Displaying publications 1 - 20 of 28 in total

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  1. Choi JR, Liu Z, Hu J, Tang R, Gong Y, Feng S, et al.
    Anal Chem, 2016 06 21;88(12):6254-64.
    PMID: 27012657 DOI: 10.1021/acs.analchem.6b00195
    In nucleic acid testing (NAT), gold nanoparticle (AuNP)-based lateral flow assays (LFAs) have received significant attention due to their cost-effectiveness, rapidity, and the ability to produce a simple colorimetric readout. However, the poor sensitivity of AuNP-based LFAs limits its widespread applications. Even though various efforts have been made to improve the assay sensitivity, most methods are inappropriate for integration into LFA for sample-to-answer NAT at the point-of-care (POC), usually due to the complicated fabrication processes or incompatible chemicals used. To address this, we propose a novel strategy of integrating a simple fluidic control strategy into LFA. The strategy involves incorporating a piece of paper-based shunt and a polydimethylsiloxane (PDMS) barrier to the strip to achieve optimum fluidic delays for LFA signal enhancement, resulting in 10-fold signal enhancement over unmodified LFA. The phenomena of fluidic delay were also evaluated by mathematical simulation, through which we found the movement of fluid throughout the shunt and the tortuosity effects in the presence of PDMS barrier, which significantly affect the detection sensitivity. To demonstrate the potential of integrating this strategy into a LFA with sample-in-answer-out capability, we further applied this strategy into our prototype sample-to-answer LFA to sensitively detect the Hepatitis B virus (HBV) in clinical blood samples. The proposed strategy offers great potential for highly sensitive detection of various targets for wide application in the near future.
  2. Guo L, Liu X, Zhao C, Hu Z, Xu X, Cheng KK, et al.
    Anal Chem, 2022 Oct 25;94(42):14522-14529.
    PMID: 36223650 DOI: 10.1021/acs.analchem.2c01456
    Spatial segmentation is a critical procedure in mass spectrometry imaging (MSI)-based biochemical analysis. However, the commonly used unsupervised MSI segmentation methods may lead to inappropriate segmentation results as the MSI data is characterized by high dimensionality and low signal-to-noise ratio. This process can be improved by the incorporation of precise prior knowledge, which is hard to obtain in most cases. In this study, we show that the incorporation of partial or coarse prior knowledge from different sources such as reference images or biological knowledge may also help to improve MSI segmentation results. Here, we propose a novel interactive segmentation strategy for MSI data called iSegMSI, which incorporates prior information in the form of scribble-regularization of the unsupervised model to fine-tune the segmentation results. By using two typical MSI data sets (including a whole-body mouse fetus and human thyroid cancer), the present results demonstrate the effectiveness of the iSegMSI strategy in improving the MSI segmentations. Specifically, the method can be used to subdivide a region into several subregions specified by the user-defined scribbles or to merge several subregions into a single region. Additionally, these fine-tuned results are highly tolerant to the imprecision of the scribbles. Our results suggest that the proposed iSegMSI method may be an effective preprocessing strategy to facilitate the analysis of MSI data.
  3. Guo L, Zhu J, Wang K, Cheng KK, Xu J, Dong L, et al.
    Anal Chem, 2023 Jun 27;95(25):9714-9721.
    PMID: 37296503 DOI: 10.1021/acs.analchem.3c02002
    High-resolution reconstruction has attracted increasing research interest in mass spectrometry imaging (MSI), but it remains a challenging ill-posed problem. In the present study, we proposed a deep learning model to fuse multimodal images to enhance the spatial resolution of MSI data, namely, DeepFERE. Hematoxylin and eosin (H&E) stain microscopy imaging was used to pose constraints in the process of high-resolution reconstruction to alleviate the ill-posedness. A novel model architecture was designed to achieve multi-task optimization by incorporating multi-modal image registration and fusion in a mutually reinforced framework. Experimental results demonstrated that the proposed DeepFERE model is able to produce high-resolution reconstruction images with rich chemical information and a detailed structure on both visual inspection and quantitative evaluation. In addition, our method was found to be able to improve the delimitation of the boundary between cancerous and para-cancerous regions in the MSI image. Furthermore, the reconstruction of low-resolution spatial transcriptomics data demonstrated that the developed DeepFERE model may find wider applications in biomedical fields.
