bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice
Authors: Claar Leslie D. , Rembado Irene , Kuyat Jacqulyn R. , Russo Simone , Marks Lydia C. , Olsen Shawn R. , Koch Christof 
Published: July 2022

ABSTRACTPerturbational complexity analysis predicts the presence of consciousness in volunteers and patients by stimulating the brain with brief pulses, recording electroencephalographic (EEG) responses, and computing their spatiotemporal complexity. We examined the underlying neural circuits in mice by directly stimulating cortex while recording with EEG and Neuropixels probes during wakefulness and isoflurane anesthesia. When mice are awake, stimulation of deep cortical layers reliably evokes locally a brief pulse of excitation, followed by a bi-phasic sequence of 120 ms profoundoffperiod and areboundexcitation. A similar pattern, partially attributed to burst spiking, is seen in thalamic nuclei, and is associated with a pronounced late component in the evoked EEG. We infer that cortico-thalamo-cortical interactions drive the long-lasting evoked EEG signals elicited by deep cortical stimulation during the awake state. The cortical and thalamic off period and rebound excitation, and the late component in the EEG, are reduced during running and absent during anesthesia.
Regulatory roles of three-dimensional structures of chromatin domains
Authors: Li Kelly Yichen , Cao Qin , Wang Huating , Leung Danny , Yip Kevin Y. 
Published: July 2022

1AbstractTranscriptional enhancers usually, but not always, regulate genes within the same topologically associating domain (TAD). We hypothesize that this incomplete insulation is due to three-dimensional structures of corresponding chromatin domains in individual cells: Whereas enhancers and genes buried inside the “core” of a domain interact mostly with other regions in the same domain, those on the “surface” can more easily interact with the outside. Here we show that a simple measure, the intra-TAD ratio, can quantify the “coreness” of a region with respect to single-cell domains it belongs. We show that domain surfaces are permissive for high gene expression, and cell type-specific active cis-regulatory elements (CREs), active histone marks, and transcription factor binding sites are enriched on domain surfaces, most strongly in chromatin subcompartments typically considered inactive. These findings suggest a “domain surface CRE” model of gene regulation. We also find that disease-associated non-coding variants are enriched on domain surfaces.
Temporal regulation of TAK1 to counteract muscular dystrophy
Authors: Roy Anirban , Koike Tatiana E. , Joshi Aniket S. , da Silva Meiricris Tomaz , Mathukumalli Kavya , Wu Mingfu , Kumar Ashok 
Published: July 2022

AbstractMuscular dystrophy is a group of genetic neuromuscular disorders that involves severe muscle wasting. Transforming growth factor β-activated kinase 1 (TAK1) is an important signaling protein that regulates cell survival, growth, and inflammation. TAK1 has been recently found to promote myofiber growth in skeletal muscle of adult mice. However, the role of TAK1 in muscle disorders remains poorly understood. In the present study, we have investigated how TAK1 affects progression of dystrophic phenotype in the mdx mouse model of Duchnne muscular dystrophy (DMD). TAK1 is highly activated during peak necrotic phase in mdx mice. Targeted inducible inactivation of TAK1 inhibits muscle injury, necroptosis, and accumulation of macrophages in dystrophic muscle of mdx mice. Additionally, targeted inactivation of TAK1 leads to the activation of autophagy and Notch and Wnt signaling in the dystrophic muscle. However, inactivation of TAK1 significantly reduces myofiber size and muscle contractile function in both young and adult mdx mice. Forced activation of TAK1 in skeletal muscle after peak necrotic phase induces myofiber growth and improves muscle histopathology in mdx mice. Our results suggest that targeted activation of TAK1 can ameliorate disease progression and improve muscle growth in DMD.One Sentence SummaryOur results demonstrate that duly regulation of TAK1 activity ameliorates dystrophic phenotype in a mouse model of Duchnne Muscular Dystrophy.
hnRNPA1/2 homologhrpa-1coordinates with miRNAs to regulate gene expression duringC. elegansdevelopment
Authors: Hebbar Shilpa , Panzade Ganesh , Zinovyeva Anna 
Published: July 2022

AbstractmicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in development and in disease. miRNAs associate with Argonaute proteins to form miRNA Induced Silencing Complexes (miRISCs), which post-transcriptionally repress gene expression. miRNA-mediated gene repression itself is subject to regulation by factors that can affect miRNA biogenesis or function. We previously identified HRPA-1, an hnRNPA/B homolog, as a putative physical interactor of miRNAs. Here, we report characterizations of both physical and genetic interactions between HRPA-1 and miRISC components. We confirmed HRPA-1 precipitation in let-7 and miR-58 pulldowns and detected an interaction between HRPA-1 and Argonaute. Deletion ofhrpa-1in amir-48 mir-241(nDf51)background enhanced themir-48 mir-241developmental defects, suggesting thathrpa-1may be important forlet-7family miRNA activity. Similarly, loss ofhrpa-1strongly enhanced developmental defects associated with two other miRNA mutants,lsy-6(ot150)andlet-7(n2853). Depletion of HRPA-1 modestly disrupted miRNA levels and affected global gene expression profiles. We identified a potential target ofhrpa-1, R06C1.4, whose knockdown partially recapitulates thehrpa-1(-)effects on miRNA mutant phenotypes. Overall, we demonstratehrpa-1andR06C1.4roles inC. elegansdevelopmental timing regulation and propose models describing possible coordinating modes of gene regulation by HRPA-1 and miRNAs.
p53 restoration in small cell lung cancer identifies a latent Cyclophilin-dependent necrosis mechanism
Authors: Acosta Jonuelle , Li Qinglan , Freeburg Nelson F. , Murali Nivitha , Grothusen Grant P. , Cicchini Michelle , Mai Hung , Gladstein Amy C. , Adler Keren M. , Doerig Katherine R. , Li Jinyang , Ruiz-Torres Miguel , Manning Kimberly L. , Stanger Ben Z. , Busino Luca , Wan Liling , Feldser David M. 
Published: July 2022

AbstractThe p53 tumor suppressor regulates multiple context-dependent tumor suppressive programs. Although p53 is mutated in ∼90% of small cell lung cancer (SCLC) tumors, how p53 mediates tumor suppression in this context is unknown. Here, using a mouse model of SCLC in which endogenous p53 expression can be conditionally and temporally regulated, we show that SCLC tumors maintain a requirement for p53 inactivation. However, we identified tumor subtype heterogeneity between SCLC tumors such that p53 reactivation induces a canonical senescence response in a subset of tumors, while, in others, p53 induces a non-apoptotic form of cell death that culminates in necrosis. We pinpointed the cyclophilin family of peptidyl prolyl cis-trans isomerases as critical determinants of a p53-induced transcriptional program that is specific to SCLC tumors and cell lines that are poised to undergo p53-mediated necrosis. Importantly, inhibition of cyclophilin isomerase activity suppresses SCLC subtype-specific p53-mediated death by limiting p53 transcriptional output without impacting chromatin binding. Our study demonstrates that intertumoral heterogeneity in SCLC can influence the biological response to p53 restoration, describes a novel mechanism of p53-regulated necrotic cell death, and uncovers new targets for the treatment of this most-recalcitrant tumor type.
Automated prediction of site and sequence of protein modification with ATRP initiators
Authors: Patel Arth , Smith Paige N. , Russell Alan J. , Carmali Sheiliza 
Published: July 2022

AbstractOne of the most straightforward and commonly used chemical modifications of proteins is to react surface amino groups (lysine residues) with activated esters. This chemistry has been used to generate protein-polymer conjugates, many of which are now approved therapeutics. Similar conjugates have also been generated by reacting activated ester atom transfer polymerization initiators with lysine residues to create biomacromolecular initiators for polymerization reactions. The reaction between activated esters and lysine amino groups is rapid and has been consistently described in almost every publication on the topic as a “random reaction”. A random reaction implies that every accessible lysine amino group on a protein molecule is equally reactive, and as a result, that the reaction is indiscriminate. Nonetheless, the literature contradicts itself by also suggesting that some lysine amino groups are more reactive than others (as a function of pKa, surface accessibility, temperature, and local environment). If the latter assumption is correct, then the outcome of these reactions cannot be random at all, and we should be able to predict the outcome from the structure of the protein. Predicting the non-random outcome of a reaction between surface lysines and reactive esters could transform the speed at which active bioconjugates can be developed and engineered. Herein, we describe a robust integrated tool that predicts the activated ester reactivity of every lysine in a protein, thereby allowing us to calculate the non-random sequence of reaction as a function of reaction conditions. Specifically, we have predicted the intrinsic reactivity of each lysine in multiple proteins with a bromine-functionalised N-hydroxysuccinimide initiator molecule. We have also shown that the model applied to PEGylation. The rules-based analysis has been coupled together in a single Python program that can bypass tedious trial and error experiments usually needed in protein-polymer conjugate design and synthesis.
EvoBind: in silico directed evolution of peptide binders with AlphaFold
Authors: Bryant Patrick , Elofsson Arne 
Published: July 2022

