The facile and economical identification of pathogenic bacteria, especially their antibiotic-resistance, is crucial in the realm of human health and safety. The presence of Escherichia coli (E. coli) ...is considered as an indicator of water contamination and is closely related to human health. Herein, inspired by the biocatalysis of bacterial surfaces, we developed a simple and cost-effective colorimetric- and electrochemical-based bioassay that is capable of analyzing both the presence of E. coli and its relative level of antibiotic resistance. In this approach, p-benzoquinone is used as a redox mediator to monitor the bacterial concentration and specifically distinguish E. coli from four other common clinical bacteria, namely, Staphylococcus aureus (S. aureus), Enterococcus faecalis (E. faecalis), Salmonella pullorum (S. pullorum), and Streptococcus mutans (S. mutans). A visible color change, captured with a smartphone using a “light box”, without relying on any complex instruments, can reflect the concentration of bacteria. The accurate quantification of E. coli was investigated with an electrochemical system in the concentration ranges of 1.0 × 103 to 1.0 × 109 CFU/mL. We further demonstrated the capability of the presented biosensor in identifying drug-resistant bacteria with two artificially induced antibiotic-resistant bacteria. Therefore, the presented bioassay is not only capable of detecting E. coli with high sensitivity and specificity but also provides a rapid solution to evaluate E. coli antibiotic resistance.
•The complex drug interactions impede the optimization of combinatorial drug therapy.•Microfluidic devices raise screening efficiency but optimization strategies are also required.•Phenotype-based ...methods and synergy models expedite the optimization process.•A three-step optimization strategy may increase chances of success in clinical translation.
Designing optimal combinatorial drug therapies is challenging, because the drug interactions depend not only on the drugs involved, but also on their doses. With recent advances, combinatorial drug therapy is closer than ever to clinical application. Herein, we summarize approaches and advances over the past decade for identifying and optimizing drug combination therapies, with innovations across research fields, covering physical laboratory platforms for combination screening to computational models and algorithms designed for synergism prediction and optimization. By comparing different types of approach, we detail a three-step workflow that could maximize the overall optimization efficiency, thus enabling the application of personalized optimization of combinatorial drug therapy.
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•A simple and cost-effective colorimetric bioassay based on GOD/HRP bienzyme system was designed for real time monitoring of foodborne bacterial viability.•This bienzyme system is ...free of any chemical synthesis and only requires 3 sample handling steps.•The color response could be easily observed by naked eyes in less than 20 mins.
Foodborne bacterial infection poses a serious threat to human health. As most diseases are caused by living bacteria, real-time assessment of bacterial viability is vitally important to the public health sector. Herein, we developed a simple and novel colorimetric assay based on the Glucose oxidase (GOD)/Horseradish peroxidase (HRP) bienzyme system for real-time monitoring of bacterial viability in food and drinking water. This bienzyme system is free of any chemical synthesis and only requires 3 sample handling steps. The color response is easily observable with the naked eye or recordable with a smartphone for precise determination of bacterial viability. The proposed strategy was validated with various bacteria both Gram-positive and Gram-negative, indicating its capability for broad-spectrum bacteria viability detection. Therefore, the proposed strategy shows promise for rapid and reliable quality control in food and drinking water.
With ever increasing drug resistance and emergence of new diseases, demand for new drug development is at an unprecedented urgency. This fact has led to extensive recent efforts to develop new drugs ...and novel techniques for efficient drug screening. However, new drug development is commonly hindered by cost and time span. Thus, developing more accessible, cost-effective methods for drug screening is necessary. Compared with conventional drug screening methods, a microfluidic-based system has superior advantages in sample consumption, reaction time, and cost of the operation. In this paper, the advantages of microfluidic technology in drug screening as well as the critical factors for device design are described. The strategies and applications of microfluidics for drug screening are reviewed. Moreover, current limitations and future prospects for a drug screening microdevice are also discussed.
