Cellular Systems Research Articles

Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches

Substantial advances have been made in the development of promising HIV vaccines to eliminate HIV-1 infection. For the first time, one hundred of the most submitted HIV subtypes and CRFs were retrieved from the LANL database, and the consensus sequences of the eleven HIV proteins were obtained to design vaccines for human and mouse hosts. By using various servers and filters, highly qualified B-cell epitopes, as well as HTL and CD8 + epitopes that were common between mouse and human alleles and were also located in the conserved domains of HIV proteins, were considered in the vaccine constructs. With 90% coverage worldwide, the human vaccine model covers a diverse allelic population, making it widely available. Codon optimization and in silico cloning in prokaryotic and eukaryotic vectors guarantee high expression of the vaccine models in human and E. coli hosts. Molecular dynamics confirmed the stable interaction of the vaccine constructs with TLR3, TLR4, and TLR9, leading to a substantial immunogenic response to the designed vaccine. Vaccine models effectively target the humoral and cellular immune systems in humans and mice; however, experimental validation is needed to confirm these findings in silico.

Comparative proteomics analysis of the mouse mini-gut organoid: insights into markers of gluten challenge from celiac disease intestinal biopsies.

Organoid models enable three-dimensional representation of cellular systems, providing flexible and accessible research tools, and can highlight key biomolecules. Such models of the intestinal epithelium can provide significant knowledge for the study of celiac disease and provide an additional context for the nature of markers observed from patient biopsy data. Using LC-MS/MS, the proteomes of the crypt and enterocyte-like states of a mouse mini-gut organoid model were measured. The data were further compared with published biopsy data by comparing the changes induced by gluten challenge after a gluten-free diet. These analyses identified 4,850 protein groups and revealed how 400 putative biomarkers of dietary challenge were differentially expressed in the organoid model. In addition to the extensive changes within the differentiated cells, the data reiterated the disruption of the crypt-villus axis after gluten challenge. The mass spectrometry data are available via ProteomeXchange with the identifier PXD025690.

Multi-Level Behavioral Mechanisms and Kinematic Modeling Research of Cellular Space Robot

The cellular space robot (CSR) is a new type of self-reconfigurable robot. It can adapt the variety of on-orbit service tasks with large space spans through multi-level reconfiguration mechanisms. As the CSR has a large configuration space, kinematic solving becomes a key problem affecting on-orbit operation capability, and kinematic automatic solving research must be conducted. In order to solve this problem, firstly, the cellular space robot system capable of realizing multi-level self-reconfiguration is proposed for the demand of space on-orbit service, and the kinematic equations of modules are constructed by considering a single module function using screw theory. Secondly, the kinematics of the cellular space robot are encapsulated and divided into multiple levels, and the multilevel-assembly relationship-description method for robotic systems is proposed based on graph theory. On this basis, the pathway-solving algorithm is proposed to express the robot organization reachability information. Finally, the module–organ–robot multilevel kinematics solving algorithm is proposed in combination with screw theory. In order to verify the effectiveness of the algorithm in this paper, numerical simulation is used to compare with the proposed algorithm. The results show that compared with the traditional algorithm, the method in this paper only needs to update part of the assembly relations after organ migration, which simplifies the kinematic modeling operation and improves the efficiency of kinematic computation.

MosGraphGen: a novel tool to generate multi-omics signaling graphs to facilitate integrative and interpretable graph AI model development.

Multi-omics data, i.e., genomics, epigenomics, transcriptomics, proteomics, characterize cellular complex signaling systems from multi-level and multi-view and provide a holistic view of complex cellular signaling pathways. However, it remains challenging to integrate and interpret multi-omics data for mining key disease targets and signaling pathways. Graph AI models have been widely used to analyze graph-structure datasets, and are ideal for integrative multi-omics data analysis because they can naturally integrate and represent multi-omics data as a biologically meaningful multi-level signaling graph and interpret multi-omics data via graph node and edge ranking analysis. However, it is non-trivial for graph-AI model developers to pre-analyze multi-omics data and convert the data into biologically meaningful graphs, which can be directly fed into graph-AI models. To resolve this challenge, we developed mosGraphGen (multi-omics signaling graph generator), generating Multi-omics Signaling graphs (mos-graph) of individual samples by mapping multi-omics data onto a biologically meaningful multi-level background signaling network with data normalization by aggregating measurements and aligning to the reference genome. With mosGraphGen, AI model developers can directly apply and evaluate their models using these mos-graphs. In the results, mosGraphGen was used and illustrated using two widely used multi-omics datasets of TCGA and Alzheimer's disease (AD) samples. The code of mosGraphGen is open-source and publicly available via GitHub: https://github.com/FuhaiLiAiLab/mosGraphGen.

