Decoding Biomechanical Cues Based on DNA Sensors.

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Paclitaxel Aggravating Radiation-Induced Pulmonary Fibrosis Is Associated with the Down-Regulation of the Negative Regulatory Function of Spry2.

Paclitaxel (PTX) is capable of aggravating radiation-induced pulmonary fibrosis (RIPF), but the mechanism is unknown. Spry2 is a negative regulator of receptor tyrosine kinase-related Ras/Raf/extracellular signal regulated kinase (ERK) pathway. This experiment was aimed at exploring whether the aggravation of RIPF by PTX is related to Spry2. The RIPF model was established with C57BL/6 mice by thoracic irradiation, and PTX was administered concurrently. Western blot was used to detect the expression level of ERK signaling molecules and the distribution of Spry2 in the plasma membrane/cytoplasm. Co-immunoprecipitation (co-IP) and immunofluorescence were used to observe the colocalization of Spry2 with the plasma membrane and tubulin. The results showed that PTX-concurrent radiotherapy could aggravate fibrotic lesions in RIPF, downregulate the content of membrane Spry2, and upregulate the levels of p-c-Raf and p-ERK in lung tissue. It was found that knockdown of Spry2 in fibroblast abolished the upregulation of p-c-Raf and p-ERK by PTX. Both co-IP results and immunofluorescence staining showed that PTX increased the binding of Spry2 to tubulin, and microtubule depolymerizing agents could abolish PTX's inhibition of Spry2 membrane distribution and inhibit PTX's upregulation of Raf/ERK signaling. Both nintedanib and ERK inhibitor were effective in relieving PTX-exacerbated RIPF. Taken together, the mechanism of PTX's aggravating RIPF was related to its ability to enhance Spry2's binding to tubulin, thus attenuating Spry2's negative regulation on Raf/ERK pathway. SIGNIFICANCE STATEMENT: This study revealed that paclitaxel (PTX) concurrent radiation therapy exacerbates radiation-induced pulmonary fibrosis during the treatment of thoracic tumors, which is associated with PTX restraining Spry2 and upregulating the Raf/extracellular signal regulated kinase signaling pathway, and provided drug targets for mitigating this complication.

Dual Enzymolysis Assisted by Acrylate or Phosphate Grafting: Influences on the Structural and Functional Properties of Jujube Residue Dietary Fiber.

Jujube residue is an abundant and low-cost dietary fiber resource, but its relatively lower hydration and functional properties limit its utilization as an ingredient of functional food. Thus, cellulase and hemicellulase hydrolysis, enzymatic hydrolysis assisted by phosphate grafting (EPG), and enzymatic hydrolysis assisted by acrylate grafting (EAG) were used to improve the functional properties of jujube residue dietary fiber (JRDF) in this study. The results evidenced that these modifications all increased the porosity of the microstructure of JRDF and increased the soluble fiber content, surface area, and hydration properties, but reduced its brightness (p < 0.05). Moreover, JRDF modified by enzymolysis combined with acrylate grafting offered the highest extractable polyphenol content, oil, sodium cholate, and nitrite ion sorption abilities. Meanwhile, JRDF modified via enzymolysis assisted by phosphate grafting showed the highest soluble fiber content (23.53 g∙100 g-1), water-retention ability (12.84 g∙g-1), viscosity (9.37 cP), water-swelling volume (10.80 mL∙g-1), and sorption ability of copper (II) and lead (II) ions. Alternatively, JRDF modified with cellulase hydrolysis alone exhibited the highest glucose adsorption capacity (21.9 g∙100 g-1) at pH 7.0. These results indicate that EPG is an effective way to improve the hypolipidemic effects of JRDF, while EAG is a good choice to enhance its hydration and hypoglycemic properties.

Reliable Detection of Extracellular PD-L1 by DNA Computation-Mediated Microfluidics.

