bluuebunny/crossref_metadata_2025_split huggingface dataset:
E6AP is important for HPV E6’s role in regulating epithelial homeostasis and its loss impairs keratinocyte commitment to differentiation
Authors: Yin Wen , Egawa Nagayasu , Zheng Ke , Griffin Heather , Aiyenuro Ademola , Bornstein Jacob , Doorbar John 
Published: June 2022

AbstractHuman papillomaviruses (HPV) typically cause chronic infections by modulating homeostasis of infected basal cell to ensure persistence. Using FUCCI and cell-cell competition assays, we established the role of two common viral targets of low-risk and high-risk E6 proteins, E6AP and NHERF1, on four key components of epithelial homeostasis. These includes cell density, proliferation, commitment to differentiation and basal layer delamination. Our RNA sequencing results validated E6’s effects on homeostasis and revealed similar transcriptional gene regulation of E6-expressing cells and E6AP-/- cells. For example, yes-associated protein (YAP) target genes were up-regulated by either E6 expression or E6AP depletion. This is also supported by YAP expression pattern in both monolayer cell culture and HPV-infected clinical tissues. As the conserved binding partner of Alpha group HPV E6 proteins, the precise role of E6AP in modulating keratinocyte phenotype and associated signalling pathways have not been defined. We demonstrate that deletion of E6AP in keratinocytes delayed the onset of differentiation and the abundance of E6AP is reduced in HPV-infected tissue. This suggests that Alpha E6 regulates epithelium homeostasis by inhibiting E6AP’s activity, leading to alteration of multiple downstream pathways including YAP activation. Potential treatments can thus be developed to resolve the reservoir of HPV infection.
Sampling from commercial vessel routes can capture marine biodiversity distributions effectively
Authors: Boyse Elizabeth , Beger Maria , Valsecchi Elena , Goodman Simon 
Published: June 2022

AbstractCollecting fine-scale occurrence data for marine species across large spatial scales is logistically challenging, but is important to determine species distributions and for conservation planning. Inaccurate descriptions of species ranges could result in designating protected areas with inappropriate locations or boundaries. Optimising sampling strategies therefore is a priority for scaling up survey approaches using tools such as environmental DNA (eDNA) to capture species distributions. eDNA can detect diverse taxa simultaneously, but to date has rarely been applied across large spatial scales relevant for conservation planning. In a marine context, commercial vessels, such as ferries, could provide sampling platforms allowing access to under-sampled areas and repeatable sampling over time to track community changes. However, sample collection from commercial vessels could be biased and may not represent biological and environmental variability. Here, we evaluate whether sampling along Mediterranean ferry routes can yield unbiased biodiversity survey outcomes, based on perfect knowledge from a stacked species distribution model (SSDM) of marine megafauna. Simulations were carried out representing different sampling strategies (random vs systematic), frames (ferry routes vs unconstrained) and number of sampling points. SSDMs were remade from different sampling simulations and compared to the ‘perfect knowledge’ SSDM to quantify the bias associated with different sampling strategies. Ferry routes detected more species and were able to recover known patterns in species richness at smaller sample sizes better than unconstrained sampling points. However, to minimise potential bias, ferry routes should be chosen to cover the variability in species composition and its environmental predictors in the SSDMs. The workflow presented here can be used to design effective eDNA sampling strategies using commercial vessel routes globally. This approach has potential to provide a cost-effective method to access remote oceanic areas on a regular basis, and can recover meaningful data on spatiotemporal biodiversity patterns.
Using canavanine resistance to measure mutation rates in Schizosaccharomyces pombe
Authors: Pai Chen-Chun , Heitzer Ellen , Bertrand Sibyl , Toumazou Sophia , Humphrey Timothy C. , Kearsey Stephen E. 
Published: June 2022

