bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monoclonal antibodies derived from B cells in subjects with cystic fibrosis reducePseudomonas aeruginosaburden in mice
Authors: Hale Malika , Takehara Kennidy K. , Thouvenel Christopher D. , Moustafa Dina A. , Repele Andrea , Fontana Mary F. , Netland Jason , McNamara Sharon , Gibson Ronald L. , Goldberg Joanna B. , Rawlings David J. , Pepper Marion 
Published: April 2024

AbstractPseudomonas aeruginosa(PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across 3 donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.
Light exposure induces phenotypic plasticity of the upside-down jellyfishCassiopeaand its endosymbiotic dinoflagellates
Authors: Salas Rebecca , Anthony Colin J , Bentlage Bastian 
Published: April 2024

AbstractThe upside-down jellyfish,Cassiopea, is an increasingly popular model organism gaining prominence for both its endosymbiotic dinoflagellates from the family Symbiodiniaceae and its behavioral changes of bell pulsations associated with environmental cues. Pulsation provides a unique window into the host’s response to environmental conditions, a typically difficult to access component of other symbiotic cnidarians. Pulsation has also been hypothesized to play a regulatory role on the endosymbiotic assemblage, but the magnitude of this regulatory effect is not well understood. Here, we used two light-acclimation experiments to help disentangle the complex phenotypic responses of the cnidarian host and its endosymbiotic dinoflagellates. The first experiment examined the phenotypic plasticity (size, behavior, color) ofCassiopeasp. in response to repeated ambient light acclimation trials to determine the rate and magnitude of phenotypic plasticity. The second experiment compared the acclimation response of jellyfish across three experimental groups to test whether a variable environment and resulting short acclimation times destabilized the host-endosymbiont relationship. Our goal was to identify covarying host-endosymbiont phenotypes to gain new insights into the dynamics of this relationship. We employed flow cytometric phenotypic profiling for high-throughput phenotypic characterization of endosymbiotic dinoflagellates in addition to pulse-amplitude modulated (PAM) fluorometry to characterize photosynthetic efficiency (Fv/Fm). Host phenotypes responded predictably to light-dark cycles, and stabilized after nine to twelve days of exposure to consistent light conditions. However, disruption of this acclimation period affected both the host’s circadian rhythm and the endosymbionts’ phenotypic profile. We also found evidence that phenotypic responses of the host and endosymbionts were generally decoupled, indicating a stronger regulatory response of light conditions on phenotypes than possible host-regulatory strategies on the endosymbiotic assemblage. This study provides unique insights into the acclimation strategies of upside-down jellyfish, an emerging model for the study of cnidarian-dinoflagellate symbiosis.HighlightsCassiopeabehavior and color respond predictably to changing light conditionsInadequate acclimation time destabilizes the host’s circadian rhythm and causes unique phenotypic characteristics of the endosymbiontsLight may be a stronger influence on host and endosymbiont phenotypes than host-endosymbiont relationships
The causal arrows ̶ from genotype, environment and management to plant phenotype ̶ are double headed
Authors: Sadras Victor O , Hayman Peter T 
Published: April 2024

