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Rapid point-of-care (POC) diagnosis of bacterial infection diseases provides clinical benefits of prompt initiation of antimicrobial therapy and reduction of the overuse/misuse of unnecessary antibiotics for nonbacterial infections. We present here a POC compatible method for rapid bacterial infection detection in 10 min. We use a large-volume solution scattering imaging (LVSi) system with low magnifications (1-2×) to visualize bacteria in clinical samples, thus eliminating the need for culture-based isolation and enrichment. We tracked multiple intrinsic phenotypic features of individual cells in a short video. By clustering these features with a simple machine learning algorithm, we can differentiate

Silage maize (Zea mays L.) is one of the most important forages in the world, and its yield and quality properties are critical parameters for livestock production and assessment of forage values. However, relationships between its yield and quality properties and the controlling factors are not well documented. In this study, we collected 5,663 observations from 196 publications across the country to identify the relationships between yield and quality properties of silage maize and to assess the impact of management practices and climatic factors on its yield and quality in China. The average dry matter yield of silage maize was (19.98±6.93) Mg ha

Extending knowledge on ecosystem stability to larger spatial scales is urgently needed because present local-scale studies are generally ineffective in guiding management and conservation decisions of an entire region with diverse plant communities. We investigated stability of plant productivity across spatial scales and hierarchical levels of organization and analyzed impacts of dominant species, species diversity, and climatic factors using a multisite survey of Inner Mongolian grassland. We found that regional stability across distant local communities was related to stability and asynchrony of local communities. Using only dominant instead of all-species dynamics explained regional stability almost equally well. The diversity of all or only dominant species had comparatively weak effects on stability and synchrony, whereas a lower mean and higher variation of precipitation destabilized regional and local communities by reducing population stability and synchronizing species dynamics. We demonstrate that, for semi-arid temperate grassland with highly uneven species abundances, the stability of regional communities is increased by stability and asynchrony of local communities and these are more affected by climate rather than species diversity. Reduced amounts and increased variation of precipitation in the future may compromise the sustainable provision of ecosystem services to human well-being in this region.

Quantification of molecular interactions on a surface is typically achieved via label-free techniques such as surface plasmon resonance (SPR). The sensitivity of SPR originates from the characteristic that the SPR angle is sensitive to the surface refractive index change. Analogously, in another interfacial optical phenomenon, total internal reflection, the critical angle is also refractive index dependent. Therefore, surface refractive index change can also be quantified by measuring the reflectivity near the critical angle. Based on this concept, we develop a method called critical angle reflection (CAR) imaging to quantify molecular interactions on glass surface. CAR imaging can be performed on SPR imaging setups. Through a side-by-side comparison, we show that CAR is capable of most molecular interaction measurements that SPR performs, including proteins, nucleic acids and cell-based detections. In addition, we show that CAR can detect small molecule bindings and intracellular signals beyond SPR sensing range. CAR exhibits several distinct characteristics, including tunable sensitivity and dynamic range, deeper vertical sensing range, fluorescence compatibility, broader wavelength and polarization of light selection, and glass surface chemistry. We anticipate CAR can expand SPR′s capability in small molecule detection, whole cell-based detection, simultaneous fluorescence imaging, and broader conjugation chemistry., Here, the authors present a method for quantifying molecular interactions on a glass surface, based on measuring surface refractive index changes via the reflectivity near the critical angle. They demonstrate tunable sensitivity and dynamic range, deep vertical sensing range, also for intracellular signals.

Ferroptosis, a form of cell death caused by the excessive accumulation of iron-dependent lipid peroxides. Studies over the last decade have identified multiple pathways that affect the sensitivity of cells to ferroptosis. Renal diseases, the tenth leading cause of death in the world, has been affecting the life of people for a long time. Numerous studies have shown that ferroptosis is inextricably linked to damage to kidney cells. Here, we review the pathophysiological features of the kidney, the basic pathways of ferroptosis, and the mechanisms of ferroptosis-induced kidney injury. It is proposed a promising outlook for the treatment of renal diseases by influencing ferroptosis.

Exposure to particulate matter has been associated with diseases of the respiratory and cardiovascular systems. Owing to the dense vasculature of the kidney, it has also been identified as a PM2.5 target organ. A potential contributor to PM2.5-mediated damage may be the promotion of inflammation. The essential oil 2-undecanone (2-methyl nonyl ketone) is an H. cordata isolate, and it has been shown to possess diverse pharmacologic effects, including anti-inflammatory properties. In this study we explored the ability of 2-undecanone to protect against PM2.5-induced kidney inflammation and the exact mechanisms in this process. We found that PM2.5 elevated the levels of certain inflammatory cytokines in BALB/c mice and in HEK 293 cells. Supplementation with 2-undecanone attenuated this PM2.5-induced inflammatory injury. Interestingly, in HEK 293 cells, the PM2.5-associated inflammation was aggravated by the mitophagy inhibitor Medivi-1, while it was attenuated by rapamycin, indicating that the mechanism of 2-undecanone-mediated inhibition of inflammation may relate to mitophagy. Meanwhile, 2-undecanone induces mitophagy in HEK 293 cells by suppressing Akt1-mTOR signaling. These results indicate that PM2.5 can induce kidney inflammation, and mitophagy induced by 2-undecanone may play a protective role against this renal inflammation.

Measuring the binding kinetics of single proteins represents one of the most important and challenging tasks in protein analysis. Here we show that this is possible using a surface plasmon resonance (SPR) scattering technique. SPR is a popular label-free detection technology because of its extraordinary sensitivity, but it has never been used for imaging single proteins. We overcome this limitation by imaging scattering of surface plasmonic waves by proteins. This allows us to image single proteins, measure their sizes, and identify them based on their specific binding to antibodies. We further show that it is possible to quantify protein binding kinetics by counting the binding of individual molecules, providing a digital method to measure binding kinetics and analyze heterogeneity of protein behavior. We anticipate that this imaging method will become an important tool for single protein analysis, especially for low volume samples, such as single cells., Editor’s summary Plasmonic scattering microscopy (PSM) enables the imaging of single proteins on SPR instruments. The method enables measurement of protein size and binding kinetics and is fully compatible with simultaneous traditional SPR measurements.

