bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunoproteasomal Processing of Isolevuglandin Adducts in Hypertension
Authors: de la Visitación Néstor , Chen Wei , Krishnan Jaya , Van Beusecum Justin P. , Amarnath Venkataraman , Hennen Elizabeth M. , Zhao Shilin , Saleem Mohammad , Ao Mingfang , Harrison David G. , Patrick David M. 
Published: April 2023

SUMMARYAbstract FigureGraphical AbstractIsolevuglandins (isoLGs) are lipid aldehydes that form in the presence of reactive oxygen species (ROS) and drive immune activation. We found that isoLG-adducts are presented within the context of major histocompatibility complexes (MHC-I) by an immunoproteasome dependent mechanism.Pharmacologic inhibition of LMP7, the chymotrypsin subunit of the immunoproteasome, attenuates hypertension and tissue inflammation in the angiotensin II (Ang II) model of hypertension. Genetic loss of function of all immunoproteasome subunits or conditional deletion of LMP7 in dendritic cell (DCs) or endothelial cells (ECs) attenuated hypertension, reduced aortic T cell infiltration, and reduced isoLG-adduct MHC-I interaction. Furthermore, isoLG adducts structurally resemble double-stranded DNA and contribute to the activation of STING in ECs. These studies define a critical role of the immunoproteasome in the processing and presentation of isoLG-adducts. Moreover they define a role of LMP7 as a regulator of T cell activation and tissue infiltration in hypertension.
Optogenetic stimulation reveals frequency-dependent resonance and encoding in V1 excitatory and inhibitory neurons
Authors: Broggini Ana Clara , Onorato Irene , Tzanou Athanasia , Sotomayor-Gómez Boris , Uran Cem , Vinck Martin 
Published: April 2023

AbstractCortical information processing is thought to be facilitated by the resonant properties of individual neurons and neuronal networks, which selectively amplify inputs at specific frequencies. We used optogenetics to test how different input frequencies are encoded by excitatory cells and parvalbumin-expressing (PV) interneurons in mouse V1. Spike phase-locking and power increased with frequency, reaching a broad peak around 80-100Hz. This effect was observed only for Chronos, a fast-kinetic opsin, but not for Channelrhodopsin-2. Surprisingly, neurons did not exhibit narrow-band resonance in specific frequency-ranges, and showed reliably phase-locking up to 140Hz. Strong phase-locking at high frequencies reflected non-linear input/output transformations, with neurons firing only in a narrow part of the cycle. By contrast, low-frequency inputs were encoded in a more continuous manner. Correspondingly, spectral coherence and firing rates showed little dependence on frequency and did not reflect transferred power. To investigate whether strong phase-locking facilitated the reliable encoding of inputs, we analyzed various spike-train distances and Fano factor. Interestingly, responses to lower rather than higher frequencies had more globally reliable spike-counts and timing structure. These findings have various practical implications for understanding the effects of optogenetic stimulation and choice of opsin. Furthermore, they show both PV and excitatory neurons respond with more local precision, i.e. phase-locking, to high-frequency inputs, but have more globally reliable responses to low-frequency inputs, suggesting differential coding regimes for these frequencies.
Quantifying the relationship between spreading depolarization and perivascular cerebrospinal fluid flow
Authors: Mukherjee Saikat , Mirzaee Mahsa , Tithof Jeffrey 
Published: April 2023

