Optimizing the synthesis of dimeric peptides: influence of the reaction medium and effects that modulate kinetics and reaction yield

Peptides are remarkably interesting alternatives to several applications. In particular, antimicrobial sequences have raised major interest of the scientific community due to the resistance acquired by commonly used antibiotics. Amongst these, some dimeric peptides have shown very promising characteristics as strong biological activities and resistance against degradation by peptidases. However, despite such promising characteristics, a relatively small number of studies address dimeric peptides, mainly due to the synthesis-related obstacles in their production, whereas the well-implemented routines of solid phase peptide synthesis-which includes the possibility of automation-makes life significantly easier. Here, we present kinetic investigations of the dimerization of a cysteine-containing sequence to obtain the homodimeric antimicrobial peptide homotarsinin. Based on the structural and membrane interaction data already available for the dimer and its monomeric chain, we have proposed distinct dimerization protocols in selected environments, namely, aqueous buffer, TFE:H2O and micellar solutions. The experimental results were adjusted by a theoretical model. Both the kinetic profiles and the reaction yields are dependent on the reaction medium, clearly indicating that aggregation, peptide structure, and peptide-membrane interactions play major roles in the formation of the disulfide bond. Finally, the rationalization of the different aspects addressed here is expected to contribute to research and applications that demand the obtainment of dimeric peptides.

The E3 Ubiquitin Ligase SCF Cyclin F Promotes Sequestosome-1/p62 Insolubility and Foci Formation and is Dysregulated in ALS and FTD Pathogenesis

Amyotrophic lateral sclerosis (ALS)- and frontotemporal dementia (FTD)-linked mutations in CCNF have been shown to cause dysregulation to protein homeostasis. CCNF encodes for cyclin F, which is part of the cyclin F-E3 ligase complex SCFcyclinF known to ubiquitylate substrates for proteasomal degradation. In this study, we identified a function of cyclin F to regulate substrate solubility and show how cyclin F mechanistically underlies ALS and FTD disease pathogenesis. We demonstrated that ALS and FTD-associated protein sequestosome-1/p62 (p62) was a canonical substrate of cyclin F which was ubiquitylated by the SCFcyclinF complex. We found that SCFcyclin F ubiquitylated p62 at lysine(K)281, and that K281 regulated the propensity of p62 to aggregate. Further, cyclin F expression promoted the aggregation of p62 into the insoluble fraction, which corresponded to an increased number of p62 foci. Notably, ALS and FTD-linked mutant cyclin F p.S621G aberrantly ubiquitylated p62, dysregulated p62 solubility in neuronal-like cells, patient-derived fibroblasts and induced pluripotent stem cells and dysregulated p62 foci formation. Consistently, motor neurons from patient spinal cord tissue exhibited increased p62 ubiquitylation. We suggest that the p.S621G mutation impairs the functions of cyclin F to promote p62 foci formation and shift p62 into the insoluble fraction, which may be associated to aberrant mutant cyclin F-mediated ubiquitylation of p62. Given that p62 dysregulation is common across the ALS and FTD spectrum, our study provides insights into p62 regulation and demonstrates that ALS and FTD-linked cyclin F mutant p.S621G can drive p62 pathogenesis associated with ALS and FTD.

Truncation or proteolysis of α-synuclein in Parkinsonism

Posttranslational modifications of α-synuclein, such as truncation or abnormal proteolysis, are implicated in Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). A key focus of this article includes the proteases responsible for inducing truncation, the specific sites susceptible to truncation, and the resultant influence of these truncated species on the seeding and aggregation of endogenous α-synuclein. We also shed light on the unique structural attributes of these truncated species, and how these modifications can lead to distinctive forms of synucleinopathies. In addition, we explore the comparative toxic potentials of various α-synuclein species. An extensive analysis of available evidence of truncated α-synuclein species in human-synucleinopathy brains is also provided. Lastly, we delve into the detrimental impact of truncated species on key cellular structures such as the mitochondria and endoplasmic reticulum. Our article discusses enzymes involved in α-synuclein truncation, including 20 S proteasome, cathepsins, asparagine endopeptidase, caspase-1, calpain-1, neurosin/kallikrein-6, matrix metalloproteinase-1/-3, and plasmin. Truncation patterns impact α-synuclein aggregation - C-terminal truncation accelerates aggregation with larger truncations correlated with shortened aggregation lag times. N-terminal truncation affects aggregation differently based on the truncation location. C-terminally truncated α-synuclein forms compact, shorter fibrils compared to the full-length (FL) protein. N-terminally truncated monomers form fibrils similar in length to FL α-synuclein. Truncated forms show distinct fibril morphologies, increased β-sheet structures, and greater protease resistance. Misfolded α-synuclein can adopt various conformations, leading to unique aggregates and distinct synucleinopathies. Fibrils, with prion-like transmission, are potentially more toxic than oligomers, though this is still debated. Different α-synuclein variants with N- and C-terminal truncations, namely 5-140, 39-140, 65-140, 66-140, 68-140, 71-140, 1-139, 1-135, 1-133, 1-122, 1-119, 1-115, 1-110, and 1-103 have been found in PD, DLB, and MSA patients' brains. In Parkinsonism, excess misfolded α-synuclein overwhelms the proteasome degradation system, resulting in truncated protein production and accumulation in the mitochondria and endoplasmic reticulum.

The role of tandem repeats in bacterial functional amyloids

Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.

Bovine liver catalase turns into three conformational states after exposure to an anionic surfactant

The mechanism by which anionic surfactants promote amyloid fibril is not well understood. Here, we investigated how sodium dodecyl sulfate (SDS), a negatively charged surfactant, affects the fibrillation of the partially unfolded random-coiled bovine liver catalase (BLC) at a pH of 2.0. We used several methods, including turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM imaging, to evaluate the conformational changes of BLC in vitro in response to SDS treatment. BLC is a multimeric protein and well folded at physiological pH but forms a random coil structure at pH 2.0. Intrinsic fluorescence and far-UV CD data showed that below 0.1 mM SDS, random coiled BLC turned into a native-like structure. BLC incubated with an SDS concentration ranging from 0.1 to 2.0 mM led to the formation of aggregates. The ThT fluorescence intensity was enhanced in the aggregated BLC samples (0.1-2.0 mM SDS), and cross beta-sheeted structure was detected by the far UV CD measurements. BLC adopts a complete alpha-helical structure upon interacting with SDS at a more than 2.0 mM concentration at pH 2.0. Understanding the mechanism of surfactant- or lipid-induced fibrillation is important for therapeutic purposes.

The ice age - A review on formulation of Adeno-associated virus therapeutics

Gene therapies offer promising therapeutic alternatives for many disorders that currently lack efficient treatment options. Due to their chemical nature and physico-chemical properties, delivery of polynucleic acids into target cells and subcellular compartments remains a significant challenge. Adeno-associated viruses (AAV) have gained a lot of interest for the efficient delivery of therapeutic single-stranded DNA (ssDNA) genomes over the past decades. More than a hundred products have been tested in clinical settings and three products have received market authorization by the US FDA in recent years. A lot of effort is being made to generate potent recombinant AAV (rAAV) vectors that show favorable safety and immunogenicity profiles for either local or systemic administration. Manufacturing processes are gradually being optimized to deliver a consistently high product quality and to serve potential market needs beyond rare indications. In contrast to protein therapeutics, most rAAV products are still supplied as frozen liquids within rather simple formulation buffers to enable sufficient product shelf life, significantly hampering global distribution and access. In this review, we aim to outline the hurdles of rAAV drug product development and discuss critical formulation and composition aspects of rAAV products under clinical evaluation. Further, we highlight recent development efforts in order to achieve stable liquid or lyophilized products. This review therefore provides a comprehensive overview on current state-of-the-art rAAV formulations and can further serve as a map for rational formulation development activities in the future.

p53 amyloid pathology is correlated with higher cancer grade irrespective of the mutant or wild-type form

p53 (also known as TP53) mutation and amyloid formation are long associated with cancer pathogenesis; however, the direct demonstration of the link between p53 amyloid load and cancer progression is lacking. Using multi-disciplinary techniques and 59 tissues (53 oral and stomach cancer tumor tissue samples from Indian individuals with cancer and six non-cancer oral and stomach tissue samples), we showed that p53 amyloid load and cancer grades are highly correlated. Furthermore, next-generation sequencing (NGS) data suggest that not only mutant p53 (e.g. single-nucleotide variants, deletions, and insertions) but wild-type p53 also formed amyloids either in the nucleus (50%) and/or in the cytoplasm in most cancer tissues. Interestingly, in all these cancer tissues, p53 displays a loss of DNA-binding and transcriptional activities, suggesting that the level of amyloid load correlates with the degree of loss and an increase in cancer grades. The p53 amyloids also sequester higher amounts of the related p63 and p73 (also known as TP63 and TP73, respectively) protein in higher-grade tumor tissues. The data suggest p53 misfolding and/or aggregation, and subsequent amyloid formation, lead to loss of the tumor-suppressive function and the gain of oncogenic function, aggravation of which might determine the cancer grade.

