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Genome Biology and Evolution Jun 2024Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (non-obligate...
Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (non-obligate cryophilic) snow algae. Both can accumulate significant biomasses on glacier and snow habitats and play major roles in global climate dynamics. Despite their significance, genomic studies on these organisms remain scarce, hindering our understanding of their evolutionary history and adaptive mechanisms in the face of climate change. Here, we present the draft genome assembly and annotation of the psychrophilic snow algal strain CCCryo 101-99 (cf. Sphaerocystis sp.). The draft haploid genome assembly is 122.5 Mb in length and is represented by 664 contigs with an N50 of 0.86 Mb, a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 92.9% (n = 1519), a maximum contig length of 5.3 Mb, and a GC content of 53.1%. In total, 28.98% of the genome (35.5 Mb) contains repetitive elements. We identified 417 non-coding RNAs (ncRNAs) and annotated the chloroplast genome. The predicted proteome comprises 14,805 genes with a BUSCO completeness of 97.8%. Our preliminary analyses reveal a genome with a higher repeat content compared to mesophilic chlorophyte relatives, alongside enrichment in gene families associated with photosynthesis and flagella functions. Our current data will facilitate future comparative studies, improving our understanding of the likely response of polar algae to a warming climate as well as their evolutionary trajectories in permanently cold environments.
PubMed: 38941446
DOI: 10.1093/gbe/evae140 -
Journal of Integrative Neuroscience Jun 2024The majority of neuromyelitis optica spectrum disorders (NMOSD) patients are seropositive for aquaporin-4 (AQP4)-specific antibodies [also named neuromyelitis optica...
OBJECTIVES
The majority of neuromyelitis optica spectrum disorders (NMOSD) patients are seropositive for aquaporin-4 (AQP4)-specific antibodies [also named neuromyelitis optica immunoglobulin G antibodies (NMO-IgG)]. Although NMO-IgG can induce pathological changes in the central nervous system (CNS), the immunological changes in the CNS and peripheral tissue remain largely unknown. We investigated whether NMO-IgG binds to tissue expressing AQP4 and induces immunological changes in the peripheral tissue and CNS.
METHODS
C57BL/6 female mice were assigned into an NMOSD or control group. Pathological and immunological changes in peripheral tissue and CNS were measured by immunostaining and flow cytometry, respectively. Motor impairment was measured by open-field test.
RESULTS
We found that NMO-IgG did bind to astrocyte- and AQP4-expressing peripheral tissue, but induced glial fibrillary acidic protein and AQP4 loss only in the CNS. NMO-IgG induced the activation of microglia and modulated microglia polarization toward the classical (M1) phenotype, but did not affect innate or adaptive immune cells in the peripheral immune system, such as macrophages, neutrophils, Th17/Th1, or IL-10-producing B cells. In addition, NMOSD mice showed significantly less total distance traveled and higher immobility time in the open field.
CONCLUSIONS
We found that injection of human NMO-IgG led to astrocytopathic lesions with microglial activation in the CNS. However, there were no significant pathological or immunological changes in the peripheral tissues.
Topics: Animals; Neuromyelitis Optica; Mice, Inbred C57BL; Immunoglobulin G; Aquaporin 4; Female; Humans; Mice; Disease Models, Animal; Microglia; Autoantibodies; Astrocytes; Glial Fibrillary Acidic Protein; Central Nervous System
PubMed: 38940087
DOI: 10.31083/j.jin2306119 -
ACS Sustainable Chemistry & Engineering Jun 2024Understanding the properties of polymers, such as their crystallinity, is crucial for their material performance and predicting their behavior during and after use,...
Understanding the properties of polymers, such as their crystallinity, is crucial for their material performance and predicting their behavior during and after use, especially in the case of environmentally friendly (bio)degradable polymers, enabling optimized design. In this work, for the first time, a pressure-induced condis crystal-like mesophase of poly(butylene succinate--butylene adipate) (PBSA) is presented. The phase behavior of pressed films obtained from commercial PBSA with 25% butylene adipate units is investigated at various processing temperatures from room temperature to 100 °C, pressed at a pressure of the press jaws and at 2-5 t for 1-5 min. The characterization and quantification evaluation of the condis crystal-like mesophase of pressed PBSA formed at temperatures above the glass transition is investigated by X-ray diffraction, polarized optical microscopy (POM), and differential scanning calorimetry (DSC) methods. Our results demonstrate that pressed PBSA films at 60 °C show a condis crystal-like mesophase, characterized by the presence of reflections at wide angles, birefringence by POM, as well as a higher melting point (endotherm) by DSC. The resulting oriented mesomorphic green polymer can, in a sustainable manner, expand further technological applications of (bio)degradable polymers, especially in the medical field, and open up opportunities for further research that could provide such polymers with tailored persistence and degradation, thus changing the shelf life.