  4. Han H, Sabani NB, Nobusawa K, Takei F, Nakatani K, Yamashita I
    Anal Chem, 2023 Jul 04;95(26):9729-9733.
    PMID: 37341999 DOI: 10.1021/acs.analchem.3c01126
    We have developed a DNA sensor that can be finalized to detect a specific target on demand. The electrode surface was modified with 2,7-diamino-1,8-naphthyridine (DANP), a small molecule with nanomolar affinity for the cytosine bulge structure. The electrode was immersed in a solution of synthetic probe-DNA that had a cytosine bulge structure at one end and a complementary sequence to the target DNA at the other end. The strong binding between the cytosine bulge and DANP anchored the probe DNAs to the electrode surface, and the electrode became ready for target DNA sensing. The complementary sequence portion of the probe DNA can be changed as requested, allowing for the detection of a wide variety of targets. Electrochemical impedance spectroscopy (EIS) with the modified electrode detected target DNAs with a high sensitivity. The charge transfer resistance (Rct) extracted from EIS showed a logarithmic relationship with the concentration of target DNA. The limit of detection (LoD) was less than 0.01 μM. By this method, highly sensitive DNA sensors for various target sequences could be easily produced.
  5. Jajuli MN, Hussin MH, Saad B, Rahim AA, Hébrant M, Herzog G
    Anal Chem, 2019 06 04;91(11):7466-7473.
    PMID: 31050400 DOI: 10.1021/acs.analchem.9b01674
    A new sample preparation method is proposed for the extraction of pharmaceutical compounds (Metformin, Phenyl biguanide, and Phenformin) of varied hydrophilicity, dissolved in an aqueous sample. When in contact with an organic phase, an interfacial potential is imposed by the presence of an ion, tetramethylammonium (TMA+), common to each phase. The interfacial potential difference drives the transfer of ionic analytes across the interface and allows it to reach up to nearly 100% extraction efficiency and a 60-fold enrichment factor in optimized extraction conditions as determined by HPLC analysis.
  6. Joshi P, Okada T, Miyabayashi K, Miyake M
    Anal Chem, 2018 May 15;90(10):6116-6123.
    PMID: 29613775 DOI: 10.1021/acs.analchem.8b00247
    Organically (octyl amine, OA) surface modified electrocatalyst (OA-Pt/CB) was studied for its oxygen reduction reaction (ORR) activity via dc methods and its charge and mass transfer properties were studied via electrochemical impedance spectroscopy (EIS). Comparison with a commercial catalyst (TEC10V30E) with similar Pt content was also carried out. In EIS, both the catalysts showed a single time-constant with an emerging high-frequency semicircle of very small diameter which was fitted using suitable equivalent circuits. The organically modified catalyst showed lower charge-transfer resistance and hence, low polarization resistance in high potential region as compared to the commercial catalyst. The dominance of kinetic processes was observed at 0.925-1.000 V, whereas domination of diffusion based processes was observed at lower potential region for the organic catalyst. No effect due to the presence of carbon was observed in the EIS spectra. Using the hydrodynamic method, higher current penetration depth was obtained for the organically modified catalyst at 1600 rpm. Exchange current density and Tafel slopes for both the electrocatalysts were calculated from the polarization resistance obtained from EIS which was in correlation with the results obtained from dc methods.
  7. Leo BF, Fearn S, Gonzalez-Cater D, Theodorou I, Ruenraroengsak P, Goode AE, et al.
    Anal Chem, 2019 Sep 03;91(17):11098-11107.
