bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of mtROS-sensitive processes in activated CD4+T cells
Authors: Meston Daniel , Bi Wenjie , Rietschel Tina , van Ham Marco , Leichert Lars I. , Jänsch Lothar 
Published: June 2020

AbstractT lymphocytes are key components in adaptive immunity and their activation naturally involves mitochondrial-derived oxygen species (mtROS). In particular, H2O2has been implicated as an important signaling molecule regulating major T cell functions. H2O2targets the oxidation status of functional cysteine residues but knowledge if and where this happens in T cell signaling networks is widely missing. This study aimed to identify mtROS-sensitive processes in activated primary human CD4+T cells. By using a thiol-specific redox proteomic approach we examined the oxidation state of 4784 cysteine-containing peptides ofex vivostimulated T cells from healthy individuals. Upon activation, a shift in oxidation was observed at catalytic cysteine residues of peroxiredoxins (PRDX5 & PRDX6), and T cells were found to maintain their global thiol-redox homeostasis. In parallel, a distinct set of 88 cysteine residues were found to be differentially oxidized upon T cell activation suggesting novel functional thiol switches. In mitochondria, cysteine oxidations selectively modified regulators of respiration (NDUFA2, NDUFA8, and UQCRH) confirming electron leakage from electron transport complexes I and III. The majority of oxidations occurred outside mitochondria and enriched sensitive thiols at regulators of cytoskeleton dynamics (e.g. CYFIP2 and ARPC1B) and known immune functions including the non-receptor tyrosine phosphatase PTPN7. Conversely, cysteine reduction occurred predominantly at transcriptional regulators and sites that coordinate zinc-binding in zinc-finger motifs. Indeed, fluorescence microscopy revealed a colocalization of zinc-rich microenvironments and mitochondria in T cells suggesting mtROS-dependent zinc-release of identified transcriptional regulators including ZFP36, RPL37A and CRIP2. In conclusion, this study complements knowledge on the mtROS signaling network and suggests zinc-dependent thiol switches as a mechanism of how mtROS affects transcription and translation in T cells.
Novel ACE2-IgG1 fusions with improvedin vitroandin vivoactivity against SARS-CoV2
Authors: Iwanaga Naoki , Cooper Laura , Rong Lijun , Beddingfield Brandon , Crabtree Jackelyn , Tripp Ralph A. , Qin Xuebin , Kolls Jay K. 
Published: June 2020

AbstractSARS-CoV2, the etiologic agent of COVID-19, uses ACE2 as a cell entry receptor. Soluble ACE2 has been shown to have neutralizing antiviral activity but has a short half-life and no active transport mechanism from the circulation into the alveolar spaces of the lung. To overcome this, we constructed an ACE2-human IgG1 fusion protein with mutations in the catalytic domain of ACE2. This fusion protein contained a LALA mutation that abrogates Fcrγ binding, but retains FcRN binding to prolong the half-life, as well as achieve therapeutic concentrations in the lung lavage. Interestingly, a mutation in the catalytic domain of ACE2, MDR504, completely abrogated catalytic activity, but significantly increased binding to SARS-CoV2 spike proteinin vitro. This feature correlated with more potent viral neutralization in a plaque assay. Parental administration of the protein showed stable serum concentrations with a serum half-life of ∼ 145 hours with excellent bioavailability in the epithelial lining fluid of the lung. Prophylactic administration of MDR504 significantly attenuated SARS-CoV2 infection in a murine model. These data support that the MDR504 hACE2-Fc is an excellent candidate for pre or post-exposure prophylaxis or treatment of COVID-19.
Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations
Authors: Bubnis Greg , Grubmüller Helmut 
Published: June 2020

