bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thriving in the heat – Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermoactive PEP-synthase
Authors: Albanese Pascal , Song Wenfei , van Keulen Siri , Koendjbiharie Jeroen , Koh Fujiet , Steigenberger Barbara , Vincent Tomoko , Konijnenberg Albert , Heck Albert J.R. , Kengen Servé W.M. , Bonvin Alexandre M.J.J. , Förster Friedrich , Scheltema Richard A. 
Published: August 2022

AbstractOver time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of Pyrococcus furious, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of P. furiosus. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes.
Imaging increased metabolism in the spinal cord in mice after middle cerebral artery occlusion
Authors: Ni Ruiqing , Straumann Nadja , Fazio Serana , Dean-Ben Xose Luis , Louloudis Georgios , Keller Claudia , Razansky Daniel , Ametamey Simon , Mu Linjing , Nombela-Arrieta César , Klohs Jan 
Published: August 2022

AbstractEmerging evidence indicates crosstalk between the brain and the hematopoietic system following cerebral ischemia. Here, we investigated metabolism and oxygenation in the spleen and spinal cord in a transient middle cerebral artery occlusion (tMCAO) mouse model that is widely used in focal cerebral ischemia research. Naïve, sham and tMCAO mice underwent positron emission tomography (PET) using [18F]fluorodeoxyglucose (FDG) for assessing glucose metabolism and multispectral optoacoustic tomography (MSOT) assisted with quantitative model-based reconstruction and unmixing algorithms for accurate mapping of oxygenation patterns in the peripheral tissues at 24 h after reperfusion. We found increased levels of [18F]FDG uptake and reduced MSOT oxygen saturation, indicating hypoxia in the thoracic spinal cord of tMCAO mice compared with sham-operated mice but not in the spleen. A positive correlation was observed between splenic and ipsilateral striatal [18F]FDG uptake. Reduced spleen size was observed in tMCAO mice compared with sham-operated miceex vivo. tMCAO led to a significant increase in the numbers of mature T cells (CD4 and CD8) in femoral bone marrow tissues, concomitant with a stark reduction in these cell subsets in the spleen and their decrease in peripheral blood. The numbers of mature granulocytes (determined as CD11b+Gr1hicells) decreased in bone marrow tissues and blood but increased in the spleen. The combination of quantitative PET and MSOT thus enabled the observation of hypoxia and increased metabolic activity in the spinal cord of tMCAO mice at 24 h after occlusion compared to sham-operated mice.
IL-12/18/21 pre-activation enhances the anti-tumor efficacy of expanded γδT cells and overcomes resistance to anti-PD-L1 treatment
Authors: Teo Huey Yee , Song Yuan , Yong Kylie Su Mei , Liu Yonghao , Mei Yu , Hanafi Zuhairah Binte , Zhu Ying , Gascoigne Nicholas R. J. , Chen Qingfeng , Liu Haiyan 
Published: August 2022

AbstractγδT cells are promising candidates for cellular immunotherapy due to their immune regulation through cytokine production and MHC-independent direct cytotoxicity against a broad spectrum of tumors. However, current γδT cell-based cancer immunotherapy has limited efficacies and novel strategies are needed to improve its clinical outcomes. Here, we report that cytokine pre-treatment with IL-12/18, IL-12/15/18, IL-12/18/21 and IL-12/15/18/21 could effectively enhance the activation and cytotoxicity ofin vitroexpanded murine and human γδT cells. However, only adoptive transfer of IL-12/18/21 pre-activated γδT cells significantly inhibited tumor growth in a murine melanoma model and a hepatocellular carcinoma model. Both IL-12/18/21 pre-activated antibody-expanded and zoledronate-expanded human γδT cells effectively controlled tumor growth in a humanized mouse model. IL-12/18/21 pre-activation promoted γδT cell proliferation and cytokine productionin vivoand enhanced IFN-γ and TNF-α production, as well as granzyme B expression by endogenous CD8+T cells in a cell-cell contact dependent manner. Furthermore, the adoptive transfer of IL-12/18/21 pre-activated γδT cells could overcome the resistance to anti-PD-L1 therapy, and the combination therapy had a synergistic effect on the therapeutic outcomes. Moreover, the enhanced anti-tumor function of adoptively transferred IL-12/18/21 pre-activated γδT cells was largely diminished in the absent of endogenous CD8+T cells when administered alone or in combination with anti-PD-L1, suggesting a CD8+T cell-dependent mechanism. Taken together, IL-12/18/21 pre-activation could promote γδT cell anti-tumor function and overcome the resistance to checkpoint blockade therapy, indicating an effective combinational cancer immunotherapeutic strategy.SynopsisIL-12/18/21 pre-activation enhances the anti-tumor efficacy of adoptively transferred γδT cells by promoting its proliferation, activation, and cytotoxicity, as well as activating endogenous CD8+T cells.Adoptive transfer of IL-12/18/21 pre-activated γδT cells could overcome the resistance to anti-PD-L1 therapy, indicating an effective combinational cancer immunotherapeutic strategy.
A mechanism of uncompetitive inhibition of the serotonin transporter
Authors: Bhat Shreyas , El-Kasaby Ali , Kasture Ameya , Boytsov Danila , Reichelt Julian B. , Hummel Thomas , Sucic Sonja , Pifl Christian , Freissmuth Michael , Sandtner Walter 
Published: August 2022

