Enrichment Method Research Articles

REMEMProt: a resource of membrane-enriched proteome profiles, their disease associations, and biomarker status.

The differential expression of plasma membrane proteins is integrally analyzed for their diagnosis, prognosis, and therapeutic applications in diverse clinical manifestations. Necessarily, distinct membrane protein enrichment methods and mass spectrometry platforms are employed for their global and relative quantitation. First of its kind to explore, we compiled membrane-associated proteomes in human and mouse systems into a database named, Resource of Experimental Membrane-Enriched Mass spectrometry-derived Proteome (REMEMProt). It currently hosts 14,626 proteins (9,507 proteins in Homo sapiens; 5,119 proteins in Mus musculus) with information on their membrane-protein enrichment methods, experimental/physiological context of detection in cells or tissues, transmembrane domain analysis, and their current attribution as biomarkers. Based on these annotations and the transmembrane domain analysis in proteins or their binary/complex protein-protein interactors, REMEMProt facilitates the assessment of the plasma membrane localization potential of proteins through batch query. A cross-study enrichment analysis platform is enabled in REMEMProt for comparative analysis of proteomes using novel/modified membrane enrichment methods and evaluation of methods for targeted enrichment of membrane proteins. REMEMProt data are made freely accessible to explore and download at https://rememprot.ciods.in/.

Towards elevated perfluorooctanoic acid (PFOA) enrichment in water: Sequential liquid-liquid extraction pretreatment for ion chromatography detection

The widespread detection of perfluorooctanoic acid (PFOA) in the environment has raised significant concerns. The standard PFOA analytical method relies on expensive solid-phase extraction (SPE) and liquid chromatography tandem mass spectrometry (LC-MS/MS) instruments, making routine use prohibitive. We herein proposed a cost-effective yet novel enrichment method for determining PFOA at ng L−1 level. This method entailed a two-step sample preparation process: firstly, PFOA was extracted and enriched using a forward-extraction under acidic conditions, followed by a backward-extraction and enrichment step utilizing alkaline water. The enriched samples were subsequently subjected to a common ion chromatography (IC). Results reveal that maintaining a forward-extraction pH below its pKa value (2.8) is essential, as protonated PFOA proves effective in enhancing the enrichment factor (EF). The challenge lied in driving PFOA from forward-extractant to aqueous backward-extractant due to the decreased hydrophobicity of deprotonated PFOA (log Kow2 = 1.0). In addition, we found that evaporating forward-extractant with alkaline backward-extractant (containing 5% methanol) reduced potential analytical uncertainties associated with PFOA evaporation and sorption. Under optimal conditions, the method achieved a detection limit of 9.2 ng L−1 and an impressive EF value of 719. Comparison with SPE-LC-MS/MS confirmed the proposed method as a promising alternative for PFOA determination. Although initially targeted for PFOA, the novel methodology is likely applicable to preconcentration of other poly-fluoroalkyl substances.

A novel enrichment and sensitive method for rapid determination of 4 sulfonamide antibiotics residues in fish

Sulfonamide antibiotics with superior performance are widely used in aquaculture. However, the residues of sulfonamide antibiotics in aquatic products may pose a threat to human health. In this work, a novel type of magnetic molecularly imprinted polymer (mMIP) was synthesized and coupled with ultra-high performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) for the selective separation and determination of 4 sulfonamide antibiotics residues in tilapia. The structure and adsorption properties of the polymers were characterized and evaluated. The key mMIP variables were investigated to determine the optimal magnetic solid phase extraction conditions. Results showed that the mMIPs had saturated adsorption capacities of 137.4, 78.7, 65.2, and 58.4 mg/g for trimethoprim, sulfadiazine, sulfamethazine, and sulfamethoxazole, respectively. Under optimized conditions, the linear range of the method for the detection of the 4 sulfonamides was 0.1–100 ng mL−1 (R > 0.991), the detection limit was 0.015 μg kg−1 (S/N = 3), the recovery rate was 78.6–101%, and the relative standard deviation (RSD%) was 4.2–7.8%. This new rapid and ultra-sensitive pretreatment method was successfully applied to the monitoring of trace sulfonamide antibiotics residues in fish samples.

