bluuebunny/crossref_metadata_2025_split huggingface dataset:
Punishment resistance for cocaine is associated with inflexible habits in rats
Authors: Jones Bradley O. , Paladino Morgan S. , Cruz Adelis M. , Spencer Haley F. , Kahanek Payton L. , Scarborough Lauren N. , Georges Sandra F. , Smith Rachel J. 
Published: June 2023

AbstractAddiction is characterized by continued drug use despite negative consequences. In an animal model, a subset of rats continues to self-administer cocaine despite footshock consequences, showing punishment resistance. We sought to test the hypothesis that punishment resistance arises from failure to exert goal-directed control over habitual cocaine seeking. While habits are not inherently permanent or maladaptive, continued use of habits under conditions that should encourage goal-directed control makes them maladaptive and inflexible. We trained male and female Sprague Dawley rats on a seeking-taking chained schedule of cocaine self-administration (2 h/day). We then exposed them to 4 days of punishment testing, in which footshock (0.4 mA, 0.3 s) was delivered randomly on one-third of trials, immediately following completion of seeking and prior to extension of the taking lever. Before and after punishment testing (4 days pre-punishment and ≥4 days post-punishment), we assessed whether cocaine seeking was goal-directed or habitual using outcome devaluation via cocaine satiety. We found that punishment resistance was associated with continued use of habits, whereas punishment sensitivity was associated with increased goal-directed control. Although punishment resistance was not predicted by habitual responding pre-punishment, it was associated with habitual responding post-punishment. In parallel studies of food self-administration, we similarly observed that punishment resistance was associated with habitual responding post-punishment but not pre-punishment. These findings indicate that punishment resistance is related to habits that have become inflexible and persist under conditions that should encourage a transition to goal-directed behavior.
Tapered Drug delivery, Optical stimulation, and Electrophysiology (T-DOpE) probes reveal the importance of cannabinoid signaling in hippocampal CA1 oscillations in behaving mice
Authors: Kim Jongwoon , Huang Hengji , Gilbert Earl , Arndt Kaiser , English Daniel Fine , Jia Xiaoting 
Published: June 2023

AbstractUnderstanding the neural basis of behavior requires monitoring and manipulating combinations of physiological elements and their interactions in behaving animals. Here we developed a thermal tapering process (TTP) which enables the fabrication of novel, low-cost, flexible probes that combine ultrafine features of dense electrodes, optical waveguides, and microfluidic channels. Furthermore, we developed a semi-automated backend connection allowing scalable assembly of the probes. We demonstrate that our T-DOpE (TaperedDrug delivery,Optical stimulation, andElectrophysiology) probe achieves in a single neuron-scale device (1) high-fidelity electrophysiological recording (2) focal drug delivery and (3) optical stimulation. With a tapered geometry, the device tip can be minimized (as small as 50 μm) to ensure minimal tissue damage while the backend is ~20 times larger allowing for direct integration with industrial-scale connectorization. Acute and chronic implantation of the probes in mouse hippocampus CA1 revealed canonical neuronal activity at the level of local field potentials and spiking. Taking advantage of the triple-functionality of the T-DOpE probe, we monitored local field potentials with simultaneous manipulation of endogenous type 1 cannabinoid receptors (CB1R; via microfluidic agonist delivery) and CA1 pyramidal cell membrane potential (optogenetic activation). Electro-pharmacological experiments revealed that focal infusion of CB1R agonist CP-55,940 in dorsal CA1 downregulated theta and sharp wave-ripple oscillations. Furthermore, using the full electro-pharmacological-optical feature set of the T-DOpE probe we found that CB1R activation reduces sharp wave-ripples (SPW-Rs) by impairing the innate SPW-R-generating ability of the CA1 circuit.
A Cost-Effective CRISPR/Cas9-Based Method for Sequencing the Functional Antibody Kappa Chain cDNA from Hybridomas Expressing Aberrant Kappa Chain mRNAs
Authors: Ahnoud Armin , He Chong , Strainic Michael , Zhai Wenwu 
Published: June 2023