AbstractCurrently, there is no accurate method to computationally design peptide binders towards a specific protein interface using only a target structure. Experimental methods such as phage display can produce strong binders, but it is impossible to know where these bind without solving the structures. Using AlphaFold2 (AF) and other AI methods to distinguish true binders has proven highly successful but relies on the availability of binding scaffolds. Here, we develop EvoBind, an in silico directed-evolution platform based on AF that designs peptide binders towards an interface using only sequence information. We show that AF can distinguish between native and mutated peptide binders using the plDDT score and find that AF adapts the receptor interface structure to the binders during optimisation. We analyse previously designed minibinder proteins and show that AF can distinguish designed binders from non-binders. We compare ELISA ratios of different peptide binders and find the affinity can not be distinguished among binders, possibly due to varying binding sites and low AF confidence. We test the recovery of binding motifs and find that up to 75% of motifs are recovered. In principle, EvoBind can be used to design binders towards any interface conditioned on if AF can predict these. We expect that EvoBind will aid experimentalists substantially, providing a starting point for further laboratory analysis and optimisation. We hope that the use of AI-based methods will come to make binder design significantly cheaper and more accurate in tackling unmet clinical needs. EvoBind is freely available at: https://colab.research.google.com/github/patrickbryant1/EvoBind/blob/master/EvoBind.ipynb
Inositol acylation of phosphatidylinositol mannosides: a rapid mass response to membrane fluidization in mycobacteria
Authors: Nguyen Peter P. , Kado Takehiro , Prithviraj Malavika , Siegrist M. Sloan , Morita Yasu S. 
Published: July 2022

AbstractMycobacteria share an unusually complex, multilayered cell envelope, which contributes to adaptation to changing environments. The plasma membrane is the deepest layer of the cell envelope and acts as the final permeability barrier against outside molecules. There is an obvious need to maintain the plasma membrane integrity, but the adaptive responses of plasma membrane to stress exposure remain poorly understood. Using chemical treatment and heat stress to fluidize the membrane, we show here that phosphatidylinositol (PI)-anchored plasma membrane glycolipids known as PI mannosides (PIMs) rapidly remodel their structures upon membrane fluidization in Mycobacterium smegmatis. Without membrane stress, PIMs are predominantly in a tri-acylated form: two acyl chains of PI moiety plus one acyl chain modified at one of the mannose residues. Upon membrane fluidization, the fourth fatty acid is added to the inositol moiety of PIMs, making them tetra-acylated variants. PIM inositol acylation is a rapid response independent of de novo protein synthesis, representing one of the fastest mass conversions of lipid molecules found in nature. Strikingly, we found that M. smegmatis is more resistant to the bactericidal effect of a cationic detergent after benzyl alcohol preexposure. We further demonstrate that fluidization-induced PIM inositol acylation is conserved in pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. Our results demonstrate that mycobacteria possess a mechanism to sense plasma membrane fluidity change. We suggest that inositol acylation of PIMs is a novel membrane stress response that enables mycobacterial cells to resist membrane fluidization.
Fully Automated Multi-Grid Cryo-EM Screening using Smart Leginon
Authors: Cheng Anchi , Kim Paul , Kuang Huihui , Mendez Joshua H. , Chua Eugene Y.D. , Maruthi Kashyap , Wei Hui , Sawh Anjelique , Aragon Mahira F. , Serbynovskyi Viacheslav , Neselu Kasahun , Eng Edward T. , Potter Clinton S. , Carragher Bridget , Bepler Tristan , Noble Alex J. 
Published: July 2022

