bluuebunny/crossref_metadata_2025 huggingface dataset:
Astrocytes gate long-term potentiation in hippocampal interneurons
Authors: Shen Weida , Tang Yejiao , Yang Jing , Zhu Linjing , Zhou Wen , Xiang Liyang , Zhu Feng , Dong Jingyin , Xie Yicheng , Zeng Ling-Hui
Published: June 2023

Long-term potentiation is involved in physiological processes such as learning and memory, motor learning and sensory processing, and pathological conditions such as addiction. In contrast to the extensive studies on the mechanism of long-term potentiation on excitatory glutamatergic synapses onto excitatory neurons (LTPE→E), the mechanism of LTP on excitatory glutamatergic synapses onto inhibitory neurons (LTPE→I) remains largely unknown. In the central nervous system, astrocytes play an important role in regulating synaptic activity and participate in the process of LTPE→E, but their functions in LTPE→Iremain incompletely defined., We studied the role of astrocytes in regulating LTPE→Iin the hippocampal CA1 region and their impact on cognitive function using electrophysiological, pharmacological, confocal calcium imaging, chemogenetics and behavior tests. We showed that LTPE→Iin the stratum oriens of hippocampal CA1 is astrocyte independent. However, in the stratum radiatum, synaptically released endocannabinoids increase astrocyte Ca2+via type-1 cannabinoid receptors, stimulate D-serine release, and potentiate excitatory synaptic transmission on inhibitory neurons through the activation of (N-methyl-D-aspartate) NMDA receptors. We also revealed that chemogenetic activation of astrocytes is sufficient for inducing NMDA-dependentde novoLTPE→Iin the stratum radiatum of the hippocampus. Furthermore, we found that disrupting LTPE→Iby knocking down γCaMKII in interneurons of the stratum radiatum resulted in dramatic memory impairment. Our findings suggest that astrocytes release D-serine, which activates NMDA receptors to regulate LTPE→I, and that cognitive function is intricately linked with the proper functioning of this LTPE→Ipathway.
Classification of patients with COVID-19 by blood RNA endotype: A prospective cohort study
Authors: Yoshimura Jumpei , Togami Yuki , Ebihara Takeshi , Mastumoto Hisatake , Mitsuyama Yumi , Sugihara Fuminori , Hirata Haruhiko , Okuzaki Daisuke , Ogura Hiroshi
Published: June 2023

Background

Although the development of vaccines has considerably reduced the severity of COVID-19, its incidence is still high. Hence, a targeted approach based on RNA endotypes of a population should be developed to help design biomarker-based therapies for COVID-19.

Objectives

We evaluated the major RNAs transcribed in blood cells during COVID-19 using PCR to further elucidate its pathogenesis and determine predictive phenotypes in COVID-19 patients.

Study design

In a discovery cohort of 40 patients with COVID-19, 26,354 RNAs were measured on day 1 and day 7. Five RNAs associated with disease severity and prognosis were derived. In a validation cohort of 153 patients with COVID-19 treated in the intensive care unit, we focused on prolactin (PRL), and toll-like receptor 3 (TLR3) among RNAs, which have a strong association with prognosis, and evaluated the accuracy for predicting survival of PRL-to-TL3 ratios (PRL/TLR3) with the areas under the ROC curves (AUC). The validation cohort was divided into two groups based on the cut-off value in the ROC curve with the maximum AUC. The two groups were defined by high PRL/TLR3 (n=47) and low PRL/TLR3 groups (n=106) and the clinical outcomes were compared.

Results

In the validation cohort, the AUC for PRL/TLR3 was 0.79, showing superior prognostic ability compared to severity scores such as APACHE II and SOFA. The high PRL/TLR3 group had a significantly higher 28-day mortality than the low PRL/TLR3 group (17.0% vs 0.9%, P<0.01).

Conclusions

A new RNA endotype classified using high PRL/TLR3 was associated with mortality in COVID-19 patients.
A cytokinetic ring-driven cell rotation achieves Hertwig’s rule in early development
Authors: Middelkoop Teije C. , Neipel Jonas , Cornell Caitlin E. , Naumann Ronald , Pimpale Lokesh G. , Jülicher Frank , Grill Stephan W.
Published: June 2023

Cells tend to divide along the direction in which they are longest, as famously stated by Oscar Hertwig in 1884 in his ‘long axis’ rule1,2. The orientation of the mitotic spindle determines the cell division axis3, and Hertwig’s long axis rule is usually ensured by forces stemming from microtubules4. Pulling on the spindle from the cell cortex can give rise to unstable behaviors5,6, and we here set out to understand how Hertwig’s long axis rule is realized in early embryonic divisions where cortical pulling forces are prevalent. We focus on earlyC. elegansdevelopment, where we compressed embryos to reveal that cortical pulling forces favor an alignment of the spindle with the cell’s short axis. Strikingly, we find that this misalignment is corrected by an actomyosin-based mechanism that rotates the entire cell, including the mitotic spindle. We uncover that myosin-driven contractility in the cytokinetic ring generates inward forces that align it with the short axis, and thereby the spindle with the long axis. A theoretical model together with experiments using slightly compressed mouse zygotes suggest that a constricting cytokinetic ring can ensure Hertwig’s long axis rule in cells that are free to rotate inside a confining structure, thereby generalizing the underlying principle.
Rapid Prototyping of Thermoplastic Microfluidic 3D Cell Culture Devices by Creating Regional Hydrophilicity Discrepancy
Authors: Bai Haiqing , Olson Kristen N. Peters , Pan Ming , Marshall Thomas , Singh Hardeep , Ma Jingzhe , Gilbride Paige , Yuan Yu-Chieh , Si Longlong , Maharjan Sushila , Huang Di , Qian Xiaohua , Livermore Carol , Zhang Yu Shrike , Xie Xin
Published: June 2023