AbstractWe constructed a panel of S. pombe strains expressing DNA polymerase ε variants associated with cancer, specifically POLES297F, POLEV411L, POLEL424V, POLES4459F and used these to compare mutation rates determined by canavanine resistance with other selective methods. Canavanine-resistance mutation rates are broadly similar to those seen with reversion of the ade-485 mutation to adenine prototrophy, but lower than 5-fluoroorotic acid (FOA)-resistance rates (inactivation of ura4+ or ura5+ genes). Inactivation of several genes has been associated with canavanine-resistance in S. pombe but surprisingly whole genome sequencing showed that 8/8 spontaneous canavanine-resistance mutants have an R175C mutation in the any1/arn1 gene. This gene encodes a β-arrestin-like protein involved in mediating Pub1 ubiquitylation of target proteins, and the phenotypic resistance to canavanine by this single mutation is similar to that shown by the original “can1-1” strain, which also has the any1R175C mutation. Some of the spontaneous mutants have additional mutations in arginine transporters, suggesting that this may marginally increase resistance to canavanine. The any1R175C strain showed internalisation of the Cat1 arginine transporter, explaining the canavanine-resistance phenotype. In addition, any1R175C cells were elongated compared to wild type. The mitotic activator Cdc25 has been identified as a Pub1 ubiquitylation target, and since Wee1 inhibition of Cdc2 is counteracted by Cdc25, it is likely that Cdc25 ubiquitylation and downregulation by Any1R175C-Pub1 delays mitotic entry
Phenotypic screening of the ReFrame Drug Repurposing Library to discover new drugs for treating sickle cell disease
Authors: Metaferia Belhu , Cellmer Troy , Dunkelberger Emily B. , Li Quan , Henry Eric R. , Hofrichter James , Staton Dwayne , Hsieh Matthew M. , Conrey Anna K. , Tisdale John F. , Chatterjee Arnab K. , Thein Swee Lay , Eaton William A. 
Published: June 2022

AbstractStem-cell transplantation and genetic therapies offer potential cures for patients with sickle cell disease (SCD) but these options require advanced medical facilities and are expensive. Consequently, these treatments will not be available to the vast majority of patients suffering from this disease for many years. What is urgently needed now is an inexpensive oral drug in addition to hydroxyurea, the only successful drug approved by the FDA that inhibits sickle-hemoglobin polymerization. Here we report results of the first phase of our phenotypic screen of the 12,657 compounds of the Scripps ReFrame drug repurposing library using a recently developed high-throughput assay to measure sickling times following deoxygenation to 0% oxygen of red cells from sickle trait individuals. The ReFrame library is a very important collection because the compounds are either FDA-approved drugs or have been tested in clinical trials. From dose-response measurements, 106 of the 12,657 compounds exhibit statistically significant anti-sickling at concentrations ranging from 31 nM to 10 μM. Compounds that inhibit sickling of trait cells are also effective with SCD cells. As many as 21 of the 106 anti-sickling compounds emerge as potential drugs. This estimate is based on a comparison of inhibitory concentrations with free concentrations of oral drugs in human serum. Moreover, the expected therapeutic effect for each level of inhibition can be predicted from measurements of sickling times for cells from individuals with sickle-syndromes of varying severity. Our results should motivate others to develop one or more of these 106 compounds into drugs for treating SCD.Significance StatementThe vast majority of patients suffering from sickle cell disease live in under-resourced countries. Consequently, advanced medical facilities required for curative therapies, such as stem cell transplantation and gene therapy, will be unavailable to them for a long time. Hydroxyurea, approved by the FDA in 1998, is the only effective drug that inhibits polymerization of the mutant hemoglobin S that stiffens and distorts (“sickles”) red cells, the root cause of the pathology. What is urgently needed now for these patients are additional, inexpensive oral anti-sickling drugs. Our high throughput phenotypic screen of the ReFrame drug repurposing library reported here discovered 106 compounds that are anti-sickling. On a statistical concentration basis, as many as 21 are predicted to be potential drugs.
Novel populations of CD4+T cells associated with vaccine efficacy
Authors: Woodring Therese , Dewey Colin N. , Dos Santos Dias Lucas , He Xin , Dobson Hannah E. , Wüthrich Marcel , Klein Bruce 
Published: June 2022

