bluuebunny/crossref_metadata_2025_split huggingface dataset:
The integrated LIM-peptidase domain of the CSA1/CHS3 paired immune receptor detects changes in DA1 family peptidase inhibitors to confer Albugo candida resistance in Arabidopsis
Authors: Gu Benguo , Parkes Toby , Smith Caroline , Lu Fu-Hao , McKenzie Neil , Dong Hui , Jones Jonathan D. G. , Cevik Volkan , Bevan Michael W. 
Published: June 2022

AbstractWhite blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Arabidopsis CSA1/DAR4 (also known as CSA1/CHS3) paired immune receptor carries an Integrated Domain (ID) with homology to the DA1 family of peptidases. Using domain swaps with DA1 family members, we show that the DAR4 ID acts as an integrated decoy for DAR3, which interacts with and inhibits the peptidase activities of DA1, DAR1 and DAR2 family members. Albugo infection rapidly lowered DAR3 levels and activates DA1 peptidase activity. This promotes endoreduplication of host tissues to support pathogen growth. We propose that DAR4/CSA1 senses the actions of a putative Albugo effector that reduces DAR3 levels and initiates defense.
DHFR metabolic activity controls neurogenic transitions in the developing Human and mouse neocortex
Authors: Saha Sulov , Jungas Thomas , Ohayon David , Audouard Christophe , Ye Tao , Fawal Mohamad-Ali , Davy Alice 
Published: June 2022

ABSTRACTOne-carbon/folate (1C) metabolism supplies methyl groups required for DNA and histone methylation, and is involved in the maintenance of self-renewal in stem cells. Dihydrofolate reductase (DHFR), a key enzyme in 1C metabolism, is highly expressed in Human and mouse neural progenitors at the early stages of neocortical development. Here, we investigated the role of DHFR in the developing neocortex and report that reducing its activity in Human cerebral organoids and mouse embryonic neocortex accelerates indirect neurogenesis, a hallmark of mammalian brain evolution, thereby affecting neuronal composition of the neocortex. Further, we show that decreasing DHFR activity in neural progenitors leads to a reduction in One-carbon/folate metabolites and correlates with modifications of H3K4me3 methylation. Our findings reveal an unanticipated role for DHFR in controlling specific steps of neocortex development and indicate that variations in 1C metabolic cues impact cell fate transitions.
SUMO Activated Target Traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome
Authors: Salas-Lloret Daniel , van der Meulen Coen , Nagamalleswari Easa , Gracheva Ekaterina , de Ru Arnoud H. , Marie Otte H. Anne , van Veelen Peter A. , Pichler Andrea , Goedhart Joachim , Vertegaal Alfred C.O. , González-Prieto Román 
Published: June 2022

ABSTRACTUbiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2 and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 60,000 acceptor sites for ubiquitin and 40,000 acceptor sites for SUMO2/3. However, E3-to-target wiring is poorly understood. The limited number of SUMO E3s provides the unique opportunity to systematically study E3-substrate wiring. We developed SUMO Activated Target Traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL(ZNF451-3) and ZMIZ2. SATTs enabled us to identify 590 SUMO1 and 1195 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference, even at the substrate isoform level. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool (https://amsterdamstudygroup.shinyapps.io/PolaRVolcaNoseR/) to browse the dataset in an interactive manner, increasing the accessibility of this resource for the community. Overall, we uncover E3-to-target wiring of 1681 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
A CRISPR-engineered Isogenic Model Reveals Altered Neuronal Phenotypes of the 22q11.2 A-B Syndromic Deletion
Authors: Paranjape Neha , Lin Yu-Hsiu T. , Flores-Ramirez Quetzal , Sarin Vishesh , Johnson Amanda Brooke , Chu Julia , Paredes Mercedes , Wiita Arun P. 
Published: June 2022