Membrane topology changes such as poration, stalk formation, and hemi-fusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our atomistic simulations, we developed a novel “gizmo” potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid head-groups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes.STATEMENT OF SIGNIFICANCEThe primary steps and nucleation of lipid membrane pore formation are key to membrane fusion, viral infection, and vesicular cellular transport. Despite decades experimental and theoretical studies, the underlying mechanisms are still not fully understood at the atomic level. Using a committor-based reaction coordinate and atomistic simulations, we report new structural and energetics insight into the full poration process. We find that the pore nucleates via an elastic indentation rather than by forming a hydrophobic defect. Subsequently, water pierces the thinned slab as a prerequisite for the following axial merger of the first lipid headgroups from opposite monolayers, which precedes and best characterizes the transition state. We also identify a metastable prepore basin, thereby explaining previous indirect experimental evidence.
Structure of a dominant negative mutant reveals a stalled intermediate state of anthrax protective antigen pore maturation
Authors: Scott Harry , Huang Wei , Gonti Srinivas , Zhang Kaiming , Mehzabeen Nurjahan , Day Alexander , Battaile Kevin P. , Lovell Scott , Bann James G. , Taylor Derek J. 
Published: June 2020

AbstractAnthrax is a severe bacterial infection caused byBacillus anthracis, which produces a tripartite toxin that includes protective antigen (PA), lethal factor (LF) and edema factor (EF). A series of dominant-negative mutations have been previously identified that prevent the heptameric PA prepore from forming the pH-induced, membrane spanning beta-barrel pore that is required for translocation of EF and LF to the cytoplasm of the infected cell. Here we show that the dominant negative D425A mutation stalls the formation of the pore at a reversible intermediate maturation state, which exhibits many of the structural aspects of the pore but fails to form the phi(ϕ)-clamp and beta-barrel structure needed for full pore maturation. Overall, this structure reveals that ϕ-clamp and beta-barrel pore formation are later steps in the pathway to pore formation, thereby providing a regulatory mechanism to prevent premature translocation of EF and LF.
Competitive hierarchies, antibiosis, and the distribution of bacterial life history traits in a microbiome*
Authors: Humphrey Parris T , Satterlee Trang T , Whiteman Noah K 
Published: June 2020

AbstractMicrobiome manipulation requires an understanding of how species interact within communities. Can outcomes of ecological interactions be predicted from microbial life history traits, the identity of the species, or both? We addressed these questions by studying the competitive interaction network in a community of 40 endophyticPseudomonasspp. bacterial isolates from a native plant. Pairwise competition experiments revealed competitive dominance ofP. fluorescensoverP. syringaestrains within this microbiome-derived community.P. syringaestrains with higher growth rates won more contests, whileP. fluorescensstrains with shorter lag times and lower growth rates won more contests. Adding to their competitive dominance,P. fluorescensstrains often produced antibiotics to which fewP. syringaestrains were resistant. Many competitive outcomes amongP. syringaestrains were predicted to be reversed byP. fluorescensinhibitors because indirect benefits accrued to less competitive strains.P. fluorescensstrains frequently changed competitive outcomes, suggesting a critical role of strains within this bacterial clade in structuring plant microbiome communities. Microbial traits also may provide a handle for directing the outcome of colonization processes within microbiomes.
Diet-regulated production of PDGFcc by macrophages controls energy storage
Authors: Cox Nehemiah , Crozet Lucile , Holtman Inge R. , Loyher Pierre-Louis , Lazarov Tomi , Mass Elvira , Stanley E. Richard , Glass Christopher K. , Geissmann Frederic 
Published: June 2020

