bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Evolution of SARS-CoV-2 Challenges Human Defenses
Authors: Duarte Carlos M. , Ketcheson David , Eguíluz Víctor M. , Agustí Susana , Fernández-Gracia Juan , Jamil Tahira , Laiolo Elisa , Gojobori Takashi , Alam Intikhab 
Published: March 2021

AbstractEvolutionary ecology theory provides an avenue to anticipate the future behavior of SARS-CoV-2. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein believed to determine infectivity. We estimate that 384 million people were infected by March 1st, 2021, producing up to 1021copies of the virus, with one new RBD variant appearing for every 600,000 human infections, resulting in approximately three new effective RBD variants produced daily. Doubling the number of RBD variants every 71.67 days followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics.One-Sentence SummaryAccelerating evolution of SARS-CoV-2 demands formulating universal vaccines and treatments based on big-data simulations of possible new variants.
Dynamic phase separation of the androgen receptor and its coactivators to regulate gene expression
Authors: Zhang Fan , Wong Samantha , Lee Joseph , Lingadahalli Shreyas , Wells Christopher , Saxena Neetu , Sanchez Christophe , Sun Bei , Parra-Nuñez Ana Karla , Chan Novia , Bui Jennifer M. , Wang Yuzhuo , Rennie Paul S. , Lack Nathan , Cherkasov Artem , Gleave Martin , Gsponer Jörg , Lallous Nada 
Published: March 2021

AbstractNumerous cancers, including prostate cancer (PCa), are addicted to transcription programs driven by superenhancers (SEs). The transcription of genes at SEs is enabled by the formation of phase-separated condensates by transcription factors and co-activators with intrinsically disordered regions. The androgen receptor (AR), main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the co-activator MED1 to SEs to promote oncogenic programs. In this work, we show that dynamic AR-rich, liquid-like foci form in PCa models upon androgen stimulation and correlate with AR transcriptional activity. The co-activator MED1 plays an essential role in the formation of AR foci while AR antagonists hinder their formation. These results suggest that enhanced compartmentalization of AR and co-activators at SEs may play an important role in the activation of oncogenic transcription programs in PCa. A better understanding of the assembly and the regulation of these AR-rich compartments may provide novel therapeutic options.
Decoding regulatory specificity of human ribosomal proteins
Authors: Luan Yizhao , Tang Nan , Yang Jiaqi , Chen Congying , Liu Shuting , Cheng Chichi , Wang Yan , Guo Ya-nan , Wang Hongwei , Xiang Mengqing , Ju Rong , Xie Zhi 
Published: March 2021

AbstractHuman ribosomes, made of around 80 ribosomal proteins (RPs) and four ribosomal RNAs, have long been thought as uniform passive protein-making factories with little regulatory function. Recently, accumulating evidence showed heterogeneity of RP composition in ribosomes responsible for regulating gene expression in development and tumorigenesis. However, a comprehensive understanding of regulatory spectrum of RPs is still lacking. In this study, we conducted a systematic survey of regulatory specificity of human RPs on global gene expression. We quantified translational and transcriptional changes of gene expression upon deficiency of 75 RPs, including 44 from the large subunit (60S) and 31 from the small subunit (40S), by ribosomal profiling and RNA sequencing analysis. We showed that RP deficiency induced diverse expression changes, particularly at the translational level. RPs were subjected to co-translational regulation under ribosomal stress where deficiency of the 60S and the 40S RPs had opposite effects on the two subunits. RP deficiency perturbed expression of genes related to cell cycle, cellular metabolism, signal transduction and development. Deficiency of RPs from the 60S led to a greater repression effect on cell growth than that from the 40S by perturbing P53 signaling and cell cycle pathways. To demonstrate functional specificity of RPs, we showed thatRPS8deficiency stimulated cellular apoptosis andRPL13orRPL18deficiency promoted cellular senescence. We also showed thatRPL11andRPL15played important roles in retina development and angiogenesis, respectively. Overall, our study demonstrated a widespread regulatory role of RPs in controlling cellular activity, providing an important resource which can offer novel insights into ribosome regulation in human diseases and cancer.
Validating Pore Size Estimates in a Complex Microfibre Environment on a Human MRI System
Authors: Huang Chu-Chung , Hsu Chih-Chin Heather , Zhou Feng-Lei , Kusmia Slawomir , Drakesmith Mark , Parker Geoff J.M. , Lin Ching-Po , Jones Derek K. 
Published: March 2021