Development of a decision support tool to compare diagnostic strategies for establishing the herd status for infectious diseases: An example with Salmonella Dublin infection in dairies

The diagnosis of infectious diseases at herd level can be challenging as different stakeholders can have conflicting priorities. The current study proposes a “proof of concept” of an approach that considers a reasonable number of criteria to rank plausible diagnostic strategies using multi-criteria decision analysis (MCDA) methods. The example of Salmonella Dublin diagnostic in Québec dairy herds is presented according to two epidemiological contexts: (i) in herds with no history of S. Dublin infection and absence of clinical signs, (ii) in herds with a previous history of infection, but absence of clinical signs at the moment of testing. Multiple multiparty exchanges were conducted to determine: 1) stakeholders’ groups; 2) the decision problem; 3) solutions to the problem (options) or diagnostic strategies to be ordered; 4) criteria and indicators; 5) criteria weights; 6) the construction of a performance matrix for each option; 7) the multi-criteria analyses using the visual preference ranking organization method for enrichment of evaluations approach; 8) the sensitivity analyses, and 9) the final decision. A total of nine people from four Québec’s organizations (the dairy producers provincial association along with the DHI company, the ministry of agriculture, the association of veterinary practitioners, and experts in epidemiology) composed the MCDA team. The decision problem was “What is the optimal diagnostic strategy for establishing the status of a dairy herd for S. Dublin infection when there are no clinical signs of infection?”. Fourteen diagnostic strategies composed of the three following parameters were considered: 1) biological samples (bulk tank milk or blood from 10 heifers aged over three months); 2) sampling frequencies (one to three samples collection visits); 3) case definitions to conclude to a positive status using imperfect milk- or blood-ELISA tests. The top-ranking diagnostic strategy was the same in the two contexts: testing the bulk tank milk and the blood samples, all samples collected during one visit and the herd being assigned a S. Dublin positive status if one sample is ELISA-positive. The final decision favored the top-ranking option for both contexts. This MCDA approach and its application to S. Dublin infection in dairy herds allowed a consensual, rational, and transparent ranking of feasible diagnostic strategies while taking into account the diagnostic tests accuracy, socio-economic, logistic, and perception considerations of the key actors in the dairy industry. This promising tool can be applied to other infectious diseases that lack a well-established diagnostic procedure to define a herd status.

Fluorescent-protein co-expression to select CHO cells expressing high quantities of vaccine antigens.

Cell line development for production of vaccine antigens or therapeutic proteins typically involves transfection, selection, and enrichment for high-expressing cells. Enrichment methods include minipool enrichment, antibody-based enrichment, and enrichment based on co-expressed fluorescent biosensor proteins. However, these methods have limitations regarding labor and cost intensity, the generation of antibodies and assurance of their viral safety, and potential expression-interference or signal-saturation of the co-expressed fluorescent protein. To improve the method of fluorescent-protein co-expression, expression constructs were created that constitutively express a model vaccine antigen together with one of three fluorescent proteins having translation initiation controlled by a wildtype or mutant internal ribosome entry site (IRES), for a total of six constructs. The constructs were transfected into Chinese hamster ovary cells (CHO) cells, enriched for high fluorescence, cultured, and tested in a mini bioreactor to identify the most promising construct. The fluorescent protein, Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) with a mutant IRES performed best and was further tested with three additional vaccine antigens. Across the four vaccine antigens, the FUCCI fluorescent protein yielded productivity enhancements, without the need for generating an antibody and assuring its viral safety. Furthermore, FUCCI protein was present in negligible quantities in the cell supernatant, indicating a low risk for contaminating drug substances or vaccine antigen.

High throughput Targeted Transcriptome Sequencing of Bone Marrow Mononuclear Cells identifies a Rare Leukemia-Specific T Cell Subset.

Abstract Many applications of scRNA-seq are focused on cell type identification, gene regulatory networks, or biomarker discovery. These applications often do not require surveying the whole transcriptome (WT), but rather require the interrogation of specific sets of well-characterized genes. In these cases, sequencing the entire transcriptome may be adding unnecessary costs. To increase throughput and minimize sequencing costs, the development of a targeted gene enrichment method is required. Here, we demonstrate an approach to combine split-pool combinatorial barcoding with enrichment of 1000 genes (Immune1000 panel) representing immune cell markers and pathways. We use this gene panel to characterize 730,000 human bone marrow mononuclear cells (BMMCs) from four leukemia and four healthy donors. We found that enrichment with the Immune1000 Panel enabled the characterization of all major immune cell types at low sequencing depth and allowed for the detection of known leukemia-associated shifts in cell type proportions. Moreover, our targeted sequencing method enabled the detection of a rare (~0.35%), leukemia-specific T cell population that showed highly proliferative and cytotoxic potential. Overall, we demonstrate our modular enrichment strategy preserves biological structure and allows for deep characterization of rare disease-relevant cell types and gene signatures with less sequencing.