AbstractSingle particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection. Screening is a major bottleneck for new cryoEM projects because grids must be optimized over several factors, including grid type, grid hole size, sample concentration, buffer conditions, ice thickness, and particle behaviors. Even for mature projects, multiple grids are commonly screened to select a subset for high-resolution data collection. Here, machine learning and novel, purpose-built image processing and microscope-handling algorithms are incorporated into the automated data collection software, Leginon, to provide an open-source solution for fully automated, high-throughput grid screening. This new version, broadly called Smart Leginon, emulates the actions of an operator in identifying areas on the grid to explore as potentially useful for data collection. Smart Leginon Autoscreen sequentially loads and examines grids from an automated specimen exchange system to provide completely unattended grid screening across a set of grids. Comparisons between a multi-grid Autoscreen session and conventional manual screening by five expert microscope operators are presented. On average, Autoscreen reduces operator time from ∼6 hours to <10 minutes and provides a comparable percentage of suitable images for evaluation as the best operator. Smart Leginon’s ability to target holes that are particularly difficult to identify is analyzed. Finally, Smart Leginon’s utility is illustrated with three real-world multi-grid user screening/collection sessions, demonstrating the efficiency and flexibility of the software package. Smart Leginon’s fully automated functionality significantly reduces the burden on operator screening time, improves the throughput of screening, and recovers idle microscope time, thereby improving availability of cryoEM services.
Brain fingerprint is based on the aperiodic, scale-free, neuronal activity
Authors: Sorrentino P , Troisi-Lopez E , Romano A , Sorrentino G , Jirsa V 
Published: July 2022

AbstractThe possibility to identify subjects from their brain activity was met enthusiastically, as it bears the possibility to individualize brain analyses. However, the nature of the processes generating subject-specific features remains unknown, as the literature does not point to specific mechanisms. In particular, most of the current literature uses techniques that are based on the assumption of stationarity (e.g. Pearson’s correlation), which do not hypothesize any mechanisms, and crashes against a large body of literature showing the complex, highly non-linear nature of brain activity. In this paper, we hypothesize that intermittent moments when large, non-linear perturbations spread across the brain (defined as neuronal avalanches in the context of critical dynamics) are the ones that carry subject-specific information, and that contribute the most to identifiability. To test this hypothesis, we apply the recently-developed avalanche transition matrix (ATM) to source reconstructed magnetoencephalographic data, as to characterize subject-speficic fast dynamics. Then, we perform identifiability analysis based on the ATMs, and compared the performance to more classical ways of estimating large-scale connections (which assume stationareity). We demonstrate that selecting the moments and places where neuronal avalanches spread improves identifiability (p<0.0001, permutation testing), despite the fact that most ot the data (i.e. the linear part) are discarded. Our results show that the non-linear part of the brain signals carries most of the subject-specific information, shading light on the nature of the processes that underlie subject-identifiability. Borrowing from statistical mechanics, a solid branch of physics, we provide a principled way to link emergent large-scale personalized activations to non-observable, microscopic processes.
Aversive bimodal associations impact visual and olfactory memory performance in Drosophila
Authors: Thiagarajan Devasena , Eberl Franziska , Veit Daniel , Hansson Bill S. , Knaden Markus , Sachse Silke 
Published: July 2022

