bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsic bias at non-canonical, β-arrestin-coupled seven transmembrane receptors
Authors: Pandey Shubhi , Kumari Punita , Baidya Mithu , Kise Ryoji , Cao Yubo , Dwivedi-Agnihotri Hemlata , Banerjee Ramanuj , Li Xaria X. , Cui Cedric S. , Lee John D. , Kawakami Kouki , Chaturvedi Madhu , Ranjan Ashutosh , Laporte Stéphane A. , Woodruff Trent M. , Inoue Asuka , Shukla Arun K. 
Published: February 2021

AbstractG protein-coupled receptors (GPCRs) are typically characterized by their seven transmembrane (7TM) architecture, and interaction with two universal signal-transducers namely, the heterotrimeric G-proteins and β-arrestins (βarrs). Synthetic ligands and receptor mutants have been designed to elicit transducer-coupling preferences and distinct downstream signaling outcomes for many GPCRs. This raises the question if some naturally-occurring 7TMRs may selectively engage one of these two signal-transducers, even in response to their endogenous agonists. Although there are scattered hints in the literature that some 7TMRs lack G-protein coupling but interact with βarrs, an in-depth understanding of their transducer-coupling preference, GRK-engagement, downstream signaling and structural mechanism remains elusive. Here, we use an array of cellular, biochemical and structural approaches to comprehensively characterize two non-canonical 7TMRs namely, the human decoy D6 receptor (D6R) and the human complement C5a receptor (C5aR2), in parallel with their canonical GPCR counterparts, CCR2 and C5aR1, respectively. We discover that D6R and C5aR2 couple exclusively to βarrs, exhibit distinct GRK-preference, and activate non-canonical downstream signaling partners. We also observe that βarrs, in complex with these receptors, adopt distinct conformations compared to their canonical GPCR counterparts despite being activated by a common natural agonist. Our study therefore establishes D6R and C5aR2 as bona-fide arrestin-coupled receptors (ACRs), and provides important insights into their regulation by GRKs and downstream signaling with direct implications for biased agonism.
Amplification of the epigenetic (gestational) age acceleration signal
Authors: Lee Yunsung , Bohlin Jon 
Published: February 2021

ABSTRACTBackgroundEpigenetic (gestational) age acceleration (E(G)AA) is associated with environmental exposures and health outcomes in humans. However, E(G)AA is the residual term from a regression of epigenetic age (outcome) on chronological (gestational) age (predictor) and therefore strongly obscured by ‘noise’ from multiple sources. Here, we propose a simple procedure, based on regression, principal component analysis (PCA), and the Lasso, that amplifies E(G)AA signals. More specifically, we first regress given (gestational) age against each CpG used for epigenetic (gestational) age prediction. The CpGs are typically taken from one of several epigenetic clocks available. PCA is subsequently performed on the resulting matrix of residual vectors for each CpG as it projects the E(G)AA signal onto perpendicular principal components (PCs), thereby separating ‘signal’ from noise. Finally, we use the Lasso to select PCs associated with an outcome of interest. We apply our method to previous studies: EAA in patients with Down’s syndrome and Werner’s syndrome and EGAA of newborns exposed to prenatal smoking as well as associations with maternal BMI.ResultsThe extracted EAA components computed using our proposed procedure revealed a significant association with Down’s syndrome (PB<0.05, Bonferroni adjusted for multiple testing) as well as for Werner’s Syndrome (PB<0.05). For EGAA we find a significant association with maternal prenatal smoking (PB<0.05, also Bonferroni adjusted) and maternal BMI (PB<0.05). Additionally, by examining the loadings of the PCs of interest, and contrary to residual EGAA, our method can identify implicated CpGs.ConclusionsOur findings suggest that our proposed procedure leads to a remarkable amplification of the E(G)AA signal. Furthermore, our method reveals that E(G)AA is a composite signal that can be driven by multiple independent factors.
Wilms Tumorigenesis in Human Kidney Organoids
Authors: Waehle Verena , Ungricht Rosemarie , Hoppe Philipp S. , Betschinger Joerg 
Published: February 2021

SUMMARYThe loss or failure of cell differentiation is a hallmark of cancer, yet whether perturbation of differentiation is causal or consequential to malignant transformation is largely unclear. Wilms tumor is the most widespread kidney cancer in children. Here, we establish a model for Wilms tumorigenesis in human kidney organoids. We show that loss of the tumor suppressor WT1 during organoid formation induces overgrowth of kidney progenitor cells at the expense of differentiating tubules. Functional and gene expression analyses demonstrate that absence of WT1 halts progenitor cell progression at a pre-epithelialized cell state and recapitulates the transcriptional changes detected in a subgroup of Wilms tumor patients with ectopic myogenesis. By “transplanting” WT1 mutant cells into wild-type kidney organoids, we find that their propagation requires an untransformed microenvironment. Genetic engineering of cancer lesions in human organoids therefore permits phenotypic modeling of tumor initiation and progression, and complements the current toolbox of pre-clinical Wilms tumor models.
PolyQ expansion does not alter the Huntingtin-HAP40 complex
Authors: Huang Bin , Guo Qiang , Niedermeier Marie L. , Cheng Jingdong , Engler Tatjana , Maurer Melanie , Pautsch Alexander , Baumeister Wolfgang , Stengel Florian , Kochanek Stefan , Fernández-Busnadiego Rubén 
Published: February 2021