ABSTRACTThe 22q11.2 deletion syndrome (22q11.2DS), associated with congenital and neuropsychiatric anomalies, is the most common copy number variant (CNV)-associated syndrome. Patient-derived, induced pluripotent stem cell (iPS) models have provided important insight into the mechanisms of phenotypic features of this condition. However, patient-derived iPS models may harbor underlying genetic heterogeneity that can confound analysis of pathogenic CNV effects. Furthermore, the ∼1.5 Mb “A-B” deletion at this locus is inherited at higher frequency than the more common ∼3 Mb “A-D” deletion, but remains under-studied due to lack of relevant models. To address these issues, here we leveraged a CRISPR-based strategy in Cas9-expressing iPS cells to engineer novel isogenic models of the 22q11.2 “A-B” deletion. After in vitro differentiation to excitatory neurons, integrated transcriptomic and cell surface proteomics identified deletion-associated alterations in surface adhesion and cell signaling. Furthermore, implantation of iPS-derived neuronal progenitor cells into the cortex of neonatal mice found accelerated neuronal maturation within a relevant microenvironment. Taken together, our results suggest pathogenic mechanisms of the 22q11.2 “A-B” deletion in driving neuronal and neurodevelopmental phenotypes, both in vitro and in vivo. We further propose that the isogenic models generated here will provide a unique resource to study this less-common variant of the 22q11.2 microdeletion syndrome.
Large-scale genetic screens identify BET-1 as a cytoskeleton regulator promoting actin health and lifespan
Authors: Garcia Gilberto , Bar-Ziv Raz , Dutta Naibedya , Moaddeli Darius , Averbukh Maxim , Torres Toni Castro , Alcala Athena , Tsui C. Kimberly , Moehle Erica A. , Shalem Ophir , Thorwald Max A. , Higuchi-Sanabria Ryo 
Published: June 2022

AbstractThe actin cytoskeleton is a three-dimensional scaffold of proteins that is a regulatory, energy-consuming network with dynamic properties to shape the structure and function of the cell. Proper actin function is required for many cellular pathways, including cell division, autophagy, chaperone function, endocytosis, and exocytosis. Deterioration of these processes manifests during aging and exposure to stress, which is in part due to the breakdown of the actin cytoskeleton. However, the regulatory mechanisms involved in preservation of cytoskeletal form and function are not well understood. Here, we performed a multi-pronged, cross-organismal screen combining a whole-genome CRISPR-Cas9 screen in human fibroblasts with in vivo C. elegans synthetic lethality screening. We identified the bromodomain protein, BET-1, as a key regulator of actin health and longevity. Overexpression of bet-1 preserves actin health at late age and promotes lifespan and healthspan in C. elegans. These beneficial effects are mediated through actin preservation by the transcriptional regulator function of BET-1. Together, our discovery assigns a key role for BET-1 in cytoskeletal health, highlighting regulatory cellular networks promoting cytoskeletal homeostasis.
A Single Anodal Transcranial Direct Current Stimulation Session to Enhance Sport-Specific Performance in Trained Individuals? A Systematic Review and Meta-Analysis
Authors: Maudrich Tom , Ragert Patrick , Perrey Stephane , Kenville Rouven 
Published: June 2022

