Search Results (29)

Continuous-flow microfluidic biochips (CFMBs) automatically execute various bioassays by precisely controlling the transport of fluid samples, which is driven by pressure delivered through fluidic ports. High-level synthesis, as an important stage in the design flow of CFMBs, generates binding and scheduling solutions whose quality directly affects the efficiency of the execution of bioassays. Existing high-level synthesis methods perform numerous transport tasks concurrently to increase efficiency. However, fluidic ports cannot be shared between concurrently executing transport tasks, resulting in a large number of fluidic ports introduced by existing methods. Increasing the number of fluidic ports undermines the integration, reduces the reliability, and increases the manufacturing cost. In this paper, we propose a port-driven high-level synthesis method based on integer linear programming (ILP) called SlimPort, integrating the optimization of fluidic port number into high-level synthesis, which has never been considered in prior work. Meanwhile, to ensure bioassay correctness, volume management between devices with a non-fixed input/output ratio is realized. Additionally, two acceleration strategies for ILP, scheduling constraint reduction and upper boundary estimation of fluidic port number, are proposed to improve the efficiency of SlimPort. Experimental results from multiple benchmarks demonstrate that SlimPort leads to high assay execution efficiency and a low number of fluidic ports. Full article

Biomolecular detection plays essential and irreplaceable roles in safeguarding human health, impeding the transmission of diseases, and augmenting the efficacy of treatments. The precise and specific identification of biomarkers holds profound significance for the early diagnosis, real-time surveillance, and targeted treatment of various diseases. In the initial phases of numerous diseases, the absence of distinct biomarkers in the bloodstream often leads to weak detection signals when using traditional immune detection methods such as enzyme-linked immunosorbent assays (ELISAs), chemiluminescence, and fluorescence chromatography. With the surge in research on surface plasmons, innovative approaches have recently emerged that combine surface plasmon resonance (SPR) with immunological detection techniques, reducing the detection sensitivity to 283 ag/mL, shrinking the sensor size to 2.228 µm², and shortening the detection time to 5.5 min. This review provides an overview of the theoretical foundations of surface plasmon resonance and immunoassays and then delves into the latest advancements in biosensors based on these principles, categorizing them according to their detection mechanisms and methodologies. Finally, we discuss future research directions, opportunities, and the challenges hindering the development of highly sensitive immuno-biochips. Full article

The development of bionic organ-on-a-chip technology relies heavily on advancements in in situ sensors and biochip packaging. By integrating precise biological and fluid condition sensing with microfluidics and electronic components, long-term dynamic closed-loop culture systems can be achieved. This study aims to develop biocompatible heterogeneous packaging and laser surface modification techniques to enable the encapsulation of electronic components while minimizing their impact on fluid dynamics. Using a kidney-on-a-chip as a case study, a non-toxic packaging process and fluid interface control methods have been successfully developed. Experimentally, miniature pressure sensors and control circuit boards were encapsulated using parylene-C, a biocompatible material, to isolate biochemical fluids from electronic components. Ultraviolet laser processing was employed to fabricate structures on parylene-C. The results demonstrate that through precise control of processing parameters, the wettability of the material can be tuned freely within a contact angle range of 60° to 110°. Morphological observations and MTT assays confirmed that the material and the processing methods do not induce cytotoxicity. This technology will facilitate the packaging of various miniature electronic components and biochips in the future. Furthermore, laser processing enables rapid and precise control of interface conditions across different regions within the chip, demonstrating a high potential for customized mass production of biochips. The proposed innovations provide a solution for in situ sensing in organ-on-a-chip systems and advanced biochip packaging. We believe that the development of this technology is a critical step toward realizing the concept of “organ twin”. Full article

Infections caused by nontuberculous mycobacteria (NTM) are rising globally throughout the world. The number of species isolated from clinical samples is steadily growing, which demands the implementation of a robust diagnostic method with wide specificity. This study was carried out in in 2022–2024 in three clinical antituberculosis centers in the biggest cities of Russia: Moscow, Saint Petersburg, and Novosibirsk. We developed the DNA hybridization assay ‘Myco-biochip’ that allows the identification of 79 mycobacterial species and analyzed 3119 samples from 2221 patients. Sixty-eight mycobacterial species were identified in clinics, including the three novel species phylogenetically related to M. duvalii, M. lentiflavum, and M. talmoniae. The identification of a close relative of M. talmoniae adds to the existence of separate clade between M. terrae, M. triviale complexes and other slow-growing Mycobacteria, which supports the thesis against the splitting of Mycobacteria into five separate genera. Adding to the list of potentially pathogenic species, we identified M. adipatum and M. terramassiliense, which were previously described as natural habitats. The diversity of acid-fast bacilli identified in TB-suspected persons was not limited to the Mycobacteria genus and also includes species from genera Nocardia, Gordonia, Corynebacterium, Tsukamurella, and Rhodococcus of the order Mycobacteriales. The revealed bacterial diversity in patients with suspected NTM-diseases requires the implementation of relevant species identification assays as the first step in the laboratory diagnostic pipeline. Full article

