Biochips beyond DNA: technologies and applications

Diminishing Immune Responses against Variants of Concern in Dialysis Patients 4 Months after SARS-CoV-2 mRNA Vaccination

Patients undergoing chronic hemodialysis were among the first to receive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccinations because of their increased risk for severe coronavirus disease and high case-fatality rates. By using a previously reported cohort from Germany of at-risk hemodialysis patients and healthy donors, where antibody responses were examined 3 weeks after the second vaccination, we assessed systemic cellular and humoral immune responses in serum and saliva 4 months after vaccination with the Pfizer-BioNTech BNT162b2 vaccine using an interferon-γ release assay and multiplex-based IgG measurements. We further compared neutralization capacity of vaccination-induced IgG against 4 SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) by angiotensin-converting enzyme 2 receptor-binding domain competition assay. Sixteen weeks after second vaccination, compared with 3 weeks after, cellular and humoral responses against the original SARS-CoV-2 isolate and variants of concern were substantially reduced. Some dialysis patients even had no detectable B- or T-cell responses.

Bioengineering Microgels and Hydrogel Microparticles for Sensing Biomolecular Targets

Hydrogels, and in particular microgels, are playing an increasingly important role in a diverse range of applications due to their hydrophilic, biocompatible, and highly flexible chemical characteristics. On this basis, solution-like environment, non-fouling nature, easy probe accessibility and target diffusion, effective inclusion of reporting moieties can be achieved, making them ideal substrates for bio-sensing applications. In fact, hydrogels are already successfully used in immunoassays as well as sensitive nucleic acid assays, also enabling hydrogel-based suspension arrays. In this review, we discuss key parameters of hydrogels in the form of micron-sized particles to be used in sensing applications, paying attention to the protein and oligonucleotides (i.e., miRNAs) targets as most representative kind of biomarkers.

High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots

DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.

Surface plasmon resonance biosensorics in urine proteomics

Surface plasmon resonance (SPR) is a novel biophysical detection method. In combination with sophisticated surface chemistries and sensing instrumentations, SPR biosensors are approved as tools for molecular interaction studies. SPR plays also a role in interaction proteomics. Once being detected in urine, SPR helps to unravel the functions of new proteins. Due to its outstanding analytical characteristics, SPR also moves more and more into the realm of quantitative analyses in the clinical laboratory. Complex urine determinations of proteins and/or metabolites will bring the SPR biosensor both to the core lab and to point-of-care-testing.This review delineates first the optical phenomena of SPR near to the gold surface, and also the main features of bioconjugation chemistry on a solid-state surface. Then the kinetic calculation of molecular interaction analysis using SPR is introduced. In order to portray the capability of the method, new applications in urine proteomics and proteinuria diagnostics are finally described in detail.

Mass spectrometry of self-assembled monolayers: a new tool for molecular surface science

Most reactions can be performed in solution and on a surface, yet the challenges faced in applying known reactions or in developing entirely new reactions for modifying surfaces remain formidable. The products of many reactions performed in solution can be characterized in minutes, and even products having complex structures can be characterized in hours. When performed on surfaces, even the most basic reactions require a substantial effort--requiring several weeks--to characterize the yields and structures of the products. This contrast stems from the lack of convenient analytical tools that provide rapid information on the structures of molecules attached to a surface. This review describes recent work that has established mass spectrometry as a powerful method for developing and characterizing a broad range of chemical reactions of molecules attached to self-assembled monolayers of alkanethiolates on gold. The SAMDI-TOF mass spectrometry technique will enable a next generation of applications of molecularly defined surfaces to problems in chemistry and biology.

Monolithic integration of well-ordered nanoporous structures in the microfluidic channels for bioseparation

Gel electrophoresis and capillary gel electrophoresis are widely used for the separation of biomolecules. With increasing demand in the miniaturized devices such as lab-on-a-chip, it is necessary to integrate such a separation component into a chip format. Here, we describe a simple approach to fabricate robust three-dimensional periodic porous nanostructures inside the microchannels for the separation of DNA molecules. In our approach, the colloidal crystals were first grown inside the microchannel using evaporation assisted self-assembly process. Then the void spaces among the colloidal crystals were filled with epoxy-based negative tone photoresist (SU-8). UV radiation was used to cure the photoresist at the desired area inside the microchannel. After subsequent development and nanoparticle removal, the well-ordered nanoporous structures inside the microchannel were obtained. Our results indicated that it was possible to construct periodic porous nanostructures inside the microchannels with cavity size around 300 nm and interconnecting pores around 30 nm. The mobility of large DNA molecules with different sizes was measured as a function of the applied electric field in the nanoporous materials. It was also demonstrated that 1 kilo-base pair (kbp) DNA ladders could be separated in such an integrated system within 10 min under moderate electric field.