AbstractBackgroundTranscranial direct current stimulation (tDCS) has emerged as a promising and feasible method to improve motor performance in healthy and clinical populations. However, the potential of tDCS to enhance sport-specific motor performance in athletes remains elusive.ObjectiveWe aimed at analyzing the acute effects of a single anodal tDCS session on sport-specific motor performance changes in athletes compared to sham.MethodsA systematic review and meta-analysis was conducted in the electronic databases PubMed, Web of Science, and SPORTDiscus with publication dates through April 2022. The meta-analysis was performed using an inverse variance method and a random-effects model. Additionally, two subgroup analyses were conducted (1) depending on the stimulated brain areas (i.e., primary motor cortex (M1), temporal cortex (TC), prefrontal cortex (PFC), cerebellum (CB)), and (2) studies clustered in subgroups according to different sports performance domains (endurance, strength, and visuomotor skill).ResultsA total number of 18 studies enrolling a sample size of 245 athletes were deemed eligible for inclusion. Across all included studies, a significant moderate standardized mean difference (SMD) favoring anodal tDCS to enhance sport-specific motor performance could be observed (SMD = 0.27, 95%CI [0.10, 0.44], p = 0.002). Subgroup analysis depending on cortical target areas of tDCS indicated non-significant moderate to high SMD in favor of anodal tDCS compared to sham for M1 (SMD = 0.24, 95%CI [-0.01, 0.49], p = 0.06), TC (SMD = 0.40, 95%CI [-0.10, 0.89], p = 0.12), PFC (SMD = 0.23, 95%CI [-0.04, 0.50], p = 0.09) and CB (SMD = 0.89, 95%CI [-0.15, 1.94], p = 0.09). Performance domain subgroup analysis revealed non-significant moderate SMD favoring anodal tDCS compared to sham: endurance domain (SMD = 0.23, 95%CI [-0.01, 0.47], p = 0.06), strength domain (SMD = 0.44, 95%CI [-0.14, 1.01], p = 0.14, Chi2 = 0.31) and visuomotor skill domain (SMD = 0.30, 95%CI [-0.03, 0.62], p = 0.07).ConclusionA single anodal tDCS session leads to performance enhancement in athletes in sport-specific motor tasks. Although no conclusions can be drawn regarding the modes of action as a function of performance domain or stimulation site, these results imply intriguing possibilities concerning sports performance enhancement. Furthermore, this study highlights the need to investigate tDCS applications under real-life conditions rather than in highly controlled laboratory settings to uncover the true potential of non-invasive brain stimulation as a performance enhancement not only in sports but also in the context of prevention or rehabilitation of neurological diseases.
A novel inovirus reprograms metabolism and motility of marine Alteromonas
Authors: Jia Kuntong , Peng Yongyi , Chen Xueji , Jian Huahua , Jin Min , Yi Zhiwei , Su Ming , Dong Xiyang , Yi Meisheng 
Published: June 2022

AbstractMembers from the Inoviridae family with striking features are widespread, highly diverse and ecologically pervasive across multiple hosts and environments; however, very small amount of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ϕAFP1, was isolated from the South China Sea and represented as a novel genus of Inoviridae. ϕAFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed ϕAFP1 could be regarded as genetic mosaics, which especially came from Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to ϕAFP1 infection reveals that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways and degradation of multiple amino acid pathways at plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that ϕAFP1 might hijack the energy of the host for the synthesis of phage proteins. ϕAFP1 exerted the step-by-step control on host genes through the appropriate level of the utilizing host resources, affirming a new non-standard regulatory strategy of viral temperately control over the host transcriptional profile. Our study provides novel information for a better understanding of filamentous phage characteristics and phage-host interactions.
CaMKII binding to GluN2B flips a β-adrenergic switch from synaptic depression to potentiation
Authors: Buonarati Olivia R. , Larsen Matthew E. , Qian Hai , Hell Johannes W. , Bayer K. Ulrich 
Published: June 2022

