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Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eukaryotic translation initiation factor-2α (eIF2α). In T1D, maladaptive unfolded protein response (UPR) in insulin-producing β cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PKR-like ER kinase (PERK), a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved β cell mass in T1D-susceptible mice. Single-cell RNA-Seq of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen-processing and presentation pathways in β cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein programmed death-ligand 1 (PD-L1) in β cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-βH1 human β cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity and that inhibition of PERK may offer a strategy for preventing or delaying the development of T1D.

Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.

Background Lysine carbamylation is a biomarker of rheumatoid arthritis and kidney diseases. However, its cellular function is understudied due to the lack of tools for systematic analysis of this post-translational modification (PTM). Methods We adapted a method to analyze carbamylated peptides by co-affinity purification with acetylated peptides based on the cross-reactivity of anti-acetyllysine antibodies. We also performed immobilized-metal affinity chromatography to enrich for phosphopeptides, which allowed us to obtain multi-PTM information from the same samples. Results By testing the pipeline with RAW 264.7 macrophages treated with bacterial lipopolysaccharide, 7,299, 8,923 and 47,637 acetylated, carbamylated, and phosphorylated peptides were identified, respectively. Our analysis showed that carbamylation occurs on proteins from a variety of functions on sites with similar as well as distinct motifs compared to acetylation. To investigate possible PTM crosstalk, we integrated the carbamylation data with acetylation and phosphorylation data, leading to the identification 1,183 proteins that were modified by all 3 PTMs. Among these proteins, 54 had all 3 PTMs regulated by lipopolysaccharide and were enriched in immune signaling pathways, and in particular, the ubiquitin-proteasome pathway. We found that carbamylation of linear diubiquitin blocks the activity of the anti-inflammatory deubiquitinase OTULIN. Conclusions Overall, our data show that anti-acetyllysine antibodies can be used for effective enrichment of carbamylated peptides. Moreover, carbamylation may play a role in PTM crosstalk with acetylation and phosphorylation, and that it is involved in regulating ubiquitination in vitro. Graphical Abstract 9DSWmM7hoJm8b3LaxSLrsC Video Abstract

Plasma is a unique phase of matter constituting positively or negatively charged atoms, excited atoms, neutral atoms, electrons, radicals, etcetera displaying a unique role in the nuclear fusion research besides studying electrical discharges in the domain of switching devices and biomedical applications lately. We discuss in this extensive proposition the fundamental plasma characteristics such as Debye length, plasma oscillations, plasma sheath and condition for sustainability and confinement of plasmas, besides examining the elementary waves in plasmas namely zero waves, electron plasma wave and ion plasma wave. The inherent electron plasma wave and ion plasma wave is associated with the driving of plasma currents which in turn depends upon the density perturbation and thermal velocities of the electrons and ions. The application of external electromagnetic radiation such as laser (pump wave) into the plasma modifies the dispersion relations of electron and ion plasma wave, respectively. The laser stimulates a plethora of waves in the plasma and undergoes remarkable physical phenomena such as self-focusing and filamentation of laser beams. The excitation of sideband waves of the laser beams into the plasma plays a key role in imparting ponderomotive force on the electron plasma waves leading to turbulence in the plasmas due to coupling of the waves. The oscillatory velocity of the electron due to pump wave, plasma density perturbation, ponderomotive force and current densities are associated with the excitation of instabilities in the plasma. Conclusively, such waves and instabilities in unmagnetized and magnetized plasma is comprehensively studied and concluded by proposing the investigation of unexplored twisted electromagnetic wave-plasma interaction.

Background Lipids are regulators of insulitis and β-cell death in type 1 diabetes development, but the underlying mechanisms are poorly understood. Here, we investigated how the islet lipid composition and downstream signaling regulate β-cell death. Methods We performed lipidomics using three models of insulitis: human islets and EndoC-βH1 β cells treated with the pro-inflammatory cytokines interlukine-1β and interferon-γ, and islets from pre-diabetic non-obese mice. We also performed mass spectrometry and fluorescence imaging to determine the localization of lipids and enzyme in islets. RNAi, apoptotic assay, and qPCR were performed to determine the role of a specific factor in lipid-mediated cytokine signaling. Results Across all three models, lipidomic analyses showed a consistent increase of lysophosphatidylcholine species and phosphatidylcholines with polyunsaturated fatty acids and a reduction of triacylglycerol species. Imaging assays showed that phosphatidylcholines with polyunsaturated fatty acids and their hydrolyzing enzyme phospholipase PLA2G6 are enriched in islets. In downstream signaling, omega-3 fatty acids reduce cytokine-induced β-cell death by improving the expression of ADP-ribosylhydrolase ARH3. The mechanism involves omega-3 fatty acid-mediated reduction of the histone methylation polycomb complex PRC2 component Suz12, upregulating the expression of Arh3 , which in turn decreases cell apoptosis. Conclusions Our data provide insights into the change of lipidomics landscape in β cells during insulitis and identify a protective mechanism by omega-3 fatty acids. -ATVUCqmTNz-ui1hDGfVzb Video Abstract

