bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphorylation of Gαi shapes canonical Gα(i)βγ/GPCR signaling
Authors: Roy Suchismita , Sinha Saptarshi , Silas Ananta James , Ghassemian Majid , Kufareva Irina , Ghosh Pradipta 
Published: September 2022

AbstractA long-standing question in the field of signal transduction is to understand the interplay between distinct signaling pathways that control cell behavior. For growth factors and heterotrimeric G proteins, the two major signaling hubs in eukaryotes, the mechanisms of independent signal transduction have been extensively characterized; however, if/how they may cross talk remains obscure. Here we use linear-ion-trap mass spectrometry in combination with cell-based biophysical, biochemical, and phenotypic assays to chart at least three distinct ways in which growth factors may impact canonical Gα(i)βγ signaling downstream of a GPCR (CXCR4) via phosphorylation of Gαi. Phosphomimicking mutations in a cluster of residues in the αE helix (Y154/Y155) result in the suppression of agonist-induced Gα(i) activation while promoting constitutive Gβγ signaling; others in the P-loop (Ser44, Ser47, Thr48) suppress Gi activation entirely thus completely segregating the growth factor and GPCR pathways. While most phosphoevents appear to impact, as expected, the core properties of Gα(i) (conformational stability, nucleotide binding, Gβγ association and release, etc.), one phosphomimicking mutation promoted mislocalization of Gαi from the plasma membrane: a novel and unexpected mechanism of GPCR signal suppression. A phosphomutation of C-terminal Y320was sufficient to orchestrate such suppression by protein compartmentalization. Findings not only elucidate how growth factor and chemokine signals crosstalk through phosphomodulation of Gαi, but also how such crosstalk may generate signal diversity.
Practical scan-length considerations for mapping upper limb movements to the somatosensory/motor cortex at 7T
Authors: Rangaprakash D , Rowe Olivia E , Song Hyungeun , Gutierrez-Arango Samantha , Fernandez Michael F , Israel Erica A , Herr Hugh M , Barry Robert L 
Published: September 2022

AbstractThe relationship between motor cortex (M1) and upper limb movements has been investigated extensively using functional MRI (fMRI). While most research has focused on applications, very few studies have focused on practical aspects related to developing the fMRI protocol. Thus, the effect of scan length on M1 activations during various upper limb movements remains unclear. Scan length constraints are important for conducting motor experiments within a 60- or 90-min scan session. We targeted this gap by studying 7T fMRI activations in a male participant while performing eight different upper limb movements (of the fingers, wrist, and elbow) across 16 task runs (8 with the left arm, 8 with the right arm, 88 mins total fMRI duration). Standard activation analyses were performed (Z>3.1, p<0.01, cluster thresholded) independently for 14 different cases (2 runs through 8 runs, left and right arm) and compared. We found diminishing returns with higher number of runs (activations gradually plateaued with runs). We observed two clusters of movements, one with generally higher activation (more activated voxels and higher Z-stats) and the other with lower activation. To achieve similar statistical power, movements with lower activation required longer scanning (more runs). Based on these observations, we propose a ‘one size does not fit all’ practical protocol within a 60-, 75-, or 90-min scan session, wherein different number of runs are assigned for different movements. Our study could benefit researchers who are designing upper limb fMRI experiments.
The parthenogenesis mechanism and venom complement of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent
Authors: Inwood Sarah N. , Harrop Thomas W.R. , Dearden Peter K. 
Published: September 2022

AbstractA biocontrol system in New Zealand using the endoparasitoid Microctonus hyperodae is failing, despite once being one of the most successful examples of classical biocontrol worldwide. In this study, RNA-seq was used to characterise two key traits of M. hyperodae in this system, the venom complement, critical for the initial success of biocontrol, and the asexual reproduction, which influenced the decline. Full characterisation of M. hyperodae venom revealed 82 candidate venom transcripts with both signal peptides and significantly higher expression in venom. Among these were many involved in manipulating the host environment to source nutrition for the parasitoid egg, preventing a host immune response against the egg, as well as two components that may stimulate the host’s innate immune system. Notably lacking from this list was calreticulin, as it also had high expression in the ovaries. In-situ hybridisation revealed expression was localised to the follicle cells, which may result in the deposition of calreticulin into the egg exochorion. Investigating the asexual reproduction of M. hyperodae revealed core meiosis-specific genes had conserved expression patterns with the highest expression in the ovaries, suggesting M. hyperodae parthenogenesis involves meiosis and the potential for sexual reproduction may have been retained. Upregulation of genes involved in endoreduplication provides a potential mechanism for the restoration of diploidy in eggs after meiosis.
Epiphenomenal neural activity in the primate cortex
Authors: Tremblay Sébastien , Testard Camille , Inchauspé Jeanne , Petrides Michael 
Published: September 2022

