A Bioinspired Design of Protective Al2O3/Polyurethane Hierarchical Composite Film Through Layer-By-Layer Deposition.

Structural materials such as ceramics, metals, and carbon fiber-reinforced plastics (CFRP) are frequently threatened by large compressive and impact forces. Energy absorption layers, i.e., polyurethane and silicone foams with excellent damping properties, are applied on the surfaces of different substrates to absorb energy. However, the amount of energy dissipation and penetration resistance are limited in commercial polyurethane foams. Herein, a distinctive nacre-like architecture design strategy is proposed by integrating hard porous ceramic frameworks and flexible polyurethane buffers to improve energy absorption and impact resistance. Experimental investigations reveal the bioinspired designs exhibit optimized hardness, strength, and modulus compared to that of polyurethane. Due to the multiscale energy dissipation mechanisms, the resulting normalized absorbed energy (≈8.557 MJ m-3) is ≈20 times higher than polyurethane foams under 50% quasi-static compression. The bioinspired composites provide superior protection for structural materials (CFRP, glass, and steel), surpassing polyurethane films under impact loadings. It is shown CFRP coated with the designed materials can withstand more than ten impact loadings (in energy of 10 J) without obvious damage, which otherwise delaminates after a single impact. This biomimetic design strategy holds the potential to offer valuable insights for the development of lightweight, energy-absorbent, and impact-resistant materials.

TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing.

BACKGROUND: High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently. RESULTS: Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base 'N's, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. CONCLUSIONS: The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.

The lipid globotriaosylceramide promotes germinal center B cell responses and antiviral immunity.

Influenza viruses escape immunity owing to rapid antigenic evolution, which requires vaccination strategies that allow for broadly protective antibody responses. We found that the lipid globotriaosylceramide (Gb3) expressed on germinal center (GC) B cells is essential for the production of high-affinity antibodies. Mechanistically, Gb3 bound and disengaged CD19 from its chaperone CD81, permitting CD19 to translocate to the B cell receptor complex to trigger signaling. Moreover, Gb3 regulated major histocompatibility complex class II expression to increase diversity of T follicular helper and GC B cells reactive with subdominant epitopes. In influenza infection, elevating Gb3, either endogenously or exogenously, promoted broadly reactive antibody responses and cross-protection. These data demonstrate that Gb3 determines the affinity and breadth of B cell immunity and has potential as a vaccine adjuvant.

The lipid Gb3 promotes germinal center B cell responses and anti-viral immunity.

Influenza viruses escape immunity due to rapid antigenic evolution, which requires vaccination strategies that allow for broadly protective antibody responses. Here, we demonstrate that the lipid globotriaosylceramide (Gb3) expressed on germinal center (GC) B cells is essential for the production of high-affinity antibodies. Mechanistically, Gb3 binds and disengages CD19 from its chaperone CD81 for subsequent translocation to the B cell receptor (BCR) complex to trigger signaling. Abundance of Gb3 amplifies the PI3-kinase/Akt/Foxo1 pathway to drive affinity maturation. Moreover, this lipid regulates MHC-II expression to increase diversity of T follicular helper (Tfh) and GC B cells reactive with subdominant epitopes. In influenza infection, Gb3 promotes broadly reactive antibody responses and cross-protection. Thus, we show that Gb3 determines affinity as well as breadth in B cell immunity and propose this lipid as novel vaccine adjuvant against viral infection. One Sentence Summary: Gb3 abundance on GC B cells selects antibodies with high affinity and broad epitope reactivities, which are cross-protective against heterologous influenza infection.

Friction and Wear in Nanoscratching of Single Crystals: Effect of Adhesion and Plasticity.

Friction and wear are two main tribological behaviors that are quite different for contact surfaces of distinct properties. Conventional studies generally focus on a specific material (e.g., copper or iron) such that the tribological result is not applicable to the other contact systems. In this paper, using a group of virtual materials characterized by coarse-grained potentials, we studied the effect of interfacial adhesion and material plasticity on friction and wear by scratching a rigid tip over an atomic smooth surface. Due to the combined effects of adhesion and plasticity on the nanoscratch process, the following findings are revealed: (1) For shallow contact where interfacial adhesion dominates friction, both friction coefficient and wear rate increase as the adhesion increases to a critical value. For deep contact where plasticity prevails, the variation of friction coefficient and wear rate is limited as the adhesion varies. (2) For weak and strong interfacial adhesions, the friction coefficient exhibits different dependence on the scratch depth, whereas the wear rate becomes higher as the scratch depth increases. (3) As the material hardness increases, both the friction coefficient and wear rate decrease in shallow and deep contacts.