Bottom-up synthetic immunology.

Infectious diseases and cancer evade immune surveillance using similar mechanisms. Targeting immune mechanisms using common strategies thus represents a promising avenue to improve prevention and treatment. Synthetic immunology can provide such strategies by applying engineering principles from synthetic biology to immunology. Synthetic biologists engineer cells by top-down genetic manipulation or bottom-up assembly from nanoscale building blocks. Recent successes in treating advanced tumours and diseases using genetically engineered immune cells highlight the power of the top-down synthetic immunology approach. However, genetic immune engineering is mostly limited to ex vivo applications and is subject to complex counter-regulation inherent to immune functions. Bottom-up synthetic biology can harness the rich nanotechnology toolbox to engineer molecular and cellular systems from scratch and equip them with desired functions. These are beginning to be tailored to perform targeted immune functions and should hence allow intervention strategies by rational design. In this Perspective we conceptualize bottom-up synthetic immunology as a new frontier field that uses nanotechnology for crucial innovations in therapy and the prevention of infectious diseases and cancer.

Toward DNA-Based Recording of Biological Processes.

Exploiting the inherent compatibility of DNA-based data storage with living cells, various cellular recording approaches have been developed for recording and retrieving biologically relevant signals in otherwise inaccessible locations, such as inside the body. This review provides an overview of the current state of engineered cellular memory systems, highlighting their design principles, advantages, and limitations. We examine various technologies, including CRISPR-Cas systems, recombinases, retrons, and DNA methylation, that enable these recording systems. Additionally, we discuss potential strategies for improving recording accuracy, scalability, and durability to address current limitations in the field. This emerging modality of biological measurement will be key to gaining novel insights into diverse biological processes and fostering the development of various biotechnological applications, from environmental sensing to disease monitoring and beyond.

Survey on 5G Physical Layer Security Threats and Countermeasures.

With the expansion of wireless mobile networks into both the daily lives of individuals as well as into the widely developing market of connected devices, communication is an increasingly attractive target for attackers. As the complexity of mobile cellular systems grows and the respective countermeasures are implemented to secure data transmissions, the attacks have become increasingly sophisticated on the one hand, but at the same time the system complexity can open up expanded opportunities for security and privacy breaches. After an in-depth summary of possible entry points to attacks to mobile networks, this paper first briefly reviews the basic principles of the physical layer implementation of 4G/5G systems, then gives an overview of possible attacks from a physical layer perspective. It also provides an overview of the software frameworks and hardware tool-software defined radios currently in use for experimenting with 4G/5G mobile networks, and it discusses their basic capabilities. In the final part, the paper summarizes the currently most promising families of techniques to detect illegitimate base stations-the machine-learning-based, localization-based, and behavior-based methods.

Immunomodulatory and antioxidant effect of liposomal auraptene against cyclophosphamide-induced immunosuppression in BALB/c mice