SummaryThe abnormal amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington disease (HD). At the protein level, this translates into the expansion of a poly-glutamine (polyQ) stretch located at the HTT N-terminus, which renders it aggregation-prone by unknown mechanisms. Here we investigated the effects of polyQ expansion on HTT in a complex with its stabilizing interaction partner huntingtin-associated protein 40 (HAP40). Surprisingly, our comprehensive biophysical, crosslinking mass spectrometry and cryo-EM experiments revealed no major differences in the conformation of HTT-HAP40 complexes of various polyQ length, including 17QHTT-HAP40 (wild type), 46QHTT-HAP40 (typical polyQ length in HD patients) and 128QHTT-HAP40 (extreme polyQ length). Thus, HTT polyQ expansion does not alter the global structure of HTT when associated with HAP40.
MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction
Authors: Murigneux Valentine , Roberts Leah W. , Forde Brian M. , Phan Minh-Duy , Nhu Nguyen Thi Khanh , Irwin Adam D. , Harris Patrick N. A. , Paterson David L. , Schembri Mark A. , Whiley David M. , Beatson Scott A. 
Published: February 2021

AbstractOxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers; however, easy and automated construction of high-quality bacterial genomes remains challenging. Here we present MicroPIPE: a reproducible end-to-end bacterial genome assembly pipeline for ONT and Illumina sequencing. To construct MicroPIPE, we evaluated the performance of several tools for genome reconstruction and assessed overall genome accuracy using ONT both natively and with Illumina. Further validation of MicroPIPE was carried out using 11 sequence type (ST)131 Escherichia coli and eight publicly available Gram-negative and Gram-positive bacterial isolates. MicroPIPE uses Singularity containers and the workflow manager Nextflow and is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe.
Animal-appropriate housing of ball pythons (Python regius) — Behavior-based evaluation of two types of housing systems
Authors: Hollandt Tina , Baur Markus , Wöhr Caroline 
Published: February 2021

AbstractConsidering animal welfare, animals should be kept in animal-appropriate and stress-free housing conditions in all circumstances. To assure such conditions, not only basic needs must be met, but also possibilities must be provided that allow animals in captive care to express all species-typical behaviors. Rack housing systems for snakes have become increasingly popular and are widely used; however, from an animal welfare perspective, they are no alternative to furnished terrariums. In this study, we therefore evaluated two types of housing systems for ball pythons (Python regius) by considering the welfare aspect animal behavior. In Part 1 of the study, ball pythons (n= 35) were housed individually in a conventional rack system. The pythons were provided with a hiding place and a water bowl, temperature control was automatic, and the lighting in the room served as indirect illumination. In Part 2 of the study, the same ball pythons, after at least 8 weeks, were housed individually in furnished terrariums. The size of each terrarium was correlated with the body length of each python. The terrariums contained substrate, a hiding place, possibilities for climbing, a water basin for bathing, an elevated basking spot, and living plants. The temperature was controlled automatically, and illumination was provided by a fluorescent tube and a UV lamp. The shown behavior spectrum differed significantly between the two housing systems (p< 0.05). The four behaviors basking, climbing, burrowing, and bathing could only be expressed in the terrarium. Abnormal behaviors that could indicate stereotypies were almost exclusively seen in the rack system. The results show that the housing of ball pythons in a rack system leads to a considerable restriction in species-typical behaviors; thus, the rack system does not meet the requirements for animal-appropriate housing.
The Arabidopsis AAC Proteins CIL and CIA2 Are Sub-functionalized Paralogs involved in Chloroplast Development
Authors: Li Mingjiu , Ruwe Hannes , Melzer Michael , Junker Astrid , Hensel Götz , Tschiersch Henning , Schwenkert Serena , Chamas Sindy , Schmitz-Linneweber Christian , Börner Thomas , Stein Nils 
Published: February 2021