AbstractUnidirectional, cause-and-effect arrows are drawn from genotype (G), environment (E), and agronomic management (M) to the plant phenotype in crop stands. Here we focus on the overlooked bidirectionality of these arrows. The phenotype-to-genotype arrow includes increased mutation rates in stressed phenotypes, relative to basal rates. From a developmental viewpoint, the phenotype modulates gene expression returning multiple cellular phenotypes with a common genome. From a computational viewpoint, the phenotype influences gene expression in a process of downward causation. The phenotype-to-environment arrow is captured in the process of niche construction, which spans from persistent and global (e.g., photosynthetic archaea and cyanobacteria that emerged ∼3.4 billion years agocreatedthe oxygen-rich atmosphere thatenabledthe evolution of aerobic organisms and eukaryotes) to transient and local (e.g., lucerne tap root constructs soil biopores that influence the root phenotype of the following wheat crop). Research on crop rotations illustrates but is divorced of niche construction theory. The phenotype-to-management arrow involves, for example, a diseased crop that triggers fungicide treatments. Making explicit the bidirectionality of the arrows in the G×E×M model allows to connect crop improvement and agronomy with other, theoretically rich scientific fields.HighlightIn the G×E×M model, the plant phenotype is not only influenced by but also influences G, E and M.
MRAP2 modifies the signaling and oligomerization state of the melanocortin-4 receptor
Authors: Sohail Iqra , Laurin Suli-Anne , Kleinau Gunnar , Chunilal Vidicha , Morton Andrew , Kagiali Zeynep Cansu Uretmen , Tello Javier A. , Lohse Martin J. , Scheerer Patrick , Bouvier Michel , McCormick Peter , Annibale Paolo , Biebermann Heike 
Published: April 2024

ABSTRACTThe melanocortin-4 receptor (MC4R) is a G protein-coupled receptor (GPCR) and a key regulator of appetite and metabolism. It can interact with the melanocortin-receptor accessory protein 2 (MRAP2), a single transmembrane helix protein known to interact with several different GPCRs. However, the consequences of this interaction are not completely understood. Here we report that co-expression of MRAP2 has multiple effects on the MC4R: it enhances G protein-mediated signaling and simultaneously impairs β-arrestin2 recruitment and, consequently, internalization. In addition, co-expression of MRAP2 leads to an increased number of monomers of MC4R by disrupting receptor oligomers. A structural homology model of the active state MC4R–MRAP2– Gs complex suggests interaction sites between MRAP2 and MC4R that are relevant for receptor activation. Taken together, our data indicate that MRAP2 is an accessory protein that interacts with and influences MC4R structure, biasing its signaling towards G protein-mediated effects.
Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions
Authors: Schmid Ernst W. , Walter Johannes C. 
Published: April 2024

SummaryProtein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying biochemical processes is lacking. Although AlphaFold-Multimer (AF-M) has the potential to fill this knowledge gap, standard AF-M confidence metrics do not reliably separate relevant PPIs from an abundance of false positive predictions. To address this limitation, we used machine learning on well curated datasets to train aStructurePrediction andOmics informedClassifier called SPOC that shows excellent performance in separating true and false PPIs, including in proteome-wide screens. We applied SPOC to an all-by-all matrix of nearly 300 human genome maintenance proteins, generating ∼40,000 predictions that can be viewed at predictomes.org, where users can also score their own predictions with SPOC. High confidence PPIs discovered using our approach suggest novel hypotheses in genome maintenance. Our results provide a framework for interpreting large scale AF-M screens and help lay the foundation for a proteome-wide structural interactome.
Non-negative matrix factorization and deconvolution as dual simplex problem
Authors: Kleverov Denis , Aladyeva Ekaterina , Serdyukov Alexey , Artyomov Maxim N. 
Published: April 2024

AbstractNon-negative matrix factorization (NMF) is one of the most powerful linear algebra tools, which has found application in various areas of data analysis, including computational biology. Despite numerous optimization methods devised for NMF, our comprehension of the inherent topological structure within factorizable matrices remains limited. In this work, we reveal the topological properties of the linear mixture data, which allow for a remarkable reduction in the dimensionality of the NMF problem and reformulation of the NMF problem as an optimization problem with onlyK(K−1)variables, with K representing the number of pure components, irrespective of the initial data matrix dimensionality. This is achieved by uncovering the dual simplex structure of the data, with complementary simplex structures existing in both the features’ and samples’ spaces and leveraging the Sinkhorn transformation to uncover the relationship between these simplexes. We validate this approach in the context of an unconstrained general mixed images scenario and achieve a significant improvement in decomposition accuracy. Furthermore, we successfully apply the proposed approach in the biological context of bulk RNA-seq gene expression data unmixing and single-cell RNA-seq data clustering.
A narrow ratio of nucleic acid to SARS-CoV-2 N-protein enables phase separation
Authors: Laughlin Patrick M. , Young Kimberly , Gonzalez-Gutierrez Giovanni , Wang Joseph C.Y. , Zlotnick Adam 
Published: April 2024