Extracellular vesicle PD-L1 (programmed death-1 ligand 1) is of greater value in tumor diagnosis, prognosis, and efficacy monitoring of anti-PD-1/PD-L1 immunotherapy. However, soluble PD-L1 interferes with the accurate detection of extracellular vesicle (EV) PD-L1. Here, we developed a microfluidic differentiation method for the detection of extracellular PD-L1, without the interference of soluble, by DNA computation with lipid probes and PD-L1 aptamer as inputs (DECLA). For the developed DECLA method, a cholesterol-DNA probe was designed that efficiently embeds into the EV membrane, and an aptamer-based PD-L1 probe was used for PD-L1 recognition. Due to the stable secondary structure of the designed connector, only cobinding of cholesterol-DNA and PD-L1 affinity probe induced biotin-labeled connector activation, while soluble PD-L1 cannot hybridize. As a result, PD-L1 EVs can be efficiently captured by streptavidin-functioned herringbone chip and quantified by anti-CD63-induced fluorescence signal. The high specificity of dual-input DNA computation allied to the high sensitivity of microfluidic-based detection was suitable for distinguishing lung cancer patients from healthy donors, highlighting its potential translation to clinical diagnosis and therapy monitoring.

Older patients benefit more from sequential courses of washed microbiota transplantation than younger population with ulcerative colitis.

OBJECTIVES: The short-term efficacy of fecal microbiota transplantation (FMT) for ulcerative colitis (UC) has increasingly been evaluated. However, few studies have examined the long-term efficacy and its predictors. This study aimed to assess the clinical factors affecting the long-term efficacy of FMT for patients with UC. METHODS: This is a retrospective analysis of a prospective trial (NCT01790061) for patients with UC undergoing washed microbiota transplantation (WMT), which is the improved methodology of FMT. The long-term clinical efficacy of WMT and the factors affecting efficacy were analyzed. RESULTS: A total of 259 patients were included for analysis. Of 70.7% (183/259) of patients achieved a clinical response at 1 month after WMT and 29.7% (77/259) achieved steroid-free clinical remission 6 months after WMT. Total 44 patients maintained a clinical response for ≥24 months, and 33 (17.1%, 33/193) achieved steroid-free clinical remission for ≥24 months with WMT monotherapy. Patients with age at UC onset of ≥60 years, mild disease severity and undergoing ≥2 courses of WMT during the response within 6 months were more likely to achieve steroid-free clinical remission 6 months after WMT. Besides, independent factors associated with the long-term response of WMT for UC were age at onset of ≥60 years and ≥2 courses of WMT during the response. CONCLUSIONS: This study indicated WMT could induce short-term steroid-free clinical remission and maintain long-term response in UC, especially for older patients and patients undergoing sequential courses.

Elucidating the Effect of Nanoscale Receptor-Binding Domain Organization on SARS-CoV-2 Infection and Immunity Activation with DNA Origami.

Multivalent display of SARS-CoV-2 RBDs (receptor-binding domains, prime proteins for viral infection and as vaccine immunogens) affects infectivity and as immunogens on a virus-like particle (VLP) can enhance immune response. However, the viral attachment and immune response initiated by the copy number and distribution pattern of SARS-CoV-2 RBDs remain poorly understood. Here, we organize SARS-CoV-2 RBDs on DNA nanoballs of ∼74 nm diameter by an aptamer-guided assembly for a systematic interrogation. We find that both the affinity and the rate of the DNA-based VLP binding to the host cell increase with the RBD number (10-90). In addition, a concentrated RBD distribution promotes faster and stronger interaction to the host cell than an even RBD distribution. Moreover, it is interesting to learn that the immunity activation does not increase linearly with RBD numbers on the VLP. As few as 20 evenly distributed RBDs per VLP can elicit up to 86% immunity of macrophage cells. Overall, the work provides a new tool to study SARS-CoV-2 infection and VLP-based immunity activation, which should deepen our understanding of viral infection and facilitate the development of highly effective antiviral vaccines.

Spatially Patterned Neutralizing Icosahedral DNA Nanocage for Efficient SARS-CoV-2 Blocking.