Anionic surfactant causes dual conformational changes in insulin

Amyloid fibrillation is a process by which proteins aggregate and form insoluble fibrils that are implicated in several neurodegenerative diseases. In n this study, we aimed to investigate the impact of the negatively charged detergent sodium dodecyl sulfate (SDS) on insulin amyloid fibrillation at pH 7.4 and 2.0, as SDS has been linked to the acceleration of amyloid fibrillation in vitro, but the underlying molecular mechanism is not fully understood. Our findings show that insulin forms amyloid-like aggregates in the presence of SDS at concentrations ranging from 0.05 to 1.8 mM at pH 2.0, while no aggregates were observed at SDS concentrations greater than 1.8 mM, and insulin remained soluble. However, at pH 7.4, insulin remained soluble regardless of the concentration of SDS. Interestingly, the aggregated insulin had a cross-β sheet secondary structure, and when incubated with higher SDS concentrations, it gained more alpha-helix. The electrostatics and hydrophobic interaction of SDS and insulin may contribute to amyloid induction. Moreover, the SDS-induced aggregation was not affected by the presence of salts. Furthermore, as the concentration of SDS increased, the preformed insulin amyloid induced by SDS began to disintegrate. Overall, our study sheds light on the mechanism of surfactant-induced amyloid fibrillation in insulin protein.

Consensus-based clustering and data aggregation in decentralized network of multi-agent systems

Multi-agent systems are promising for applications in various fields. However, they require optimization algorithms that can handle large number of agents and heterogeneously connected networks in clustered environments. Planning algorithms performed in the decentralized communication model and clustered environment require precise knowledge about cluster information by compensating noise from other clusters. This article proposes a decentralized data aggregation algorithm using consensus method to perform COUNT and SUM aggregation in a clustered environment. The proposed algorithm introduces a trust value to perform accurate aggregation on cluster level. The correction parameter is used to adjust the accuracy of the solution and the computation time. The proposed algorithm is evaluated in simulations with large and sparse networks and small bandwidth. The results show that the proposed algorithm can achieve convergence on the aggregated data with reasonable accuracy and convergence time. In the future, the proposed tools will be useful for developing a robust decentralized task assignment algorithm in a heterogeneous multi-agent multi-task environment.

Chaotic aging: intrinsically disordered proteins in aging-related processes

The development of aging is associated with the disruption of key cellular processes manifested as well-established hallmarks of aging. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) have no stable tertiary structure that provide them a power to be configurable hubs in signaling cascades and regulate many processes, potentially including those related to aging. There is a need to clarify the roles of IDPs/IDRs in aging. The dataset of 1702 aging-related proteins was collected from established aging databases and experimental studies. There is a noticeable presence of IDPs/IDRs, accounting for about 36% of the aging-related dataset, which is however less than the disorder content of the whole human proteome (about 40%). A Gene Ontology analysis of the used here aging proteome reveals an abundance of IDPs/IDRs in one-third of aging-associated processes, especially in genome regulation. Signaling pathways associated with aging also contain IDPs/IDRs on different hierarchical levels, revealing the importance of "structure-function continuum" in aging. Protein-protein interaction network analysis showed that IDPs present in different clusters associated with different aging hallmarks. Protein cluster with IDPs enrichment has simultaneously high liquid-liquid phase separation (LLPS) probability, "nuclear" localization and DNA-associated functions, related to aging hallmarks: genomic instability, telomere attrition, epigenetic alterations, and stem cells exhaustion. Intrinsic disorder, LLPS, and aggregation propensity should be considered as features that could be markers of pathogenic proteins. Overall, our analyses indicate that IDPs/IDRs play significant roles in aging-associated processes, particularly in the regulation of DNA functioning. IDP aggregation, which can lead to loss of function and toxicity, could be critically harmful to the cell. A structure-based analysis of aging and the identification of proteins that are particularly susceptible to disturbances can enhance our understanding of the molecular mechanisms of aging and open up new avenues for slowing it down.

Selective Photodynamic Activity of Tetrakis(4-aminophenyl)porphyrins with and without Acetyl Protecting Groups on Cancer and Normal Cells

Tetrakis(4-aminophenyl)porphyrin (1) and tetrakis(4-acetamidophenyl)porphyrin (2) were dissolved in water with the incorporation of a polysaccharide (λ-carrageenan (CGN)) as a water-solubilizing agent. Although the photodynamic activity of the CGN-2 complex was considerably lower than that of the CGN-1 complex, the selectivity index (SI; IC50 in a normal cell/IC50 in a cancer cell) of the CGN-2 complex was considerably higher than that of the CGN-1 complex. This is because the photodynamic activity of the CGN-2 complex was significantly affected by the intracellular uptakes by the normal and cancer cells. During in vivo experiments, the CGN-2 complex inhibited tumor growth under light irradiation with high blood retention compared with the CGN-1 complex and Photofrin, which exhibited lower blood retention. This study showed that the photodynamic activity and SI are influenced by substituent groups of arene in the meso-positions of porphyrin analogs.

Promotion effect of ultraviolet light on graphene oxide aggregation in the presence of different climatic zone's humic and fulvic acid

Aggregation of graphene oxide (GO) is significantly affected by dissolved organic matter (DOM) in natural waters, while DOM's climate zone and light irradiation is seldom considered. This study investigated the effect of humic/fulvic acid (HA/FA) from various climate zones of China on aggregation of small (200 nm) and large (500 nm) GO under 120-h UV irradiation. GO aggregation was promoted by HA/FA because UV irradiation decreased hydrophilicity of GO and steric forces among particles. GO generated electron and hole pair under UV irradiation, which reduce GO with more hydrophilic oxygen-containing functional group (C-O) to rGO with high hydrophobicity and oxidize DOM into organic matter with smaller molecular weight. Most severe GO aggregation was observed with Makou HA from Subtropical Monsoon climate zone and Maqin FA from Plateau and Mountain climate zone, which was primarily because HA/FA's high molecular weight and aromaticity dispersed GO initially that facilitated UV penetration. GO aggregation ratio was positively correlated with graphitic fraction content (R2 = 0.82-0.99) and negatively correlated with C-O group content (R2 = 0.61-0.98) in the presence of DOM under UV irradiation. This work highlights different dispersity of GO during photochemical reactions in various climate zones, providing new insight into the environmental implications of nanomaterial release.

TMEM106B aggregation in neurodegenerative diseases: linking genetics to function

BACKGROUND

Mutations of the gene TMEM106B are risk factors for diverse neurodegenerative diseases. Previous understanding of the underlying mechanism focused on the impairment of lysosome biogenesis caused by TMEM106B loss-of-function. However, mutations in TMEM106B increase its expression level, thus the molecular process linking these mutations to the apparent disruption in TMEM106B function remains mysterious.

MAIN BODY

Recent new studies reported that TMEM106B proteins form intracellular amyloid filaments which universally exist in various neurodegenerative diseases, sometimes being the dominant form of protein aggregation. In light of these new findings, in this review we systematically examined previous efforts in understanding the function of TMEM106B in physiological and pathological conditions. We propose that TMEM106B aggregations could recruit normal TMEM106B proteins and interfere with their function.

CONCLUSIONS

TMEM106B mutations could lead to lysosome dysfunction by promoting the aggregation of TMEM106B and reducing these aggregations may restore lysosomal function, providing a potential therapeutic target for various neurodegenerative diseases.

