bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroimmune characterization of optineurin insufficiency mouse model during ageing
Authors: Mohovic Nikolina , Peradinovic Josip , Markovinovic Andrea , Cimbro Raffaello , Minic Zeljka , Dominovic Marin , Jakovac Hrvoje , Nimac Jerneja , Rogelj Boris , Munitic Ivana 
Published: March 2023

AbstractOptineurin is a multifunctional polyubiquitin-binding protein implicated in inflammatory signalling. Optineurin mutations are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), neurodegenerative diseases characterised by neuronal loss, neuroinflammation, and peripheral immune disbalance. However, the pathogenic role of optineurin mutations is unclear. We previously observed no phenotype in the unmanipulated young optineurin insufficiency mice (Optn470T), designed to mimic ALS/FTD-linked truncations deficient in polyubiquitin binding. The purpose of this study was to investigate whether ageing would trigger neurodegeneration. We performed a neuroimmune characterization of ageing wild-type (WT) and Optn470Tmice. No motor or cognitive differences were detected between the genotypes. Neuropathological analyses demonstrated signs of ageing including lipofuscin accumulation and microglial activation. However, this was not worsened in Optn470Tmice, and they did not exhibit TAR DNA-binding protein 43 (TDP-43) aggregation or neuronal loss. Spleen immunophenotyping uncovered T cell immunosenescence at two years but without notable differences between the WT and Optn470Tmice. Conventional dendritic cells (cDC) and macrophages exhibited increased expression of activation markers in two-year-old Optn470Tmales but not females, although the numbers of innate immune cells were similar between genotypes. Altogether, a combination of optineurin insufficiency and ageing did not induce ALS/FTD-like neuropathology in mice.
Time-Resolved Chemical Phenotyping of Whole Plant Roots with Printed Electrochemical Sensors and Machine Learning
Authors: Coatsworth Philip , Cotur Yasin , Naik Atharv , Asfour Tarek , Collins Alex Silva-Pinto , Olenik Selin , Gonzalez-Macia Laura , Bozkurt Tolga , Chao Dai-Yin , Güder Firat 
Published: March 2023

AbstractPlants are non-equilibrium systems consisting of time-dependent biological processes. Phenotyping of chemical responses, however, is typically performed using plant tissues, which behave differently to whole plants, in one-off measurements. Single point measurements cannot capture the information rich time-resolved changes in chemical signals in plants associated with nutrient uptake, immunity or growth. In this work, we report a high-throughput, modular, real-time chemical phenotyping platform for continuous monitoring of chemical signals in the often-neglected root environment of whole plants: TETRIS (Time-resolvedElectrochemicalTechnology for plantRootIn-situchemicalSensing). TETRIS consists of screen-printed electrochemical sensors for monitoring concentrations of salt, pH and H2O2in the root environment of whole plants. TETRIS can detect time-sensitive chemical signals and be operated in parallel through multiplexing to elucidate the overall chemical behavior of living plants. Using TETRIS, we determined the rates of uptake of a range of ions (including nutrients and heavy metals) inBrassica oleracea acephala.We also modulated ion uptake using the ion channel blocker LaCl3, which we could monitor using TETRIS. We developed a machine learning model to predict the rates of uptake of salts, both harmful and beneficial, demonstrating that TETRIS can be used for rapid mapping of ion uptake for new plant varieties. TETRIS has the potential to overcome the urgent “bottleneck” in high-throughput screening in producing high yielding plant varieties with improved resistance against stress.
Dimerization and autophosphorylation of the MST family of kinases are controlled by the same set of residues
Authors: Weingartner Kyler A. , Tran Thao , Tripp Katherine W. , Kavran Jennifer M. 
Published: March 2023