Microfluidic three-dimensional cell culture devices that enable the recapitulation of key aspects of organ structures and functionsin vivorepresent a promising preclinical platform to improve translational success during drug discovery. Essential to these engineered devices is the spatial patterning of cells from different tissue types within a confined microenvironment. Traditional fabrication strategies lack the scalability, cost-effectiveness, and rapid prototyping capabilities required for industrial applications, especially for processes involving thermoplastic materials. Here, we introduce an approach to pattern fluid guides inside microchannels by establishing differential hydrophilicity using pressure-sensitive adhesives as masks and a subsequent selective coating with a biocompatible polymer. We identified optimal coating conditions using polyvinylpyrrolidone, which resulted in rapid and consistent hydrogel flow in both the open-chip prototype and the fully bonded device containing additional features for medium perfusion. We tested the suitability of our device for dynamic 3D cell culture by growing human hepatocytes in the device under controlled fluid flow for a 14-day period. Additionally, we demonstrated the potential of using our device for pharmaceutical high-throughput screening applications, such as predicting drug-induced liver injury. Our approach offers a facile strategy of rapid prototyping thermoplastic microfluidic organ chips with varying geometries, microstructures, and substrate materials.
Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer
Authors: Murray Joseph C. , Sivapalan Lavanya , Hummelink Karlijn , Balan Archana , White James R. , Niknafs Noushin , Rhymee Lamia , Pereira Gavin , Rao Nisha , Phallen Jillian , Leal Alessandro , Bartlett David L. , Marrone Kristen A. , Naidoo Jarushka , Levy Benjamin , Rosner Samuel , Hann Christine L. , Scott Susan C. , Feliciano Josephine , Lam Vincent K. , Ettinger David S. , Li Qing Kay , Illei Peter B. , Monkhorst Kim , Zaidi Ali H. , Scharpf Robert B. , Brahmer Julie R. , Velculescu Victor E. , Forde Patrick M. , Anagnostou Valsamo
Published: June 2023

Purpose

Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect -especially in the setting of stable disease-call for the development of molecularly-informed real-time minimally invasive predictive biomarkers. In addition to capturing tumor regression, liquid biopsies may be informative in evaluating immune-related adverse events (irAEs).

Experimental design

We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response for each patient. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles.

Results

Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank p=0.0003) and overall survival (log-rank p=0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, peripheral blood T-cell repertoire reshaping, assessed by significant TCR clonotypic expansions and regressions were noted on-treatment.

Conclusions

Molecular responses assist with interpretation of heterogeneous clinical responses especially for patients with stable disease. Our complementary assessment of the tumor and immune compartments by liquid biopsies provides an approach for monitoring of clinical benefit and immune-related toxicities for patients with NSCLC receiving immunotherapy.

Statement of translational relevance

Longitudinal dynamic changes in cell-free tumor load and reshaping of the peripheral T-cell repertoire capture clinical outcomes and immune-related toxicities during immunotherapy for patients with non-small cell lung cancer.
Neurological Imaging Order Selection Using Natural Language Processing and a Support Vector Classifier
Authors: Mehta Videet , Dharia Rohan , Desai Nilesh
Published: June 2023

Purpose

To develop an algorithm for automated medical imaging order selection based on provider-input signs and symptoms using natural language processing and machine learning. The aim is to reduce the frequency of inappropriate physician imaging orders, which currently accounts for 25.7% of cases, and thereby mitigate potential patient health concerns.

Materials and Methods

The study was conducted retrospectively with a four-step analysis process. The data used for training in the study consisted of anonymized imaging records and associated provider-input symptoms for CT and MRI orders in 40,667 patients from a tertiary children’s hospital. First, the data were normalized using keyword filtering and lemmatization. Second, an entity-embedding ML model converted the symptoms to high-dimensional numerical vectors suitable for model comprehension, which we used to balance the dataset through k-nearest-neighbor-based synthetic sampling. Third, a Support Vector Classifier (ML model) was trained and hyperparameter-tuned using the embedded symptoms to predict modality (CT/MRI), contrast (with/without), and anatomical region (head, neck, etc.) for the imaging orders. Finally, a web application was developed to package the model, which analyzes user-input symptoms and outputs the predicted order.