Aggregation and stability of selenium nanoparticles: Complex roles of surface coating, electrolytes and natural organic matter

The application of selenium nanoparticles (SeNPs) as nanofertilizers may lead to the release of SeNPs into aquatic systems. However, the environmental behavior of SeNPs is rarely studied. In this study, using alginate-coated SeNPs (Alg-SeNPs) and polyvinyl alcohol-coated SeNPs (PVA-SeNPs) as models, we systematically investigated the aggregation and stability of SeNPs under various water conditions. PVA-SeNPs were highly stable in mono- and polyvalent electrolytes, probably due to the strong steric hindrance of the capping agent. Alg-SeNPs only suffered from a limited increase in size, even at 2500 mmol/L NaCl and 200 mmol/L MgCl₂, while they underwent apparent aggregation in CaCl₂ and LaCl₃ solutions. The binding of Ca²⁺ and La³⁺ with the guluronic acid part in alginate induced the formation of cross-linking aggregates. Natural organic matter enhanced the stability of Alg-SeNPs in monovalent electrolytes, while accelerated the attachment of Alg-SeNPs in polyvalent electrolytes, due to the cation bridge effects. The long-term stability of SeNPs in natural water showed that the aggregation sizes of Alg-SeNPs and PVA-SeNPs increased to several hundreds of nanometers or above 10 µm after 30 days, implying that SeNPs may be suspended in the water column or further settle down, depending on the surrounding water chemistry. The study may contribute to the deep insight into the fate and mobility of SeNPs in the aquatic environment. The varying fate of SeNPs in different natural waters also suggests that the risks of SeNPs to organisms living in diverse depths in the aquatic compartment should be concerned.

Characterization of Virus Particles and Submicron-Sized Particulate Impurities in Recombinant Adeno-Associated Virus Drug Product

Characterization of particulate impurities such as aggregates is necessary to develop safe and efficacious adeno-associated virus (AAV) drug products. Although aggregation of AAVs can reduce the bioavailability of the virus, only a limited number of studies focus on the analysis of aggregates. We explored three technologies for their capability to characterize AAV monomers and aggregates in the submicron (<1 µm) size range: (i) mass photometry (MP), (ii) asymmetric flow field flow fractionation coupled to a UV-detector (AF4-UV/Vis) and (iii) microfluidic resistive pulse sensing (MRPS). Although low counts for aggregates impeded a quantitative analysis, MP was affirmed as an accurate and rapid method for quantifying the genome content of empty/filled/double-filled capsids, consistent with sedimentation velocity analytical ultracentrifugation results. MRPS and AF4-UV/Vis enabled the detection and quantification of aggregate content. The developed AF4-UV/Vis method separated AAV monomers from smaller aggregates, thereby enabling a quantification of aggregates <200 nm. MRPS was experienced as a straightforward method to determine the particle concentration and size distribution between 250-2000 nm, provided that the samples do not block the microfluidic cartridge. Overall, within this study we explored the benefits and limitations of the complementary technologies for assessing aggregate content in AAV samples.

(Dys)functional insights into nucleic acids and RNA-binding proteins modulation of the prion protein and α-synuclein phase separation

Prion diseases are prototype of infectious diseases transmitted by a protein, the prion protein (PrP), and are still not understandable at the molecular level. Heterogenous species of aggregated PrP can be generated from its monomer. α-synuclein (αSyn), related to Parkinson's disease, has also shown a prion-like pathogenic character, and likewise PrP interacts with nucleic acids (NAs), which in turn modulate their aggregation. Recently, our group and others have characterized that NAs and/or RNA-binding proteins (RBPs) modulate recombinant PrP and/or αSyn condensates formation, and uncontrolled condensation might precede pathological aggregation. Tackling abnormal phase separation of neurodegenerative disease-related proteins has been proposed as a promising therapeutic target. Therefore, understanding the mechanism by which polyanions, like NAs, modulate phase transitions intracellularly, is key to assess their role on toxicity promotion and neuronal death. Herein we discuss data on the nucleic acids binding properties and phase separation ability of PrP and αSyn with a special focus on their modulation by NAs and RBPs. Furthermore, we provide insights into condensation of PrP and/or αSyn in the light of non-trivial subcellular locations such as the nuclear and cytosolic environments.

Protein aggregation model to explain the bioactivity of condensed tannins

Tannins are involved in the taste of foods and multi bioactivity of traditional herbal medicines. The characteristics of tannins are believed to derive from their connectivity with proteins. However, the mode of interaction between proteins and tannins is not yet understood because of the complexity of the tannin structure. Then this study aimed to elucidate the detail binding mode of tannin and protein by the ¹H-¹⁵N HSQC NMR method using the ¹⁵N-labeled MMP-1that have not been used so far. The HSQC results suggested cross-link sites between MMP-1s, which cause protein aggregation and inhibit MMP-1 activity. This study presents the first 3D protein aggregation model of condensed tannins, which is important for understanding the bioactivity of polyphenols. Furthermore, it can broaden the understanding of the range of interactions between other proteins and polyphenols.

Early stages in Aβ1-42 spontaneous aggregation: An unbiased dataset from coarse-grained molecular dynamics simulations

The small soluble aggregates of Aβ_1-42 are broadly documented as potential targets for the development of new compounds with the capacity to inhibit the early stages of Alzheimer´s disease. Nevertheless, Aβ_1-42 peptides show an intrinsically disordered character with a high propensity for aggregation, which complicates the identification of conserved structural patterns. Because of this, experimental techniques find substantial difficulties in the characterization of such soluble oligomers. Theoretical techniques, such as molecular dynamics (MD) simulations, provide a possible workaround for this problem. However, the computational cost associated with comprehensively sampling the vast conformational space accessible to these peptides might become prohibitive. In this sense, coarse-grained (CG) simulations can effectively overcome that hurdle at a fraction of the computational cost. In this dataset, we furnish an extensive collection of Aβ_1-42 peptides in dimeric conformation generated with the SIRAH force field for CG MD simulation. It comprises 25 independent trajectories in .xtc (gromacs) format of Aβ_1-42 couples of peptides that evolve towards dimeric states along eleven µs-long unbiased simulations. Thanks to the backmapping capabilities of our force field, pseudo atomistic coordinates can be straightforwardly recovered from MD trajectories reported here and analyzed with popular molecular editing programs. This set of simulations performed at room conditions and physiological salt concentrations may furnish a complete collection of inter-peptide interfaces that can be used in high-throughput docking or as new starting states for peptide oligomerization seeding of Aβ_1-42 dimerization.

Multicellular dynamics on structured surfaces: Stress concentration is a key to controlling complex microtissue morphology on engineered scaffolds

Tissue engineers have utilised a variety of three-dimensional (3D) scaffolds for controlling multicellular dynamics and the resulting tissue microstructures. In particular, cutting-edge microfabrication technologies, such as 3D bioprinting, provide increasingly complex structures. However, unpredictable microtissue detachment from scaffolds, which ruins desired tissue structures, is becoming an evident problem. To overcome this issue, we elucidated the mechanism underlying collective cellular detachment by combining a new computational simulation method with quantitative tissue-culture experiments. We first quantified the stochastic processes of cellular detachment shown by vascular smooth muscle cells on model curved scaffolds and found that microtissue morphologies vary drastically depending on cell contractility, substrate curvature, and cell-substrate adhesion strength. To explore this mechanism, we developed a new particle-based model that explicitly describes stochastic processes of multicellular dynamics, such as adhesion, rupture, and large deformation of microtissues on structured surfaces. Computational simulations using the developed model successfully reproduced characteristic detachment processes observed in experiments. Crucially, simulations revealed that cellular contractility-induced stress is locally concentrated at the cell-substrate interface, subsequently inducing a catastrophic process of collective cellular detachment, which can be suppressed by modulating cell contractility, substrate curvature, and cell-substrate adhesion. These results show that the developed computational method is useful for predicting engineered tissue dynamics as a platform for prediction-guided scaffold design. STATEMENT OF SIGNIFICANCE: Microfabrication technologies aiming to control multicellular dynamics by engineering 3D scaffolds are attracting increasing attention for modelling in cell biology and regenerative medicine. However, obtaining microtissues with the desired 3D structures is made considerably more difficult by microtissue detachments from scaffolds. This study reveals a key mechanism behind this detachment by developing a novel computational method for simulating multicellular dynamics on designed scaffolds. This method enabled us to predict microtissue dynamics on structured surfaces, based on cell mechanics, substrate geometry, and cell-substrate interaction. This study provides a platform for the physics-based design of micro-engineered scaffolds and thus contributes to prediction-guided biomaterials design in the future.