Enhanced Adsorption of Sulfonamides by Attapulgite-Doped Biochar Prepared with Calcination.

The extensive use of sulfonamides seriously threatens the safety and stability of the ecological environment. Developing green inexpensive and effective adsorbents is critically needed for the elimination of sulfonamides from wastewater. The non-modified biochar exhibited limited adsorption capacity for sulfonamides. In this study, the attapulgite-doped biochar adsorbent (ATP/BC) was produced from attapulgite and rice straw by calcination. Compared with non-modified biochar, the specific surface area of ATP/BC increased by 73.53−131.26%, and the average pore width of ATP/BC decreased 1.77−3.60 nm. The removal rates of sulfadiazine and sulfamethazine by ATP/BC were 98.63% and 98.24%, respectively, at the mass ratio of ATP to rice straw = 1:10, time = 4 h, dosage = 2 g∙L−1, pH = 5, initial concentration = 1 mg∙L−1, and temperature = 20 °C. A pseudo-second-order kinetic model (R2 = 0.99) and the Freundlich isothermal model (R2 = 0.99) well described the process of sulfonamide adsorption on ATP/BC. Thermodynamic calculations showed that the adsorption behavior of sulfonamides on the ATP/BC was an endothermic (ΔH > 0), random (ΔS > 0), spontaneous reaction (ΔG < 0) that was dominated by chemisorption (−20 kJ∙mol−1 > ΔG). The potential adsorption mechanisms include electrostatic interaction, hydrogen bonding, π−π interaction, and Lewis acid−base interactions. This study provides an optional material to treat sulfonamides in wastewater and groundwater.

Human neural cell type-specific extracellular vesicle proteome defines disease-related molecules associated with activated astrocytes in Alzheimer's disease brain.

In neurodegenerative diseases, extracellular vesicles (EVs) transfer pathogenic molecules and are consequently involved in disease progression. We have investigated the proteomic profiles of EVs that were isolated from four different human-induced pluripotent stem cell-derived neural cell types (excitatory neurons, astrocytes, microglia-like cells, and oligodendrocyte-like cells). Novel cell type-specific EV protein markers were then identified for the excitatory neurons (ATP1A3, NCAM1), astrocytes (LRP1, ITGA6), microglia-like cells (ITGAM, LCP1), and oligodendrocyte-like cells (LAMP2, FTH1), as well as 16 pan-EV marker candidates, including integrins and annexins. To further demonstrate how cell-type-specific EVs may be involved in Alzheimer's disease (AD), we performed protein co-expression network analysis and conducted cell type assessments for the proteomes of brain-derived EVs from the control, mild cognitive impairment, and AD cases. A protein module enriched in astrocyte-specific EV markers was most significantly associated with the AD pathology and cognitive impairment, suggesting an important role in AD progression. The hub protein from this module, integrin-ß1 (ITGB1), was found to be significantly elevated in astrocyte-specific EVs enriched from the total brain-derived AD EVs and associated with the brain ß-amyloid and tau load in independent cohorts. Thus, our study provides a featured framework and rich resource for the future analyses of EV functions in neurodegenerative diseases in a cell type-specific manner.

Enrichment of Phosphorylated Tau (Thr181) and Functionally Interacting Molecules in Chronic Traumatic Encephalopathy Brain-derived Extracellular Vesicles.

Chronic Traumatic Encephalopathy (CTE) is a tauopathy that affects individuals with a history of mild repetitive brain injury. The initial neuropathologic changes of CTE include perivascular deposition of phosphorylated microtubule-associated protein tau (p-tau). Extracellular vesicles (EVs) are known to carry pathogenic molecules, such as tau in Alzheimer's disease and CTE suggesting their contribution in pathogenesis. We therefore examined the protein composition of EVs separated from CTE and an age-matched control brain tissues by tandem mass tag -mass spectrometry. The reporter ion intensity was used to quantify the identified molecules. A total of 516 common proteins were identified among three sets of experiments. Weighted protein co-expression network analysis identified 18 unique modules of co-expressed proteins. Two modules were significantly correlated with total tau (t-tau) and p-tau protein in the isolated EVs and enriched in cellular components and biological processes for synaptic vesicle secretion and multivesicular body-plasma membrane fusion. The p-tau (Thr181) level is significantly higher in CTE EVs compared to control EVs and can distinguish the two groups with 73.6% accuracy. A combination of t-tau or p-tau (Thr181) with SNAP-25, PLXNA4 or UBA1, enhanced the accuracy to 96.3, 93.8 and 93.8%, respectively. Bioinformatic protein-protein interaction analysis revealed the functional interaction of SNAP-25 and PLXNA4 with tau, suggesting their interaction in CTE EVs. These data indicate the future application of identified EV proteins for monitoring the CTE risk assessments and understanding the EV-mediated disease progression mechanism.