AbstractRecent studies have linked spreading depolarization (SD, an electro-chemical wave in the brain following stroke, migraine, traumatic brain injury, and more) with increase in cerebrospinal fluid (CSF) flow through the perivascular spaces (PVSs, annular channels lining the brain vasculature). We develop a novel computational model that couples SD and CSF flow. We first use high order numerical simulations to solve a system of physiologically realistic reaction-diffusion equations which govern the spatiotemporal dynamics of ions in the extracellular and intracellular spaces of the brain cortex during SD. We then couple the SD wave with a 1D CSF flow model that captures the change in cross-sectional area, pressure, and volume flow rate through the PVSs. The coupling is modelled using an empirical relationship between the excess potassium ion concentration in the extracellular space following SD and the vessel radius. We find that the CSF volumetric flow rate depends intricately on the length and width of the PVS, as well as the vessel radius and the angle of incidence of the SD wave. We derive analytical expressions for pressure and volumetric flow rates of CSF through the PVS for a given SD wave and quantify CSF flow variations when two SD waves collide. Our numerical approach is very general and could be extended in the future to obtain novel, quantitative insights into how CSF flow in the brain couples with slow waves, functional hyperemia, seizures, or externally applied neural stimulations.
A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments
Authors: Han Yingchun , Zhang Chuwen , Zhao Zhuoming , Peng Yongyi , Liao Jing , Jiang Qiuyun , Liu Qing , Shao Zongze , Dong Xiyang 
Published: April 2023

AbstractCold seeps harbor abundant and diverse microbes that represent a tremendous potential for biological applications and also have a significant influence on biogeochemical cycles. Though recent metagenomic studies have expanded our understanding of the microbial community and function of seep microorganisms, the knowledge of diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic data from 16 cold seep sites across the globe to construct comprehensive gene and genome catalogs. The non-redundant gene catalog was comprised of 147 million genes (clustered at 95% amino acid identity), and 35.72% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) are obtained, most of which (94.31%) belong to novel species. Of them, 81 ANME species are identified covering all subclades except ANME-2d, and 23 syntrophic SRB species spanning Seep-SRB1a Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAGs catalogs are a valuable resource that enables expanded knowledge of the structure and functions of cold seep microbiomes.
Palmitoylethanolamide shows limited efficacy in controlling cerebral cryptococcosisin vivo
Authors: Munzen Melissa E. , Reguera-Gomez Marta , Hamed Mohamed F. , Enriquez Vanessa , Charles-Nino Claudia L. , Dores Michael R. , Alviña Karina , Martinez Luis R. 
Published: April 2023

ABSTRACTCryptococcus neoformans(Cn) is an encapsulated neurotropic fungal pathogen and the causative agent of cryptococcal meningoencephalitis (CME) in humans. Recommended treatment for CME is Amphotericin B (AmpB) and 5-fluorocytosine (5-FC). Though effective, AmpB has displayed numerous adverse side effects due to its potency and nephrotoxicity, prompting investigation into alternative treatments. Palmitoylethanolamide (PEA) is an immunomodulatory compound capable of promoting neuroprotection and reducing inflammation. To investigate the efficacy of PEA as a therapeutic alternative for CME, we intracerebrally infected mice withCnand treated them with PEA or AmpB alone or in combination. Our results demonstrate that PEA alone does not significantly prolong survival nor reduce fungal burden, but when combined with AmpB, PEA exerts an additive effect and promotes both survivability and fungal clearance. However, we compared this combination to traditional AmpB and 5-FC treatment in a survivability study and observed lower efficacy. Overall, our study revealed that PEA alone is not effective as an antifungal agent in the treatment of CME. Importantly, we describe the therapeutic capability of PEA in the context ofCninfection and show that its immunomodulatory properties may confer limited protection when combined with an effective fungicidal agent.
Deletion of Neuroligins from Astrocytes Does Not Detectably Alter Synapse Numbers or Astrocyte Cytoarchitecture by Maturity
Authors: Golf Samantha R. , Trotter Justin H. , Wang Jinzhao , Nakahara George , Han Xiao , Wernig Marius , Südhof Thomas C. 
Published: April 2023

