bluuebunny/crossref_metadata_2025_split huggingface dataset:
AUG-3387, a Human-Derived Monoclonal Antibody Neutralizes SARS-CoV-2 Variants and Reduces Viral Load from Therapeutic Treatment of Hamsters In Vivo
Authors: Emig Christopher J. , Mena Marco A. , Henry Steven J. , Vitug Adela , Ventura Christian John , Fox Douglas , Nguyenla Xammy Huu , Xu Haiyue , Moon Chaeho , Sahakijjpijarn Sawittree , Kuehl Philip J. , Revelli David , Cui Zengrong , Williams Robert O. , Christensen Dale J. 
Published: October 2021

AbstractInfections from the SARS-CoV-2 virus have killed over 4.6 million people since it began spreading through human populations in late 2019. In order to develop a therapeutic or prophylactic antibody to help mitigate the effects of the pandemic, a human monoclonal antibody (mAb) that binds to the SARS-CoV-2 spike protein was isolated from a convalescent patient following recovery from COVID-19 disease. This mAb, designated AUG-3387, demonstrates a high affinity for the spike protein of the original viral strains and all variants tested to date. In vitro pseudovirus neutralization and SARS-CoV-2 neutralization activity has been demonstrated in vitro. In addition, a dry powder formulation has been prepared using a Thin-Film Freezing (TFF) process that exhibited a fine particle fraction (FPF) of 50.95 ± 7.69% and a mass median aerodynamic diameter (MMAD) and geometric standard deviation (GSD) of 3.74 ± 0.73 µm and 2.73 ± 0.20, respectively. The dry powder is suitable for delivery directly to the lungs of infected patients using a dry powder inhaler device. Importantly, AUG-3387, administered as a liquid by intraperitoneal injection or the dry powder formulation delivered intratracheally into Syrian hamsters 24 hours after intranasal SARS-CoV-2 infection, demonstrated a dose-dependent reduction in the lung viral load of the virus. These data suggest that AUG-3387 formulated as a dry powder demonstrates potential to treat COVID-19.
Vht hydrogenase is required for hydrogen cycling during nitrogen fixation by the non-hydrogenotrophic methanogen Methanosarcina acetivorans
Authors: Hoerr Jadelyn M. , Dhamad Ahmed E. , Deere Thomas M. , Chanderban Melissa , Lessner Daniel J. 
Published: October 2021

ABSTRACTMethanosarcina acetivorans is the primary model to understand the physiology of methanogens that do not use hydrogenase to consume or produce hydrogen (H2) during methanogenesis. The genome of M. acetivorans encodes putative methanophenazine-reducing hydrogenases (Vht and Vhx), F420-reducing hydrogenase (Frh), and hydrogenase maturation machinery (Hyp), yet cells lack significant hydrogenase activity under all growth conditions tested to date. Thus, the importance of hydrogenase to the physiology of M. acetivorans has remained a mystery. M. acetivorans can fix dinitrogen (N2) using nitrogenase that is documented in bacteria to produce H2 during the reduction of N2 to ammonia. Therefore, we hypothesized that M. acetivorans uses hydrogenase to recycle H2 produced by nitrogenase during N2 fixation. Results demonstrate that hydrogenase expression and activity is higher in N2-grown cells compared to cells grown with fixed nitrogen (NH4Cl). To test the importance of each hydrogenase and the maturation machinery, the CRISPRi-dCas9 system was used to generate separate M. acetivorans strains where transcription of the vht, frh, vhx, or hyp operons is repressed. Repression of vhx and frh does not alter growth with either NH4Cl or N2 and has no effect on H2 metabolism. However, repression of vht or hyp results in impaired growth with N2 but not NH4Cl. Importantly, H2 produced endogenously by nitrogenase is detected in the headspace of culture tubes containing the vht or hyp repression strains. Overall, the results reveal that Vht hydrogenase recycles H2 produced by nitrogenase that is required for optimal growth of M. acetivorans during N2 fixation.IMPORTANCEThe metabolism of M. acetivorans and closely related Methanosarcinales is thought to not involve H2. Here we show for the first time M. acetivorans is capable of H2 cycling like hydrogenotrophic Methanosarcinales (e.g., Methanosarcina barkeri). However, unlike M. barkeri hydrogenase activity and H2 cycling is tightly regulated in M. acetivorans and is only utilized during N2 fixation to consume H2 production endogenously by nitrogenase. The in vivo production of H2 by nitrogenase during N2 reduction is also demonstrated for the first time in a methanogen. Overall, the results provide new insight into the evolution and diversity of methanogen metabolism and new details about methanogen nitrogenase that could be leveraged for practical applications, such as nitrogenase-dependent production of H2 as a biofuel.
Investigating the Role of Chromatin Remodeler FOXA1 in Ferroptotic Cell Death
Authors: Logie Emilie , Maes Louis , Van Meenen Joris , De Rijk Peter , Strazisar Mojca , Joris Geert , Cuypers Bart , Laukens Kris , Berghe Wim Vanden 
Published: October 2021