AbstractWhen neuroscientists record neural activity from the brain, they often conclude that neural responses observed during task performance are indicative of the functional role of the brain area(s) studied. In humans and nonhuman primates, it is often hard to combine recordings and causal techniques within the same experiment, leaving the possibility that the activity recorded may be epiphenomenal rather than reflecting a specific functional role. Currently, the prevalence of epiphenomenal neural activity in the cortex is unknown. To estimate the extent of such activity in primates, we chronically recorded neural activity in the prefrontal cortex of the same monkeys using the same neural implants during the performance of four different cognitive tasks. The four tasks were carefully selected such that only one of them causally depends on the brain area recorded, as demonstrated by previous double dissociation studies. Using the four most common single neuron analyses methods in the field, we found that the prevalence and strength of neural correlates were just as high across all four tasks, including for the three tasks that do not depend on this brain area. These results suggest that the probability of observing epiphenomenal activity in primate cortex is high, which can mislead investigators relying on neural recording or imaging to map brain function.One-Sentence SummaryTremblay, Testard and colleagues show that inferring a brain area’s function from neural recordings alone could be misleading.
Camel urine limits proliferation and modifies cell morphology in human renal tumoral and non-tumoral cells
Authors: Pastrana Carlos Iglesias , Sgobba Maria Noemi , Navas González Francisco Javier , Delgado Bermejo Juan Vicente , Duarte Iola F. , Lentini Giovanni , Sayed Osman Taher Kamal , Guerra Lorenzo , Ciani Elena 
Published: September 2022

AbstractThe widespread ethnomedical practice of dromedary urinotherapy as a remedy against various illnesses is well recognized in traditional dromedary countries, and multiple researchers tried to unravel its bioactive potential and provide scientific evidence through in vivo and in vitro experiments. None of these studies (i) measured urine osmolarity prior to bioactivity testing, which could deeply influence the results of in vitro tests, nor (ii) addressed issues related to cells’ morphological changes after exposure to camel urines. Taken together, the above aspects point to the need for a “good practice” to be shared by researchers in this field, in order to reduce the variability of in vitro testing of camel urine bioactivity. In this work, using a set of biological samples from animals differing in sex, age, and physiological status, we investigated, the antiproliferative activity of camel urine towards human non-tumoral (HK2) and tumoral renal cells (Caki-1), through cell viability and microscopy analysis, and taking the possible influence of osmolarity into account. We employed cell lines commonly used in toxicological research which, to the best of our knowledge, have not been previously exposed to camel urine. HK2 and Caki-1 cells tolerated well mannitol-induced hyperosmolarity up to 500 mOsm/L. Significant antiproliferative effects were observed only in Caki-1 cells, when exposed to urine solutions (diluted to <500 mOsm/L) from two males out of the ten tested samples, while effects on cell morphology (elongation) were observed only in HK2 cells, when exposed to urine solutions from six samples. The significant antiproliferative effect observed only in tumoral cells looks promising for forthcoming developments in the cancer treatment field. Finally, the presented approach may serve as a guide for future research in this specific, multidisciplinary field.
Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation
Authors: Landshammer Alexandro , Bolondi Adriano , Kretzmer Helene , Much Christian , Buschow René , Rose Alina , Wu Hua-Jun , Mackowiak Sebastian , Braendl Bjoern , Giesselmann Pay , Tornisiello Rosaria , Parsi Krishna Mohan , Huey Jack , Mielke Thorsten , Meierhofer David , Maehr René , Hnisz Denes , Michor Franziska , Rinn John L. , Meissner Alexander 
Published: September 2022

ABSTRACTLong non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously not annotated lncRNA that is transcribed upstream of the SOX17 gene and located within the same topologically associating domain. We termed it LNCSOX17 and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of LNCSOX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. We identified and characterized LNCSOX17 as an essential new actor in early human endoderm, thereby further expanding the list of functionally important non-coding regulators.
Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes
Authors: McAdams Zachary L , Busi Susheel Bhanu , Gustafson Kevin L , Bivens Nathan , Franklin Craig L , Wilmes Paul , Ericsson Aaron C 
Published: September 2022

AbstractHost genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiontSaccharimonadaceae. Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.
Redefining hypo- and hyper-responding phenotypes of CFTR mutants for understanding and therapy
Authors: Hillenaar Tamara , Beekman Jeffrey , van der Sluijs Peter , Braakman Ineke 
Published: September 2022

ABSTRACTMutations in CFTR cause misfolding and decreased or absent ion-channel function, resulting in the disease Cystic Fibrosis. Fortunately, a triple-modulator combination therapy (Trikafta) has been FDA approved for 178 mutations, including all patients who have F508del on one allele. That so many CFTR mutants respond well to modulators developed for a single mutation is due to the nature of the folding process of this multidomain protein. We have addressed the question ‘What characterizes the exceptions: the mutants that functionally respond either not or extremely well’.A functional response is the product of the number of CFTR molecules on the cell surface, open probability, and conductivity of the CFTR chloride channel. By combining biosynthetic radiolabeling with protease-susceptibility assays, we have followed CF-causing mutants during early and late stages of folding in presence and absence of modulators. Most CFTR mutants showed typical biochemical responses for each modulator, such as a TMD1 conformational change or an increase of (cell-surface) stability, regardless of a functional response. These modulators thus should still be considered for hypo-responder genotypes. Understanding both biochemical and functional phenotypes of outlier mutations will boost our insights into CFTR folding and misfolding, and lead to improved therapeutic strategies.
Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics
Authors: Doellinger Joerg , Blumenscheit Christian , Schneider Andy , Lasch Peter 
Published: September 2022