AbstractSARS-CoV-2 Nucleocapsid protein (N) is a viral structural protein that packages the 30kb genomic RNA inside virions and forms condensates within infected cells through liquid-liquid phase separation (LLPS). N, in both soluble and condensed forms, has accessory roles in the viral life cycle including genome replication and immunosuppression. The ability to perform these tasks depends on phase separation and its reversibility. The conditions that stabilize and destabilize N condensates and the role of N-N interactions are poorly understood. We have investigated LLPS formation and dissolution in a minimalist system comprised of N protein and an ssDNA oligomer just long enough to support assembly. The short oligo allows us to focus on the role of N-N interaction. We have developed a sensitive FRET assay to interrogate LLPS assembly reactions from the perspective of the oligonucleotide. We find that N alone can form oligomers but that oligonucleotide enables their assembly into a three-dimensional phase. At a ∼1:1 ratio of N to oligonucleotide LLPS formation is maximal. We find that a modest excess of N or of nucleic acid causes the LLPS to break down catastrophically. Under the conditions examined here assembly has a critical concentration of about 1 µM. The responsiveness of N condensates to their environment may have biological consequences. A better understanding of how nucleic acid modulates N-N association will shed light on condensate activity and could inform antiviral strategies targeting LLPS.
Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation
Authors: Olea-Flores Monserrat , Sharma Tapan , Verdejo-Torres Odette , DiBartolomeo Imaru , Thompson Paul R. , Padilla-Benavides Teresita , Imbalzano Anthony N. 
Published: April 2024

ABSTRACTPyruvate kinase is a glycolytic enzyme that converts phosphoenolpyruvate and ADP into pyruvate and ATP. There are two genes that encode pyruvate kinase in vertebrates;PkmandPklencode muscle- and liver/erythrocyte-specific forms, respectively. Each gene encodes two isoenzymes due to alternative splicing. Both muscle-specific enzymes, Pkm1 and Pkm2, function in glycolysis, but Pkm2 also has been implicated in gene regulation due to its ability to phosphorylate histone 3 threonine 11 (H3T11) in cancer cells. Here, we examined the roles of Pkm1 and Pkm2 during myoblast differentiation. RNA-seq analysis revealed that Pkm2 promotes the expression ofDpf2/Baf45dandBaf250a/Arid1A. Dpf2 and Baf250a are subunits that identify a specific sub-family of the mammalian SWI/SNF (mSWI/SNF) of chromatin remodeling enzymes that is required for activation of myogenic gene expression during differentiation. Pkm2 also mediated the incorporation of Dpf2 and Baf250a into the regulatory sequences controlling myogenic gene expression. Pkm1 did not affect expression but was required for nuclear localization of Dpf2. Additionally, Pkm2 was required not only for the incorporation of phosphorylated H3T11 in myogenic promoters, but also for the incorporation of phosphorylated H3T6 and H3T45 at myogenic promoters via regulation of AKT and protein kinase C isoforms that phosphorylate those amino acids. Our results identify multiple unique roles for Pkm2 and a novel function for Pkm1 in gene expression and chromatin regulation during myoblast differentiation.
Anin silicoframework for the rational design of vaginal probiotic therapy
Authors: Lee Christina Y. , Bonakdar Sina , Arnold Kelly B. 
Published: April 2024