    PMID: 31310103 DOI: 10.1021/acs.analchem.9b01704
    There are no methods sensitive enough to detect enzymes within cells, without the use of analyte labeling. Here we show that it is possible to detect protein ion signals of three different H2S-synthesizing enzymes inside microglia after pretreatment with silver nanowires (AgNW) using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Protein fragment ions, including the fragment of amino acid (C4H8N+ = 70 amu), fragments of the sulfur-producing cystathionine-containing enzymes, and the Ag+ ion signal could be detected without the use of any labels; the cells were mapped using the C4H8N+ amino acid fragment. Scanning electron microscopy imaging and energy-dispersive X-ray chemical analysis showed that the AgNWs were inside the same cells imaged by TOF-SIMS and transformed chemically into crystalline Ag2S within cells in which the sulfur-producing proteins were detected. The presence of these sulfur-producing cystathionine-containing enzymes within the cells was confirmed by Western blots and confocal microscopy images of fluorescently labeled antibodies against the sulfur-producing enzymes. Label-free TOF-SIMS is very promising for the label-free identification of H2S-contributing enzymes and their cellular localization in biological systems. The technique could in the future be used to identify which of these enzymes are most contributory.
  8. Lin G, Dong L, Cheng KK, Xu X, Wang Y, Deng L, et al.
    Anal Chem, 2023 Aug 22;95(33):12505-12513.
    PMID: 37557184 DOI: 10.1021/acs.analchem.3c02246
    Metabolic pathways are regarded as functional and basic components of the biological system. In metabolomics, metabolite set enrichment analysis (MSEA) is often used to identify the altered metabolic pathways (metabolite sets) associated with phenotypes of interest (POI), e.g., disease. However, in most studies, MSEA suffers from the limitation of low metabolite coverage. Random walk (RW)-based algorithms can be used to propagate the perturbation of detected metabolites to the undetected metabolites through a metabolite network model prior to MSEA. Nevertheless, most of the existing RW-based algorithms run on a general metabolite network constructed based on public databases, such as KEGG, without taking into consideration the potential influence of POI on the metabolite network, which may reduce the phenotypic specificities of the MSEA results. To solve this problem, a novel pathway analysis strategy, namely, differential correlation-informed MSEA (dci-MSEA), is proposed in this paper. Statistically, differential correlations between metabolites are used to evaluate the influence of POI on the metabolite network, so that a phenotype-specific metabolite network is constructed for RW-based propagation. The experimental results show that dci-MSEA outperforms the conventional RW-based MSEA in identifying the altered metabolic pathways associated with colorectal cancer. In addition, by incorporating the individual-specific metabolite network, the dci-MSEA strategy is easily extended to disease heterogeneity analysis. Here, dci-MSEA was used to decipher the heterogeneity of colorectal cancer. The present results highlight the clustering of colorectal cancer samples with their cluster-specific selection of differential pathways and demonstrate the feasibility of dci-MSEA in heterogeneity analysis. Taken together, the proposed dci-MSEA may provide insights into disease mechanisms and determination of disease heterogeneity.
  9. Liu Y, Sairi M, Neusser G, Kranz C, Arrigan DW
    Anal Chem, 2015 Jun 2;87(11):5486-90.
    PMID: 25962586 DOI: 10.1021/acs.analchem.5b01162
    In this work, independent radial diffusion at arrayed nanointerfaces between two immiscible electrolyte solutions (nanoITIES) was achieved. The arrays were formed at nanopores fabricated by focused ion beam milling of silicon nitride (SiN) membranes, enabling the reproducible and systematic design of five arrays with different ratios of pore center-to-center distance (rc) to pore radius (ra). Voltammetry across water-1,6-dichlorohexane nanoITIES formed at these arrays was examined by the interfacial transfer of tetrapropylammonium ions. The diffusion-limited ion-transfer current increased with the ratio rc/ra, reaching a plateau for rc/ra ≥ 56, which was equivalent to the theoretical current for radial diffusion to an array of independent nanoITIES. As a result, mass transport to the nanoITIES arrays was greatly enhanced due to the decreased overlap of diffusion zones at adjacent nanoITIES, allowing each interface in the array to behave independently. When the rc/ra ratio increased from 13 to 56, the analytical performance parameters of sensitivity and limit of detection were improved from 0.50 (±0.02) A M(-1) to 0.76 (±0.02) A M(-1) and from 0.101 (±0.003) μM to 0.072 (±0.002) μM, respectively. These results provide an experimental basis for the design of arrayed nanointerfaces for electrochemical sensing.
