bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymph Node Fibroblastic Reticular Cells Attenuate Immune Responses Through Induction of Tolerogenic Macrophages at Early Stage of Transplantation
Authors: Liu Beichen , Liu Huihui , Liu Siwei , Qin Chenchen , He Xiaoya , Song Zhengyang , Dong Yujun , Ren Hanyun 
Published: July 2022

Background.
Fibroblastic reticular cells (FRCs) are a type of stromal cells located in the T zone in secondary lymphoid organs. Previous studies showed that FRCs possess the potential to promote myeloid differentiation. We aim to investigate whether FRCs in lymph nodes (LNs) could induce tolerogenic macrophage generation and further influence T-cell immunity at an early stage of allogeneic hematopoietic stem cell transplantation (allo-HSCT).

Methods.
LNs were assayed to confirm the existence of proliferating macrophages after allo-HSCT. Ex vivo—expanded FRCs and bone marrow cells were cocultured to verify the generation of macrophages. Real-time quantitative PCR and ELISA assays were performed to observe the cytokines expressed by FRC. Transcriptome sequencing was performed to compare the difference between FRC-induced macrophages (FMs) and conventional macrophages. Mixed lymphocyte reaction and the utilization of FMs in acute graft-versus-host disease (aGVHD) mice were used to test the inhibitory function of FMs in T-cell immunity in vitro and in vivo.

Results.
We found a large number of proliferating macrophages near FRCs in LNs with tolerogenic phenotype under allo-HSCT conditions. Neutralizing anti–macrophage colony-stimulating factor receptor antibody abolished FMs generation in vitro. Phenotypic analysis and transcriptome sequencing suggested FMs possessed immunoinhibitory function. Mixed lymphocyte reaction proved that FMs could inhibit T-cell activation and differentiation toward Th1/Tc1 cells. Injection of FMs in aGVHD mice effectively attenuated aGVHD severity and mortality.

Conclusions.
This study has revealed a novel mechanism of immune regulation through the generation of FRC-induced tolerogenic macrophages in LNs at an early stage of allo-HSCT.
Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy
Authors: Fichtner Miriam L. , Hoehn Kenneth B. , Ford Easton E. , Mane-Damas Marina , Oh Sangwook , Waters Patrick , Payne Aimee S. , Smith Melissa L. , Watson Corey T. , Losen Mario , Martinez-Martinez Pilar , Nowak Richard J. , Kleinstein Steven H. , O’Connor Kevin C. 
Published: July 2022

AbstractMyasthenia gravis (MG) is an autoantibody-mediated autoimmune disorder of the neuromuscular junction. In a subset of patients with MG, muscle-specific tyrosine kinase (MuSK) autoantibodies are present. MuSK MG patients respond well to CD20-mediated B cell depletion therapy (BCDT); most achieve complete stable remission. However, relapse often occurs. To further understand the immunomechanisms underlying relapse, we sought to study autoantibody-producing B cells over the course of BCDT. We developed a fluorescently labeled antigen to enrich for MuSK-specific B cells, which was validated with a novel Nalm6 cell line engineered to express a human MuSK-specific B cell receptor. B cells (≅ 2.6 million) from 12 different samples collected from nine MuSK MG patients were screened for MuSK specificity. We successfully isolated two MuSK-specific IgG4 subclass-expressing plasmablasts from two of these patients, who were experiencing a relapse after a BCDT-induced remission. Human recombinant MuSK mAbs were then generated to validate binding specificity and characterize their molecular properties. Both mAbs were strong MuSK binders, they recognized the Ig1-like domain of MuSK, and showed pathogenic capacity when tested in an AChR clustering assay. The presence of persistent clonal relatives of these MuSK-specific B cell clones was investigated through B cell receptor repertoire tracing of 63,977 unique clones derived from longitudinal samples collected from these two patients. Clonal variants were detected at multiple timepoints spanning more than five years and reemerged after BCDT-mediated remission, predating disease relapse by several months. These results indicate that a reservoir of rare pathogenic MuSK autoantibody-expressing B cell clones survive BCDT and reemerge into circulation prior to manifestation of clinical relapse. This study provides both a mechanistic understanding of MuSK MG relapse and a valuable candidate biomarker for relapse prediction.
Age- or lifestyle-induced accumulation of genotoxicity is associated with a generalized shutdown of long gene transcription
Authors: Ibañez-Solé Olga , Izeta Ander 
Published: July 2022