Broad-spectrum anti-SARS-CoV-2 strategies that can inhibit the infection of wild-type and mutant strains would alleviate their threats to global public health. Here, we propose an icosahedral DNA framework for the assembly of up to 30 spatially arranged neutralizing aptamers (IDNA-30) to inhibit viral infection. Each triangular plane of IDNA-30 is composed of three precisely positioned aptamers topologically matching the SARS-CoV-2 spike trimer, thus forming a multivalent spatially patterned binding. Due to its multiple binding sites and moderate size, multifaced IDNA-30 induces aggregation of viruses. The rigid icosahedron framework afforded by four helixes not only forms a steric barrier to prevent the virus from binding to the host but also limits the conformational transformation of the SARS-CoV-2 spike trimer. Combining multivalent topologically patterned aptamers with structurally well-defined nanoformulations, IDNA-30 exhibits excellent broad-spectrum neutralization against SARS-CoV-2, including almost completely blocking the infection of Omicron pseudovirus. Overall, this multidimensional neutralizing strategy provides a new direction for the assembly of neutralizing reagents to enhance their inhibitory effect against SARS-CoV-2 infection and combat other disease-causing viruses.

Countering Malicious DeepFakes: Survey, Battleground, and Horizon.

The creation or manipulation of facial appearance through deep generative approaches, known as DeepFake, have achieved significant progress and promoted a wide range of benign and malicious applications, e.g., visual effect assistance in movie and misinformation generation by faking famous persons. The evil side of this new technique poses another popular study, i.e., DeepFake detection aiming to identify the fake faces from the real ones. With the rapid development of the DeepFake-related studies in the community, both sides (i.e., DeepFake generation and detection) have formed the relationship of battleground, pushing the improvements of each other and inspiring new directions, e.g., the evasion of DeepFake detection. Nevertheless, the overview of such battleground and the new direction is unclear and neglected by recent surveys due to the rapid increase of related publications, limiting the in-depth understanding of the tendency and future works. To fill this gap, in this paper, we provide a comprehensive overview and detailed analysis of the research work on the topic of DeepFake generation, DeepFake detection as well as evasion of DeepFake detection, with more than 318 research papers carefully surveyed. We present the taxonomy of various DeepFake generation methods and the categorization of various DeepFake detection methods, and more importantly, we showcase the battleground between the two parties with detailed interactions between the adversaries (DeepFake generation) and the defenders (DeepFake detection). The battleground allows fresh perspective into the latest landscape of the DeepFake research and can provide valuable analysis towards the research challenges and opportunities as well as research trends and future directions. We also elaborately design interactive diagrams (http://www.xujuefei.com/dfsurvey) to allow researchers to explore their own interests on popular DeepFake generators or detectors.

Ammonia-induced excess ROS causes impairment and apoptosis in porcine IPEC-J2 intestinal epithelial cells.

Ammonia is one of the most important toxic metabolites in the intestine of animals. It can cause intestinal damage and associated intestinal diseases through different endogenous or exogenous stimuli. However, the definition of harmful ammonia concentration and the molecular mechanism of ammonia - induced intestinal epithelial injury remain unclear. In this study, we found that the viability of porcine IPEC-J2 intestinal epithelial cells significantly decreased with the increase of NH4Cl dose (20-80 mM). Ammonia (40 mM NH4Cl) increased the expression level of ammonia transporter RHCG and disrupted the intestinal barrier function of IPEC-J2 cells by reducing the expression levels of the tight junction molecules ZO-1 and Claudin-1. Ammonia caused elevated levels of ROS and apoptosis in IPEC-J2 cells. This was manifested by decreased activity of antioxidant enzymes SOD and GPx, decreased mitochondrial membrane potential, and increased cytoplasmic Ca2+ concentration. In addition, the expression levels of apoptosis-related molecules Caspase-9, Caspase-3, Fas, Caspase-8, p53 and Bax were increased, the expression level of anti-apoptotic molecule Bcl-2 was decreased. Moreover, the antioxidant NAC (N-acetyl-L-cysteamine) effectively alleviated ammonia-induced cytotoxicity, reduced ROS level, Ca2+ concentration, and the apoptosis of IPEC-J2 cells. The results suggest that ammonia-induced excess ROS triggered apoptosis through mitochondrial pathway, death receptor pathway and DNA damage. This study can provide reference and theoretical basis for the definition of harmful ammonia concentration in pig intestine and the effect and mechanism of ammonia on pig intestinal health.

Production of Trans-Cinnamic Acid by Immobilization of the Bambusa oldhamii BoPAL1 and BoPAL2 Phenylalanine Ammonia-Lyases on Electrospun Nanofibers.