The harm of air pollution to public health has become a research hotspot, especially atmospheric fine-particulate matter (PM

Expansions of short nucleotide repeats account for more than 50 neurological or neuromuscular diseases. Many repeat expansion-containing RNAs can generate toxic repeat proteins through repeat-associated non-AUG (RAN) translation in all the reading frames. Understanding how RAN translation occurs and what cellular factors regulate this process will help decipher the basic mechanism of the molecular process and disease pathogenesis. Using reporter systems to quantitatively measure RAN translation provides a platform to examine candidate genes/pathways and screen for modifiers of this non-canonical pathway. In this chapter, we describe the dual-luciferase reporter system to measure RAN translation using C9ORF72 GGGGCC

Exposure to Di (2-ethylhexyl) phthalate (DEHP) has been associated with toxic effects of the reproductive system. However, the exact mechanism remains to be elucidated. In this study we explored the testicular toxicity induced by DEHP, and the probable molecular mechanism in the process. In vivo, the results demonstrated that DEHP affected testosterone levels and blood-testosterone barrier (BTB) integrity and caused ferroptosis. We further demonstrated that DEHP up-regulated the expression of p38α, p-p38α, p53, p-p53, SAT1, ALOX15. This view has also been confirmed in TM4 cells. After pre-treatment with fer-1 or si-MAPK14, the expression of either p53, p-p53, SAT1 and ALOX15 up-regulated by MEHP was inhibited in vitro. Interestingly, p38α can prevent the accumulation of lipid ROS, and the production of lipid ROS in turn promoted the expression of p38α, thus forming a feedback loop during the ferroptosis. In this process, a vicious cycle consisting of p38α, p53, SAT1, ALOX15, lipid ROS was involved. This study provides new mechanistic insights into DEHP-induced toxicity of the reproductive system.

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

Rapid and sensitive detection of biomarkers is the key to the diagnosis of acute diseases. One example is the detection of troponin in myocardial infarction. Here we report a gradient-based digital immunoassay method, which can achieve high-sensitivity cardiac troponin T (hs-cTnT) detection with only 1 microliter of plasma sample. We designed a multizone microfluidic channel functionalized with capture antibody specific to troponin. Taking advantage of limited sample volume, a troponin concentration gradient is created along the channel because of binding induced depletion. We quantified the concentration gradient by counting the detection antibody conjugated gold nanoparticles bound to different test zones with optical imaging. Differential counting between the zones removes most common noises and non-specific bindings. The total analytical time is about 30 minutes, and the limit of quantification is 6.2 ng/L. We examined 41 clinical plasma samples from 15 patients and the change in hs-cTnT concentration in serial samples showed good linear correlation with clinical results (R(2) = 0.98). Therefore, this simple and sensitive gradient-based digital immunoassay method is a promising technology for clinical hs-cTnT detection and could be adapted for detection of other biomarkers.

C9ORF72 hexanucleotide GGGGCC repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-containing RNA mediates toxicity through nuclear granules and dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG translation. However, it remains unclear how the intron-localized repeats are exported and translated in the cytoplasm. We use single molecule imaging approach to examine the molecular identity and spatiotemporal dynamics of the repeat RNA. We demonstrate that the spliced intron with G-rich repeats is stabilized in a circular form due to defective lariat debranching. The spliced circular intron, instead of pre-mRNA, serves as the translation template. The NXF1-NXT1 pathway plays an important role in the nuclear export of the circular intron and modulates toxic DPR production. This study reveals an uncharacterized disease-causing RNA species mediated by repeat expansion and demonstrates the importance of RNA spatial localization to understand disease etiology., Hexanucleotide repeat expansion in the intron 1 of the C9ORF72 gene can cause amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). Here the authors use single molecule imaging to show nuclear export and translation of circular repeat-containing C9ORF72 intronic RNA.

Patulin (PAT), a kind of mycotoxin, is produced by many common fungi in fruit and vegetable-based products. It has been shown to cause hepatotoxicity. However, the possible mechanisms are not completely elucidated. The present study aimed to characterize the role of autophagic-inflammasomal pathway on pyroptosis induced by PAT. In mouse livers, PAT induced pyroptosis, and increased inflammation through the activation of NLRP3 inflammasome. In liver cells, we noticed that PAT induced pyroptotic cell death, which was confirmed by the activation of GSDMD, caspase-1, the release of LDH, and the result of PI/Hoechst assay. In addition, PAT-induced pyroptosis was dependent upon the activation of NLRP3 inflammasome and the release of cathepsin B. Cells had less expression of caspase-1 and IL-1β protein levels after treated by NLRP3 inhibitor MCC950 or cathepsin B inhibitor CA-074Me. The expression of GSDMD and IL-1β protein levels were also decrease after treated by caspase-1 inhibitor Ac-YVAD-cmk. Moreover, autophagy inhibitor 3-methyladenine (3-MA) attenuated PAT-induced increase in cytoplasmic cathepsin B expression, and subsequent LDH release, the activation of NLRP3 inflamosomes, pyroptotic cell death, and inflammation. These findings suggested that PAT-induced pyroptosis maybe through autophagy-cathepsin B-inflammasomal pathway in the liver. These results provide new mechanistic insights into PAT-induced hepatotoxicity.