Ku70 suppresses alternative end joining in G1-arrested progenitor B cells.

Classical nonhomologous end joining (C-NHEJ) repairs DNA double-strand breaks (DSBs) throughout interphase but predominates in G1 phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/ligase IV (Lig4) core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While XRCC4/Lig4 are absolutely required for joining RAG1/2 endonuclease ("RAG")-initiated DSBs during V(D)J recombination in G1-phase progenitor lymphocytes, cycling cells deficient for XRCC4/Lig4 also can join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination by XRCC4/Lig4-mediated joining has been attributed to RAG shepherding V(D)J DSBs exclusively into the C-NHEJ pathway. Here, we report that A-EJ of DSB ends generated by RAG1/2, Cas9:gRNA, and Zinc finger endonucleases in Lig4-deficient G1-arrested progenitor B cell lines is suppressed by Ku. Thus, while diverse DSBs remain largely as free broken ends in Lig4-deficient G1-arrested progenitor B cells, deletion of Ku70 increases DSB rejoining and translocation levels to those observed in Ku70-deficient counterparts. Correspondingly, while RAG-initiated V(D)J DSB joining is abrogated in Lig4-deficient G1-arrested progenitor B cell lines, joining of RAG-generated DSBs in Ku70-deficient and Ku70/Lig4 double-deficient lines occurs through a translocation-like A-EJ mechanism. Thus, in G1-arrested, Lig4-deficient progenitor B cells are functionally end-joining suppressed due to Ku-dependent blockage of A-EJ, potentially in association with G1-phase down-regulation of Lig1. Finally, we suggest that differential impacts of Ku deficiency versus Lig4 deficiency on V(D)J recombination, neuronal apoptosis, and embryonic development results from Ku-mediated inhibition of A-EJ in the G1 cell cycle phase in Lig4-deficient developing lymphocyte and neuronal cells.

Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer's Disease Mouse Models.

Extracellular vesicles (EVs) are secreted by any neural cells in the central nervous system for molecular clearance, cellular communications, and disease spread in multiple neurodegenerative diseases, including Alzheimer's disease (AD), although their exact molecular mechanism is poorly understood. We hypothesize that high-resolution proteomic profiling of EVs separated from animal models of AD would determine the composition of EV contents and their cellular origin. Here, we examined recently developed transgenic mice (CAST.APP/PS1), which express familial AD-linked mutations of amyloid precursor protein (APP) and presenilin-1 (PS1) in the CAST/EiJ mouse strain and develop hippocampal neurodegeneration. Quantitative proteomics analysis of EVs separated from CAST.APP/PS1 and age-matched control mice by tandem mass tag-mass spectrometry identified a total of 3444 unique proteins, which are enriched in neuron-, astrocyte-, oligodendrocyte-, and microglia-specific molecules. CAST.APP/PS1-derived EVs show significant enrichment of Psen1, APP, and Itgax and reduction of Wdr61, Pmpca, Aldh1a2, Calu, Anp32b, Actn4, and Ndufv2 compared to WT-derived EVs, suggesting the involvement of Aß-processing complex and disease-associated/neurodegenerative microglia (DAM/MGnD) in EV secretion. In addition, Itgax and Apoe, DAM/MGnD markers, in EVs show a positive correlation with Itgax and Apoe mRNA expression from brain tissue in CAST.APP/PS1 mice. These datasets indicate the significant contribution of Aß plaque and neurodegeneration-induced DAM/MGnD microglia for EV secretion in CAST.APP/PS1 mice and shed light on understanding AD pathogenesis.

Alzheimer's disease brain-derived extracellular vesicles spread tau pathology in interneurons.