AbstractThe serotonin transporter (SERT/SLC6A4) is arguably the most extensively studied solute carrier (SLC). During its eponymous action - i.e., the retrieval of serotonin from the extracellular space - SERT undergoes a conformational cycle. Typical inhibitors (antidepressant drugs and cocaine), partial and full substrates (amphetamines and their derivatives) and atypical inhibitors (ibogaine analogues) bind preferentially to different states in this cycle. This results in competitive or non-competitive transport inhibition. Here, we explored the action of N-formyl-1,3-bis (3,4-methylenedioxyphenyl)-prop-2-yl-amine (ECSI#6) on SERT: inhibition of serotonin uptake by ECSI#6 was enhanced with increasing serotonin concentration. Conversely, the KM for serotonin was lowered by augmenting ECSI#6. ECSI#6 bound with low affinity to the outward-facing state of SERT but with increased affinity to a potassium-bound state. Electrophysiological recordings showed that ECSI#6 preferentially interacted with the inward-facing state. Kinetic modeling recapitulated the experimental data and verified that uncompetitive inhibition arose from preferential binding of ECSI#6 to the K+-bound, inward-facing conformation of SERT. This binding mode predicted a pharmacochaperoning action of ECSI#6, which was confirmed by examining its effect on the folding-deficient mutant SERT-PG601,602AA: pre-incubation of HEK293 cells with ECSI#6 restored export of SERT-PG601,602AA from the endoplasmic reticulum and substrate transport. Similarly, in transgenic flies, administration of ECSI#6 promoted delivery of SERT-PG601,602AA to the presynaptic specialization of serotonergic neurons. To the best of our knowledge, ECSI#6 is the first example of an uncompetitive SLC inhibitor. Pharmacochaperones endowed with the binding mode of ECSI#6 are attractive, because they can rescue misfolded transporters at concentrations, which cause modest transport inhibition.
Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules
Authors: Hashimoto Hideharu , Ramirez Daniel H. , Lautier Ophélie , Pawlak Natalie , Blobel Günter , Palancade Benoît , Debler Erik W. 
Published: August 2022

AbstractInSaccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside theSaccharomycetaceaefamily are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure ofScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyondSaccharomycetaceae, e.g. inSchizosaccharomyces pombeor human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix aC in the zf-C3HC and Rsm1 modules, and an extra helix αAB’ in the Rsm1 module. Conservation of key residues responsible for its distinct features identifiesS. pombeRsm1 andHomo sapiensNIPA/ZC3HC1 as structural orthologs ofScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function ofScPml39 inS. cerevisiae.
Accessible, interactive and cloud-enabled genomic workflows integrated with the NCI Genomic Data Commons
Authors: Hung Ling-Hong , Fukuda Bryce , Schmitz Robert , Hoang Varik , Lloyd Wes , Yeung Ka Yee 
Published: August 2022

ABSTRACTLarge scale data resources such as the NCI’s Cancer Research Data Commons (CRDC) and the Genotype-Tissue Expression (GTEx) portal have the potential to simplify the analysis of cancer data by providing data that can be used as standards or controls. However, comparisons with data that is processed using different methodologies or even different versions of software, parameters and supporting datasets can lead to artefactual results. Reproducing the exact workflows from text-based standard operating procedures (SOPs) is problematic as the documentation can be incomplete or out of date, especially for complex workflows involving many executables and scripts. We extend our open-source Biodepot-workflow-builder (Bwb) platform to provide a dynamic solution that disseminates the computational protocols to process large-scale sequencing data developed by the National Cancer Institute (NCI) Genomic Data Commons (GDC). Specifically, we converted the GDC DNA sequencing (DNA-Seq) and the GDC mRNA sequencing (mRNA-Seq) SOPs into reproducible, self-installing, containerized, and interactive graphical workflows. Secure integration with protected-access CRDC data is achieved using the Data Commons Framework Services (DCFS) Gen3 protocol. These graphical workflows can be applied to reproducibly analyze datasets across other repositories and/or custom user data. Analyses can be performed on a local laptop, desktop, or cloud providers. With RNA-Seq datasets from the GDC and GTEx, we illustrate the importance of uniform analysis of control and treatment data for accurate inference of differentially expressed genes. Furthermore, we demonstrate that these best practices for analyzing RNA-seq data from different sources can be achieved using our accessible workflows. Most importantly, we demonstrate how our reproducible distribution of the methodology can transform the analyses of cancer genomic data by enabling researchers to leverage datasets across multiple repositories to enhance data interpretation.
An evaluation of the early impact of the COVID-19 pandemic on Zambia’s routine immunization program
Authors: Winter Amy K. , Takahashi Saki , Carcelén Andrea , Hayford Kyla , Mutale Wilbroad , Mwansa Francis , Sinyange Nyambe , Ngula David , Moss William J. , Mutembo Simon 
Published: August 2022