ABSTRACTPurposeRecent advances in diffusion-weighted MRI provide ‘restricted diffusion signal fraction’ and restricting pore size estimates. Materials based on co-electrospun oriented hollow cylinders have been introduced to provide validation for such methods. This study extends this work, exploring accuracy and repeatability using an extended acquisition on a 300 mT/m gradient human MRI scanner, in substrates closely mimicking tissue, i.e., non-circular cross-sections, intra-voxel fibre crossing, intra-voxeldistributionsof pore-sizes and smaller pore-sizes overall.MethodsIn a single-blind experiment, diffusion-weighted data were collected from a biomimetic phantom on a 3T Connectom system using multiple gradient directions/diffusion times. Repeated scans established short-term and long-term repeatability. The total scan time (54 minutes) matched similar protocols used in human studies. The number of distinct fibre populations was estimated using spherical deconvolution, and median pore size estimated through the combination of CHARMED and AxCaliber3D framework. Diffusion-based estimates were compared with measurements derived from scanning electron microscopy.ResultsThe phantom contained substrates with different orientations, fibre configurations and pore size distributions. Irrespective of one or two populations within the voxel, the pore-size estimates (~5μm) and orientation-estimates showed excellent agreement with the median values of pore-size derived from scanning electron microscope and phantom configuration. Measurement repeatability depended on substrate complexity, with lower values seen in samples containing crossing-fibres. Sample-level repeatability was found to be good.ConclusionWhile no phantom mimics tissue completely, this study takes a step closer to validating diffusion microstructure measurements for usein vivoby demonstrating the ability to quantify microgeometry in relatively complex configurations.
The formation of the bacterial RNA polymerase–promoter open complex involves a branched pathway
Authors: Malinen Anssi M. , Bakermans Jacob , Aalto-Setälä Emil , Blessing Martin , Bauer David L.V. , Parilova Olena , Belogurov Georgiy A. , Dulin David , Kapanidis Achillefs N. 
Published: March 2021

AbstractThe expression of most bacterial genes commences with the binding of RNA polymerase (RNAP)–σ70holoenzyme to the promoter DNA. This initial RNAP–promoter closed complex undergoes a series of conformational changes, including the formation of a transcription bubble on the promoter and the loading of template DNA strand into the RNAP active site; these changes lead to the catalytically active open complex (RPO) state. Recent cryo-electron microscopy studies have provided detailed structural insight on the RPOand putative intermediates on its formation pathway. Here, we employ single-molecule fluorescence microscopy to interrogate the conformational dynamics and reaction kinetics during real-time RPOformation. We find that the RPOpathway is branched, generating RPOcomplexes with different stabilities. The RNAP cleft loops, and especially the β’ rudder, stabilise the transcription bubble. The RNAP interactions with the promoter upstream sequence (beyond −35) stimulate transcription bubble nucleation and tune the reaction path towards stable forms of the RPO. The mechanistic heterogeneity of the RPOpathway may be a prerequisite for its regulation since such heterogeneity allows the amplification of small promoter sequence or transcription-factor-dependent changes in the free energy profile of the RPOpathway to large differences in transcription efficiency.
Learning brain dynamics for decoding and predicting individual differences
Authors: Pessoa Luiz , Limbachia Chirag , Misra Joyneel , Surampudi Srinivas Govinda , Venkatesh Manasij , Jaja Joseph 
Published: March 2021

AbstractInsights from functional Magnetic Resonance Imaging (fMRI), as well as recordings of large numbers of neurons, reveal that many cognitive, emotional, and motor functions depend on the multivariate interactions of brain signals. Todecodebrain dynamics, we propose an architecture based on recurrent neural networks to uncover distributed spatiotemporal signatures. We demonstrate the potential of the approach using human fMRI data during movie-watching data and a continuous experimental paradigm. The model was able to learn spatiotemporal patterns that supported 15-way movie-clip classification (~90%) at the level of brain regions, and binary classification of experimental conditions (~60%) at the level of voxels. The model was also able to learn individual differences in measures of fluid intelligence and verbal IQ at levels comparable or better than existing techniques. We propose a dimensionality reduction approach that uncovers low-dimensional trajectories and captures essential informational (i.e., classification related) properties of brain dynamics. Finally, saliency maps were employed to characterize brain-region/voxel importance, and uncovered how dynamic but consistent changes in fMRI activation influenced decoding performance. When applied at the level of voxels, our framework implements a dynamic version of multivariate pattern analysis. We believe our approach provides a powerful framework for visualizing, analyzing, and discovering dynamic spatially distributed brain representations during naturalistic conditions.1Author summaryBrain signals are inherently dynamic and evolve in both space and time as a function of cognitive or emotional task condition or mental state. To characterize brain dynamics, we employed an architecture based on recurrent neural networks, and applied it to functional magnetic resonance imaging data from humans watching movies or during continuous experimental conditions. The model learned spatiotemporal patterns that allowed it to correctly classify which clip a participant was watching based entirely on data from other participants; the model also learned a binary classification of experimental conditions at the level of voxels. We developed a dimensionality reduction approach that uncovered low-dimensional “trajectories” and captured essential information properties of brain dynamics. When applied at the level of voxels, our framework implements a dynamic version of multivariate pattern analysis. We believe our approach provides a powerful framework for visualizing, analyzing, and discovering dynamic spatially distributed brain representations during naturalistic conditions.
Regenerating vascular mural cells in zebrafish fin blood vessels are not derived from pre-existing ones and differentially requirepdgfrbsignaling for their development
Authors: Leonard Elvin V. , Figueroa Ricardo J. , Bussmann Jeroen , Lawson Nathan D. , Amigo Julio D. , Siekmann Arndt F. 
Published: March 2021