ABSTRACTAstrocytes perform multifarious roles in the formation, regulation, and function of synapses in the brain, but the mechanisms involved are incompletely understood. Interestingly, astrocytes abundantly express neuroligins, postsynaptic adhesion molecules that function as synaptic organizers by binding to presynaptic neurexins. Here we examined the function of neuroligins in astrocytes with a rigorous genetic approach that uses the conditional deletion of all major neuroligins (Nlgn1-3) in astrocytesin vivoand complemented this approach by a genetic deletion of neuroligins in glia cells that are co-cultured with human neurons. Our results show that early postnatal deletion of neuroligins from astrocytes in vivo has no detectable effect on cortical or hippocampal synapses and does not alter the cytoarchitecture of astrocytes when evaluated in young adult mice. Moreover, deletion of astrocytic neuroligins in co-cultures of human neurons produced no detectable consequences for the formation and function of synapses. Thus, astrocytic neuroligins are unlikely to fundamentally shape synapse formation or astrocyte morphogenesis but likely perform other important roles that remain to be discovered.
miR-125b-5p impacts extracellular vesicle biogenesis, trafficking, and EV subpopulation release in the porcine trophoblast by regulating ESCRT-dependent pathway
Authors: Guzewska Maria M. , Witek Krzysztof J. , Karnas Elżbieta , Rawski Michał , Zuba-Surma Ewa , Kaczmarek Monika M. 
Published: April 2023

1.ABSTRACTIntercellular communication is a critical process that ensures cooperation between distinct cell types at the embryo–maternal interface. Extracellular vesicles (EVs) are considered to be potent mediators of this communication by transferring biological information in their cargo (e.g. miRNAs) to the recipient cells. miRNAs are small non-coding RNAs that affect the function and fate of neighboring and distant cells by regulating gene expression. Focusing on the maternal side of the dialog, we recently revealed the impact of embryonic signals, including miRNAs, on EV-mediated cell-to-cell communication. In this study, we show the regulatory mechanism of the miR-125b-5p ESCRT-mediated EV biogenesis pathway and the further secretion of EVs by trophoblasts at the time when the crucial steps of implantation are taking place.To test the ability of miR-125b-5p to influence the expression of genes involved in the generation and release of EV subpopulations in porcine conceptuses, we used an ex vivo approach. Next, in silico and in vitro analyses were performed to confirm miRNA–mRNA interactions. Finally, EV trafficking and release were assessed using several imaging and particle analysis tools.Our results indicated that conceptus development and implantation are accompanied by changes in the abundance of EV biogenesis and trafficking machinery. ESCRT-dependent EV biogenesis and the further secretion of EVs were modulated by miR-125b-5p, specifically impacting the ESCRT-II complex (via VPS36) and EV trafficking in primary porcine trophoblast cells. The identified miRNA–ESCRT interplay led to the generation and secretion of specific subpopulations of EVs.miRNA present at the embryo–maternal interface governs EV-mediated communication between the mother and the developing conceptus, leading to the generation, trafficking, and release of characteristic subpopulations of EVs.
Myosin in autoinhibitedoffstate(s), stabilized by mavacamten, can be recruited via inotropic effectors
Authors: Ma Weikang , del Rio Carlos L. , Qi Lin , Prodanovic Momcilo , Mijailovich Srboljub , Zambataro Christopher , Gong Henry , Shimkunas Rafael , Gollapudi Sampath , Nag Suman , Irving Thomas C. 
Published: April 2023

AbstractMavacamten is a novel, FDA-approved, small molecule therapeutic designed to regulate cardiac function by selectively but reversibly inhibiting the enzymatic activity of myosin. It shifts myosin towards orderedoffstates close to the thick filament backbone. It remains unresolved whether mavacamten permanently sequesters these myosin heads in theoffstate(s) or whether these heads can be recruited in response to physiological stimuli when required to boost cardiac output. We show that cardiac myosins stabilized in theseoffstate(s) by mavacamten are recruitable by Ca2+, increased heart rate, stretch, and β-adrenergic (β-AR) stimulation, all known physiological inotropic effectors. At the molecular level, we show that, in presence of mavacamten, Ca2+increases myosin ATPase activity by shifting myosin heads from the reserve super-relaxed (SRX) state to the active disordered relaxed (DRX) state. At the myofilament level, both Ca2+and passive lengthening can shift orderedoffmyosin heads from positions close to the thick filament backbone to disorderedonstates closer to the thin filaments in the presence of mavacamten. In isolated rat cardiomyocytes, increased stimulation rates enhanced shortening fraction in mavacamten-treated cells. This observation was confirmedin vivoin telemetered rats, where left-ventricular dP/dtmax,an index of inotropy, increased with heart rate in mavacamten treated animals. Finally, we show that β-AR stimulationin vivoincreases left-ventricular function and stroke volume in the setting of mavacamten. Our data demonstrate that the mavacamten-promotedoffstates of myosin in the thick filament are activable, at least partially, thus leading to preservation of cardiac reserve mechanisms.Significance statementMavacamten is the first myosin-targeted small molecule inhibitor approved by the FDA to treat obstructive hypertrophic cardiomyopathy by attenuating myocardial hyperdynamic contraction. The recruitment of cardiac contractility is, however, vital to ensure sufficient cardiac output during increased physiological demand. Here we show that major inotropic effectors are at least partially preserved in the setting of mavacamten, resulting in maintenance of cardiac reserve mechanisms. These results not only suggest an alternative mechanistic explanation, beyond mere LV outflow tract obstruction removal, for the clinically observed increase in peak oxygen uptake with exercise in HCM patients receiving mavacamten, but also lay the groundwork for a potential methodology to investigate the sarcomeric basis of chronotropic incompetence in disease states to motivate new therapeutic interventions.
Two Ascending Thermosensory Pathways from the Lateral Parabrachial Nucleus That Mediate Behavioral and Autonomous Thermoregulation
Authors: Yahiro Takaki , Kataoka Naoya , Nakamura Kazuhiro 
Published: April 2023

