bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot
Authors: Wang Qian , Bowen Anthony , Valdez Riccardo , Gherasim Carmen , Gordon Aubree , Liu Lihong , Ho David D. 
Published: October 2022

AbstractThe SARS-CoV-2 Omicron variant and its numerous sub-lineages have exhibited a striking ability to evade humoral immune responses induced by prior vaccination or infection. The Food and Drug Administration (FDA) has recently granted Emergency Use Authorizations (EUAs) to new bivalent formulations of the original Moderna and Pfizer mRNA SARS-CoV-2 vaccines that target both the ancestral strain as well as the Omicron BA.4/BA.5 variant. Despite their widespread use as a vaccine boost, little is known about the antibody responses induced in humans. Here, we collected sera from several clinical cohorts: individuals after three or four doses of the original monovalent mRNA vaccines, individuals receiving the new bivalent vaccines as a fourth dose, and individuals with BA.4/BA.5 breakthrough infection following mRNA vaccination. Using pseudovirus neutralization assays, these sera were tested for neutralization against an ancestral SARS-CoV-2 strain, several Omicron sub-lineages, and several related sarbecoviruses. At ~3-5 weeks post booster shot, individuals who received a fourth vaccine dose with a bivalent mRNA vaccine targeting BA.4/BA.5 had similar neutralizing antibody titers as those receiving a fourth monovalent mRNA vaccine against all SARS-CoV-2 variants tested, including BA.4/BA.5. Those who received a fourth monovalent vaccine dose had a slightly higher neutralizing antibody titers than those who received the bivalent vaccine against three related sarbecoviruses: SARS-CoV, GD-Pangolin, and WIV1. When given as a fourth dose, a bivalent mRNA vaccine targeting Omicron BA.4/BA.5 and an ancestral SARS-CoV-2 strain did not induce superior neutralizing antibody responses in humans, at the time period tested, compared to the original monovalent vaccine formulation.
Visualizing the Dynamics of DNA Replication and Repair at the Single-Molecule Molecule Level
Authors: Berger Scott , Chistol Gheorghe 
Published: October 2022

AbstractDuring cell division, the genome of each eukaryotic cell is copied by thousands of replisomes – large protein complexes consisting of several dozen proteins. Recent studies suggest that the eukaryotic replisome is much more dynamic than previously thought. To directly visualize replisome dynamics in a physiological context, we recently developed a single-molecule approach for imaging replication proteins inXenopusegg extracts. These extracts contain all the soluble nuclear proteins and faithfully recapitulate DNA replication and repairin vitro, serving as a powerful platform for studying the mechanisms of genome maintenance. Here we present detailed protocols for conducting single-molecule experiments in nuclear egg extracts and preparing key reagents. This workflow can be easily adapted to visualize the dynamics and function of other proteins implicated in DNA replication and repair.
Membrane localization accelerates association under conditions relevant to cellular signaling
Authors: Huang William Y. C. , Boxer Steven G. , Ferrell James E. 
Published: October 2022

AbstractTranslocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association should be faster in the cytosol because membrane diffusion is slow. Here we directly compare an identical association reaction in solution and on supported membranes. The measured rate constants show that for 10 μm-radius spherical cell, association is 15-25-fold faster at the membrane than in the cytoplasm. The advantage is cell size-dependent, and for typical ~1 μm prokaryotic cells it should be essentially negligible. Rate enhancement is attributable to a combination of closer proximity of the signaling molecule to its targets after translocation and the higher efficiency of a two-dimensional search.
PhISCO: a simple method to infer phenotypes from protein sequences
Authors: Hernandez-Berthet Ayelén S. , Aptekmann Ariel A. , Tejero Jesús , Sánchez Ignacio E. , Noguera Martín E. , Roman Ernesto A. 
Published: October 2022

AbstractAlthough protein sequences encode the information for folding and function, understanding their link is not an easy task. Unluckily, the prediction of how specific amino acids contribute to these features is still considerably impaired. Here, we developed PhISCO, Phenotype Inference from Sequence COmparisons, a simple algorithm that finds positions associated with any quantitative phenotype and predicts their values. From a few hundred sequences from four different protein families, we performed multiple sequence alignments and calculated per-position pairwise differences for both the sequence and the observed phenotypes. We found that from 3 to 10 positions, depending on the studied case, were enough to identify positions associated with the phenotypes and perform quantitative predictions of them. Here we show that these strong correlations can be found using individual positions while an improvement is achieved when the most correlated positions are jointly analyzed. Noteworthy, we performed phenotype predictions using a simple linear model that links per-position divergences and differences in observed phenotypes. We also show that although extremely simple, predictions are comparable to the state-of-art methodologies which, in most of the cases, are far more complex. All of the calculations are obtained at a very low information cost since the only input needed is a multiple sequence alignment of protein sequences with their associated quantitative phenotype. The diversity of the explored systems makes PhISCO a valuable tool to find sequence determinants of biological activity modulation and to predict various functional features for uncharacterized members of a protein family.
Responses of carbapenemase-producing and non-producing carbapenem-resistantPseudomonas aeruginosastrains to meropenem revealed by quantitative tandem mass spectrometry proteomics
Authors: Salvà-Serra Francisco , Jaén-Luchoro Daniel , Marathe Nachiket P. , Adlerberth Ingegerd , Moore Edward R. B. , Karlsson Roger 
Published: October 2022