AbstractVascular networks are comprised of endothelial cells and mural cells, which include pericytes and smooth muscle cells. It is well established that new endothelial cells are derived from pre-existing ones during the angiogenic phase of blood vessel growth. By contrast, mural cell ontogeny is less clear with an ongoing debate whether mural cells possess mesenchymal stem cell properties. To elucidate the mechanisms controlling mural cell recruitment during development and tissue regeneration, we studied the formation of zebrafish caudal fin arteries. Mural cells showed morphological heterogeneity: cells colonizing arteries proximal to the body wrapped around them, while those in more distal regions extended protrusions along the proximo-distal vascular axis. Despite these differences, both cell populations expressed platelet-derived growth factor receptor beta (Pdgfrb) and the smooth muscle cell marker myosin heavy chain 11a (Myh11a). Loss of Pdgfrb signalling during development or tissue regeneration resulted in a substantial decrease in mural cells at the vascular front, while those proximal to the body were less affected. Using lineage tracing, we demonstrate that precursor cells located in periarterial regions of the caudal fin and expressing Pgdfrb can give rise to mural cells, while in regeneration newly formed mural cells were not derived from pre-existing ones. Together, our findings reveal conserved roles for pdgfrb signalling in development and regeneration, while at the same time illustrating a limited capacity of mural cells to self-renew or contribute to other cell types during tissue regeneration.
Consensus tetratricopeptide repeat proteins are complex superhelical nanosprings
Authors: Synakewicz Marie , Eapen Rohan S. , Perez-Riba Albert , Bauer Daniela , Weißl Andreas , Fischer Gerhard , Hyvönen Marko , Rief Matthias , Itzhaki Laura S. , Stigler Johannes 
Published: March 2021

AbstractTandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs) — superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between folded and unfolded conformations. We rationalise the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the centre towards both termini simultaneously. Strikingly, we also directly observe the protein’s superhelical tertiary structure in the force signal. Using protein engineering, crystallography and single-molecule experiments, we show how the superhelical geometry can be altered by carefully placed amino-acid substitutions and examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.Significance statementRepetition of biological building blocks is crucial to modulating and diversifying structure and function of biomolecules across all organisms. In tandem-repeat proteins, the linear arrangement of small structural motifs leads to the formation of striking supramolecular shapes. Using a combination of single-molecule biophysical techniques and modelling approaches, we dissect the spring-like nature of a designed repeat protein and demonstrate how its shape and mechanics can be manipulated by design. These novel insights into the biomechanical and biochemical characteristics of this protein class give us a methodological basis from which to understand the biological functions of repeat proteins and to exploit them in nanotechnology and biomedicine.
mTORC2 contributes to murine systemic autoimmunity
Authors: Zhou Xian , Qi Haiyu , Li Meilu , Li Yanfeng , Zhu Xingxing , Amin Shreyasee , Alexander Mariam , Diadhiou Catherine , Davidson Anne , Zeng Hu 
Published: March 2021

ABSTRACTThe development of many systemic autoimmune diseases, including systemic lupus erythematosus, is associated with overactivation of the type I interferon (IFN) pathway, lymphopenia, and increased follicular helper T (Tfh) cell differentiation. However, the cellular and molecular mechanisms underlying these immunological perturbations remain incompletely understood. Here we show that the mechanistic target of rapamycin complex 2 (mTORC2) promotes Tfh differentiation and disrupts Treg homeostasis. Inactivation of mTORC2 in total T cells, but not in Tregs, greatly ameliorated the immunopathology in a systemic autoimmunity mouse model. This was associated with reduced Tfh differentiation, B cell activation, and reduced T cell glucose metabolism. Finally, we show that type I IFN can synergize with TCR ligation to activate mTORC2 in T cells, which partially contributes to T cell lymphopenia. These data indicate that mTORC2 may act as downstream of type I IFN, TCR, and costimulatory receptor ICOS, to promote glucose metabolism, Tfh differentiation, and T cell lymphopenia, but not to suppress Treg function in systemic autoimmunity. Our results suggest that mTORC2 might be a rational target for systemic autoimmunity treatment.
Cell trajectory modeling identifies a primitive trophoblast state defined by BCAM enrichment
Authors: Shannon Matthew , Baltayeva Jennet , Castellana Barbara , Wächter Jasmin , Yoon Samantha , Treissman Jenna , Le Hoa T. , Lavoie Pascal M. , Beristain Alexander G. 
Published: March 2021