AbstractThermoregulatory behavior in homeothermic animals is an innate behavior to defend body core temperature from environmental thermal challenges in coordination with autonomous thermoregulatory responses. In contrast to the progress in understanding the central mechanisms of autonomous thermoregulation, those of behavioral thermoregulation remain poorly understood. We have previously shown that the lateral parabrachial nucleus (LPB) mediates cutaneous thermosensory afferent signaling for thermoregulation. To understand the thermosensory neural network for behavioral thermoregulation, in the present study, we investigated the roles of ascending thermosensory pathways from the LPB in avoidance behavior from innocuous heat and cold in rats. Neuronal tracing revealed two segregated groups of LPB neurons projecting to the median preoptic nucleus (MnPO), a thermoregulatory center (LPB→MnPO neurons), and those projecting to the central amygdaloid nucleus (CeA), a limbic emotion center (LPB→CeA neurons). While LPB→MnPO neurons include separate subgroups activated by heat or cold exposure of rats, LPB→CeA neurons were only activated by cold exposure. By selectively inhibiting LPB→MnPO or LPB→CeA neurons using tetanus toxin light chain or chemogenetic or optogenetic techniques, we found that LPB→MnPO transmission mediates heat avoidance, whereas LPB→CeA transmission contributes to cold avoidance.In vivoelectrophysiological experiments showed that skin cooling-evoked thermogenesis in brown adipose tissue requires not only LPB→MnPO neurons but also LPB→CeA neurons, providing a novel insight into the central mechanism of autonomous thermoregulation. Our findings reveal an important framework of central thermosensory afferent pathways to coordinate behavioral and autonomous thermoregulation and to generate the emotions of thermal comfort and discomfort that drive thermoregulatory behavior.
Interviewer Biases in Medical Survey Data: The Example of Blood Pressure Measurements
Authors: Geldsetzer Pascal , Chang Andrew Young , Meijer Erik , Sudharsanan Nikkil , Charu Vivek , Kramlinger Peter , Haarburger Richard 
Published: April 2023

