bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid immunity elicits potent cross-variant ADCC against SARS-CoV-2 through a combination of anti-S1 and S2 antibodies
Authors: Grant Michael D. , Bentley Kirsten , Fielding Ceri A. , Hatfield Keeley M. , Ings Danielle P. , Harnum Debbie , Wang Eddie , Stanton Richard , Holder Kayla A. 
Published: March 2023

AbstractAntibodies capable of neutralising SARS-CoV-2 have been well studied, but the Fc receptor-dependent antibody activities that also significantly impact the course of infection have not been studied in such depth. SARS-CoV-2 infection induces antibody-dependent NK cell responses targeting multiple antigens, however, as most vaccines induce only anti-spike antibodies, we investigated spike-specific antibody-dependent cellular cytotoxicity (ADCC). Vaccination produced antibodies that only weakly induced ADCC, however, antibodies from individuals who were infected prior to vaccination (‘hybrid’ immunity) elicited much stronger anti-spike ADCC. Quantitative and qualitative aspects of humoral immunity contributed to this capability, with infection skewing IgG antibody production towards S2, vaccination skewing towards S1 and hybrid immunity evoking strong responses against both domains. The capacity for hybrid immunity to provide superior spike-directed ADCC was associated with selectively increased antibody responses against epitopes within both S1 and S2. Antibodies targeting both spike domains were important for strong antibody-dependent NK cell activation, with three regions of antibody reactivity outside the receptor-binding domain (RBD) corresponding with potent anti-spike ADCC. Consequently, ADCC induced by hybrid immunity with ancestral antigen was conserved against variants containing neutralisation escape mutations in the RBD [Delta and Omicron (BA.1)]. Induction of antibodies recognizing a broad range of spike epitopes and eliciting strong and durable ADCC may partially explain why hybrid immunity provides superior protection against infection and disease than vaccination alone, and demonstrates that spike-only subunit vaccines would benefit from strategies to induce a combination of S1- and S2-specific antibody responses.SignificanceNeutralising antibodies prevent the entry of cell-free virus, however, antibodies that promote Fc-dependent activities such as ADCC are critical to control cell-associated virus. Although current SARS-CoV-2 vaccines induce potent neutralising antibodies, they fail to induce robust ADCC. Our demonstration that hybrid immunity induces superior ADCC with pan-variant activity may partially explain why hybrid immunity offers enhanced protection against reinfection. It also highlights that vaccine strategies based on expression of the spike subunit alone should not focus solely on inducing antibody responses targeting the receptor binding domain.
Identifying Fibrogenic Cells Following Salivary Gland Obstructive Injury
Authors: Altrieth Amber L. , O’Keefe Kevin J. , Gellatly Victoria A. , Tavarez Joey R. , Feminella Sage M. , Moskwa Nicholas L. , Cordi Carmalena V. , Turrieta Judy C. , Nelson Deirdre A. , Larsen Melinda 
Published: March 2023

AbstractFibrosis results from excess extracellular matrix accumulation, which alters normal tissue architecture and impedes function. In the salivary gland, fibrosis can be induced by irradiation treatment for cancer therapy, Sjögren’s Disease, and other causes; however, it is unclear which stromal cells and signals participate in injury responses and disease progression. As hedgehog signaling has been implicated in fibrosis of the salivary gland and other organs, we examined contributions of the hedgehog effector, Gli1, to fibrotic responses in salivary glands. To experimentally induce a fibrotic response in female murine submandibular salivary glands, we performed ductal ligation surgery. We detected a progressive fibrotic response where both extracellular matrix accumulation and actively remodeled collagen trended upwards at 7 days and significantly increased at 14 days post- ligation. Macrophages, which participate in extracellular matrix remodeling, Gli1+and PDGFRα+stromal cells, which may deposit extracellular matrix, both increased with injury. Using single-cell RNA-sequencing, we found that a majority ofGli1+cells at embryonic day 16 also expressPdgfraand/orPdgfrb.However, in adult mice, only a small subset of Gli1+cells express PDGFRα and/or PDGFRβ at the protein level. Using lineage-tracing mice, we found that Gli1-derived cells expand with ductal ligation injury. Although some of the Gli1 lineage-traced tdTomato+cells expressed vimentin and PDGFRβ following injury, there was no increase in the classic myofibroblast marker, smooth muscle alpha-actin. Additionally, there was little change in extracellular matrix area, remodeled collagen area, PDGFRα, PDGFRβ, endothelial cells, neurons, or macrophages in Gli1 null salivary glands following injury when compared with controls, suggesting that Gli1 signaling and Gli1+cells have only a minor contribution to mechanical injury-induced fibrotic changes in the salivary gland. We used scRNA-seq to examine cell populations that expand with ligation and/or showed increased expression of matrisome genes.Pdgfra+/Pdgfrb+stromal cell subpopulations both expanded in response to ligation, showed increased expression and a greater diversity of matrisome genes expressed, consistent with these cells being fibrogenic. Defining the signaling pathways driving fibrotic responses in stromal cell sub-types could reveal future therapeutic targets.
Hepatic Lipid Droplet-Associated Proteome Changes Distinguish Dietary-Induced Fatty Liver from Insulin Resistance in Male Mice
Authors: Woerkom Andries Van , Harney Dylan J , Nagarajan Shilpa R. , Hakeem-Sanni Mariam F. , Lin Jinfeng , Hooke Matthew , Pulpitel Tamara , Cooney Gregory J , Larance Mark , Saunders Darren N. , Brandon Amanda E , Hoy Andrew J. 
Published: March 2023