AbstractPseudomonas aeruginosais an opportunistic pathogen with increasing incidence of multidrug-resistant strains, including resistance to last-resort antibiotics, such as carbapenems. Resistances are often due to complex interplays of naturally and acquired resistance mechanisms that are enhanced by its remarkably large regulatory network.This study describes the proteomic responses of two carbapenem-resistantP. aeruginosastrains of high-risk clones ST235 and ST395 to subminimal inhibitory concentrations (sub-MICs) of meropenem by identifying differentially expressed proteins and pathways. Strain CCUG 51971, carries a VIM-4 metallo-β-lactamase or ‘classical’ carbapenemase, and strain CCUG 70744 carries no known acquired carbapenem-resistance genes and exhibits ‘non-classical’ carbapenem-resistance. Each strain was cultivated with different sub-MICs of meropenem, and analyzed, using quantitative shotgun proteomics, based on tandem mass tag (TMT) isobaric labeling followed by nano-liquid chromatography tandem-mass spectrometry.Exposure of both strains to sub-MICs meropenem resulted in hundreds of differentially expressed proteins, including β-lactamases, proteins associated with transport, peptidoglycan metabolism, cell wall organization, and regulatory proteins. Strain CCUG 51971 showed up-regulation of intrinsic β-lactamases and VIM-4 carbapenemase, while CCUG 70744 exhibited a combination of up-regulated intrinsic β-lactamases, efflux pumps, penicillin-binding proteins and down-regulation of porins. All components of the H1 type VI secretion system were up-regulated in strain CCUG 51971. Enrichment analyses revealed multiple metabolic pathways affected in both strains.Sub-MICs of meropenem cause marked changes in the proteomes of carbapenem-resistant strains ofP. aeruginosaexhibiting different resistance mechanisms, involving a wide range of proteins, many uncharacterized, which might play a role in the susceptibility ofP. aeruginosato meropenem.
Exploring The Behavior of Bioelectric Circuits using Evolution Heuristic Search
Authors: Hazan Hananel , Levin Michael 
Published: October 2022

AbstractCharacteristic spatial differences of cellular resting potential across tissues have been shown to act as instructive bioelectric prepatterns regulating embryonic and regenerative morphogenesis, as well as cancer suppression. Indeed, modulation of bioelectric patterns via specific ion channel-targeting drugs, channel misexpression, or optogenetics has been used to control growth and form in vitro, showing promise in regenerative medicine and synthetic bioengineering. Repair of defects, injury, and transformation requires quantitative understanding of bioelectric dynamics within tissues so that these can be modulated toward desired outcomes in organ patterning or the creation of entirely novel synthetic constructs. The major gap in the discovery of interventions for rational control of organ-level outcomes is the inability to predict large-scale bioelectric patterns - their emergence from symmetry breaking (given a set of channels expressed on the tissue) and their change as a function of time under specific bioelectrical interventions. It is thus essential to develop machine learning and other computational tools to help human scientists identify bioelectric states with desirable properties. Here, we tested the ability of a heuristic search algorithm to explore the parameter space of bio-electrical circuits by adjusting the parameters of simulated cells. We show that while bioelectrical space is not easy to search, it does contain parameter sets that encode rich and interesting patterning behaviors. We demonstrate proof of principle of using a computational search platform to identify circuits with desired properties, as a first step toward the design of machine learning tools for improved bioelectric control of growth and form.
The trans-regulatory landscape of gene networks in plants
Authors: Hummel Niklas F. C. , Zhou Andy , Li Baohua , Markel Kasey , Ornelas Izaiah J. , Shih Patrick M. 
Published: October 2022

AbstractThe effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative effector domains of over 400Arabidopsis thalianatranscription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how newly characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.
Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination
Authors: Wang Ling , Watters John W. , Ju Xiangwu , Liu Shixin 
Published: October 2022