Phenylalanine ammonia-lyase (PAL) catalyzes the nonoxidative deamination of phenylalanine to yield trans-cinnamic acid and ammonia. Recombinant Bambusa oldhamii BoPAL1/2 proteins were immobilized onto electrospun nanofibers by dextran polyaldehyde as a cross-linking agent. A central composite design (CCD)-response surface methodology (RSM) was utilized to optimize the electrospinning parameters. Escherichia coli expressed eBoPAL2 exhibited the highest catalytic efficiency among four enzymes. The optimum conditions for fabricating nanofibers were determined as follows: flow rate of 0.10 mL/h, voltage of 13.8 kV, and distance of 13 cm. The response surface models were used to obtain the smaller the fiber diameters as well as the highest PAL activity in the enzyme immobilization. Compared with free BoPALs, immobilized BoPALs can be reused for at least 6 consecutive cycles. The remained activity of the immobilized BoPAL proteins after storage at 4 °C for 30 days were between 75 and 83%. In addition, the tolerance against denaturants of the immobilized BoPAL proteins were significantly enhanced. As a result, the dextran polyaldehyde natural cross-linking agent can effectively replace traditional chemical cross-linking agents for the immobilization of the BoPAL enzymes. The PAL/nylon 6/polyvinyl alcohol (PVA)/chitosan (CS) nanofibers made are extremely stable and are practical for industrial applications in the future.

NLIP and HAD-like Domains of Pah1 and Lipin 1 Phosphatidate Phosphatases Are Essential for Their Catalytic Activities.

Saccharomyces cerevisiae Pah1 phosphatidate phosphatase (PAP) catalyzes the dephosphorylation of phosphatidate to yield diacylglycerol, controlling phospholipids and triacylglycerol metabolisms. Pah1 and human Lipin 1 are intrinsically disordered proteins with 56% and 43% unfolded regions, respectively. Truncation analysis of the conserved and non-conserved regions showed that N- and C-conserved regions are essential for the catalytic activity of Pah1. PAP activities can be detected in the conserved N-terminal Lipin (NLIP) domain and C-terminal Lipin (CLIP)/haloacid dehalogenase (HAD)-like domain of Pah1 and Lipin 1, suggesting that the evolutionarily conserved domains are essential for the catalytic activity. The removal of disordered hydrophilic regions drastically reduced the protein solubility of Pah1. Thioredoxin is an efficient fusion protein for production of soluble NLIP-HAD recombinant proteins in Escherichia coli.

Reversible Self-Assembly Nanovesicle of UCST Response Prepared with Multi-l-arginyl-poly-l-aspartate Conjugated with Polyethylene Glycol.

Multi-L-arginyl-poly-L-aspartate (MAPA), also known as cyanophycin, containing a backbone of polyaspartate with arginine and lysine as side chains, was prepared with recombinant Escherichia coli. The insoluble part (iMAPA) was conjugated with polyethylene glycol (PEG) at two different levels, high (iMAPA(PEG)h) and low (iMAPA(PEG)l). Both levels of conjugation exhibited UCST (upper critical solution temperature)-type responses in the pH range of 3-10 at a concentration of 2 mg/mL. The cloud-point temperature of each conjugate also showed a positive correlation with concentration in PBS, falling between 20 to 58 °C at a concentration from 0.1 to 3 mg/mL. Hysteresis was observed to follow approximate paths under the same condition during repeated heating and cooling. Notably, the reversible formation of core-shell vesicles appeared at room temperature in PBS with a size of around 25 to 60 nm, as measured by DLS and observed under TEM. The reversibility was further employed to encapsulate doxorubicin (Dox) at different weight ratios of Dox to iMAPA(PEG)h. An encapsulation efficiency could reach as high as 70% with an equivalent loading capacity of 1.5 mg Dox/mg iMAPA(PEG)h. The Dox-loaded vesicles stayed stable at 4 °C for up to 4 weeks, with a minimal leakage below 2% and a slightly dilated morphology. Temperature-triggered release of Dox from the vesicles could be achieved by a step change of 5 °C successively from 37 to 62 °C in an effort to induce an initial 10% release at 37 °C gradually to complete release at 62 °C.