ABSTRACTFatty liver is characterised by the expansion of lipid droplets and is associated with the development of many metabolic diseases, including insulin resistance, dyslipidaemia and cardiovascular disease. We assessed the morphology of hepatic lipid droplets and performed quantitative proteomics in lean, glucose-tolerant mice compared to high-fat diet (HFD) fed mice that displayed hepatic steatosis and glucose intolerance as well as high-starch diet (HStD) fed mice who exhibited similar levels of hepatic steatosis but remained glucose tolerant. Both HFD and HStD-fed mice had more and larger lipid droplets than Chow-fed animals. We observed striking differences in liver lipid droplet proteomes of HFD and HStD-fed mice compared to Chow-fed mice, with fewer differences between HFD and HStD. Taking advantage of our diet strategy, we identified a fatty liver lipid droplet proteome consisting of proteins common in HFD- and HStD-fed mice. Likewise, a proteome associated with glucose tolerance that included proteins common in Chow and HStD but not HFD-fed mice was identified. Notably, glucose intolerance was associated with changes in the ratio of adipose triglyceride lipase (ATGL) to perilipin 5 (PLIN5) in the lipid droplet proteome, suggesting dysregulation of neutral lipid homeostasis in glucose-intolerant fatty liver, which supports bioactive lipid synthesis and impairs hepatic insulin action. We conclude that our novel dietary approach uncouples ectopic lipid burden from insulin resistance-associated changes in the hepatic lipid droplet proteome.
Inducible expression of the restriction enzyme uncovered genome-wide distribution and dynamic behavior of histones H4K16ac and H2A.Z at DNA double-strand breaks inArabidopsis
Authors: Kawaguchi Kohei , Kazama Mei , Hata Takayuki , Matsuo Mitsuhiro , Obokata Junichi , Satoh Soichirou 
Published: March 2023

AbstractDNA double-strand breaks (DSBs) are among the most serious types of DNA damage and cause mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, in mammals, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed. However, this DSB induction system is not suitable for investigating chromatin remodeling during and after DSB repair, and such approach has not been performed in plants. Here, we established a transgenicArabidopsisplant harboring a restriction enzyme geneSbfI driven by a heat-inducible promoter. Using this transgenic plant, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated dynamics of these histone marks around the endogenous 623SbfI recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by ChIP-seq procedures. From the results,SbfI-induced DSBs were detected at 360 loci and induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be a highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs inArabidopsis.
Flaviviruses alter endoplasmic reticulum-mitochondria contacts to regulate respiration and apoptosis
Authors: Freppel Wesley , Anton Anaïs , Nouhi Zaynab , Mazeaud Clément , Gilbert Claudia , Tremblay Nicolas , Torres Viviana Andrea Barragan , Sow Aïssatou Aïcha , Laulhé Xavier , Lamarre Alain , Rodrigue-Gervais Ian Gaël , Pichlmair Andreas , Scaturro Pietro , Hulea Laura , Chatel-Chaix Laurent 
Published: March 2023