Results

The model was found to have a final overall accuracy of 93.2% on a 4,704-case test set (p <0.001). The AUCs for the eight classes ranged from 96% to 100%, and the average F1-score was 0.92.

Conclusion

This algorithm looks to act as a clinical decision support tool to help augment the present physician imaging order selection accuracy and improve patient health.
Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS-COV-2 targeting main protease and papain-like protease
Authors: Choudhary Shweta , Nehul Sanketkumar , Singh Ankur , Panda Prasan Kumar , Kumar Pravindra , Sharma Gaurav Kumar , Tomar Shailly
Published: June 2023

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be over, but its variants continue to emerge, and patients with mild symptoms having long COVID is still under investigation. SARS-CoV-2 infection leading to elevated cytokine levels and suppressed immune responses set off cytokine storm, fatal systemic inflammation, tissue damage, and multi-organ failure. Thus, drug molecules targeting the SARS-CoV-2 virus-specific proteins or capable of suppressing the host inflammatory responses to viral infection would provide an effective antiviral therapy against emerging variants of concern. Evolutionarily conserved papain-like protease (PLpro) and main protease (Mpro) play an indispensable role in the virus life cycle and immune evasion. Direct-acting antivirals targeting both these viral proteases represent an attractive antiviral strategy that is also expected to reduce viral inflammation. The present study has evaluated the antiviral and anti-inflammatory potential of natural triterpenoids: azadirachtin, withanolide_A, and isoginkgetin. These molecules inhibit the Mpro and PLpro proteolytic activities with half-maximal inhibitory concentrations (IC50) values ranging from 1.42 to 32.7 µM. Isothermal titration calorimetry (ITC) analysis validated the binding of these compounds to Mpro and PLpro. As expected, the two compounds, withanolide_A and azadirachtin, exhibit potent anti-SARS-CoV-2 activity in cell-based assays, with half- maximum effective concentration (EC50) values of 21.73 µM and 31.19 µM, respectively. The anti-inflammatory role of azadirachtin and withanolide_A when assessed using HEK293T cells were found to significantly reduce the levels of CXCL10, TNFα, IL6, and IL8 cytokines, which are elevated in severe cases of COVID-19. Interestingly, azadirachtin and withanolide_A were also found to rescue the decreased type-I interferon response (IFN-α1). The results of this study clearly highlight the role of triterpenoids as effective antiviral molecules that target SARS-CoV-2 specific enzymes and also host immune pathways involved in virus mediated inflammation.
Immortalization and transformation of primary cells mediated by engineered ecDNAs
Authors: Pradella Davide , Zhang Minsi , Gao Rui , Yao Melissa A. , Gluchowska Katarzyna M. , Florez Ylenia Cendon , Mishra Tanmay , Rocca Gaspare La , Weigl Moritz , Jiao Ziqi , Nguyen Hieu H.M. , Grimm Felix , Lisi Marta , Mastroleo Chiara , Chen Kevin , Luebeck Jens , Bafna Vineet , Antonescu Cristina R. , Ventura Andrea
Published: June 2023

Focal gene amplifications are among the most common cancer-associated mutations, but their evolution and contribution to tumorigenesis have proven challenging to recapitulate in primary cells and model organisms. Here we describe a general approach to engineer large (>1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs, also known as “double minutes”) in a spatiotemporally controlled manner in cancer cell lines and in primary cells derived from genetically engineered mice. With this strategy, ecDNA formation can be coupled with expression of fluorescent reporters or other selectable markers to enable the identification and tracking of ecDNA-containing cells. We demonstrate the feasibility of this approach by engineering MDM2-containing ecDNAs in near-diploid human cells, showing that GFP expression can be used to track ecDNA dynamics under physiological conditions or in the presence of specific selective pressures. We also apply this approach to generate mice harboring inducibleMyc- andMdm2-containing ecDNAs analogous to those spontaneously occurring in human cancers. We show that the engineered ecDNAs rapidly accumulate in primary cells derived from these animals, promoting proliferation, immortalization, and transformation.
Genome reduction occurred in earlyProchlorococcuswith an unusually low effective population size
Authors: Zhang Hao , Hellweger Ferdi L. , Luo Haiwei
Published: June 2023

In the oligotrophic sunlit ocean, the most abundant free-living planktonic bacterial lineages evolve convergently through genome reduction. The cyanobacteriumProchlorococcusresponsible for 10% global oxygen production is a prominent example. The dominant theory known as ‘genome streamlining’ posits that they have extremely large effective population sizes (Ne) such that selection for metabolic efficiency acts to drive genome reduction. Because genome reduction largely took place anciently, this theory builds on the assumption that their ancestors’Newas similarly large. ConstrainingNefor ancient ancestors is challenging because experimental measurements of extinct organisms are impossible and alternatively reconstructing ancestralNewith phylogenetic models gives large uncertainties. Here, we develop a new strategy that leverages agent-based modeling to simulate the change ofNeproxy for ancient ancestors, the genome-wide ratio of radical to conservative nonsynonymous nucleotide substitution rate (dR/dC), in response to the change ofNe. Surprisingly, this proxy shows expected increases with decreases ofNeonly whenNefalls to about 10k – 100k or lower, magnitudes characteristic ofNeof obligate endosymbiont species where drift drives genome reduction. We therefore conclude that drift, rather than selection, is the primary force that droveProchlorococcusgenome reduction.
WITHDRAWN: How rate information is collectively coded in input to the cerebellum: a hypothesis and simulation
Authors: Gilbert Mike , Rasmussen Anders
Published: June 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to the fact that it is a previous draft of the paper titled: “What if…? The granular layer, the input layer of the cerebellar network: a theory”. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Foraging specialization and body size in seabirds
Authors: Hernandez Juan , Arroyo José Ignacio
Published: June 2023