Ferroptosis is a lipid peroxidation-dependent mechanism of regulated cell death known to suppress tumor proliferation and progression. Although several genetic and protein hallmarks have been identified in ferroptotic cell death, it remains challenging to fully characterize ferroptosis signaling pathways and to find suitable biomarkers. Moreover, changes taking place in the epigenome of ferroptotic cells remain poorly studied. In this context, we aimed to investigate the role of chromatin remodeler forkhead box protein A1 (FOXA1) in RSL3-treated multiple myeloma cells because, similar to ferroptosis, this transcription factor has been associated with changes in the lipid metabolism, DNA damage, and epithelial-to-mesenchymal transition (EMT). RNA sequencing and Western blot analysis revealed that FOXA1 expression is consistently upregulated upon ferroptosis induction in different in vitro and in vivo disease models. In silico motif analysis and transcription factor enrichment analysis further suggested that ferroptosis-mediated FOXA1 expression is orchestrated by specificity protein 1 (Sp1), a transcription factor known to be influenced by lipid peroxidation. Remarkably, FOXA1 upregulation in ferroptotic myeloma cells did not alter hormone signaling or EMT, two key downstream signaling pathways of FOXA1. CUT&RUN genome-wide transcriptional binding site profiling showed that GPX4-inhibition by RSL3 triggered loss of binding of FOXA1 to pericentromeric regions in multiple myeloma cells, suggesting that this transcription factor is possibly involved in genomic instability, DNA damage, or cellular senescence under ferroptotic conditions.Abstract Figure
Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors
Authors: Hilliard Sylvia , Tortelote Giovane , Liu Hongbing , Chen Chao-Hui , El-Dahr Samir S. 
Published: October 2021