IntroductionCyclophosphamide (CP), which is a commonly used chemotherapy drug, can lead to a range of side effects such as immunosuppression, bone marrow suppression, leukopenia, and oxidative stress. This study aims to explore the effects of Auraptene (AUR), which has immunomodulatory and antioxidant properties, on immune function in mice that are experiencing suppression induced by CP. Materials and methodsThe experiment involved 60 male BALB/c mice that underwent a 10-day treatment. On days 1, 3, and 9, CP was given at 80 mg/kg IP doses to induce immunosuppression. The mice were divided into five groups: Control group, CP group, CP + liposomal AUR 0.2 mg/kg (AUR 0.2), CP + liposomal AUR 0.25 mg/kg (AUR 0.25), and liposomal vehicle group. Various parameters were measured, including mouse weight, immune organ weight index (spleen and thymus), spleen and thymus histopathology, levels of inflammatory cytokines (IL2, IL10, IL4, IFN-γ), TH1/TH2 balance ratio, IgG and IgM immunoglobulin levels, white blood cell count, platelets, neutrophils, lymphocytes, and oxidative activity measured by MDA, SOD, and Total Antioxidant. ResultsIn the group treated with CP, the mice showed a significant decrease in weight compared to the control group. In contrast, the group treated with AUR maintained their weight and did not show a significant difference from the control group. AUR 0.25 reduced the damage to the spleen and thymus caused by CP. Additionally, AUR 0.25 demonstrated a significant decrease in IL4 and IL10 levels compared to the CP group (p = 0.04), approaching the levels of the control group. Furthermore, IL2 and IFN-γ levels in the AUR 0.25 group significantly increased (p = 0.04) compared to the CP group, reaching levels similar to the control group. AUR also increased serum IgM and IgG levels two to three times compared to the CP group, approaching the levels of the control group. MDA levels in the AUR 0.25 group decreased to normal and control levels. AUR 0.25 also showed increased SOD and Total Antioxidant levels. Additionally, white blood cells, platelets, neutrophils, and lymphocytes in the AUR group significantly increased compared to the CP group, reaching normal levels similar to the control group. The TH1/TH2 ratio in the AUR group exhibited a significant increase of two and a half times (p = 0.002) compared to the CP group. ConclusionThese results show that AUR protects against the side effects of CP by increasing the function of the humoral and cellular immune system through the balance of TH1/TH2 and increasing the level of immunoglobulins, as well as increasing the antioxidant activity and the protective role of cytotoxicity.

Temperature influences immune cell development and body length in purple sea urchin larvae

Anthropogenic climate change has increased the frequency and intensity of marine heatwaves that may broadly impact the health of marine invertebrates. Rising ocean temperatures lead to increases in disease prevalence in marine organisms; it is therefore critical to understand how marine heatwaves impact immune system development. The purple sea urchin (Strongylocentrotus purpuratus) is an ecologically important, broadcast-spawning, omnivore that primarily inhabits kelp forests in the northeastern Pacific Ocean. The S. purpuratus life cycle includes a relatively long-lived (∼2 months) planktotrophic larval stage. Larvae have a well-characterized cellular immune system that is mediated, in part, by a subset of mesenchymal cells known as pigment cells. To assess the role of environmental temperature on the development of larval immune cells, embryos were generated from adult sea urchins conditioned at 14 °C. Embryos were then cultured in either ambient (14 °C) or elevated (18 °C) seawater. Results indicate that larvae raised in an elevated temperature were slightly larger and had more pigment cells than those raised at ambient temperature. Further, the larval phenotypes varied significantly among genetic crosses, which highlights the importance of genotype in structuring how the immune system develops in the context of the environment. Overall, these results indicate that larvae are phenotypically plastic in modulating their immune cells and body length in response to adverse developmental conditions.

Polystyrene nanoplastics significantly facilitate largemouth bass ranavirus infection of host cells

Novel pollutants nanoplastics (NPs) are widely distributed in aquatic environments and may pose a health threat to aquatic organisms. Notably, the contribution of NPs to the occurrence of viral diseases in aquatic animals remains largely uncertain. In this study, the effects of polystyrene nanoplastics (PS-NPs) on Largemouth bass ranavirus (LMBV)-infected MsF cells were investigated. MsF cells took up PS-NPs in a time- and dose-dependent manner and significantly affect cell viability at an exposure concentration of 500 μg/mL. Western blot and qPCR assays indicated that exposure to PS-NPs accelerated LMBV replication in MsF cells. PS-NPs act synergistically with LMBV to disrupt the cellular antioxidant system, as evidenced by increased ROS production and decreased mRNA levels of antioxidant-associated genes. Furthermore, PS-NPs was found to exacerbate LMBV-induced inflammatory responses, as demonstrated by disturbed expression of inflammation-related factors. In addition, our results suggest that PS-NPs reduce IFN production by inhibiting the expression of molecules related to the cGAS-STING signaling pathway, thereby promoting viral replication. Collectively, our findings suggest the potential threat of NPs to infectious diseases caused by freshwater fish viruses and provide new insights for fish disease prevention and control.