SummaryMacrophages control inflammation in obese animals, and may also directly or indirectly regulate energy storage. In a genetic screen we identify a PDGF-family growth factor,Pvf3, produced by macrophages and required for lipid storage inDrosophilalarvae’s fat body cells. We next demonstrate using genetic and pharmacological approaches thatPvf3ortholog PDGFcc, produced byCcr2-independent embryo-derived tissue macrophages, is also required for storage in mammalian white adipose tissue. PDGFcc production by resident macrophages is regulated by diet, acts on white adipocytes in a paracrine manner, and controls adipocyte hypertrophy in high-fat diet fed and genetically hyperphagic mice. Upon PDGFcc blockade, excess lipids are redirected at the organismal level toward thermogenesis and hepatic storage in adults. This process is altogether independent from inflammation and insulin resistance promoted byCcr2-dependent monocytes/macrophages. Our data identify a conserved macrophagedependent mechanism that controls energy storage, conducive to the design of pharmacological interventions.
Previous oil exposure alters oil avoidance behavior in a common marsh fish, the Gulf KillifishFundulus grandis
Authors: Martin Charles W. , McDonald Ashley M. , Rieucau Guillaume , Roberts Brian J. 
Published: June 2020

AbstractOil spills threaten the structure and function of ecological communities. In the northern Gulf of Mexico, the 2010 Deepwater Horizon spill was among the largest marine disasters in history. While many predicted catastrophic consequences for nearshore fishes, field studies indicate surprising resilience in populations and communities. One potential mechanism for this resilience is the recognition and behavioral avoidance at small spatial scales of the toxic chemical constituents found in oil. Previous research indicates many marsh fishes have the capacity to avoid oil contaminated areas. Here, we test whether prior oil exposure of a common marsh fish, the Gulf killifishFundulus grandis, alters this avoidance response. Using choice tests between unoiled and a range of oiled sediments, we found that, even at low levels of previous exposure, killifish lose recognition of oiled sediments. Preference for unoiled sediments was lost across the entire range of oil concentrations tested here after oil exposure, and some evidence for preference of oiled sediments was even demonstrated. These results provide evidence for lack of response to toxic environments in exposed individuals, suggesting sublethal impairment of sensory mechanisms on an individual level despite organism survival. Future research should highlight additional sublethal consequences that affect ecosystem and food web functioning.
Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes
Authors: Hobson Benjamin D. , Kong Linghao , Hartwick Erik W. , Gonzalez Ruben L. , Sims Peter A. 
Published: June 2020

ABSTRACTPuromycin is an amino-acyl transfer RNA analog widely employed in studies of protein synthesis. Since puromycin is covalently incorporated into nascent polypeptide chains, anti-puromycin immunofluorescence enables visualization of nascent protein synthesis. A common assumption in studies of local messenger RNA translation is that the anti-puromycin staining of puromycylated nascent polypeptides in fixed cells accurately reports on their original site of translation, particularly when ribosomes are stalled with elongation inhibitors prior to puromycin treatment. However, when we attempted to implement a proximity ligation assay to detect ribosome-puromycin complexes, we found no evidence to support this assumption. We further demonstrated, using biochemical assays and live cell imaging of nascent polypeptides, that puromycylated nascent polypeptides rapidly dissociate from ribosomes even in the presence of elongation inhibitors. Our results suggest that attempts to define precise subcellular translation sites using anti-puromycin immunostaining may be confounded by release of puromycylated nascent polypeptide chains prior to fixation.
A learned map for places and concepts in the human MTL
Authors: Herweg Nora A. , Kunz Lukas , Schonhaut Daniel R. , Brandt Armin , Wanda Paul A. , Sharan Ashwini D. , Sperling Michael R. , Schulze-Bonhage Andreas , Kahana Michael J. 
Published: June 2020

