bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based data analysis of tissue growth in thin 3D printed scaffolds
Authors: Browning Alexander P , Maclaren Oliver J , Buenzli Pascal R , Lanaro Matthew , Allenby Mark C , Woodruff Maria A , Simpson Matthew J 
Published: March 2021

AbstractTissue growth in three-dimensional (3D) printed scaffolds enables exploration and control of cell behaviour in biologically realistic geometries. Cell proliferation and migration in these experiments have yet to be explicitly characterised, limiting the ability of experimentalists to determine the effects of various experimental conditions, such as scaffold geometry, on cell behaviour. We consider tissue growth by osteoblastic cells in melt electro-written scaffolds that comprise thin square pores with sizes that we deliberately vary. We collect highly detailed temporal measurements of the average cell density, tissue coverage, and tissue geometry. To quantify tissue growth in terms of the underlying cell proliferation and migration processes, we introduce and calibrate a mechanistic mathematical model based on the Porous-Fisher reaction-diffusion equation. Parameter estimates and uncertainty quantification through profile likelihood analysis reveal consistency in the rate of cell proliferation and steady-state cell density between pore sizes. This analysis also serves as an important model verification tool: while the use of reaction-diffusion models in biology is widespread, the appropriateness of these models to describe tissue growth in 3D scaffolds has yet to be explored. We find that the Porous-Fisher model is able to capture features relating to the cell density and tissue coverage, but is not able to capture geometric features relating to the circularity of the tissue interface. Our analysis identifies two distinct stages of tissue growth, suggests several areas for model refinement, and provides guidance for future experimental work that explores tissue growth in 3D printed scaffolds.Author SummaryAdvances in 3D printing technology have led to cell culture experiments that realistically capture natural biological environments. Despite the necessity of quantifying cell behaviour with parameters that can be compared between experiments, many existing mathematical models of tissue growth in these experiments neglect information relating to population size. We consider tissue growth by cells on 3D printed scaffolds that comprise square pores of various sizes in this work. We apply a relatively simple mathematical model based on the Porous-Fisher reaction-diffusion equation to interpret highly detailed measurements relating to both the cell density and the quantity of tissue deposited. We analyse the efficacy of such a model in capturing cell behaviour seen in the experiments and quantify cell behaviour in terms of parameters that carry a biologically meaningful interpretation. Our analysis identifies important areas for model refinement and provides guidance for future data-collection and experimentation that explores tissue growth in 3D printed scaffolds.
Evolved changes in DNA methylation in response to the sustained loss of parental care in the burying beetle
Authors: Mashoodh R , Sarkies P , Westoby J , Kilner RM 
Published: March 2021

AbstractLevels of parental care critically influence the developmental environment with the capacity to impact the growth, survival, physiology, and behaviour of offspring. Plastic changes in DNA methylation have been hypothesised to modulate gene expression responses to parental environments. Moreover, these effects can be inherited and so may affect the process of adaptive evolution. In this study, using experimental evolution, we investigated how plastic changes in DNA methylation induced by the loss of parental care have evolved in a biparental insect (Nicrophorus vespilloides) using experimental evolution. We show that removal of care in a single generation is associated with changes in gene expression in stress-related pathways in 1st instar larvae. However, in larvae that have adapted to the loss of parental care after being deprived of care for 30 generations, gene expression is shifted from stress-related gene expression towards growth and brain development pathways. We found that changes in gene body methylation arose both as a direct response to the loss of parental care and stochastically as populations diverged. Overall, our results suggest that a complex interplay between transcription and DNA methylation shapes the molecular adaptation to environmental change.
Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs
Authors: Batista Marcelo Bueno , Brett Paul , Appia-Ayme Corinne , Wang Yi-Ping , Dixon Ray 
Published: March 2021