  10. Makhsin SR, Goddard NJ, Gupta R, Gardner P, Scully PJ
    Anal Chem, 2020 11 17;92(22):14907-14914.
    PMID: 32378876 DOI: 10.1021/acs.analchem.0c00586
    The metal-clad leaky waveguide (MCLW) is an optical biosensor consisting of a metal layer and a low index waveguide layer on a glass substrate. This label-free sensor measures refractive index (RI) changes within the waveguide layer. This work shows the development and optimization of acrylate based-hydrogel as the waveguide layer formed from PEG diacrylate (PEGDA, Mn 700), PEG methyl ether acrylate (PEGMEA, Mn 480), and acrylate-PEG2000-NHS fabricated on a substrate coated with 9.5 nm of titanium. The acrylate-based hydrogel is a synthetic polymer, so properties such as optical transparency, porosity, and hydrogel functionalization by a well-controlled reactive group can be tailored for immobilization of the bioreceptor within the hydrogel matrix. The waveguide sensor demonstrated an equal response to solutions of identical RI containing small (glycerol) and large (bovine serum albumin; BSA) analyte molecules, indicating that the hydrogel waveguide film is highly porous to both sizes of molecule, thus potentially allowing penetration of a range of analytes within the porous matrix. The final optimized MCLW chip was formed from a total hydrogel concentration of 40% v/v of PEGMEA-PEGDA (Mn 700), functionalized with 2.5% v/v of acrylate-PEG2000-NHS. The sensor generated a single-moded waveguide signal with a RI sensitivity of 128.61 ± 0.15° RIU-1 and limit of detection obtained at 2.2 × 10-6 RIU with excellent signal-to-noise ratio for the glycerol detection. The sensor demonstrated RI detection by monitoring changes in the out-coupled angle resulting from successful binding of d-biotin to streptavidin immobilized on functionalized acrylate hydrogel, generating a binding signal of (12.379 ± 0.452) × 10-3°.
  11. Nasrollahpour H, Khalilzadeh B, Naseri A, Sillanpää M, Chia CH
    Anal Chem, 2022 Jan 11;94(1):349-365.
    PMID: 34878242 DOI: 10.1021/acs.analchem.1c03909
  12. Ng JK, Tay FH, Wray PS, Mohd Saberi SS, Ken Ting KK, Khor SM, et al.
    Anal Chem, 2021 11 16;93(45):15015-15023.
    PMID: 34730329 DOI: 10.1021/acs.analchem.1c02652
    The onset of Covid-19 pandemic has resulted in the exponential growth of alcohol-based hand rub (ABHR)/hand sanitizer use. Reports have emerged of ABHR products containing methanol, a highly toxic compound to humans, exposing users to acute and chronic medical illnesses. While gas chromatography-mass spectrometry (GC-MS) remains the gold-standard method for the detection and identification of impurities in ABHRs, there exist limitations at widespread volume testing. This paper demonstrates the capability of an inexpensive portable pyroelectric linear array infrared spectrometer to rapidly test ABHR and compare the performance with a benchtop Fourier transform infrared spectrometer and HS-GC-MS. Multicomponent partial least square quantification models were built with performance found to be comparable between the two spectrometers and with the HS-GC-MS. Furthermore, the portable spectrometer was field-tested with real-world samples in Malaysia on both retail products (Group A) and freely deployed public dispensers (Group B) between May and November 2020. A total of 386 samples were tested. Only 75.2% of Group A met the criteria of safe and effective ABHR [no detectable methanol and alcohol concentration above 60% (v/v)], while <50% of Group B did. In addition, 7.4 and 18.8% of Group A and Group B, respectively, were found to contain methanol above permissible limits. The high percentage of sub-standard and methanol-containing samples combined with the frequent use of ABHR by the public highlights the need for and importance of a portable and rapid testing device for widespread screening of ABHR against falsified products and protects the general public.
