Cerebral organoids with chromosome 21 trisomy secrete Alzheimer's disease-related soluble aggregates detectable by single-molecule-fluorescence and super-resolution microscopy.

Understanding the role of small, soluble aggregates of beta-amyloid (Aß) and tau in Alzheimer's disease (AD) is of great importance for the rational design of preventative therapies. Here we report a set of methods for the detection, quantification, and characterisation of soluble aggregates in conditioned media of cerebral organoids derived from human iPSCs with trisomy 21, thus containing an extra copy of the amyloid precursor protein (APP) gene. We detected soluble beta-amyloid (Aß) and tau aggregates secreted by cerebral organoids from both control and the isogenic trisomy 21 (T21) genotype. We developed a novel method to normalise measurements to the number of live neurons within organoid-conditioned media based on glucose consumption. Thus normalised, T21 organoids produced 2.5-fold more Aß aggregates with a higher proportion of larger (300-2000 nm2) and more fibrillary-shaped aggregates than controls, along with 1.3-fold more soluble phosphorylated tau (pTau) aggregates, increased inflammasome ASC-specks, and a higher level of oxidative stress inducing thioredoxin-interacting protein (TXNIP). Importantly, all this was detectable prior to the appearance of histological amyloid plaques or intraneuronal tau-pathology in organoid slices, demonstrating the feasibility to model the initial pathogenic mechanisms for AD in-vitro using cells from live genetically pre-disposed donors before the onset of clinical disease. Then, using different iPSC clones generated from the same donor at different times in two independent experiments, we tested the reproducibility of findings in organoids. While there were differences in rates of disease progression between the experiments, the disease mechanisms were conserved. Overall, our results show that it is possible to non-invasively follow the development of pathology in organoid models of AD over time, by monitoring changes in the aggregates and proteins in the conditioned media, and open possibilities to study the time-course of the key pathogenic processes taking place.

Imaging Protein Aggregates in Parkinson's Disease Serum Using Aptamer-Assisted Single-Molecule Pull-Down.

The formation of soluble α-synuclein (α-syn) and amyloid-ß (Aß) aggregates is associated with the development of Parkinson's disease (PD). Current methods mainly focus on the measurement of the aggregate concentration and are unable to determine their heterogeneous size and shape, which potentially also change during the development of PD due to increased protein aggregation. In this work, we introduce aptamer-assisted single-molecule pull-down (APSiMPull) combined with super-resolution fluorescence imaging of α-syn and Aß aggregates in human serum from early PD patients and age-matched controls. Our diffraction-limited imaging results indicate that the proportion of α-syn aggregates (α-syn/(α-syn+Aß)) can be used to distinguish PD and control groups with an area under the curve (AUC) of 0.85. Further, super resolution fluorescence imaging reveals that PD serums have a higher portion of larger and rounder α-syn aggregates than controls. Little difference was observed for Aß aggregates. Combining these two metrics, we constructed a new biomarker and achieved an AUC of 0.90. The combination of the aggregate number and morphology provides a new approach to early PD diagnosis.

Imaging protein aggregates in the serum and cerebrospinal fluid in Parkinson's disease.

Aggregation of α-synuclein plays a key role in the development of Parkinson's disease. Soluble aggregates are present not only within human brain but also the CSF and blood. Characterizing the aggregates present in these biofluids may provide insights into disease mechanisms and also have potential for aiding diagnosis. We used two optical single-molecule imaging methods called aptamer DNA-PAINT and single-aggregate confocal fluorescence, together with high-resolution atomic force microscopy for specific detection and characterization of individual aggregates with intermolecular ß-sheet structure, present in the CSF and serum of 15 early stage Parkinson's disease patients compared to 10 healthy age-matched controls. We found aggregates ranging in size from 20 nm to 200 nm, in both CSF and serum. There was a difference in aggregate size distribution between Parkinson's disease and control groups with a significantly increased number of larger aggregates (longer than 150 nm) in the serum of patients with Parkinson's disease. To determine the chemical composition of the aggregates, we performed aptamer DNA-PAINT on serum following α-synuclein and amyloid-ß immunodepletion in an independent cohort of 11 patients with early stage Parkinson's disease and 10 control subjects. ß-Sheet aggregates in the serum of Parkinson's disease patients were found to consist of, on average, 50% α-synuclein and 50% amyloid-ß in contrast to 30% α-synuclein and 70% amyloid-ß in control serum [the differences in the proportion of these aggregates were statistically significant between diseased and control groups (P = 1.7 × 10-5 for each species)]. The ratio of the number of ß-sheet α-synuclein aggregates to ß-sheet amyloid-ß aggregates in serum extracted using our super-resolution method discriminated Parkinson's disease cases from controls with an accuracy of 98.2% (AUC = 98.2%, P = 4.3 × 10-5). Our data suggest that studying the protein aggregates present in serum can provide information about the disruption of protein homeostasis occurring in Parkinson's disease and warrants further investigation as a potential biomarker of disease.

PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning.

MOTIVATION: Peptide is a promising candidate for therapeutic and diagnostic development due to its great physiological versatility and structural simplicity. Thus, identifying therapeutic peptides and investigating their properties are fundamentally important. As an inexpensive and fast approach, machine learning-based predictors have shown their strength in therapeutic peptide identification due to excellences in massive data processing. To date, no reported therapeutic peptide predictor can perform high-quality generic prediction and informative physicochemical properties (IPPs) identification simultaneously. RESULTS: In this work, Physicochemical Property-based Therapeutic Peptide Predictor (PPTPP), a Random Forest-based prediction method was presented to address this issue. A novel feature encoding and learning scheme were initiated to produce and rank physicochemical property-related features. Besides being capable of predicting multiple therapeutics peptides with high comparability to established predictors, the presented method is also able to identify peptides' informative IPP. Results presented in this work not only illustrated the soundness of its working capacity but also demonstrated its potential for investigating other therapeutic peptides. AVAILABILITY AND IMPLEMENTATION: https://github.com/YPZ858/PPTPP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Determination of the residue dynamics and dietary risk of thiamethoxam and its metabolite clothianidin in citrus and soil by LC-MS/MS.

A modified quick, easy, cheap, effective, rugged and safe (QuEChERS) method was developed for the determination of thiamethoxam and its metabolite clothianidin in citrus (including the whole citrus, peel and pulp) and soil samples by liquid chromatography-tandem mass spectrometry. The sample was extracted with acetonitrile and purified with octadecylsilane. The detection limits of both compounds were 0.0001-0.0002 mg kg-1, while the limit of quantification of thiamethoxam was 0.002 mg kg-1 and the limit of quantitation of metabolites was 0.001 mg kg-1. The recovery was 70.37%-109.76%, with inter-day relative standard deviations (RSD) (n = 15) values ≤9.46% for the two compounds in the four matrices. The degradation curve of thiamethoxam in whole citrus and soil was plotted using the first-order kinetic model. The half-life of the whole citrus was 1.9-6.2 days, and the half-life of the soil was 3.9-4.2 days. The terminal residue of thiamethoxam (the sum of thiamethoxam and clothianidin, expressed as thiamethoxam) was found to be concentrated on the peel. The final residual amount of thiamethoxam in the edible portion (pulp) was less than 0.061 mg kg-1. The risk quotient values were all below 1, indicating that thiamethoxam as a citrus insecticide does not pose a health risk to humans at the recommended dosage.

Evaluation of photolysis and hydrolysis of pyraclostrobin in aqueous solutions and its degradation products in paddy water.

This study evaluated the hydrolysis and photolysis kinetics of pyraclostrobin in an aqueous solution using ultra-high-performance liquid chromatography-photodiode array detection and identified the resulting metabolites of pyraclostrobin by hydrolysis and photolysis in paddy water using high-resolution mass spectrometry coupled with liquid chromatography. The effect of solution pH, metal ions and surfactants on the hydrolysis of pyraclostrobin was explored. The hydrolysis half-lives of pyraclostrobin were 23.1-115.5 days and were stable in buffer solution at pH 5.0. The degradation rate of pyraclostrobin in an aqueous solution under sunlight was slower than that under UV photolysis reaction. The half-lives of pyraclostrobin in a buffer solution at pH 5.0, 7.0, 9.0 and in paddy water were less than 12 h under the two light irradiation types. The metabolites of the two processes were identified and compared to further understand the mechanisms underlying hydrolysis and photolysis of pyraclostrobin in natural water. The extracted ions obtained from paddy water were automatically annotated by Compound Discoverer software with manual confirmation of their fragments. Two metabolites were detected and identified in the pyraclostrobin hydrolysis, whereas three metabolites were detected and identified in the photolysis in paddy water.

Degradation dynamics, residues and risk assessment of Dufulin enantiomers in corn plants and corn by LC/MS/MS.

The degradation dynamics and terminal residues of dufulin enantiomers were investigated in two typical corn plants. A convenient and precise chiral method by high-performance liquid chromatography coupled with tandem triple quadrupole mass spectrometry (HPLC/MS/MS) using a Chiralpak IC column was developed and validated for measuring dufulin enantiomers in corn plants and corn. The two enantiomers of dufulin quickly dissipated in the corn plant, and no noticeable stereoselectivity was observed during degradation or in the final residues. After 30% rac-dufulin wettable powder with a 1- to 1.5-fold dose of the recommended value was sprayed two to three times on corn plants, the residue levels of S-(+)-dufulin and R-(-)-dufulin in corn from both sites were lower than or equal to 0.0520 mg kg-1 on days 7, 14 and 21 after the last application. The dietary risk assessment indicated that dufulin did not exhibit obvious dietary health risks in corn samples when good agricultural practices were implemented. The findings from this study may be used to better understand the chiral profiles of dufulin in the environment and the effect of dufulin residues in corn on health.