AbstractThe energetic requirements for biological nitrogen fixation necessitate stringent regulation of this process in response to diverse environmental constraints. To ensure that the nitrogen fixation machinery is expressed only under appropriate physiological conditions, the dedicated NifL-NifA regulatory system, prevalent in Proteobacteria, plays a crucial role in integrating signals of the oxygen, carbon and nitrogen status to control transcription of nitrogen fixation (nif) genes. Greater understanding of the intricate molecular mechanisms driving transcriptional control ofnifgenes may provide a blueprint for engineering diazotrophs that associate with cereals. In this study, we investigated the properties of a single amino acid substitution in NifA, (NifA-E356K) which disrupts the hierarchy ofnifregulation in response to carbon and nitrogen status inAzotobacter vinelandii. The NifA-E356K substitution enabled overexpression of nitrogenase in the presence of excess fixed nitrogen and release of ammonia outside the cell. However, both of these properties were conditional upon the nature of the carbon source. Our studies reveal that the uncoupling of nitrogen fixation from its assimilation is likely to result from feedback regulation of glutamine synthetase, allowing surplus fixed nitrogen to be excreted. Reciprocal substitutions in NifA from other Proteobacteria yielded similar properties to theA. vinelandiicounterpart, suggesting that this variant protein may facilitate engineering of carbon source-dependent ammonia excretion amongst diverse members of this family.SignificanceThe NifL-NifA regulatory system provides dedicated signal transduction machinery to regulate nitrogen fixation in diverse Proteobacteria. Understanding how the balance of nitrogen and carbon resources is signalled via NifL-NifA for precise control of nitrogen fixation may lead to broadly applicable translational outputs. Here, we characterize a NifA variant that bypasses nitrogen regulation but is still dependent on the carbon status to enable ammonia excretion in soil diazotrophs. Disruption of the regulatory hierarchy in response to nitrogen and carbon suggests how the integration of environmental stimuli could be harnessed to engineer conditional release of fixed nitrogen for the benefit of cereal crops.
Comparing two circular distributions: advice for effective implementation of statistical procedures in biology
Authors: Landler Lukas , Ruxton Graeme D. , Malkemper E. Pascal 
Published: March 2021

AbstractMany biological variables, often involving timings of events or directions, are recorded on a circular rather than linear scale, and need different statistical treatment for that reason. A common question that is asked of such circular data involves comparison between two groups or treatments: Are the populations from which the two samples drawn differently distributed around the circle? For example, we might ask whether the distribution of directions from which a stalking predator approaches its prey differs between sunny and cloudy conditions; or whether the time of day of mating attempts differs between lab mice subject to one of two hormone treatments. An array of statistical approaches to these questions have been developed. We compared 18 of these (by simulation) in terms of both abilities to control type I error rate near the nominal value, and statistical power. We found that only eight tests offered good control of type I error in all our test situations. Of these eight, we are able to identify Watson’s U2test and MANOVA based on trigonometric functions of the data as offering the best power in the overwhelming majority of our test circumstances. There was often little to choose between these tests in terms of power, and no situation where either of the remaining six tests offered substantially better power than either of these. Hence, we recommend the routine use of either Watson’s U2test or MANOVA when comparing two samples of circular data.
Structural insights into GlcNAc-1-phosphotransferase that directs lysosomal protein transport
Authors: Du Shuo , Wang Guopeng , Zhang Zhiying , Ma Chengying , Gao Ning , Xiao Junyu 
Published: March 2021

AbstractGlcNAc-1-phosphotransferase (GNPT) catalyzes the initial step in the formation of the mannose-6-phosphate tag that labels ∼60 lysosomal proteins for transport. Mutations in GNPT cause lysosomal storage disorders such as mucolipidoses. However, the molecular mechanism of GNPT remains unclear. Mammalian GNPTs are α2β2γ2 hexamers in which the core catalytic α- and β-subunits are derived from GNPTAB. Here, we present the cryo-electron microscopy structure of theDrosophila melanogasterGNPTAB homolog (DmGNPTAB). Four conserved regions located far apart in the sequence fold into the catalytic domain, which exhibits structural similarity to that of the UDP-glucose glycoprotein glucosyltransferase (UGGT). Comparison with UGGT revealed a putative donor substrate-binding site, and the functional requirements of critical residues in human GNPTAB were validated usingGNPTAB-knockout cells. DmGNPTAB forms an evolutionarily conserved homodimer, and perturbing the dimer interface undermines the maturation and activity of human GNPTAB. These results provide important insights into GNPT function and related diseases.
MEG cortical microstates: spatiotemporal characteristics, dynamic functional connectivity and stimulus-evoked responses
Authors: Tait Luke , Zhang Jiaxiang 
Published: March 2021