ABSTRACTThe Hippo pathway controls tissue growth and regulates stem cell fate through the activities of core kinase cassette that begins with the Sterile 20-like kinase MST1/2. Activation of MST1/2 relies ontrans-autophosphorylation but the details of the mechanisms regulating that reaction are not fully elucidated. Proposals include dimerization as a first step and include multiple models for potential kinase-domain dimers. Efforts to verify and link these dimers totrans-autophosphorylation were unsuccessful. We explored the link between dimerization andtrans-autophosphorylation for MST2 and the entire family of MST kinases. We analyzed crystal lattice contacts of structures of MST kinases and identified an ensemble of kinase-domain dimers compatible withtrans-autophosphorylation. These dimers share a common dimerization interface comprised of the activation loop and αG-helix while the arrangements of the kinase-domains within the dimer varied depending on their activation state. We then verified the dimerization interface and determined its function using MST2. Variants bearing alanine substitutions of the αG-helix prevented dimerization of the MST2 kinase domain both in solution and in cells. These substitutions also blocked autophosphorylation of full-length MST2 and itsDrosophilahomolog Hippo in cells. These variants retain the same secondary structure as wild-type and capacity to phosphorylate a protein substrate, indicating the loss of MST2 activation can be directly attributed to a loss of dimerization rather than loss of either fold or catalytic function. Together this data functionally links dimerization and autophosphorylation for MST2 and suggests this activation mechanism is conserved across both species and the entire MST family.
Drosophilaoocyte specification is maintained by the dynamic duo of microtubule polymerase Mini spindles/XMAP215 and dynein
Authors: Lu Wen , Lakonishok Margot , Gelfand Vladimir I 
Published: March 2023

AbstractIn many species, only one oocyte is specified among a group of interconnected germline sister cells. InDrosophila melanogaster, 16-cell interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), theDrosophilahomolog of XMAP215, is essential for the oocyte fate determination. mRNA encoding Msps is concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown ofmspsblocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, enhancing dynein-dependent nurse cell-to-oocyte transport and transforming a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination.Significance statementOocyte determination inDrosophila melanogasterprovides a valuable model for studying cell fate specification. We describe the crucial role of the duo of microtubule polymerase Mini spindles (Msps) and cytoplasmic dynein in this process. We show that Msps is essential for oocyte fate determination. Msps concentration in the oocyte is achieved through dynein-dependent transport ofmspsmRNA along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, further enhancing nurse cell-to-oocyte transport by dynein. This creates a positive feedback loop that transforms a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination. Our findings provide important insights into the mechanisms of oocyte specification and have implications for understanding the development of multicellular organisms.
The loss of antioxidant activities impairs intestinal epithelium homeostasis by altering lipid metabolism
Authors: Ramos-León Javier , Valencia Concepción , Gutiérrez-Mariscal Mariana , Rivera-Miranda David-David-Alejandro , García-Meléndrez Celina , Covarrubias Luis 
Published: March 2023

ABSTRACTThe increase in reactive oxygens species (ROS) with aging could be at the origin of many diseases of the elderly. Here we investigated the role of ROS in the renewal of the intestinal epithelium in mice lacking catalase (CAT) and/or nicotinamide nucleotide transhydrogenase (NNT) activities.Cat-/-mice have delayed intestinal epithelium renewal and were prone to develop necrotizing enterocolitis upon starvation. Interestingly, crypts lacking CAT showed fewer intestinal stem cells (ISC) and lower stem cell activity than wild-type, together with less LYS in Paneth cells. In contrast, crypts lacking NNT showed a similar number of ISCs and amount of LYS as wild-type but increased stem cell activity, which was also impaired by the loss of CAT.Catdeficiency caused fat accumulation in crypts, and a fall in the remarkable high amount of adipose triglyceride lipase (ATGL) in PCs. Supporting a role of ATGL in the regulation of ISC activity, its inhibition halt intestinal organoid development. These data suggest that the reduction of the intestine renewal capacity along aging originates from fatty acid metabolic alterations caused by peroxisomal ROS.Summary statementMice with increased peroxisomal or mitochondrial reactive oxygen species develop intestinal phenotypes that are associated with aging and originate from a defective stem cell niche with impaired fatty acid metabolism.
Mediolateral foot placement control can be trained: Older adults learn to walk more stable, when ankle moments are constrained
Authors: Mahaki M. , van Leeuwen A.M. , Bruijn S.M. , Van der Velde N. , van Dieën J.H. 
Published: March 2023

