bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental shift in testosterone influence on prefrontal emotion control
Authors: Tyborowska Anna , Volman Inge , Niermann Hannah C. M. , Dapprich Anna L. , Smeekens Sanny , Cillessen Antonius H. N. , Toni Ivan , Roelofs Karin 
Published: September 2022

AbstractA paradox of testosterone effects is seen in adolescents vs. adults in social emotional approach-avoidance behavior. During adolescence, high testosterone levels are associated with increased anterior prefrontal (aPFC) involvement in emotion control, whereas during adulthood this neuro-endocrine relation is reversed. Rodent work shows that, during puberty, testosterone transitions from a neuro-developmental to a social-sexual activating hormone. In this study, we explored whether this functional transition is also present in human adolescents and young adults. Using a prospective longitudinal design, we investigated the role of testosterone on neural control of social emotional behavior during the transitions from middle to late adolescence and into young adulthood. Seventy-one individuals (tested at ages 14, 17, and 20 years) performed an fMRI-adapted approach-avoidance (AA) task involving automatic and controlled actions in response to social emotional stimuli. In line with predictions from animal models, the effect of testosterone on aPFC engagement decreased between middle and late adolescence, and shifted into an activational role by young adulthood - impeding neural control of emotions. This change in testosterone function was accompanied by increased testosterone-modulated amygdala reactivity. These findings qualify the testosterone-dependent maturation of the prefrontal-amygdala circuit supporting emotion control during the transition from middle adolescence into young adulthood.
Conceptual associations generate sensory predictions
Authors: Yan Chuyao , de Lange Floris P. , Richter David 
Published: September 2022

AbstractA crucial ability of the human brain is to learn and exploit probabilistic associations between stimuli to facilitate perception and behavior by predicting future events. While studies have shown how perceptual relationships are used to predict sensory inputs, relational knowledge is often between concepts rather than percepts (e.g., we learned to associate cats with dogs, rather than specific images of cats and dogs). Here we asked if and how sensory responses to visual input may be modulated by predictions derived from conceptual associations. To this end we exposed participants to arbitrary word-word pairs (e.g., car – dog) repeatedly, creating an expectation of the second word, conditional on the occurrence of the first. In a subsequent session, we exposed participants to novel word-picture pairs, while measuring fMRI BOLD responses. All word-picture pairs were equally likely, but half of the pairs conformed to the previously formed conceptual (word-word) associations, whereas the other half violated this association. Results showed suppressed sensory responses throughout the ventral visual stream, including early visual cortex, to pictures that corresponded to the previously expected words compared to unexpected words. This suggests that the learned conceptual associations were used to generate sensory predictions that modulated processing of the picture stimuli. Moreover, these modulations were tuning-specific, selectively suppressing neural populations tuned towards the expected input. Combined, our results suggest that recently acquired conceptual priors are generalized across domains and used by the sensory brain to generate feature specific predictions, facilitating processing of expected visual input.
Activity-dependent glassy cell mechanics I : Mechanical properties measured with active microrheology
Authors: Ebata H. , Umeda K. , Nishizawa K. , Nagao W. , Inokuchi S. , Sugino Y. , Miyamoto T. , Mizuno D. 
Published: September 2022