AbstractEEG microstate analysis is a useful approach for studying brain states - nicknamed ‘atoms of thought’ - and their fast transitions in healthy cognition and disease. A key limitation of conventional microstate analysis is that it must be performed at the sensor level, and therefore gives limited anatomical insight into the cortical mechanisms underpinning these states. In this study, we generalise the microstate methodology to be applicable to source-reconstructed electrophysiological data. Using simulations of a neural-mass network model, we first established the validity and robustness of the proposed method. Using MEG resting-state data, we uncovered ten microstates with distinct spatial distributions of cortical activation. Multivariate pattern analysis demonstrated that source-level MEG microstates were associated with distinct functional connectivity patterns. Using a passive auditory paradigm, we further demonstrated that the occurrence probability of MEG microstates were altered by evoked auditory responses, exhibiting a hyperactivity of the microstate including the auditory cortex. Our results support the use of MEG source-level microstates as a data-driven method for investigating brain dynamic activity and connectivity at the millisecond scale.
Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes
Authors: Ragsdale Aaron P. 
Published: March 2021

AbstractSelected mutations interfere and interact with evolutionary processes at nearby loci, distorting allele frequency trajectories and creating correlations between pairs of mutations. A number of recent studies have used patterns of linkage disequilibrium (LD) between selected variants to test for selective interference and epistatic interactions, with some disagreement over interpreting observations from data. Interpretation is hindered by a lack of analytic or even numerical expectations for patterns of variation between pairs of loci under the combined effects of selection, dominance, epistasis, and demography. Here, I develop a numerical approach to compute the expected two-locus sampling distribution under diploid selection with arbitrary epistasis and dominance, recombination, and variable population size. I use this to explore how epistasis and dominance affect expected signed LD, including for non-steadystate demography relevant to human populations. Using whole-genome sequencing data from humans, I explore genome-wide patterns of LD within protein-coding genes. I show that positive LD between missense mutations within genes is driven by strong positive allele-frequency correlations between pairs of mutations that fall within the same annotated conserved domain, pointing to compensatory mutations or antagonistic epistasis as the prevailing mode of interaction within conserved genic elements. LD between missense mutations is reduced outside of conserved domains, as would expected under Hill-Robertson interference. This variation in both mutational fitness effects and selective interactions within proteincoding genes calls for more refined inferences of the joint distribution of fitness and interactive effects, and the methods presented here should prove useful in that pursuit.
Volume-transmitted GABA waves pace epileptiform rhythms in the hippocampal network
Authors: Magloire Vincent , Savtchenko Leonid P. , Sylantyev Sergyi , Jensen Thomas P. , Cole Nicholas , Marvin Jonathan S. , Looger Loren L. , Kullmann Dimitri M. , Walker Matthew C. , Pavlov Ivan , Rusakov Dmitri A. 
Published: March 2021

SUMMARYMechanisms that entrain and drive rhythmic epileptiform discharges remain debated. Traditionally, this quest has been focusing on interneuronal networks driven by GABAergic connections that activate synaptic or extrasynaptic receptors. However, synchronised interneuronal discharges could also trigger a transient elevation of extracellular GABA across the tissue volume, thus raising tonic GABAAreceptor conductance (Gtonic) in multiple cells. Here, we use patch-clamp GABA ‘sniffer’ and optical GABA sensor to show that periodic epileptiform discharges are preceded by region-wide, rising waves of extracellular GABA. Neural network simulations that incorporate volume-transmitted GABA signals point to mechanistic principles underpinning this relationship. We validate this hypothesis using simultaneous patch-clamp recordings from multiple nerve cells, selective optogenetic stimulation of fast-spiking interneurons. Critically, we manipulate GABA uptake to suppress extracellular GABA waves but not synaptic GABAergic transmission, which shows a clear effect on rhythm generation. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA actions in pacing regenerative rhythmic activity in brain networks.
Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner
Authors: Fusco Claudia M. , Desch Kristina , Dörrbaum Aline R. , Wang Mantian , Staab Anja , Chan Ivy C.W. , Vail Eleanor , Villeri Veronica , Langer Julian D. , Schuman Erin M. 
Published: March 2021

SUMMARYOwing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs quickly associated with translating ribosomes in the cytoplasm and that this incorporation is independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (in response to oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing remote neuronal synapses a rapid solution to the relatively slow and energy-demanding requirement of nuclear ribosome biogenesis.
Purkinje cell outputs selectively inhibit a subset of unipolar brush cells in the input layer of the cerebellar cortex
Authors: Guo Chong , Rudolph Stephanie , Neuwirth Morgan E. , Regehr Wade G. 
Published: March 2021

