bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microstructure Aware Modeling Of Biochemical Transport In Arterial Blood Clots
Authors: Teeraratkul Chayut , Mukherjee Debanjan 
Published: January 2021

AbstractFlow-mediated transport of biochemical species is central to thrombotic phenomena. Comprehensive three-dimensional modeling of flow-mediated transport around realistic macroscale thrombi poses challenges owing to their arbitrary heterogeneous microstructure. Here, we develop a microstructure aware model for species transport within and around a macroscale thrombus by devising a custom preconditioned fictitious domain formulation for thrombus-hemodynamics interactions, and coupling it with a fictitious domain advection-diffusion formulation for transport. Microstructural heterogeneities are accounted through a hybrid discrete particle-continuum approach for the thrombus interior. We present systematic numerical investigations on unsteady arterial flow within and around a three-dimensional macroscale thrombus; demonstrate the formation of coherent flow structures around the thrombus which organize advective transport; illustrate the role of the permeation processes at the thrombus boundary and subsequent intra-thrombus transport; and characterize species transport from bulk flow to the thrombus boundary and vice versa.
RBD11, a bioengineered Rab11-binding module for visualizing and analyzing endogenous Rab11
Authors: Osaki Futaba , Matsui Takahide , Hiragi Shu , Homma Yuta , Fukuda Mitsunori 
Published: January 2021

ABSTRACTThe small GTPase Rab11 plays pivotal roles in diverse physiological phenomena, including the recycling of membrane proteins, cytokinesis, neurite outgrowth, and epithelial morphogenesis. One effective method of analyzing the function of endogenous Rab11 is to overexpress a Rab11-binding domain of one of its effectors, e.g., the C-terminal domain of Rab11-FIP2 (Rab11-FIP2-C), as a dominant-negative construct. However, the drawback of this method is the broader Rab binding specificity of the effector domain, because Rab11-FIP2-C binds to Rabs other than Rab11, e.g., to Rab14 and Rab25. In this study, we bioengineered an artificial Rab11-specific binding domain, named RBD11. Expression of RBD11 visualized endogenous Rab11 without affecting its localization or function, whereas expression of a tandem RBD11, named 2×RBD11, inhibited epithelial morphogenesis and induced a multi-lumen phenotype characteristic of Rab11-deficient cysts. We also developed two tools for temporally and reversibly analyzing Rab11-dependent membrane trafficking: tetracycline-inducible 2×RBD11 and an artificially oligomerized domain (FM)-tagged RBD11.
The rapid evolution of flagellar ion-selectivity in experimental populations ofE. coli
Authors: Ridone Pietro , Ishida Tsubasa , Lin Angela , Humphreys David T , Giannoulatou Eleni , Sowa Yoshiyuki , Baker Matthew A. B. 
Published: January 2021

ABSTRACTDetermining which cellular processes facilitate adaptation requires a tractable experimental model where an environmental cue can generate variants which rescue function. The Bacterial Flagellar Motor (BFM) is an excellent candidate – an ancient and highly conserved molecular complex for propulsion which navigates bacteria towards favourable environments. In most species, rotation is powered by H+or Na+ion transit through the torque-generating stator subunit of the motor complex. The ion that drives the rotor has changed over evolutionary timescales but the molecular basis of this selectivity remains unknown.Here we used CRISPR engineering to replace the nativeEscherichia coliH+-powered stator with Na+-powered stator genes and report the rapid and spontaneous reversion of our edit in a low sodium environment. We followed the evolution of the stators during their reversion to H+-powered motility and used whole genome and transcriptome sequencing to identify both flagellar- and non-flagellar-associated genes involved in the cell’s adaptation. Our transplant of an unfit protein and the cells’ rapid response to this edit demonstrates the adaptability of the stator subunit and highlights the hierarchical modularity of the flagellar motor.
HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization
Authors: Biswas Saikat , Karslake Joshua D. , Chen Ziyuan , Farhat Ali , Freddolino Peter L. , Biteen Julie S. , Ragunathan Kaushik 
Published: January 2021