A rapid and sensitive method to detect cardiac troponin I (cTnI) in human blood is critical to the diagnosis and treatment of acute myocardial infarction (AMI). Here, we describe a simple one-step digital immunoassay for single-molecule detection without washing steps. A sample containing cTnI mixed with detection antibody-conjugated gold nanoparticles (AuNPs) is added to a capture antibody-coated sensor surface and the formation of the antibody-cTnI-antibody sandwich is detected by digitally counting the binding of the individual gold nanoparticles to the sensor surface in real time using a bright-field optical imaging setup together with a differential imaging algorithm. The digital immunoassay detects cTnI in undiluted human plasma, which achieves a detection limit of 5.7 ng/L within a detection time of only 10 min, which meets the requirement of current clinical high-sensitivity troponin assay (∼70 ng/L cutoff). We anticipate that the one-step and real-time digital immunoassay can be applied to the detection of other disease biomarkers in blood.

LncRNAs plays an important role in the regulation of gene expression. Identification of cancer-related lncRNAs GO terms and KEGG pathways is great helpful for revealing cancer-related functional biological processes. Therefore, in this study, we proposed a computational method to identify novel cancer-related lncRNAs GO terms and KEGG pathways. By using existing lncRNA database and Max-relevance Min-redundancy (mRMR) method, GO terms and KEGG pathways were evaluated based on their importance on distinguishing cancer-related and non-cancer-related lncRNAs. Finally, GO terms and KEGG pathways with high importance were presented and analyzed. Our literature reviewing showed that the top 10 ranked GO terms and pathways were really related to interpretable tumorigenesis according to recent publications.

Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most prevalent genetic cause ofamyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism isthe aberrant accumulation of dipeptide repeat (DPR) proteins produced by the unconventional translation of expanded RNA repeats. Here, we performed genome-wide CRISPR-Cas9 screens for modifiers of DPR protein production in human cells.We found that DDX3X, an RNA helicase, suppresses the repeat-associated non-AUG translation of GGGGCC repeats. DDX3X directly binds to (GGGGCC)n RNAs but not antisense (CCCCGG)n RNAs. Its helicase activity is essential for the translation repression. Reduction of DDX3X increases DPR levels in C9ORF72-ALS/FTD patient cells and enhances (GGGGCC)n-mediated toxicity in Drosophila. Elevating DDX3X expression is sufficient to decrease DPR levels, rescue nucleocytoplasmic transport abnormalities, and improve survival of patient iPSC-differentiated neurons. This work identifies genetic modifiers of DPR protein production and provides potential therapeutic targets for C9ORF72-ALS/FTD.

Membrane proteins play vital roles in cellular signaling processes and serve as the most popular drug targets. A key task in studying cellular functions and developing drugs is to measure the binding kinetics of ligands with the membrane proteins. However, this has been a long-standing challenge because one must perform the measurement in a membrane environment to maintain the conformations and functions of the membrane proteins. Here, we report a new method to measure ligand binding kinetics to membrane proteins using self-assembled virion oscillators. Virions of human herpesvirus were used to display human G-protein-coupled receptors (GPCRs) on their viral envelopes. Each virion was then attached to a gold-coated glass surface via a flexible polymer to form an oscillator and driven into oscillation with an alternating electric field. By tracking changes in the oscillation amplitude in real-time with subnanometer precision, the binding kinetics between ligands and GPCRs was measured. We anticipate that this new label-free detection technology can be readily applied to measure small or large ligand binding to any type of membrane proteins and thus contribute to the understanding of cellular functions and screening of drugs.

Colorectal cancer is the third most common cancer in males and second in females. This disease can be caused by genetic and acquired/environmental factors. Microsatellite instability (MSI) is one of the major mechanisms in colorectal cancer. This mechanism is a specific condition of genetic hyper mutability that results from incompetent DNA mismatch repair. MSI has been applied to classify different colorectal cancer subtypes. However, the effects of MSI status on gene expression are largely unknown. In our study, we integrated the gene expression profile and MSI status of all CRC samples from the TCGA database, and then categorized the CRC samples into three subgroups, namely, MSI-stable, MSI-low, and MSI-high, according to the MSI status. We applied a novel computational method based on machine learning and screened the genes specifically expressed for the different colorectal cancer subtypes. The results showed the distinct mechanisms of the different colorectal cancer subtypes with MSI status and provided the genes that may be the optimal standards to further classify the various molecular subtypes of colorectal cancer with distinct MSI status.

Patulin (PAT) is a secondary metabolite produced by certain species of Penicillium, Byssochlamys and Aspergillus. It has been shown to induce liver toxicity, but the possible molecular mechanisms are not completely elucidated. In our study, we treated Human Hepatoma G2 (HepG2) cells by 3-methyladenine (3-MA), an autophagosome formation inhibitor, and rapamycin, an autophagosome formation stimulator. The results showed that 3-MA protected the HepG2 cells against PAT cytotoxicity, while rapamycin decreased the cell viability. Thus, autophagy may play an important role in PAT-induced toxicity. To uncover the mechanism by which cells decrease proliferation and activation of autophagy, we found that collapses of mitochondrial membrane potential (ΔΨm) and reactive oxygen species (ROS) level were increased under treatment with PAT. Further, we elucidated that the expression of p-Akt1 and p-MTOR was inhibited during this process. N-acetyl-l-cysteine (NAC), a ROS inhibitor, protected against PAT-induced cytotoxicity, decreased the protein expression of LC3-II, and up-regulated the level of p-Akt1 and p-MTOR. These findings suggested that PAT-induced autophagic cell death was ROS-dependent in HepG2 cells. In conclusion, it is possible that PAT elicited autophagy through ROS-Akt1-MTOR pathway in the HepG2 cells.