Influence of suspended particles and dissolved organic matters on virus enrichment in reclaimed water by two-step tangential flow ultrafiltration: Phenomena and mechanisms

Enteric virus concentration in large-volume water samples is crucial for detection and essential for assessing water safety. Certain dissolution and suspension components can affect the enrichment process. In this study, tangential flow ultrafiltration (TFUF) was used as an enrichment method for recovering enteric virus in water samples. Interestingly, the bacteriophage MS2 recovery in reclaimed water and the reclaimed water without particles were higher than that in ultrapure water. The simulated reclaimed water experiments showed that humic acid (HA) (92.16% ± 4.32%) and tryptophan (Try) (81.50 ± 7.71%) enhanced MS2 recovery, while the presence of kaolin (Kaolin) inhibited MS2 recovery with an efficiency of 63.13% ± 11.17%. Furthermore, Atomic force microscopy (AFM) revealed that the MS2-HA cluster and the MS2-Try cluster had larger roughness values on the membrane surface, making it difficult to be eluted, whereas MS2-Kaolin cluster had compact surfaces making it difficult to be eluted. Additionally, the MS2-HA cluster is bound to the membrane by single hydrogen bond with SO, whereas both the MS2-Try cluster and the MS2-Kaolin cluster are bound to the membrane by two hydrogen bonds, making eluting MS2 challenging. These findings have potential implications for validating standardized methods for virus enrichment in water samples.

Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA

Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplification of minute amounts of Mtb DNA to enable WGS as an alternative to other Mtb enrichment methods. Purified genomic Mtb-DNA (0.1, 0.5, 1, and 5 pg) was encapsulated and amplified using the Samplix Xdrop-instrument and sequenced alongside a control sample using standard Illumina protocols followed by MAGMA-analysis. The control and 5 pg input dMDA samples underwent nanopore sequencing followed by Nanoseq and TB-profiler analysis. dMDA generated 105-2400 ng DNA from the 0.1-5 pg input DNA, respectively. Followed by Illumina WGS, dMDA raised mean sequencing depth from 7 × for 0.1 pg input DNA to ≥ 60 × for 5 pg input and the control sample. Bioinformatic analysis revealed a high number of false positive and false negative variants when amplifying ≤ 0.5 pg input DNA. Nanopore sequencing of the 5 pg dMDA sample presented excellent coverage depth, breadth, and accurate strain characterization, albeit elevated false positive and false negative variants compared to Illumina-sequenced dMDA sample with identical Mtb DNA input. dMDA coupled with Illumina WGS for samples with ≥ 5 pg purified Mtb DNA, equating to approximately 1000 copies of the Mtb genome, offers precision for drug resistance, phylogeny, and transmission insights.

Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern.

To control the SARS-CoV-2 pandemic, healthcare systems have focused on ramping up their capacity for epidemiological surveillance through viral whole genome sequencing. In this paper, we tested the performance of two protocols of SARS-CoV-2 nucleic acid enrichment, an amplicon enrichment using different versions of the ARTIC primer panel and a hybrid-capture method using KAPA RNA Hypercap. We focused on the challenge of the Omicron variant sequencing, the advantages of automated library preparation and the influence of the bioinformatic analysis in the final consensus sequence. All 94 samples were sequenced using Illumina iSeq 100 and analysed with two bioinformatic pipelines: a custom-made pipeline and an Illumina-owned pipeline. We were unsuccessful in sequencing six samples using the capture enrichment due to low reads. On the other hand, amplicon dropout and mispriming caused the loss of mutation G21987A and the erroneous addition of mutation T15521A respectively using amplicon enrichment. Overall, we found high sequence agreement regardless of method of enrichment, bioinformatic pipeline or the use of automation for library preparation in eight different SARS-CoV-2 variants. Automation and the use of a simple app for bioinformatic analysis can simplify the genotyping process, making it available for more diagnostic facilities and increasing global vigilance.

Comparative transcriptomic profiling of the two-stage response of rice to Xanthomonas oryzae pv. oryzicola interaction with two different pathogenic strains.