AbstractActive microrheology was conducted in living cells by applying an optical-trapping force to vigorously-fluctuating tracer beads with feedback-tracking technology. The complex shear viscoelastic modulusG(ω) =G′(ω) –iG″(ω) was measured in HeLa cells in an epithelial-like confluent monolayer. We found thatG(ω) ∝ (−iω)1/2over a wide range of frequencies (1 Hz <ω/2π<10 kHz). Actin disruption and cell-cycle progression from G1 to S and G2 phases only had a limited effect onG(ω) in living cells. On the other hand,G(ω) was found to be dependent on cell metabolism; ATP-depleted cells showed an increased elastic modulusG′(ω) at low frequencies, giving rise to a constant plateau such thatG(ω) =G0+A(−iω)1/2. Both the plateau and the additional frequency dependency ∝ (−iω)1/2of ATP-depleted cells are consistent with a rheological response typical of colloidal jamming. On the other hand, the plateauG0disappeared in ordinary metabolically active cells, implying that living cells fluidize their internal states such that they approach the critical jamming point.Statement of SignificanceIntracellular mechanical properties were measured using optical-trap-based microrheology. Despite expectations to the contrary, shear viscoelasticity was hardly affected by reorganization of cytoskeletal structures during cell-cycle progression (G1 to S and G2 phases), nor by artificial disruption of the actin cytoskeleton induced by chemical inhibitors. Rather, the mechanics of cell interiors is governed by the glassy cytoplasm. Cells depleted of ATP solidified, whereas living cells that maintained metabolic activities were more fluid-like. Instead of a completely fluid response, however, we observed a characteristic power-law viscoelasticityG(ω) ∝ (−iω)1/2over the whole range of frequencies measured. Based on our current understanding of jamming rheology, we discuss how cells fluidize their internal state in a way that pushes the system towards the critical jamming transition.
Hyperaerated metalation calculator for E. coli strain JM109 (DE3) grown in LB media
Authors: Clough Sophie E. , Osman Deenah , Young Tessa R. , Robinson Nigel J. 
Published: September 2022

AbstractWe recently produced three web-based calculators that predict in vivo metal occupancies of proteins, based on the metal affinities of a protein of interest along with estimates of the availabilities of the labile buffered pools of metals inside a cell. Metal availabilities were calculated from the calibrated responses of DNA-binding, metal-sensing, transcriptional regulators. The availability of intracellular Fe(II) was estimated to be similar in E. coli grown under anaerobic conditions compared to cells grown aerobically in LB medium. The purpose of this article is to archive the background data that underpins the release of a new calculator for hyperaerated cells grown in flasks with baffles, with relatively low culture volumes plus high shaking speeds to give elevated oxygenation. The intracellular availability of Fe(II) calculated from the responses of the intracellular Fe(II) sensor Fur was estimated to be significantly lower in these hyperaerated cells than either of the previous values determined for anaerobic or aerobic cultures. The total number of atoms of Mn(II) per cell increased in hyperaerated cells albeit with only modest change in intracellular Mn(II) availability as estimated from the responses of the Mn(II) sensor MntR. Accurate determination of intracellular Ni(II) availability will require further calibration of the magnitude of the responses of the Ni(II) sensor NikR in hyperaerated cells to take account of the state of Fnr. The hyperaerated metalation calculator is made available online and as a spreadsheet, for use by others.
Attenuation of polysialic acid biosynthesis in cells by the small molecule inhibitor 8-keto-sialic acid
Authors: Hunter Carmanah , Gao Zhizeng , Chen Hong-Ming , Thompson Nicole , Wakarchuk Warren , Nitz Mark , Withers Stephen G. , Willis Lisa M. 
Published: September 2022

AbstractSialic acids are key mediators of cell function, particularly with regards to cellular interactions with the surrounding environment. Reagents that modulate the display of specific sialyl glycoforms at the cell surface would be useful biochemical tools and potentially allow for therapeutic intervention in numerous challenging chronic diseases. While multiple strategies are being explored for the control of cell surface sialosides, none that shows high selectivity between sialyltransferases or that targets a specific sialyl glycoform has yet to emerge. Here we describe a strategy to block the formation of α2,8-linked sialic acid chains (oligo- and polysialic acid) through the use of 8-keto-sialic acid as a chain-terminating metabolic inhibitor that, if incorporated, can not be elongated. 8-Keto-sialic acid is non-toxic at effective concentrations and serves to block polysialic acid synthesis in cancer cell lines and primary immune cells, with minimal effects on other sialyl glycoforms.
A role for BCL2L13 and autophagy in germline purifying selection of mtDNA
Authors: Kremer Laura S. , Bozhilova Lyuba V. , Rubalcava-Gracia Diana , Filograna Roberta , Upadhyay Mamta , Koolmeister Camilla , Chinnery Patrick F. , Larsson Nils-Göran 
Published: September 2022