AbstractFalls are a problem, especially for older adults. Placing our feet accurately relative to the center-of-mass helps us to prevent falling during gait. The degree of foot placement control with respect to the center-of mass kinematic state is decreased in older as compared to young adults. Here, we attempted to train mediolateral foot placement control in healthy older adults. Ten older adults trained by walking on shoes with a narrow ridge underneath (LesSchuh), restricting mediolateral center-of-pressure shifts. As a training effect, we expected improved foot placement control during normal walking. A training session consisted of a normal walking condition, followed by a training condition on LesSchuh and finally an after-effect condition. Participants performed six of such training sessions, spread across three weeks. As a control, before the first training session, we included two similar sessions, but on normal shoes only. We evaluated whether a training effect was observed across sessions and weeks in a repeated-measures design. Whilst walking with LesSchuh, the magnitude of foot placement error reduced half-a-millimeter between sessions within a week (cohen’sd=0.394). As a training effect in normal walking, the magnitude of foot placement errors was significantly lower compared to the control week, by one millimeter in weeks 2 (cohen’sd=0.686) and 3 (cohen’sd=0.780) and by two millimeters in week 4 (cohen’sd=0.875). Local dynamic stability of normal walking also improved significantly. More precise foot placement may thus have led to improved stability. It remains to be determined whether the training effects were the result of walking on LesSchuh or from repeated treadmill walking itself. Moreover, enhancement of mechanisms beyond the scope of our outcome measures may have improved stability. At the retention test, gait stability returned to similar levels as in the control week. Yet, a reduction in foot placement error persisted.
Natural variation in theCaenorhabditis elegansegg-laying circuit modulates an intergenerational fitness trade-off
Authors: Mignerot Laure , Gimond Clotilde , Bolelli Lucie , Bouleau Charlotte , Sandjak Asma , Boulin Thomas , Braendle Christian 
Published: March 2023

ABSTRACTEvolutionary shifts from egg-laying (oviparity) to live birth (viviparity) are common across diverse taxa, and some species exhibit variability in egg-laying modes or an intermediate mode with eggs containing embryos at various stages of development. How such natural quantitative variation in egg retention arises through differences in genetics, behaviour, and physiology – and how this variation ultimately connects to variation in specific fitness components – remains poorly understood. Here, we investigate intraspecific variation in egg retention in the nematodeCaenorhabditis elegansusing a panel of 316 wild strains. We observe highly variable intra-uterine egg retention, with some strains exhibiting strongly reduced or increased retention with internal hatching. We identify multiple evolutionary origins of these phenotypic extremes and pinpoint candidate loci responsible for the observed variation. Analysis of a subset of strains confirms that natural variation in egg-laying behaviour contributes to differences in egg retention. Using neuromodulatory agents and CRISPR-Cas9-mediated genetic manipulation, we demonstrate that this behavioural variation arises from an evolutionarily divergent neuromodulatory architecture in the egg-laying circuitry. In addressing the question of why natural variation inC. elegansegg retention is maintained, we find that strong egg retention can reduce maternal fertility and survival due to detrimental hatchingin utero. However, genotypes with strong egg retention may benefit from improved offspring protection against environmental insults and gain a competitive advantage with offspring exhibiting a shortened development time to reproductive maturity outside the uterus. The observed natural variation in egg-laying behaviour inC. eleganscould therefore reflect modifications of a trade-off between alternative fitness components across generations. Our study reveals previously underappreciated diversity in theC. elegansegg-laying circuit and provides insights into the fitness consequences of this behavioural variation. We propose that intraspecific variation in nematode egg-laying behaviour offers an ideal system to identify molecular changes underlying evolutionary transitions between oviparity and viviparity in invertebrates.
Real-time in vivo thoracic spinal glutamate sensing reveals spinal hyperactivity during myocardial ischemia
Authors: Salavatian Siamak , Robbins Elaine Marie , Kuwabara Yuki , Castagnola Elisa , Cui Xinyan Tracy , Mahajan Aman 
Published: March 2023