ABSTRACTWith no therapeutics available, there is an urgent need to better understand the pathogenesis of flaviviruses which constitute a threat to public health worldwide. During infection, dengue virus (DENV) and Zika virus (ZIKV), two flaviviruses induce alterations of mitochondria morphology to favor viral replication, suggesting a viral co-opting of mitochondria functions. Here, we performed an extensive transmission electron microscopy-based quantitative analysis to demonstrate that both DENV and ZIKV alter endoplasmic reticulum-mitochondria contacts (ERMC). This correlated at the molecular level with an impairment of ERMC tethering protein complexes located at the surface of both organelles. Furthermore, virus infection, as well as NS4B expression modulated the mitochondrial oxygen consumption rate. Consistently, metabolomic and mitoproteomic analyses revealed a decrease in the abundance of several metabolites of the Krebs cycle and changes in the stoichiometry of the electron transport chain. Most importantly, ERMC destabilization by protein knockdown increased virus replication while dampening ZIKV-induced apoptosis. Overall, our results support the notion that flaviviruses hijack ERMCs to generate a cytoplasmic environment beneficial for sustained and efficient replication.
A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses
Authors: Elek Claire K. A. , Brown Teagan L. , Viet Thanh Le , Evans Rhiannon , Baker David J. , Telatin Andrea , Tiwari Sumeet K. , Al-Khanaq Haider , Thilliez Gaëtan , Kingsley Robert A. , Hall Lindsay J. , Webber Mark A. , Adriaenssens Evelien M. 
Published: March 2023

ABSTRACTBacteriophages (phages) within thePrzondovirusgenus are T7-like podoviruses belonging to theStudiervirinaesubfamily, within theAutographiviridaefamily and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targetingKlebsiellaspp. We describe HYPPA – aHYbrid andPoly-polishPhageAssembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.IMPACT STATEMENTThe current workflows employed for phage genome assembly are often error-prone and can lead to many incomplete phage genomes being deposited within databases. This can create challenges when performing comparative genomics, and may also lead to incorrect taxonomic assignment. To overcome these challenges we proposed HYPPA, a workflow that can produce complete and high-quality phage genomes without the need for laborious lab-based validation.DATA SUMMARYPhage raw reads are available from the National Centre for Biotechnology Information Sequence Read Archive (NCBI-SRA) under the BioProject number PRJNA914245. Phage annotated genomes have been deposited at GenBank under the accessionsOQ579023-OQ579032(Table 1). Bacterial WGS data for clinical preterm infant samples have been deposited at GenBank under BioProject accession PRJNA471164 (Table S1). Bacterial raw reads for food samples are available from NCBI-SRA with individual accessions (SAMN33593347-SAMN33593351), and can be found under the BioProject number PRJNA941224 (Table S1). Strain-specific details for bacteria and publicly-available phages used in these analyses, along with accessions for the latter can be found inTable S1andTable S6, respectively. The CL1-CL8 clinicalKlebsiellastrains (Table S1) were under a Materials Transfer Agreement, for which sequencing data and strain information is not available.
Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses
Authors: Maestri Renan , Perez-Lamarque Benoît , Zhukova Anna , Morlon Hélène 
Published: March 2023

AbstractSeveral coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversificationversusrecent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus–host codiversification have been largely over-estimated.
Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses
Authors: Park Seo-Young , Choi Dong-Hyuk , Song Jinsung , Park Uiseon , Cho Hyeran , Hong Bee Hak , Silberberg Yaron R. , Lee Dong-Yup 
Published: March 2023

ABSTRACTDesigning and selecting cell culture media and feed are a key strategy to maximize culture performance in industrial biopharmaceutical processes. However, this is a major challenge for therapeutic proteins production since mammalian cells are very sensitive to their culture environment and require specific nutritional needs to grow and produce high-quality proteins such as antibodies. In this regard, in our previous study, we developed data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design a new media formulation. To expand our exploration to feed, in this study, we evaluated two chemically defined feed media, A and B, in Ambr15 bioreactor runs using a monoclonal antibody-producing CHO K1 cell line. The feeds had a significant impact on cell growth, longevity, viability, and productivity and toxic metabolites production. Specifically, concentrated feed A was not sufficient to support prolonged cell culture and high titer compared to feed B. The framework systematically characterized the major metabolic bottlenecks in the TCA cycle and its related amino acid transferase reactions, and identified key design components, such as asparagine, aspartate, and glutamate, needed for highly productive cell cultures. From our results, we designed three new feeds by adjusting the levels of those amino acids and successfully validated their effectiveness in promoting cell growth and/or titer.
Self-assembly and contraction of micron-scale DNA rings
Authors: Illig Maja , Jahnke Kevin , Scheffold Marlene , Mersdorf Ulrike , Drechsler Hauke , Diez Stefan , Göpfrich Kerstin 
Published: March 2023