Body size affects many biological processes since it predicts traits, timing, and biological rates. Some of these relationships are explained by the metabolic theory of ecology, which predicts that they should scale according to a power law with exponents multiples of. Here we study the relationships between foraging specialization, particularly the number of dietary categories and prey capture strategies, and seabird species size, based on a database of 342 species (representing more than 95 % of all species). In our analysis, we found a negative relationship between the number of dietary categories and the number of capture strategies with body size with exponents of -0.83±0.31 and -0.76±0.06. To explain these relationships in terms of first principles, we developed a simple model to explain the origin of this scaling based on well-established ecological scaling relationships. Our study suggests that foraging specialization is constrained by the energy used by an organism, providing a basis for future theoretical developments.
Massage and Exercise Increase Body Awareness in Healthy Adults: A Randomized Placebo Controlled Trial
Authors: Danner Ursula , Avian Alexander , Mittermaier Christian
Published: June 2023

Objective

Physiotherapists are supposed to have a great impact on the body awareness of their clients through passive and active measures. The aim of this study was to investigate the effect of a single session of manual massage or exercise on body awareness.

Methods

A three-arm randomized controlled study including 96 healthy volunteers (18 - 65 years) was conducted at the Institute of Physical Medicine & Rehabilitation, at the Kepler University Hospital in Linz/Austria. Anonymous questionnaire assessments and analysis with intention-to-treat approach were performed. Participants were assigned to a single intervention of massage (full-body massage with slow strokes and gentle kneading), exercise (moderate body workout, video-based exercise instructions) or lecture on medicinal herbs (video-based lecture, control group). Primary endpoints were the changes of body awareness recorded with the non-verbal Awareness Body Chart test. Secondary endpoints were the changes of body awareness scored with a German body awareness questionnaire (Kurzer Fragebogen zur Eigenwahrnehmung des Koerpers, KEKS) and changes in mood scored with a German questionnaire on mood (Befindlichkeitsfragebogen).

Results

The Awareness Body Chart total score increased in both intervention groups but not in the control group with significant differences in the change between control group and both other groups (massage vs. control: +0.47, 95% CI 0.30 to 0.64; exercise vs. control: +0.31, 95% CI 0.15 to 0.45; massage vs. exercise: +0.19, 95% CI -0.02 to 0.34). An increase of the KEKS total score was found in the exercise in comparison to the control group. Mood significantly improved in both intervention groups compared to the control group.

Conclusions

In this study single session interventions of massage or exercise presented immediate positive impact on body awareness and furthermore on mood. The trial may serve as a prototype for further research on body awareness.

Trial Registration

Registered in theclinicaltrials.govdatabase (NCT05004272)
Delayed primacy recall performance predicts post mortem Alzheimers disease pathology from unimpaired ante mortem cognitive baseline
Authors: Bruno Davide , Gicas Kristina , Jauregi Zinkunegi Ainara , Mueller Kimberly D , Lamar Melissa
Published: June 2023

INTRODUCTION: We propose a novel method to assess delayed primacy in the CERAD memory test. We then examine whether this measure predicts post mortem Alzheimers disease (AD) neuropathology in individuals who were clinically unimpaired at baseline. METHODS: A total of 1096 individuals were selected from the Rush Alzheimers Disease Center database registry. All participants were clinically unimpaired at baseline, and had subsequently undergone brain autopsy. Average age at baseline was 78.8 (6.92). A Bayesian regression analysis was carried out with global pathology as outcome; demographic, clinical and APOE data as covariates; and cognitive predictors, including delayed primacy. RESULTS: Global AD pathology was best predicted by delayed primacy. Secondary analyses showed that delayed primacy was mostly associated with neuritic plaques, whereas total delayed recall was associated with neurofibrillary tangles. DISCUSSION: We conclude that CERAD-derived delayed primacy is a useful metric for early detection and diagnosis of AD in unimpaired individuals.
Screening of leaf extraction and storage conditions for eco-metabolomics studies
Authors: Lang Jakob , Ramos Sergio E. , Smohunova Marharyta , Bigler Laurent , Schuman Meredith C.
Published: June 2023