Regulation of nitrogen transformation and microbial community by inoculation during livestock manure composting.

This study examined the effects of three Bacillus strains and one Saccharomyces cerevisiae strain on nitrogen transformation and microbial communities in pig and chicken manure compost. The findings revealed that the use of compound microbial inoculants increased the compost temperature, accelerated moisture reduction, enhanced cellulase activity, and stimulated the accumulation of NH4 +-N, NO3 --N, and total nitrogen (TN), resulting in a 9% increase in TN content. The abundance of Firmicutes decreased by 3.95% at the maturation phase, while Actinobacteria and Bacteroidetes increased by 1.64% and 1.85%, respectively. Inoculation led to an increase in amoA, nxrA and nifH gene copy numbers, while simultaneously reducing the abundance of nirK, nosZ and nirS genes. It also resulted in an increase in functional enzyme levels, specifically nif and amo, with a corresponding decrease in nor. Clostridium, Phascolarctobacterium, Eubacterium and Faecalibacterium from the class Clostridium, which have a significant correlation with nifH and nxrA genes, suggest their likely crucial role in nitrogen retention and fixation. Inoculation aided in the removal of pathogenic bacteria and antibiotic resistance genes (ARGs) like fluoroquinolones, nucleosides and nitroimidazole. This study provides effective theoretical support for the mechanism of nitrogen retention and fixation, and for improving the quality of compost.

Comparison between washed microbiota transplantation and infliximab: Medical cost during long-term management in patients with inflammatory bowel disease.

BACKGROUND: Both infliximab (IFX) and fecal microbiota transplantation (FMT) have shown the efficacy for inflammatory bowel disease (IBD). However, there has no head-to-head study on the cost-value of the such treatments on IBD. This study aimed to compare the medical costs using IFX and the new method of FMT (washed microbiota transplantation [WMT]) in the long-term management for IBD under the current health economic condition in China. METHODS: Patients with IBD who underwent initial WMT via upper gastrointestinal endoscopy, mid-gut tube, or colonic transendoscopic enteral tubing at a university hospital between April 2013 and August 2021 and achieved the long-term sustainment with WMT or WMT combined with mesalazine until August 2022 were recruited in the real-world. The costs and hospitalizations were analyzed among two therapies mentioned above and IFX standard therapy. The charge of WMT was stable in the long term at our center, and the charge of IFX came from virtual statistics publicized by China Healthcare Security. RESULTS: Sixty eligible patients with IBD were included in the study. The long-term costs of patients using WMT monotherapy annually or per hospitalization were lower than those on WMT combined with mesalazine, respectively ( p < 0.001, respectively). The cumulative costs of IFX at the time of 0.52 and 0.85 years exceeded that of the above WMT, respectively ( p < 0.001, respectively). Besides, patients on WMT monotherapy paid 51.1 k CNY annually in the nonsustain phase but cut down the costs by 7.2 k CNY and duration of hospitalization by 5.1 days per hospitalization when reaching the goal of sustainment. CONCLUSION: This study demonstrated that WMT could dramatically reduce the cost and duration of hospitalizations in the long-term sustainment in the current Chinese IBD cohort. Compared with IFX, WMT could be a good way for the patients with IBD achieving long-term sustainment and saving medical costs.

An effective preserving strategy for strawberries by constructing pectin/starch coatings reinforced with functionalized eggshell fillers.

Food waste occurs frequently worldwide, though hunger and malnutrition issues have received global attention. Short-term spoilage of perishable foods causes a significant proportion of food waste. Developing simple, green, and low-cost strategies to preserve the freshness of perishable foods is important to address this issue and improving food safety. By using strawberries as the model perishable fruit, this study reported a pectin/carboxy methyl starch sodium (PC) based coating using epigallocatechin gallate-loaded eggshell powder (ES@EGCG) as the functional fillers. In comparison to PC coating, the PC-ES@EGCG coating displayed much-enhanced performance, such as enhanced mechanical (2 folds) and barrier (water vapor & oxygen) properties. This composite coating reduced the weight loss of strawberries from over 60% to around 30% after 7-day storage. Coated strawberries exhibit better freshness retention, which achieves the purpose of preserving strawberries during storage. This study provided a cost-effective and eco-friendly coating strategy for reducing food waste.

Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.

BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported. AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT. METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure. RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT. CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.

The long-term efficacy of imatinib with hepatic resection or other local treatment for gastrointestinal stromal tumours liver metastases: a retrospective cohort study.

BACKGROUND: The liver is the most common site of metastasis from gastrointestinal stromal tumors (GISTs). The authors aimed to evaluate imatinib (IM) combined with hepatic resection (HR) or other local treatments such as radiofrequency ablation (RFA) and transarterial chemoembolization (TACE), compared to IM monotherapy in long-term survival benefits in patients suffering from GIST liver metastases. METHODS: Our research encompassed 238 patients diagnosed with liver metastases of GISTs from January 2002 to April 2022 at the First Affiliated Hospital of Sun Yat-Sen University. The oncological outcomes of concern included overall survival (OS), progression-free survival (PFS), and liver-specific PFS. RESULTS: Of all 238 patients, 126 were treated with IM alone (IM group), 81 with IM combined with HR (IM+HR group), and 31 with IM combined with RFA/TACE (IM+RFA/TACE group). The median follow-up time was 44.83 months. The median OS in the IM group was 132.60 months and was not reached in either the IM+HR group or the IM+RFA/TACE group. The 10-year OS rate in the IM+HR group was significantly superior to the IM group and the IM+RFA/TACE group (91.9% vs. 61.1% vs. 55.2%, respectively, P =0.015), and the liver-specific PFS ( P =0.642) and PFS ( P =0.369) in the three groups showed a beneficial trend in the combined treatment group. Multivariate analyses showed that age less than or equal to 60 years (HR 0.280, P< 0.001) and IM+HR (HR 0.361, P =0.047) were independently associated with better OS. Achieving no evidence of disease through surgical intervention was independently correlated with enhanced OS (HR 0.099, P =0.034), liver-specific PFS (HR 0.388, P =0.014), and PFS (HR 0.402, P =0.004). CONCLUSIONS: In patients with GIST liver metastases, IM combined with HR might improve OS in selected patients compared with IM alone and IM combined with RFA/TACE. Achieving no evidence of disease status with surgical treatment of patients results in significant prolonging of OS, liver-specific PFS, and PFS.

Diverse SARS-CoV-2 aptamers overcome variant antigenic shift.

SARS-CoV-2 mutates rapidly as evidenced by the emergence of Omicron which causes changes in the recognition epitopes of most current neutralizing antibodies and immune evasion. Although aptamers are potential neutralizing agents for SARS-CoV-2 due to their unique molecular properties, it is difficult to compare their performances as assay conditions vary greatly, and their activity levels against variants remain unknown. Here, we evaluated the performances of 14 SARS-CoV-2 aptamers and provided a comprehensive analysis them, which we expect will improve the development of aptamer tools for SARS-CoV-2 diagnostics and therapeutics.

Microfluidic Enrichment of Intact SARS-CoV-2 Viral Particles by Stoichiometric Balanced DNA Computation.

Health diagnostic tools for community safety and environmental monitoring require selective and quantitatively accurate active viral load assessment. Herein, we report a microfluidic enrichment strategy to separate intact SARS-CoV-2 particles by AND logic gate with inputs of cholesterol oligonucleotides for the envelope and aptamers for the spike viral proteins. Considering the unequal quantity of endogenous spikes and lipid membranes on SARS-CoV-2, a dual-domain binding strategy, with two aptamers targeting different spike domains, was applied to balance the spike-envelope stoichiometric ratio. By balancing the stoichiometric with DNA computation and promoting microscale mass transfer of the herringbone chip, the developed strategy enabled high sensitivity detection of pseudotyped SARS-CoV-2 with a limit of detection as low as 37 active virions/µL while distinguishing it from inactive counterparts, other nontarget viruses, and free spike protein. Moreover, the captured viral particles can be released through DNase I treatment with up to 90% efficiency, which is fully compatible with virus culture and sequencing. Overall, the developed strategy not only identified SARS-CoV-2-infected patients (n = 14) with 100% identification from healthy donors (n = 8) but also provided a fresh perspective on the regulation of stoichiometric ratio to achieve a more biologically relevant DNA computation.