AbstractMyocardial ischemia-reperfusion (IR) can cause ventricular arrhythmias and sudden cardiac death via sympathoexcitation. The spinal cord neural network is crucial in triggering these arrhythmias and evaluating its neurotransmitter activity during IR is critical for understanding ventricular excitability control. To assess the real-timein vivospinal neural activity in a large animal model, we developed a flexible glutamate-sensing multielectrode array. To record the glutamate signaling during IR injury, we inserted the probe into the dorsal horn of the thoracic spinal cord at the T2-T3 where neural signals generated by the cardiac sensory neurons are processed and provide sympathoexcitatory feedback to the heart. Using the glutamate sensing probe, we found that the spinal neural network was excited during IR, especially after 15 mins, and remained elevated during reperfusion. Higher glutamate signaling was correlated with the reduction in the cardiac myocyte activation recovery interval, showing higher sympathoexcitation, as well as dispersion of the repolarization which is a marker for increased risk of arrhythmias. This study illustrates a new technique for measuring the spinal glutamate at different spinal cord levels as a surrogate for the spinal neural network activity during cardiac interventions that engage the cardio-spinal neural pathway.Graphical abstract
In vitrocomparison of SARS-CoV-2 variants
Authors: Phadke Kruttika S. , Higdon Nathaniel B. A. , Bellaire Bryan H. 
Published: March 2023

ABSTRACTThe Coronaviridae family hosts various coronaviruses responsible for many diseases, from the common cold, severe lung infections to pneumonia. SARS-CoV-2 was discovered to be the etiologic agent of the Coronavirus pandemic, and numerous basic and applied laboratory techniques were utilized in virus culture and examination of the disease. Understanding the replication kinetics and characterizing the virus’ effect on different cell lines is crucial for developingin vitrostudies. With the emergence of multiple variants of SARS-CoV-2, a comparison between their infectivity and replication in common cell lines will give us a clear understanding of the characteristic differences in pathogenicity. In this study, we compared the cytopathic effect (CPE) and replication of Wild Type (WT), Omicron (B.1.1.529), and Delta (B.1.617.2) variants on 5 different cell lines; VeroE6, VeroE6 expressing high endogenous ACE2, VeroE6 highly expressing human ACE2 (VeroE6/ACE2) and TMPRSS2 (VeroE6/hACE2/ TMPRSS2), Calu3 cells highly expressing human ACE2 and A549 cells. All 3 VeroE6 cell lines were susceptible to WT strain, where CPE and replication were observed. Along with being susceptible to Wild type, VeroE6/hACE2/TMPRSS2 cells were susceptible to both omicron and delta strains, whereas VeroE6/ACE2 cells were only susceptible to omicron in a dose-dependent manner. No CPE was observed in both human lung cell lines, A549 and Calu3/hACE2, but Wild type and omicron replication was observed. As SAR-CoV-2 continues to evolve, this data will benefit researchers in experimental planning, viral pathogenicity analysis, and providing a baseline for testing future variants.
Self-regulating living material with temperature-dependent light absorption
Authors: Xiong Lealia L. , Garrett Michael A. , Kornfield Julia A. , Shapiro Mikhail G. 
Published: March 2023

ABSTRACTEngineered living materials (ELMs) exhibit desirable characteristics of the living component, including growth and repair, and responsiveness to external stimuli.Escherichia coliare a promising constituent of ELMs because they are very tractable to genetic engineering, produce heterologous proteins readily, and grow exponentially. However, seasonal variation in ambient temperature presents a challenge in deploying ELMs outside of a laboratory environment, becauseE. coligrowth rate is impaired both below and above 37°C. Here, we develop a genetically-encoded mechanism for autonomous temperature homeostasis in ELMs containingE. coliby engineering circuits that control the expression of a light-absorptive chromophore in response to changes in temperature. We demonstrate that below 36°C, our engineeredE. coliincrease in pigmentation, causing an increase in sample temperature and growth rate above non-pigmented counterparts in a model planar ELM. On the other hand, above 36°C, they decrease in pigmentation, protecting their growth compared to bacteria with temperature-independent high pigmentation. Integrating our temperature homeostasis circuit into an ELM has the potential to improve living material performance by optimizing growth and protein production in the face of seasonal temperature changes.
A molecular glue approach to control the half-life of CRISPR-based technologies
Authors: Sreekanth Vedagopuram , Jan Max , Zhao Kevin T. , Lim Donghyun , Davis Jessie R. , McConkey Marie , Kovalcik Veronica , Barkal Sam , Law Benjamin K. , Fife James , Tian Ruilin , Vinyard Michael E. , Becerra Basheer , Kampmann Martin , Sherwood Richard I. , Pinello Luca , Liu David R. , Ebert Benjamin L. , Choudhary Amit 
Published: March 2023