AbstractInsects rely heavily on sampling information from their environment for survival and fitness. Different sensory channels with dedicated downstream neural substrates are programmed to fine tune these signals and translate them into usable instructions to mediate complex behaviors. Sensory information can also be learned and stored as memories that influence decisions in the future. The learning of unimodal sensory signals, especially olfaction, has been studied extensively in different conditioning paradigms in different insects. Using the Drosophila melanogaster model in our work, we first investigated differences in the efficiencies of aversive associative visual and olfactory learning using sensory cues that are innately very attractive, such as blue or green light as well as food odors found in fruits or yeast. We then combined the presentation of visual and olfactory sensory stimuli during training to study the effect of bimodal integration on learning performance. When trained unimodally, flies did not easily learn visual stimuli, but when trained bimodally, they developed a significant short-term visual memory after a single learning trial. The bimodal training also suppressed the phototaxis response of the flies to near abolishment. However, a similar training did not enhance the short-term olfactory memory and in some cases, even caused reduction in strength. An enhancement after bimodal training was only seen with a weak long-term olfactory memory retrieved after 24h. Our study demonstrates that bimodal sensory integration is not always synergistic, but is conditional upon the training paradigm and inherent learning abilities of the sensory modalities involved.
Comparison between optical tissue clearing methods for detecting administered mesenchymal stromal cells in mouse lungs
Authors: Pichardo Alejandra Hernandez , Amadeo Francesco , Wilm Bettina , Lévy Raphaël , Ressel Lorenzo , Murray Patricia , Sée Violaine 
Published: July 2022

AbstractOptical tissue clearing of lung tissue enables the intact lung to be imaged using fluorescence microscopy. Several clearing protocols have been developed in recent years, including the Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC), stabilised 3D imaging of solvent-cleared organs (s-DISCO) and Ethyl cinnamate (ECi) methods. Here we compared these protocols with the aim of determining the biodistribution of mesenchymal stroma cells (MSCs) and understanding how they interact with host cells in the mouse lung. First, we evaluated how each method affected the size, morphology, and transparency of the lungs. Then, we compared the preservation of the fluorescence of the protein tdTomato expressed by the MSCs, and of the organic dye Evans Blue which labels the vasculature. In addition, we tested the compatibility of the methods with immunofluorescence staining. We found that CUBIC clearing is the only method that enables direct imaging of fluorescently labelled MSCs in the lungs thereby allowing the study of the MSC interaction with endothelial and immune cells when combined with immunofluorescence staining. Overall, 3D imaging of CUBIC cleared lungs confirmed that injected MSCs are initially retained in the pulmonary microvasculature, and that most cells are eliminated from the lungs within the first 24 h.Summary statementWe present a tissue clearing approach to visualize exogenous MSCs in the mouse lung and study their effects in the host.
In vivofunctional genomics identifies essentiality of potassium homeostasis in medulloblastoma
Authors: Fan Jerry J. , Wang Xin , Erickson Anders W. , Skowron Patryk , Wang Xian , Chen Xin , Shan Guanqiao , Bahrampour Shahrzad , Xiong Yi , Dong Weifan , Abeysundara Namal , Francisco Michelle A. , Pusong Ronwell J. , Suárez Raúl A. , Farooq Hamza , Holgado Borja L. , Wu Xiaochong , Daniels Craig , Dupuy Adam J. , Cadiñanos Juan , Bradley Allan , Bagchi Anindya , Moriarity Branden S. , Largaespada David A. , Sorana Morrissy A. , Ramaswamy Vijay , Mack Stephen C. , Garzia Livia , Dirks Peter B. , Wanggou Siyi , Li Xuejun , Sun Yu , Taylor Michael D. , Huang Xi 
Published: July 2022

ABSTRACTThe identification of cancer maintenance genes—driver genes essential to tumor survival—is fundamental for developing effective cancer therapy. Transposon-based insertional mutagenesis screens can identify cancer driver genes broadly but not discriminate maintenance from progression or initiation drivers, which contribute to cancer phenotypes and tumorigenesis, respectively. We engineered a nested, double-jumping transposon system to first dysregulate gene expression during tumorigenesis and then restore gene expression following tumor induction, allowing for genome-wide screening of maintenance essentialityin vivo. In a mouse model of medulloblastoma, the most common pediatric malignancy, insertion and remobilization of this nested transposon uncovers potassium channel genes as recurrent maintenance drivers. In human medulloblastoma, KCNB2 is the most overexpressed potassium channel across Group 3, Group 4, and SHH subgroups, andKcnb2knockout in mice diminishes the replicative potential of medulloblastoma-propagating cells to mitigate tumor growth. Kcnb2 governs potassium homeostasis to regulate plasma membrane tension-gated EGFR signaling, which drives proliferative expansion of medulloblastoma-propagating cells. Thus, our novel transposon system reveals potassium homeostasis as essential to tumor maintenance through biomechanical modulation of membrane signaling.