Dissipation and translocation of saisenxin in tobacco and soil under conventional field and controlled laboratory conditions.

The aim of this investigation was to investigate the fate and translocation characteristics of saisenxin (SSX), a novel organic zinc fungicide, in the environment and tobacco plants under conventional field and laboratory conditions. A rapid and sensitive analytical technique based on high-performance liquid chromatography was used for determination of SSX, in soil samples and tobacco leaf, stem and root samples. The method had satisfactiry linearity (R2 = 0.9999) and the limits of detection and of quantitation of the target compound were 0.06 and 0.20 mg kg-1, respectively. The average recoveries were in the range of 89.74-94.24% in soil, leaf, stem and root samples, with relative standard deviations of <8%. For conventional field trials, the half-life (t1/2) of SSX was 5.9-6.5 days in soil and 4.8-5.3 days in tobacco leaves; the corresponding values under controlled laboratory conditions were extended to 7.1 and 7.6 days. The translocation factor (TF) values were in the range of 0-2.25 and 0-0.25 for foliage and root irrigation treatments, respectively. The TFs of SSX in tobacco indicated that tobacco had a high ability to transfer SSX upward.

Single-molecule characterization of salivary protein aggregates from Parkinson's disease patients: a pilot study.

Saliva is a convenient and accessible biofluid that has potential as a future diagnostic tool for Parkinson's disease. Candidate diagnostic tests for Parkinson's disease to date have predominantly focused on measurements of α-synuclein in CSF, but there is a need for accurate tests utilizing more easily accessible sample types. Prior studies utilizing saliva have used bulk measurements of salivary α-synuclein to provide diagnostic insight. Aggregate structure may influence the contribution of α-synuclein to disease pathology. Single-molecule approaches can characterize the structure of individual aggregates present in the biofluid and may, therefore, provide greater insight than bulk measurements. We have employed an antibody-based single-molecule pulldown assay to quantify salivary α-synuclein and amyloid-ß peptide aggregate numbers and subsequently super-resolved captured aggregates using direct Stochastic Optical Reconstruction Microscopy to describe their morphological features. We show that the salivary α-synuclein aggregate/amyloid-ß aggregate ratio is increased almost 2-fold in patients with Parkinson's disease (n = 20) compared with controls (n = 20, P < 0.05). Morphological information also provides insight, with saliva from patients with Parkinson's disease containing a greater proportion of larger and more fibrillar amyloid-ß aggregates than control saliva (P < 0.05). Furthermore, the combination of count and morphology data provides greater diagnostic value than either measure alone, distinguishing between patients with Parkinson's disease (n = 17) and controls (n = 18) with a high degree of accuracy (area under the curve = 0.87, P < 0.001) and a larger dynamic range. We, therefore, demonstrate for the first time the application of highly sensitive single-molecule imaging techniques to saliva. In addition, we show that aggregates present within saliva retain relevant structural information, further expanding the potential utility of saliva-based diagnostic methods.

Improved Imaging Surface for Quantitative Single-Molecule Microscopy.

Preventing nonspecific binding is essential for sensitive surface-based quantitative single-molecule microscopy. Here we report a much-simplified RainX-F127 (RF-127) surface with improved passivation. This surface achieves up to 100-fold less nonspecific binding from protein aggregates compared to commonly used polyethylene glycol (PEG) surfaces. The method is compatible with common single-molecule techniques including single-molecule pull-down (SiMPull), super-resolution imaging, antibody-binding screening and single exosome visualization. This method is also able to specifically detect alpha-synuclein (α-syn) and tau aggregates from a wide range of biofluids including human serum, brain extracts, cerebrospinal fluid (CSF) and saliva. The simplicity of this method further allows the functionalization of microplates for robot-assisted high-throughput single-molecule experiments. Overall, this simple but improved surface offers a versatile platform for quantitative single-molecule microscopy without the need for specialized equipment or personnel.

Co-aggregation with Apolipoprotein E modulates the function of Amyloid-ß in Alzheimer's disease.

