bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precisely patterned nanofibers made from extendable protein multiplexes
Authors: Bethel Neville P. , Borst Andrew J. , Parmeggiani Fabio , Bick Matthew J. , Brunette TJ , Nguyen Hannah , Kang Alex , Bera Asim K. , Carter Lauren , Miranda Marcos C. , Kibler Ryan , Lamb Mila , Li Xinting , Sankaran Banumathi , Baker David 
Published: October 2022

AbstractMolecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha helical coiled coils have such symmetric extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here, we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2to C8and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibers can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibers can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
Differential chondrogenic differentiation between iPSC-derived from healthy and OA cartilage is associated with changes in epigenetic regulation and metabolic transcriptomic signatures
Authors: Khan Nazir M. , Diaz-Hernandez Martha Elena , Chihab Samir , Priyadarshani Priyanka , Bhattaram Pallavi , Mortensen Luke J. , Guzzo Rosa M , Drissi Hicham 
Published: October 2022

ABSTRACTInduced pluripotent stem cells (iPSCs) are potential cell sources for regenerative medicine. The iPSCs exhibit a preference for lineage differentiation to the donor cell type indicating the existence of memory of origin. Although the intrinsic effect of the donor cell type on differentiation of iPSCs is well recognized, whether disease-specific factors of donor cells influence the differentiation capacity of iPSC remains unknown. Using viral based reprogramming, we demonstrated the generation of iPSCs from chondrocytes isolated from healthy (AC-iPSCs) and osteoarthritis cartilage (OA-iPSCs). These reprogrammed cells acquired markers of pluripotency and differentiated into uncommitted-mesenchymal progenitors. Interestingly, AC-iPSCs exhibited enhanced chondrogenic potential as compared OA-iPSCs and showed increased expression of chondrogenic genes. Pan-transcriptome analysis showed that chondrocytes derived from AC-iPSCs were enriched in molecular pathways related to energy metabolism and epigenetic regulation, together with distinct expression signature that distinguishes them from OA-iPSCs. The molecular tracing data demonstrated that epigenetic and metabolic marks were imprint of original cell sources from healthy and OA-chondrocytes. Our results suggest that the epigenetic and metabolic memory of disease may predispose OA-iPSCs for their reduced chondrogenic differentiation and thus regulation at epigenetic and metabolic level may be an effective strategy for controlling the chondrogenic potential of iPSCs.
Broad SARS-CoV-2 Neutralization by Monoclonal and Bispecific Antibodies Derived from a Gamma-infected Individual
Authors: Guerra Denise , Beaumont Tim , Radić Laura , Kerster Gius , van der Straten Karlijn , Yuan Meng , Torres Jonathan L. , Lee Wen-Hsin , Liu Hejun , Poniman Meliawati , Bontjer Ilja , Burger Judith A. , Claireaux Mathieu , Caniels Tom G. , Snitselaar Jonne L. , Bijl Tom P. L. , Kruijer Sabine , Ozorowski Gabriel , Gideonse David , Sliepen Kwinten , Ward Andrew B. , Eggink Dirk , de Bree Godelieve J. , Wilson Ian A. , Sanders Rogier W. , van Gils Marit J. 
Published: October 2022

ABSTRACTThe worldwide pandemic caused by SARS-CoV-2 has remained a human medical threat due to the continued evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants for therapeutic and prophylactic use. A stabilized autologous SARS-CoV-2 spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants of concern, with COVA309-35 being the most potent against the autologous virus, as well as against Omicron BA.1 and BA.2. When combining the COVA309 mAbs as cocktails or bispecific antibody formats, the breadth and potency was significantly improved against all tested variants. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.
CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands
Authors: Rouillon Clément , Eckhardt Bruna V. , Kollenstart Leonie , Gruss Fabian , Verkennis Alexander E.E. , Rondeel Inge , Krijger Peter H.L. , Ricci Giulia , Biran Alva , van Laar Theo , Delvaux de Fenffe Charlotte M. , Luppens Georgiana , Albanese Pascal , Scheltema Richard A. , de Laat Wouter , Dekker Nynke H. , Groth Anja , Mattiroli Francesca 
Published: October 2022