Elimination of Human Papillomavirus 16-Positive Tumors by a Mucosal rAd5 Therapeutic Vaccination in a Pre-Clinical Murine Study.

Therapeutic vaccination can harness the body's cellular immune system to target and destroy cancerous cells. Several treatment options are available to eliminate pre-cancerous and cancerous lesions caused by human papillomaviruses (HPV), but may not result in a long-term cure. Therapeutic vaccination may offer an effective, durable, and minimally intrusive alternative. We developed mucosally delivered, recombinant, non-replicating human adenovirus type 5 (rAd5)-vectored vaccines that encode HPV16's oncogenic proteins E6 and E7 alongside a molecular dsRNA adjuvant. The induction of antigen-specific T cells and the therapeutic efficacy of rAd5 were evaluated in a mouse model of HPV tumorigenesis where E6E7-transformed cells, TC-1, were implanted subcutaneously in C57BL/6 mice. After tumor growth, mice were treated intranasally with rAd5 vaccines expressing the wildtype form of E6E7 (rAd5-16/E6E7Wt) in combination with an anti-PD-1 antibody or isotype control. Animals treated with rAd5-16/E6E7Wt with and without anti-PD-1 had significant reductions in tumor volume and increased survival compared to controls. Further, animals treated with rAd5-16/E6E7Wt had increased CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) and produced a cytotoxic tumor microenvironment. In a second study, the immunogenicity of a non-transformative form of E6E7 (rAd5-16/E6E7Mu) and a vaccine encoding predicted T cell epitopes of E6E7 (rAd5-16/E6E7epi) were evaluated. These vaccines elicited significant reductions in TC-1 tumor volume and increased survival of animals. Antigen-specific CD8+ T effector memory cells were observed in the animals treated with E6E7-encoding rAd5, but not in the rAd5-empty group. The work described here demonstrates that this mucosal vaccination can be used therapeutically to elicit specific cellular immunity and further identifies a clinical candidate with great potential for the treatment and prevention of human cervical cancer.

The Spiral Model of Evolution: Stable Life Forms of Organisms and Unstable Life Forms of Cancers.

If one must prioritize among the vast array of contributing factors to cancer evolution, environmental-stress-mediated chromosome instability (CIN) should easily surpass individual gene mutations. CIN leads to the emergence of genomically unstable life forms, enabling them to grow dominantly within the stable life form of the host. In contrast, stochastic gene mutations play a role in aiding the growth of the cancer population, with their importance depending on the initial emergence of the new system. Furthermore, many specific gene mutations among the many available can perform this function, decreasing the clinical value of any specific gene mutation. Since these unstable life forms can respond to treatment differently than stable ones, cancer often escapes from drug treatment by forming new systems, which leads to problems during the treatment for patients. To understand how diverse factors impact CIN-mediated macroevolution and genome integrity-ensured microevolution, the concept of two-phased cancer evolution is used to reconcile some major characteristics of cancer, such as bioenergetic, unicellular, and multicellular evolution. Specifically, the spiral of life function model is proposed, which integrates major historical evolutionary innovations and conservation with information management. Unlike normal organismal evolution in the microevolutionary phase, where a given species occupies a specific location within the spiral, cancer populations are highly heterogenous at multiple levels, including epigenetic levels. Individual cells occupy different levels and positions within the spiral, leading to supersystems of mixed cellular populations that exhibit both macro and microevolution. This analysis, utilizing karyotype to define the genetic networks of the cellular system and CIN to determine the instability of the system, as well as considering gene mutation and epigenetics as modifiers of the system for information amplification and usage, explores the high evolutionary potential of cancer. It provides a new, unified understanding of cancer as a supersystem, encouraging efforts to leverage the dynamics of CIN to develop improved treatment options. Moreover, it offers a historically contingent model for organismal evolution that reconciles the roles of both evolutionary innovation and conservation through macroevolution and microevolution, respectively.

Shikonin protects skin cells against oxidative stress and cellular dysfunction induced by fine particulate matter.