Cellular membranes are important biomaterials with highly dynamic structures. Membrane dynamics plays an important role in numerous cellular processes, but precise tracking it is challenging due to the lack of tools with a highly sensitive and fast detection capability. Here we demonstrate a broad bandwidth optical imaging technique to measure cellular membrane displacements in the normal direction at sub-nm level detection limits and 20 μs temporal resolution (1 Hz-50 kHz). This capability allows us to study the intrinsic cellular membrane dynamics over a broad temporal and spatial spectrum. We measured the nanometer-scale stochastic fluctuations of the plasma membrane of HEK-293 cells, and found them to be highly dependent on the cytoskeletal structure of the cells. By analyzing the fluctuations, we further determine the mechanical properties of the cellular membranes. We anticipate that the method will contribute to the understanding of the basic cellular processes, and applications, such as mechanical phenotyping of cells at the single-cell level.

Hexanucleotide repeat expansion in C9ORF72 is the most frequent cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we demonstrate that the repeat-associated non-AUG (RAN) translation of (GGGGCC)n-containing RNAs into poly-dipeptides can initiate in vivo without a 5′-cap. The primary RNA substrate for RAN translation of C9ORF72 sense repeats is shown to be the spliced first intron, following its excision from the initial pre-mRNA and transport to the cytoplasm. Cap-independent RAN translation is shown to be upregulated by various stress stimuli through phosphorylation of the α subunit of eukaryotic initiation factor-2 (eIF2α), the core event of an integrated stress response (ISR). Compounds inhibiting phospho-eIF2α-signaling pathways are shown to suppress RAN translation. Since the poly-dipeptides can themselves induce stress, these findings support a feedforward loop with initial repeat-mediated toxicity enhancing RAN translation and subsequent production of additional poly-dipeptides through ISR, thereby promoting progressive disease., Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most frequent cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here the authors show that (GGGGCC)n translation can initiate without a 5′-cap, and this cap-independent translation is upregulated by stress mediated through eIF2α phosphorylation.

Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely noninvasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold. We further demonstrated the realization of Boolean logic functions by using DNA strand displacement reactions, which include multi-input and sequential cell logic gates (AND, OR, XOR, and AND-OR). This study provides a highly generic tool for self-organization of biological systems.

Mono (2-ethylhexyl) phthalate (MEHP) is the principal metabolite of di (2-etylhexyl) phthalate, which is widely used as a plasticizer, especially in medical devices. MEHP has toxic effects on cardiovascular system. The aim of this study was to investigate the possibility that 6-gingerol may inhibit the oxidative DNA damage of MEHP in human umbilical vein endothelial cells (HUVECs) and the potential mechanism. The comet assay was used to monitor DNA strand breaks. We have shown that 6-gingerol significantly reduced the DNA strand breaks caused by MEHP. MEHP increased the levels of reactive oxygen species and malondialdehyde, decreased the level of glutathione and activity of superoxide dismutase, and altered the mitochondrial membrane potential. In addition, DNA damage-associated proteins (p53 and p-Chk2 (T68)) were significantly increased by the treatment of MEHP. Those effects can all be protected by 6-gingerol. The results firmly indicate that 6-gingerol may have a strong protective ability against the DNA damage caused by MEHP in HUVECs, and the mechanism may relate to the antioxidant activity.

Timely diagnosis of acute diseases improves treatment outcomes and saves lives, but it requires fast and precision quantification of biomarkers. Here we report a time-resolved digital immunoassay based on plasmonic imaging of binding of single nanoparticles to biomarkers captured on a sensor surface. The real-time and high contrast of plasmonic imaging lead to fast and precise counting of the individual biomarkers over a wide dynamic range. We demonstrated the detection principle, evaluated the performance of the method using procalcitonin (PCT) as an example, and achieved a limit of detection of ~ 3 pg/mL, dynamic range of 4-12500 pg/mL, for a total detection time of ~ 25 mins.

The emergence of antibiotic resistance has prompted the development of rapid antimicrobial susceptibility testing (AST) technologies that will enable evidence-based treatment and promote antimicrobial stewardship. To date, many rapid AST methods have been developed, but few are able to be performed on clinical samples directly. Here we developed a large volume light scattering microscopy (LVM) technique that tracks phenotypic features of single bacterial cells directly in clinical urine samples without sample enrichment or culturing. The technique demonstrated rapid (90 min) detection of Escherichia coli in 24 clinical urine samples with 100% sensitivity and 83% specificity and rapid (90 min) AST in 12 urine samples with 87.5% categorical agreement with two antibiotics, ampicillin and ciprofloxacin.

Human G protein-coupled receptors (GPCRs) respond to various ligands and stimuli. However, GPCRs rely on membrane for proper folding, making their biochemical properties difficult to study. By displaying GPCRs in viral envelopes, we fabricated a Virion Display (VirD) array containing 315 non-olfactory human GPCRs for functional characterization. Using this array, we found that 10 of 20 anti-GPCR mAbs were ultra-specific. We further demonstrated that those failed in the mAb assays could recognize their canonical ligands, suggesting proper folding. Next, using two peptide ligands on the VirD-GPCR array, we identified expected interactions and novel interactions. Finally, we screened the array with group B Streptococcus, a major cause of neonatal meningitis, and demonstrated that inhibition of a newly identified target, CysLTR1, reduced bacterial penetration both in vitro and in vivo. We believe that the VirD-GPCR array holds great potential for high-throughput screening for small molecule drugs, affinity reagents, and ligand deorphanization., G protein-coupled receptors (GPCRs) are important targets for drug discovery. Here, the authors develop a Virion Display array of 315 functional non-odorant GPCRs, providing a platform for high-throughput, unbiased screening for small molecule drugs, affinity reagents, and microbial interactions.