AbstractMammalian mitochondrial DNA (mtDNA) is inherited uniparentally through the female germline without undergoing recombination. This poses a major problem as deleterious mtDNA mutations must be eliminated to avoid a mutational meltdown over generations. At least two mechanisms that can decrease the mutation load during maternal transmission are operational: a stochastic bottleneck for mtDNA transmission from mother to child, and a directed purifying selection against transmission of deleterious mtDNA mutations. However, the molecular mechanisms controlling these processes remain unknown. In this study, we systematically tested whether decreased autophagy contributes to purifying selection by crossing the C5024T mouse model harbouring a single pathogenic heteroplasmic mutation in the tRNAAla gene of the mtDNA with different autophagy-deficient mouse models, including knockouts of Parkin, Bcl2l13, Ulk1, and Ulk2. Our study reveals a robust effect of knockout of Bcl2l13 on the selection process, and weaker evidence for the effect of Ulk1 and potentially Ulk2, while no statistically significant impact is seen for knockout of Parkin. This points at distinctive roles of these players in germline purifying selection. Overall, our approach provides a framework for investigating the roles of other important factors involved in the enigmatic process of purifying selection and guides further investigations for the role of BCL2L13 in the elimination of non-synonymous mutations in protein-coding genes.
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)
Authors: Chihara Kotaro , Gerovac Milan , Hör Jens , Vogel Jörg 
Published: September 2022

ABSTRACTNew methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq toEscherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ∼500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.
Improved Genome Editing by an Engineered CRISPR-Cas12a
Authors: Ma Enbo , Chen Kai , Shi Honglue , Stahl Elizabeth C. , Adler Ben , Liu Junjie , Zhou Kaihong , Ye Jinjuan , Doudna Jennifer A. 
Published: September 2022

ABSTRACTCRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a (LbCas12a) that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold depending on the genomic locus. Finally, we found that a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy of coupled rational engineering and directed evolution establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The availability of experimental and predicted structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome editing proteins.
The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins
Authors: Miller Alexandria N. , Houlihan Patrick R. , Matamala Ella , Cabezas-Bratesco Deny , Lee Gi Young , Cristofori-Armstrong Ben , Dilan Tanya L. , Sanchez-Martinez Silvia , Matthies Doreen , Yan Rui , Yu Zhiheng , Ren Dejian , Brauchi Sebastian E. , Clapham David E. 
Published: September 2022

AbstractThe severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
High resolution photocatalytic mapping of SARS-CoV-2 Spike protein-host cell membrane interactions
Authors: Datta Suprama , Tavares Alexander H. , Reyes-Robles Tamara , Ryu Keun Ah , Khan Nazimuddin , Bechtel Tyler J. , Bertoch Jayde M. , White Cory H. , Hazuda Daria J. , Vora Kalpit A. , Hett Erik C. , Fadeyi Olugbeminiyi O. , Oslund Rob C. , Saeed Mohsan , Emili Andrew 
Published: September 2022

AbstractIdentifying protein environments at the virus-host cell interface can improve our understanding of viral entry and pathogenesis. SARS-CoV-2, the virus behind the ongoing COVID-19 pandemic, uses the cell surface ACE2 protein as a major receptor, but the contribution of other cellular proteins in the entry process is unknown. To probe the microenvironment of SARS-CoV-2 Spike-ACE2 protein interactomes on human cells, we developed a photocatalyst-based viral-host protein microenvironment mapping platform (ViraMap) employing iridium photocatalysts conjugated to Spike for visible-light driven proximity labelling on host cells. Application of ViraMap on ACE2-expressing cells captured ACE2, the established co-receptor NRP1, as well as other proteins implicated in host cell entry and immunomodulation. We further investigated these enriched proteins via loss-of-function and over-expression in pseudotype and authentic infection models and observed that the Ig receptor PTGFRN and tyrosine kinase ligand EFNB1 can serve as SARS-CoV-2 entry factors. Our results highlight additional host targets that participate infection and showcase ViraMap for interrogating virus-host cell surface interactomes.
SOGO-SOFI, light-modulated super-resolution optical fluctuation imaging using only 20 raw frames for high-fidelity reconstruction
Authors: Xue Fudong , He Wenting , Peng Dingming , You Hui , Zhang Mingshu , Xu Pingyong 
Published: September 2022