In the field of in vitro diagnostics, detection of nucleic acids and proteins from biological samples is typically performed with independent platforms; however, co-detection remains a major ...technical challenge. Specifically, during the coronavirus disease 2019 (COVID-19) pandemic, the ability to simultaneously detect viral RNA and human antibodies would prove highly useful for efficient diagnosis and disease course management. Herein, we present a multiplex one-pot pre-coated interface proximity extension (OPIPE) assay that facilitates the simultaneous recognition of antibodies using a pre-coated antigen interface and a pair of anti-antibodies labeled with oligonucleotides. Following anti-antibody-bound nucleic acid chain extension to form templates in proximity, antibody signals can be amplified, together with that of targeted RNA, via a reverse transcription-polymerase chain reaction. Using four-color fluorescent TaqMan probes, we demonstrate the co-detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies and viral nucleic acids in a single bio-complex sample, including nucleocapsid protein-specific IgG and IgM, and the RNA fragments of RdRp and E genes. The serum detection limit for this platform is 100 fg/mL (0.67 fM) for the anti-SARS-CoV-2 antibody and 10 copies/μL for viral RNA. The OPIPE assay offers a practical and affordable solution for ultrasensitive co-detection of nucleic acids and antibodies from the same trace biological sample without the additional requirement of complicated equipment.
•One-pot pre-coated interface proximity extension assay (OPIPE) for co-detection is developed.•A 100-fold enhancement in sensitivity was achieved relative to microfluidic ELISA with as little as 1 μL serum.•The serum detection limit for the anti-SARS-CoV-2 antibody is 100 fg/mL (0.67 fM) and for viral RNA is 10 copies/μL.•OPIPE assay detect anti-SARS-CoV-2 antibodies and viral RNA simultaneously from one clinical sample with only PCR equipments.
Label-free proteomics with trace clinical samples provides a wealth of actionable insights for personalized medicine. Clinically acquired primary cells, such as circulating tumor cells (CTCs), are ...usually with low abundance that is prohibitive for conventional label-free proteomics analysis. Here, we present a sickle-like inertial microfluidic system for online rare cell separation and tandem label-free proteomics (namely, Orcs-proteomics). Orcs-proteomics adopts a buffer system with 0.1% N-dodecyl β-d-maltoside (DDM), 1 mM Tris (2-carboxyethyl) phosphine (TCEP), and 2 mM 2-chloroacetamide (CAA) for cell lysis and reductive alkylation. We demonstrate the application of Orcs-proteomics with 293T cells and manage to identify 913, 1563, 2271, and 2770 protein groups with 4, 13, 68, and 119 cells, respectively. We then spike MCF7 cells with white blood cells (WBCs) to simulate the patient’s blood sample. Orcs-proteomics identifies more than 2000 protein groups with an average of 61 MCF7 cells. We further recruit two advanced breast cancer patients and collect 5 and 7 CTCs from each patient through minimally invasive blood drawing. Orcs-proteomics manages to identify 973 and 1135 protein groups for each patient. Therefore, Orcs-proteomics empowers rare cells simultaneously to be separated and counted for proteomics and provides technical support for personalized treatment decision making with rare primary patient samples.
Abstract
Motivation
High-dimensional mass cytometry (CyTOF), which provides both cellular signatures and inter-cluster interactions like the antagonism between immune activation and suppression, and ...the pro-inflammatory synergy, sheds light on the cellular and molecular basis of disease pathogenesis. However, revealing the aberrance of inter-cluster communication networks in CyTOF datasets remains a significant challenge.
Results
Here, we developed Sample Classification and direct Association Network among Cell clusters (SCANCell) that quantifies the direct association (DA) network of cell clusters. SCANCell was applied to profile inter-cluster interaction patterns of a well-recruited systemic lupus erythematosus (SLE) cohort, including 8 healthy controls, 10 active SLE patients (APs) and 8 remission SLE patients (RPs). SCANCell identified decreased inter-cluster interactions of CD8+ T cells in APs compared with RPs, and enhanced DA of CD8+ T cells after stimulation with immunostimulatory cytokine interleukin-2 in vitro. These discoveries prove that SCANCell can uncover pathology- and drug stimulation-associated inter-cluster interactions, which potentially benefits understanding of pathogenesis and novel therapeutic strategies.
Availability and implementation
The main processing scripts of SCNACell are available at https://github.com/Lxc417/SCANCell. Other codes for the following data statistics are available from the corresponding author upon request.
Supplementary information
Supplementary data are available at Bioinformatics online.