Impact of wood-derived biochar on the hydrologic performance of bioretention media: Effects on aggregation, root growth, and water retention

Bioretention systems are one example of green stormwater infrastructure that may mitigate the hydrologic impact of stormwater runoff. To improve water retention while maintaining rapid stormwater infiltration, conventional bioretention soil media (BSM) might be augmented with biochar. Biochar may improve the BSM's structure by increasing soil aggregation, which might improve water retention and increase stormwater infiltration while also improving root growth. Pots with BSMs representing high and moderate sand content media were amended with a wood-derived biochar, planted with switchgrass, and subjected to weekly storms for 20 weeks, followed by a 10-week drought. In the high sand content medium (NC mix), biochar amendment increased hydraulic conductivity (K_sat), and this effect increased with time. At 0 weeks, 2% and 4% (w/w) biochar increased K_sat by 4 ± 2% and 10 ± 4%, respectively, while at 30 weeks the increase was 30 ± 10 and 70 ± 20%, respectively, above biochar-free media. Similar improvements were seen in plant available water (PAW) in NC mix. However, minimal improvements in K_sat and PAW from biochar amendment were found in the moderate sand content BSM that contained compost and mulch (DE mix). Where biochar promoted K_sat, this was correlated with increased water-stable aggregate size (r = 0.86), fine root volume (r = 0.88), and below ground biomass (r = 0.83). Important factors affecting K_sat and aggregation in the NC mix were biochar's influence on organo-mineral association, fungal hyphae length, and plant roots. Wood-derived biochar amendment to BSM may obviate the need for compost/mulch since biochar has similar effects on improving BSM hydrology and root growth without the risk of undesired nutrient leaching.

A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is characterized by the intra- and extracellular accumulation of amyloid-β (Aβ) peptides. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously.

METHODS

We quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and membrane filter assays. Protein changes in different mouse tissues were analyzed by MS-based proteomics using label-free quantification; resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in cerebrospinal fluid (CSF) from AD patients and controls using ELISAs.

RESULTS

Experiments revealed faster accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, with more protein abundance changes in hippocampus, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease-relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in human AD brain tissue. Arl8b protein levels were significantly increased in CSF of AD patients.

CONCLUSIONS

We report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker.

Vapor phase-grown TiO2 and ZnO nanoparticles inside electrospun polymer fibers and their calcination-induced organization

The spatial organization of metal oxide nanoparticles represents an important factor in the chemical utilization of resulting structures. For the production of networks that are composed of metal oxide nanoparticle chains, we dispersed vapor phase-grown TiO2 and ZnO nanoparticles homogeneously in an aqueous polyvinyl alcohol solution. After electrospinning, we analyzed the sizes and diameters of the compositionally homogeneous electrospun fibers and discussed the size distribution and morphology of the nanoparticles inside. Calcination-induced polymer removal gives rise to self-supported nanoparticle-based nanofibers. Particle coarsening by a factor of ~ 2 for TiO2 and ~ 3 for ZnO nanoparticles is observed.

Graphical abstract

Targeting the glycine-rich domain of TDP-43 with antibodies prevents its aggregation in vitro and reduces neurofilament levels in vivo

Cytoplasmic aggregation and concomitant nuclear clearance of the RNA-binding protein TDP-43 are found in ~ 90% of cases of amyotrophic lateral sclerosis and ~ 45% of patients living with frontotemporal lobar degeneration, but no disease-modifying therapy is available. Antibody therapy targeting other aggregating proteins associated with neurodegenerative disorders has shown beneficial effects in animal models and clinical trials. The most effective epitopes for safe antibody therapy targeting TDP-43 are unknown. Here, we identified safe and effective epitopes in TDP-43 for active and potential future passive immunotherapy. We prescreened 15 peptide antigens covering all regions of TDP-43 to identify the most immunogenic epitopes and to raise novel monoclonal antibodies in wild-type mice. Most peptides induced a considerable antibody response and no antigen triggered obvious side effects. Thus, we immunized mice with rapidly progressing TDP-43 proteinopathy ("rNLS8" model) with the nine most immunogenic peptides in five pools prior to TDP-43ΔNLS transgene induction. Strikingly, combined administration of two N-terminal peptides induced genetic background-specific sudden lethality in several mice and was therefore discontinued. Despite a strong antibody response, no TDP-43 peptide prevented the rapid body weight loss or reduced phospho-TDP-43 levels as well as the profound astrogliosis and microgliosis in rNLS8 mice. However, immunization with a C-terminal peptide containing the disease-associated phospho-serines 409/410 significantly lowered serum neurofilament light chain levels, indicative of reduced neuroaxonal damage. Transcriptomic profiling showed a pronounced neuroinflammatory signature (IL-1β, TNF-α, NfκB) in rNLS8 mice and suggested modest benefits of immunization targeting the glycine-rich region. Several novel monoclonal antibodies targeting the glycine-rich domain potently reduced phase separation and aggregation of TDP-43 in vitro and prevented cellular uptake of preformed aggregates. Our unbiased screen suggests that targeting the RRM2 domain and the C-terminal region of TDP-43 by active or passive immunization may be beneficial in TDP-43 proteinopathies by inhibiting cardinal processes of disease progression.

Ocean acidification enhances the embryotoxicity of CuO nanoparticles to Oryzias melastigma

Concerns are raised towards individual effects of ocean acidification (OA) and engineered nanoparticles (NPs) on marine organisms. However, there are scarce studies regarding nanotoxicity under OA conditions. We investigated the combined effects of OA (pHs, 7.70 and 7.40) and CuO NPs on the embryotoxicity of marine medaka Oryzias melastigma and the bioavailability of CuO NPs in embryos. The results showed that OA alleviated the aggregation of CuO NPs and promoted the dissolution of CuO NPs in seawater (increased by 0.010 and 0.029 mg/L under pHs 7.70 and 7.40, respectively). Synergistic effects of OA with CuO NPs on medaka embryos were observed as indicated by much higher mortality and oxidative damage. Importantly, the enhanced toxicity of CuO NPs to medaka embryos under OA conditions mainly originated from the higher bioavailability of particulate CuO (e.g., 30.28 mg/kg at pH 7.40) rather than their released Cu²⁺ ions (e.g. 3.04 mg/kg at pH 7.40). The weaker aggregation of NPs under OA conditions resulted in higher penetration of individual particles (or small aggregates) into embryos through the micropyle and chorionic pores, causing enhanced bioavailability of NPs. The obtained results provided underlying insights into understanding the risk of NPs to marine ecosystem under OA conditions.

Scavenging of copper(II) ions, phosphate(V) ions, and diuron from aqueous media by goethite modified with chitosan or poly(acrylic acid)

Goethite was modified by chitosan (CS) or poly(acrylic acid) (PAA) to improve its adsorptive abilities toward components of agrochemicals, i.e., copper ions (Cu), phosphate ions (P), and diuron. The pristine goethite effectively bound Cu (7.68 mg/g, 63.71%) and P (6.31 mg/g, 50.46%) only in their mixed systems. In the one adsorbate solutions, the adsorption levels accounted for 3.82 mg/g (30.57%) for Cu, 3.22 mg/g (25.74%) for P, and 0.15 mg/g (12.15%) for diuron. Goethite modification with CS or PAA did not yield spectacular results in adsorption. The maximum increase in adsorbed amount was noted for Cu ions (8.28%) after PAA modification as well as for P (6.02%) and diuron (24.04%) after CS modification. Both goethite modifications contributed to clear reduction in desorption of pollutants (even by 20.26% for Cu after PAA coating), which was mainly dictated by electrostatic attractive forces and hydrogen bonds formation occurring between macromolecules and impurities. The only exception in this phenomenon was Cu desorption from CS-modified solid-the polymer made it higher (to 95.00%). The Cu adsorption on PAA-modified goethite enhanced solid aggregation and thus facilitated metal cation separation from aqueous media. Consequently, the goethite modification with PAA was considered more promising for environmental remediation.

Plant growth-promoting bacterial consortia improved the physiology and growth of maize by regulating osmolytes and antioxidants balance under salt-affected field conditions

This study was undertaken to see how microbial consortia influenced maize development and yield under salt-affected conditions. The efficacy of the pre-isolated bacterial strains Burkholderia phytofirmans, Bacillussubtilis, Enterobacter aerogenes, and Pseudomonas syringae and Pseudomonas fluorescens to decrease the detrimental effects of salt on maize was tested in four distinct combinations using Randomized Complete Block Design with three replicates. The results revealed that these strains were compatible and collaborated synergistically, with an 80% co-aggregation percentage under salt-affected conditions. Following that, these strains were tested for their ability to increase maize growth and yield under salt-affected field conditions. The photosynthetic rate (11-50%), relative water content (10-34%), and grain yield (13-21%) of maize were all increased by these various combinations. However, when Burkholderia phytofirmans, Enterobacter aerogenes and Pseudomonas fluorescens were combined, the greatest increase was seen above the un-inoculated control. Furthermore, as compared to the un-inoculated control, the same combination resulted in a 1.5-fold increase in catalase and a 2.0-fold increase in ascorbate concentration. These findings showed that a multi-strain consortium might boost maize's total yield response as a result of better growth under salt stress.