G protein-coupled receptors (GPCRs) are the largest protein family for cell signal transduction, and most of them are crucial drug targets. Conventional label-free assays lack the spatial information to address the heterogeneous response from single cells after GPCRs activation. Here, we reported a GPCRs study in live cells using plasmonic-based electrochemical impedance microscopy. This label-free optical imaging platform is able to resolve responses from individual cells with subcellular resolution. Using this platform, we studied the histamine mediated GPCRs activation and revealed spatiotemporal heterogeneity of cellular downstream responses. Triphasic responses were observed from individual HeLa cells upon histamine stimulation. A quick peak P1 in less than 10 s was attributed to the GPCRs triggered calcium release. An inverted P2 phase within 1 min was attributed to the alternations of cell-matrix adhesion after the activation of Protein Kinase C (PKC). The main peak (P3) around 3-6 min after the histamine treatment was due to dynamic mass redistribution and showed a dose-dependent response with a half-maximal effective concentration (EC50) of 3.9 ± 1.2 μM. Heterogeneous P3 responses among individual cells were observed, particularly at high histamine concentration, indicating diverse histamine H1 receptor expression level in the cell population.

With the increasing prevalence of antibiotic resistance, the need to develop antimicrobial susceptibility testing (AST) technologies is urgent. The current challenge has been to perform the antibiotic susceptibility testing in short time, directly with clinical samples, and with antibiotics over a broad dynamic range of clinically relevant concentrations. Here we develop a technology for point-of-care diagnosis of antimicrobial-resistant bacteria in urinary tract infections (UTI), by imaging the clinical urine samples directly with an innovative large-image-volume solution scattering imaging (LVSi) system and analyzing the image sequences with a single-cell division tracking method. The high sensitivity of single-cell division tracking associated with large volume imaging enabled rapid antibiotic susceptibility testing directly on the clinical urine samples. The results demonstrated direct detection of bacterial infections in 60 clinical urine samples with a 60 min LVSi video, and digital AST of 30 positive clinical samples with 100% categorical agreement with both the clinical culture results and the on-site agar plating validation results. This technology provides opportunities for precise antibiotic prescription and prompt proper treatment of the patient within a single clinic visit.

Patulin (PAT) is a compound produced by fungi including those of the Aspergillus, Penicillium, and Byssochlamys species. PAT has been linked with negative outcomes in certain microorganisms and animal species, but how it causes hepatotoxicity is poorly understood. In this study, we determined that, by treating HepG2 cells using PAT, these cells could be induced to rapidly undergo autophagy, and this was followed within 12 h of treatment by lysosomal membrane permeabilization (LMP) and cathepsin B release. We were able to block these outcomes if cells were treated with 3-methyladenine (3MA), an inhibitor of autophagy, prior to PAT treatment. Moreover, PAT-induced collapse of mitochondrial membrane potential (ΔΨm) depended both on cathepsin B and autophagy. 3MA was further able to reduce the induction of apoptosis in response to PAT, suggesting that autophagy is a driving mechanism for this apoptotic induction. Inhibiting cathepsin B using CA-074 Me further reduced PAT-induced collapses of ΔΨm, mitochondiral cytochrome c release, and apoptosis. We also found that extended treatment of HepG2 cells using PAT over a period of 24 h led to the impairment of mitophagy such that morphologically swollen mitochondria accumulated within cells, and PINK1 failed to colocalize with LC3. Together these data reveal that PAT treatment can promote the induction of apoptosis in HepG2 cells in a manner dependent upon autophagy that progresses via the lysosomal-mitochondrial axis. This study thereby affords new insights into the mechanisms by which PAT drives hepatotoxicity.

Aim and Objective: Leukemia is the second common blood cancer after lymphoma, and its incidence rate has an increasing trend in recent years. Leukemia can be classified into four types: acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myelogenous leukemia (CML). More than forty drugs are applicable to different types of leukemia based on the discrepant pathogenesis. Therefore, the identification of specific drug-targeted biological processes and pathways is helpful to determinate the underlying pathogenesis among such four types of leukemia. Methods: In this study, the gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were highly related to drugs for leukemia were investigated for the first time. The enrichment scores for associated GO terms and KEGG pathways were calculated to evaluate the drugs and leukemia. The feature selection method, minimum redundancy maximum relevance (mRMR), was used to analyze and identify important GO terms and KEGG pathways. Results: Twenty Go terms and two KEGG pathways with high scores have all been confirmed to effectively distinguish four types of leukemia. Conclusion: This analysis may provide a useful tool for the discrepant pathogenesis and drug design of different types of leukemia.

Timely determination of antimicrobial susceptibility for a bacterial infection enables precision prescription, shortens treatment time, and helps minimize the spread of antibiotic resistant infections. Current antimicrobial susceptibility testing (AST) methods often take several days and thus impede these clinical and health benefits. Here, we present an AST method by imaging freely moving bacterial cells in urine in real time and analyzing the videos with a deep learning algorithm. The deep learning algorithm determines if an antibiotic inhibits a bacterial cell by learning multiple phenotypic features of the cell without the need for defining and quantifying each feature. We apply the method to urinary tract infection, a common infection that affects millions of people, to determine the minimum inhibitory concentration of pathogens from human urine specimens spiked with lab strain E. coli (ATCC 43888) and an E. coli strain isolated from a clinical urine sample for different antibiotics within 30 min and validate the results with the gold standard broth macrodilution method. The deep learning video microscopy-based AST holds great potential to contribute to the solution of increasing drug-resistant infections.

Action potentials in neurons have been studied traditionally by intracellular electrophysiological recordings and more recently by the fluorescence detection methods. Here we describe a label-free optical imaging method that can measure mechanical motion in single cells with a sub-nanometer detection limit. Using the method, we have observed sub-nanometer mechanical motion accompanying the action potential in single mammalian neurons by averaging the repeated action potential spikes. The shape and width of the transient displacement are similar to those of the electrically recorded action potential, but the amplitude varies from neuron to neuron, and from one region of a neuron to another, ranging from 0.2–0.4 nm. The work indicates that action potentials may be studied noninvasively in single mammalian neurons by label-free imaging of the accompanying sub-nanometer mechanical motion.