AbstractA causative role for DNA damage as a molecular driver of aging has long been advocated. Transcription-blocking lesions (TBLs) accumulate with age in a stochastic manner. Thus, gene expression data might reflect the gene length-dependent accumulation of TBLs. Here we present an analysis of gene expression as a function of gene length in several independent single-cell RNA sequencing datasets of mouse and human aging. We found a pervasive age-associated downregulation of long gene expression, which is seen across species, datasets, sexes, tissues and cell types. Furthermore, long gene downregulation was also observed in premature aging models such as UV-radiation and smoke exposure, and in gene expression data from progeroid diseases Cockayne syndrome and trichothiodystrophy. Finally, we analyzed the length of differentially expressed genes associated to age in both mice and humans. Downregulated genes were significantly longer than upregulated genes. These data highlight a previously undetected hallmark of cellular aging and provide strong support for age-associated accumulation of genotoxic damage inducing a generalized shutdown of RNA polymerase II-mediated long gene transcription.Abstract Figure
Waning and boosting of functional humoral immunity to SARS-CoV-2
Authors: Tong X. , McNamara R.P. , Avendaño M.J. , Serrano E.F. , García-Salum T. , Pardo-Roa C. , Levican J. , Poblete E. , Salina E. , Muñoz A. , Riquelme A. , Alter G. , Medina R.A. 
Published: July 2022

SummarySince the emergence of the SARS-CoV-2 virus, we have witnessed a revolution in vaccine development with the rapid emergence and deployment of both traditional and novel vaccine platforms. The inactivated CoronaVac vaccine and the mRNA-based Pfizer/BNT162b2 vaccine are among the most widely distributed vaccines, both demonstrating high, albeit variable, vaccine effectiveness against severe COVID-19 over time. Beyond the ability of the vaccines to generate neutralizing antibodies, antibodies can attenuate disease via their ability to recruit the cytotoxic and opsinophagocytic functions of the immune response. However, whether Fc-effector functions are induced differentially, wane with different kinetics, and are boostable, remains unknown. Here, using systems serology, we profiled the Fc-effector profiles induced by the CoronaVac and BNT162b2 vaccines, over time. Despite the significantly higher antibody functional responses induced by the BNT162b2 vaccine, CoronaVac responses waned more slowly, albeit still found at levels below those present in the systemic circulation of BNT162b2 immunized individuals. However, mRNA boosting of the CoronaVac vaccine responses resulted in the induction of significantly higher peak antibody functional responses with increased humoral breadth, including to Omicron. Collectively, the data presented here point to striking differences in vaccine platform-induced functional humoral immune responses, that wane with different kinetics, and can be functionally rescued and expanded with boosting.
The burden of human coronavirus infection in children hospitalised with lower respiratory tract infection in Cape Town, South Africa
Authors: Aliyu Abdulmumuni S. , Masu Adelaide N. , Kagina Benjamin M. , Muloiwa Rudzani 
Published: July 2022

ABSTRACTIntroductionHuman coronaviruses (HCoV) NL63, HKU, OC43 and 229E are known to cause various respiratory infections including croup, pneumonia, and bronchitis in young children. The role of these four HCoV strains in the aetiology of pneumonia is little described in South Africa.MethodsWe used data collected between September 2012 – September 2013 from children aged <13 years with lower respiratory illness at Red Cross War Memorial Children’s Hospital. Respiratory samples including a nasopharyngeal swab (NP) and induced sputum (IS) were taken and tested for the four strains of coronaviruses using FTD33 multiplex real-time PCR.ResultsA total of 460 respiratory samples were analysed. Of these, 258 (56.0%) were male and 19 (4.1%) HIV infected. The median age of the children was 8 (IQR 4-18) months.Nasopharyngeal (NP) samples were obtained from 460 children while induced sputum (IS) was not available for six children due to sample loss prior to analysis, leaving 454 available for analysis. A total of 42 (9.1%, 95% CI 6.7-12.1%) participants tested positive for HCoV in at least one of the two specimens. PCR was able to detect a total of 35 (7.7%) cases from the 454 tested IS specimens compared to 23 (5.0%) detected out of 460 NP samples.The commonest detected HCoVs were coronavirus OC43 with 20 (4.3%) detected from either specimen followed by coronavirus NL63 or coronavirus HKU detected in 14 (3.0%) and 10 (2.2%) of positive test samples, respectively. The least common virus detected HCoV was coronavirus 229E detected in both positive test samples of one participant.Overall HCoVs were detected in 23 (8.9%) of boys compared to 19 (9.1%) of the girls who returned a positive test; p=0.856. The overall age distribution of children with PCR detected HCoVs was similar to that of children with a negative result with median age of 10 (IQR 5-16) months and median of 8 (IQR 4-19) months, respectively; p=0.535. Prevalence of HCoV was 11/192 (5.7%), 23/153 (15.0%) and 8/115 (7.0%) in children <6 months old, 6-18 months and over 18 months respectively; p=0.008.ConclusionChildren aged 6 to 18 months had double the risk of other age groups.
Reduced Olfactory Bulb Volume Accompanies Olfactory Dysfunction After Mild SARS-CoV-2 Infection
Authors: Petersen Marvin , Becker Benjamin , Schell Maximilian , Mayer Carola , Nägele Felix L. , Petersen Elina , Twerenbold Raphael , Thomalla Götz , Cheng Bastian , Betz Christian , Hoffmann Anna S. 
Published: July 2022