We investigated the rise of nontuberculous mycobacteria (NTM) infections in Bulgaria, focusing on species identification and distribution from 2018 to 2022. Utilizing advanced diagnostic tools, including the Hain Mycobacterium CM/AS method, Myco-biochip assay, and whole-genome sequencing, the study identifies and characterizes a diverse range of Mycobacterium species from clinical samples. While M. avium, M. gordonae, M. fortuitum, and M. chelonae were dominating, a number of rare species were also found. They include such species as M. marseillense and M. celatum. Moreover, the noticeable prevalence of M. terrae complex species missed by conventional testing was observed. We identified a rare species, highly homologous to previously described strains from Japan; based on genome–genome distance data, we propose its reannotation as a new species. Further, a novel species was identified, which is significantly distinct from its closest neighbor, M. iranicum, with ANI = 87.18%. Based on the SeqCode procedure, we propose to name this new species Mycobacterium bulgaricum sp. nov. Dynamic changes in NTM species prevalence in Bulgaria observed from 2011 to 2022 highlight the emergence of new species and variations tied to environmental and demographic factors. This underscores the importance of accurate species identification and genotyping for understanding NTM epidemiology, informing public health strategies, and enhancing diagnostic accuracy and treatment protocols. Full article

Access to clean water is fundamental to public health and safety, serving as the cornerstone of well-being in communities. Despite the significant investments of millions of dollars in water testing and treatment processes, the United States continues to grapple with over 7 million waterborne-related cases annually. This persistent challenge underscores the pressing need for the development of a new, efficient, rapid, low-cost, and reliable method for ensuring water quality. The urgency of this endeavor cannot be overstated, as it holds the potential to safeguard countless lives and mitigate the pervasive risks associated with contaminated water sources. In this study, we introduce a biochip LAMP assay tailored for water source monitoring. Our method swiftly detects even extremely low concentrations of Escherichia coli (E. coli) in water, and 10 copies/μL of E. coli aqueous solution could yield positive results within 15 min on a PC-MEDA biochip. This innovation marks a significant departure from the current reliance on lab-dependent methods, which typically necessitate several days for bacterial culture and colony counting. Our multifunctional biochip system not only enables the real-time LAMP testing of crude E. coli samples but also holds promise for future modifications to facilitate on-site usage, thereby revolutionizing water quality assessment and ensuring rapid responses to potential contamination events. Full article

Due to advances in additive manufacturing and prototyping, affordable and rapid microfluidic sensor-integrated assays can be fabricated using additive manufacturing, xurography and electrode shadow masking to create versatile platform technologies aimed toward qualitative assessment of acute cytotoxic or cytolytic events using stand-alone biochip platforms in the context of environmental risk assessment. In the current study, we established a nasal mucosa biosensing platform using RPMI2650 mucosa cells inside a membrane-integrated impedance-sensing biochip using exclusively rapid prototyping technologies. In a final proof-of-concept, we applied this biosensing platform to create human cell models of nasal mucosa for monitoring the acute cytotoxic effect of zinc oxide reference nanoparticles. Our data generated with the biochip platform successfully monitored the acute toxicity and cytolytic activity of 6 mM zinc oxide nanoparticles, which was non-invasively monitored as a negative impedance slope on nasal epithelial models, demonstrating the feasibility of rapid prototyping technologies such as additive manufacturing and xurography for cell-based platform development. Full article

Intracranial chondroid tumors are a heterogeneous group of neoplasms characterized by the presence of a cartilage matrix. These tumors exhibit overlapping clinical and histological features. Mutations in IDH1/2 genes serve as important diagnostic markers of tumor type, particularly chondrosarcoma. To improve the accuracy of IDH1/2 diagnostics, we compared three methods: biochip assay, real-time PCR with DNA melting analysis using TaqMan probes and sequencing (qPCR-DMA-Sanger), and immunohistochemistry (IHC). Tumor samples from 96 patients were investigated. The IDH1 mutations were detected in 34/64 (53%) chondrosarcomas; IHC detected 27/56 (48.2%) mutations, the qPCR-DMA-Sanger method 27/59 (46%) mutations, and the biochip assay revealed 29/60 (48.3%) mutations. The detection of IDH1 mutations in chordoma (2/15) and osteosarcoma (2/7) suggested the need for a revised diagnosis. In benign tumors, IDH1 mutations were present in chondroma (4/6), but absent in chondromyxoid fibroma (0/4). The most frequent IDH1 mutations were R132C (60%), R132L, and R132G (13.5% each), R132H (8%), and R132S (5%). The concordance between the biochip assay and IHC was 90%, between IHC and PCR-DMA-Sanger 83%, and between biochip assay and qPCR-DMA-Sanger was 98%, respectively. No IDH2 mutations were found. The use of independent diagnostic methods may improve the detection of IDH-mutant specimens in chondroid tumors. Full article