Measuring molecular binding to membrane proteins is critical for understanding cellular functions, validating biomarkers, and screening drugs. Despite the importance, developing such a capability has been a difficult challenge, especially for small-molecule binding to membrane proteins in their native cellular environment. Here we show that the binding of both large and small molecules to membrane proteins can be quantified on single cells by trapping single cells with a microfluidic device and detecting binding-induced cellular membrane deformation on the nanometer scale with label-free optical imaging. We develop a thermodynamic model to describe the binding-induced membrane deformation, validate the model by examining the dependence of membrane deformation on cell stiffness, membrane protein expression level, and binding affinity, and study four major types of membrane proteins, including glycoproteins, ion channels, G-protein coupled receptors, and tyrosine kinase receptors. The single-cell detection capability reveals the importance of local membrane environment on molecular binding and variability in the binding kinetics of different cell lines and heterogeneity of different cells within the same cell line.

Epidermal growth factor receptor (EGFR, also known as ErbB-1 or HER-1) is a membrane bound protein that has been associated with a variety of solid tumors and the control of cell survival, proliferation, and metabolism. Quantification of the EGFR expression level in cell membranes and the interaction kinetics with drugs are thus important for cancer diagnosis and treatment. Here we report mapping of the distribution and interaction kinetics of EGFR in their native environment with the surface plasmon resonance imaging (SPRi) technique. The monoclonal anti-EGFR antibody was used as a model drug in this study. The binding of the antibody to EGFR overexpressed A431 cells was monitored in real time, which was found to follow the first-order kinetics with an association rate constant (ka) and dissociation rate constant (kd) of (2.7 ± 0.6) × 10(5) M(-1) s(-1) and (1.4 ± 0.5) × 10(-4) s(-1), respectively. The dissociation constant (KD) was determined to be 0.53 ± 0.26 nM with up to seven-fold variation among different individual A431 cells. In addition, the averaged A431 cell surface EGFR density was found to be 636/μm(2) with an estimation of 5 × 10(5) EGFR per cell. Additional measurement also revealed that different EGFR positive cell lines (A431, HeLa, and A549) show receptor density dependent anti-EGFR binding kinetics. The results demonstrate that SPRi is a valuable tool for direct quantification of membrane protein expression level and ligand binding kinetics at single cell resolution. Our findings show that the local environment affects the drug-receptor interactions, and in situ measurement of membrane protein binding kinetics is important.

S-Palmitoylation is a key regulatory mechanism controlling protein targeting, localization, stability, and activity. Since increasing evidence shows that its disruption is implicated in many human diseases, the identification of palmitoylation sites is attracting more attention. However, the computational methods that are published so far for this purpose have suffered from a poor balance of sensitivity and specificity; hence, it is difficult to get a good generalized prediction ability on an external validation set, which holds back the further analysis of associations between disruption of palmitoylation and human inherited diseases. In this work, we present a reliable identification method for protein S-palmitoylation sites, called SeqPalm, based on a series of newly composed features from protein sequences and the synthetic minority oversampling technique. With only 16 extracted key features, this approach achieves the most favorable prediction performance up to now with sensitivity, specificity, and Matthew's correlation coefficient values of 95.4%, 96.3%, and 0.917, respectively. Then, all known disease-associated variations are studied by SeqPalm. It is found that 243 potential loss or gain of palmitoylation sites are highly associated with human inherited disease. The analysis presents several potential therapeutic targets for inherited diseases associated with loss or gain of palmitoylation function. There are even biological evidence that are coordinate with our prediction results. Therefore, this work presents a novel approach to discover the molecular basis of pathogenesis associated with abnormal palmitoylation. SeqPalm is now available online at http://lishuyan.lzu.edu.cn/seqpalm , which can not only annotate the palmitoylation sites of proteins but also distinguish loss or gain of palmitoylation sites by protein variations.

Antibody-conjugated nanomaterials have attracted much attention because of their applications in nanomedicine and nanotheranostics, and amplification of detection signals. For many of these applications, the nanoconjugates must bind with a cell membrane receptor (antigen) specifically before entering the cells and reaching the final target, which is thus important but not well understood. Here, a plasmonic imaging study of the binding kinetics of antibody-conjugated gold nanoparticles with antigen-expressing cells is presented, and the results are compared with that of the nanoparticle-free antibody. It is found that the nanoconjugates can significantly affect the binding kinetics compared with free antibody molecules, depending on the density of the antibody conjugated on the nanoparticles, and expressing level of the antigen on the cell membrane. The results are analyzed in terms of a transition from monovalent binding model to a bivalent binding model when the conjugation density and expressing level increase. These findings help optimize the design of functional nanomaterials for drug delivery and correct interpretation of data obtained with nanoparticle signal amplification.

The occurrence, distribution, bioconcentration and diet safety via seafood consumption of 19 antibiotics were investigated in eight closed mariculture ponds, four estuaries, two nearshore areas and one offshore area from the Beibu Gulf. Seventeen, 16, 15 and 7 antibiotics were detected at total concentrations of 43.2 − 885 ng L−1, 22.4 − 118 ng L−1, 22.7 − 24.5 ng L−1, and 1.81–3.23 ng L−1 in the water of the above different areas, respectively. This indicates that the mariculture ponds are important sources of antibiotic pollution on the coast of the Beibu Gulf. Ten antibiotics were detected in feed samples with concentrations ranging from 0.03 to 95.4 ng g−1, demonstrating the presence of antibiotics in the feed and/or residual antibiotics in the raw material of the feed. The field bioconcentration factors (BCFs) of the antibiotics calculated in different culture organisms ranged from 0.55 to 10,774 L kg−1. The estimated daily intakes (EDIs) of sulphonamides, fluoroquinolones, macrolides and chloramphenicols via aquatic products were 19.8–105, 33.7–178, 34.9–186 and 6.9–37.1 ng d−1, respectively. According to the acceptable daily intakes (ADIs) and maximum residue limits (MRLs) proposed by different organisations, these aquatic products (shrimp, crab and oyster) reached the standard of safe consumption and could not pose a health risk to humans. However, a potential elevated risk to humans may remain because of the occurrence of multiple antibiotics in the cultured organisms, particularly for sensitive populations, such as pregnant women, the elderly and children.