Formulation Studies to Develop Low-Cost, Orally-Delivered Secretory IgA Monoclonal Antibodies for Passive Immunization Against Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is a common cause for diarrheal infections in children in low- and middle-income countries (LMICs). To date, no ETEC vaccine candidates have been approved. Passive immunization with low-cost, oral formulations of secretory IgA (sIgA) against ETEC is an alternative approach to protect high-risk populations in LMICs. Using a model sIgA monoclonal antibody (anti-LT sIgA2-mAb), the stability profiles of different formulations were assessed during storage and in in vitro digestion models (mimicking in vivo oral delivery). First, by employing various physicochemical techniques and a LT-antigen binding assay, three formulations with varying acid-neutralizing capacity (ANC) were evaluated to stabilize sIgA2-mAb during stress studies (freeze-thaw, agitation, elevated temperature) and during exposure to gastric phase digestion. Next, a low-volume, in vitro intestinal digestion model was developed to screen various additives to stabilize sIgA2-mAb in the intestinal phase. Finally, combinations of high ANC buffers and decoy proteins were assessed to collectively protect sIgA2-mAb during in vitro sequential (stomach to intestine) digestion. Based on the results, we demonstrate the feasibility of low-cost, 'single-vial', liquid formulations of sIgA-mAbs delivered orally after infant feeding for passive immunization, and we suggest future work based on a combination of in vitro and in vivo stability considerations.

Co-aggregation between whey proteins and carotenoids from yellow mombin (Spondias mombin): Impact of carotenoids' self-aggregation

The interaction between whey proteins and carotenoid is reported to improve carotenoid solubility and stability, however, the strong trend of carotenoids to aggregate when in polar systems is often neglected in papers addressing their molecular interaction. Therefore, this study focused on characterizing the aggregative behavior of the carotenoids from yellow mombin (Spondias mombin) and to understand how these carotenoids behave when added to aqueous dispersions of whey proteins. Carotenoids-rich extract, containing mainly β-cryptoxanthin and lutein, was obtained from freeze-dried yellow mombin pulp and its aggregative behavior in ethanol/water medium was studied. By increasing the medium polarity, carotenoids trend to form J-aggregation, causing a drop in the color intensity of the solution. When added to whey protein aqueous dispersions, rather than a protein-carotenoid bimolecular interaction, the formation of co-aggregates between carotenoids and whey proteins was evidenced by preparative size exclusion chromatography. These results may contribute to the developing functional food products.

Meta-analysis of engineered nanoparticles dynamic aggregation in freshwater-like systems using machine learning techniques

Predictive algorithms for exposure characterization of engineered nanoparticles (ENPs) in the ecosystems are essential to improve the development of robust nano-safety frameworks. Here, machine learning (ML) techniques were utilised for data mining and prediction of the dynamic aggregation transformation process in aqueous environments using case studies of nZnO and nTiO₂. Supervised ML models using input variables of natural organic matter, ionic strength, size, and ENPs concentration showed poor prediction performance based on statistical metric values of root mean square error (RMSE), mean absolute error (MAE), coefficient of determination (R²), and Nash-Sutcliffe efficiency (NSE) for both types of ENP. On the contrary, algorithms developed using model input parameters of zeta potential, pH, and time had good generalisation and high prediction accuracy. Among the five developed ML algorithms, random forest regression, support vector regression, and artificial neural network generated good prediction accuracy for both data sets. Therefore, the use of ML can be valuable in the development of robust nano-safety frameworks to optimise societal benefits, and for proactive long-term ecological protection.

Synthesis of mannan oligosaccharide-sialic acid conjugates and its inhibition on Aβ42 aggregation

In this work, a mannan-oligosaccharide conjugate with sialic acid capable of perturbing Aβ42 aggregation was designed and synthesized. Mannan oligosaccharides with degree polymerization of 3-13 were obtained by stepwise hydrolysis of locust bean gum using β-mannanase and α-galactosidase, named as LBOS. The activated LBOS was further chemically conjugated with sialic acid (Sia, N-acetylneuraminic acid) by fluoro-mercapto chemical coupling to synthesize a conjugate LBOS-Sia, and then phosphorylated to obtain pLBOS-Sia. The successful synthesis of pLBOS-Sia was confirmed by infrared1 chromatography, mass spectrometry, and ¹H NMR. The soluble protein analysis, microscopic observation, thioflavin T-labeling, and circular dichroism spectroscopy revealed that both LBOS-Sia and pLBOS-Sia can inhibit Aβ42 aggregation. MTT assay showed that LBOS-Sia and pLBOS-Sia had no cytotoxicity to BV-2 cells, and could substantially reduce the release of pro-inflammatory factor TNF-α induced by Aβ42 in BV-2 cells, and inhibit the occurrence of neuroinflammation. In future, this novel structure of mannan oligosaccharide-sialic acid conjugate can be potentially used to for the development of glycoconjugates against AD targeting Aβ.

Effects of size and surface charge on the sedimentation of nanoplastics in freshwater

The environmental issues caused by nanoplastics (NPs) are increasingly noticeable. Environmental behavior study of the NPs could provide vital information for their environmental impact assessment. However, associations between NPs' inherent properties and their sedimentation behaviors were seldom investigated. In this study, six types of PSNPs (polystyrene nanoplastics) with different charges (positive and negative) and particle sizes (20-50 nm, 150-190 nm and 220-250 nm) were synthesized, and their sedimentations under different environmental factors, (e.g., pH value, ionic strength (IS), electrolyte type and natural organic matter) were investigated. Results displayed that both particle size and surface charge would affect the sedimentation of PSNPs. The maximum sedimentation ratio of 26.48% was obtained in positive charged PSNPs with size of 20-50 nm, while the minimum sedimentation ratio of 1.02% was obtained in negative charged PSNPs with size of 220-250 nm at pH 7.6. The pH value shift (range of 5-10) triggered negligible changes of sedimentation ratio, the average particle size and the Zeta potential. Small size PSNPs (20-50 nm) showed higher sensitivity to IS, electrolyte type and HA condition than large size PSNPs. At high IS value ( [Formula: see text]  = 30 mM or IS_NaCl = 100 mM), the sedimentation ratios of the PSNPs all increased differently according to their properties, and the sedimentation promoting effect of CaCl₂ was more significant on negative charged PSNPs than positive charged PSNPs. When [Formula: see text] increased from 0.9 to 9 mM, the sedimentation ratios of negative charged PSNPs increased by 0.53%-23.49%, while that of positive charged PSNPs increased by less than 10%. Besides, humic acid (HA) addition (1-10 mg/L) would lead to a stable suspension status for PSNPs in water with different degree and perhaps different mechanism due to their charge characteristics. These results showed new light on influence factor studies of NPs' sedimentation and would be helpful for further knowledge of NPs' environmental behaviors.

Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis

Transthyretin amyloidosis is a progressive systemic disorder that is caused by the amyloid deposition of transthyretin in various organs. Stabilization of the native transthyretin is an effective strategy for the treatment of transthyretin amyloidosis. In this study we demonstrate that the clinically used uricosuric agent benziodarone is highly effective to stabilize the tetrameric structure of transthyretin. An acid-induced aggregation assay showed that benziodarone had strong inhibitory activity similar to that of tafamidis, which is currently used as a therapeutic agent for transthyretin amyloidosis. Moreover, a possible metabolite, 6-hydroxybenziodarone, retained the strong amyloid inhibitory activity of benziodarone. An ex vivo competitive binding assay using a fluorogenic probe showed that benziodarone and 6-hydroxybenziodarone were highly potent for selective binding to transthyretin in human plasma. An X-ray crystal structure analysis revealed that the halogenated hydroxyphenyl ring was located at the entrance of the thyroxine binding channel of transthyretin and that the benzofuran ring was located in the inner channel. These studies suggest that benziodarone and 6-hydroxybenziodarone would potentially be effective against transthyretin amyloidosis.