ABSTRACTOne prerequisite for generating recombinant antibodies for therapeutic and non-therapeutic purposes from hybridoma clones is the reliable, efficient, and cost-effective sequencing of the hybridoma clone that produces the desired antibody. However, many hybridoma fusion partners produce aberrant endogenous mRNA transcripts most of which resemble kappa chains. These aberrant kappa chain mRNAs can interfere with or even prevent the determination of the functional murine antibody kappa chain cDNA sequences during the PCR amplification step. In this paper, we report the development of a rapid and cost-effective CRISPR/Cas9 based method to eliminate the aberrant endogenous sequence. We have demonstrated the effectiveness of this method by significantly reducing the number of an endogenous aberrant kappa chain transcript known as the aberrant SP2/0 kappa chain. This transcript is produced by the commonly used fusion partner known as SP2/0 which is a myeloma-derived cell line. Here, we first cloned and sequenced two hybridoma clones using this method (clones A1E7 and A9E11). Our results showed a 24 to 25 percent reduction of the aberrant chain sequences (method 1) from the sequencing results. We then optimized this method (method 2) and used it to clone and sequence a third hybridoma clone (clone 262). This optimized method allowed us to achieve an 88% reduction of the aberrant kappa chain sequences.
Unifying sparse coding, predictive coding, and divisive normalization
Authors: Lian Yanbo , Burkitt Anthony N. 
Published: June 2023

AbstractSparse coding, predictive coding and divisive normalization have each been found to be principles that underlie the function of neural circuits in many parts of the brain, supported by substantial experimental evidence. However, the connections between these related principles are still poorly understood. In this paper, we show how sparse coding, predictive coding, and divisive normalization can be described within a unified framework, and illustrate this explicitly within the context of a two-layer neural model. This two-layer model is constructed in a way that implements sparse coding with a network structure that is constructed by implementing predictive coding. The results demonstrate how a homeostatic function that regulates neural responses in the model can shape the nonlinearity of neural responses in a way that replicates different forms of divisive normalization. The equivalence of the model to divisive normalization in a single-neuron case is shown analytically. Simulations show that the model can learn simple cells in the primary visual cortex with the property of contrast saturation, which has previously been explained by divisive normalization. In summary, the study demonstrates that the three principles of sparse coding, predictive coding, and divisive normalization can be unified to provide a learning framework based on biophysical properties, such as Hebbian learning and homeostasis, and this framework incorporates both learning and more diverse response nonlinearities observed experimentally. This framework has the potential to also be used to explain how the brain learns to integrate input from different sensory modalities.
An exosome-based gene delivery platform for cell-specific CRISPR/Cas9 genome editing
Authors: Dubey Sunil , Chen Zhe , Talis Austin , Molotkov Andrei , Ali Alessandra , Mintz Akiva , Momen-Heravi Fatemeh 
Published: June 2023