ABSTRACTHP1 proteins bind with low affinity but high specificity to histone H3 lysine 9 methylation (H3K9me), forming transcriptionally inactive genomic compartments referred to as heterochromatin. How HP1 proteins traverse a complex and crowded chromatin landscape on the millisecond timescale and yet recognize H3K9me with high specificity remains paradoxical. Here, we visualize the single-molecule dynamics of an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By analyzing the motions of individual Swi6 molecules, we identify mobility states that map to discrete biochemical intermediates. Using mutants that perturb Swi6 H3K9me recognition, oligomerization, or nucleic acid binding, we parse the mechanism by which each biochemical property affects protein dynamics. We find that rather than enhancing chromatin binding, nucleic acid interactions, compete with and titrates Swi6 away from heterochromatin. However, as few as four tandem Swi6 chromodomains are necessary and sufficient to restore H3K9me-dependent localization. Our studies propose propose that HP1 oligomerization stabilizes higher-order protein configurations of a defined stoichiometry that facilitates high-specificity H3K9me recognition and outcompetes the inhibitory effects of nucleic acid-binding.
A Developmental Role for Microglial Presenilin 1 in Memory
Authors: Ledo Jose Henrique , Azevedo Estefania P. , Medrihan Lucian , Cheng Jia , Silva Hernandez M. , McCabe Kathryn , Bamkole Michael , Lafaille Juan J. , Friedman Jeffrey M. , Stevens Beth , Greengard Paul 
Published: January 2021

SummaryMicroglia, the macrophages of the brain, are increasingly recognized to play a key role in synaptic plasticity and function; however, the underlying mechanisms remain elusive. Presenilin 1 (PS1) is an essential protein involved in learning and memory, through neuronal mechanisms. Loss of Presenilin function in neurons impairs synapse plasticity and causes cognitive deficits in mice. Surprisingly, here we show memoryenhancementin mice by deleting PS1 selectively in microglia. We further demonstrate increased synapse transmission andin vivoneuronal activity in mice by depleting PS1 during microglial development, but not after microglial maturation. Remarkably, conditional deletion of PS1 in microglia during development increased memory retention in adulthood and was dependent on the NMDA receptor subunit GluN2B. In vivo calcium imaging of freely behaving mice revealed increased amplitude of neuronal Ca2+ transients in the CA1 hippocampus ofPS1 cKOmice compared to control mice, suggesting a greater CA1 engagement during novel object exploration. Finally, loss of PS1 in microglia mitigated synaptic and cognitive deficits in a mouse model of Alzheimer’s disease. Together our results reveal a novel mechanism and function of PS1 in microglia in which modulation can enhance neuronal activity, learning and memory in mice.
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2
Authors: Vanshylla Kanika , Di Cristanziano Veronica , Kleipass Franziska , Dewald Felix , Schommers Philipp , Gieselmann Lutz , Gruell Henning , Schlotz Maike , Ercanoglu Meryem S , Stumpf Ricarda , Mayer Petra , Heger Eva , Johannis Wibke , Horn Carola , Suárez Isabelle , Jung Norma , Salomon Susanne , Eberhardt Kirsten Alexandra , Fätkenheuer Gerd , Pfeifer Nico , Eggeling Ralf , Augustin Max , Lehmann Clara , Klein Florian 
Published: January 2021

AbstractA detailed understanding of antibody-based SARS-CoV-2 immunity has critical implications for overcoming the COVID-19 pandemic and for informing on vaccination strategies. In this study, we evaluated the dynamics of the SARS-CoV-2 antibody response in a cohort of 963 recovered individuals over a period of 10 months. Investigating a total of 2,146 samples, we detected an initial SARS-CoV-2 antibody response in 94.4% of individuals, with 82% and 79% exhibiting serum and IgG neutralization, respectively. Approximately 3% of recovered patients demonstrated exceptional SARS-CoV-2 neutralizing activity, defining them as ‘elite neutralizers’. These individuals also possessed effective cross-neutralizing IgG antibodies to SARS-CoV-1 without any known prior exposure to this virus. By applying multivariate statistical modeling, we found that sero-reactivity, age, time since disease onset, and fever are key factors predicting SARS-CoV-2 neutralizing activity in mild courses of COVID-19. Investigating longevity of the antibody response, we detected loss of anti-spike reactivity in 13% of individuals 10 months after infection. Moreover, neutralizing activity had an initial half-life of 6.7 weeks in serum versus 30.8 weeks in purified IgG samples indicating the presence of a more stable and long-term memory IgG B cell repertoire in the majority of individuals recovered from COVID-19. Our results demonstrate a broad spectrum of the initial SARS-CoV-2 neutralizing antibody response depending on clinical characteristics, with antibodies being maintained in the majority of individuals for the first 10 months after mild course of COVID-19.
Do examinations prepare students for higher education? A lesson from the Covid-19 lockdown
Authors: Harriet L Jones , Valentina Zini , Jon R Green , John R Prendergast , Jon Scott 
Published: January 2021