AbstractBackgroundImplications of the COVID-19 pandemic for both populations and healthcare systems are vast. In addition to morbidity and mortality from COVID-19, the pandemic also has disrupted local health systems, including reductions or delays in routine vaccination services and catch-up vaccination campaigns that could lead to outbreaks of other infectious diseases that result in an additional burden of disease and strain on the healthcare system.Methods and FindingsWe evaluated the impact of the COVID-19 pandemic on Zambia’s routine childhood immunization program in 2020 using multiple sources of data. We relied on district-level administrative vaccination coverage data and Zambia’s 2018 Demographic and Health Survey to project disruptions to routine childhood vaccination within the pandemic year 2020 (N=5,670). Next, we leveraged serological data to predict age-specific measles seroprevalence and assessed the impact of changes in vaccination coverage on measles outbreak risk in each district. We found minor disruptions to routine administration of measles-rubella and pentavalent vaccines in 2020. This was in part due to Zambia’s Child Health Week held in June of 2020 which helped to reach children missed during the first six months of the year. We estimated that the two-month delay in a measles-rubella vaccination campaign, originally planned for September of 2020 but conducted in November of 2020 as a result of the pandemic, had little impact on modeled district-specific measles outbreak risks.ConclusionsThe pandemic only minimally increased the number of children missed by measles-rubella and pentavalent vaccines in 2020. However, the ongoing SARS-CoV-2 transmission since our analysis concluded means efforts to maintain routine immunization services and minimize the risk of measles outbreaks will continue to be critical. Fortunately, the methodological framework developed in this analysis relied on routinely collected data and can be used to evaluate COVID-19 pandemic disruptions in Zambia following 2020 and in other countries or for other vaccines at a sub-national level.
ATF3 Preserves Skeletal Muscle Stem Cell Quiescence by Preventing Precocious Activation
Authors: Zhang Suyang , Huang Yile , Yang Feng , He Liangqiang , Li Yuying , Esther Wan Yi Ching , Ding Yingzhe , Chan Kui Ming , Xie Ting , Sun Hao , Wang Huating 
Published: August 2022

AbstractSkeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how the SC quiescence is preserved. Here we report that AP-1 family member ATF3 preserves the SC quiescence by preventing their premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, and however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances SC activation during resistance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, which reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a novel mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.
Accumulation of defense systems in phage resistant strains ofPseudomonas aeruginosa
Authors: Costa Ana Rita , van den Berg Daan F. , Esser Jelger Q. , Muralidharan Aswin , van den Bossche Halewijn , Bonilla Boris Estrada , van der Steen Baltus A. , Haagsma Anna C. , Fluit Ad C. , Nobrega Franklin L. , Haas Pieter-Jan , Brouns Stan J.J. 
Published: August 2022

AbstractProkaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains ofPseudomonas aeruginosaand a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems are specific to phage genera, and that defense systems with complementary phage specificities co-occur inP. aeruginosagenomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes ofP. aeruginosawith at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistantP. aeruginosastrains.
Phosphorylation Status Of MUS81 Is A Modifier Of Olaparib Sensitivity In BRCA2-Deficient Cells
Authors: Blandino Francesca , Malacaria Eva , Figlioli Carolina , Noto Alessandro , Pugliese Giusj Monia , Franchitto Annapaola , Pichierri Pietro 
Published: August 2022