ABSTRACTExosomes are naturally occurring vesicles that have the potential to be manipulated to become promising drug delivery vehicles for on-demand in vitro and in vivo gene editing. Here, we developed the modular safeEXO platform, a prototype exosome delivery vehicle that is mostly devoid of endogenous RNA and can efficaciously deliver RNA and ribonucleoprotein (RNP) complexes to their intended intracellular targets manifested by downstream biologic activity. We also successfully engineered producer cells to produce safeEXO vehicles that contain endogenous Cas9 (safeEXO-CAS) to effectively deliver efficient ribonucleoprotein (RNP)-mediated CRISPR genome editing machinery to organs or diseased cells in vitro and in vivo. We confirmed that safeEXO-CAS exosomes could co-deliver ssDNA, sgRNA and siRNA, and efficaciously mediate gene insertion in a dose-dependent manner. We demonstrated the potential to target safeEXO-CAS exosomes by engineering exosomes to express a tissue-specific moiety, integrin alpha-6 (safeEXO-CAS-ITGA6), which increased their uptake to lung epithelial cells in vitro and in vivo. We tested the ability of safeEXO-CAS-ITGA6 loaded with EMX1 sgRNAs to induce lung-targeted editing in mice, which demonstrated significant gene editing in the lungs with no signs of morbidity or detectable changes in immune cell populations. Our results demonstrate that our modular safeEXO platform represents a targetable, safe and efficacious vehicle to deliver nucleic acid-based therapeutics that successfully reach their intracellular targets. Furthermore, safeEXO producer cells can be genetically manipulated to produce safeEXO vehicles containing CRISPR machinery for more efficient RNP-mediated genome editing. This platform has the potential to improve current therapies and increase the landscape of treatment for various human diseases using RNAi and CRISPR approaches.
Pentose Phosphate Pathway Inhibition activates Macrophages towards phagocytic Lymphoma Cell Clearance
Authors: Beielstein Anna C. , Izquierdo Elena , Blakemore Stuart , Nickel Nadine , Michalik Michael , Chawan Samruddhi , Brinker Reinhild , Bartel Hans-Henrik , Vorholt Daniela , Nolte Janica L. , Linke Rebecca , Costa Picossi Carolina Raissa , Sáiz Jorge , Picard Felix , Florin Alexandra , Meinel Jörn , Büttner Reinhard , Villaseñor Alma , Winkels Holger , Hallek Michael , Krüger Marcus , Barbas Coral , Pallasch Christian P. 
Published: June 2023

SummaryMacrophages in the B-cell lymphoma microenvironment represent a functional node in progression and therapeutic response. We assessed metabolic regulation of macrophages in the context of therapeutic antibody-mediated phagocytosis. Pentose phosphate pathway (PPP) inhibition by specific compounds and shRNA targeting induced increased phagocytic lymphoma cell clearance.Moreover, macrophages provided decreased support for survival of lymphoma cells. PPP inhibition induced metabolic activation, cytoskeletal re-modelling and pro-inflammatory polarization of macrophages. A link between PPP and immune regulation was identified as mechanism of macrophage repolarization. Inhibition of the PPP causes suppression of glycogen synthesis and subsequent modulation of the immune modulatory UDPG-Stat1-Irg1-Itaconate axis. PPP inhibition rewired macrophage maturation and activationin vivo. Addition of the PPP inhibitor S3 to antibody therapy achieved significantly prolonged overall survival in an aggressive B-cell lymphoma mouse model.We hypothesize the PPP as key regulator and targetable modulator of macrophage activity in lymphoma to improve efficacy of immunotherapies.HighlightsMacrophage-mediated lymphoma cell phagocytosis is increased by pentose phosphate pathway (PPP) inhibition as an immune regulatory switch for macrophage function and polarizationPPP inhibition is linked to decreased glycogen synthesis and subsequent modulation of the UDPG-Stat1-Irg1-Itaconate axisPPP inhibition is tolerablein vivoand facilitates therapeutic targeting of B-cell lymphoma
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS
Authors: Trimbour Remi , Deutschmann Ina Maria , Cantini Laura 
Published: June 2023

AbstractThe molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation.Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation.We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMus in terms of TF targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs.
IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells
Authors: Fischer Sabrina , Weber Lisa M. , Stielow Bastian , Frech Miriam , Simon Clara , Könnecke Julie , Forné Ignasi , Nist Andrea , Bauer Uta Maria , Stiewe Thorsten , Neubauer Andreas , Liefke Robert 
Published: June 2023

AbstractAcute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may therefore represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.
Touch sensation requires the mechanically-gated ion channel Elkin1
Authors: Chakrabarti Sampurna , Klich Jasmin D. , Khallaf Mohammed A. , Sánchez-Carranza Oscar , Baran Zuzanna M. , Rossi Alice , Huang Angela Tzu-Lun , Pohl Tobias , Fleischer Raluca , Fürst Carina , Hammes Annette , Bégay Valérie , Hörnberg Hanna , Poole Kate , Lewin Gary R. 
Published: June 2023