Cancers are regarded as malignant proliferations of tumor cells present in many tissues and organs, which can severely curtail the quality of human life. The potential of using plasma DNA for cancer detection has been widely recognized, leading to the need of mapping the tissue-of-origin through the identification of somatic mutations. With cutting-edge technologies, such as next-generation sequencing, numerous somatic mutations have been identified, and the mutation signatures have been uncovered across different cancer types. However, somatic mutations are not independent events in carcinogenesis but exert functional effects. In this study, we applied a pan-cancer analysis to five types of cancers: (I) breast cancer (BRCA), (II) colorectal adenocarcinoma (COADREAD), (III) head and neck squamous cell carcinoma (HNSC), (IV) kidney renal clear cell carcinoma (KIRC), and (V) ovarian cancer (OV). Based on the mutated genes of patients suffering from one of the aforementioned cancer types, patients they were encoded into a large number of numerical values based upon the enrichment theory of gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We analyzed these features with the Monte-Carlo Feature Selection (MCFS) method, followed by the incremental feature selection (IFS) method to identify functional alteration features that could be used to build the support vector machine (SVM)-based classifier for distinguishing the five types of cancers. Our results showed that the optimal classifier with the selected 344 features had the highest Matthews correlation coefficient value of 0.523. Sixteen decision rules produced by the MCFS method can yield an overall accuracy of 0.498 for the classification of the five cancer types. Further analysis indicated that some of these features and rules were supported by previous experiments. This study not only presents a new approach to mapping the tissue-of-origin for cancer detection but also unveils the specific functional alterations of each cancer type, providing insight into cancer-specific functional aberrations as potential therapeutic targets. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

In this manuscript, a disposable paper-based analytical device comprised of a closed bipolar electrode (BPE) was fabricated for the ultrasensitive electrochemiluminescence (ECL) detection of intracellular H

Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing. Results: Hypertension implicated a remarkable gut dysbiosis with significant reduction in within-sample diversity and shift in microbial composition. Metagenome-wide association study (MGWAS) revealed 53,953 microbial genes that differ in distribution between the patients and healthy controls (false discovery rate, 0.05) and can be grouped into 68 clusters representing bacterial species. Opportunistic pathogenic taxa, such as, Klebsiella spp., Streptococcus spp., and Parabacteroides merdae were frequently distributed in hypertensive gut microbiome, whereas the short-chain fatty acid producer, such as, Roseburia spp. and Faecalibacterium prausnitzii, were higher in controls. The number of hypertension-associated species also showed stronger correlation to the severity of disease. Functionally, the hypertensive gut microbiome exhibited higher membrane transport, lipopolysaccharide biosynthesis and steroid degradation, while in controls the metabolism of amino acid, cofactors and vitamins was found to be higher. We further provided the microbial markers for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.78, demonstrating the potential of gut microbiota in prediction of hypertension. Conclusion: These findings represent specific alterations in microbial diversity, genes, species and functions of the hypertensive gut microbiome. Further studies on the causality relationship between hypertension and gut microbiota will offer new prospects for treating and preventing the hypertension and its associated diseases.

Adult neural stem cells (NSCs) are a group of multi-potent, self-renewing progenitor cells that contribute to the generation of new neurons and oligodendrocytes. Three subtypes of NSCs can be isolated based on the stages of the NSC lineage, including quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs). Although it is widely accepted that these three groups of NSCs play different roles in the development of the nervous system, their molecular signatures are poorly understood. In this study, we applied the Monte-Carlo Feature Selection (MCFS) method to identify the gene expression signatures, which can yield a Matthews correlation coefficient (MCC) value of 0.918 with a support vector machine evaluated by ten-fold cross-validation. In addition, some classification rules yielded by the MCFS program for distinguishing above three subtypes were reported. Our results not only demonstrate a high classification capacity and subtype-specific gene expression patterns but also quantitatively reflect the pattern of the gene expression levels across the NSC lineage, providing insight into deciphering the molecular basis of NSC differentiation. This article is protected by copyright. All rights reserved

Background: As one of essential post-translational modifications (PTMs), the citrullination or deimination on an arginine residue would change the molecular weight and electrostatic charge of its side-chain. And it has been found that the citrullination in protein sequences was catalyzed by a type of Ca2+-dependent enzyme family called peptidylarginine deiminase (PAD), which include five isotypes: PAD1, 2, 3, 4/5, and 6. Citrullinated proteins participate in many biological processes, e.g. the citrullination of myelin basic protein (MBP) assists the early development of central nervous system. However, abnormal modifications on citrullinated proteins would also lead to some severe human diseases including multiple sclerosis and rheumatoid arthritis. Objective: Therefore, it is necessary and important to identify the citrullination sites in protein sequences. The information about the location of citrulliantion sites in protein sequences will be useful to investigate the molecular functions and disease mechanisms related to citrullinated proteins. Materials and Methods: In this study, we investigated the peptide segments that contain the citrullination sites in the centers, which were encoded into numeric digits from four aspects. Thus, we yielded a training set with 116 positive samples and 232 negative samples. Then, a reliable feature selection technique, called maximum-relevance-minimum-redundancy (mRMR), was applied to analyze these features, and four algorithms, including random forest (RF), Dagging, nearest neighbor algorithm (NNA), and support vector machine (SVM), together with the incremental feature selection (IFS) method were adopted to extract important features. Results: Finally an optimal classifier derived from RF algorithm was constructed to predict citrullination sites. 44 most prominent features were comprehensively analyzed and their biological characteristics in citrullination catalysis were also revealed. Conclusion: We believed that the biological features obtained in this pioneering work would provide some useful insights into the formation and function of citrullination and the optimal classifier could be a useful tool to identify citrullination sites in protein sequences.

