bluuebunny/crossref_metadata_2025_split huggingface dataset:
FreiBox: A versatile open-source behavioral setup for investigating the neuronal correlates of behavioral flexibility via 1-photon imaging in freely moving mice
Authors: Crompe Brice De La , Schneck Megan , Steenbergen Florian , Schneider Artur , Diester Ilka 
Published: November 2022

AbstractTo survive in a complex and changing environment, animals must adapt their behavior. This ability is called behavioral flexibility and is classically evaluated by a reversal learning paradigm. During such a paradigm, the animals adapt their behavior according to a change of the reward contingencies. To study these complex cognitive functions (from outcome evaluation to motor adaptation), we developed a versatile, low-cost, open-source platform, allowing us to investigate the neuronal correlates of behavioral flexibility with 1-photon calcium imaging. This platform consists of FreiBox, a novel low-cost Arduino behavioral setup, as well as further open-source tools which we developed and integrated into our framework. FreiBox is controlled by a custom Python interface and integrates a new licking sensor (Strain Gauge lickometer) for controlling spatial licking behavioral tasks. In addition to allowing both discriminative and serial reversal learning, the Arduino can track mouse licking behavior in real time to control task events in a sub-millisecond timescale. To complete our setup, we also developed and validated an affordable commutator, crucial for recording calcium imaging with the Miniscope V4 in freely moving mice. Further, we demonstrated that FreiBox can be associated with 1-photon imaging and other open-source initiatives (e.g., Open Ephys), to form a versatile platform for exploring the neuronal substrates of licking based behavioral flexibility in mice. The combination of the FreiBox behavioral setup and our low-cost commutator represents a highly competitive and complementary addition to the recently emerging battery of open-source initiatives.Significance StatementBehavioral flexibility is essential to survive in a complex and changing environment. To study this cognitive ability in freely-moving mice, we developed a versatile, low-cost, open-source behavioral setup, called FreiBox, allowing us to investigate the neuronal correlates of licking-based behavioral flexibility. FreiBox is controlled by a custom Python interface and integrates a new licking sensor for controlling spatial licking behavioral tasks (e.g. discriminative learning, reversal learning). We also developed and validated an active commutator to record calcium imaging with the Miniscope V4 in freely moving mice. Finally, we demonstrated that FreiBox can be associated with 1-photon imaging and other open-source initiatives, to form a versatile platform for exploring the neuronal substrates of licking based behavioral flexibility in mice.
Replication-induced DNA secondary structures drive fork uncoupling and breakage
Authors: Williams Sophie L. , Casas-Delucchi Corella S. , Raguseo Federica , Guneri Dilek , Li Yunxuan , Minamino Masashi , Fletcher Emma Elisabeth , Yeeles Joseph T. P. , Keyser Ulrich F. , Waller Zoë A. E. , Antonio Marco Di , Coster Gideon 
Published: November 2022

AbstractSequences that can form DNA secondary structures, such as G-quadruplexes (G4s) and intercalated-Motifs (iMs), are abundant in the human genome and play a range of physiological roles. However, they can also pose a challenge to the replication machinery and in turn threaten genome stability. Multiple lines of evidence suggest G4s interfere with replication, but the underlying mechanism remains unclear. Moreover, there is a lack of evidence of how iMs affect the replisome. Here, we reconstitute replication of physiologically derived structure-forming sequences to find that a single G4 or iM is sufficient to arrest DNA replication. Direct single molecule structure detection within solid-state nanopores reveals structures form as a consequence of replication. A combination of genetic and biophysical characterisation establishes that structure forming capacity is a key determinant of replisome arrest. Mechanistically, replication fork arrest is caused by impaired synthesis, resulting in helicase-polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Sgs1 or Chl1. Altogether, this study provides a potential mechanism for quadruplex structure formation and resolution during replication and highlights G4s and iMs as endogenous sources of replication stress, which may explain their genomic instability and mutation frequencies in cancer.
Voltage-gated sodium channel activity mediates sea urchin larval skeletal patterning through spatial regulation of Wnt5 expression
Authors: Thomas Christopher F. , Hawkins Dakota Y. , Skidanova Viktoriya , Marrujo Simone R. , Gibson Janay , Ye Ziqing , Bradham Cynthia A. 
Published: November 2022