SUMMARYGenomic DNA is a crowded track where translocating motor proteins frequently collide. It remains unclear whether these collisions, generally thought to occur inadvertently, carry any physiological function. In this work, we developed a single-molecule assay to directly visualize the trafficking of individualE. coliRNA polymerases (RNAPs) on DNA. This assay enabled us to test the hypothesis that RNAP collisions drive bidirectional transcription termination of convergent gene pairs. We showed that the head-on collision between two converging RNAPs is necessary to prevent transcriptional readthrough, but insufficient to release the collided RNAPs from the DNA. Remarkably, co-directional collision from a trailing RNAP into the head-on collided complex dramatically increases the termination efficiency. Furthermore, a stem-loop structure formed in the nascent RNA is required for collisions to occur at well-defined positions between gene boundaries. These findings, corroborated by transcriptomic data, establish programmed RNAP collisions as an effective strategy to achieve precise gene expression and imply a broader role of genomic conflicts in cell physiology.
Molecular dynamics simulations reveal the impact of NUTD15 variants in structural conformation and dynamics
Authors: Gómez-Rubio Elena , Garcia-Marin Javier 
Published: October 2022

AbstractNUDT15 or MTH2 is a member of NUDIX protein family that catalyze the hydrolysis of nucleotides and deoxynucleotides, including thioguanine analogues. NUTD15 has been reported as a DNA sanitizer in humans, and more recent studies have proved that genomic variants are related to a poor prognosis in inmoplastic and immunologic diseases with thioguanines. Despite of this, the role of NUTD15 in physiology and molecular biology is quite unclear, as well as the mechanism of action of this enzyme. The existence of clinically relevant variants has prompted the study of this enzymes, whose capacity to bound and hydrolyze thioguanine nucleotides is still poor understood. By using a combination of biomolecular modelling techniques together with molecular dynamics we have studied the monomeric wild type NUTD15, as well as two important variants R139C and R139H. Our findings reveal not only how nucleotide binding stabilizes the enzyme, but also how two loops are responsible for keeping the enzyme in a packed close conformation. Mutations in α2 helix affect a network of hydrophobic and π-interactions that are responsible of active site enclosing.
Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes
Authors: McCully Alexandra L. , Yao McKenna Loop , Brower Kara K. , Fordyce Polly M. , Spormann Alfred M. 
Published: October 2022

AbstractOur understanding ofin situmicrobial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for novel taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of novelNegativicutesandMethanobacteriafrom stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.
Glycoengineered keratinocyte library reveals essential functions of specific glycans for all stages of HSV-1 infection
Authors: Bagdonaite Ieva , Marinova Irina N , Rudjord-Levann Asha M , Pallesen Emil MH , King-Smith Sarah , Rømer Troels B , Chen Yen-Hsi , Olofsson Sigvard , Nordén Rickard , Bergström Tomas , Dabelsteen Sally , Wandall Hans H 
Published: October 2022

AbstractViral and host glycans represent an understudied aspect of host-pathogen interactions, despite potential implications for treatment of viral infections. This is due to lack of easily accessible tools for analyzing glycan function in a meaningful context. Here we generated a glycoengineered keratinocyte library delineating human glycosylation pathways to uncover roles of specific glycans at different stages of herpes simplex virus type 1 (HSV-1) infectious cycle. We show the importance of cellular glycosaminoglycans and glycosphingolipids for HSV-1 attachment, N-glycans for entry and spread, and O-glycans for propagation. While altered virion surface structures had minimal effects on the early interactions with wild type cells, mutation of specific O-glycosylation sites affected glycoprotein surface expression and function. In conclusion, the data demonstrates the importance of specific glycans in a clinically relevant human model of HSV-1 infection and highlights the utility of genetic engineering to elucidate the roles of specific viral and cellular carbohydrate structures.
Inhibiting a mRNA motif binding protein that mediates TGF-β1 upregulation of translation attenuates pulmonary fibrosis in mice
Authors: Chen Wensheng , Pilling Darrell , Gomer Richard H. 
Published: October 2022

AbstractIn human lung cells, the profibrotic cytokine TGF-β1 increases sialidase 3 (NEU3) protein by increasingNEU3translation without increasing levels ofNEU3mRNA. To elucidate how TGF-β1 regulates translation, we treated human lung fibroblasts (HLF) with TGF-β1 and used proteomics and RNA-seq to determine the effect of TGF-β1 on proteins, mRNAs, and mRNA polysome/monosome ratios. We identified 181 mRNAs where TGF-β1 also increases translation to increase protein levels without significantly affecting mRNA levels. These mRNAs share a common 20 nucleotide motif. Deletion or insertion of this motif in mRNAs eliminates or induces the TGF-β1 regulation of translation. At least 5 RNA-binding proteins including DDX3 bind the RNA motif, and TGF-β1 regulates their protein levels and/or binding to the motif. Inhibiting DDX3, either by siRNA or small molecule inhibitors, reduced TGF-β1 induced NEU3 levels. In the mouse bleomycin model of pulmonary fibrosis, injections of the DDX3 inhibitor RK-33 starting 10 days after bleomycin potentiated survival and reduced lung inflammation, fibrosis, and lung tissue levels of DDX3, TGF-β1, and NEU3. Together, these results suggest that TGF-β1 regulates RNA-binding proteins that interact with a mRNA motif that is necessary and sufficient for TGF-β1 to regulate mRNA translation, and that blocking this effect can reduce fibrosis.
Nanoscale dynamics of streptococcal adhesion to AGE-modified collagen
Authors: Leiva-Sabadini Camila , Tiozzo-Lyon Paola , Hidalgo-Galleguillos Luis , Rivas Lina , Robles Agustín I , Fierro Angélica , Barrera Nelson P , Bozec Laurent , Schuh Christina MAP , Aguayo Sebastian 
Published: October 2022