ABSTRACTMemory T cells underpin vaccine-induced immunity but are not yet fully understood. To distinguish features of memory cells that confer protective immunity, we used single cell transcriptome analysis to compare antigen-specific CD4+T cells recalled to lungs of mice that received a protective or nonprotective subunit vaccine followed by challenge with a fungal pathogen. We unexpectedly found populations specific to protection that expressed a strong type I interferon response signature, whose distinctive transcriptional signature appeared unconventionally dependent on IFN-γ receptor. We also detected a unique population enriched in protection that highly expressed the gene for the natural killer cell marker NKG7. Lastly, we detected differences in TCR gene use and in Th1- and Th17-skewed responses after protective and nonprotective vaccine, respectively, reflecting heterogeneousIfng- andIl17a-expressing populations. Our findings highlight key features of transcriptionally diverse and distinctive antigen-specific T cells associated with protective vaccine-induced immunity.
High content image analysis in routine diagnostic histopathology predicts outcomes in HPV-associated oropharyngeal squamous cell carcinomas
Authors: Hue Jonas , Valinciute Zaneta , Thavaraj Selvam , Veschini Lorenzo 
Published: June 2022

AbstractObjectiveRoutine haematoxylin and eosin (H&E) photomicrographs from human papillomavirus-associated oropharyngeal squamous cell carcinomas (HPV+OpSCC) contain a wealth of prognostic information. In this study, we set out to develop a high content image analysis workflow to quantify features of H&E images from HPV+OpSCC patients to identify prognostic features which can be used for prediction of patient outcomes.MethodsWe have developed a dedicated image analysis workflow using open-source software, for single-cell segmentation and classification. This workflow was applied to a set of 567 images from diagnostic H&E slides in a retrospective cohort of HPV+OpSCC patients with favourable (n = 29) and unfavourable (n = 29) outcomes. Using our method, we have identified 31 quantitative prognostic features which were quantified in each sample and used to train a neural network model to predict patient outcomes. The model was validated by k-fold cross-validation using 10 folds and a test set.ResultsUnivariate and multivariate statistical analyses revealed significant differences between the two patient outcome groups in 31 and 16 variables respectively (P<0.05). The neural network model had an overall accuracy of 78.8% and 77.7% in recognising favourable and unfavourable prognosis patients when applied to the test set and k-fold cross-validation respectively.ConclusionOur open-source H&E analysis workflow and model can predict HPV+OpSCC outcomes with promising accuracy. Our work supports the use of machine learning in digital pathology to exploit clinically relevant features in routine diagnostic pathology without additional biomarkers.
Comparative transcriptomic analysis of whole blood mycobacterial growth assays and tuberculosis patients’ blood RNA profiles
Authors: Bachanová Petra , Cheyne Ashleigh , Broderick Claire , Newton Sandra M. , Levin Michael , Kaforou Myrsini 
Published: June 2022

AbstractIn vitro whole blood infection models are used for elucidating the immune response to Mycobacterium tuberculosis (Mtb). They exhibit commonalities but also differences, to the in vivo blood transcriptional response during natural human Mtb disease. Here, we present a description of concordant and discordant components of the immune response in blood, quantified through transcriptional profiling in an in vitro whole blood infection model compared to whole blood from patients with tuberculosis disease. We identified concordantly and discordantly expressed gene modules and performed in silico cell deconvolution. A high degree of concordance of gene expression between both adult and paediatric in vivo-in vitro tuberculosis infection was identified. Concordance in paediatric in vivo vs in vitro comparison is largely characterised by immune suppression, while in adults the comparison is marked by concordant immune activation, particularly that of inflammation, chemokine, and interferon signalling. Discordance between in vitro and in vivo increases over time and is driven by T-cell regulation and monocyte-related gene expression, likely due to apoptotic depletion of monocytes and increasing relative fraction of longer-lived cell types, such as T and B cells. Our approach facilitates a more informed use of the whole blood in vitro model, while also accounting for its limitations.
A potential marker for problematic mother-infant bonding revealed by magnetoencephalography study of first-time mothers listening to infant cries
Authors: Hoegholt N.F , Bonetti L. , Stevner A.B.A. , Andersen C.E. , Hughes M , Fernandes H.M. , Vuust P. , Kringelbach M.L 
Published: June 2022