STRUCTURED ABSTRACTBackgroundCis-regulatory elements (CREs), such as enhancers and promoters, and their cognate transcription factors play a central role in cell fate specification. Bulk analysis of CREs has provided insights into gene regulation in nephron progenitor cells (NPCs). However, the cellular resolution required to unravel the dynamic changes in regulatory elements associated with cell fate choices remains to be defined.MethodsWe integrated single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) in embryonic E16.5 (self-renewing) and postnatal P2 (primed) mouse Six2GFPNPCs. This analysis revealed NPC diversity and identified candidate CREs. To validate these findings and gain additional insights into more differentiated cell types, we performed a multiome analysis of E16.5 and P2 kidneys.ResultsCRE accessibility recovered the diverse states of NPCs and precursors of differentiated cells. Single-cell types such as podocytes, proximal and distal precursors are marked by differentially accessible CREs. Domains of regulatory chromatin as defined by rich CRE-gene associations identified NPC fate-determining transcription factors (TF). Likewise, key TF expression correlates well with its regulon activity. Young NPCs exhibited enrichment in accessible motifs for bHLH, homeobox, and Forkhead TFs, while older NPCs were enriched in AP-1, HNF1, and HNF4 motif activity. A subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors.ConclusionDefining the regulatory landscape of nephrogenesis at single-cell resolution informs the basic mechanisms of nephrogenesis and provides a foundation for future studies in disease states characterized by abnormal nephrogenesis.Significance StatementNephron progenitor cells (NPCs) are a multipotent population giving rise to all cell types of the nephron. At any given time, the NPC’s choice to self-renew or differentiate is determined not only by its transcription factor (TF) repertoire but also by the genome accessibility of the cognate cis-regulatory elements.Using single-cell analysis, we demonstrate the heterogeneity of NPCs at the epigenetic level and observe dynamic and cell type-specific changes in chromatin accessibility. Fate-determining TFs harbor domains rich in interactive chromatin that are established prior to gene activation.These findings illustrate the importance of chromatin-based mechanisms in the regulation of nephrogenesis and may have implications for nephron regeneration and repair.
Discovery of archaeal Fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
Authors: Moi David , Nishio Shunsuke , Li Xiaohui , Valansi Clari , Langleib Mauricio , Brukman Nicolas G. , Flyak Kateryna , Dessimoz Christophe , de Sanctis Daniele , Tunyasuvunakool Kathryn , Jumper John , Graña Martin , Romero Héctor , Aguilar Pablo S. , Jovine Luca , Podbilewicz Benjamin 
Published: October 2021

AbstractSexual reproduction consists of genome reduction by meiosis and subsequent gamete fusion. Presence of meiotic genes in prokaryotes suggests that DNA repair mechanisms evolved toward meiotic recombination; however, fusogenic proteins resembling those found in eukaryotes were not identified in prokaryotes. Here, we identify archaeal proteins that are homologs of fusexins, a superfamily of fusogens that mediate eukaryotic gamete and somatic cell fusion, as well as virus entry. The crystal structure of a trimeric archaeal Fusexin1 reveals novel features such as a six-helix bundle and an additional globular domain. Ectopically expressed Fusexin1 can fuse mammalian cells, and this process involves the additional domain and a conserved fusion loop. Archaeal fusexin genes exist within integrated mobile elements, potentially linking ancient archaeal gene exchanges and eukaryotic sex.One-Sentence SummaryCell membrane fusion proteins of viruses and eukaryotes are also present in archaea.
Modular, robust and extendible multicellular circuit design in yeast
Authors: Carignano Alberto , Chen Dai Hua , Mallory Cannon , Wright Clay , Seelig Georg , Klavins Eric 
Published: October 2021

AbstractDivision of labor between cells is ubiquitous in biology but the use of multi-cellular consortia for engineering applications is only beginning to be explored. A significant advantage of multi-cellular circuits is their potential to be modular with respect to composition but this claim has not yet been extensively tested using experiments and quantitative modeling. Here, we construct a library of 24 yeast strains capable of sending, receiving or responding to three molecular signals, characterize them experimentally and build quantitative models of their input-output relationships. We then compose these strains into two- and three-strain cascades as well a four-strain bistable switch and show that experimentally measured consortia dynamics can be predicted from the models of the constituent parts. To further explore the achievable range of behaviors, we perform a fully automated computational search over all two-, three- and four-strain consortia to identify combinations that realize target behaviors including logic gates, band-pass filters and time pulses. Strain combinations that are predicted to map onto a target behavior are further computationally optimized and then experimentally tested. Experiments closely track computational predictions. The high reliability of these model descriptions further strengthens the feasibility and highlights the potential for distributed computing in synthetic biology.
Low antigen abundance limits efficient T-cell recognition of highly conserved regions of SARS-CoV-2
Authors: Swaminathan Srividhya , Lineburg Katie E. , Ambalathingal George R. , Crooks Pauline , Grant Emma J. , Mohan Sonali V , Raju Jyothy , Panikkar Archana , Texier Laetitia Le , Tong Zheng Wei Marcus , Chew Keng Yih , Neller Michelle A. , Short Kirsty R. , Gowda Harsha , Gras Stephanie , Khanna Rajiv , Smith Corey 
Published: October 2021

SummaryUnderstanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8+ T-cell epitopes across the nucleocapsid (N), spike (S) and ORF3a proteins of SARS-CoV-2 and five CD8+ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8+ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad pre-existing immunity in the community.
Characterisation of a highly diverged mitochondrial ATP synthase peripheral stalk subunit b in Trypanosoma brucei
Authors: Dewar Caroline E. , Oeljeklaus Silke , Warscheid Bettina , Schneider André 
Published: October 2021

ABSTRACTThe mitochondrial F1Fo ATP synthase of Trypanosoma brucei has been studied in detail. Whereas its F1 moiety is relatively highly conserved in structure and composition, the same is not the case for the Fo part and the peripheral stalk. A core subunit of the latter, the normally conserved subunit b, could not be identified in trypanosomes suggesting that it might be absent. Here we have identified a 17 kDa mitochondrial protein of the inner membrane that is essential for normal growth, efficient oxidative phosphorylation and membrane potential maintenance. Pulldown experiments and native PAGE analysis indicate that the protein is associated with the F1Fo ATP synthase. Its ablation reduces the levels of Fo subunits, but not those of F1, and disturbs the cell cycle. HHpred analysis showed that the protein has structural similarities to subunit b of other species, indicating that the Fo part of the trypanosomal ATP synthase does contain a highly diverged subunit b. Thus, the Fo part of the trypanosomal ATPase synthase may be more widely conserved than initially thought.
RNA-seq, bioinformatic identification of potential MicroRNA-Like Small RNAs in the edible mushroom Agaricus bisporus and experimental approach for their validation
Authors: Marin Francisco R. , Dávalos Alberto , Kiltschewskij-Brown Dylan , Crespo Maria C. , Cairns Murray , Andres-Leon Eduardo , Soler-Rivas Cristina 
Published: October 2021

ABSTRACTAlthough genomes from many edible mushrooms are sequenced, studies on fungal miRNAs are scarce. Most of the bioinformatic tools are designed for plants or animals but fungal miRNAs processing and expression share similarities and differences with both kingdoms. Moreover, since mushroom species such as Agaricus bisporus (white button mushroom) are frequently consumed as food, controversial discussions are still evaluating whether their miRNAs might or might not be assimilated, perhaps within extracellular vesicles (i.e exosomes). Therefore, the A. bisporus RNA-seq was studied in order to identify potential de novo miRNA-like small RNAs (milRNAs) that might allow their later detection in the diet. Results pointed to 1 already known and 37 de novo milRNAss. Three milRNAss were selected for RT-qPCR experiments. Precursors and mature milRNAs were found in the edible parts (caps and stipes) validating the predictions carried out in silico. When their potential gene targets were investigated, results pointed that mostly were involved in primary and secondary metabolic regulation. However, when human transcriptome is used as target, the results suggest that they might interfere with important biological processes related with cancer, infectious process and neurodegenerative diseases.
Flow Cytometric Evaluation of Yeast-Bacterial Cell-Cell Interactions
Authors: Lei Ming , Trivedi Vikas D. , Nair Nikhil U. , Lee Kyongbum , Van Deventer James A. 
Published: October 2021

AbstractSynthetic cell-cell interaction systems can be useful for understanding multicellular communities or for screening binding molecules. We adapt a previously characterized set of synthetic cognate nanobody-antigen pairs to a yeast-bacteria coincubation format and use flow cytometry to evaluate cell-cell interactions mediated by binding between surface-displayed molecules. We further use fluorescence-activated cell sorting (FACS) to enrich for a specific yeast-displayed nanobody within a mixed yeast-display population. Finally, we demonstrate that this system supports characterization of a therapeutically relevant nanobody-antigen interaction: a previously discovered nanobody that binds to the intimin protein expressed on the surface of enterohemorrhagic E. coli. Overall, our findings indicate that the yeast-bacteria format supports efficient evaluation of ligand-target interactions. With further development, this format may facilitate systematic characterization and high throughput discovery of bacterial surface-binding molecules.
Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter
Authors: Bera Subhas C. , America Pim P. B. , Maatsola Santeri , Seifert Mona , Ostrofet Eugeniu , Cnossen Jelmer , Spermann Monika , Papini Flávia S. , Depken Martin , Malinen Anssi M. , Dulin David 
Published: October 2021