AbstractDefining pattern formation mechanisms during embryonic development is important for understanding the etiology of birth defects and to inform tissue engineering approaches. In this study, we used tricaine, a voltage-gated sodium channel (VGSC) inhibitor, to show that VGSC activity is required for normal skeletal patterning inLytechinus variegatussea urchin larvae. We demonstrate that tricaine-mediated patterning defects are rescued by an anesthetic-insensitive version of the VGSC LvScn5a. Expression of this channel is enriched in the ventrolateral ectoderm where it spatially overlaps with posterolaterally expressed Wnt5. We show that VGSC activity is required to spatially restrict Wnt5 expression to this ectodermal region that is adjacent and instructive to clusters of primary mesenchymal cells that initiate secretion of the larval skeleton as triradiates. Tricaine-mediated Wnt5 spatial expansion correlates with the formation of ectopic PMC clusters and triradiates. These defects are rescued by Wnt5 knock down, indicating that the spatial expansion Wnt5 is responsible for the patterning defects induced by VGSC inhibition. These results demonstrate a novel connection between bioelectrical status and the spatial control of patterning cue expression during embryonic pattern formation.Summary statementInhibition of voltage-gated sodium channels perturbs Wnt5-mediated patterning of the sea urchin larval skeleton
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in IAV from North American swine
Authors: Hufnagel David E. , Young Katharine M. , Arendsee Zebulun , Gay L. Claire , Caceres C. Joaquin , Rajão Daniela S. , Perez Daniel R. , Vincent Baker Amy L. , Anderson Tavis K. 
Published: November 2022

ABSTRACTInfluenza A viruses (IAV) of the H1N1 classical swine lineage became endemic in North American swine following the 1918 pandemic. Additional human-to-swine transmission events after 1918, and a spillover of H1 viruses from wild birds in Europe, potentiated a rapid increase in genomic diversity via reassortment between introductions and the endemic classical swine lineage. To determine mechanisms affecting reassortment and evolution, we conducted a phylogenetic analysis of N1 and paired HA swine IAV genes in North America between 1930 and 2020. We described fourteen N1 clades within the N1 Eurasian avian lineage (including the N1 pandemic clade) and the N1 classical swine lineage. Seven N1 genetic clades had evidence for contemporary circulation. To assess antigenic drift associated with N1 genetic diversity, we generated a panel of representative swine N1 antisera and quantified the antigenic distance between wild-type viruses using enzyme-linked lectin assays and antigenic cartography. Within the N1 lineage, antigenic similarity was variable and reflected shared evolutionary history. Sustained circulation and evolution of N1 genes in swine had resulted in significant antigenic distance between the N1 pandemic clade and classical swine lineage. We also observed a significant increase in the rate of evolution in the N1 pandemic clade relative to the classical lineage. Between 2010 and 2020, N1 clades and N1-HA pairings fluctuated in detection frequency across North America, with hotspots of diversity generally appearing and disappearing within two years. We also identified frequent N1-HA reassortment events (n = 36), which were rarely sustained (n = 6) and sometimes also concomitant with the emergence of new N1 genetic clades (n = 3). These data form a baseline from which we can identify N1 clades that expand in range or genetic diversity that may impact viral phenotypes or vaccine immunity and subsequently the health of North American swine.
A single-cell trajectory atlas of striatal development
Authors: Anderson Ashley G. , Kulkarni Ashwinikumar , Konopka Genevieve 
Published: November 2022

AbstractThe striatum integrates dense neuromodulatory inputs from many brain regions to coordinate complex behaviors. This integration relies on the coordinated responses from distinct striatal cell types. While previous studies have characterized the cellular and molecular composition of the striatum using single-cell RNA-sequencing at distinct developmental timepoints, the molecular changes spanning embryonic through postnatal development at the single-cell level have not been examined. Here, we combine published mouse striatal single-cell datasets from both embryonic and postnatal timepoints to analyze the developmental trajectory patterns and transcription factor regulatory networks within striatal cell types. Using this integrated dataset, we found that dopamine receptor-1 expressing spiny projection neurons have an extended period of postnatal development with greater transcriptional complexity compared to dopamine receptor-2 expressing neurons. Moreover, we found the transcription factor, FOXP1, exerts indirect changes to oligodendrocytes. These data can be accessed and further analyzed through an interactive website (https://cells-test.gi.ucsc.edu/?ds=mouse-striatal-dev).
Antagonism between viral infection and innate immunity at the single-cell level
Authors: Grabowski Frederic , Kochańczyk Marek , Korwek Zbigniew , Czerkies Maciej , Prus Wiktor , Lipniacki Tomasz 
Published: November 2022

AbstractWhen infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.
A new view on functions of the lysine demalonylase activity of SIRT5
Authors: Nahálková Jarmila 
Published: November 2022