AbstractHealth agencies rely upon survey-based physical measures to estimate the prevalence of key global health indicators such as hypertension. Such measures are usually collected by non-healthcare worker personnel and are potentially subject to measurement error due to variations in interviewer technique and setting, termed “interviewer effects”. In the context of physical measurements, particularly in low- and middle-income countries, interviewer-induced biases have not yet been examined. Using blood pressure as a case study, we aimed to determine the relative contribution of interviewer effects on the total variance of blood pressure measurements in three large nationally-representative health surveys from the Global South.We utilized 169,681 observations between 2008 and 2019 from three health surveys (Indonesia Family Life Survey, National Income Dynamics Study of South Africa, and Longitudinal Aging Study in India). In a linear mixed model, we modeled systolic blood pressure as a continuous dependent variable and interviewer effects as random effects alongside individual factors as covariates. To quantify the interviewer effect-induced uncertainty in hypertension prevalence, we utilized a bootstrap approach comparing sub-samples of observed blood pressure measurements to their adjusted counterparts. Our analysis revealed that the proportion of variation contributed by interviewers to blood pressure measurements was statistically significant but small: approximately 0.24-2.2% depending on the cohort. Thus, hypertension prevalence estimates were not substantially impacted at national scales. However, individual extreme interviewers could account for measurement divergences as high as 12%. Thus, highly biased interviewers could have important impacts on hypertension estimates at the sub-district level.Significance StatementPhysical measurements such as blood pressure are important indicators of countries’ health system performance. These measures are usually obtained in household surveys by study-specific interviewers, who are not clinical healthcare workers. Thus, there is a concern that they may contribute substantial measurement error. We used three large, nationally-representative health surveys from India, Indonesia, and South Africa to model the magnitude of the interviewer effect on blood pressure measurements, then projected their impact on estimations of country-level hypertension prevalence. At smaller geographic units, “extreme” interviewers could substantially bias hypertension estimates. Overall, however, the magnitude of the interviewer effects was small and, thus, unlikely to substantially bias hypertension prevalence estimates at the national level.
The TriScan: fast and sensitive 3D confocal fluorescence imaging using a simple optical design
Authors: Van den Eynde Robin , Verheyen Jon , Miclea Paul , Lazar Josef , Vandenberg Wim , Dedecker Peter 
Published: April 2023

AbstractWe present the TriScan, a compact and inexpensive fluorescence microscope that can combine the speed of widefield microscopy with the 3D-sectioning capabilities of confocal microscopy. The optical layout is based on a module that combines line-scan confocal imaging with a sensitive camera detector, realized using a simple optical layout that permits the use of arbitrarily fast scanning mirrors. The resulting design is theoretically capable of full field-of-view acquisition rates in the kilohertz regime combined with a diffraction-limited resolution and single-molecule sensitivity. In doing so, the system provides the ease-of- use and speed of widefield imaging combined with the optical sectioning of one-photon confocal imaging. The simple and inexpensive design is suitable for a broad variety of settings ranging from research to diagnostics and screening.
Computationally Engineered CRISPR-SpyCas9 High-Fidelity Variants with Improved Specificity and Reduced Non-specific DNA Damage
Authors: Rabinowitz Roy , Shor Oded , Zerbib Johanna , Herman Shay , Zelikson Natalie , Madiwale Shreyas , Yom-Tov Nataly , Ben-David Uri , Benninger Felix , Offen Daniel 
Published: April 2023

ABSTRACTThe CRISPR-Cas system holds great promise in the treatment of diseases caused by genetic variations. As wildtype SpyCas9 is known to generate many off-target effects, its use in the clinic remains controversial due to safety concerns. Several high-fidelity Cas9 variants with greater specificity have been developed using rational design and directed evolution. However, the enhancement of specificity by these methods is limited by factors like selection pressure and library diversity. Thus,in-silicoprotein engineering may provide a more efficient route for enhancing specificity, although computationally testing these proteins remains challenging. We recently demonstrated the advantage of normal mode analysis to simulate and predict the enzymatic function of SpyCas9 in the presence of mismatches. Here, we report several mathematical models describing the entropy and functionality relationships in the CRISPR-Cas9 system. We demonstrate the invariant characteristics of these models across different conformational structures. Based on these invariant models, we developed ComPE, a novel computational protein engineering method to modify the protein and measure the vibrational entropy of wildtype or variant SpyCas9 in complex with its sgRNA and target DNA. Using this platform, we discovered novel high-fidelity Cas9 variants with improved specificity. We functionally validated the improved specificity of four variants, and the intact on-target activity in one of them. Lastly, we demonstrate their reduced off-target editing and non-specific gRNA-independent DNA damage, highlighting their advantages for clinical applications. The described method could be applied to a wide range of proteins, from CRISPR-Cas orthologs to distinct proteins in any field where engineered proteins can improve biological processes.