Mono(2-ethylhexyl) phthalate (MEHP), the active metabolite of di(2-ethylhexyl) phthalate (DEHP), has been known to have adverse effects on the reproductive system, urologic systems, hepatic, developmental toxicities and carcinogenicity. However, the effect of MEHP on cardiovascular toxicity remains unclear. Therefore, we aimed to evaluate the cytotoxic effects of MEHP and the possible molecular mechanism. We found that treatment of EA.hy 926 cells with MEHP induced autophagy at earlier time (6 h) in this study. Lysosomal membrane permeabilization (LMP) occurred, after treatment with MEHP for 12 h, followed by the release of cathepsin B. Autophagy inhibitor 3-methyladenine (3MA) attenuated MEHP-induced LMP and the release of cathepsin B in EA.hy 926 cells. Additionally, MEHP induced collapse of mitochondrial transmembrane potential, which was evidenced by JC-1 staining. Addition of 3MA relieved MEHP-induced apoptosis as assessed by the expression of caspase 3 and TUNEL assay, indicating that MEHP-induced apoptosis was autophagy-dependent. Cathepsin B inhibitor, CA-074 Me, suppressed MEHP-induced the mitochondria release of cytochrome c and apoptosis as well. In summary, our results suggest that MEHP induced autophagy-dependent apoptosis in EA.hy 926 cells through the lysosomal-mitochondrial axis. This study provides new mechanistic insights into MEHP-induced cardiovascular toxicity.

As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients’ personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR) algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases.

Mono-(2-ethylhexyl) phthalate (MEHP) is an active metabolite of di-(2-ethylhexyl) phthalate (DEHP). MEHP has toxic effects on cardiovascular system, but the possible molecular mechanisms are not completely elucidated. In our study, 3-methyladenine (3-MA), an autophagosome formation inhibitor, protected the EA.hy926 cells against MEHP cytotoxicity, and rapamycin, an autophagosome formation stimulator, further decreased the cell viability in the MEHP-treated EA.hy926 cells. Thus, autophagy may play an important role in MEHP-induced toxicity. MEHP increased the autophagosome number in EA.hy926 cells detected under transmission electron microscope. Collapses of ΔΨm and reactive oxygen species (ROS) level were increased in a dose-dependent manner under treatment with 0-200μM MEHP for 24h. N-acetyl-l-cysteine (NAC), a ROS inhibitor, protected against MEHP-induced cytotoxicity and decreased the protein expression of LC3-II. These findings suggested that MEHP-induced autophagic cell death was ROS-dependent in EA.hy926 cells. Knockdown of Akt1 with Akt1 siRNA aggravated MEHP-induced cell death, and insulin, an Akt1 activator, alleviated MEHP-induced cell death. These results were consistent with the expression of LC3-II using western blot. The phospho-Akt1(Ser473) (p-Akt1) level was enhanced after pretreatment with NAC. In conclusion, it is possible that ROS elicited autophagy through Akt1 pathway in the MEHP-treated EA.hy926 cells.

During the display of peptide/human leukocyte antigen (HLA) -I complex for further immune recognition, the cleaved and transported antigenic peptides have to bind to HLA-I protein and the binding affinity between peptide epitopes and HLA proteins directly influences the immune recognition ability in human beings. Key factors affecting the binding affinity during the generation, selection and presentation processes of HLA-I complex have not yet been fully discovered. In this study, a new method describing the HLA class I-peptide interactions was proposed. Three hundred and forty features of HLA I proteins and peptide sequences were utilized for analysis by four candidate algorithms, screening the optimal classifier. Features derived from the optimal classifier were further selected and systematically analyzed, revealing the core regulators. The results validated the hypothesis that features of HLA I proteins and related peptides simultaneously affect the binding process, though with discrepant redundancy. Besides, the high relative ratio (16/20) of the amino acid composition features suggests the unique role of sequence signatures for the binding processes. Integrating biological, evolutionary and chemical features of both HLA I molecules and peptides, this study may provide a new perspective of the underlying mechanisms of HLA I-mediated immune reactions.

A drug's biological half-life is defined as the time required for the human body to metabolize or eliminate 50% of the initial drug dosage. Correctly measuring the half-life of a given drug is helpful for the safe and accurate usage of the drug. In this study, we investigated which gene ontology (GO) terms and biological pathways were highly related to the determination of drug half-life. The investigated drugs, with known half-lives, were analyzed based on their enrichment scores for associated GO terms and KEGG pathways. These scores indicate which GO terms or KEGG pathways the drug targets. The feature selection method, minimum redundancy maximum relevance, was used to analyze these GO terms and KEGG pathways and to identify important GO terms and pathways, such as sodium-independent organic anion transmembrane transporter activity (GO:0015347), monoamine transmembrane transporter activity (GO:0008504), negative regulation of synaptic transmission (GO:0050805), neuroactive ligand-receptor interaction (hsa04080), serotonergic synapse (hsa04726), and linoleic acid metabolism (hsa00591), among others. This analysis confirmed our results and may show evidence for a new method in studying drug half-lives and building effective computational methods for the prediction of drug half-lives.

Pancreatic cancer is a serious disease that results in more than thirty thousand deaths around the world per year. To design effective treatments, many investigators have devoted themselves to the study of biological processes and mechanisms underlying this disease. However, it is far from complete. In this study, we tried to extract important gene ontology (GO) terms and KEGG pathways for pancreatic cancer by adopting some existing computational methods. Genes that have been validated to be related to pancreatic cancer and have not been validated were represented by features derived from GO terms and KEGG pathways using the enrichment theory. A popular feature selection method, minimum redundancy maximum relevance, was employed to analyze these features and extract important GO terms and KEGG pathways. An extensive analysis of the obtained GO terms and KEGG pathways was provided to confirm the correlations between them and pancreatic cancer.

Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1 and CDH2 and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.