Mass spectrometry-based plant metabolomics is frequently used to identify novel natural products or study the effect of specific treatments on a plant’s metabolism. Reliable sample handling is required to avoid artifacts, which is why most protocols mandate shock freezing of plant tissue in liquid nitrogen and an uninterrupted cooling chain. However, the logistical challenges of this approach make it infeasible for many ecological studies. Especially for research in the tropics, permanent cooling poses a challenge, which is why many of those studies use dried leaf tissue instead. We screened a total of ten extraction and storage approaches for plant metabolites extracted from maize leaf tissue across two cropping seasons to develop a methodology for agroecological studies in logistically challenging tropical locations. All methods were evaluated based on changes in the metabolite profile across a 2-month storage period at different temperatures with the goal of reproducing the metabolite profile of the living plant as closely as possible. We show that our newly developed on-site liquid-liquid extraction protocol provides a good compromise between sample replicability, extraction efficiency, material logistics, and metabolite profile stability. We further discuss alternative methods which showed promising results and feasibility of on-site sample handling for field studies.

Highlight

We developed an on-site metabolite extraction method for leaf tissue samples from field studies in challenging logistical circumstances. We highlight extract stability and reproducibility compared to frozen or dried tissue.
Mixed structure- and sequence-based approach for protein graph neural networks with application to antibody developability prediction
Authors: Khade Pranav M. , Maser Michael , Gligorijevic Vladimir , Watkins Andrew
Published: June 2023

There are hundreds of thousands of known proteins but significantly fewer unique protein folds. Furthermore, proteins often have conserved and even repeating geometric patterns, which can be captured by models of protein structure and function. In this work, we use Delaunay tessellations andα-shapes, which capture these conserved geometric patterns, to define graph adjacency in Graph Convolutional Networks (GCN). We demonstrate the utility of the resulting GCN model on antibody developability prediction. Compared to the frequently used graph adjacencies based on k-nearest-neighbors or a fixed cutoff radius, the Delaunay tessellation andα-shapes better capture residue-specific interactions at a lower computational cost for a given system size. The resulting models achieve state-of-the-art performance on an antibody developability prediction task. Finally, we propose an extension of the model which does not require known or predicted structures but uses an “archetypical” antibody structure to infer likely contacts.
Data-driven discovery of innate immunomodulators via machine learning-guided high throughput screening
Authors: Tang Yifeng , Kim Jeremiah Y. , IP Carman KM , Bahmani Azadeh , Chen Qing , Rosenberger Matthew G. , Esser-Kahn Aaron P. , Ferguson Andrew L.
Published: June 2023

The innate immune response is vital for the success of prophylactic vaccines and immunotherapies. Control of signaling in innate immune pathways can improve prophylactic vaccines by inhibiting unfavorable systemic inflammation and immunotherapies by enhancing immune stimulation. In this work, we developed a machine learning-enabled active learning pipeline to guidein vitroexperimental screening and discovery of small molecule immunomodulators that improve immune responses by altering the signaling activity of innate immune responses stimulated by traditional pattern recognition receptor agonists. Molecules were tested byin vitrohigh throughput screening (HTS) where we measured modulation of the nuclear factorκ-light-chain-enhancer of activated B-cells (NF-κB) and the interferon regulatory factors (IRF) pathways. These data were used to train data-driven predictive models linking molecular structure to modulation of the NF-κB and IRF responses using deep representational learning, Gaussian process regression, and Bayesian optimization. By interleaving successive rounds of model training andin vitroHTS, we performed an active learning-guided traversal of a 139,998 molecule library. After sampling only∼2% of the library, we discovered viable molecules with unprecedented immunomodulatory capacity, including those capable of suppressing NF-κB activity by up to 15-fold, elevating NF-κB activity by up to 5-fold, and elevating IRF activity by up to 6-fold. We extracted chemical design rules identifying particular chemical fragments as principal drivers of specific immunomodulation behaviors. We validated the immunomodulatory effect of a subset of our top candidates by measuring cytokine release profiles. Of these, one molecule induced a 3-fold enhancement in IFN-βproduction when delivered with a cyclic di-nucleotide stimulator of interferon genes (STING) agonist. In sum, our machine learning-enabled screening approach presents an efficient immunomodulator discovery pipeline that has furnished a library of novel small molecules with a strong capacity to enhance or suppress innate immune signaling pathways to shape and improve prophylactic vaccination and immunotherapies.
Opioidergic activation of descending pain inhibitory system underlies placebo analgesia
Authors: Neyama Hiroyuki , Wu Yuping , Nakaya Yuka , Kato Shigeki , Shimizu Tomoko , Tahara Tsuyoshi , Shigeta Mika , Inoue Michiko , Miyamichi Kazunari , Matsushita Natsuki , Mashimo Tomoji , Miyasaka Yoshiki , Watanabe Yasuyoshi , Kobayashi Masayuki , Kobayashi Kazuto , Cui Yilong
Published: June 2023

Placebo analgesia is caused by inactive treatment, implicating endogenous brain function involvement. However, the underlying neurobiological mechanisms remain unclear. We found that μ-opioid signals in the medial prefrontal cortex (mPFC) activate the descending pain inhibitory system to initiate placebo analgesia in neuropathic pain rats. Chemogenetic manipulation demonstrated that specific activation of μ-opioid receptor-positive (MOR+) neurons in the mPFC or suppression of the mPFC-ventrolateral periaqueductal gray (vlPAG) circuit inhibited placebo analgesia in rats. MOR+neurons in the mPFC are monosynaptically connected and directly inhibit L5 pyramidal neurons that project to the vlPAG via GABAAreceptors. Thus, intrinsic opioid signaling in the mPFC disinhibits excitatory outflow to the vlPAG by suppressing MOR+neurons, leading to descending pain inhibitory system activation that initiates placebo analgesia.