ABSTRACTDuring every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 cooperates with the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitution, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Polε) for PCNA binding, but not with the lagging strand DNA polymerase Delta (Polδ). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand both processes are coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.
HvSL1andHvMADS16promote stamen identity to restrict multiple ovary formation in barley
Authors: Selva Caterina , Yang Xiujuan , Shirley Neil J. , Whitford Ryan , Baumann Ute , Tucker Matthew R. 
Published: October 2022

AbstractCorrect floral development is a consequence of a sophisticated balance between environmental and molecular cues. Floral mutants provide insight into the main genetic determinants that integrate these cues, as well as providing opportunities to assess functional conservation across species. In this study, we characterize the barley (Hordeum vulgare) multiovary mutantsmov2.gandmov1and propose causative gene sequences: a C2H2 zinc-fingerHvSL1and a B-class geneHvMADS16, respectively. In the absence ofHvSL1,flowers lack stamens but exhibit functional supernumerary carpels resulting in multiple seeds per floret when artificially pollinated. Deletion ofHvMADS16inmov1causes homeotic conversion of lodicules and stamens into bract-like organs and carpels that contain non-functional ovules. Based on developmental, genetic, and molecular data we propose a model by which stamen specification in barley is defined by HvSL1 acting upstream of barley B-class genes, specifically the transcriptional up-regulation ofHvMADS16. The present work identifies strong conservation of stamen formation pathways with rice, but also reveals intriguing species-specific differences. The findings lay the foundation for a better understanding of floral architecture inTriticeae, a key target for crop improvement.HighlightAnalysis of the barley multiovarymov1andmov2loci indicates that HvSL1 and HvMADS16 exhibit both unique and conserved roles in the specification and development of cereal flowers.
Peritubular macrophages phagocyte remains of undifferentiated spermatogonia in mouse testis
Authors: Marra María Fernanda , Ibañez Jorge , Millán María Elisa , Freites Carlos Leandro , Fernandez Dario , Lopez Luis Alberto 
Published: October 2022

AbstractThe cells involved in spermatogenesis are germ-cells, called spermatogonia, classified as: type A-undifferentiated, type A-intermediate and type B. During the spermatogenesis, more than 75% of the germ-cells undergo apoptosis and most of them are phagocyted by Sertoli cells. Peritubular macrophages in adult mouse testis are macrophages that both stimulate the proliferation and differentiation of undifferentiated spermatogonia in the wall of the seminiferous tubule. They have long processes and ramified appearance that squished between the lateral sides of neighbor myoid cells. We show, that a population of peritubular macrophages, grouped in pairs and activated, phagocyted undifferentiated spermatogonia in apoptosis. In adult mouse testis, 3.3x 105undifferentiated spermatogonia are in the germinal epithelium and 8,250 of them are in apoptosis. We counted in the testis 2,634.2 ±160 peritubular macrophages with phagocytic activity. If each one phagocyted one undifferentiated spermatogonia in apoptosis, it may indicated that peritubular macrophages phagocyted 31.9 % of the total undifferentiated spermatogonia in apoptosis. According to our knowledges, this is the first time that it is shown that undifferentiated spermatogonia in apoptosis are cleaned by peritubular macrophages.Summary SentenceWe report that peritubular macrophages of adult mouse testis, phagocytic remains of apoptotic undifferentiated spermatogonia. These results show that peritubular macrophages, like Sertoli cells, participate in the remotion of germinal cells in the testis.
Fibril elongation by human islet amyloid polypeptide is the main event linking aggregation to membrane damage
Authors: Elenbaas Barend O.W. , Kremsreiter Stefanie M. , Khemtemourian Lucie , Killian J. Antoinette , Sinnige Tessa 
Published: October 2022