Shikonin, an herbal naphthoquinone, demonstrates a broad spectrum of pharmacological properties. Owing to increasingly adverse environmental conditions, human skin is vulnerable to harmful influences from dust particles. This study explored the antioxidant capabilities of shikonin and its ability to protect human keratinocytes from oxidative stress induced by fine particulate matter (PM2.5). We found that shikonin at a concentration of 3 µM was nontoxic to human keratinocytes and effectively scavenged reactive oxygen species (ROS) while increasing the production of reduced glutathione (GSH). Furthermore, shikonin enhanced GSH level by upregulating glutamate-cysteine ligase catalytic subunit and glutathione synthetase mediated by nuclear factor-erythroid 2-related factor. Shikonin reduced ROS levels induced by PM2.5, leading to recovering PM2.5-impaired cellular biomolecules and cell viability. Shikonin restored the GSH level in PM2.5-exposed keratinocytes via enhancing the expression of GSH-synthesizing enzymes. Notably, buthionine sulphoximine, an inhibitor of GSH synthesis, diminished effect of shikonin against PM2.5-induced cell damage, confirming the role of GSH in shikonin-induced cytoprotection. Collectively, these findings indicated that shikonin could provide substantial cytoprotection against the adverse effects of PM2.5 through direct ROS scavenging and modulation of cellular antioxidant system.

Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system.

Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.

Ferroptosis in Obstetrical and Gynecological Diseases: A Mini Review.

Ferroptosis is an iron-dependent form of non-apoptotic cell programmed death, characterized by the disturbance of iron metabolism, accumulation of lipid peroxides and disruption of cellular antioxidant system. Ferroptosis induces oxidative cell death through decrease of antioxidant capacity and accumulation of lipid reactive oxygen species (ROS) in cells. In recent years, studies have confirmed that ferroptosis is closely related to numerous organ injuries, degenerative pathologies and even the tumorigenesis and therapeutic resistance of tumors. While the effect of ferroptosis in obstetrical and gynecological diseases remains unclear and the relevant researches are still limited. In this review, we summarize the current understanding of the molecular mechanisms and regulatory networks of ferroptosis, together with the potential physiological functions and pathological roles of ferroptosis in clinical obstetrical and gynecological diseases. Importantly, our review also aims to provide references for further understanding of its pathogenesis and explore potential therapeutic strategies for targeting ferroptosis in clinical obstetrical and gynecological diseases.

Transit Archimedes optimization algorithm enabled deep learning for power and resource allocation NOMA technique for 5G cellular systems

Summary5G communication technology is projected to provide extreme data rates that surpass user exposure, low power consumption, and greater short latency. A diverged multi‐layer approach is implemented by cellular networks with macro‐cells and various schemes of small cells to aid users with diverged quality of service (QoS) that affects more research by employing intervention management in 5G networks. Along with the escalating requirement for cellular services and adequate resources to furnish it and capable of handling the network traffic has become a resource distribution concern. The major concern is to facilitate the network jam having QoS. To overcome this concern, a potent investigation is developed for power and resource allocation, which is named as transit Archimedes optimization algorithm (TAOA). First, the non‐orthogonal multiple access (NOMA) system module is created with the aid of power consumption and energy modules. Then, user clustering (UC) is performed to gather the NOMA users into single or multiple clusters utilizing deep embedded clustering (DEC) in accordance with user grouping parameters, like signal‐to‐interference and noise ratio (SINR), position, initial power, and channel gain. After that, sub‐channel assignment and power allocation are done by the back propagation neural network (BPNN). Lastly, the presented module TAOA is performed to update the network parameters of BPNN, where TAOA is developed by the fusion of transit search (TS) optimization and Archimedes optimization algorithm (AOA). The analytic metrics utilized for finding the performance of the proposed TAOA‐BPNN are achievable rate, energy efficiency, sum rate, and throughput. The experimental results demonstrate that the proposed method offers good performance with the achievable rate of 3.273 Mbits, energy efficiency of 0.00000000473 J, sum rate of 0.00000248 s, and throughput of 0.00000346 Mbps.

Testing the PEST hypothesis using relevant Rett mutations in MeCP2 E1 and E2 isoforms.