AbstractCas9 is a programmable nuclease that has furnished transformative technologies, including base editors and transcription modulators (e.g., CRISPRi/a), but several applications of these technologies, including therapeutics, mandatorily require precision control of their half-life. For example, such control can help avert any potential immunological and adverse events in clinical trials. Current genome editing technologies to control the half-life of Cas9 are slow, have lower activity, involve fusion of large response elements (> 230 amino acids), utilize expensive controllers with poor pharmacological attributes, and cannot be implementedin vivoon several CRISPR-based technologies. We report a general platform for half-life control using the molecular glue, pomalidomide, that binds to a ubiquitin ligase complex and a response-element bearing CRISPR-based technology, thereby causing the latter’s rapid ubiquitination and degradation. Using pomalidomide, we were able to control the half-life of large CRISPR-based technologies (e.g., base editors, CRISPRi) and small anti-CRISPRs that inhibit such technologies, allowing us to build the first examples of on-switch for base editors. The ability to switch on, fine-tune and switch-off CRISPR-based technologies with pomalidomide allowed complete control over their activity, specificity, and genome editing outcome. Importantly, the miniature size of the response element and favorable pharmacological attributes of the drug pomalidomide allowed control of activity of base editorin vivousing AAV as the delivery vehicle. These studies provide methods and reagents to precisely control the dosage and half-life of CRISPR-based technologies, propelling their therapeutic development.
NRF2 deficiency promotes ferroptosis of astrocytes mediated by oxidative stress in Alzheimer’s disease
Authors: Tang Zhi , Chen Zhuyi , Min Guo , Peng Yaqian , Xiao Yan , Guan ZhiZhong , Ni Ruiqing , Qi Xiaolan 
Published: March 2023

AbstractOxidative stress is involved in the pathogenesis of Alzheimer’s disease (AD), which is linked to reactive oxygen species (ROS), lipid peroxidation, and neurotoxicity. Emerging evidence suggests a role of nuclear factor (erythroid-derived 2)-like 2 (Nrf2), a major source of antioxidant response elements in AD. The molecular mechanism of oxidative stress and ferroptosis in astrocytes in AD is not yet fully understood. Here, we aim to investigate the mechanism by which Nrf2 regulates the ferroptosis of astrocytes in AD. Postmortem frontal cortex tissues from patients with AD and nondemented controls and brain tissue from the 3×Tg AD mouse model and wild-type mice (10 months old) were used. Immunofluorescence staining for Nrf2, the ROS marker NADPH oxidase 4 (NOX4), and GFAP was performed. We further induced Nrf2 deficiency in mouse astrocytes by using RNAi and assessed the changes in ROS, ferroptosis, lipid peroxidation, and mitochondrial dysfunction by using western blotting and immunofluorescence staining. We found decreased expression of Nrf2 and upregulated expression of NOX4 in the frontal cortex from patients with AD and in the cortex of 3×Tg mice compared to control mice. We demonstrated that Nrf2 deficiency led to ferroptosis-dependent oxidative stress-induced ROS with downregulated heme oxygenase-1 and glutathione peroxidase 4 and upregulated cystine glutamate expression. Moreover, Nrf2 deficiency increased lipid peroxidation, DNA oxidation, and mitochondrial fragmentation in mouse astrocytes. In conclusion, these results suggest that Nrf2 promotes ferroptosis of astrocytes involving oxidative stress in AD.