Which isoforms of apolipoprotein E (apoE) we inherit determine our risk of developing late-onset Alzheimer's Disease (AD), but the mechanism underlying this link is poorly understood. In particular, the relevance of direct interactions between apoE and amyloid-ß (Aß) remains controversial. Here, single-molecule imaging shows that all isoforms of apoE associate with Aß in the early stages of aggregation and then fall away as fibrillation happens. ApoE-Aß co-aggregates account for ~50% of the mass of diffusible Aß aggregates detected in the frontal cortices of homozygotes with the higher-risk APOE4 gene. We show how dynamic interactions between apoE and Aß tune disease-related functions of Aß aggregates throughout the course of aggregation. Our results connect inherited APOE genotype with the risk of developing AD by demonstrating how, in an isoform- and lipidation-specific way, apoE modulates the aggregation, clearance and toxicity of Aß. Selectively removing non-lipidated apoE4-Aß co-aggregates enhances clearance of toxic Aß by glial cells, and reduces secretion of inflammatory markers and membrane damage, demonstrating a clear path to AD therapeutics.

An antibody scanning method for the detection of α-synuclein oligomers in the serum of Parkinson's disease patients.

Misfolded α-synuclein oligomers are closely implicated in the pathology of Parkinson's disease and related synucleinopathies. The elusive nature of these aberrant assemblies makes it challenging to develop quantitative methods to detect them and modify their behavior. Existing detection methods use antibodies to bind α-synuclein aggregates in biofluids, although it remains challenging to raise antibodies against α-synuclein oligomers. To address this problem, we used an antibody scanning approach in which we designed a panel of 9 single-domain epitope-specific antibodies against α-synuclein. We screened these antibodies for their ability to inhibit the aggregation process of α-synuclein, finding that they affected the generation of α-synuclein oligomers to different extents. We then used these antibodies to investigate the size distribution and morphology of soluble α-synuclein aggregates in serum and cerebrospinal fluid samples from Parkinson's disease patients. Our results indicate that the approach that we present offers a promising route for the development of antibodies to characterize soluble α-synuclein aggregates in biofluids.

Small soluble α-synuclein aggregates are the toxic species in Parkinson's disease.

Soluble α-synuclein aggregates varying in size, structure, and morphology have been closely linked to neuronal death in Parkinson's disease. However, the heterogeneity of different co-existing aggregate species makes it hard to isolate and study their individual toxic properties. Here, we show a reliable non-perturbative method to separate a heterogeneous mixture of protein aggregates by size. We find that aggregates of wild-type α-synuclein smaller than 200 nm in length, formed during an in vitro aggregation reaction, cause inflammation and permeabilization of single-liposome membranes and that larger aggregates are less toxic. Studying soluble aggregates extracted from post-mortem human brains also reveals that these aggregates are similar in size and structure to the smaller aggregates formed in aggregation reactions in the test tube. Furthermore, we find that the soluble aggregates present in Parkinson's disease brains are smaller, largely less than 100 nm, and more inflammatory compared to the larger aggregates present in control brains. This study suggests that the small non-fibrillar α-synuclein aggregates are the critical species driving neuroinflammation and disease progression.

A Comparative Study of High-Contrast Fluorescence Lifetime Probes for Imaging Amyloid in Tissue.

Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium derivatives, prominently Thioflavin T, have been the state-of-the-art fluorescent probes for amyloid aggregates, but their optical, structural, and binding properties typically limit them to in vitro applications. This study compares the use of novel uncharged derivative, PAP_1, with parent Thioflavin T as a fluorescence lifetime imaging probe. This is applied specifically to imaging recombinant α-synuclein aggregates doped into brain tissue. Despite the 100-fold lower brightness of PAP_1 compared to that of Thioflavin T, PAP_1 binds to α-synuclein aggregates with an affinity several orders of magnitude greater than Thioflavin T; thus, we observe a specific decrease in the fluorescence lifetime of PAP_1 bound to α-synuclein aggregates, resulting in a separation of >1.4 standard deviations between PAP_1-stained brain tissue background and α-synuclein aggregates that is not observed with Thioflavin T. This enables contrast between highly fluorescent background tissue and amyloid fibrils that is attributed to the greater affinity of PAP_1 for α-synuclein aggregates, avoiding the substantial off-target staining observed with Thioflavin T.

Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer's disease.

Protein aggregation likely plays a key role in the initiation and spreading of Alzheimer's disease pathology through the brain. Soluble aggregates of amyloid beta are believed to play a key role in this process. However, the aggregates present in humans are still poorly characterized due to a lack of suitable methods required for characterizing the low concentration of heterogeneous aggregates present. We have used a variety of biophysical methods to characterize the aggregates present in human Alzheimer's disease brains at Braak stage III. We find soluble amyloid beta-containing aggregates in all regions of the brain up to 200 nm in length, capable of causing an inflammatory response. Rather than aggregates spreading through the brain as disease progresses, it appears that aggregation occurs all over the brain and that different brain regions are at earlier or later stages of the same process, with the later stages causing increased inflammation.