PubMed: 38939870
DOI: 10.1021/acssuschemeng.4c03285 -
Exploration (Beijing, China) Jun 2024Myocardial infarction (MI) is a leading cause of death worldwide. Few drugs hold the ability to depress cardiac electrical and structural remodeling simultaneously after...
Myocardial infarction (MI) is a leading cause of death worldwide. Few drugs hold the ability to depress cardiac electrical and structural remodeling simultaneously after MI, which is crucial for the treatment of MI. The aim of this study is to investigate an effective therapy to improve both electrical and structural remodeling of the heart caused by MI. Here, an "ion cocktail therapy" is proposed to simultaneously reverse cardiac structural and electrical remodeling post-MI in rats and minipigs by applying a unique combination of silicate, strontium (Sr) and copper (Cu) ions due to their specific regulatory effects on the behavior of the key cells involved in MI including angiogenesis of endothelial cells, M2 polarization of macrophages and apoptosis of cardiomyocyte. The results demonstrate that ion cocktail treatment attenuates structural remodeling post-MI by ameliorating infarct size, promoting angiogenesis in both peri-infarct and infarct areas. Meantime, to some extent, ion cocktail treatment reverses the deteriorative electrical remodeling by reducing the incidence rate of early/delayed afterdepolarizations and minimizing the heterogeneity of cardiac electrophysiology. This ion cocktail therapy reveals a new strategy to effectively treat MI with great clinical translation potential due to the high effectiveness and safety of the ion cocktail combination.
PubMed: 38939858
DOI: 10.1002/EXP.20230067 -
Journal of Extracellular Biology Aug 2023EVs released by adipose derived stem cells (ADSCs) have shown promise as a therapeutic for tissue repair because of their purported immune-regulatory properties....
EVs released by adipose derived stem cells (ADSCs) have shown promise as a therapeutic for tissue repair because of their purported immune-regulatory properties. Extracellular vesicles (EVs) from ADSCs could be beneficial in improving graft retention rates for autologous fat grafting (AFG) post-mastectomy as, currently, grafted tissue rates are variable. Enriching grafted tissue with ADSC-EVs may improve retention rates by modulating macrophages resident within both the breast and lipoaspirate. We aimed to identify key macrophage phenotypes that are modulated by ADSC-EVs in vitro. ADSCs were isolated from lipoaspirates of women undergoing AFG and characterised by flow cytometry and differentiation potential. ADSC-EVs were isolated from culture media and characterised by tuneable resistive pulse sensing, transmission electron microscopy and Western blot. Primary monocyte-derived macrophages were polarized to an M1-like (GM-CSF, IFNγ), M2-like phenotype (M-CSF, IL-4) or maintained (M0-like; M-CSF) and ADSC-EVs were co-cultured with macrophages for 48 h. Flow cytometry and high-dimensional analysis clustered macrophages post co-culture. A manual gating strategy was generated to recapitulate these clusters and was applied to a repeat experimental run. Both runs were analysed to examine the prevalence of each cluster, representing a unique macrophage phenotype, with and without ADSC-EVs. Following the addition of ADSC-EVs, M0-like macrophages demonstrated a reciprocal shift of cell distribution from a cluster with a 'high inflammatory profile' (CD36CD206CD86; 16.5 ± 7.0%; < 0.0001) to a cluster with a 'lower inflammatory profile' (CD36CD86+; 35 ± 21.5%; < 0.05). M1-like macrophages shifted from a cluster with a 'high inflammatory profile' (CD206CD11bCD36CD163; 26.1 ± 9.4%; = 0.0024) to a 'lower inflammatory profile' (CD206CD11bCD36; 72.8 ± 8.7%; = 0.0007). There was no shift in M2-like clusters following ADSC-EV treatment. ADSC-EVs are complex regulators of macrophage phenotype that can shift macrophages away from a heightened pro-inflammatory state.