AbstractThe aggregation of human islet amyloid polypeptide (hIAPP) is linked to the death of pancreatic β-cells in type II diabetes. The process of fibril formation by hIAPP is thought to cause membrane damage, but the precise mechanisms are still unclear. Previously, we showed that the aggregation of hIAPP in the presence of membranes containing anionic lipids is dominated by secondary nucleation events, which occur at the interface between existing fibrils and the membrane surface. Here, we used vesicles with different lipid composition to explore the connection between hIAPP aggregation and vesicle leakage. We found that different anionic lipids promote hIAPP aggregation to the same extent, whereas remarkably stochastic behaviour is observed on purely zwitterionic membranes. Vesicle leakage induced by hIAPP consists of two distinct phases for any of the used membrane compositions: (i) an initial phase in which hIAPP binding causes a certain level of leakage that is strongly dependent on osmotic conditions, membrane composition and the used dye, and (ii) a main leakage event that we attribute to elongation of hIAPP fibrils, based on seeded experiments. Altogether, our results shed more light on the relationship between hIAPP fibril formation and membrane damage, and strongly suggest that oligomeric intermediates do not considerably contribute to vesicle leakage.
Crosstalk between paralogous ComRS quorum-sensing systems diversifies the competence/bacteriocin networks of oral streptococci
Authors: Li Jinbei W. , Wyllie Ryan M. , Jensen Paul A. 
Published: October 2022

AbstractComRS quorum-sensing systems regulate competence and bacteriocin production in the mutans streptococci that cause dental caries (tooth decay). We recently discovered a new class of ComRS (Type IV) in the oral pathogenStreptococcus sobrinus. We now show that every species of mutans streptococci has at least one Type IV ComRS system.S. mutans, S. ratti, S. macacae, andS. ferushave both a Type II and a Type IV ComRS system;S. cricetihas one Type IV ComRS system; andS. downeiandS. sobrinushave two Type IV ComRS systems. Gene deletion and reporter assays reveal that, in general, competence is regulated by one ComRS system, while a second ComRS system—when present—regulates bacteriocin production. However, crosstalk in species with two ComRS systems leads to a diverse set of competence/bacteriocin network structures. InS. mutans, for example, the Type IV ComRS can potentiate competence by kickstarting the well-studied Type II system, while the Type II system shows spillover activation of the Type IV system. Differences in ComR DNA binding sequences determine the specificity of the ComR paralogs, and sometimes a single base pair change can integrate the two systems. Our work reveals similarities and differences among the competence/bacteriocin networks in naturally competent streptococci, suggesting that paralogous regulation may provide evolutionary flexibility in genetic networks.
Synaptojanin1 regulates lysosomal functions in ventral midbrain neurons
Authors: Zhu Xinyu , Prakash Sanjana Surya , McAuliffe Geoffrey , Pan Ping-Yue 
Published: October 2022