Introduction: array technology - an overview

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.

Detection of metazoan species as a public health issue: simple methods for the validation of food safety and quality

Species identification represents a critical issue in food chain safety and quality control. Several procedures are available to detect animal proteins in cattle feed or to trace transgenic foods. The most effective approach is based on the use of DNA as a marker. Amplification of DNA provides rapid, sensitive and specific protocols. Several target genes can be used, but new insights come from the mitochondrial genome, which is naturally amplified in each cell and shows a remarkable resistance to degradation. These are key points when analysing complex matrices such as foods, animal feedstuff or environmental samples. Traceability is important to prevent BSE or to monitor novel foods, such as genetically modified organisms. Amplification is commonly performed, but it requires expertise and a molecular biology laboratory to perform restriction analysis, electrophoresis or gel staining for the visualisation of results. Hereby, we consider a strategy based on multiple nested amplification and reverse hybridisation assay that virtually requires only a thermocycler and a water bath. The protocol is rapid and simple and can simultaneously detect different species in a DNA sample. This promising approach allows microarray developments, opening up to further perspectives. An international application has been published under the patent cooperation treaty. Presently, a ban on feeding ruminants on cattle-derived proteins is in force in Europe and USA. The identification of metazoan traces in a sample is not only a mere preventive measure for BSE, but represents a possible screening system for monitoring biotechnology products and procedures, as well as a quality control strategy to assure consumer's rights.

Proteomics: applications relevant to transfusion medicine

With the completion of the human genome sequence, it is now possible to analyze the many individual components that comprise complex biologic systems. Despite this sequence data, understanding the biologic relationships of all proteins of a given cell or biologic sample (the proteome) is still an exceedingly difficult task. However, new technology developments mean that proteomics research can be used to investigate a variety of biologic systems. Already, these studies have given valuable insight for the development of improved diagnostic and therapeutic products. The present review aims to provide a basic understanding of proteomics research by discussing the methods used to study large numbers of proteins and by reviewing the application of proteomics methods to transfusion medicine.

An electrochemical RNA hybridization assay for detection of the fecal indicator bacterium Escherichia coli

Monitoring waters for indicator bacteria is required to protect the public from exposure to fecal pollution. Our proof-of-concept study describes a method for detecting fecal coliforms. The coliform Escherichia coli was used as a model fecal indicator. DNA probe-coated magnetic beads in combination with the electrochemical monitoring of the oxidation state of guanine nucleotides should allow for direct detection of bacterial RNA. To demonstrate this concept, we used voltammetry in connection with pencil electrodes to detect isolated E. coli 16S rRNA. Using this approach, 10(7) cells of E. coli were detected in a quantitative, reproducible fashion in 4h. Detection was achieved without a nucleic acid amplification step. The specificity of the assay for coliforms was demonstrated by testing against a panel of bacterial RNA. We also show that E. coli RNA can be detected directly from cell extracts. The method could be used for on-site detection and shows promise for adaptation into automated biosensors for water-quality monitoring.

Survey of the year 2003 commercial optical biosensor literature

In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.