PubMed: 38939512
DOI: 10.1002/jex2.104 -
Journal of Extracellular Biology Jan 2024Extracellular vesicles (EVs) secreted by human-induced pluripotent stem cells (hiPSCs) have great potential as cell-free therapies in various diseases, including...
Extracellular vesicles (EVs) secreted by human-induced pluripotent stem cells (hiPSCs) have great potential as cell-free therapies in various diseases, including prevention of blood-brain barrier senescence and stroke. However, there are still challenges in pre-clinical and clinical use of hiPSC-EVs due to the need for large-scale production of a large quantity. Vertical-Wheel bioreactors (VWBRs) have design features that allow the biomanufacturing of hiPSC-EVs using a scalable aggregate or microcarrier-based culture system under low shear stress. EV secretion by undifferentiated hiPSCs expanded as 3-D aggregates and on Synthemax II microcarriers in VWBRs were investigated. Additionally, two types of EV collection media, mTeSR and HBM, were compared. The hiPSCs were characterized by metabolite and transcriptome analysis as well as EV biogenesis markers. Protein and microRNA cargo were analysed by proteomics and microRNA-seq, respectively. The functional assays of microglia stimulation and proliferation were conducted. HiPSCs expanded as 3-D aggregates and on microcarriers had comparable cell number, while microcarrier culture had higher glucose consumption, higher glycolysis and lower autophagy gene expression based on mRNA-seq. The microcarrier cultures had at least 17-23 fold higher EV secretion, and EV collection in mTeSR had 2.7-3.7 fold higher yield than HBM medium. Microcarrier culture with mTeSR EV collection had a smaller EV size than other groups, and the cargo was enriched with proteins (proteomics) and miRNAs (microRNA-seq) reducing apoptosis and promoting cell proliferation (e.g. Wnt-related pathways). hiPSC-EVs demonstrated the ability of stimulating proliferation and M2 polarization of microglia . HiPSC expansion on microcarriers produces much higher yields of EVs than hiPSC aggregates in VWBRs. EV collection in mTeSR increases yield compared to HBM. The biomanufactured EVs from microcarrier culture in mTeSR have exosomal characteristics and are functional in microglia stimulation, which paves the ways for future in vivo anti-aging study.
PubMed: 38938678
DOI: 10.1002/jex2.133 -
Journal of Extracellular Biology Jan 2024Extracellular vesicles (EVs) are membranous structures released by cells into the extracellular space and are thought to be involved in cell-to-cell communication. While...
Extracellular vesicles (EVs) are membranous structures released by cells into the extracellular space and are thought to be involved in cell-to-cell communication. While EVs and their cargo are promising biomarker candidates, sorting mechanisms of proteins to EVs remain unclear. In this study, we ask if it is possible to determine EV association based on the protein sequence. Additionally, we ask what the most important determinants are for EV association. We answer these questions with explainable AI models, using human proteome data from EV databases to train and validate the model. It is essential to correct the datasets for contaminants introduced by coarse EV isolation workflows and for experimental bias caused by mass spectrometry. In this study, we show that it is indeed possible to predict EV association from the protein sequence: a simple sequence-based model for predicting EV proteins achieved an area under the curve of 0.77 ± 0.01, which increased further to 0.84 ± 0.00 when incorporating curated post-translational modification (PTM) annotations. Feature analysis shows that EV-associated proteins are stable, polar, and structured with low isoelectric point compared to non-EV proteins. PTM annotations emerged as the most important features for correct classification; specifically, palmitoylation is one of the most prevalent EV sorting mechanisms for unique proteins. Palmitoylation and nitrosylation sites are especially prevalent in EV proteins that are determined by very strict isolation protocols, indicating they could potentially serve as quality control criteria for future studies. This computational study offers an effective sequence-based predictor of EV associated proteins with extensive characterisation of the human EV proteome that can explain for individual proteins which factors contribute to their EV association.
PubMed: 38938677
DOI: 10.1002/jex2.120 -
Biomaterials Research 2024The management of infected wounds poses a significant challenge due to the growing issue of antibiotic resistance, underscoring the urgent necessity to innovate and...