AbstractA major pathological hallmark of Parkinson’s Disease (PD) is the manifestation of Lewy bodies comprised of alpha-synuclein (α-syn). The accumulation of α-syn enriched protein aggregates is thought to arise from dysfunction in degradation systems within the brain. Recently, missense mutations ofSYNJ1encoding the SAC1 and 5’-phosphatase domains have been found in families with hereditary early-onset Parkinsonism. Previous studies showed thatSynj1haploinsufficiency (Synj1+/-) leads to PD-like behavioral and pathological changes in mice, including the accumulation of the autophagy substrate p62 and pathological α-syn proteins in the midbrain (MB) and striatum. In this study, we aim to investigate the neuronal degradation pathway using theSynj1+/-MB culture as a model. Our data suggests that autophagy flux and cumulative autophagosome formation is unaltered at baseline inSynj1+/-MB neurons. However, lysosome number is reduced with a similar decrease in lysosomal proteins, including LAMP1, LAMP2, and LAMP2A. Lysosomes are hyperacidified with enhanced enzymatic activity inSynj1+/-MB neurons. Using a combination of light and electron microscopy, we show that lysosomal changes are primarily associated with a lack of SAC1 activity. Consistently, expressing the SYNJ1 R258Q mutant in N2a cells reduces the lysosome number. Interestingly, the lysosomal defects in Synj1+/- neurons does not impact the clearance of exogenously expressed wild-type α-syn; however, the clearance of α-syn A53T was impaired in the axons ofSynj1+/-MB neurons. Taken together, our results suggest axonal vulnerability to lysosomal defects in Synj1 deficient MB neurons.Significance StatementIn the study, Zhu et al. discovered a previously uncharacterized role of Synj1 in regulating lysosomal number, protein, and acidity in ventral midbrain neurons. These alterations are associated with a specific impairment in the clearance of α-syn A53T, but not WT α-syn in axons, suggesting an essential role of Synj1 in axonal degradative capacity under pathological stress. This work in cultured mammalian neurons complements recent research efforts inDrosophila, C. elegans andzebra fish, and provides a novel insight for the role Synj1 in neuronal autolysosomal function.
An experimental demonstration of ensemble epistasis in the lac repressor
Authors: Morrison Anneliese J. , Harms Michael J. 
Published: October 2022

ABSTRACTEpistatic, non-additive, interactions between mutations reveal the functional architecture of living systems, strongly shape evolution, and present a difficult challenge for bioengineers. Interpreting and modeling epistasis requires knowledge of the mechanisms that bring it about. We recently argued that “ensemble epistasis” could be a generic mechanism for epistasis between mutations introduced into a single macromolecule. Because proteins exist as ensembles of interconverting conformations, a mutation could induce epistasis by subtly altering ensemble composition and thus the effects of subsequent mutations. Here we show experimentally that the thermodynamic ensemble does indeed yield high magnitude epistasis in the lac repressor. We observed two- and three-way epistasis in DNA binding, with magnitudes as large or larger than the individual effects of mutations. This biophysical effect propagated to substantial epistasis in gene expressionin vivo. As predicted in previous theoretical work, IPTG concentration tunes the magnitude of ensemble epistasis. Further, our observations could all be captured with a rigorous mathematical model of the lac repressor ensemble. Given that conformational ensembles are unavoidable features of macromolecules, we expect this is a ubiquitous and underappreciated cause of intramolecular epistasis.
Computational investigation of the effect of reduced dynein velocity and reduced cargo diffusivity on slow axonal transport
Authors: Kuznetsov Ivan A. , Kuznetsov Andrey V. 
Published: October 2022

AbstractContributions of three components of slow axonal transport (SAT) were studied using a computational model: the anterograde motor (kinesin)-driven component, the retrograde motor (dynein)-driven component, and the diffusion-driven component. The contribution of these three components of SAT was investigated in three different segments of the axon: the proximal portion, the central portion, and the distal portion of the axon. MAP1B protein was used as a model system to study SAT because there are published experimental data reporting MAP1B distribution along the axon length and average velocity of MAP1B transport in the axon. This allows the optimization approach to be used to find values of model kinetic constants that give the best fit with published experimental data. The effects of decreasing the value of cargo diffusivity on the diffusion-driven component of SAT and decreasing the value of dynein velocity on the retrograde motor-driven component of SAT were investigated. We found that for the case when protein diffusivity and dynein velocity are very small, it is possible to obtain an analytical solution to model equations. We found that, in this case, the protein concentration in the axon is uniform. This shows that anterograde motor-driven transport alone cannot simulate a variation of cargo concentration in the axon. Most proteins are non-uniformly distributed in axons. They may exhibit, for example, an increased concentration closer to the synapse. The need to reproduce a non-uniform distribution of protein concentration may explain why SAT is bidirectional (in addition to an anterograde component, it also contains a retrograde component).
Serial visualization of Glucose-insulin metabolism in thin young Indians with prediabetes reveals early failure of beta cell secretion in relation to decreasing insulin sensitivity
Authors: Tiwari Pradeep , Phatak Sanat , Bandopadhyay Souvik , Sethi Tavpritesh , Fall Caroline HD , Yajnik Chittaranjan 
Published: October 2022