Functionalized nanocrystal-tagged fluorescent polymer beads: synthesis, physicochemical characterization, and immunolabeling application

A methodology for incorporating solubilized CdSe/ZnS core/shell nanocrystals (NCs) into functionalized carboxylated polystyrene latexes 0.3-1 microm in diameter via a swelling procedure was developed and used for the production of homogeneous, highly fluorescent polymeric beads (HFPBs), which were found to be comparable in brightness to standard polymeric microspheres doped with organic fluorophores and more photostable than the latter by more than 50 times (Fluoresbrite yellow-orange microspheres were used as an example). The three-dimensional (3D) confocal analysis of individual 1-microm HFPB demonstrated that the beads were doped with the NCs almost homogeneously. HFPBs 0.3 microm in diameter were conjugated with anti-mouse polyvalent immunoglobulins and used for immunofluorescent detection of p-glycoprotein, a mediator of the multidrug resistance phenotype, overexpressed in the membrane of MCF7r breast adenocarcinoma cells. The photostability of NCs-tagged HFPBs offers obvious advantages for the reconstruction of 3D confocal fluorescence images of antigen distribution, and their exceptionally high brightness combined with photostability permits the detection of a single antigen molecule using a standard epifluorescence microscope.

From differential gene expression to differential gene function and back

Following the decoding of several plant and animal genomes, the identification of all corresponding transcripts and proteins and understanding how their expression corresponds to physiological and pathological states is the obvious next step. Nucleic acid quantification methods have become increasingly high-throughput and relatively low-cost, and moving ahead, combinations of technologies monitoring differential gene expression and those defining differential cellular function will yield maximum benefit in furthering biology and for drug target identification and validation.:

An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays

A flat microdevice which incorporates a thin-film amorphous silicon (a-Si:H) photodetector with an upper layer of functionalized SiO2 is used to quantify the density of both immobilized and hybridized DNA oligonucleotides labeled with a fluorophore. The device is based on the photoconductivity of hydrogenated amorphous silicon in a coplanar electrode configuration. Excitation, with near UV/blue light, of a single-stranded DNA molecule tagged with the fluorophore 1-(3-(succinimidyloxycarbonyl)benzyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl) pyridinium bromide (PyMPO), results in the emission of visible light. The emitted light is then converted into an electrical signal in the photodetector, thus allowing the optoelectronic detection of the DNA molecules. The detection limit of the present device is of the order of 1 x 10(12) molecules/cm2 and is limited by the efficiency of the filtering of the excitation light. A surface density of 33.5 +/- 4.0 pmol/cm2 was measured for DNA covalently immobilized to the functionalized SiO2 thin film and a surface density of 3.7 +/- 1.5 pmol/cm2 was measured for the complementary DNA hybridized to the bound DNA. The detection concept explored can enable on-chip electronic data acquisition, improving both the speed and the reliability of DNA microarrays.

Assessing Cellular Protein Phosphorylation: High Throughput Drug Discovery Technologies

Changes in protein phosphorylation mediate much of cellular physiology. Perturbations in the activity of the kinases that catalyze these reactions underlie numerous human pathologies, including metabolic and inflammatory disorders and most notably, cancer. HTS techniques that determine the activity of protein kinases in vitro are useful in the development of small molecule kinase inhibitors, but do not address underlying mechanistic concerns or efficient in vivo targeting. Observing protein phosphorylation in cell lysates and fixed cells in a high throughput manner is fundamental to understanding the mechanism of action of lead molecules and whether they target signaling pathways of interest. Herein we discuss several higher throughput techniques to study cellular protein kinase signal transduction and the strategies for implementation in kinase drug discovery.

Microscopy-based multicolor tissue cytometry at the single-cell level

Cytomics is a novel perspective from which to look at life. As with genomics and proteomics before, this discipline requires novel and innovative techniques and technologies to focus on its substrate of research--the cytome. With cytomics being the discipline that analyzes cellular systems and their interdependencies, advanced microscopy represents a key technology in cytomics research. Yet, conventional microscopy-based investigations, i.e., "look and conclude" analyses, do not meet the major cytomics criteria of 1) relating multiple parameters to each other, 2) within large populations of cells, 3) on a single-cell basis, and 4) in a quantitative and observer-independent manner. However, emerging improvements in the fields of fluorophore technology, sensitive fluorescence detection devices, and sophisticated image analysis procedures, are important and necessary steps into the cytomics era. Tissue represents an important class of cytomes, hence tissue cytometry--on the single cell level--can be expected to become an important cytomics technology. In this report, the techniques and technologies of microscopy-based multicolor tissue cytometry (MMTC) are outlined and applications are discussed, including the phenotypic characterization of tissue infiltrating leukocytes, in situ quantification of proliferation markers and tumor suppressors, and in situ quantification of apoptosis.