ABSTRACTThe combination of short liquid chromatography (LC) gradients and data independent acquisition (DIA) by mass spectrometry (MS) has proven its huge potential for high-throughput proteomics. This methodology benefits from the speed of the latest generation of mass spectrometers, which enable short MS cycle times needed to provide sufficient sampling of sharp LC peaks. However, the optimization of isolation window schemes resulting in a certain number of data points per peak (DPPP) is understudied, although it is one of the most important parameters for the outcome of this methodology. In this study, we show that substantially reducing the number of DPPP for short gradient DIA massively increases protein identifications while maintaining quantitative precision. A deeper analysis of the underlying effects shows that a reduction of DPPP increases the selectivity of the data analysis, allowing fragment ions to be tracked over a longer period of the LC gradient. This in turn increases the number of precursors identified per protein, keeping the number of data points per protein nearly constant even at long cycle times. When proteins are inferred from its precursors, quantitative precision is maintained at low DPPP while greatly increasing proteomic depth. This strategy enabled us quantifying 6018 HeLa proteins (> 80,000 precursor identifications) with coefficients of variation below 20% in 30 min using a Q Exactive Orbitrap mass spectrometer, which corresponds to a throughput of 29 samples per day. This indicates that the potential of high-throughput DIA-MS has not been fully exploited yet.
The mediodorsal thalamus supports adaptive responding based on stimulus-outcome associations
Authors: Morceau Sarah , Faugère Angélique , Coutureau Etienne , Wolff Mathieu 
Published: September 2022

AbstractThe ability to engage into flexible behaviors is crucial in dynamic environments. We recently showed that in addition to the well described role of the orbitofrontal cortex (OFC), its thalamic input from the submedius thalamic nucleus (Sub) also contributes to adaptive responding during Pavlovian degradation. In the present study, we examined the role of the mediodorsal thalamus (MD) which is the other main thalamic input to the OFC. To this end, we assessed the effect of both pre- and post-training MD lesions in rats performing a Pavlovian contingency degradation task. Pre-training lesions mildly impeded the establishment of stimulus-outcome associations during the initial training of Pavlovian conditioning without interfering with Pavlovian degradation training when the sensory feedback provided by the outcome rewards were available to animals. However, we found that both pre- and post-training MD lesions produced a selective impairment during a test conducted under extinction conditions, during which only current mental representation could guide behavior. Altogether, these data suggest a role for the MD in the successful encoding and representation of Pavlovian associations.
A phase-separated biomolecular condensate nucleates polymerization of the tubulin homolog FtsZ to spatiotemporally regulate bacterial cell division
Authors: Ramm Beatrice , Schumacher Dominik , Harms Andrea , Heermann Tamara , Klos Philipp , Müller Franziska , Schwille Petra , Søgaard-Andersen Lotte 
Published: September 2022

SummaryCell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social, predatory bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single large megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we studied the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization, suggesting a novel cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. PomY-nucleated FtsZ polymerization shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanism’s ancient origin.
Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition
Authors: Mattia Zaghi , Banfi Federica , Massimino Luca , Volpin Monica , Bellini Edoardo , Brusco Simone , Merelli Ivan , Barone Cristiana , Bruni Michela , Bossini Linda , Lamparelli Luigi Antonio , Pintado Laura , D’Aliberti Deborah , Spinelli Silvia , Mologni Luca , Colasante Gaia , Ungaro Federica , Cioni Jean-Michel , Azzoni Emanuele , Piazza Rocco , Montini Eugenio , Broccoli Vania , Sessa Alessandro 
Published: September 2022

SUMMARYWithin the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the onco-protein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that conditions in which SET is accumulated, including the severe Schinzel-Giedion Syndrome (SGS), are characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of the SET-related disorders in humans, including SGS, neurodevelopmental disorders, myeloproliferative diseases, and cancer.
Structural basis for mTORC1-dependent regulation of the lysosomal and autophagic transcription factor TFEB
Authors: Cui Zhicheng , Napolitano Gennaro , de Araujo Mariana E. G. , Esposito Alessandra , Monfregola Jlenia , Huber Lukas A. , Ballabio Andrea , Hurley James H. 
Published: September 2022

AbstractThe transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino-acid-mediated activation of the RagC GAP FLCN. TFEB lacks the TOR signaling (TOS) motif responsible for the recruitment of other mTORC1 substrates. We used cryo-electron microscopy (cryo-EM) to determine the structure of TFEB as presented to mTORC1 for phosphorylation. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first via a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB in a RagCGDP-dependent aspartate clamp in the cleft between the Rag G domains. Mutation of the clamp drives TFEB constitutively into the nucleus whilst having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. This structure presents the phosphorylatable Ser residues of TFEB to the mTORC1 active site in a suitable geometry for their phosphorylation. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state.