Progress in macrophage research is crucial for numerous applications in medicine, including cancer and infectious diseases. However, the existing methods to manipulate living macrophages are labor-intense and inconvenient. Here, we show that macrophage membranes can be reconstituted after storage for months at 4 °C, with their CD206 receptor selectivity and specificity being similar to those in the living cells. Then, we have developed a mannose ligand, specific to CD206, linked with PEG as an IR spectroscopy marker to detect binding with the macrophage receptor. PEG was selected due to its unique adsorption band of the C–O–C group at IR spectra, which does not overlap with other biomolecules’ spectroscopic feature. Next, competitive binding assay versus the PEG-bound ligand has enabled the selection of other higher-affinity ligands specific to CD206. Furthermore, those higher-affinity ligands were used to differentiate activated macrophages in a patient’s bronchoalveolar (BAL) or nasopharyngeal (NPL) lavage. CD206− control cells (HEK293T) showed only non-specific binding. Therefore, biochips based on reconstituted macrophage membranes as well as PEG-trimannoside as an IR spectroscopic marker can be used to develop new methods facilitating macrophage research and macrophage-focused drug discovery. Full article

Bacterial infections represent a serious and global threat in modern medicine; thus, it is very important to rapidly detect pathogenic bacteria, such as Escherichia coli (E. coli) O157:H7. Once treatments are delayed after the commencement of symptoms, the patient’s health quickly deteriorates. Hence, real-time detection and monitoring of infectious agents are highly critical in early diagnosis for correct treatment and safeguarding public health. To detect these pathogenic bacteria, many approaches have been applied by the biosensors community, for example, widely-used polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), culture-based method, and adenosine triphosphate (ATP) bioluminescence. However, these approaches have drawbacks, such as time-consumption, expensive equipment, and being labor-intensive, making it critical to develop ultra-sensitive and highly selective detection. The microfluidic platform based on surface plasmon resonance (SPR), electrochemical sensing, and rolling circle amplification (RCA) offers proper alternatives capable of supplementing the technological gap for pathogen detection. Note that the microfluidic biochip allows to develop rapid, sensitive, portable, and point-of-care (POC) diagnostic tools. This review focuses on recent studies regarding accurate and rapid detection of E. coli O157:H7, with an emphasis on POC methods and devices that complement microfluidic systems. We also examine the efficient whole-body detection by employing antimicrobial peptides (AMPs), which has attracted growing attention in many applications. Full article

In vitro cell cultures are used as models for drug discovery. The detection of cell damage biomarkers such as adenylate kinase (AK) is often used in drug screening and cell biology experiments. A microfluidic platform for AK detection was developed with the capability of detecting the AK resulting from the lysis of 10–100 human colorectal adenocarcinoma HCT116 cells. For this assay, AK was captured on the surface of microbeads integrated into a microfluidic device and optically detected using a fluorescently labelled anti-AK antibody. Microfluidic technologies have in addition been used to develop two- and three-dimensional cell culture models that have the potential to accelerate drug discovery. The microfluidic platform was used to detect the AK resulting from the lysis of HCT116 cells cultivated in a microfluidic biochip, demonstrating the potential for the integration of the miniaturised biosensor with the cell chip. Full article

This study focused on the identification of bacterial profiles of semen in normozoospermic men and their possible involvement in changes to the sperm structural integrity and functional activity. Furthermore, we studied possible fluctuations of selected cytokines, oxidative markers, and antibacterial proteins as a result of bacterial presence in the ejaculate. Sperm motility was assessed with computer-assisted sperm analysis, while sperm apoptosis, necrosis and acrosome integrity were examined with fluorescent methods. Reactive oxygen species (ROS) generation was quantified via luminometry, sperm DNA fragmentation was evaluated using the TUNEL protocol and chromatin-dispersion test, while the JC-1 assay was applied to evaluate the mitochondrial membrane potential. Cytokine levels were quantified with the biochip assay, whilst selected antibacterial proteins were quantified using the ELISA method. The predominant species identified by the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were Staphylococcus hominis, Staphylococcus capitis and Micrococcus luteus. The results revealed that the sperm quality decreased proportionally to the increasing bacterial load and occurrence of conditionally pathogenic bacteria, including Enterococcus faecalis, Staphylococcus aureus and Escherichia coli. Antimicrobial susceptibility tests revealed a substantial resistance of randomly selected bacterial strains to ampicillin, vancomycin, tobramycin, and tetracycline. Furthermore, an increased bacterial quantity in semen was accompanied by elevated levels of pro-inflammatory cytokines, including interleukin-1, interleukin-2, interleukin-6, tumor necrosis factor alpha as well as ROS overproduction and lipid peroxidation of the sperm membranes. Our results suggest that semen quality may be notably affected by the bacterial quantity as well as quality. It seems that bacteriospermia may be associated with inflammatory processes, oxidative stress, sperm structural deterioration, and a subsequent risk for the development of subfertility, even in normozoospermic males. Full article