  13. Ng KL, Khor SM
    Anal Chem, 2017 09 19;89(18):10004-10012.
    PMID: 28845664 DOI: 10.1021/acs.analchem.7b02432
    Guanine (G), adenine (A), thymine (T), and cytosine (C) are the four basic constituents of DNA. Studies on DNA composition have focused especially on DNA damage and genotoxicity. However, the development of a rapid, simple, and multiplex method for the simultaneous measurement of the four DNA bases remains a challenge. In this study, we describe a graphite-based nanocomposite electrode (Au-rGO/MWCNT/graphite) that uses a simple electro-co-deposition approach. We successfully applied the developed sensor for multiplex detection of G, A, T, and C, using square-wave voltammetry. The sensor was tested using real animal and plant DNA samples in which the hydrolysis of T and C could be achieved with 8 mol L-1 of acid. The electrochemical sensor exhibited excellent sensitivity (G = 178.8 nA/μg mL-1, A = 92.9 nA/μg mL-1, T = 1.4 nA/μg mL-1, and C = 15.1 9 nA/μg mL-1), low limit of detection (G, A = 0.5 μg mL-1; T, C = 1.0 μg mL-1), and high selectivity in the presence of common interfering factors from biological matrixes. The reliability of the established method was assessed by method validation and comparison with the ultraperformance liquid chromatography technique, and a correlation of 103.7% was achieved.
  14. Okazaki T, Orii T, Tan SY, Watanabe T, Taguchi A, Rahman FA, et al.
    Anal Chem, 2020 07 21;92(14):9714-9721.
    PMID: 32551577 DOI: 10.1021/acs.analchem.0c01062
    We present an electrochemical long period fiber grating (LPFG) sensor for electroactive species with an optically transparent electrode. The sensor was fabricated by coating indium tin oxide onto the surface of LPFG using a polygonal barrel-sputtering method. LPFG was produced by an electric arc-induced technique. The sensing is based on change in the detection of electron density on the electrode surface during potential application and its reduction by electrochemical redox of analytes. Four typical electroactive species of methylene blue, hexaammineruthenium(III), ferrocyanide, and ferrocenedimethanol were used to investigate the sensor performance. The concentrations of analytes were determined by the modulation of the potential as the change in transmittance around the resonance band of LPFG. The sensitivity of the sensor, particularly to methylene blue, was high, and the sensor responded to a wide concentration range of 0.001 mM to 1 mM.
  15. Promja S, Puenpa J, Achakulvisut T, Poovorawan Y, Lee SY, Athamanolap P, et al.
    Anal Chem, 2023 Jan 12.
    PMID: 36633573 DOI: 10.1021/acs.analchem.2c05112
    Since the declaration of COVID-19 as a pandemic in early 2020, multiple variants of the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) have been detected. The emergence of multiple variants has raised concerns due to their impact on public health. Therefore, it is crucial to distinguish between different viral variants. Here, we developed a machine learning web-based application for SARS-CoV-2 variant identification via duplex real-time polymerase chain reaction (PCR) coupled with high-resolution melt (qPCR-HRM) analysis. As a proof-of-concept, we investigated the platform's ability to identify the Alpha, Delta, and wild-type strains using two sets of primers. The duplex qPCR-HRM could identify the two variants reliably in as low as 100 copies/μL. Finally, the platform was validated with 167 nasopharyngeal swab samples, which gave a sensitivity of 95.2%. This work demonstrates the potential for use as automated, cost-effective, and large-scale viral variant surveillance.
  16. Samat N, Tan PJ, Shaari K, Abas F, Lee HB
    Anal Chem, 2014 Feb 4;86(3):1324-31.