SUMMARYBackgroundDespite its high prevalence, the determinants of smelling impairment in COVID-19 remain not fully understood. In this work, we aimed to examine the association between olfactory bulb volume and the clinical trajectory of COVID-19-related smelling impairment in a large-scale magnetic resonance imaging (MRI) analysis.Methodology/PrincipalData of non-vaccinated COVID-19 convalescents recruited within the framework of the Hamburg City Health Study COVID Program between March and December 2020 were analyzed. On average 8 months after recruitment,, participants underwent MRI and neuropsychological testing as well as a structured questionnaire for olfactory function. Between March and April 2022 olfactory function was assessed at an additional timepoint including quantitative olfactometric testing with Sniffin’ Sticks.ResultsThis study included 233 individuals recovered from mainly mild to moderate SARS-CoV-2 infections. Longitudinal assessment demonstrated a declining prevalence of olfactory dysfunction from 67.1% at acute infection, 21.0% at baseline examination and 17.5% at follow-up. Participants with post-acute olfactory dysfunction had a significantly lower olfactory bulb volume at scan-time than normally smelling individuals. Olfactory bulb volume predicted olfactometric scores at follow-up. Performance in neuropsychological testing was not significantly associated with the olfactory bulb volume.ConclusionsOur work demonstrates an association of long-term smelling dysfunction and olfactory bulb integrity in a sample of individuals recovered from mainly mild to moderate COVID-19. Collectively, our results highlight olfactory bulb volume as a surrogate marker that may inform diagnosis and guide rehabilitation strategies in COVID-19.
Translation in the cell under fierce competition for shared resources: a mathematical model
Authors: Katz Rami , Attias Elad , Tuller Tamir , Margaliot Michael 
Published: July 2022

AbstractDuring the process of translation the mRNAs in the cell “compete” for shared resources like tRNA molecules and ribosomes. This creates an indirect and intricate coupling between the mRNAs. For example, if ribosomal “traffic jams” evolve on some mRNA then the abundance of free ribosomes may decrease leading to lower initiation rates in the other mRNAs. When the shared resources are abundant the coupling between mRNAs due to this competition is weak. However, when the resources are scarce, e.g., when the pool of free ribosomes is starved, the competition may have a dramatic effect on the dynamics of translation in the cell. This scenario may be relevant for example under stress conditions or during a high yield viral infection, where the viral mRNAs “hijack” components of the translation machinery. Fierce competition for shared resources may also take place in synthetic or engineered systems such as cell free systems or in the case of high-throughput heteroglougs gene expression.We study this scenario using a mathematical model that includes a network ofmribosome flow models (RFMs) interconnected via a pool of free ribosomes. Each RFM is a non-linear dynamical model for ribosome flow along a single mRNA molecule, and the interconnection via the pool encapsulates the competition for shared resources. We analyze the case wheremis large, i.e., a there is a large number of mRNAs. This implies that many ribosomes are attached to the mRNAs and thus the pool is starved.Our model allows quantitative and qualitative analysis of the network steady state when the pool is starved. Our analysis results show that adding an mRNA to the network always decreases the steady state pool density. This makes sense, as every new mRNA “consumes” ribosomes. We also show that adding an mRNA has an intricate effect on the total protein production in the network: on the one-hand, the new mRNA produces new proteins. On the other-hand, the other mRNAs produce less proteins, as the pool that feeds these mRNAs now has a smaller abundance of ribosomes. Our analysis yields an explicit bound for the total production rate of the network when the number of RFMIOs is very large. In particular, we analyze how the total density of ribosomes in the network bounds the total production rate. This bound demonstrates that when the number of mRNAs increases, the marginal utility of adding another mRNA diminishes, and the total protein production rate saturates to a limiting value. We demonstrate our analysis approach using an example of producing insulin in a cell free system.
Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites
Authors: Rizos Iris , Debeljak Pavla , Finet Thomas , Klein Dylan , Ayata Sakina-Dorothée , Not Fabrice , Bittner Lucie 
Published: July 2022

AbstractMarine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2 171 unassigned clusters exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 38 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community’s variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.
The host range and the role of O-antigen in P1 transduction with its alternative S’ tail fibre
Authors: Huan Yang W. , Fa-arun Jidapha , Wang Baojun 
Published: July 2022