Several factors can affect the allergen content and profile of a specific food, including processing procedures often leading to a decrease in allergenicity, although no change, or even an increase, have also been reported. Evaluation of the effectiveness of a processing procedure requires the availability of reliable methodologies to assess the variation in molecules able to induce allergic reactions in the analyzed food. Conventional and innovative strategies and methodologies can be exploited to identify allergenic proteins in foodstuffs. However, depending on the specific purposes, different methods can be used. In this review, we have critically reviewed the advantages of an innovative method, the multiplex allergen microarray-based immunoassay, in the detection of allergens in foodstuffs. In particular, we have analyzed some studies reporting the exploitation of an IgE-binding inhibition assay on multiplex allergen biochips, which has not yet been reviewed in the available literature. Unlike the others, this methodology enables the identification of many allergenic proteins, some of which are still unknown, which are recognized by IgE from allergic patients, with a single test. The examined literature suggests that the inhibition test associated with the multiplex allergen immunoassay is a promising methodology exploitable for the detection of IgE-binding proteins in food samples. Full article

Mycotoxins are secondary metabolites produced by fungal species, which pose significant risk to humans and livestock. The mycotoxins which are produced from Aspergillus, Penicillium, and Fusarium are considered most important and therefore regulated in food- and feedstuffs. Analyses are predominantly performed by official laboratory methods in centralized labs by expert technicians. There is an urgent demand for new low-cost, easy-to-use, and portable analytical devices for rapid on-site determination. Most significant advances were realized in the field bioanalytical techniques based on molecular recognition. This review aims to discuss recent progress in the generation of native biomolecules and new bioinspired materials towards mycotoxins for the development of reliable bioreceptor-based analytical methods. After brief presentation of basic knowledge regarding characteristics of most important mycotoxins, the generation, benefits, and limitations of present and emerging biorecognition molecules, such as polyclonal (pAb), monoclonal (mAb), recombinant antibodies (rAb), aptamers, short peptides, and molecularly imprinted polymers (MIPs), are discussed. Hereinafter, the use of binders in different areas of application, including sample preparation, microplate- and tube-based assays, lateral flow devices, and biosensors, is highlighted. Special focus, on a global scale, is placed on commercial availability of single receptor molecules, test-kits, and biosensor platforms using multiplexed bead-based suspension assays and planar biochip arrays. Future outlook is given with special emphasis on new challenges, such as increasing use of rAb based on synthetic and naïve antibody libraries to renounce animal immunization, multiple-analyte test-kits and high-throughput multiplexing, and determination of masked mycotoxins, including stereoisomeric degradation products. Full article

Background: The detection of anti-acetylcholine receptor (AChR) and anti-muscle-specific tyrosine kinase (MuSK) antibodies is useful in myasthenia gravis (MG) diagnosis and management. BIOCHIP mosaic-based indirect immunofluorescence is a novel analytical method, which employs the simultaneous detection of anti-AChR and anti-MuSK antibodies in a single miniature incubation field. In this study, we compare, for the first time, the BIOCHIP MG mosaic with conventional enzyme-linked immunosorbent assay (ELISA) in the diagnosis of MG. Methods: A total of 71 patients with MG diagnosis were included in the study. Anti-AChR and anti-MuSK antibodies were measured separately by two different ELISA and simultaneously by BIOCHIP. The results were then compared. Results: The overall concordance between ELISA and BIOCHIP for anti-AChR reactivity was 74%. Cohen’s kappa was 0.51 (95% CI 0.32–0.71), which corresponds to 90% of the maximum possible kappa (0.57), given the observed marginal frequencies. The overall concordance for anti-MuSK reactivity was 84%. Cohen’s kappa was 0.11 (95% CI 0.00–0.36), which corresponds to 41% of the maximum possible kappa (0.27). Conclusion: The overall concordance among assays is not optimal. Full article