AbstractLearning, memory and cognition are thought to require forms of synaptic plasticity such as hippocampal long-term potentiation and depression (LTP and LTD), and such plasticity can be modulated by β-adrenergic stimulation with isoproterenol or norepinephrine. For instance, LTP versus LTD is induced by high-versus low-frequency stimulation (HFS versus LFS) but, stimulating β-adrenergic receptors (βARs) enables LTP induction also by LFS. In contrast to HFS-LTP, such βAR-LTP requires signaling by L-type voltage-gated Ca2+-channels, not NMDA-type glutamate receptors (NMDARs). Surprisingly, we found that βAR-LTP still required a non-ionotropic NMDAR function: the stimulus-induced binding of the Ca2+/calmodulin-dependent protein kinase II (CaMKII) that mediates CaMKII movement to excitatory synapses. In hippocampal neurons, β-adrenergic stimulation with isoproterenol transformed LTD-type CaMKII movement to LTP-type movement, resulting in CaMKII movement to excitatory instead of inhibitory synapses. Additionally, isoproterenol enabled induction of a major cell-biological feature of LTP in response to LTD stimuli: increased SEP-GluA1 surface expression. Like for the βAR-LTP in hippocampal slices, the effects of isoproterenol on CaMKII movement and SEP-GluA1 surface expression involved L-type Ca2+-channels. Taken together, these results indicate that isoproterenol transforms LTD stimuli to LTP signals by switching CaMKII movement and GluN2B binding to LTP mode.One Sentence SummaryBuonarati et al. show that β-adrenergic stimulation enables LTP induction in response to LTD stimuli by switching synaptic CaMKII movement to LTP mode.
Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains
Authors: Hay Iain M. , Shamin Maria , Caroe Eve R. , Mohammed Ahmed S. A. , Svergun Dmitri I. , Jeffries Cy M. , Graham Stephen C. , Sharpe Hayley J. , Deane Janet E. 
Published: June 2022

ABSTRACTThe type IIB receptor protein tyrosine phosphatases (R2B RPTPs) are cell surface transmembrane proteins that engage in cell adhesion via their extracellular domains (ECDs) and cell signaling via their cytoplasmic phosphatase domains. The ECDs of R2B RPTPs form stable, homophilic, trans interactions between adjacent cell membranes. Previous work has demonstrated how one family member, PTPRM, forms homodimers; however, the determinants of homophilic specificity remain unknown. We have solved the X-ray crystal structure of the membrane-distal, N-terminal domains of PTPRK that form a head-to-tail dimer consistent with intermembrane adhesion. Comparison with the PTPRM structure demonstrates inter-domain conformational differences that may define homophilic specificity. Using small-angle X-ray scattering we determined the solution structures of the full-length ECDs of PTPRM and PTPRK, identifying that both are rigid, extended molecules that differ in their overall long-range conformation. Furthermore, we identify one residue, W351, within the interaction interface that differs between PTPRM and PTPRK and show that mutation to glycine, the equivalent residue in PTPRM, abolishes PTPRK dimer formation in vitro. This comparison of two members of the receptor tyrosine phosphatase family suggest that homophilic specificity is driven by a combination of shape complementarity and specific but limited sequence differences.SIGNIFICANCE STATEMENTCell-cell contacts are dynamically regulated, in part, by the actions of tyrosine kinases and phosphatases. The R2B family of receptor tyrosine phosphatases combine an adhesive extracellular domain with intracellular catalytic domains that bind and dephosphorylate key cell adhesion and polarity proteins. Previous work demonstrated that the extracellular domains form head-to-tail homodimers but, as the interface was composed of residues conserved across the family, homophilic specificity determinants remained unclear. We have used a range of structural techniques including X-ray crystallography, small angle X-ray scattering and AlphaFold modelling to demonstrate that, despite their similarity, two members of the R2B family possess significant differences in their overall shape. Our results support that a combination of subtle shape and sequence variations may determine homophilic binding.
DESIGN OF A CHIMERIC ACE-2/Fc-SILENT FUSION PROTEIN WITH ULTRAHIGH AFFINITY AND NEUTRALIZING CAPACITY FOR SARS-CoV-2 VARIANTS
Authors: Bodie Neil M. , Connolly David , Chu Jennifer , Uhal Bruce D 
Published: June 2022