Picocyanobacteria-A non-negligible group for the export of biomineral silica to ocean depth

Diatoms have long been thought to dominate the marine silicon (Si) cycle, as well as play an important role in the ocean's carbon (C) export, due to density-driven particle sedimentation. Research in the past decade has shed new light on the potential importance of picocyanobacteria to C export, although the sinking mechanism is still unclear. Interestingly, the recent discovery of Si accumulation by picocyanobacteria of the genus Synechococcus has strong implications for the marine Si cycle, which may also have profound influence on the oceanic C export. Understanding the mechanisms of Synechococcus Si accumulation and its ecological effects are therefore critical for addressing wider issues such as Si and C exports by small cells via biological pump. Here, we show that recent advances in process studies indicate that the presence of Si within picocyanobacteria may be a common and universal feature. Subsequently, we generalize four biochemical forms of Si potentially present in picocyanobacterial cells, which are all different from diatomaceous opal-A, and hypothesize that these various structures of Si phases may be several stage products of Si precipitation. At the same time, several aspects of Si dynamics in Synechococcus are also discussed emphatically. In addition, we provide a first estimate of picocyanobacteria Si stock and production for the global ocean, accounting for 12% of the global Si inventory and 45% of the global annual Si production in the surface ocean, respectively. The implication is that picocyanobacteria may exert a significant influence on the marine Si cycle, which is likely to alter our understanding of the long-term control of the oceanic Si cycling by diatoms. Finally, we summarize three possible mechanisms and pathways through which picocyanobacteria-derived Si can be transported to the deep ocean. Altogether, marine picocyanobacteria, despite very small in cell size, are a non-negligible group for the export of biomineral Si to deeper waters and ocean sediments.

Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer's Disease drug candidate

BACKGROUND

Apolipoprotein E (ApoE) ε4 genotype is the most prevalent risk factor for late-onset Alzheimer's Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by the C112R mutation, the molecular mechanism of its proteinopathy is unknown.

METHODS

Here, we reveal the molecular mechanism of ApoE4 aggregation using a combination of experimental and computational techniques, including X-ray crystallography, site-directed mutagenesis, hydrogen-deuterium mass spectrometry (HDX-MS), static light scattering and molecular dynamics simulations. Treatment of ApoE ε3/ε3 and ε4/ε4 cerebral organoids with tramiprosate was used to compare the effect of tramiprosate on ApoE4 aggregation at the cellular level.

RESULTS

We found that C112R substitution in ApoE4 induces long-distance (> 15 Å) conformational changes leading to the formation of a V-shaped dimeric unit that is geometrically different and more aggregation-prone than the ApoE3 structure. AD drug candidate tramiprosate and its metabolite 3-sulfopropanoic acid induce ApoE3-like conformational behavior in ApoE4 and reduce its aggregation propensity. Analysis of ApoE ε4/ε4 cerebral organoids treated with tramiprosate revealed its effect on cholesteryl esters, the storage products of excess cholesterol.

CONCLUSIONS

Our results connect the ApoE4 structure with its aggregation propensity, providing a new druggable target for neurodegeneration and ageing.

Firmly interlocked Janus-type metallic Ni3Sn2S2-carbon nanotube heterostructure suppresses polysulfide dissolution and Sn aggregation

Ternary transition-metal tin chalcogenides, with their diverse compositions, abundant constituents, high theoretical capacities, acceptable working potentials, excellent conductivities, and synergistic active/inactive multi-components, hold promise as anode materials for metal-ion batteries. However, abnormal aggregation of Sn nanocrystals and the shuttling of intermediate polysulfides during electrochemical tests detrimentally affect the reversibility of redox reactions and lead to rapid capacity fading within a limited number of cycles. In this study, we present the development of a robust Janus-type metallic Ni₃Sn₂S₂-carbon nanotube (NSSC) heterostructured anode for Li-ion batteries (LIBs). The synergistic effects of Ni₃Sn₂S₂ nanoparticles and a carbon network successfully generate abundant heterointerfaces with steady chemical bridges, thereby enhancing ion and electron transport, preventing the aggregation of Ni and Sn nanoparticles, mitigating the oxidation and shuttling of polysulfides, facilitating the reforming of Ni₃Sn₂S₂ nanocrystals during delithiation, creating a uniform solid-electrolyte interphase (SEI) layer, protecting the mechanical integrity of electrode materials, and ultimately enabling highly reversible lithium storage. Consequently, the NSSC hybrid exhibits an excellent initial Coulombic efficiency (ICE > 83 %) and superb cyclic performance (1218 mAh/g after 500 cycles at 0.2 A/g and 752 mAh/g after 1050 cycles at 1 A/g). This research provides practical solutions for the intrinsic challenges associated with multi-component alloying and conversion-type electrode materials in next-generation metal-ion batteries.

Adaptive aggregation for longitudinal quantile regression based on censored history process

Most of the studies for longitudinal quantile regression are based on the correct specification. Nevertheless, one specific model can hardly perform precisely under different conditions and assessing which conditions are (approximately) satisfied to determine the optimal one is rather difficult. In the case of the mixed effect model, the misspecification of the fixed effect part will cause a lack of predicting accuracy of random effects, and affect the efficiency of the cumulative function estimator. On the other hand, limited research has focused on incorporating multiple candidate procedures in longitudinal data analysis, which is of current emergency. This paper proposes an exponential aggregation weighting algorithm for longitudinal quantile regression. Based on the secondary smoothing loss function, we establish oracle inequalities for aggregated estimator. The proposed method is applied to evaluate the cumulative τ th quantile function for additive mixed effect model with right-censored history process, and an aggregation-based best linear prediction for random effects is constructed as well. We show that the asymptotic properties are conveniently imposed owing to the smoothing scheme. Simulation studies are carried out to exhibit the rationality, and our method is illustrated to analyze the data set from a multicenter automatic defibrillator implantation trial.

Intertwined synergistic abiotic and biotic degradation of polypropylene pellets in marine mesocosms

The accumulation of plastic waste in the oceans has caused growing concern for its effects on marine life. The interactions of plastics with environmental factors have been linked to fragmentation to micro- and nanoparticles with different properties and consequences, but the mechanism of fragmentation has not been fully understood yet. In this work, we investigate the combined effect of marine communities and ultraviolet (UV) radiation towards the degradation of virgin and artificially weathered polypropylene (PP) pellets after a long-term incubation period in marine mesocosms. The surface chemical alterations and deterioration of the polymer, in conjunction with the attachment and evolution of marine bacterial communities, the development of biofilm and exopolymeric substances (EPS), as well as the colloidal properties (zeta-potential and hydrodynamic diameter) of the mesocosms were studied. The surface area of both types of pellets decreased over time, despite no concrete weight change being observed. Cell growth, EPS production and colloid particle size were correlated to the loss of area. Therefore, we propose that surface area could be effectively monitored, instead of weight loss, as an alternative indicator of polymer degradation in biodegradation experiments. Changes in the chemical structure of the polymer, in addition to the evolution of the biological factors, implied that a complex degradation process alternated between two phases: an abiotic phase, when UV irradiation contributes to the deterioration of the polymer surface layers and a biotic phase, when marine communities degrade the weathered polymer surface to reveal the underlying layer of virgin polymer. Finally, microscopic particles, produced as a result of the decrease in pellet area, promoted the aggregation of colloidal particles. The role and impacts of these colloidal particles in marine ecosystems are yet as unidentified as that of micro- and nano-sized plastic particles and call for further investigation.

Effect of atmospheric pin-to-plate cold plasma on oat protein: Structural, chemical, and foaming characteristics

The impact of novel pin-to-plate atmospheric cold plasma was investigated with input voltage (170 V, 230 V) and exposure time (15 & 30 min) on oat protein by studying structural (FTIR, circular dichroism (CD), UV-vis, Fluorescence), morphological (particle size analysis, SEM, turbidity), chemical (pH, redox potential (ORP), ζ potential, carbonyl, sulfhydryl, surface hydrophobicity), and foaming characteristics. The plasma treatment reduced the pH while increasing the ORP of the dispersions. These ionic environment changes affected the ζ potential and particle size leading to the formation of larger aggregates (170-15; 230-15) and distorted smaller ones (170-30; 230-30) as confirmed by SEM. The FTIR spectra showed reduced intensity at specific amide bands (1600-1700 cm^-1) and also an increase in carbonyl stretching (1743 cm^-1) representing oxidative carbonylation (increase in carbonyl content). Thus, the partial exposure of hydrophobic amino acids increases surface hydrophobicity. The altered secondary structure (rise in α-helix, decrement in β-sheets and turns), and tertiary structures were observed in circular dichroism (CD) and UV absorbance and fluorescence characteristics of proteins respectively. Furthermore, the increase in free sulfhydryl content and disulfide content was highly affected by the plasma treatments due to observed protein unfolding and aggregations. Besides, the increased solubility and reduced surface tension contributed to the improved foaming characteristics. Thus, plasma processing influences protein structure affecting their characteristics and other functionalities.