Extracellular vesicles are highly transmissible and play critical roles in the propagation of tau pathology, although the underlying mechanism remains elusive. Here, for the first time, we comprehensively characterized the physicochemical structure and pathogenic function of human brain-derived extracellular vesicles isolated from Alzheimer's disease, prodromal Alzheimer's disease, and non-demented control cases. Alzheimer's disease extracellular vesicles were significantly enriched in epitope-specific tau oligomers in comparison to prodromal Alzheimer's disease or control extracellular vesicles as determined by dot blot and atomic force microscopy. Alzheimer's disease extracellular vesicles were more efficiently internalized by murine cortical neurons, as well as more efficient in transferring and misfolding tau, than prodromal Alzheimer's disease and control extracellular vesicles in vitro. Strikingly, the inoculation of Alzheimer's disease or prodromal Alzheimer's disease extracellular vesicles containing only 300 pg of tau into the outer molecular layer of the dentate gyrus of 18-month-old C57BL/6 mice resulted in the accumulation of abnormally phosphorylated tau throughout the hippocampus by 4.5 months, whereas inoculation of an equal amount of tau from control extracellular vesicles, isolated tau oligomers, or fibrils from the same Alzheimer's disease donor showed little tau pathology. Furthermore, Alzheimer's disease extracellular vesicles induced misfolding of endogenous tau in both oligomeric and sarkosyl-insoluble forms in the hippocampal region. Unexpectedly, phosphorylated tau was primarily accumulated in glutamic acid decarboxylase 67 (GAD67) GABAergic interneurons and, to a lesser extent, glutamate receptor 2/3-positive excitatory mossy cells, showing preferential extracellular vesicle-mediated GABAergic interneuronal tau propagation. Whole-cell patch clamp recordings of CA1 pyramidal cells showed significant reduction in the amplitude of spontaneous inhibitory post-synaptic currents. This was accompanied by reductions in c-fos+ GAD67+ neurons and GAD67+ neuronal puncta surrounding pyramidal neurons in the CA1 region, confirming reduced GABAergic transmission in this region. Our study posits a novel mechanism for the spread of tau in hippocampal GABAergic interneurons via brain-derived extracellular vesicles and their subsequent neuronal dysfunction.

P2RX7 inhibitor suppresses exosome secretion and disease phenotype in P301S tau transgenic mice.

BACKGROUND: Neuronal accumulation of misfolded microtubule-associated protein tau is a hallmark of neuropathology in Alzheimer's disease, frontotemporal dementia, and other tauopathies, and has been a therapeutic target. Microglia can spread tau pathology by secreting tau-containing exosomes, although the specific molecular target is yet to be identified for the therapeutic intervention. P2X purinoceptor 7 (P2RX7) is an ATP-gated cation channel, enriched in microglia and triggers exosome secretion. The purpose of the study is to examine the therapeutic effect of an orally applicable, CNS-penetrant P2RX7 specific inhibitor on the early disease stage of a tauopathy mouse model. METHODS: Three-months-old P301S tau mice were treated with P2RX7-specific inhibitor GSK1482160 or vehicle for 30 days, followed by behavioral, biochemical and immunohistochemical assessment. GSK1482160 was also tested for exosome secretion from primary cultured murine astrocytes, neurons and microglia in vitro. RESULTS: Oral administration of GSK1482160 significantly reduced accumulation of MC1+ and Alz50+ misfolded tau in hippocampal regions, which was accompanied with reduced accumulation of Tsg101, an exosome marker, in hippocampal neurons. Proximity ligation assay demonstrated complex formation of Alz50+ tau and Tsg101 in hippocampal neurons, which was reduced by GSK1482160. On the other hand, GSK1482160 had no effect on microglial ramification or CD68 expression, which was significantly enhanced in P301S mice, or pro/anti-inflammatory cytokine gene expression. Strikingly, GSK1482160-treated P301S mice show significantly improved working and contextual memory as determined by Y-maze and fear conditioning tests. GSK1482160 also significantly increased accumulation of Tsg101 and CD81 in microglia in vivo, suggesting its suppression of P2RX7-induced exosome secretion from microglia. This effect was confirmed in vitro, as ATP-induced secretion of tau-containing exosome was significantly suppressed by GSK1482160 treatment from primary murine microglia, but not from neurons or astrocytes. DISCUSSION: The oral administration of P2RX7 inhibition mitigates disease phenotypes in P301S mice, likely by suppressing release of microglial exosomes. P2RX7 could be a novel therapeutic target for the early stage tauopathy development.

Predicting the flow stress and dominant yielding mechanisms: analytical models based on discrete dislocation plasticity.

Dislocations are the carriers of plasticity in crystalline materials. Their collective interaction behavior is dependent on the strain rate and sample size. In small specimens, details of the nucleation process are of particular importance. In the present work, discrete dislocation dynamics (DDD) simulations are performed to investigate the dominant yielding mechanisms in single crystalline copper pillars with diameters ranging from 100 to 800 nm. Based on our simulations with different strain rates and sample size, we observe a transition of the relevant nucleation mechanism from "dislocation multiplication" to "surface nucleation". Two physics-based analytical models are established to quantitatively predict this transition, showing a good agreement for different strain rates with our DDD simulation data and with available experimental data. Therefore, the proposed analytical models help to understand the interplay between different physical parameters and nucleation mechanisms and are well suitable to estimate the material strength for different material properties and under given loading conditions.