bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new concept on anti-SARS-CoV-2 vaccines: strong CD8+ T-cell immune response in both spleen and lung induced in mice by endogenously engineered extracellular vesicles
Authors: Ferrantelli Flavia , Chiozzini Chiara , Manfredi Francesco , Leone Patrizia , Federico Maurizio 
Published: December 2020

AbstractSevere acute respiratory syndrome coronavirus (SARS-CoV)-2 is spreading rapidly in the absence of validated tools to control the growing epidemic besides social distancing and masks. Many efforts are ongoing for the development of vaccines against SARS-CoV-2 since there is an imminent need to develop effective interventions for controlling and preventing SARS-CoV-2 spread. Essentially all vaccines in most advanced phases are based on the induction of antibody response against either whole or part of spike (S) protein. Differently, we developed an original strategy to induce CD8+ T cytotoxic lymphocyte (CTL) immunity based on in vivo engineering of extracellular vesicles (EVs). We exploited this technology with the aim to identify a clinical candidate defined as DNA vectors expressing SARS-CoV-2 antigens inducing a robust CD8+ T-cell response. This is a new vaccination approach employing a DNA expression vector encoding a biologically inactive HIV-1 Nef protein (Nefmut) showing an unusually high efficiency of incorporation into EVs even when foreign polypeptides are fused to its C-terminus. Nanovesicles containing Nefmut-fused antigens released by muscle cells are internalized by antigen-presenting cells leading to cross-presentation of the associated antigens thereby priming of antigen-specific CD8+ T-cells. To apply this technology to a design of anti-SARS-CoV-2 vaccine, we recovered DNA vectors expressing the products of fusion between Nefmut and four viral antigens, namely N- and C-terminal moieties of S (referred to as S1 and S2), M, and N. All fusion products are efficiently uploaded in EVs. When the respective DNA vectors were injected in mice, a strong antigen-specific CD8+ T cell immunity was generated. Most important, high levels of virus-specific CD8+ T cells were found in bronchoalveolar lavages of immunized mice. Co-injection of DNA vectors expressing the diverse SARS-CoV-2 antigens resulted in additive immune responses in both spleen and lung. EVs engineered with SARS-CoV-2 antigens proved immunogenic also in the human system through cross-priming assays carried out with ex vivo human cells. Hence, DNA vectors expressing Nefmut-based fusion proteins can be proposed as anti-SARS-CoV-2 vaccine candidates.
QTL Mapping in Outbred Tetraploid (and Diploid) Diallel Populations
Authors: Amadeu Rodrigo R. , Munoz Patricio R. , Zheng Chaozhi , Endelman Jeffrey B. 
Published: December 2020

ABSTRACTOver the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multi-allelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and non-additive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with 3 tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.
Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS
Authors: de Souza Degenhardt Maximilia F. , Vitale Phelipe A. M. , Abiko Layara A. , Zacharias Martin , Sattler Michael , Oliveira Cristiano L. P. , Salinas Roberto K. 
Published: December 2020

ABSTRACTNa+/Ca2+exchangers (NCX) are secondary active transporters that couple the translocation of Na+with the transport of Ca2+in the opposite direction. The exchanger is an essential Ca2+extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+-sensor called CBD12. Binding of intracellular Ca2+to CBD12 activates the NCX but inhibits the Na+/Ca2+exchanger ofDrosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant inter-domain flexibility in the Apo state, but assume rigid inter-domain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the Apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the Apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N RDCs) and Small-Angle X-Ray Scattering (SAXS) data in a combined modelling strategy that generated atomistic information on the most representative conformations. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, while the wide-open inter-domain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+binding shifts the CBD12 conformational ensemble towards extended conformers, which could be a key step in the Na+/Ca2+exchangers’ allosteric regulation mechanism. The present strategy, combining MD with NMR and SAXS, provides a powerful approach to select representative structures from ensembles of conformations, which could be applied to other flexible multi-domain systems.SIGNIFICANCEThe conformational ensemble of CALX-CBD12, the main Ca2+-sensor ofDrosophila’s Na+/Ca2+exchanger, was characterized by a combination of MD simulations with SAXS and NMR data using the EOM approach. This analysis showed that this two-domain construct experiences opening-closing motions, providing molecular information about CALX-CBD12 in the Apo state. Ca2+-binding shifts the conformational ensemble towards extended conformers. These findings are consistent with a model according to which Ca2+modulation of CBD12 plasticity is a key step in the Ca2+-regulation mechanism of the full-length exchanger.
The polybasic cleavage site in the SARS-CoV-2 spike modulates viral sensitivity to Type I IFN and IFITM2
Authors: Winstone Helena , Lista Maria Jose , Reid Alisha , Pickering Suzanne , Doores Katie J , Swanson Chad , Neil Stuart J D 
Published: December 2020