AbstractThe adhesion of initial colonizers such asStreptococcus mutansto collagen is critical for dentinal and root caries progression. One of the most described pathological and aging-associated changes in collagen – including dentinal collagen – is the generation of advanced glycation end-products (AGEs) such as methylglyoxal (MGO)-derived AGEs. Despite previous reports suggesting that AGEs alter bacterial adhesion to collagen, the biophysics driving oral streptococcal attachment to MGO-modified collagen remains largely understudied. Thus, the aim of this work was to unravel the dynamics of the initial adhesion ofS. mutansto type-I collagen in the presence and absence of MGO-derived AGEs, by employing bacterial cell force-spectroscopy with atomic force microscopy (AFM). Type-I collagen gels were treated with 10mM MGO to induce AGE formation, which was characterized with microscopy and ELISA. Subsequently, AFM cantilevers were functionalized with livingS. mutansUA 159 orS. sanguinisSK 36 cells and probed against collagen surfaces to obtain force-curves displaying bacterial attachment in real-time, from which the adhesion force, number of events, Poisson analysis, and contour and rupture lengths for each individual detachment event were computed. Furthermore, in-silico docking studies between the relevantS. mutansUA 159 collagen-binding protein SpaP and collagen were computed, in the presence and absence of MGO. Overall, results showed that MGO modification increased both the number and adhesion force of single-unbinding events betweenS. mutansand collagen, without altering the contour or rupture lengths. Both experimental and in-silico simulations suggest that this effect is due to increased specific and non-specific forces and interactions betweenS. mutansUA 159 and MGO-modified collagen substrates. In summary, these results suggest that collagen alterations due to glycation and AGE formation may play a role in early bacterial adherence to oral tissues, associated with conditions such as aging or chronic hyperglycemia, amongst others.
Junctophilin-2 promotes cardiomyocyte survival by blocking MURF1-mediated Junctin ubiquitination and proteasome-dependentdegradation
Authors: Ji Xiaoyun , Huang Yifan , Ni Rui , Zheng Dong , Fan Guo-Chang , Jones Douglas L , Song Long-Sheng , Chakrabarti Subrata , Su Zhaoliang , Peng Tianqing 
Published: October 2022

AbstractAimsJunctophilin-2 is required for the development, maturation and integrity of the t-tubule system and the gating stability of RyR2 in cardiomyocytes. This study investigated whether and how junctophilin-2 maintained junctin, a scaffold protein stabilizing RyR2, to prevent cardiomyocyte death under stress.MethodsCardiomyocytes were exposed to conditions of stress including palmitate, doxorubicin, or hypoxia/re-oxygenation. Adenoviral vectors were employed to manipulate expression of junctophilin-2 and junctin in cardiomyocytes. Molecular/cellular/biochemical analyses were conducted.ResultsDifferent conditions of stress decreased junctophilin-2 expression through aberrant autophagy and concomitantly induced a reduction of junctin protein in cardiomyocytes. Over-expression of junctophilin-2 preserved the protein levels of junctin and attenuated cytosolic Ca2+and apoptosis in cardiomyocytes under stress. Knockdown of junctophilin-2 reproduced the detrimental phenotypes of stress in cardiomyocytes. Notably, over-expression of junctin prevented cardiomyocyte death under stress whereas knockdown of junctin offset the protective effects conferred by junctophilin-2 over-expression. Mechanistically, junctophilin-2 blocked MURF1-junctin interaction thereby preventing junctin ubiquitination and proteasome-dependent degradation. Mass spectrometry analysis identified multiple ubiquitination sites on the junctin protein and the non-ubiquitinated junctin mutant (K8A/K102A/K107A/K140A) was resistant to degradation.ConclusionsThis study uncovers an unrecognized role of junctophilin-2 in preventing junctin ubiquitination and degradation in maintaining cytosolic Ca2+homeostasis. Both junctophilin-2 and junctin represent two new survival factors of cardiomyocytes and thus, may be new therapeutic targets for cardiac protection.