AbstractAs the coronavirus SARS-CoV-2 continues to mutate into Variants of Concern (VOC), there is a growing and urgent need to develop effective antivirals to combat the newly emerged infectious disease COVID-19. Recent data indicate that monoclonal antibodies developed early in the pandemic are no longer capable of effectively neutralizing currently active VOCs. This report describes the design of a class of variant-agnostic chimeric molecules consisting of an Angiotensin Converting Enzyme-2 (ACE-2) domain mutated to retain ultrahigh affinity binding to a wide variety of SARS-CoV-2 variants, coupled to an Fc-silent immunoglobulin domain that eliminates antibody-dependent enhancement (ADE) and simultaneously extends biological half-life compared to existing mABs. Molecular modeling revealed that ACE-2 mutations L27, V34 and E90 resulted in ultrahigh affinity binding of the LVE-ACE-2 domain to the widest variety of VOCs, with KDs of 93 pM, 507 pM and 73 pM for binding to the Alpha B1.1.7, Delta B.1.617.2 and Omicron B.1.1.529 variants, and notably, 78fM affinity to the Omicron BA.2 variant, respectively. Surrogate viral neutralization assays (sVNT) revealed titers of ≥4.9ng/ml, for neutralization of recombinant viral proteins corresponding to the Alpha, Delta and Omicron variants. The values above were obtained with LVE-ACE-2/mAB chimeras containing the Y-T-E sequence that enhances binding to the FcRn receptor, which in turn is expected to extend biological half-life 3-4-fold. It is proposed that this new class of chimeric ACE-2/mABs will constitute variant-agnostic and cost-effective prophylactics against SARS-CoV-2, particularly when administered by nasal delivery systems.
Structural stability of Human serum albumin is modified in rheumatoid arthritis
Authors: Lin Hsien-Jung L. , Parkinson David H. , Holman J. Connor , Thompson W. Chad , Anderson Christian N. K. , Hadfield Marcus , Ames Stephen , Pina Nathan R. Zuniga , Bowden Jared N. , Quinn Colette , Hansen Lee D. , Price John C. 
Published: June 2022

ABSTRACTDifferential scanning calorimetry (DSC) can interrogate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes are a result of either concentration or altered thermal stabilities for 7-10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of the most abundant protein, human serum albumin (HSA). By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.
Inflammasome targeting with an NLRP3 agonist therapy is feasible but ineffective in murine hepatocellular carcinoma models with liver damage
Authors: Pu Zhangya , Liu Zelong , Chen Jiang , Inoue Koetsu , Ruan Zhiping , Zhu Lingling , Kikuchi Hiroto , Matsui Aya , Huang Peigen , Duda Dan G. 
Published: June 2022

AbstractCo-inhibition of programmed cell death receptor-1 (PD-1) and vascular endothelial growth factor receptor (VEGFR) pathway has shown efficacy in hepatocellular carcinoma (HCC). NLRP3 is a component of the inflammasome involved in the initiation, development, and progression of multiple cancers. We examined whether adding an NLRP3 agonist to dual PD-1/VEGFR inhibitors is feasible and can address treatment resistance in orthotopic HCC in mice with underlying liver damage. Mice with established tumors were treated with an NLRP3 agonist alone, combination of anti-VEGFR2 or the multikinase inhibitor regorafenib with anti-PD1 antibodies, or their combination. In all models tested, NLRP3 agonist therapy showed acceptable toxicity but no effect on tumor growth delay, disease morbidity, or survival. Pharmacodynamic analyses confirmed the effects of NLRP3 agonist therapy on inflammasome, evidenced by a significant elevation in plasma levels of pro-inflammatory cytokines such as IL-1β. However, these changes were not detectable in tumor tissues, where we detected increased expression of immunosuppressive markers IL-6, KC/GRO, CCL9, and IL-18, and immune checkpoint molecules (PD1, PD-L1, and CTLA-4) after NLRP3 agonist therapy. Thus, modulation of the inflammasome with a novel NLRP3 agonist was feasible in mice with orthotopic HCC and liver damage but did not enhance efficacy when combined with anti-PD1/VEGFR therapies.