Two-tiered plant immune responses involve cross-talk among defense-responsive (DR) genes involved in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), effector-triggered immunity (ETI) and effector-triggered susceptibility (ETS). Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an important bacterial disease that causes serious threats to rice yield and quality. Transcriptomic profiling provides an effective approach for the comprehensive and large-scale detection of DR genes that participate in the interactions between rice and Xoc. In this study, we used RNA-seq to analyze the differentially expressed genes (DEGs) in susceptible rice after inoculation with two naturally pathogenic Xoc strains, a hypervirulent strain, HGA4, and a relatively hypovirulent strain, RS105. First, bacterial growth curve and biomass quantification revealed that differential growth occurred beginning at 1day post inoculation (dpi) and became more significant at 3 dpi. Additionally, we analyzed the DEGs at 12h and 3 days post inoculation with two strains, representing the DR genes involved in the PTI and ETI/ETS responses, respectively. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the common DEGs, which included 4380 upregulated and 4019 downregulated genes and 930 upregulated and 1383 downregulated genes identified for the two strains at 12h post inoculation (hpi) and 3 dpi, respectively. Compared to those at 12 hpi, at 3 dpi the number of common DEGs decreased, while the degree of differential expression was intensified. In addition, more disease-related GO pathways were enriched, and more transcription activator-like effector (TALE) putative target genes were upregulated in plants inoculated with HGA4 than in those inoculated with RS105 at 3 dpi. Then, four DRs were randomly selected for the BLS resistance assay. We found that CDP3.10, LOC_Os11g03820, and OsDSR2 positively regulated rice resistance to Xoc, while OsSPX3 negatively regulated rice resistance. By using an enrichment method for RNA-seq, we identified a group of DEGs related to the two stages of response to the Xoc strain, which included four functionally identified DR genes.

Passive eDNA sampling facilitates biodiversity monitoring and rare species detection

Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.

Screening for colorectal cancer: Study on the shedding cells of feces.

The objective of this study was to explore the enrichment efficiency of an improved fecal exfoliated cell enrichment method and its application in colorectal cancer screening. Samples were collected from a cohort of 100 colorectal cancer patients being treated at the First Hospital of Hebei Medical University from January 2021 to June 2022. Patient samples were equally divided between control and experimental groups corresponding to the enrichment method being applied to the fecal exfoliated cells. Samples consisted of natural stool and bowel cleansing enema solution samples. The control group received the traditional three-layer integrated screen method, and the experimental group used nano-Fe3O4 folic acid magnetic beads to enrich the fecal exfoliated cells. The morphology of the extracted cells was observed by light microscopy through hematoxylin and eosin staining, and the positive rate of fecal occult blood test (FOBT) and the detection rate of colorectal cancer was compared between the two groups. The FOBT-positive rates of natural feces and intestinal cleansing liquid in the control group were 74.00% and 90.00%, respectively, and the FOBT-positive rates of natural feces and intestinal cleansing liquid in the experimental group were 76.00% and 92.00%, respectively. The positive FOBT rate was high, and the difference was statistically significant (P = 0.037 and P = 0.029). The sensitivities of natural fecal exfoliation cytology in the control and experimental groups were 82.00% and 92.00%, respectively. The sensitivity of the experimental group was higher than that of the control group, and the difference was not statistically significant (P = 0.137). The sensitivities of the exfoliated cytology examination of the intestinal cleansing liquid in the control and experimental groups were 88.00% and 98.00%, respectively. The sensitivity of the experimental group was significantly higher than that of the control group, and the difference was statistically significant (P = 0.050). Cell smear results show that the exfoliated cells collected by the three-layer integrated sieve method are unevenly distributed, with overlapping cells and a large number of impurities blurring the background, seriously affecting the observation of cell morphology. The cell structure is blurred, stained unevenly, and arranged in a disorderly manner. The exfoliated cells collected by the nanofolic acid magnetic bead enrichment method are relatively evenly distributed, with no overlapping of cells in patches. The background is clear, and the morphology of each cell can be clearly observed. The cell structure is relatively clear, stained evenly, and distributed evenly. In the cytological examination of fecal exfoliation of colorectal cancer, the nano-Fe3O4 folic acid magnetic bead enrichment method can enrich more target cells compared with the traditional three-layer integrated screen method, improve the detection rate of colorectal cancer, and ensure the exfoliation The cell smears are of higher quality, providing a better sample for clinical assessment of the exfoliated cells. Nano-Fe3O4 folic acid magnetic beads enrichment method can become a simple, efficient, and relatively safe screening method for colorectal cancer, positively affecting early screening developments and diagnosis of colorectal cancer.