AbstractThe COVID-19 pandemic caused severe disruption to education in the UK in 2020, with most of the school teaching moving online and national school examinations being cancelled. This was particularly disruptive for those taking end of school examinations in preparation for higher education. Biological science courses require students to absorb a lot of new vocabulary and concepts, with examinations traditionally focusing on content recall rather than reasoning. Students who had entered university in September 2019 were compared with those arriving in September 2020 with respect to their knowledge of bioscience vocabulary and understanding of key concepts. Results showed no significant difference between those who had gone through the examination process in 2019 relative to those who had not, in 2020. This suggests the cramming of information for examinations has no detectable effect on the knowledge and understanding of biology that students take with them to university.
Dendritic membrane resistance modulates activity-induced Ca2+influx in oxytocinergic magnocellular neurons of mouse PVN
Authors: Sheng Wanhui , Harden Scott W. , Tan Yalun , Krause Eric G. , Frazier Charles J. 
Published: January 2021

ABSTRACTHypothalamic oxytocinergic magnocellular neurons have a fascinating ability to release peptide from both their axon terminals and from their dendrites. Existing data indicates there is a flexible relationship between somatic activity and dendritic release, but the mechanisms governing this relationship are not completely understood. Here we use a combination of electrical and optical recording techniques to quantify activity-dependent calcium influx in proximal vs. distal dendrites of oxytocinergic magnocellular neurons located in the paraventricular nucleus of the hypothalamus (OT-MCNs). Results reveal that the dendrites of OT-MCNs are weak conductors of somatic voltage changes, and yet activity-induced dendritic calcium influx can be robustly regulated by a diverse set of stimuli that open or close ionophores located along the dendritic membrane. Overall, this study reveals that dendritic membrane resistance is a dynamic and endogenously regulated feature of OT-MCNs that is likely to have substantial functional impact on central oxytocin release.IMPACT STATEMENTActivity-induced dendritic calcium influx in oxytocinergic magnocellular neurons can be robustly modulated by a highly diverse set of stimuli acting on distinct types of ionophores expressed along the dendritic membrane.
RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration
Authors: Becchi Matteo , Chiarantoni Pietro , Suma Antonio , Micheletti Cristian 
Published: January 2021

ABSTRACTWe use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide long xrRNA from Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either one of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on timescales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, both for activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing-downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings ought to be useful as a reference to interpret and design future theoretical and experimental studies of RNA translocation.
Mechanotaxis directsPseudomonas aeruginosatwitching motility
Authors: Kühn Marco J. , Talà Lorenzo , Inclan Yuki , Patino Ramiro , Pierrat Xavier , Vos Iscia , Al-Mayyah Zainebe , MacMillan Henriette , Negrete Jose , Engel Joanne N. , Persat Alexandre 
Published: January 2021

AbstractThe opportunistic pathogenPseudomonas aeruginosaexplores surfaces using twitching motility powered by retractile extracellular filaments called type IV pili. Single cells twitch by successive pili extension, attachment and retraction. However, whether and how single cells control twitching migration remains unclear. We discovered thatP. aeruginosaactively directs twitching in the direction of mechanical input from type IV pili, in a process we call mechanotaxis. The Chp chemotaxis-like system controls the balance of forward and reverse twitching migration of single cells in response to the mechanical signal. On surfaces, Chp senses type IV pili attachment at one pole thereby sensing a spatially-resolved signal. As a result, the Chp response regulators PilG and PilH control the polarization of the extension motor PilB. PilG stimulates polarization favoring forward migration, while PilH inhibits polarization inducing reversal. Subcellular segregation of PilG and PilH efficiently orchestrates their antagonistic functions, ultimately enabling rapid reversals upon perturbations. This distinct localization of response regulators establishes a signaling landscape known as local-excitation, global-inhibition in higher order organisms, identifying a conserved strategy to transduce spatially-resolved signals. Our discovery finally resolves the function of the Chp system and expands our view of the signals regulating motility.
Deep learning-based real-time detection of novel pathogens during sequencing
Authors: Bartoszewicz Jakub M. , Genske Ulrich , Renard Bernhard Y. 
Published: January 2021