The management of infected wounds poses a significant challenge due to the growing issue of antibiotic resistance, underscoring the urgent necessity to innovate and implement alternative therapeutic strategies. These strategies should be capable of eliminating bacterial infections in infected wounds while circumventing the induction of multi-drug resistance. In the current study, we developed an easily prepared and injectable fibrin gel (FG) loaded with nanoparticles (NPs) that exhibit antibacterial and immunomodulatory properties to facilitate the healing of infected wounds. Initially, a novel type of NP was generated through the electrostatic interaction between the photothermal agent, mPEG-modified polydopamine (MPDA), and the nitric oxide (NO) donor, S-nitrosocysteamine (SNO). This interaction resulted in the formation of NPs referred to as SNO-loaded MPDA (SMPDA). Subsequently, the SMPDA was encapsulated into the FG using a double-barreled syringe, thereby producing the SMPDA-loaded FG (SMPDA/G). Experimental results revealed that SMPDA/G could effectively eliminate bacterial infections and alter the immune microenvironment. This efficacy is attributed to the synergistic combination of NO therapy and photothermal therapy, along with the role of SMPDA in facilitating M2 macrophage polarization within the gel. Accordingly, these findings suggest that the SMPDA/G holds substantial promise for clinical application in infected wound healing.
PubMed: 38938648
DOI: 10.34133/bmr.0019 -
International Journal of Genomics 2024In the context of hepatocellular carcinoma (HCC), tumor-associated macrophages (TAMs) are pivotal for the immunosuppressive nature of the tumor microenvironment (TME)....
BACKGROUND
In the context of hepatocellular carcinoma (HCC), tumor-associated macrophages (TAMs) are pivotal for the immunosuppressive nature of the tumor microenvironment (TME). This investigation delves into the functional transformations of TAMs within the TME by leveraging single-cell transcriptomics to pinpoint critical genes influencing TAM subset polarization.
METHODS
We procured single-cell and bulk transcriptomic data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), implementing quality assurance, dimensional reduction, clustering, and annotation on the single-cell sequencing data. To examine cellular interactions, CellChat was utilized, while single-cell regulatory network inference and clustering (SCENIC) was applied to deduce transcription factors (TFs) and their associated targets. Through gene enrichment, survival, and immune infiltration correlation analyses, we sought to pinpoint and validate influential genes. A TAM model under HCC conditions was then established to confirm the expression levels of these key genes.
RESULTS
Our analysis encompassed 74,742 cells and 23,110 genes. Through postdimensional reduction and clustering, we identified seven distinct cell types and nine TAM subtypes. Analysis via CellChat highlighted a predominance of M2-phenotype-inclined TAM subsets within the tumor's core. SCENIC pinpointed the transcription factor PRDM1 and its target genes as pivotal in this region. Further analysis indicated these genes' involvement in macrophage polarization. Employing trajectory analysis, survival analysis, and immune infiltration correlation, we scrutinized and validated genes likely directing M2 polarization. Experimental validation confirmed PRDM1's heightened expression in TAMs conditioned by HCC.
CONCLUSIONS
Our findings suggest the PRDM1 gene is a key regulator of M2 macrophage polarization, contributing to the immunosuppressive TME in HCC.
PubMed: 38938448
DOI: 10.1155/2024/7263358 -
Frontiers in Human Neuroscience 2024During the first year of life, infants start to learn the lexicon of their native language. Word learning includes the establishment of longer-term representations for...
During the first year of life, infants start to learn the lexicon of their native language. Word learning includes the establishment of longer-term representations for the phonological form and the meaning of the word in the brain, as well as the link between them. However, it is not known how the brain processes word forms immediately after they have been learned. We familiarized 12-month-old infants (N = 52) with two pseudowords and studied their neural signatures. Specifically, we determined whether a newly learned word form elicits neural signatures similar to those observed when a known word is recognized (i.e., when a well-established word representation is activated, eliciting enhanced mismatch responses) or whether the processing of a newly learned word form shows the suppression of the neural response along with the principles of predictive coding of a learned rule (i.e., the order of the syllables of the new word form). The pattern of results obtained in the current study suggests that recognized word forms elicit a mismatch response of negative polarity, similar to newly learned and previously known words with an established representation in long-term memory. In contrast, prediction errors caused by acoustic novelty or deviation from the expected order in a sequence of (pseudo)words elicit responses of positive polarity. This suggests that electric brain activity is not fully explained by the predictive coding framework.
PubMed: 38938291
DOI: 10.3389/fnhum.2024.1386207