AbstractTranscription initiation is the first step in gene expression, and is therefore strongly regulated in all domains of life. The RNA polymerase (RNAP) first associates with the initiation factorσto form a holoenzyme, which binds, bends and opens the promoter in a succession of reversible states. These states are critical for transcription regulation, but remain poorly understood. Here, we addressed the mechanism of open complex formation by monitoring its assembly/disassembly kinetics on individual consensuslacUV5promoters using high-throughput single-molecule magnetic tweezers. We probed the key protein–DNA interactions governing the open-complex formation and dissociation pathway by modulating the dynamics at different concentrations of monovalent salts and varying temperatures. Consistent with ensemble studies, we observed that RPOis a stable, slowly reversible state that is preceded by a kinetically significant open intermediate (RPI), from which the holoenzyme dissociates. A strong anion concentration and type dependence indicates that the RPOstabilization may involve sequence-independent interactions between the DNA and the holoenzyme, driven by a non-Coulombic effect consistent with the non-template DNA strand interacting withσand the RNAPβsubunit. The temperature dependence provides the energy scale of open-complex formation and further supports the existence of additional intermediates.
Prolonged HPA axis dysregulation in postpartum depression associated with adverse life experiences during development: a cross-species translational study for a novel therapeutic approach
Authors: Niwa Minae , Lockhart Sedona , Wood Daniel J. , Yang Kun , Francis-Oliveira Jose , Kin Kyohei , Ahmed Adeel , Wand Gary S. , Kano Shin-ichi , Payne Jennifer L. , Sawa Akira 
Published: October 2021

AbstractStress during childhood and adolescence increases the risk for postpartum depression (PPD). Patients with depression who have experienced adverse life events tend to be treatment refractory. However, the mechanism by which stress during childhood and adolescence are involved in the pathophysiology of PPD remains unclear. We investigated the longitudinal effects of adolescent stress on the hypothalamic-pituitary-adrenal (HPA) axis and behaviors in the postpartum period through mouse and human studies. We observed that adolescent social isolation caused an aberrantly sustained elevation of glucocorticoids via dysregulation of the HPA axis, leading to long-lasting postpartum behavioral changes in female mice. The postpartum behavioral changes elicited by this adolescent stress were not ameliorated by the medicines currently used for PPD treatment. However, a post-delivery treatment with a glucocorticoid receptor antagonist effectively ameliorated the behavioral changes in mice. We also demonstrated a significant impact of stress during childhood and adolescence on the HPA axis dysregulation and PPD in women. We provide experimental evidence that suggests a mechanism-driven therapeutic strategy (repurposing a GR antagonist) for at least some cases of treatment refractory PPD.
Epigenetic clock and methylation studies in gray short-tailed opossums
Authors: Horvath Steve , Haghani Amin , Zoller Joseph A. , Raj Ken , Sinha Ishani , Talbot Annais , Ruiz Yadiamaris Aviles , Sears Karen E. 
Published: October 2021

ABSTRACTThe opossum (Monodelphis domestica), with its sequenced genome, ease of laboratory care and experimental manipulation, and unique biology, is the most used laboratory marsupial. Using the mammalian methylation array, we generated DNA methylation data from n=100 opossum tissues including blood, liver, and tail. We contrast age-related changes in the opossum methylome to those of C57BL/6J mice. We present several epigenetic clocks for opossums that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (opossum and human). Two dual-species human-opossum pan-tissue clocks accurately measure chronological age and relative age, respectively. These human-opossum epigenetic clocks are expected to provide a significant boost to the attractiveness of opossum as a biological model.