One Sentence Summary

Sugar pills relieve pain by activating the intrinsic pain inhibitory system via opioidergic signals in the prefrontal cortex.
Genetic Screen Identified Prmt5 as a Neuroprotection Target against Cerebral Ischemia
Authors: Wu Haoyang , Lv Peiyuan , Wang Jinyu , Bennett Brian , Wang Jiajia , Li Pishun , Peng Yi , Hu Guang , Lin Jiaji
Published: June 2023

Epigenetic regulators present novel opportunities for both ischemic stroke research and therapeutic interventions. While previous work has implicated that they may provide neuroprotection by potentially influencing coordinated sets of genes and pathways, most of them remains largely uncharacterized in ischemic conditions. In this study, we used the oxygen-glucose deprivation (OGD) model in the immortalized mouse hippocampal neuronal cell line HT-22 and carried out an RNAi screen on epigenetic regulators. We identified Prmt5 as a novel negative regulator of neuronal cell survival after OGD, which presented a phenotype of translocation from the cytosol to the nucleus upon oxygen and energy depletion bothin vitroandin vivo. Prmt5 bound to the chromatin and a large number of promoter regions to repress downstream gene expression. Silencing Prmt5 significantly dampened the OGD-induced changes for a large-scale of genes, and gene ontology analysis showed that Prmt5-target genes were highly enriched for Hedgehog signaling. Encouraged by the above observation, we treated mice with middle cerebral artery occlusion (MCAO) with the Prmt5 inhibitor EPZ015666 and found that Prmt5 inhibition sustain protection against neuronal deathin vivo. Together, our findings revealed a novel epigenetic mechanism of Prmt5 in cerebral ischemia and uncovered a potential target for neuroprotection.
Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization
Authors: Behrmann Megan S. , Perera Himasha M. , Welikala Malisha U. , Matthews Jacquelynn E. , Trakselis Michael A.
Published: June 2023

Repair of DNA damage begins with the elicitation of targeted cellular responses to restore the genome. InE. coli, major products of DNA damage result in the buildup of single-stranded DNA (ssDNA) that is rapidly bound by cooperative filamentation of RecA to initiate the SOS response. The replicative helicase, DnaB, is a central component of the replisome, unwinding duplex DNA in concert with Pol III template dependent synthesis. Interestingly, helicase unwinding is heavily regulated, and the unwinding rate can be reduced by over 10-fold if DnaB becomes decoupled from Pol III. However, if DnaB is dysregulated by mutations that enforce a faster more constricted conformation, unwinding can continue independently, generating excess ssDNA resulting in severe cellular stress. This surplus ssDNA can stimulate RecA recruitment for recombinational repair or activation of SOS to increase the available repair protein pool. To better understand the consequences of dysregulated unwinding, we combined targeteddnaBmutations with an inducible plasmid-based RecA filament inhibition strategy to examine the dependencies on RecA in counteracting decoupling. We find that RecA filamentation is instrumental for processing daughter strand gaps left behind from decoupled unwinding and synthesis to prevent DNA breaks. Without functional RecA filaments,dnaBmutant strains had a greater burden from endogenous damage but without a compensatory increase in mutagenesis. Overall, RecA plays a critical role in strain survival by processing DNA gaps and protecting from breaks caused by dysregulated or interrupted helicase activityin vivo.

AUTHOR SUMMARY

Coupled DNA unwinding and synthesis is a genomic protection strategy used during DNA replication to prevent excessive buildup of labile single-stranded DNA (ssDNA). The helicase and polymerase enzymes have evolved multidimensional regulation tactics to maintain this connection despite different individual kinetic rates and differential responses to genomic obstacles. For one, the DnaB helicase inE. colican alter its hexameric ring structure by dilating to slow down or constricting to speed up DNA unwinding. Here, we have utilized persistently constricted mutants of DnaBin vitroor genomically editeddnaB in vivoto induce decoupling in the replisome. Constricted DnaB mutants limit total leading strand synthesis by Pol III, indicating that lost kinetic regulation between these enzymes results in inefficient replication. Using an inducible plasmid-based system to disrupt Rad51 filamentation in vivo, we show that RecA is responsible for the increased mutagenesis, a filamented cellular phenotype, and mitigating DNA breaks from excess ssDNA caused by decoupling. These results reveal a role for RecA filamentation in mediating excess ssDNA resulting from decoupling to maintain survival and adaptation.
Beyond venomous fangs: Uloboridae spiders have lost their venom but not their toxicity
Authors: Peng Xiaojing , Dersch Ludwig , Dresler Josephine , Lüddecke Tim , Dederichs Tim , Michalik Peter , Peigneur Steve , Tytgat Jan , Hassan Afrah , Mucciolo Antonio , Robinson-Rechavi Marc , Zancolli Giulia
Published: June 2023