AbstractContractile rings formed from cytoskeletal filaments mediate the division of cells. The reverse-engineering of synthetic contractile rings could shed light on fundamental physical principles of the ring self-assembly and dynamics independent of the natural protein-based compounds. Here, we engineer DNA nanotubes and crosslink them with a synthetic peptide-functionalized star-PEG construct. The star-PEG construct induces the formation of DNA nanotube bundles composed of several tens of individual DNA nanotubes. Importantly, the DNA nanotube bundles curve into closed micron-scale DNA rings in a high-yield one-pot self-assembly process resulting in several thousand rings per microliter. The crosslinked DNA rings can undergo contraction to less than half of their initial diameter by two distinct mechanisms, triggered by increasing molecular crowding or temperature. DNA-based contractile rings expand the toolbox of DNA nanotechnology and could be a future element of an artificial division machinery in synthetic cells.
Melanin concentrating hormone and orexin shape social affective behavior via action in the insular cortex of rat
Authors: Barretto-de-Souza Lucas , Joseph Shemar A. , Lynch Francesca M. , Ng Alexandra J. , Chrsitianson John P. 
Published: March 2023

ABSTRACTRationaleIn a social context, individuals are able to detect external information from others and coordinate behavioral responses according to the situation, a phenomenon called social decision-making. Social decision-making is multifaceted, influenced by emotional and motivational factors like stress, sickness and hunger. However, the neurobiological basis for motivational state competition and interaction are not well known.ObjectiveWe investigated possible neural mechanisms through which internal states could shape social behavior in a social affective preference (SAP) test. In the SAP test, experimental rats given a choice to interact with naïve or stressed conspecifics exhibit an age-dependent preference to interact with stressed juvenile conspecifics, but avoid stressed adult conspecifics. First, we assessed the effect of hunger on SAP behavior. Behavior in the SAP test requires the insular cortex, which receives input from the hunger-related peptides melanin-concentrating hormone (MCH) and orexin neurons of the lateral hypothalamus (LH). This study aimed to evaluate the role of LH and insular MCH and orexin in SAP test.MethodsSAP tests were conducted in rats that were sated, food deprived or allowed 1 h of access to food after 14 h of deprivation (relieved condition). Separate cohorts of sated rats received cannula implants for microinjection of drugs to inhibit the LH or to block or stimulate MCH or orexin receptors in the insula prior to SAP tests or social interaction tests.ResultsFood and water deprivation prior to SAP tests with juvenile rats caused a shift in preference away from the stressed rat toward the naïve juveniles. Pharmacological inhibition of LH with muscimol (100 ng/side) abolished the preference for the juvenile stressed conspecific, as well as the preference for the adult naïve conspecific. The blockade of MCHr1 or orexin receptors in the insular cortex with SNAP94847 (50µM) or TCS1102 (1µM), respectively, also abolished the preference for the stressed juvenile conspecific, but only the antagonism of orexin receptors was able to abolish the preference for the adult naïve conspecific. Microinjection of increasing doses (50 or 500 nM) of MCH or orexin-A in the insular cortex increased the interaction time in the one-on-one social interactions test with juvenile conspecifics, however only the microinjection of orexin-A increased the interaction time with adult naïve conspecifics.ConclusionsTaken together, these results suggest that lateral hypothalamus peptides shape the direction of social approach or avoidance via actions MCH and orexin neurotransmission in the insular cortex.
A rapid and sensitive multiplex, whole mount RNA fluorescencein situhybridization and immunohistochemistry protocol
Authors: Huang Tian , Guillotin Bruno , Rahni Ramin , Birnbaum Ken , Wagner Doris 
Published: March 2023

AbstractIn the past few years, there has been an explosion in single-cell transcriptomics datasets, yetin vivoconfirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescencein situhybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.