AbstractNovel pathogens evolve quickly and may emerge rapidly, causing dangerous outbreaks or even global pandemics. Next-generation sequencing is the state-of-the-art in open-view pathogen detection, and one of the few methods available at the earliest stages of an epidemic, even when the biological threat is unknown. Analyzing the samples as the sequencer is running can greatly reduce the turnaround time, but existing tools rely on close matches to lists of known pathogens and perform poorly on novel species. Machine learning approaches can predict if single reads originate from more distant, unknown pathogens, but require relatively long input sequences and processed data from a finished sequencing run. Incomplete sequences contain less information, leading to a trade-off between sequencing time and detection accuracy. Using a workflow for real-time pathogenic potential prediction, we investigate which subsequences already allow accurate inference. We train deep neural networks to classify Illumina and Nanopore reads and integrate the models with HiLive2, a real-time Illumina mapper. This approach outperforms alternatives based on machine learning and sequence alignment on simulated and real data, including SARS-CoV-2 sequencing runs. After just 50 Illumina cycles, we observe an 80-fold sensitivity increase compared to real-time mapping. The first 250bp of Nanopore reads, corresponding to 0.5s of sequencing time, are enough to yield predictions more accurate than mapping the finished long reads. The approach could also be used for screening synthetic sequences against biosecurity threats.
Selective uptake into inflamed human intestinal tissue and immune cell targeting by wormlike polymer micelles
Authors: Gardey Elena , Sobotta Fabian H. , Haziri Drilon , Grunert Philip C. , Kuchenbrod Maren T. , Gruschwitz Franka V. , Hoeppener Stephanie , Schumann Michael , Gaßler Nikolaus , Stallmach Andreas , Brendel Johannes C. 
Published: January 2021

AbstractOver the 21st century, inflammatory bowel disease (IBD) has become a global disease with no causal therapeutic options. Selective targeting of inflamed areas in the gastrointestinal tract could be an effective treatment circumventing severe side effects for healthy tissue. Our study demonstrates that the shape of polymeric nanostructures represents so far rarely addressed key to required tissue selectivity in the intestine.Ex vivoexperiments on human colonic biopsies revealed that crosslinked wormlike micelles featuring a dense poly(ethylene oxide) (PEO) shell exclusively enter the inflamed human mucosa without affecting healthy tissue. Similarly designed spherical micelles (∼25 nm) or vesicles (∼120 nm) penetrate both tissues or were barely uptaken at all, respectively. Moreover, it was found that the particles colocalize with immune cells in the lamina propria facilitating a specific targeting of the main pro-inflammatory cells within the diseased human mucosa. These findings demonstrate an untapped potential in particle design and enable new vistas for an effective treatment of IBD.
Generating novel protein sequences using Gibbs sampling of masked language models
Authors: Johnson Sean R. , Monaco Sarah , Massie Kenneth , Syed Zaid 
Published: January 2021

AbstractRecently developed language models (LMs) based on deep neural networks have demonstrated the ability to generate fluent natural language text. LMs pre-trained on protein sequences have shown state of the art performance on a variety of downstream tasks. Protein LMs have also been used to generate novel protein sequences. In the present work we use Gibbs sampling of BERT-style LMs, pre-trained on protein sequences using the masked language modeling task, to generate novel protein sequences. We evaluate the quality of the generated sequences by comparing them to natural sequences from the same family. In particular, we focus on proteins from the chorismate mutase type II family, which has been used in previous work as an example target for protein generative models. We find that the Gibbs sampling process on BERT-style models pretrained on millions to billions of protein sequences is able to generate novel sequences that retain key features of related natural sequences. Further, we find that smaller models fine-tuned or trained from scratch on family-specific data are able to equal or surpass the generation quality of large pre-trained models by some metrics. The ability to generate novel natural-like protein sequences could contribute to the development of improved protein therapeutics and protein-catalysts for industrial chemical production.
Computational Analysis of Protein Stability and Allosteric Interaction Networks in Distinct Conformational Forms of the SARS-CoV-2 Spike D614G Mutant: Reconciling Functional Mechanisms through Allosteric Model of Spike Regulation
Authors: Verkhivker Gennady M. , Agajanian Steve , Oztas Denis , Gupta Grace 
Published: January 2021

AbstractStructural and biochemical studies SARS-CoV-2 spike mutants with the enhanced infectivity have attracted significant attention and offered several mechanisms to explain the experimental data. The development of a unified view and a working model which is consistent with the diverse experimental data is an important focal point of the current work. In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis along with network-based community analysis to simulate structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. The results demonstrated that the D614 position anchors a key regulatory cluster that dictates functional transitions between open and closed states. Using molecular simulations and mutational sensitivity analysis of the SARS-CoV-2 spike proteins we showed that the D614G mutation can improve stability of the spike protein in both closed and open forms, but shifting thermodynamic preferences towards the open mutant form. The results offer support to the reduced shedding mechanism of S1 domain as a driver of the increased infectivity triggered by the D614G mutation. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike engine. By employing network community analysis of the SARS-CoV-2 spike proteins, our results revealed that the D614G mutation can promote the increased number of stable communities and allosteric hub centers in the open form by reorganizing and enhancing the stability of the S1-S2 inter-domain interactions and restricting mobility of the S1 regions. This study provides atomistic-based view of the allosteric interactions and communications in the SARS-CoV-2 spike proteins, suggesting that the D614G mutation can exert its primary effect through allosterically induced changes on stability and communications in the residue interaction networks.