ABSTRACTIn early placental development, progenitor cytotrophoblasts (CTBs) differentiate along one of two cellular trajectories: the villous or extravillous pathways. CTBs committed to the villous pathway fuse with neighboring CTBs to form the outer multinucleated syncytiotrophoblast (SCT), while CTBs committed to the extravillous pathway differentiate into invasive extravillous trophoblasts (EVT). Unfortunately, little is known about the processes controlling human CTB progenitor maintenance and differentiation. To address this, we established a single cell RNA sequencing (scRNA-seq) dataset from first trimester placentas to identify cell states important in trophoblast progenitor establishment, renewal, and differentiation. Multiple distinct trophoblast states were identified, representing progenitor CTBs, column CTBs, SCT precursors, and EVT. Lineage trajectory analysis identified a progenitor origin that was reproduced in human trophoblast stem cell organoids. Heightened expression of basal cell adhesion molecule (BCAM) defined this primitive state, where BCAM enrichment or gene silencing resulted in enhanced or diminished organoid growth. Together, this work describes at high-resolution trophoblast heterogeneity within the first trimester, resolves gene networks within human CTB progenitors, and identifies BCAM as a primitive progenitor marker and possible regulator.Summary StatementLineage trajectory modeling identifies multiple human progenitor trophoblast states and defines trophoblast differentiation kinetics, where BCAM-expressing progenitors demonstrate enhanced regenerative ability.
A second specificity-determining loop in Class A sortases: Biochemical characterization of natural sequence variation in chimeric SrtA enzymes
Authors: Piper Isabel M. , Struyvenberg Sarah A. , Valgardson Jordan D. , Johnson D. Alex , Gao Melody , Johnston Katherine , Svendsen Justin E. , Kodama Hanna M. , Hvorecny Kelli L. , Antos John M. , Amacher Jeanine F. 
Published: March 2021

AbstractGram-positive bacteria contain sortase enzymes on their cell surfaces that catalyze transpeptidation reactions critical for proper cellular function.In vitro, sortases are used in sortase-mediated ligation (SML) reactions for a variety of protein engineering applications. Historically, sortase A fromStaphylococcus aureus(saSrtA) has been the enzyme of choice for SML reactions. However, the stringent specificity of saSrtA for the sequence motif LPXTG limits its uses. Here, we use principal component analysis to identify a structurally conserved loop with a high degree of variability in all classes of sortases. We investigate the contribution of this β7-β8 loop, located between the catalytic cysteine and arginine residues and immediately adjacent to the target binding cleft, by designing and testing chimeric sortase enzymes. Our chimeras utilize natural sequence variation of Class A sortases from 8 species engineered into the SrtA sequence fromStreptococcus pneumoniae(spSrtA). While some of our chimeric enzymes mimic the activity and selectivity of the wild-type protein from which the loop sequence is derived (e.g., that of saSrtA), others result in chimeric spSrtA enzymes able to accommodate a range of residues in the final position of the substrate motif (LPXTX). Using mutagenesis, structural, and sequence analyses, we identify three interactions facilitated by β7-β8 loop residues that appear to be broadly characteristic of Class A sortase enzymes. These studies provide the foundation for a deeper understanding of sortase target selectivity and can expand the sortase toolbox for future SML applications.
Building code amendment and building resilience: perspective of building code users in New Zealand
Authors: Nwadike Amarachukwu Nnadozie , Wilkinson Suzanne 
Published: March 2021

PurposeThe process followed in amending building code creates problems for code users within the building industry. These problems include the need and frequency of changes made to building code, access to updated documents, method of communication, amendment interval and amendment pathway. This study aims to explore the viewpoints of building code users regarding building code amendments in New Zealand.Design/methodology/approachUsing a closed-ended questionnaire survey, this paper examined the New Zealand building code amendments by evaluating the views of experienced and relevant stakeholders within the research area.FindingsA high proportion (50.90%) of the survey participants agreed to a three-years building code amendment cycle, as against the current biannual Amendment practiced in New Zealand. Findings from the study affirmed the necessity for building code amendment and the support for free amended building code documents to the public and other building standards. The study concludes with strong support to the use of intensive research and learning gained from disasters in building code amendment in New Zealand. Implementing the code users opinions encourages disaster resilience through effective application of the building code requirements in design and construction.Originality/valueThe contribution from this study offered a unique insight into the perspectives of building code users on building code amendment in New Zealand and ways of incorporating the findings in the building code later updates to improve disaster resilience in the built environment.