ABSTRACTThe Arabidopsis geneChloroplast Import Apparatus 2 (CIA2)encodes a transcription factor that positively affects the activity of nuclear genes for chloroplast ribosomal proteins and chloroplast protein import machineries.CIA2-like (CIL)is the paralogous gene ofCIA2. We generated acilmutant by site-directed mutagenesis and compared it withcia2andcia2cildouble mutant. Phenotype of thecilmutant did not differ from the wild type under our growth conditions, except faster growth and earlier time to flowering. Compared tocia2,thecia2cilmutant showed more impaired chloroplast functions and reduced amounts of plastid ribosomal RNAs.In silicoanalyses predict for CIA2 and CIL a C-terminal CCT domain and an N-terminal chloroplast transit peptide (cTP). Chloroplast (and potentially nuclear) localization was previously shown for HvCMF3 and HvCMF7, the homologs of CIA2 and CIL in barley. We observed nuclear localization of CIL after transient expression in Arabidopsis protoplasts. Surprisingly, transformation ofcia2withHvCMF3, HvCMF7or with a truncatedCIA2lacking the predicted cTP could partially rescue the pale-green phenotype ofcia2. These data are discussed with respect to potentially overlapping functions between CIA2, CIL and their barley homologs and to the function of the putative cTPs of CIA2 and CIL.HIGHLIGHTThe nucleus-localized CCT domain proteins CIA2 and CIL in Arabidopsis and the homologous chloroplast-localized HvCMF3 and HvCMF7 in barley retained partially overlapping functions in chloroplast development.
Extracellular membrane tubules involved in suberin deposition in plant cell walls
Authors: De Bellis Damien , Kalmbach Lothar , Marhavy Peter , Daraspe Jean , Geldner Niko , Barberon Marie 
Published: February 2021

AbstractSuberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots, the outer layers of stems and roots with secondary growth, as well as in wound-induced tissues. Its presence allows organs to resist various environmental stresses, such as pathogen attack, drought or excessive salt concentrations. Suberin is a mostly aliphatic polyester of long-chain fatty acids and alcohols, often co-occurring with lignin-like polymers in the same cells. Most suberizing cells appear to deposit suberin in the form of lamellae just outside of the plasma membrane, below the primary cell wall. The monomeric precursors of suberin are thought to be glycerated fatty acids, synthesized at the endoplasmic reticulum. However, it has remained obscure how these monomers are transported outside of the cell, where they will be polymerized to form suberin lamellae. Here, we demonstrate that extracellular vesicular-tubular structures accumulate specifically in suberizing cells. By employing various, independent mutational and hormonal challenges, known to affect suberization in distinct ways, we demonstrate that their presence correlates perfectly with root suberization. Surprisingly, no endosomal compartment marker showed any conspicuous changes upon induction of suberization, suggesting that this compartment might not derive from endosomal multi-vesicular bodies, but possibly form directly from endoplasmic reticulum subdomains. Consistent with this, we could block formation of both, suberin deposition and vesicle accumulation by a pharmacogenetic manipulation affecting early steps in the secretory pathway. Whereas many previous reports have described extracellular vesicle occurrence in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in suberin formation.One Sentence SummarySuberin lamellae formation is associated with extracellular membrane tubules.
Investigation of USP30 inhibition to enhance Parkin-mediated mitophagy: tools and approaches
Authors: Tsefou Eliona , Walker Alison S. , Clark Emily H. , Hicks Amy R. , Luft Christin , Takeda Kunitoshi , Watanabe Toru , Ramazio Bianca , Staddon James M. , Briston Thomas , Ketteler Robin 
Published: February 2021

SummaryMitochondrial dysfunction is implicated in Parkinson disease (PD). Mutations in Parkin, an E3 ubiquitin ligase, can cause juvenile-onset Parkinsonism probably through impairment of mitophagy. Inhibition of the de-ubiquitinating enzyme USP30 may counter this effect to enhance mitophagy. Using different tools and cellular approaches, we wanted to independently confirm this claimed role for USP30. Pharmacological characterization of additional tool compounds that selectively inhibit USP30 are reported. The consequence of USP30 inhibition by these compounds, siRNA knockdown and overexpression of dominant-negative USP30 in the mitophagy pathway in different disease-relevant cellular models was explored. Knockdown and inhibition of USP30 showed increased p-Ser65-ubiquitin levels and mitophagy in neuronal cell models. Furthermore, patient-derived fibroblasts carrying pathogenic mutations in Parkin showed reduced p-Ser65-ubiquitin levels compared to wild-type cells, levels that could be restored using either USP30 inhibitor or dominant-negative USP30 expression. Our data provide additional support for USP30 inhibition as a regulator of the mitophagy pathway.
Evidence for spatiotemporal shift in demersal fisheries management priority areas in the western Mediterranean
Authors: Paradinas Iosu , Giménez Joan , Conesa David , López-Quílez Antonio , Pennino Maria Grazia 
Published: February 2021