ABSTRACTThe cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein (S). The presence of a polybasic cleavage site in SARS-CoV-2 S at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the S precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons, and more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2 and the degree of this restriction is governed by route of viral entry. Removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH- and cathepsin-dependent in late endosomes where, like SARS-CoV-1 S, it is more sensitive to IFITM2 restriction. Furthermore, we find that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 S may reduce viral replication through the activity of type I IFNs.IMPORTANCEThe furin cleavage site in the S protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2, and that the sensitivity is exacerbated by deletion of the furin cleavage site which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus may represent a potential therapeutic target for COVID-19 treatment development.
Mutation of a conserved Gln residue does not abolish desensitization of acid-sensing ion channel 1
Authors: Rook Matthew L , Miaro Megan , Couch Tyler , Kneisley Dana L , Musgaard Maria , MacLean David M. 
Published: December 2020

AbstractDesensitization is a common feature of ligand-gated ion channels although the molecular cause varies widely between channel types. Mutations that substantially reduce or abolish desensitization have been described for many ligand-gated ion channels including glutamate, GABA, glycine and nicotinic receptors but not for acid-sensing ion channels (ASICs) until recently. Mutating Gln276 to a glycine in human ASIC1a was reported to mostly abolish desensitization at both the macroscopic and single channel levels, potentially providing a valuable tool for subsequent studies. However, we find that in both human and chicken ASIC1 the effect of Q276G is modest. In chicken ASIC1, the equivalent Q277G slightly reduces desensitization when using pH 6.5 as a stimulus but desensitizes essentially like wild type when using more acidic pH values. In addition, steady-state desensitization is intact, albeit right-shifted, and recovery from desensitization is accelerated. Molecular dynamics simulations indicate that the Gln277 side chain participates in a hydrogen bond network that might stabilize the desensitized conformation. Consistent with this, destabilizing this network with the Q277N or Q277L mutations largely mimics the Q277G phenotype. In human ASIC1a, Q276G does not substantially reduce desensitization but surprisingly slows entry to and exit from the desensitized state, thus requiring longer agonist applications to reach equilibrium. Our data reveal that while the Q/G mutation does not substantially impair desensitization as previously reported, it does point to unexpected differences between chicken and human ASICs and the need for careful scrutiny before using this mutation in future studies.
Patient-derived cancer organoid tracking with widefield one-photon redox imaging to assess treatment response
Authors: Gil Daniel A. , Deming Dustin , Skala Melissa C. 
Published: December 2020

AbstractMotivationAccessible tools are needed for rapid, non-destructive imaging of patient-derived cancer organoid (PCO) treatment response to accelerate drug discovery and streamline treatment planning for individual patients.AimSegment and track individual PCOs with widefield one-photon redox imaging to extract morphological and metabolic variables of treatment response.ApproachRedox imaging of the endogenous fluorophores, NAD(P)H and FAD, was used to monitor the metabolic state and morphology of PCOs. Redox imaging was performed on a widefield one-photon epifluorescence microscope to evaluate drug response in two colorectal PCO lines. An automated image analysis framework was developed to track PCOs across multiple time points over 48 hours. Variables quantified for each PCO captured metabolic and morphological response to drug treatment, including the optical redox ratio and organoid area.ResultsThe optical redox ratio (NAD(P)H/(FAD+NAD(P)H)) was independent of PCO morphology pre-tieatment. Drugs that induced cell death decreased the optical redox ratio and growth rate compared to control. Multivariate analysis of redox and morphology variables identified distinct PCO sub-populations. Single-organoid tracking improved sensitivity to drug treatment compared to pooled organoid analysis.ConclusionWidefield one-photon redox imaging can monitor metabolic and morphological changes on a single organoid-level, providing an accessible, non-destructive tool to screen drugs in patient-matched samples.
Projecting the combined healthcare burden of seasonal influenza and COVID-19
Authors: Du Zhanwei , Fox Spencer J. , Ingle Tanvi , Pignone Michael P. , Meyers Lauren Ancel 
Published: December 2020

