner Michael , Garg Saurabh K. , Mullendorf Karin , Woltjer Randall L. , Mandel Gail 
Published: July 2020

AbstractBackgroundThe transcriptional repressor, RE1 Silencing Transcription Factor (REST), recognized historically as a master regulator of neuronal gene expression during mouse development, has recently been ascribed roles in human aging and neurodegenerative disorders. However, REST’s role in healthy adult human brain, and how faithfully mouse models reproduce REST function in human brain, is not known.ResultsHere, we present the first genome-wide binding profile for REST in both mouse and human postnatal hippocampus. We find the majority of REST-bound sites in human hippocampus are unique compared to both mouse hippocampus and to all other reported human ENCODE cell types. Genes associated with unique REST-bound sites include previously unidentified categories related to innate immunity and inflammation signaling, suggesting species specific roles for REST in protecting human brain health.ConclusionsOur results suggest newly evolved functions for REST in maintaining human brain health.