AbstractCircuitry of the cerebellar cortex is regionally and functionally specialized. Unipolar brush cells (UBCs), and Purkinje cell (PC) synapses made by axon collaterals in the granular layer, are both enriched in areas that control balance and eye-movement. Here we find a link between these specializations: PCs preferentially inhibit mGluR1-expressing UBCs that respond to mossy fiber inputs with long lasting increases in firing, but PCs do not inhibit mGluR1-lacking UBCs. PCs inhibit about 29% of mGluR1-expressing UBCs by activating GABAAreceptors (GABAARs) and inhibit almost all mGluR1-expressing UBCs by activating GABABRs. PC to UBC synapses allow PC output to regulate the input layer of the cerebellar cortex in diverse ways. GABAAR-mediated feedback is fast, unreliable, noisy, and suited to linearizing input-output curves and decreasing gain. Slow GABABR-mediated inhibition allows elevated PC activity to sharpen the input-output transformation of UBCs, and allows dynamic inhibitory feedback of mGluR1-expressing UBCs.
Dynamic distortion of orientation representation after learning in the mouse primary visual cortex
Authors: Corbo Julien , McClure John P. , Erkat O. Batuhan , Polack Pierre-Olivier 
Published: March 2021

Learning is an essential cognitive mechanism allowing behavioral adaptation through adjustments in neuronal processing. It is associated with changes in the activity of sensory cortical neurons evoked by task-relevant stimuli. However, the exact nature of those modifications and the computational advantages they may confer are still debated. Here, we investigated how learning an orientation discrimination task alters the neuronal representations of the cues orientations in the primary visual cortex (V1) of male and female mice. When comparing the activity evoked by the task stimuli in naïve mice and mice performing the task, we found that the representations of the orientation of the rewarded and non-rewarded cues were more accurate and stable in trained mice. This better cue representation in trained mice was associated with a distortion of the orientation representation space such that stimuli flanking the task-relevant orientations were represented as the task stimuli themselves, suggesting that those stimuli were generalized as the task cues. This distortion was context dependent as it was absent in trained mice passively viewing the task cues and enhanced in the behavioral sessions where mice performed best. Those modifications of the V1 population orientation representation in performing mice were supported by a suppression of the activity of neurons tuned for orientations neighboring the orientations of the task cues. Thus, visual processing in V1 is dynamically adapted to enhance the reliability of the representation of the learned cues and favor generalization in the task-relevant computational space.Significance statementPerformance improvement in a task often requires facilitating the extraction of the information necessary to its execution. Here, we demonstrate the existence of a suppression mechanism that improves the representation of the orientations of the task stimuli in the V1 of mice performing an orientation discrimination task. We also show that this mechanism distorts the V1 orientation representation space, leading stimuli flanking the task stimuli orientations to be generalized as the task stimuli themselves.
Computational assessment of the spike protein antigenicity reveals diversity in B cell epitopes but stability in T cell epitopes across SARS-CoV-2 variants
Authors: Ge Anni , Rioux Melissa , Kelvin Alyson A. 
Published: March 2021

AbstractSince its emergence into the human population at the end of 2019, SARS-CoV-2 has caused significant morbidity and mortality worldwide. Efforts to develop a protective vaccine against COVID-19 have yielded several vaccine platforms currently in distribution targeting the original SARS-CoV-2 spike protein sequence from the first cases of infection. In recent months, variants of SARS-CoV-2 have raised concerns that viral mutation may undermine vaccination efforts through viral escape of host immune memory acquired from infection or vaccination. We therefore used a computational approach to predict changes in spike protein antigenicity with respect to host B cell and CD8+ T cell immunity across six SARS-CoV-2 variants (D614G, B.1.1.7, B.1.351, P.1, B.1.429, and mink-related). Our epitope analysis using DiscoTope suggests possible changes in B cell epitopes in the S1 region of the spike protein across variants, in particular the B.1.1.7 and B.1.351 lineages, which may influence immunodominance. Additionally, we show that high-affinity MHC-I-binding peptides and glycosylation sites on the spike protein appear consistent between variants with the exception of an extra glycosylation site in the P.1 variant. Together, these analyses suggests T cell vaccine strategies have the most longevity before reformulation.
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Authors: Maier Wolfgang , Bray Simon , van den Beek Marius , Bouvier Dave , Coraor Nathaniel , Miladi Milad , Singh Babita , De Argila Jordi Rambla , Baker Dannon , Roach Nathan , Gladman Simon , Coppens Frederik , Martin Darren P , Lonie Andrew , Grüning Björn , Kosakovsky Pond Sergei L. , Nekrutenko Anton 
Published: March 2021

AbstractThe COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available athttps://covid19.galaxyproject.org.