AbstractThe overlapping 2020-2021 influenza season and COVID-19 pandemic may overwhelm hospitals throughout the Northern Hemisphere. Using a mathematical model, we project that COVID-19 burden will dwarf that of influenza. If non-pharmacological mitigation efforts fail, increasing influenza vaccination coverage by 30% points would avert 54 hospitalizations per 100,000 people.
A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC
Authors: Lewis Aaron J. O. , Hegde Ramanujan S. 
Published: December 2020

AbstractCells use transporters to move protein across membranes, but the origins of the most ancient transporters are unknown. Here, we analyse the ubiquitous protein-conducting channel SecY. Features conserved by its two duplicated halves suggest that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY’s halves detect exceptional similarity with the only other ubiquitous protein transporter, YidC. Their shared fold comprises a three-helix bundle interrupted by a helical hairpin. In YidC this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY it is transmembrane and forms the substrate-binding lateral gate helices. In both, the three-helix bundle forms a protein-conducting hydrophilic groove, delimited by a conserved hydrophobic residue. We propose that SecY originated as a homodimeric YidC homolog. Many YidC homologs now use this interface to heterodimerise with a conserved partner. Unification of the two ubiquitous protein transporters would reconstruct a key step in the evolution of cells.
Factors Associated with Longitudinal Psychological and Physiological Stress in Health Care Workers During the COVID-19 Pandemic
Authors: Hirten Robert P. , Danieletto Matteo , Tomalin Lewis , Choi Katie Hyewon , Zweig Micol , Golden Eddye , Kaur Sparshdeep , Helmus Drew , Biello Anthony , Pyzik Renata , Calcogna Claudia , Freeman Robert , Sands Bruce E , Charney Dennis , Bottinger Erwin P , Keefer Laurie , Suarez-Farinas Mayte , Nadkarni Girish N. , Fayad Zahi A. 
Published: December 2020

ABSTRACTIntroductionThe Coronavirus Disease 2019 (COVID-19) pandemic has resulted in psychological distress in health care workers (HCWs). There is a need to characterize which HCWs are at increased risk of psychological sequela from the pandemic.MethodsHCWs across seven hospitals in New York City were prospectively followed in an ongoing observational digital study using the custom Warrior Watch Study App. Participants wore an Apple Watch for the duration of the study measuring HRV throughout the follow up period. Surveys were obtained daily.ResultsThree hundred and sixty-one HCWs were enrolled. Multivariable analysis found New York City COVID-19 case count to be significantly associated with increased longitudinal stress (p=0.008). A non-significant decrease in stress (p=0.23) was observed following COVID-19 diagnosis, though there was a borderline significant increase following the 4-week period after a COVID-19 diagnosis via nasal PCR (p=0.05). Baseline emotional support, baseline quality of life and baseline resilience were associated with decreased longitudinal stress (p<0.001). Baseline resilience and emotional support were found to buffer against stressors, with a significant reduction in stress during the 4-week period after COVID-19 diagnosis observed only in participants in the highest tertial of emotional support and resilience (effect estimate −0.97, p=0.03; estimate −1.78, p=0.006). A significant trend between New York City COVID-19 case count and longitudinal stress was observed only in the high tertial emotional support group (estimate 1.22, p=0.005), and was borderline significant in the high and medium resilience tertials (estimate 1.29, p=0.098; estimate 1.14, p=0.09). Participants in the highest tertial of baseline emotional support and resilience had significantly reduced amplitude and acrophase of the circadian pattern of longitudinally collected heart rate variability.ConclusionOur findings demonstrate that low resilience, emotional support, and quality of life identify HCWs at risk of high perceived longitudinal stress secondary to the COVID-19 pandemic and have a distinct physiological stress profile. Assessment of HCWs for these features can identify and permit allocation of psychological support to these at-risk individuals as the COVID-19 pandemic and its psychological effects continue in this vulnerable population.
Dynamic regulation of hierarchical heterogeneity in Acute Myeloid Leukemia serves as a tumor immunoevasion mechanism
Authors: Pospori Constandina , Grey William , Anton Sara Gonzalez , Gibson Shayin , Georgiou Christiana , Birch Flora , Stevens Georgia , Williams Thomas , Khorshed Reema , Haltalli Myriam , Skoufou-Papoutsaki Maria-Nefeli , Sloan Katherine , Encabo Hector Huerga , Hopkins Jack , Christodoulidou Chrysi , Stampoulis Dimitris , Hearn-Yeates Francesca , Gribben John , Stauss Hans J. , Chakraverty Ronjon , Bonnet Dominique , Lo Celso Cristina 
Published: December 2020