Tactile, Auditory, and Visual Stimulation as Sensory Enrichment for Dairy Cattle.

Several types of enrichment can be used to improve animal welfare. This review summarizes the literature on the use of mechanical brushes, tactile udder stimulation, music, and visual stimuli as enrichment methods for dairy cows. Mechanical brushes and tactile stimulation of the udder have been shown to have a positive effect on milk yield and overall behavioral repertoire, enhancing natural behavior. Classical music reduces stress levels and has similarly been associated with increased milk yield. A slow or moderate tempo (70 to 100 bpm) at frequencies below 70 dB is recommended to have this positive effect. Evidence on the impacts of other types of enrichment, such as visual stimulation through mirrors, pictures, and color lights, or the use of olfactory stimuli, is equivocal and requires further study.

Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp.

The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.

Multi-attribute decision-making analysis based on the bipolar N-soft PROMETHEE method

The multi-attribute decision-making (MADM) methods can deeply mine hidden information in data and make a more reliable decision with actual needs and human cognition. For this reason, this paper proposes the bipolar N-soft PROMETHEE (preference ranking organization method for enrichment of evaluation) method. The method fully embodies the advantages of the PROMETHEE method, which can limit the unconditional compensation between attribute values and effectively reflect the priority between attribute values. Further, by introducing an attribute threshold to filter research objects, the proposed method not only dramatically reduces the amount of computation but also considers the impact of the size of the attribute value itself on decision-making. Secondly, the paper proposes the concepts of attribute praise, attribute popularity, total praise, and total popularity for the first time, fully mining information from bipolar N-soft sets, which can effectively handle situations where attribute values have different orders of magnitude. In addition, this paper presents the decision-making process of the new method, closely integrating theoretical models with real life. Finally, this paper analyses and compares the proposed method with the existing ones, further verifying the effectiveness and flexibility of the proposed method.

Low-volume enrichment method supports high throughput bacteriophage screening and isolation from wastewater.

Bacteriophage therapy is a rapidly growing field of study. Narrow host ranges, bacterial resistance, and limited antibiotic availability make lytic phages a feasible therapeutic potential. Phage discovery, a critical step in developing phage therapy, is a pathway to accessible treatment. This has always been a laborious, time-consuming and resource-intensive process. In this paper, we describe a 96-well plate low-volume bacteriophage enrichment method with concentrated environmental sources to rapidly discover and isolate phages targeting multiple organisms simultaneously. Samples from natural water sources, wastewater influent, and activated sludge were tested in large volume enrichment cultures and low-volume 96-well plate format. Each plate has the capacity to run as many as 48 different combinations with multiple bacterial hosts. The time to identify the presence of phage in a sample was 5 to 10 hours in the low-volume format versus a minimum of 2 days in the traditional enrichment method. The labor and expense involved also favor the 96-well plate format. There was some loss of discovered phages using this technique, primarily targeting bacterial species less prevalent in the environment. This is an easily modifiable method that is amenable to automation and a variety of potential phage sources.

Covalent organic framework aerogel for high-performance solid-phase extraction of tetracycline antibiotics: Experiment and simulated calculation on adsorption behavior

Three-dimensional sponge-architecture covalent organic frameworks (COFs)-aerogel was successfully designed and synthesized via a freeze-drying template approach, and utilized as an efficient sorbent in solid-phase extraction (SPE). A method for selective enrichment of pharmaceutical contaminants including tetracycline, chlortetracycline, methacycline and oxytetracycline in the environment and food samples was proposed by combining with high performance liquid chromatography (HPLC). To understand the adsorption mechanism, selectivity test and molecular dynamics (MD) simulated calculation were both carried out. The experimental and in-silico results demonstrated that the COFs-aerogel possessed high selectivity for contaminants with H bond acceptors/donors and good efficiency with maximum adsorption capacity up to 294.1 mg/g. The SPE-based HPLC method worked well in the range of 8–1000 ng/mL, with the need of little dose of adsorbent and sample volume while no need of spectrometer, outgoing the reported adsorbents. Under the optimized conditions, the intra-day and inter-day relative standard deviations (RSD) of repeatability were within 2.78–6.29 % and 2.44–8.42 % (n = 5). The results meet the current detection requirement for practical applications, and could be extended for further design of promising adsorbents.

TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics

Protein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a novel tandem S-Trap-IMAC-HILIC (S-Trap: suspension trapping; IMAC: immobilized metal ion affinity chromatography; HILIC: hydrophilic interaction chromatography) strategy, termed TIMAHAC, for simultaneous analysis of plant phosphoproteomics and N-glycoproteomics. This approach integrates IMAC and HILIC into a tandem tip format, streamlining the enrichment process of phosphopeptides and N-glycopeptides. The key innovation lies in the use of a unified buffer system and an optimized enrichment sequence to enhance efficiency and reproducibility. The applicability of TIMAHAC was demonstrated by analyzing the Arabidopsis phosphoproteome and N-glycoproteome in response to abscisic acid (ABA) treatment. Up to 1954 N-glycopeptides and 11,255 phosphopeptides were identified from Arabidopsis, indicating its scalability for plant tissues. Notably, distinct perturbation patterns were observed in the phosphoproteome and N-glycoproteome, suggesting their unique contributions to ABA response. Our results reveal that TIMAHAC offers a comprehensive approach to studying complex regulatory mechanisms and PTM interplay in plant biology, paving the way for in-depth investigations into plant signaling networks.

Fermentation enrichment, structural characterization and immunostimulatory effects of β-glucan from Quinoa

We developed an efficient mixed-strain co-fermentation method to increase the yield of quinoa β-glucan (Q+). Using a 1:1 mass ratio of highly active dry yeast and Streptococcus thermophilus, solid-to-liquid ratio of 1:12 (g/mL), inoculum size of 3.8 % (mass fraction), fermentation at 32 °C for 27 h, we achieved the highest β-glucan yield of (11.13 ± 0.80)%, representing remarkable 100.18 % increase in yield compared to quinoa β-glucan(Q-) extracted using hot water. The structure of Q+ and Q- were confirmed through Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies. Q+ contained 41.66 % β-glucan, 3.93 % protein, 2.12 % uronic acid; Q- contained 37.21 % β-glucan, 11.49 % protein, and 1.73 % uronic acid. The average molecular weight of Q+(75.37 kDa) was lower than that of Q- (94.47 kDa). Both Q+ and Q- promote RAW264.7 cell proliferation without displaying toxicity. They stimulate RAW264.7 cells through the NF-κB and MAPK signaling pathways, primarily inducing NO and pro-inflammatory cytokines by upregulating CD40 expression. Notably, Q+ exhibited stronger immunostimulatory activity compared to Q-. In summary, the fermentation enrichment method yields higher content of quinoa β-glucan with increased purity and stronger immunostimulatory properties. Further study of its bioimmunological activity and structure-activity relationship may contribute to the development of new immunostimulants.

Liquid Biopsy for Detection of Pancreaticobiliary Cancers by Functional Enrichment and Immunofluorescent Profiling of Circulating Tumor Cells and Their Clusters.

Circulating tumor cells (CTCs) have historically been used for prognostication in oncology. We evaluate the performance of liquid biopsy CTC assay as a diagnostic tool in suspected pancreaticobiliary cancers (PBC). The assay utilizes functional enrichment of CTCs followed by immunofluorescent profiling of organ-specific markers. The performance of the assay was first evaluated in a multicentric case-control study of blood samples from 360 participants, including 188 PBC cases (pre-biopsy samples) and 172 healthy individuals. A subsequent prospective observational study included pre-biopsy blood samples from 88 individuals with suspicion of PBC and no prior diagnosis of cancer. CTCs were harvested using a unique functional enrichment method and used for immunofluorescent profiling for CA19.9, Maspin, EpCAM, CK, and CD45, blinded to the tissue histopathological diagnosis. TruBlood® malignant or non-malignant predictions were compared with tissue diagnoses to establish sensitivity and specificity. The test had 95.9% overall sensitivity (95% CI: 86.0-99.5%) and 92.3% specificity (95% CI: 79.13% to 98.38%) to differentiate PBC (n = 49) from benign conditions (n = 39). The high accuracy of the CTC-based TruBlood test demonstrates its potential clinical application as a diagnostic tool to assist the effective detection of PBC when tissue sampling is unviable or inconclusive.