Venom, one of nature’s most potent secretions, has played a crucial role in the evolutionary success of many animal groups, including spiders. However, Uloboridae spiders appear to lack venom and capture their prey, unlike venomous spiders, by extensive silk-wrapping and regurgitation of digestive fluids onto the entire prey. A prevailing hypothesis posits that toxins may have been reallocated from the venom to alternative secretions, like silk or digestive fluids. Yet, whether uloborids have retained venom toxins and the mechanisms underlying prey immobilisation remain unresolved. Here, we employed a multi-disciplinary approach to assess the absence of venom glands inUluborus plumipes, toxin gene expression and toxicity of digestive proteins. Our findings confirm thatU. plumipeslacks a venom apparatus, while neurotoxin-like transcripts were highly expressed in the digestive system. Midgut gland extract had comparable toxicity levels to that of the venomousParasteatoda tepidariorum. However, no inhibitory effects on sodium nor potassium channels were observed, indicating a different toxic mechanism. These findings support the hypothesis that Uloboridae spiders have lost their venom apparatus while retaining toxin-like genes. The potent toxicity of their digestive fluids, a trait conserved across spiders, likely compensate for the absence of venom, ensuring effective prey immobilisation and digestion.
Inference of Genomic Landscapes using Ordered Hidden Markov Models with Emission Densities (oHMMed)
Authors: Vogl Claus , Karapetiants Mariia , Yıldırım Burçin , Kjartansdóttir Hrönn , Kosiol Carolin , Bergman Juraj , Majka Michal , Mikula Lynette Caitlin
Published: June 2023

Background

Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim to quantify this variation, account for it during inference procedures, and ultimately determine the causal processes behind it. Since sequential observations along chromosomes are not independent, it is unsurprising that autocorrelation patterns have been observede.g.,in human base composition.

In this article, we develop a class of Hidden Markov Models (HMMs) called oHMMed (ordered HMM with emission densities, the corresponding R package of the same name is available on CRAN): They identify the number of comparably homogeneous regions within autocorrelated observed sequences. These are modelled as discrete hidden states; the observed data points are realisations of continuous probability distributions with state-specific means that enable ordering of these distributions. The observed sequence is labelled according to the hidden states, permitting only neighbouring states that are also neighbours within the ordering of their associated distributions. The parameters that characterise these state-specific distributions are inferred.

Results

We apply our oHMMed algorithms to the proportion of G and C bases (modelled as a mixture of normal distributions) and the number of genes (modelled as a mixture of poisson-gamma distributions) in windows along the human, mouse, and fruit fly genomes. This results in a partitioning of the genomes into regions by statistically distinguishable averages of these features, and in a characterisation of their continuous patterns of variation. In regard to the genomic G and C proportion, this latter result distinguishes oHMMed from segmentation algorithms based in isochore or compositional domain theory. We further use oHMMed to conduct a detailed analysis of variation of chromatin accessibility (ATAC-seq) and epigenetic markers H3K27ac and H3K27me3 (modelled as a mixture of poisson-gamma distributions) along the human chromosome 1 and their correlations.

Conclusions

Our algorithms provide a biologically assumption-free approach to characterising genomic landscapes shaped by continuous, autocorrelated patterns of variation. Despite this, the resulting genome segmentation enables extraction of compositionally distinct regions for further downstream analyses.
Mutant analysis of Kcng4b reveals how the different functional states of the voltage-gated potassium channel regulate ear development
Authors: Jędrychowska Justyna , Vardanyan Vitya , Wieczor Milosz , Marciniak Antoni , Czub Jacek , Amini Razieh , Jain Ruchi , Shen Hongyuan , Choi Hyungwon , Kuznicki Jacek , Korzh Vladimir
Published: June 2023

The voltage gated (Kv) slow-inactivating delayed rectifier channel regulates the development of hollow organs of the zebrafish. The functional tetramer consists of an electrically active subunit (Kcnb1, Kv2.1) and a modulatory silent subunit (Kcng4b, Kv6.4). The two mutations in zebrafishkcng4b - kcng4b-C1andkcng4b-C2(Gasanov et al., 2021) - have been studied during ear development using electrophysiology, developmental biology andin silicostructural modelling.kcng4b-C1mutation causes a C-terminal truncation characterized by mild Kcng4b loss-of-function (LOF) manifested by failure of kinocilia to extend and formation of ectopic otoliths. In contrast, thekcng4b-C2-/-mutation causes the C-terminal domain to elongate and the ectopic seventh transmembrane (TM) domain to form, converting the intracellular C-terminus to an extracellular one. Kcng4b-C2 acts as a Kcng4b gain-of-function (GOF) allele. Otoliths fail to develop and kinocilia are reduced inkcng4b-C2-/-. These results show that different mutations of the silent subunit Kcng4 can affect the activity of the Kv channel and cause a wide range of developmental defects.
Proximity labelling and evolutionary evidence reveal insights into IL-1α nuclear networks and function
Authors: Wellens Rose , Tapia Victor S. , Bennett Hayley , Adamson Antony , Rivers-Auty Jack , Green Jack P. , Lopez-Castejon Gloria , Brough David , Hoyle Christopher
Published: June 2023