AbstractThe slightest touch to the skin initiates tactile perception that is almost immediate1. The extraordinary speed of touch perception is enabled by mechanically-activated ion channels, the opening of which excites the endings of sensory neurons innervating the skin to initiate sensation. Here we identify a new mechanically-activated ion channel, Elkin12, that, when ablated in mice, leads to a profound behavioural touch insensitivity. Touch insensitivity inElkin1-/-mice was caused by a loss of mechanically-activated currents (MA-currents) in around half of all sensory neurons that are activated by light touch (low threshold mechanoreceptors, LTMRs). Reintroduction of Elkin1 into sensory neurons fromElkin1-/-mice acutely restored MA-currents. Piezo23–6is an established mechanosensitive ion channel required for touch sensation. In mice genetic ablation ofPiezo2renders many, but not all, LTMRs insensitive to mechanical force4,5,7. Here we show that Elkin1 underpins PIEZO2-independent touch sensation. Additionally, we find that Elkin1 is present in many nociceptive sensory neurons which detect potentially damaging and painful mechanical force. These nociceptors depend onElkin1for effectively communicating information on sustained noxious mechanical forces. We further identified molecular and functional interactions between the known mechanotransduction protein Stoml38,9and Elkin1 ion channels. Our data identify Elkin1 as a novel core component of touch transduction in mammals. The specific sensory deficits exhibited byElkin1-/-mice make Elkin1 a highly desirable target that could be harnessed to treat somatic sensory disorders including pain.
Blueprinting expandable nanomaterials with standardized protein building blocks
Authors: Huddy Timothy F. , Hsia Yang , Kibler Ryan D. , Xu Jinwei , Bethel Neville , Nagarajan Deepesh , Redler Rachel , Leung Philip J. Y. , Courbet Alexis , Yang Erin C. , Bera Asim K. , Coudray Nicolas , Calise S. John , Davila-Hernandez Fatima A. , Weidle Connor , Han Hannah L. , Li Zhe , McHugh Ryan , Reggiano Gabriella , Kang Alex , Sankaran Banumathi , Dickinson Miles S. , Coventry Brian , Brunette TJ , Liu Yulai , Dauparas Justas , Borst Andrew J. , Ekiert Damian , Kollman Justin M. , Bhabha Gira , Baker David 
Published: June 2023

AbstractA wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures1. Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight “train track” assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to “back of an envelope” architectural blueprints.
The involvement of the human prefrontal cortex in the emergence of visual awareness
Authors: Fang Zepeng , Dang Yuanyuan , Ling Zhipei , Han Yongzheng , Zhao Hulin , Xu Xin , Zhang Mingsha 
Published: June 2023

AbstractExploring the neural mechanisms of awareness is a fundamental task of cognitive neuroscience. There is an ongoing dispute regarding the role of the prefrontal cortex (PFC) in the emergence of awareness, which is partially raised by the confound between report- and awareness-related activity. To address this problem, we designed a visual awareness task that can minimize report-related motor confounding. Our results show that saccadic latency is significantly shorter in the aware trials than in the unaware trials. Local field potential (LFP) data from 6 patients consistently show early (200-300 ms) awareness-related activity in the PFC, including event-related potential and high-gamma activity. Moreover, the awareness state can be reliably decoded by the neural activity in the PFC since the early stage, and the neural pattern is dynamically changed rather than being stable during the representation of awareness. Furthermore, the enhancement of dynamic functional connectivity, through the phase modulation at low frequency, between the PFC and other brain regions in the early stage of the awareness trials may explain the mechanism of conscious access. These results indicate that the PFC is critically involved in the emergence of awareness.
Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes
Authors: Grodner Benjamin , Shi Hao , Farchione Owen , Vill Albert C. , Ntekas Ioannis , Diebold Peter J. , Zipfel Warren R. , Brito Ilana L. , De Vlaminck Iwijn 
Published: June 2023

ABSTRACTThe frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.