AbstractMarine Protected Areas (MPAs) are a promising management tool for the conservation and recovery of marine ecosystems, as well as fisheries management. MPAs are generally established as permanent closures but marine systems are dynamic, which has generated debate in favour of more dynamic designs. As a consequence, the identification of priority areas should assess their persistence in space and time. Here, we develop a step-by-step approach to assess the spatiotemporal dynamics of fisheries management priority areas using standard fishery-independent survey data. To do so, we fit Bayesian hierarchical spatiotemporal SDM models to different commercially important demersal species and use the resulting maps to fit different spatial prioritisation configurations. We use these results to assess the spatiotemporal dynamics of fisheries priority areas. The proposed method is illustrated through a western Mediterranean case study using fishery-independent trawl survey data on six commercially important species collected over 17 years. We identified two fisheries priority area patterns in the study area, each predominant during a different time-period of the study, asserting the importance of regularly re-assessing MPA designs.
H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis
Authors: Verma Ayushi , Singh Akhilesh , Nengroo Mushtaq Ahmad , Saini Krishan Kumar , Sinha Abhipsa , Singh Anup Kumar , Datta Dipak 
Published: February 2021

AbstractTriple Negative Breast Cancer (TNBC) is known to have poor prognosis and adverse clinical outcome among all breast cancer subtypes due to the absence of available targeted therapy for it. Emerging literature indicates that epigenetic reprogramming is now appreciated as a driving force for TNBC pathophysiology. High expression of epigenetic modulator EZH2 (Enhancer of zeste homolog 2) has been shown to correlate with TNBC poor prognosis but the contribution of EZH2 catalytic (H3K27me3) versus non-catalytic EZH2 (NC-EZH2) function in TNBC growth and progression remains elusive. In the process of dissecting the impact of H3K27me3 versus NC-EZH2 function in TNBC pathogenesis, we reveal that selective hyperactivation of H3K27me3 over NC-EZH2 not only promotes TNBC metastasis but also alters the metastatic landscape of TNBC. Using extensivein- vivolive animal imaging, we present conclusive evidence that peritoneal metastasis, particularly splenic metastasis of TNBC is governed by H3K27me3. Transcriptome analyses of hyperactive H3K27me3 cells lead us to discover Cytokeratin-14 (KRT14) as a new target of H3K27me3. Unlike classical H3K27me3 mediated suppression of gene expression, here; we observe that H3K27me3 enhances KRT14 transcription by attenuating the binding of transcriptional repressor Sp1 to its promoter. Further, loss of KRT14 significantly reduces TNBC migration, invasion and splenic metastasis. Finally, genetic ablation of EZH2 or pharmacological inhibition of EZH2 catalytic function by FDA approved drug tazemetostat (EPZ6438) robustly inhibits TNBC peritoneal metastasis. Altogether, our preclinical findings posit a rational insight for the clinical development of H3K27me3 inhibitor like tazemetostat as a targeted therapy against TNBC.
A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and non-vascular plants
Authors: Chini Andrea , Monte Isabel , Fernández-Barbero Gemma , Boter Marta , Hicks Glenn , Raikhel Natasha , Solano Roberto 
Published: February 2021

AbstractThe phytohormone JA-Ile regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein COI1 (Coronatine Insensitive 1) and a JAZ (Jasmonate ZIM-domain) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signalling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI-JAZ interaction and degradation of JAZ1 and JAZ9in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana)COI1-JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1- JAZ also occurs in the liverwortMarchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signalling, J4 works as an antagonist of the closely-related auxin signalling pathway, preventing TIR1/Aux-IAA interaction and auxin responsesin planta,including hormone-mediated degradation of an auxin repressor, gene expression and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways.One sentence summaryA chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and non-vascular plants.
Consciously detecting and recognizing a stimulus without knowing what it looks like
Authors: Rimsky-Robert Daphné , Lisi Matteo , Noûs Camille , Sergent Claire 
Published: February 2021

AbstractDoes conscious perception occur during initial sensory processing, or does it arise later in a supra modal fashion? If conscious access truly depends on supra modal processes, we may be able to induce “asensory perception”, where only the semantic features of a meaningful stimulus are accessed, untied to its sensory attributes. Here we tested this prediction by degrading the low-level sensory representations of visual words in the brain using pattern masking, and subsequently presenting audio words that were either semantically related to the masked word or not. We hypothesized these retrospective semantic cues would reactivate the remaining traces of the masked word in the brain, and induce awareness of any information that was not disrupted by masking. In three separate experiments we show that, when presented with retrospective cues that are semantically related to the masked word, participants are better at detecting the presence of the preceding masked word and naming it, while at the same time being unable to report its visual features. In other words, participants could consciously detect and recognize the preceding masked word, without knowing what it looked like. These findings suggest that non-sensory information can be consciously accessed in relative independence from the build-up of sensory representations.