ABSTRACTStudies using magnetoencephalography (MEG) have identified the orbitofrontal cortex (OFC) to be an important early hub for a ‘parental instinct’ in the brain. This complements the finding from functional magnetic resonance imaging (fMRI) studies linking reward, emotion regulation, empathy and mentalisation networks to the ‘parental brain’. Here, we used MEG in 43 first-time mothers listening to infant and adult cry vocalisations to investigate the link with mother-infant postpartum bonding scores and their level of sleep deprivation (assessed using both actigraphy and sleep logs). We found significant differences 800-1000ms after onset of infant compared to adult cries in source-reconstructed brain activity in areas previously linked to the parental brain. Importantly, mothers with weaker bonding scores showed decreased brain responses to infant cries in the auditory cortex, middle and superior temporal gyrus, OFC, hippocampal areas, supramarginal gyrus and inferior frontal gyrus at around 100-200ms after stimulus onset. In contrast, we did not find correlations with sleep deprivation scores. The significant changes in brain processing of an infant’s distress signals could be a novel marker of weaker infant bonding in new mothers and should be investigated in vulnerable populations.
Cell-Type-Specific Epigenetic Priming of Gene Expression in Nucleus Accumbens by Cocaine
Authors: Mews Philipp , Van der Zee Yentl , Kronman Hope , Gurung Ashik , Ramakrishnan Aarthi , Browne Caleb , Futamura Rita , Estill Molly , Ryan Meagan , Reyes Abner A , Garcia Benjamin A , Sidoli Simone , Shen Li , Nestler Eric J 
Published: June 2022

ABSTRACTA hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe a novel epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled to increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relates to aberrant gene expression upon drug relapse. The histone chaperone ANP32E removes H2A.Z from chromatin, and we demonstrate that D1 MSN-selective Anp32e knockdown prevents cocaine-induced H2A.Z depletion and blocks cocaine’s rewarding actions. By contrast, very different effects of cocaine exposure, withdrawal, and relapse were found for D2-MSNs. These findings establish histone variant exchange as an important mechanism and clinical target engaged by drugs of abuse to corrupt brain function and behavior.
Hepatocyte Rap1a Contributes To Obesity- and Statin-Associated Hyperglycemia
Authors: Wang Yating , Spolitu Stefano , Zadroga John A. , Sarecha Amesh K. , Ozcan Lale 
Published: June 2022

SUMMARYExcessive hepatic glucose production contributes to the development of hyperglycemia and is a key feature of type 2 diabetes. Here, we report that activation of hepatic Rap1a suppresses gluconeogenic gene expression and glucose production, whereas Rap1a silencing stimulates them. Rap1a activation is suppressed in obese mouse liver and restoring its activity lowers blood glucose and improves glucose intolerance. As Rap1a’s membrane localization and activation depends on its geranylgeranylation, which is inhibited by statins, we found lower active-Rap1a levels in statin-treated hepatocytes and the human liver. Similar to Rap1a inhibition, statins stimulated hepatic gluconeogenesis and increased fasting blood glucose in obese mice. Geranylgeraniol treatment, which acts as the precursor for geranylgeranyl isoprenoids, restored Rap1a activity and improved statin-mediated glucose intolerance. Mechanistically, we show that Rap1a activation induces actin polymerization, which suppresses gluconeogenesis by Akt-mediated FoxO1 inhibition. Thus, Rap1a regulates hepatic glucose homeostasis, and blocking its activity, via lowering geranylgeranyl isoprenoids, contributes to statin-induced glucose intolerance.
Immuno-electron microscopy localizes Caenorhabditis elegans vitellogenins along the classic exocytosis route
Authors: Zhai Chao , Zhang Nan , Li Xi-Xia , Tan Xue-Ke , Sun Fei , Dong Meng-Qiu 
Published: June 2022