AbstractBacterial vaginosis is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop anin silicoframework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This framework highlighted the importance of resident microbial species on the efficacy of probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) andLactobacillusspp. with candidate probiotic strains as a necessary selection criteria. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of thein silicoplatform. Results from the model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.
The NS1 protein of contemporary West African Zika virus is efficient to increase cellular permissiveness to virus replication
Authors: Dana Machmouchi , Marie-Pierre Courageot , Eva Ogire , Alain Kohl , Desprès Philippe , Marjolaine Roche 
Published: April 2024

ABSTRACTMosquito-borne Zika virus (ZIKV; orthoflavivirus,Flaviviridae) has become a global health problem due to expansion of the geographic distribution of Asian Lineage virus. Contemporary ZIKV strains of African lineage have recently gained increased attention due to their epidemic potential and their capacity to be highly teratogenic in humans. The ZIKV non-structural NS1 protein from recent West African strains Africa was been studied where with view of its importance in the pathogenicity. NS1 protein from contemporary West African ZIKV (NS1CWA) and historical African ZIKV strain MR766 (NS1MR766) differ by seven amino-acid substitutions. Expression of recombinant NS1 proteins showed differences in the subcellular distribution between NS1CWAand NS1MR766in HEK-293T cells. There was an increased secretion efficiency of soluble NS1CWAcompared to NS1MR766. The replication of a chimeric MR766/NS1CWAvirus was studied in Vero and A549 cells. Insertion of NS1CWAinto MR766 enhances virus replication in both cell lines leading to more pronounced cell death. This correlated with lower up-regulation ofIFN-βand interferon-stimulated gene mRNA in A549 cells infected by MR766/NS1CWAvirus. Our data raise the question on the importance of NS1 protein in the pathogenicity of contemporary ZIKV from West Africa, and point to differences within viral strains belonging to the same African lineage.AUTHOR SUMMARYMosquito-borne Zika virus (ZIKV) of African lineage has the potential to cause epidemic along with a high risk of fetal pathogenicity. Too little is still known on the features of contemporary ZIKV from West Africa. We find there is a remarkable conservation of NS1 amino-acid residues between ZIKV strains recently isolated in Senegal and Guinea. Analysis of recombinant ZIKV NS1 protein revealed efficient secretion of contemporary African NS1 protein from human cells. Using infectious molecular clone of African ZIKV, we showed that contemporary West Africa NS1 protein influences virus replication and innate immune activation. The NS1 protein has been proposed as playing a major role in the pathogenicity of contemporary ZIKV from West Africa.
Coatomer complex I is required for the transport of SARS-CoV-2 progeny virions from the endoplasmic reticulum-Golgi intermediate compartment
Authors: Hirabayashi Ai , Muramoto Yukiko , Takenaga Toru , Tsunoda Yugo , Wakazaki Mayumi , Sato Mayuko , Fujita-Fujiharu Yoko , Nomura Norimichi , Yamauchi Koji , Onishi Chiho , Nakano Masahiro , Toyooka Kiminori , Noda Takeshi 
Published: April 2024

AbstractSARS-CoV-2 undergoes budding within the lumen of the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and delivers progeny virions to the cell surface by employing vesicular transport. However, the molecular mechanisms remain poorly understood. Using three-dimensional electron microscopic analysis, such as array tomography and electron tomography, we found that virion-transporting vesicles possessed a coated protein on their membrane and demonstrated that the coated protein was coatomer complex I (COPI). During the later stages of SARS-CoV-2 infection, we observed a notable alteration in the distribution of COPI and ERGIC throughout the cytoplasm. Depletion of COPB2, a key component of COPI, led to the confinement of SARS-CoV-2 structural proteins in the perinuclear region, where progeny virions were accumulated within the ERGIC. While the expression levels of viral proteins within cells were comparable, this depletion significantly reduced the efficiency of virion release, leading to the significant inhibition of viral replication. Hence, our findings suggest COPI as a critical player in facilitating the transport of SARS-CoV-2 progeny virions from the ERGIC. Thus, COPI could be a promising target for the development of antivirals against SARS-CoV-2.
Single-cell imaging of the lytic phage life cycle in bacteria
Authors: Wedd Charlie , Yunusov Temur , Smith Aaron , Li Ruizhe , Hardo Georgeos , Hunter Michael , Majed Racha , Fusco Diana , Bakshi Somenath 
Published: April 2024