AbstractDistinct lines of research in both humans and animals point to a specific role of the hippocampus in both spatial and episodic memory function. The discovery of concept cells in the hippocampus and surrounding medial-temporal lobe (MTL) regions suggests that the MTL maps physical and semantic spaces with a similar neural architecture. Here, we studied the emergence of such maps using MTL micro-wire recordings from 20 patients navigating a virtual environment featuring salient landmarks with established semantic meaning. We present several key findings: The array of local field potentials in the MTL contains sufficient information to decode subjects’ instantaneous location in the environment. Closer examination revealed that the field potentials represent both the subjects’ locations in virtual space and in high-dimensional semantic space. We further show that both spatial and semantic representations strengthen over time. This learning effect appears as subjects increase their knowledge of the environment’s spatial and semantic layout. Similarly, we observe a learning effect on temporal sequence coding. Over time, field potentials come to represent future locations, even after controlling for spatial proximity. This predictive coding of future states, more so than the strength of spatial representations per se, explains variability in subjects’ navigation performance. Our results thus support the conceptualization of the MTL as a memory space, building semantic knowledge, spatial and non-spatial, from episodic experience to plan future actions and predict their outcomes.Significance statementUsing rare micro-wire recordings, we studied the representation of spatial, semantic and temporal information in the human MTL. Our findings demonstrate that subjects acquire a cognitive map that simultaneously represents the spatial and semantic relations between landmarks. We further show that the same learned representation is used to predict future states, implicating MTL cell assemblies as the building blocks of prospective memory functions.
Changes in the functional connectome and behavior after exposure to chronic stress and increasing neurogenesis
Authors: Culig Luka , Steadman Patrick E. , Kenney Justin W. , Legendre Sandra , Minier Frédéric , Hen René , Frankland Paul W. , Belzung Catherine 
Published: June 2020

AbstractAddition of new neurons to the dentate gyrus might change the activity of neural circuitry in the areas which the hippocampus projects to. The size of the hippocampus and the number of adult newborn granule cells are decreased by unpredictable chronic mild stress (UCMS). Additionally, one of the notable effects of chronic stress is the induction of ΔFosB, an unusually stable transcription factor which accumulates over time in several brain areas. This accumulation has been observed in many animal models of depression and it could have a protective role against stress, but no studies so far have explored how a specific increase in neurogenesis might regulate the induction and which brain networks might be predominately affected.We attempted to investigate the role of increasing adult hippocampal neurogenesis on stress-related behavior and the functional brain circuitry involved in mice exposed to UCMS. We usediBaxmice, in which the pro-apoptotic geneBaxcan be selectively ablated in neural stem cells, therefore inducibly enhancing survival of newborn neurons after tamoxifen administration. The animals were exposed to UCMS for 9 weeks and treated with tamoxifen in week 3 after the beginning of UCMS. In week 8, they were submitted to a battery of behavioral tests to assess depressive-like and anxiety-like behavior. In week 9, blood was collected to assess basal corticosterone levels, and the animals were sacrificed and their brain collected for ΔFosB immunohistochemistry. Brain-wide maps of ΔFosB expression were constructed and graph theoretical analyses were used to study the changes in brain networks after stress.UCMS induced negative correlations between the lateral entorhinal cortex and both the hippocampal structures and the nucleus accumbens in the VEH-treated mice, which were not present in other groups. Ranking nodes by degree reveals a strong thalamic-cortical signature in both non-stress (NS) groups. Exposure to UCMS seems to induce activity in thalamic areas and cerebral nuclei, with a different signature in the UCMS TAM group, which seems to completely “disengage” the neocortex and has most of its nodes with the most connections in the thalamic areas.
Contributions and competition of Mg2+and K+in folding and stabilization of the Twister Ribozyme
Authors: Kognole Abhishek A. , MacKerell Alexander D. 
Published: June 2020

AbstractNative folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg2+in a background of monovalent ions. In a recent study we showed how the presence of Mg2+impacts the transition from partially unfolded to folded states through a “push-pull” mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To better understand the ion atmosphere of RNA in folded and partially folded states results from atomistic Umbrella Sampling and oscillating chemical potential Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg2+and K+ions around Twister RNA. Results show the presence of 100 mM Mg2+to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K+ions. Furthermore, K+preferentially interacts with purine N7 atoms of helical regions in partially unfolded states thereby potentially stabilizing them. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K+can act as a surrogate for Mg2+by participating in specific interactions with non-sequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at sub-millimolar Mg2+concentrations.
Evolutionary transcriptomics implicatesHAND2in the origins of implantation and regulation of gestation length
Authors: Marinić Mirna , Mika Katelyn , Chigurupati Sravanthi , Lynch Vincent J. 
Published: June 2020