AbstractA substrate specificity of the pharmaceutically attractive tumor-promoter SIRT5 was already investigated multiple times by advanced proteomic tools. However, the present bioinformatic analysis brings new highlights to the knowledge about the lysine demalonylation activity of SIRT5, a member of the sirtuin family with multiple roles in aging and age-related diseases. It shows unreported functional aspects of the lysine demalonylated substrates in Eukaryotic translation elongation (ETE), Amino acid and derivative metabolism (AADM), and Selenoamino acid metabolism (SAM). The cluster of the elongation factors (EEF1A1, EEF2, EEF1D, and EEF1G) belonging to ETE participates in the peptide chain elongation and the export of the tRNA-s from the nucleus to the primary sites of the proteosynthesis. SIRT5 regulates the activity of the key enzymes with tumor-promoting functions involved in AADM (GLUD1, SHMT1, ACAT1). In contrast, SIRT5 also lysine demalonylates tumor suppressor substrates as a part of the AADM and SAM interaction networks (ALDH9A1, BHMT, GNMT). It indicates comparable functions like SIRT3, which has dual tumor promoter/oncogene functions. Similar to the roles of the sirtuins, the SAM pathway impacts longevity, protects against cardiovascular diseases, and is associated with hepatic steatosis. The selen supplementation mediates the calorie restriction effect, which increases the NAD+/NADH ratio in the cells and stimulates the expression of SIRT5 and other sirtuins. SIRT5 in turn regulates the selenocysteine synthesis through the lysine demalonylation of the participating ribosomal proteins, SECISBP2 and GNMT, which creates a regulatory loop.
Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits
Authors: Grove Daisy J. , Levine Daniel J. , Kearse Michael G. 
Published: November 2022

ABSTRACTeIF2A was the first eukaryotic initiator tRNA carrier discovered but its exact function has remained enigmatic. Uncharacteristic of translation initiation factors, eIF2A is reported to be non-cytosolic in multiple human cancer cell lines. Attempts to study eIF2A mechanistically have been limited by the inability to achieve high yield of soluble recombinant protein. Here, we developed a purification paradigm that yields ∼360-fold and ∼6,000-fold more recombinant human eIF2A fromE. coliand insect cells, respectively, than previous reports. Using a mammalianin vitrotranslation system, we found that increased levels of recombinant human eIF2A inhibit translation of multiple reporter mRNAs, including those that are translated by cognate and near-cognate start codons, and does so prior to start codon recognition. eIF2A also inhibited translation directed by all four types of cap-independent viral IRESs, including the CrPV IGR IRES that does not require initiation factors or initiator tRNA, suggesting excess eIF2A sequesters 40S subunits. Supplementation with additional 40S subunits prevented eIF2A-mediated inhibition and pull-down assays demonstrated direct binding between recombinant eIF2A and purified 40S subunits. These data support a model that eIF2A must be kept away from the translation machinery to avoid sequestering 40S ribosomal subunits.
Recombinant expression and characterisation of a lipase from the Antarctic zooplanktonSalpa thompsoni
Authors: Rayani Ekta , Cotton Alexander , Roberts Iwan , Ward John , Goodall-Copestake Will , Parker Brenda 
Published: November 2022

AbstractCold marine environments are abundant on earth and represent a rich resource for low temperature enzymes. Here we applyin silicobioprospecting methods followed byin vitroexpression and biochemical analyses to characterise a novel low temperature lipase from the Antarctic tunicateSalpa thompsoni. A 586 amino acid pancreatic lipase-like gene was identified fromS. thompsonitranscriptomic data, expressed as a hexahistadine fusion protein inEscherichia coliat 10°C and purified by affinity chromatography. Hydrolysis of the synthetic substrate ρ-nitrophenyl butyrate (PNPB) showed that this recombinant protein has optimal activity at 20 °C and pH 7, and a specific activity of 3.16 U/mg under this condition. Over 60% of enzyme activity was maintained between 15 to 25 °C, with a sharp decrease outside this range. These results are indicative of cold active psychrophilic enzyme activity. A meta-analysis of lipase activities towards PNPB showed that the novelS. thompsonilipase displays a higher activity at lower temperatures relative to previously characterised enzymes. The work demonstrates a methodology for conversion of transcriptomic toin vitroexpression data for the discovery of new cold-active biocatalysts from marine organisms.
Low-level repressive histone marks fine-tune stemness gene transcription in neural stem cells
Authors: Rajan Arjun , Anhezini Lucas , Rives-Quinto Noemi , Neville Megan C. , Larson Elizabeth D. , Goodwin Stephen F. , Harrison Melissa M. , Lee Cheng-Yu 
Published: November 2022

AbstractCoordinated regulation of stemness gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of stemness gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC(FruC) bindscis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss offruCfunction alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruCnegatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in genecis-regulatory regions. Identical tofruCloss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes stemness gene transcription in stem cells, a mechanism likely conserved from flies to humans.
PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance
Authors: Wong Chun Wai , Evangelou Christos , Sefton Kieran N. , Leshem Rotem , Sergiou Kleita , Carro Macarena Lucia Fernandez , Uzuner Erez , Mole Holly , Telfer Brian A. , Wilcock Daniel J. , Smith Michael P. , Kunii Kaiko , Perl Nicholas R. , Lorigan Paul , Williams Kaye J. , Rao Patricia E. , Nagaraju Raghavendar T. , Niepel Mario , Hurlstone Adam F.L. 
Published: November 2022