ABSTRACTVitellogenins (VITs) are the most abundant proteins in adult hermaphrodite C. elegans. VITs are synthesized in the intestine, secreted to the pseudocoelom, matured into yolk proteins (YPs), and finally deposited in oocytes to support embryonic and larval development. How VITs are secreted out of the intestine remains unclear. In this study, we use immuno-electron microscopy (immuno-EM) to characterize the wild-type subcellular structures containing VITs or YPs. In the intestinal cells of young adult worms, we identify VITs along an exocytic pathway consisting of the rough ER, the Golgi, and the lipid bilayer bounded vesicles, which we call intestinal vitellogenin vesicles (VVs). This suggests that the classic exocytotic pathway mediates secretion of VITs from the intestine to the pseudocoelom. We also show that pseudocoelomic yolk patches (PYPs) are membrane-less and amorphous. The different VITs/YPs are packed as a mixture into the above structures. The size of VVs can vary with the VIT levels and the age of the worm. On adult day 2 (AD 2), intestinal VVs (∼200 nm in diameter) are smaller than gonadal yolk organelles (YOs, ∼500 nm in diameter). VVs, PYPs, and YOs share a uniform, medium electron density by conventional EM. The morphological profiles documented in this study can serve as a reference for future studies of VITs/YPs. Surveying the findings from this study and elsewhere, we review in the discussion the post-translational modifications and protein-protein interactions of C. elegans VITs/YPs.
Hspa13 Regulates Endoplasmic Reticulum and Cytosolic Proteostasis Through Modulation of Protein Translocation
Authors: Espinoza Mateo F. , Nguyen Khanh K. , Sycks Melody M. , Lyu Ziqi , Montoya Maureen R. , Genereux Joseph C. 
Published: June 2022

ABSTRACTMost eukaryotic secretory proteins are co-translationally translocated through Sec61 into the endoplasmic reticulum (ER). Because these proteins have evolved to fold in the ER, their mistargeting is associated with toxicity. Genetic experiments have implicated the ER Hsp70 Hspa13/STCH as involved in processing of nascent secretory proteins. Herein, we evaluate the role of Hspa13 in protein import and the maintenance of cellular proteostasis. We find that Hspa13 interacts primarily with the Sec61 translocon and its associated factors. Hspa13 overexpression inhibits translocation of the secreted protein transthyretin (TTR), leading to accumulation and aggregation of immature TTR in the cytosol. ATPase inactive mutants of Hspa13 further inhibit translocation and maturation of secretory proteins. While Hspa13 overexpression inhibits cell growth and ER quality control, HSPA13 knockout destabilizes proteostasis and increases sensitivity to ER disruption. Thus, we propose that Hspa13 regulates import through the translocon to maintain both ER and cytosolic protein homeostasis.The raw mass spectrometry data associated with this manuscript has been deposited in the PRIDE archive and can be accessed at PXD033498.
Secreted Aeromonas GlcNAc binding protein GbpA stimulates epithelial cell proliferation in the zebrafish intestine
Authors: Banse Allison V. , VanBeuge Stephanie , Smith T. Jarrod , Logan Savannah L. , Guillemin Karen 
Published: June 2022

ABSTRACTIn response to microbiota colonization, the intestinal epithelia of many animals exhibit increased rates of cell proliferation. We used gnotobiotic larval zebrafish to identify a secreted factor from the mutualist Aeromonas veronii that is sufficient to promote intestinal epithelial cell proliferation. This secreted A. veronii protein is a homologue of the Vibrio cholerae GlcNAc binding protein GbpA, which was identified as a chitin-binding colonization factor in mice. GbpA was subsequently shown to be a lytic polysaccharide monooxygenase (LPMO) that can degrade recalcitrant chitin. Our phenotypic characterization of gbpA deficient A. veronii found no alterations in the mutant cells’ biogeography in the zebrafish intestine and only a modest competitive disadvantage in chitin-binding and colonization fitness when competed against the wild type strain. These results argue against the model of GbpA being a secreted adhesin that binds simultaneously to bacterial cells and GlcNAc, and instead suggests that GbpA is part of a bacterial GlcNAc utilization program. We show that the host proliferative response to GbpA occurs in the absence of bacteria upon exposure of germ-free zebrafish to preparations of native GbpA secreted from either A. veronii or V. cholerae or recombinant A. veronii GbpA.Furthermore, domain 1 of A. veronii GbpA, containing the predicted LPMO activity, is sufficient to stimulate intestinal epithelial proliferation. We conjecture that intestinal epithelia upregulate their rates of renewal in response to secreted bacterial GbpA proteins as an adaptive strategy for coexisting with bacteria that can degrade glycan constituents of the protective intestinal lining.