Most living organisms on Earth are photosensitive, including humans, and they get influenced by the solar day and night cycles created by the axial rotation of the Earth. The diurnal exposure of ultraviolet radiation (UVR) from the Sun is responsible for various skin-related diseases, including melanoma and non-melanoma skin cancers in humans. Evolutionarily, our skin has developed various protective biological mechanisms against the harmful effects of UVR, including nucleotide excision repair (NER) and melanin. In the past, the circadian clock has been shown to regulate NER and cell cycle processes, where their ability to protect from UVR changes according to the time of the day. However, the growing trend of erratic work schedule and feeding behavior has been shown to profoundly affect our circadian clock, making our body vulnerable to a host of environmental stressors, including UVR. Similar to NER, melanin, which is synthesized in melanocytes, is regarded as one of the most effective skin protectants against UVR damage, as it absorbs excess solar UVR and protects against genomic insults. Over the years, multiple signaling pathways have been shown to influence melanin biosynthesis by directly controlling the expression on a master regulator of melanogenesis, the microphthalmia-associated transcription factor (MITF). MITF is a basic helix-loop-helix melanoma proto-oncogene known to modulate critical melanocyte mechanisms by transcriptionally controlling MITF’s target genes. As the role of the transcriptional influence of the skin circadian clock on DNA repair in protecting the cells from environmental genotoxic stress is well established, what remains unknown is its connection with melanin pigmentation through MITF and a possible feedback loop that has the potential to affect the circadian clock back. Therefore, my thesis tries to understand both the clock's properties in melanocytes and their role in protecting against the solar UVR through MITF and how clock disruption mediated by MITF contributes to melanoma initiation/progression.

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eukaryotic translation initiation factor-2[alpha] (eIF2[alpha]). In T1D, maladaptive unfolded protein response (UPR) in insulin-producing [beta] cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2a kinase PKR-like ER kinase (PERK), a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved [beta] cell mass in T1D-susceptible mice. Single-cell RNA-Seq of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen-processing and presentation pathways in p cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein programmed death-ligand 1 (PD-L1) in [beta] cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-[beta]H1 human [beta] cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances [beta] cell immunogenicity and that inhibition of PERK may offer a strategy for preventing or delaying the development of T1D.

With the recent update of the SI system, all but one of the units are now based on defining the values of some fundamental constants. This development began in 1983 when the speed of light was assigned an exact fixed value. The advantage of this method is that it separates the definition from the realization, allowing new realizations to be introduced as technology advances without further redefinition. In addition, it allows unit realizations that are adapted to the scale of their intended use. Because of these advantages, we expect that one day also the last remaining object in the current SI system, the caesium atom, will also disappear. The purpose of this proposal is to outline possible paths for realizations of a future SI second based on the definition of the value of the Rydberg constant. Hydrogen and hydrogen–like systems would be the obvious candidates. The emphasis here is on the development of optical clock systems that circumvent difficulties associated with the short wavelength lasers otherwise required for cooling and driving the clock transition. The proposed clock systems based on atomic hydrogen and hydrogen–like He + , should be no more complex than current optical lattice clocks.

Background Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation and progression. Multiple clinical studies have used proteomics to identify biomarker candidates. However, most of the studies were limited to the initial candidate identification, which needs to be further validated and have assays developed for clinical use. Here we curate these studies to help prioritize biomarker candidates for validation studies and to obtain a broader view of processes regulated during disease development. Methods This systematic review was registered with Open Science Framework ( https://doi.org/10.17605/OSF.IO/N8TSA ). Using PRISMA guidelines, we conducted a systematic search of proteomics studies of T1D in the PubMed to identify putative protein biomarkers of the disease. Studies that performed mass spectrometry-based untargeted/targeted proteomic analysis of human serum/plasma of control, pre-seroconversion, post-seroconversion, and/or T1D-diagnosed subjects were included. For unbiased screening, 3 reviewers screened all the articles independently using the pre-determined criteria. Results A total of 13 studies met our inclusion criteria, resulting in the identification of 266 unique proteins, with 31 (11.6%) being identified across 3 or more studies. The circulating protein biomarkers were found to be enriched in complement, lipid metabolism, and immune response pathways, all of which are found to be dysregulated in different phases of T1D development. We found 2 subsets: 17 proteins (C3, C1R, C8G, C4B, IBP2, IBP3, ITIH1, ITIH2, BTD, APOE, TETN, C1S, C6A3, SAA4, ALS, SEPP1 and PI16) and 3 proteins (C3, CLUS and C4A) have consistent regulation in at least 2 independent studies at post-seroconversion and post-diagnosis compared to controls, respectively, making them strong candidates for clinical assay development. Conclusions Biomarkers analyzed in this systematic review highlight alterations in specific biological processes in T1D, including complement, lipid metabolism, and immune response pathways, and may have potential for further use in the clinic as prognostic or diagnostic assays.

The circadian rhythm is established by a coordinated network of peripheral clocks interlocked and regulated by a central pacemaker. This network is maintained by the rhythmic expression of core clock genes, which in turn generate oscillatory expression patterns of different sets of target proteins in a tissue-specific manner. Precise regulation of biological processes driven by the body's circadian network in response to periodic changes in the environment determines healthy life. The delicate balance in the cycling of enzymes, metabolites, cofactors, and immune regulators is essential to achieve cellular homeostasis. Disruption of this circadian homeostasis has been linked with the development and progression of various diseases including cancer. Over the years, circadian regulation of drug metabolism and processing has been employed in the treatment of diabetes, hypertension, peptic ulcers, and allergic rhinitis. Although time dictated drug administration was demonstrated many decades ago, its application in cancer treatment is limited due to insufficient mechanistic data supporting experimental results and inconsistency between clinical trials. However, timed administration of anti-cancer drugs is rapidly gaining attention as studies with animal and human models unveil molecular intricacies involved in the circadian control of biological pathways. In this regard, striking a balance between maximizing tumor responsiveness and minimizing side effects is crucial to achieve positive patient outcomes. This review focuses on regulation of the circadian clock in carcinogenesis outcomes through DNA damage and repair mechanisms and its application in therapy with specific emphasis on skin and breast cancers.