Mutations in methyl-CpG binding protein 2 (MeCP2), such as the T158M, P152R, R294X, and R306C mutations, are responsible for most Rett syndrome (RTT) cases. These mutations often result in altered protein expression that appears to correlate with changes in the nuclear size; however, the molecular details of these observations are poorly understood. Using a C2C12 cellular system expressing human MeCP2-E1 isoform as well as mouse models expressing these mutations, we show that T158M and P152R result in a decrease in MeCP2 protein, whereas R306C has a milder variation, and R294X resulted in an overall 2.5 to 3 fold increase. We also explored the potential involvement of the MeCP2 PEST domains in the proteasome-mediated regulation of MeCP2. Finally, we used the R294X mutant to gain further insight into the controversial competition between MeCP2 and histone H1 in the chromatin context. Interestingly, in R294X, MeCP2 E1 and E2 isoforms were differently affected, where the E1 isoform contributes to much of the overall protein increase observed, while E2 decreases by half. The modes of MeCP2 regulation, thus, appear to be differently regulated in the two isoforms.

Unraveling the rationale and conducting a comprehensive assessment of AdipoRon (adiponectin receptor agonist) as a candidate drug for diabetic nephropathy and cardiomyopathy prevention and intervention-a systematic review.

Type 2 diabetes mellitus (T2DM) is a widespread chronic disease characterized by persistent hyperglycemia, leading to severe complications such as diabetic cardiomyopathy and nephropathy, significantly affecting patient health and quality of life. The complex mechanisms underlying these complications include chronic inflammation, oxidative stress, and metabolic dysregulation. Diabetic cardiomyopathy, marked by structural and functional heart abnormalities, and diabetic nephropathy, characterized by progressive kidney damage, are major contributors to the increased morbidity and mortality associated with T2DM. AdipoRon, a synthetic adiponectin receptor agonist, has shown potential in preclinical studies for mimicking the beneficial effects of endogenous adiponectin, reducing inflammation and oxidative stress, and improving lipid metabolism and mitochondrial function. This systematic review evaluates the therapeutic potential of AdipoRon, focusing on its impact on diabetic cardiomyopathy and nephropathy. Through a comprehensive literature search and analysis, we highlight AdipoRon's role in ameliorating cardiovascular and renal complications in various animal models and cellular systems. The findings underscore the urgent need for translational clinical studies to validate AdipoRon's efficacy and safety in human populations, aiming to advance this promising therapeutic approach from experimental models to clinical application, potentially offering new hope for improved management of diabetic complications.

3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity.

The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF, ADCY3, TMEM18 and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 - an inflammation-responsive gene in nerve nociceptors - was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.

In Situ Generation and High Bioresistance of Trityl-based Semiquinone Methide Radicals Under Anaerobic Conditions in Cellular Systems.

Bioreduction of spin labels and polarizing agents (generally stable radicals) has been an obstacle limiting the in-cell applications of pulsed electron paramagnetic resonance (EPR) spectroscopy and dynamic nuclear polarization (DNP). In this work, we have demonstrated that two semiquinone methide radicals (OXQM⋅ and CTQM⋅) can be easily produced from the trityl-based quinone methides (OXQM and CTQM) via reduction by various reducing agents including biothiols and ascorbate under anaerobic conditions. Both radicals have relatively low pKa's and exhibit EPR single line signals at physiological pH. Moreover, the bioreduction of OXQM in three cell lysates enables quantitative generation of OXQM⋅ which was most likely mediated by flavoenzymes. Importantly, the resulting OXQM⋅ exhibited extremely high stability in the E.coli lysate under anaerobic conditions with 76- and 14.3-fold slower decay kinetics as compared to the trityl OX063 and a gem-diethyl pyrrolidine nitroxide, respectively. Intracellular delivery of OXQM into HeLa cells was also achieved by covalent conjugation with a cell-permeable peptide as evidenced by the stable intracellular EPR signal from the OXQM⋅ moiety. Owing to extremely high resistance of OXQM⋅ towards bioreduction, OXQM and its derivatives show great application potential in in-cell EPR and in-cell DNP studies for various cells which can endure short-term anoxic treatments.