Novel drug-like fluorenyl derivatives as selective butyrylcholinesterase and β-amyloid inhibitors for the treatment of Alzheimer's disease

Butyrylcholinesterase (BuChE) and amyloid β (Aβ) aggregation remain important biological target and mechanism in the search for effective treatment of Alzheimer's disease. Simultaneous inhibition thereof by the application of multifunctional agents may lead to improvement in terms of symptoms and causes of the disease. Here, we present the rational design, synthesis, biological evaluation and molecular modelling studies of novel series of fluorene-based BuChE and Aβ inhibitors with drug-like characteristics and advantageous Central Nervous System Multiparameter Optimization scores. Among 17 synthesized and tested compounds, we identified 22 as the most potent eqBuChE inhibitor with IC₅₀ of 38 nM and 37.4% of Aβ aggregation inhibition at 10 μM. Based on molecular modelling studies, including molecular dynamics, we determined the binding mode of the compounds within BuChE and explained the differences in the activity of the two enantiomers of compound 22. A novel series of fluorenyl compounds meeting the drug-likeness criteria seems to be a promising starting point for further development as anti-Alzheimer agents.

Raman spectra characterization of size-dependent aggregation and dispersion of polystyrene particles in aquatic environments

Aqueous environments are generally thought to be a source of pooling and re-distribution for both micro-plastics (MPs) and nano-plastics (NPs); however, significantly less data on NPs than MPs have been reported. The occurrence of salts, proteins, and other organic matter may promote or inhibit the aggregation of NPs to form agglomeration particles, making their detection more difficult. In this study, 80 and 500 nm polystyrene nano-plastics (PS-NPs) modified by four different functional groups (PS-Bare, PS-COOH, PS-NH₂, and PS-CHO-500 nm) were selected to mimic the flocculation and/or sedimentation of NPs in salts (NaCl, CaCl₂, and Na₂SO₄) and protein solutions. The results showed that the 80 nm PS-NPs are only colloidal in pure water. All four strong electrolyte solutions that were tested significantly promoted the aggregation of PS-NPs, including those that were protein-coated. In addition, 500 nm PS-CHO did not flocculate but gradually settled into sedimentation. Therefore, Raman spectrometry can be used to analyze assembled PS-NPs, but is not suitable for analyzing normal PS-NPs. By combining fractal morphology, this study provides insight into the comprehensive analysis of PS-NPs in water solutions, including the digestion of biological samples.

Reciprocal effects of NOM and solution electrolyte ions on aggregation of ferrihydrite nanoparticles

The effects of natural organic matter (NOM) types and electrolyte ions are crucial to the aggregation of ferrihydrite nanoparticles (Fh NPs) in the environment. Dynamic light scattering (DLS) was employed for the aggregation kinetics of Fh NPs (10 mg/L as Fe) in the present study. The critical coagulation concentration (CCC) values of Fh NPs aggregation in NaCl were obtained in the presence of 15 mg C/L NOM as SRHA (857.4 mM) > PPHA (752.3 mM) > SRFA > (420.1 mM) > ESHA (141.0 mM) > NOM-free (125.3 mM), indicating Fh NPs aggregation was inhibited as the above order. Comparatively in CaCl₂, the CCC values were measured in ESHA (0.9 mM), PPHA (2.7 mM), SRFA (3.6 mM), SRHA (5.9 mM), NOM-free (76.6 mM), implying NPs aggregation was enhanced following the order of ESHA > PPHA > SRFA > SRHA. To investigate the dominant mechanisms, the aggregation of Fh NPs was comprehensively studied under the effects of NOM types, concentrations (0-15 mg C/L) and electrolyte ions (NaCl/CaCl₂ beyond CCC). In NaCl/CaCl₂, the low concentration of NOM (<7.5 mg C/L) could accelerate NPs aggregation mainly due to patch-charge attraction. When NOM concentration was high (>7.5 mg C/L), the inhibition effect on NPs aggregation occurred in NaCl due to steric repulsion, whereas the enhancement effect in CaCl₂ of aggregation was dominated by the bridging effect. The results indicated that the effects of NOM types, concentration and electrolyte ions should be carefully considered for the environmental behavior of NPs.

Investigation of the role of cell hydrophobicity and EPS production in the aggregation of the marine diatom Cylindrotheca closterium under hypo-saline conditions

Aggregation of diatoms is of global importance to understand settling of particulate organic carbon in aquatic systems. In this study, we investigate the aggregation of the marine diatom Cylindrotheca closterium during the exponential growth phase under hypo-saline conditions. The results of the flocculation/flotation experiments show that the aggregation of the diatom depends on the salinity. In favorable growth conditions for marine diatoms (salinity of 35), the highest aggregation is achieved. To explain these observations, we used a surface approach combining atomic force microscopy (AFM) and electrochemical methods to characterize both the cell surface properties and the structure of the extracellular polymeric substances (EPS) cell produce, and to quantify the amount of surface-active organic matter released. At a salinity of 35, the results showed that diatoms are soft, hydrophobic and release only small amounts of EPS organized into individual short fibrils. In contrast, diatoms adapt to a salinity of 5 by becoming much stiffer and more hydrophilic, producing larger amounts of EPS that structurally form an EPS network. Both adaptation responses of diatoms, the hydrophobic properties of diatoms and the release of EPS, appear to play an important role in diatom aggregation and explain the behavior observed at different salinities. This biophysical study provides important evidence allowing to get a deep insight into diatom interactions at the nanoscale, which may contribute to a better understanding of large-scale aggregation phenomena in aquatic systems.

A novel fluorophore with multichromic effect and its application in LED light for the volatile vapor detection

Successfully designed and synthesized diaryl maleimide DAM, and their structure was confirmed by mass spectroscopy and NMR techniques. They investigated their photophysical properties, such as solvatochromic and the aggregation effect of AIE/ACQ on the water/DMF ratio, and other studies of solid-state mechanofluorochromic, such as grinding, exposure to solvent fumes, hydrostatic pressures, and vapochromic. Interestingly, the solvent methods gave very similar results in both the dissolving phase and the vapor phase. For the solution state from hexane to CH₂Cl_2, a greenish-yellow to orange emission was observed. From hexane to dichloromethane, naked-eye colorimetric changes (from yellow to orange in a solid state) were observed. Very interesting results were obtained, the yellow solid was ground for 1 min, it turned into an orange color, and its wavelengths were red-shifted in both absorption and emission. Subsequently, the ground sample was exposed to diethyl ether vapors, which returned to the original green-yellow emission and absorption. The applied hydrostatic pressures (0-4Mpa) in DAM gave excellent red-shifted emission, and then their hydrostatic pressures were increased to 4-16 Mpa, and the red-shifted emission gradually decreased.

Islet Amyloid Polypeptide Triggers α-synuclein Pathology in Parkinson's Disease

Pathologic aggregation and prion-like propagation of α-synuclein (α-syn) are the hallmarks of Parkinson's disease (PD). Emerging evidence shows that type 2 diabetes mellitus (T2DM) is a risk factor for PD. Interestingly, T2DM is characterized by the amyloid deposition of islet amyloid polypeptide (IAPP) in the pancreas. Although T2DM and PD share pathological similarities, the underlying molecular mechanisms bridging these two diseases remain unknown. Here, we report that IAPP co-deposits with α-syn in the brains of PD patients. IAPP interacts with α-syn and accelerates its aggregation. In addition, the IAPP-seeded α-syn fibrils show enhanced seeding activity and neurotoxicity compared with pure α-syn fibrils in vitro and in vivo. Strikingly, intravenous injection of IAPP fibrils into α-syn A53T transgenic mice or human SNCA transgenic mice accelerated the aggregation of α-syn and PD-like motor deficits. Taken together, these findings support that IAPP acts as a trigger of α-syn pathology in PD, and provide a mechanistic explanation for the increased risk and faster progression of PD in patients with T2DM.