Interleukin (IL)-1α is a suggested dual-function cytokine that diverged from IL-1β in mammals potentially by acquiring additional biological roles that relate to highly conserved regions in the pro-domain of IL-1α, including a nuclear localisation sequence (NLS) and histone acetyl transferase (HAT)-binding domains. Why evolution modified pro-IL-1α’s subcellular location and protein interactome, and how this shaped IL-1α’s intracellular role, is unknown. TurboID proximity labelling with pro-IL-1α suggested a nuclear role for pro-IL-1α that involved interaction with HATs, including EP300. We also identified and validated inactivating mutations in the pro-IL-1α NLS of multiple mammalian species. However, HAT-binding domains were also conserved in species that had lost pro-IL-1α nuclear localisation. Together, these data suggest that HAT binding and nuclear localisation occurred together, and that while some species lost the NLS in their pro-IL-1α, HAT binding was maintained. The NLS was lost from several distinct species at different evolutionary times, suggesting convergent evolution, and that the loss of the NLS confers some important biological outcome.
SALL3mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss
Authors: Lei Yingnan , Al Delbany Diana , Krivec Nuša , Regin Marius , de Deckersberg Edouard Couvreu , Janssens Charlotte , Ghosh Manjusha , Sermon Karen , Spits Claudia
Published: June 2023

Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, as cells that have acquired specific genetic abnormalities experience a selective advantage in vitro. These abnormalities are highly recurrent in hPSC lines worldwide, but currently their functional consequences in differentiating cells are scarcely described. An accurate assessment of the risk associated with these genetic variants in both research and clinical settings is therefore lacking. In this work, we established that one of these recurrent abnormalities, the loss of chromosome 18q, impairs neuroectoderm commitment and affects the cardiac progenitor differentiation of hESCs. We show that downregulation ofSALL3, a gene located in the common 18q loss region, is responsible for failed neuroectodermal differentiation. Knockdown ofSALL3in control lines impaired differentiation in a manner similar to the loss of 18q, while transgenic overexpression ofSALL3in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show by gene expression analysis that loss of 18q and downregulation ofSALL3leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, including the WNT, NOTCH, JAK-STAT, TGF-beta and NF-kB pathways, suggesting that these cells are in an altered state of pluripotency.
Nanoscale structural response of biomimetic cell membranes to controlled dehydration
Authors: Krok Emilia , Franquelim Henri G. , Chattopadhyay Madhurima , Orlikowska-Rzeznik Hanna , Schwille Petra , Piatkowski Lukasz
Published: June 2023

Although cell membranes in physiological conditions exist in excess of water, there is a number of biochemical processes, such as adsorption of biomacromolecules or membrane fusion events, that require partial or even complete, transient dehydration of lipid membranes. Even though the dehydration process is crucial for understanding all fusion events, still little is known about the structural adaptation of the lipid membranes when their interfacial hydration layer is perturbed. Here, we introduce the study on the nanoscale structural reorganization of the phase-separated, supported lipid bilayers (SLBs) under a wide range of hydration conditions. Model lipid membranes were characterized with the combination of fluorescence microscopy and atomic force microscopy, and crucially, without applying any chemical or physical modifications, that so far have been considered to be indispensable for maintaining the membrane integrity upon dehydration. We revealed that decreasing hydration state of the membrane leads to an enhanced mixing of lipids characteristic for the liquid-disordered (Ld) phase with those forming liquid-ordered (Lo) phase. This is associated with a 2-fold decrease in the hydrophobic mismatch between the Ldand Lolipid phases and a 3-fold decrease of line tension for the completely desiccated membrane. Importantly, the observed changes in the hydrophobic mismatch, line tension, and miscibility of lipids are fully reversible upon subsequent rehydration of the membrane. These findings provide deeper insights into the fundamental processes such as cell-cell fusion that require partial dehydration at the interface of two membranes.
Combinatorial selective ER-phagy remodels the ER during neurogenesis
Authors: Hoyer Melissa J. , Capitanio Cristina , Smith Ian R. , Paoli Julia C. , Bieber Anna , Jiang Yizhi , Paulo Joao A. , Gonzalez-Lozano Miguel A. , Baumeister Wolfgang , Wilfling Florian , Schulman Brenda A. , Harper J. Wade
Published: June 2023

The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis: a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodeling, as autophagy-deficient neuronsin vivodisplay axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of ER and the role of individual ER-phagy receptors is limited. Here, we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodeling duringin vitrodifferentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.