ABSTRACTEnterobacteria phage P1 expresses two types of tail fibre, S and S’. Despite the wide usage of phage P1 for transduction, the host range and the receptor for its alternative S’ tail fibre was never determined. Here, a ΔS-cin Δpac E. coli P1 lysogenic strain was generated to allow packaging of phagemid DNA into P1 phage having either S or S’ tail fibre. P1(S’) could transduce phagemid DNA into Shigella flexneri 2a 2457O, Shigella flexneri 5a M90T and Escherichia coli O3 efficiently. Mutational analysis of the O-antigen assembly genes and LPS inhibition assays indicated that P1(S’) transduction requires at least one O-antigen unit. E. coli O111:B4 LPS produced a high neutralising effect against P1(S’) transduction, indicating that this E. coli strain could be a host for P1(S’). Mutations in the O-antigen modification genes of S. flexneri 2a 2457O and S. flexneri 5a M90T did not cause significant changes to P1(S’) transduction efficiency. A higher transduction efficiency of P1(S’) improved the delivery of a cas9 antimicrobial phagemid into both S. flexneri 2457O and M90T. These findings provide novel insights into P1 tropism-switching, by identifying the host range of P1(S’) and demonstrating its potential for delivering a sequence-specific Cas9 antimicrobial into clinically relevant S. flexneri.
Efficient in vivo neuronal genome editing in the mouse brain using nanocapsules containing CRISPR-Cas9 ribonucleoproteins
Authors: Metzger Jeanette M. , Wang Yuyuan , Neuman Samuel S. , Snow Kathy J. , Murray Stephen A. , Lutz Cathleen M. , Bondarenko Viktoriya , Felton Jesi , Gimse Kirstan , Xie Ruosen , Zhao Yi , Flowers Matthew T. , Simmons Heather A. , Roy Subhojit , Saha Krishanu , Levine Jon , Emborg Marina E. , Gong Shaoqin 
Published: July 2022

ABSTRACTGenome editing of somatic cells via clustered regularly interspaced short palindromic repeats (CRISPR) offers promise for new therapeutics to treat a variety of genetic disorders, including neurological diseases. However, the dense and complex parenchyma of the brain and the post-mitotic state of neurons make efficient genome editing challenging. In vivo delivery systems for CRISPR-Cas proteins and single guide RNA (sgRNA) include both viral vectors and non-viral strategies, each presenting different advantages and disadvantages for clinical application. We developed non-viral and biodegradable PEGylated nanocapsules (NCs) that deliver preassembled Cas9-sgRNA ribonucleoproteins (RNPs). Here, we show that the RNP NCs led to robust genome editing in neurons following intracerebral injection into the mouse striatum. Genome editing was predominantly observed in medium spiny neurons (>80%), with occasional editing in cholinergic, calretinin, and parvalbumin interneurons. Glial activation was minimal and was localized along the needle tract. Our results demonstrate that the RNP NCs are capable of safe and efficient neuronal genome editing in vivo.SIGNIFICANCE STATEMENTModifying the DNA of cells in the brain could present opportunities for new treatments of neurological diseases. In this report, we describe a nanocapsule system designed to deliver the elements needed to modify the DNA of brain cells, also known as genome editing. These nanocapsules are created by chemically encapsulating the genome editing components, such that the nanocapsules are stable when prepared and biodegradable to release their payload upon entering cells. When injected into the mouse brain, our research shows that the nanocapsules lead to safe and efficient editing of DNA in neurons.
Stiffness-dependent active wetting enables optimal collective cell durotaxis
Authors: Pallarès Macià-Esteve , Pi-Jaumà Irina , Fortunato Isabela Corina , Grazu Valeria , Gómez-González Manuel , Roca-Cusachs Pere , de la Fuente Jesus M , Alert Ricard , Sunyer Raimon , Casademunt Jaume , Trepat Xavier 
Published: July 2022

AbstractThe directed migration of cellular clusters enables morphogenesis, wound healing, and collective cancer invasion. Gradients of substrate stiffness are known to direct the migration of cellular clusters in a process called collective durotaxis, but underlying mechanisms remain unclear. Here, we unveil a connection between collective durotaxis and the wetting properties of cellular clusters. We show that clusters of cancer cells dewet soft substrates and wet stiff ones. At intermediate stiffness, at the crossover from low to high wettability, clusters on uniform-stiffness substrates become maximally motile, and clusters on stiffness gradients exhibit optimal durotaxis. Durotactic velocity increases with cluster size, stiffness gradient, and actomyosin activity. We demonstrate this behavior on substrates coated with the cell-cell adhesion protein E-cadherin and then establish its generality on substrates coated with extracellular matrix. We develop a physical model of three-dimensional active wetting that explains this mode of collective durotaxis in terms of a balance between in-plane active traction and tissue contractility, and out-of-plane surface tension. Finally, we show that the distribution of cluster displacements has a heavy tail, with infrequent but large cellular hops that contribute to durotactic migration. Our study demonstrates a physical mechanism of collective durotaxis, through both cell-cell and cell-substrate adhesion ligands, based on the wetting properties of active droplets.