AbstractThe developmental origins and evolutionary histories of cell types, tissues and organ systems contribute to the ways in which their dysfunction leads to disease. In mammals for example, the nature and extent of maternal-fetal interactions, how those interactions develop, and their evolutionary history likely influence diseases of pregnancy such as infertility and preterm birth. Here we show genes that evolved to be expressed at the maternal-fetal interface in Eutherian (‘Placental’) mammals play essential roles in the evolution of pregnancy and are associated with immune system disorders and preterm birth. Among these genes is the transcription factorHAND2, which suppresses estrogen signaling, an innovation of Eutherians, thereby allowing blastocyst implantation. We found thatHAND2is dynamically expressed in the decidua throughout the menstrual cycle and pregnancy, gradually decreasing to reach a low at term. HAND2 regulates a small but distinct set of target genes in endometrial stromal fibroblasts including the cytokineIL15, which was also dynamically expressed throughout the menstrual cycle and gestation, and promoted the migration of natural killer cells and extravillous cytotrophoblasts. Remarkably, we found that theHAND2promoter loops to a distal enhancer containing SNPs implicated in the regulation of gestation length and birth weight. Collectively, these data connectHAND2expression at the maternal-fetal interface with the evolution of implantation and gestation length regulation, and preterm birth.
Role of TLR4 in persistentLeptospira interrogansinfection: a comparativein vivostudy in mice
Authors: Nair Nisha , Guedes Mariana Soares , Hajjar Adeline , Werts Catherine , Gomes-Solecki Maria 
Published: June 2020

AbstractToll-Like Receptor (TLR) 4, the LPS receptor, plays a central role in the control of leptospirosis and absence of TLR4 results in lethal infection in mice. Because human TLR4 does not sense the atypical leptospiral-LPS, we hypothesized that TLR4/MD-2 humanized transgenic mice (huTLR4) may be more susceptible to leptospirosis than wild-type mice, and thus may constitute a model of acute human leptospirosis. Therefore, we infected huTLR4 mice, which express human TLR4 but not murine TLR4, with a high but sublethal dose ofL. interrogansserovar Copenhageni FioCruz (Leptospira) in comparison to C57BL/6J wildtype (WT) and, as a control, a congenic strain in which thetlr4coding sequences are deleted (muTLR4Lps-del). We show that the huTLR4 gene is fully functional in the murine background. We found that dissemination ofLeptospirain blood, shedding in urine, colonization of the kidney and overall kinetics of leptospirosis progression is equivalent between WT and huTLR4 C57BL/6J mice. Furthermore, inflammation of the kidney appeared to be subdued in huTLR4 compared to WT mice in that we observed less infiltrates of mononuclear lymphocytes, less innate immune markers and no relevant differences in fibrosis markers. Contrary to our hypothesis, huTLR4 mice showed less inflammation and kidney pathology, and are not more susceptible to leptospirosis than WT mice. This study is significant as it indicates that one intact TLR4 gene, be it mouse or human, is necessary to control acute leptospirosis.Contribution to the fieldDifferences of recognition exist between mouse and human TLR4, in that the anchor of LPS in the outer membrane ofLeptospira(LipidA) activates murine, but not human TLR4. We hypothesized that if human TLR4 does not sense leptospiral-LPS, then transgenic mice in which murine TLR4 was replaced with human TLR4, should be more susceptible toLeptospiradissemination as compared to congenic wild-type mice, which could result in a more robust inflammatory response and pathology in the kidney. However, we found that impaired sensing of leptospiral-LPS in huTLR4 mice did not affect overall infection in comparison to wild-type mice and does not result in increased pathology of the kidney. Our study indicates that rather than leptospiral-LPS sensing, the presence of a fully functional TLR4 receptor is necessary to control acute leptospirosis.