    PMID: 24405504 DOI: 10.1021/ac403709a
    Photodynamic therapy (PDT) is an alternative treatment for cancer that involves administration of a photosensitive drug or photosensitizer that localizes at the tumor tissue followed by in situ excitation at an appropriate wavelength of light. Tumour tissues are then killed by cytotoxic reactive oxygen species generated by the photosensitizer. Targeted excitation and photokilling of affected tissues is achieved through focal light irradiation, thereby minimizing systemic side effects to the normal healthy tissues. Currently, there are only a small number of photosensitizers that are in the clinic and many of these share the same structural core based on cyclic tetrapyrroles. This paper describes how metabolic tools are utilized to prioritize natural extracts to search for structurally new photosensitizers from Malaysian biodiversity. As proof of concept, we analyzed 278 photocytotoxic extracts using a hyphenated technique of liquid chromatography-mass spectrometry coupled with principal component analysis (LC-MS-PCA) and prioritized 27 extracts that potentially contained new photosensitizers for chemical dereplication using an in-house UPLC-PDA-MS-Photocytotoxic assay platform. This led to the identification of 2 new photosensitizers with cyclic tetrapyrrolic structures, thereby demonstrating the feasibility of the metabolic approach.
  17. Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, et al.
    Anal Chem, 2023 Dec 26;95(51):18793-18802.
    PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785
    Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
  18. Tey HY, Breadmore MC, See HH
    Anal Chem, 2023 Jan 31;95(4):2134-2139.
    PMID: 36649064 DOI: 10.1021/acs.analchem.2c02937
    A polymer inclusion membrane (PIM) based sampling probe was developed for electrokinetic extraction of drugs from biological fluids. The probe was fabricated by dip-coating a nonconductive glass capillary tube in a homogeneous PIM solution for three cycles. The PIM solution comprised cellulose triacetate (CTA), 2-nitrophenyl octyl ether (NPOE), and 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [EMIM][NTf2] in a ratio of 5:4:2. The developed probe electrokinetically extracted doxorubicin from human plasma, human serum, and dried blood spot (DBS). The practicability and reliability of the electrokinetic extraction were evaluated by LC-MS/MS to quantify the desorption of extracted doxorubicin. Under the optimized conditions, a quantification limit of 0.2-2 ng/mL was achieved for the three biological samples. The probe was further integrated into a portable battery-powered device for safe low-voltage (36 V) electrokinetic extraction. The developed technique is envisioned to provide a more efficient analytical workflow in the laboratory.
  19. Thang LY, See HH, Quirino JP
    Anal Chem, 2016 Sep 26.
    PMID: 27669824
    The translation of stacking techniques used in capillary electrophoresis (CE) to microchip CE (MCE) in order to improve concentration sensitivity is an important area of study. The success in stacking relies on the generation and control of the stacking boundaries which is a challenge in MCE because the manipulation of solutions is not as straightforward as in CE with a single channel. Here, a simple and rapid on-line sample concentration (stacking strategy) in a battery operated nonaqueous MCE device with a commercially available double T-junction glass chip is presented. A multi-stacking approach was developed in order to circumvent the issues for stacking in nonaqueous MCE. The cationic analytes from the two loading channels were injected under field-enhanced conditions and were focused by micelle-to-solvent stacking. This was achieved by the application of high electric fields along the two loading channels and a low electric field in the separation channel, with one ground electrode in the reservoir closest to the junction. At the junction, the stacked zones were re-stacked under field-enhanced conditions and then injected into the separation channels. The multi-stacking was verified under a fluorescence microscope using Rhodamine 6G as the analyte, revealing a sensitivity enhancement factor (SEF) of 110. The stacking approach was also implemented in the nonaqueous MCE with contactless conductivity detection of the anticancer drug tamoxifen as well as its metabolites. The multi-stacking and analysis time was 40 s and 110 s, respectively, the limit of detections was from 10 to 35 ng/mL, and the SEFs were 20 to 50. The method was able to quantify the target analytes from breast cancer patients.
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