ABSTRACTThe MUS81 complex is crucial for preserving genome stability through resolution of branched DNA intermediates in mitosis and also for the processing of deprotected replication forks in BRCA2-deficient cells. Because of the existence of two different MUS81 complexes in mammalian cells that act in M or S-phase, whether and how the PARPi sensitivity of BRCA2-deficient cells is affected by loss of MUS81 function is unclear.Here, using a mutant of MUS81 that impairs its function in M-phase, we show that viability of BRCA2-deficient cells but not their PARPi sensitivity requires a fully-functional MUS81 complex in mitosis. In contrast, expression of a constitutively-active MUS81 is sufficient to confer PARPi resistance. From a mechanistic point of view, our data indicates that deregulated action of the mitotic active form of MUS81 in S-phase leads to the cleavage of stalled replication forks before their reversal, bypassing fork deprotection, and engaging a Polθ-dependent DSBs repair.Collectively, our findings describe a novel mechanism leading to PARPi resistance that involves unscheduled MUS81-dependent cleavage of intact, unreversed replication forks. Since this cleavage occurs mimicking the phosphorylated status of S87 of MUS81, our data suggest that hyperphosphorylation of this residue in S-phase might represent a novel biomarker to identify resistance to PARPi.
Is proteolytic cleavage essential for the activation of Hydra pore-forming toxin, HALT-4?
Authors: Wei Yuen Yap , Jung Shan Hwang 
Published: August 2022

AbstractThe mature form of Hydra actinoporin-like toxin 4 (mHALT-4) differs from other actinoporins primarily by bearing approximately 115 additional residues at the N-terminus. Five dibasic residues were found in this extended region and we assume that, when cleaved, each truncated HALT-4 (tKK1, tKK2, tRK3, tKK4 and tKK5) could exhibit an enhanced cytolytic activity. However, our results showed that mHALT-4, tKK1 and tKK2 possessed similar cytolytic activity against HeLa cells, whereas tRK3, tKK4 and tKK5 failed to kill HeLa cells. Therefore, the cleavage of KK1 or KK2 sites did not enhance the cytolytic activity of tKK1 and tKK2 but might facilitate the sorting of tKK1 and tKK2 to the regulated secretory pathway and eventually deposit them in the nematocyst. In contrast, RK3, KK4 and KK5 were unlikely to serve as the proteolytic cleavage sites since the amino acids between KK2 and RK3 are also crucial for the pore formation.HighlightsFive dibasic cleavage sites are identified at the N-terminal region of HALT-4 but they are unlikely to have a role in the enhancement of HALT-4 cytotoxicity.The first two dibasic sites, KK1 and KK2, may be involved in sorting HALT-4 to the regulated secretory pathway where HALT-4 can be transported to the nematocyst.
Low intensity repetitive transcranial magnetic stimulation modulates brain-wide functional connectivity to promote anti-correlated activity
Authors: Moretti Jessica , Terstege Dylan J. , Poh Eugenia Z. , Epp Jonathan R. , Rodger Jennifer 
Published: August 2022

AbstractBackgroundRepetitive transcranial magnetic stimulation (rTMS) induces action potentials to induce plastic changes in the brain with increasing evidence for the therapeutic importance of brain-wide functional network effects of rTMS; however, the influence of sub-action potential threshold (low-intensity; LI-) rTMS on neuronal activity is largely unknown.HypothesisWe investigated whether LI-rTMS modulates neuronal activity and functional connectivity. We also specifically assessed modulation of parvalbumin interneuron activity.MethodsWe conducted a brain-wide analysis of c-Fos, a marker for neuronal activity, in mice that received LI-rTMS to visual cortex. Mice received single or multiple sessions of excitatory 10Hz LI-rTMS with custom rodent coils or were sham controls. We assessed changes to c-Fos positive cell densities and c-Fos/parvalbumin co-expression. Peak c-Fos expression corresponded with activity during rTMS. We also assessed functional connectivity changes using brain-wide c-Fos-based network analysis.ResultsLI-rTMS modulated c-Fos expression in cortical and subcortical regions. c-Fos density changes were most prevalent with acute stimulation, however chronic stimulation decreased parvalbumin interneuron activity, most prominently in the amygdala and striatum. LI-rTMS also increased anti-correlated functional connectivity, with the most prominent effects also in the amygdala and striatum following chronic stimulation.ConclusionLI-rTMS induces changes in c-Fos expression that suggest modulation of neuronal activity and functional connectivity throughout the brain. Our results suggest that LI-rTMS promotes anticorrelated functional connectivity, possibly due to decreased parvalbumin interneuron activation induced by chronic stimulation. These changes may underpin therapeutic rTMS effects, therefore modulation of subcortical activity supports rTMS for treatment of disorders involving subcortical dysregulation.Highlights-Low-intensity rTMS increases brain-wide anti-correlated functional connectivity-Acute excitatory LI-rTMS modulates cortical and subcortical neuronal activity-Decreased parvalbumin interneuron activity may promote anti-correlated activity-Striatum and amygdala show prominent modulation with LI-rTMS