AbstractAcute Myeloid Leukemia, a hematological malignancy with poor clinical outcome, is composed of hierarchically heterogeneous cells. We examine the contribution of this heterogeneity to disease progression in the context of anti-tumor immune responses and investigate whether these responses regulate the balance between stemness and differentiation in AML. Combining phenotypic analysis with proliferation dynamics and fate-mapping of AML cells in a murine AML model, we demonstrate the presence of a terminally differentiated, chemoresistant population expressing high levels of PDL1. We show that PDL1 upregulation in AML cells, following exposure to IFNγ from activated T cells, is coupled with AML differentiation and the dynamic balance between proliferation, versus differentiation and immunosuppression, facilitates disease progression in the presence of immune responses. This microenvironment-responsive hierarchical heterogeneity in AML may be key in facilitating disease growth at the population level at multiple stages of disease, including following bone marrow transplantation and immunotherapy.
Multistability and consequent phenotypic plasticity in AMPK-Akt double negative feedback loop in cancer cells
Authors: Chedere Adithya , Hari Kishore , Kumar Saurav , Rangarajan Annapoorni , Jolly Mohit Kumar 
Published: December 2020

AbstractAdaptation and survival of cancer cells to various stress and growth factor conditions is crucial for successful metastasis. A double-negative feedback loop between two serine/threonine kinases AMPK and Akt can regulate the adaptation of breast cancer cells to matrix-deprivation stress. This feedback loop can generate majorly two phenotypes or cell states: matrix detachment-triggered pAMPKhigh/ pAktlowstate, and matrix (re)attachment-triggered pAkthigh/ pAMPKlowstate. However, whether these two cell states can exhibit phenotypic plasticity and heterogeneity in a given cell population, i.e., whether they can co-exist and undergo spontaneous switching to generate the other subpopulation, remains unclear. Here, we develop a mechanism-based mathematical model that captures the set of experimentally reported interactions among AMPK and Akt. Our simulations suggest that the AMPK-Akt feedback loop can give rise to two co-existing phenotypes (pAkthigh/ pAMPKlowand pAMPKhigh/pAktlow) in specific parameter regimes. Next, to test the model predictions, we segregated these two subpopulations in MDA-MB-231 cells and observed that each of them was capable of switching to another in adherent conditions. Finally, the predicted trends are supported by clinical data analysis of TCGA breast cancer and pan-cancer cohorts that revealed negatively correlated pAMPK and pAkt protein levels. Overall, our integrated computational-experimental approach unravels that AMPK-Akt feedback loop can generate multistability and drive phenotypic switching and heterogeneity in a cancer cell population.
Fusobacterium nucleatumfacilitates cetuximab resistance in colorectal cancer via the PI3K/AKT and JAK/STAT3 pathways
Authors: Han Hu , Li Yan , Qin Wan , Wang Lu , Yin Han , Su Beibei , Yuan Xianglin 
Published: December 2020

AbstractInfectious pathogens contribute to about 20% of the total tumor burden.Fusobacterium nucleatum(Fn) has been associated with the initiation, progression, and therapy resistance in colorectal cancer (CRC). The over-abundance ofFnhas been observed in patients with right-sided CRC than in those with left-sided CRC. While theKRAS/NRAS/BRAFwild-type status of the CRC conferred better response to cetuximab in patients with left-sided CRC than with right-sided CRC. However, treatment failure remains the leading cause of tumor relapse and poor clinical outcome in patients with CRC. Here, we have studied the association ofFnto cetuximab resistance. Our functional studies indicate thatFnfacilitates resistance of CRC to cetuximabin vitroandin vivo. Moreover,Fnwas found to target the PI3K/AKT and JAK/STAT3 pathways, which altered the response to cetuximab therapy. Therefore, assessing the levels and targetingFnand the associated signaling pathways may allow modulating the treatment regimen and improve prognoses of CRC patients.