AbstractBackground & ObjectiveDefective beta cell function in relation to impaired insulin sensitivity results in glucose intolerance. There are few studies documenting the lifecourse evolution of this relationship. The Pune Maternal Nutrition Study (PMNS) longitudinal birth cohort offered the opportunity to document these parameters from childhood in young, rural prediabetic participants and compare them to normal glucose tolerant (NGT).MethodsPMNS subjects were classified as NGT or Glucose intolerant according to their OGTT results at 18 years of age. Insulin Sensitivity (HOMA-S) and β-cell function (HOMA-β) were estimated at 6,12 and 18 years. Their inter-relationship was estimated using HOMA-β as a nonlinear function of HOMA-S, separately for NGT and Glucose intolerant individuals at 6,12 and 18 years. Rates of change of HOMA-S and HOMA-β were estimated using a linear mixed effect model and visualized using LOESS plots.ResultOf 619 participants, 177 had glucose intolerance at 18 years of age. A nonlinear hyperbolic relationship between HOMA-S and HOMA-B was observed at all time points. There was a progressive fall in HOMA-S and rise in HOMA-B with increasing age. Glucose intolerant participants had lower HOMA-B for all levels of HOMA-S as compared to NGT, manifesting as shift towards the origin in the hyperbolic curve.ConclusionWe provide evidence for early life dysregulation in glucose insulin metabolism leading to pre-diabetes at 18 years of age. Prediabetic individuals started with lower beta cell function and lower insulin sensitivity from an early age. Diabetes prevention should start from early life.
Public-private partnership in Alberta, Canada: a path dependence perspective
Authors: Opara Michael , Rankin Robert , Ling Ran , Le Thien 
Published: October 2022

PurposeIn this study, the authors revisit Alberta's public-private partnership (P3) program after 20 years of field level experience by retracing its historical emergence and institutional evolution given its political context. Specifically, the authors adopt a path dependence perspective to reconstruct and reexamine Alberta's P3 program emergence, reflect on the successes achieved, and articulate challenges that must be overcome to institutionalize P3s as part of Alberta's infrastructure delivery environment in the future.Design/methodology/approachAdopting a constructivist approach and a case-based methodology, the authors (re)analyze the activities of governmental agents, private industry, and other actors as part of a new infrastructure policy introduced in 2002 to transform the provincial institutional landscape to accommodate P3.FindingsThe authors find Alberta's P3 emergence was driven by the necessity of its infrastructure deficits, political expediency, and resource scarcity. Furthermore, with well-entrenched conservative political actors as gatekeepers, Alberta's P3 implementation demonstrated stability and incremental change simultaneously, consistent with core elements of path dependency. Following the introduction of P3 in Alberta, the province lacked formal institutional structures that would transition its P3 program from good to great and enable it to become firmly embedded in the public infrastructure delivery landscape. With the subsequent absence of P3-convinced (political) leadership and uncertainty about its P3 policy direction, Alberta was unable or unwilling to consolidate the progress made at the start of the program.Originality/valueMost recently, the emergence of new political leadership in Alberta has (re)catalyzed policy progress, pointing toward a more methodical program approach, and suggesting a rediscovered confidence in P3s in the province with the establishment of a P3 Office (P3O), including nascent formal rules for unsolicited bids. These recent changes in our view make for a much more anchored policy and could lead to program sustainability and eventual institutionalization. Given the unpredictability of the recent political change, a more robust analysis of the relationship between political party control, leadership, and P3 stability is required to anticipate future policy and organizational obstacles.