The emergence and ongoing spread of multidrug-resistant (MDR) bacteria is a major global public health threat. MDR has extensively combated the potency of antibiotics. Development of new antibiotics ...requires several years with prohibitive cost that will not last. An alternative solution is to recombine failed antibiotics, which has been proven to be not only cost-effective, but also potent. However, selection of the optimal combinations of these chemicals through conventional trial-and-error methods is challenging and slow, since M candidates with N doses lead to NM possible combinations. Herein, we present a artificial intelligence (AI) guided chemical combination optimization technique, namely Streamlined Rapid Identification of Combinatorial Therapies (STRICT), which is phenotype based and can efficiently learn and identify the optimal drug-combinations with minimal experimental efforts. With the guidance of STRICT, we successfully identified potent combinations of five antibiotics from 26 antibiotics that are individually ineffective at inhibiting an artificially induced strain of MDR bacteria. Rather than examine millions of tests, STRICT accomplished this task with only 120 carefully selected tests. Our results indicate that STRICT is a powerful platform to identify efficacious multiantibiotic combinations for the treatment of MDR bacteria. The AI-guided platform introduced here is an effective tool for drug repurposing, beneficial toward large-scale drug screening for other disease models, and also has a broad application in chemical combination optimization to deliver a desired end point for a complex system.
Recently emerged mass cytometry (cytometry by time‐of‐flight CyTOF) technology permits the identification and quantification of inherently diverse cellular systems, and the simultaneous measurement ...of functional attributes at the single‐cell resolution. By virtue of its multiplex ability with limited need for compensation, CyTOF has led a critical role in immunological research fields. Here, we present an overview of CyTOF, including the introduction of CyTOF principle and advantages that make it a standalone tool in deciphering immune mysteries. We then discuss the functional assays, introduce the bioinformatics to interpret the data yield via CyTOF, and depict the emerging clinical and research applications of CyTOF technology in sketching immune landscape in a wide variety of diseases.
1. The CyTOF technique enables immune profiling of various disease conditions.
2. The development of CyTOF‐based functional assays and bioinformatics pipelines is thriving and promising.
3. CyTOF may serve as a promising platform to facilitate the identification of immunological biomarkers and drug screening.
An effective tool to assess embryo quality in the assisted reproduction clinical practice will enhance successful implantation rates and mitigate high risks of multiple pregnancies. Potential ...biomarkers secreted into culture medium (CM) during embryo development enable rapid and noninvasive methods of assessing embryo quality. However, small volumes, low biomolecule concentrations, and impurity interference collectively preclude the identification of quality-related biomarkers in single blastocyst CM. Here, we developed a noninvasive trace multiomics approach to screen for potential markers in individual human blastocyst CM. We collected 84 CM samples and divided them into high-quality (HQ) and low-quality (LQ) groups. We evaluated the differentially expressed proteins (DEPs) and metabolites (DEMs) in HQ and LQ CM. A total of 504 proteins and 189 metabolites were detected in individual blastocyst CM. Moreover, 9 DEPs and 32 DEMs were identified in different quality embryo CM. We also categorized HQ embryos into positive implantation (PI) and negative implantation (NI) groups based on ultrasound findings on day 28. We identified 41 DEPs and 4 DEMs associated with clinical implantation outcomes in morphologically HQ embryos using a multiomics analysis approach. This study provides a noninvasive multiomics analysis technique and identifies potential biomarkers for clinical embryo developmental quality assessment.An effective tool to assess embryo quality in the assisted reproduction clinical practice will enhance successful implantation rates and mitigate high risks of multiple pregnancies. Potential biomarkers secreted into culture medium (CM) during embryo development enable rapid and noninvasive methods of assessing embryo quality. However, small volumes, low biomolecule concentrations, and impurity interference collectively preclude the identification of quality-related biomarkers in single blastocyst CM. Here, we developed a noninvasive trace multiomics approach to screen for potential markers in individual human blastocyst CM. We collected 84 CM samples and divided them into high-quality (HQ) and low-quality (LQ) groups. We evaluated the differentially expressed proteins (DEPs) and metabolites (DEMs) in HQ and LQ CM. A total of 504 proteins and 189 metabolites were detected in individual blastocyst CM. Moreover, 9 DEPs and 32 DEMs were identified in different quality embryo CM. We also categorized HQ embryos into positive implantation (PI) and negative implantation (NI) groups based on ultrasound findings on day 28. We identified 41 DEPs and 4 DEMs associated with clinical implantation outcomes in morphologically HQ embryos using a multiomics analysis approach. This study provides a noninvasive multiomics analysis technique and identifies potential biomarkers for clinical embryo developmental quality assessment.
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