Aggregation kinetics and stability of biodegradable nanoplastics in aquatic environments: Effects of UV-weathering and proteins

Plastic pollution caused by conventional plastics has promoted the development and use of biodegradable plastics. However, biodegradable plastics do not degrade readily in water; instead, they can generate micro- and nanoplastics. Compared to microplastics, nanoplastics are more likely to cause negative impacts to the aquatic environment due to their smaller size. The impacts of biodegradable nanoplastics highly depend on their aggregation behavior and colloidal stability, which still remain unknown. Here, we studied the aggregation kinetics of biodegradable nanoplastics made of polybutylene adipate co-terephthalate (PBAT) in NaCl and CaCl₂ solutions as well as in natural waters before and after weathering. We further studied the effect of proteins on aggregation kinetics with both negative-charged bovine serum albumin (BSA) and positive-charged lysozyme (LSZ). For pristine PBAT nanoplastics (before weathering), Ca^2＋ destabilized nanoplastic suspensions more aggressively than Na⁺, with the critical coagulation concentration being 20 mM in CaCl₂ vs 325 mM in NaCl. Both BSA and LSZ promoted the aggregation of pristine PBAT nanoplastics, and LSZ showed a more pronounced effect. However, no aggregation was observed for weathered PBAT nanoplastics under most experimental conditions. Further stability tests demonstrated that pristine PBAT nanoplastics aggregated substantially in seawater, but not in freshwater, and only slightly in soil pore water; while weathered PBAT nanoplastics remained stable in all natural waters. These results suggest that biodegradable nanoplastics, especially weathered biodegradable nanoplastics, are highly stable in the aquatic environment, even in the marine environment.

Tryptophan capped gold-silver bimetallic nanoclusters-based turn-off fluorescence sensor for the determination of histamine

Tryptophan capped gold-silver bimetallic nanoclusters (Trp-Au/Ag BNCs) based turn-off fluorescence sensor has been developed for the simple and rapid determination of histamine. Sensor parameters such as the effect of solvent, irradiation time etc. were optimized and further studies were done using these results. Fluorescence quenching of BNCs happens with the incremental addition of histamine. This might be due to the aggregation of BNCs induced by the electrostatic force of attraction between the negatively charged BNCs and amino functional groups of histamine. The sensor showed good sensitivity for the determination of histamine with a linear range of 8.5 × 10^-5 M to 4.0 × 10^-6 M and a limit of detection (LOD) of 9.0 × 10^-7 M. Practical utility of the proposed sensor has been proved through spike recovery analysis in synthetic physiological fluids.

Peroxyl radicals modify 6-phosphogluconolactonase from Escherichia coli via oxidation of specific amino acids and aggregation which inhibits enzyme activity

6-phosphogluconolactonase (6PGL) catalyzes the second reaction of the pentose phosphate pathway (PPP) converting 6-phosphogluconolactone to 6-phosphogluconate. The PPP is critical to the generation of NADPH and metabolic intermediates, but some of its components are susceptible to oxidative inactivation. Previous studies have characterized damage to the first (glucose-6-phosphate dehydrogenase) and third (6-phosphogluconate dehydrogenase) enzymes of the pathway, but no data are available for 6PGL. This knowledge gap is addressed here. Oxidation of Escherichia coli 6PGL by peroxyl radicals (ROO^•, from AAPH (2,2'-azobis(2-methylpropionamidine) dihydrochloride) was examined using SDS-PAGE, amino acid consumption, liquid chromatography with mass detection (LC-MS), protein carbonyl formation and computational methods. NADPH generation was assessed using mixtures all three enzymes of the oxidative phase of the PPP. Incubation of 6PGL with 10 or 100 mM AAPH resulted in protein aggregation mostly due to reducible (disulfide) bonds. High fluxes of ROO^• induced consumption of Cys, Met and Trp, with the Cys oxidation rationalizing the aggregate formation. Low levels of carbonyls were detected, while LC-MS analyses provided evidence for oxidation of selected Trp and Met residues (Met1, Trp18, Met41, Trp203, Met220 and Met221). ROO^• elicited little loss of enzymatic activity of monomeric 6PGL, but the aggregates showed diminished NADPH generation. This is consistent with in silico analyses that indicate that the modified Trp and Met are far from the 6-phosphogluconolactone binding site and the catalytic dyad (His130 and Arg179). Together these data indicate that monomeric 6PGL is a robust enzyme towards oxidative inactivation by ROO^• and when compared to other PPP enzymes.

N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates

BACKGROUND

Argonaute proteins play a central role in RNA silencing by forming protein-small RNA complexes responsible for the silencing process. While most Argonaute proteins have a short N-terminal region, Argonaute2 in Drosophila melanogaster (DmAgo2) harbors a long and unique N-terminal region. Previous in vitro biochemical studies have shown that the loss of this region does not impair the RNA silencing activity of the complex. However, an N-terminal mutant of Drosophila melanogaster has demonstrated abnormal RNA silencing activity. To explore the causes of this discrepancy between in vitro and in vivo studies, we investigated the biophysical properties of the region. The N-terminal region is highly rich in glutamine and glycine residues, which is a well-known property for prion-like domains, a subclass of amyloid-forming peptides. Therefore, the possibility of the N-terminal region functioning as an amyloid was tested.

RESULTS

Our in silico and biochemical assays demonstrated that the N-terminal region exhibits amyloid-specific properties. The region indeed formed aggregates that were not dissociated even in the presence of sodium dodecyl sulfate. Also, the aggregates enhanced the fluorescence intensity of thioflavin-T, an amyloid detection reagent. The kinetics of the aggregation followed that of typical amyloid formation exhibiting self-propagating activity. Furthermore, we directly visualized the aggregation process of the N-terminal region under fluorescence microscopy and found that the aggregations took fractal or fibril shapes. Together, the results indicate that the N-terminal region can form amyloid-like aggregates.

CONCLUSIONS

Many other amyloid-forming peptides have been reported to modulate the function of proteins through their aggregation. Therefore, our findings raise the possibility that aggregation of the N-terminal region regulates the RNA silencing activity of DmAgo2.

Five-mer peptides prevent short-term spatial memory deficits in Aβ25-35-induced Alzheimer's model mouse by suppressing Aβ25-35 aggregation and resolving its aggregate form

BACKGROUND

The development of drugs for Alzheimer's disease (AD), which is related to the misfolding and aggregation of amyloid-β (Aβ), is high in demand due to the growing number of AD patients. In this study, we screened 22 kinds of 5-mer synthetic peptides derived from the Box A region of Tob1 protein to find a peptide effective against Aβ aggregation.

METHODS

A Thioflavin T (ThT) assay was performed to evaluate aggregation and screen aggregation inhibitors. Male ICR mice (6 weeks old) were administered saline, 9 nmol Aβ25-35, or a mixture of 9 nmol Aβ25-35 and 9 nmol GSGFK in the right lateral ventricle. Short-term spatial memory was assessed through Y-maze. Microglia cells (BV-)2 cells were plated on 24-well plates (4 × 10⁴ cells/well) and incubated for 48 h, and then, the cells were treated with 0.01, 0.05, 0.1, 0.2, or 0.5 mM GSGFK. After incubation for 24 h, bead uptake was evaluated using a laser confocal microscope and Cytation 5.

RESULTS

We found two kinds of peptides, GSGNR and GSGFK, that were not only suppressed by aggregation of Aβ25-35 but also resolved the aggregated Aβ25-35. Results obtained from the Y-maze test on an Aβ25-35-induced AD model mouse indicated that GSGFK prevents the deficits in short-term memory induced by Aβ25-35. The effect of GSGFK on phagocytosis in BV-2 cells proved that GSGFK activates the phagocytic ability of microglia.

CONCLUSIONS

In conclusion, 5-mer peptides prevent short-term memory deficit in Aβ25-35 induced AD model mouse by reducing the aggregated Aβ25-35. They may also upregulate the phagocytic ability of microglia, which makes 5-mer peptides suitable candidates as therapeutic drugs against AD.

Aggregation in efficiency and productivity analysis: a brief review with new insights and justifications for constant returns to scale

The main goal of this paper is to clarify a few important aspects about the aggregation issues in efficiency and productivity analysis. By doing so we also sketch a brief historical map on how the area of aggregation in efficiency and productivity analysis has developed to where it is now and its connection to some classic studies in economic theory. As a result, this paper also serves as a tribute to the great scholars I was lucky to learn from, Rolf Färe and Shawna Grosskopf, who made a profound impact on research in economics in general and the topic of aggregation in productivity and efficiency analysis in particular.