AbstractTaking advantage of the stochastic photoswitching of genetically encodable reversibly photoswitchable fluorescent proteins (RSFPs), super-resolution optical fluctuation imaging (SOFI) and its variant photochromic stochastic optical fluctuation imaging (pcSOFI) are valuable tools for wide field super- resolution (SR) imaging. Live-cell (pc)SOFI, which requires a small number of original frames to reconstruct an SR image, is prone to structural discontinuity artifacts and low spatial resolution. Herein, we developed a repeated synchronized on- and gradually off-switching SOFI (SOGO-SOFI) that maximized the photoswitching frequency of RSFPs by light modulation and required only 20 frames for high-quality reconstruction. Live-cell SOGO-SOFI imaging of the endoplasmic reticulum (ER) exhibited 10 times higher temporal resolution (100 fps) and fewer artifacts than pcSOFI. Moreover, a combination of SOGO-SOFI with Airyscan further increased the image contrast and the resolution of Airyscan by a factor of 1.5 from 140 nm to 91 nm. The capabilities of SOGO-SOFI were further demonstrated by dual- color imaging of nucleolar proteins in mammalian cells and deep imaging of ER structures in thick brain slices (20.6 µm).
Chorography and conformational dynamism of the Soluble Human Fibrinogen in solution
Authors: Pinelo Jose Emiliano Esparza , Manandhar Pragya , Popovic Grega , Ray Katherine , Nguyen Quoc , Iavarone Anthony T. , Offenbacher Adam R. , Hudson Nathan E. , Sen Mehmet 
Published: September 2022

AbstractFibrinogen is a soluble, multi-subunit and multi-domain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin initiating polymerization that substantially contributes to clot growth. The consentaneous structural view of the soluble form of fibrinogen is relatively straight and rigid-like. However, fibrinogen contains numerous, transiently-accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there has been limited information on the solution structure and internal flexibility of soluble fibrinogen. Here, utilizing an integrative, biophysical approach involving temperature-dependent hydrogen-deuterium exchange mass spectrometry, small angle X-ray scattering, and negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Our data reveal a high degree of internal flexibility, accommodated by four major and distinct flexible sites along the central axis of the protein. We propose that the fibrinogen structure in solution consists of a complex, conformational landscape with multiple local minima, rather than a single, rigid topology. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia, and post-translational modifications, residing near fibrinogen flexions. This work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.
Attention-based GCN Integrates Multi-omics Data for Breast Cancer Subtype Classification and Patient-specific Gene Marker Identification
Authors: Guo Hui , Lv Xiang , Li Yizhou , Li Menglong 
Published: September 2022

AbstractBreast cancer is a heterogeneous disease and can be divided into several subtypes with unique prognostic and molecular characteristics. Classification of breast cancer subtypes plays an important role in the precision treatment and prognosis of breast cancer. Benefitting from the relation-aware ability of graph convolution network (GCN), we presented a multi-omics integrative method, attention-based GCN, for breast cancer molecular subtype classification using mRNA expression, copy number variation, and DNA methylation multi-omics data. Several attention mechanisms were performed and all exhibited effectiveness in integrating heterogeneous data. Column-wise attention-based GCN outperformed the other baseline methods, achieving AUC of 0.9816, ACC of 0.8743 and MCC of 0.8151 in 5-fold cross validation. Besides, Layer-wise Relevance Propagation (LRP) algorithm was used for interpretation of model decision and could identify patient-specific important biomarkers which were reported to be related to the occurrence and development of breast cancer. Our results highlighted the effectiveness of GCN and attention mechanisms in multi-omics integrative analysis and implement of LRP algorithm could provide biologically reasonable insights into model decision.Author SummaryIdentification of molecular subtype is essential to understanding the pathogenesis of cancer and advancing the development of cancer precision treatment. We have developed a graph convolution network architecture to predict the molecular subtype of breast cancer patients based on multi-omics data. The major difference between our work and other methods is that we have offered a new view for multi-omics data integration with the assistance of graph convolution network. Besides, we adopted an interpretability method to explain the model decision and prioritize the genes for biomarker discovery.