AbstractAdaptive resistance limits immune checkpoint blockade therapy (ICBT) response duration and magnitude. Interferon γ (IFNγ), a critical cytokine that promotes cellular immunity, also induces adaptive resistance to ICBT. Using syngeneic mouse tumour models, we confirmed that chronic IFNγ exposure confers resistance to anti-Programmed cell death protein 1 (α-PD-1) therapy. We identified consistent upregulation of poly-ADP ribosyl polymerase 14 (PARP14) in both chronic IFNγ-treated cancer cells and patient melanoma with elevatedIFNGexpression. Knockdown or pharmacological inhibition of PARP14 increased effector T cell infiltration into tumours derived from cells pre-treated with IFNγ and decreased the presence of regulatory T cells, leading to restoration of α-PD-1 sensitivity. Finally, we determined that tumours which spontaneously relapsed following α-PD-1 therapy could be re-sensitised upon receiving PARP14 inhibitor treatment, establishing PARP14 as an actionable target to reverse IFNγ-driven ICBT resistance.
Tracing the origin of pathologic pulmonary fibroblasts
Authors: Tsukui Tatsuya , Sheppard Dean 
Published: November 2022

AbstractFibroblasts substantially remodel extracellular matrix (ECM) in response to tissue injury and generate fibrotic scars in chronic diseases. Recent studies have identified diverse fibroblast subsets in healthy and injured tissues. However, the origin(s) and functional importance of injury-induced fibroblast lineages remain unclear. Here we show that alveolar fibroblasts, which provide a niche for maintaining alveolar type 2 cells in uninjured lungs, are the dominant source of multiple emergent fibroblast subsets that sequentially arise to facilitate fibrosis after lung injury. We demonstrate that Cthrc1+ fibroblasts, which express the highest levels of ECM proteins at injured sites, are effector cells for fibrogenesis using a novel mouse tool, Cthrc1-CreER. We use another novel mouse tool, Scube2-CreER, that uniquely targets alveolar fibroblasts, to reveal that alveolar fibroblasts are the dominant origin for multiple fibroblast subsets that emerge after lung injury. Pseudotime and in vitro analysis suggest that inflammatory cytokines initially induce chemokine-producing inflammatory fibroblasts from alveolar fibroblasts, which can differentiate into Cthrc1+ fibrotic fibroblasts in response to TGF-β. We identify similar fibroblast lineages from scRNA-seq in human pulmonary fibrosis. These results elucidate the pathologic fibroblast lineage development in response to lung injury and suggest that targeting key steps in transitions among these subsets could provide novel strategies for the treatment of fibrotic diseases.
Neutralizing antibodies to Omicron after the fourth SARS-CoV-2 mRNA vaccine dose in immunocompromised patients highlight the need of additional boosters
Authors: Rescigno Maria , Agrati Chiara , Salvarani Carlo , Giannarelli Diana , Costantini Massimo , Mantovani Alberto , Massafra Raffaella , Zinzani Pier Luigi , Morrone Aldo , Notari Stefania , Matusali Giulia , Pinter Giuseppe Lauria , Uccelli Antonio , Ciliberto Gennaro , Baldanti Fausto , Locatelli Franco , Silvestris Nicola , Sinno Valentina , Turola Elena ,   VAX4FRAIL study Group,   Maria Teresa Lupo Stanghellini, Apolone Giovanni 
Published: November 2022

AbstractImmunocompromised patients have been shown to have an impaired immune response to COVID-19 vaccines. Here we compared the B-cell, T-cell and neutralizing antibody response to WT and Omicron BA.2 SARS-CoV-2 virus after the fourth dose of mRNA COVID-19 vaccines in patients with hematological malignancies (HM, n=71), solid tumors (ST, n=39) and immune-rheumatological (ID, n=25) diseases. We show that the T-cell response is similarly boosted by the fourth dose across the different subgroups, while the antibody response is improved only in patients not receiving B-cell targeted therapies, independent on the pathology. However, 9% of patients with anti-RBD antibodies did not have neutralizing antibodies to both virus variants, while an additional 5.7% did not have neutralizing antibodies to Omicron BA.2, making these patients particularly vulnerable to SARS-CoV-2 infection. The increment of neutralizing antibodies was very similar towards Omicron BA.2 and WT virus after the third or fourth dose of vaccine, suggesting that there is no preferential skewing towards either virus variant with the booster dose. The only limited step is the amount of antibodies that are elicited after vaccination, thus increasing the probability of developing neutralizing antibodies to both variants of virus. Hence, additional booster doses are recommended to frail patients.