AbstractWhen a lytic bacteriophage infects a bacterial cell, it commandeers the cell’s resources to replicate, ultimately causing cell lysis and the release of new virions. As phages function as obligate parasites, each stage of the infection process depends on the physiological parameters of the host cell. Given the inherent variability of bacterial physiology, we ask how the phage infection dynamic reflects such heterogeneity.Here, we introduce an imaging assay for investigating the kinetics of individual infection steps by a single T7 phage on a single bacterium. The high-throughput, time-resolved nature of the assay allows us to monitor the infection progression simultaneously in multiple cells, revealing substantial heterogeneity in each step and correlations between the dynamics of infection steps and physiological properties of the infected cell. Simulations of competing phage populations with distinct lysis time distributions indicate that this heterogeneity can have considerable impact on phage fitness, recognising variability in infection kinetics as a potential evolutionary driver of phage-bacteria interactions.
Archaeal type six secretion system mediates contact-dependent antagonism
Authors: Zachs Tobias , Malit Jessie James L. , Xu Jingwei , Schürch Alexandra , Sivabalasarma Shamphavi , Nußbaum Phillip , Albers Sonja-Verena , Pilhofer Martin 
Published: April 2024

AbstractMicrobial communities are shaped by cell-cell interactions. Even though archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here we report the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time lapse imaging, we show that Halogeometricum borinquense exhibits antagonism towards Haloferax volcanii by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed CISs bound to the cytoplasmic membrane, resembling bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains with antagonistic behavior. Our data provides a mechanistic framework for understanding how archaea may shape microbial communities and impact the food webs they inhabit.TeaserT6SSs are widespread in the archaeal domain and used to kill other archaea.
Reconstitution of human DNA licensing and the structural and functional analysis of key intermediates
Authors: Wells Jennifer N. , Leber Vera , Edwardes Lucy V , Allyjaun Shenaz , Peach Matthew , Tomkins Joshua , Kefala-Stavridi Antonia , Faull Sarah V , Aramayo Ricardo , Pestana Carolina M. , Ranjha Lepakshi , Speck Christian 
Published: April 2024

SUMMARYHuman DNA licensing initiates the process of replication fork assembly. Specifically, this reaction leads to the loading of hMCM2-7 on DNA, which represents the core of the replicative helicase that unwinds DNA during S-phase. Here, we report the biochemical reconstitution of human DNA licensing using purified proteins, the structural and functional analysis of the process and reveal the impact of cancer-associated mutations on DNA licensing. We showed that thein vitroreaction is specific and results in the assembly of high-salt resistant hMCM2-7 double-hexamers, the final product of DNA licensing. We used ATPγS to block complex assembly at the hOrc1-5-Cdc6-Cdt1-MCM2-7 step. We observed that the assembly of this intermediate is independent of hOrc6, although hOrc6 enhances the loading of the second hMCM2-7 hexamer. The structural and mutational analysis of the hOrc1-5-Cdc6-Cdt1-MCM2-7 complex provides insights into hORC-Cdc6 dependent recruitment of hMCM2-7 via five hMcm winged-helix domains. The structure highlights how hOrc1 activates the hCdc6 ATPase, while the analysis of hOrc1 and hCdc6 ATPase mutants uncovered an unexpected role for hCdc6 ATPase in complex disassembly. The structure highlights that Cdc6 binding to Orc1-5 stabilises Orc2-DNA interactions and supports Mcm3-dependent recruitment of MCM2-7. Finally, the structure allowed us to locate cancer-associated mutations at the hCdc6-Mcm3 interface, which showed specific helicase loading defects.