Taming Janus-Faced Quinoline-Derived Fluorescent Probes for Dual-Channel Distinguishable Visualization of HSO3- and HClO in Dried Foods and Living Cells

With the booming development of food manufacturing, developing ideal analytical tools to precisely quantify food additives is highly sought after in the food science field. Herein, a new series of quinoline-derived multifunctional fluorescent probes has been synthesized. Bearing double reactive sites, these compounds display fluorescence response toward both bisulfite (HSO3-) and hypochlorous acid (HClO). Among these compact structures, compound ethyl-2-cyano-3-(6-(methylthio)quinolin-2-yl)acrylate (QTE) was screened out. Probe QTE not only shows ratiometric variation toward HSO3- with little cross talk but also performs turn-off signal toward HClO. In addition, probe QTE has been utilized for bioimaging of HClO in living cells. Furthermore, the HSO3- content in dried food samples has been appraised by QTE with satisfactory results. Meanwhile, relying on the apparent chromaticity change, a flexible dark-box device has been elaborated for chromatic analysis, promoting visualization of HSO3- in the field.

Rapid degradation of sulfamethoxazole by permanganate combined with bisulfite: efficiency, influence factors and mechanism

In this study, permanganate combined with bisulfite (PM/BS), a novel advanced oxidation process, was used for rapidly removing sulfamethoxazole (SMX) from contaminated water. The results showed that 80% SMX was removed within 10 s in the PM/BS system, while no obvious SMX degradation was observed in the PM or BS alone system within 300 s. Reactive manganese species (RMnS, Mn(III), Mn(V) and Mn(VI)), sulfate radical (SO4•-) and hydroxyl radical (HO•) formed in the PM/BS system all played a role in accelerated degradation of SMX. Due to the loss of RMnS, SMX degradation was significantly inhibited with the increase in pH. The best [BS]:[PM] ratio for SMX removal was 7.5:1-10:1. The presence of Cl-, HCO3- or natural organic matter (NOM) significantly inhibited the degradation of SMX, while SO42- and NO3- had little impact on SMX removal. Based on the detected transformation products, two degradation pathways of SMX by PM/BS, namely N-S bond cleavage and amino oxidation, were proposed.

Rational Construction of a Two-Photon NIR Ratiometric Fluorescent Probe for the Detection of Bisulfite in Live Cells, Tissues, and Foods

In this study, we report a novel ratiometric fluorescent probe with a blue shift of 180 nm based on a D-π-A-A structure. The probe composed of a hydroxyl moiety as a donor, a naphthyl ring as a π bridge, and benzothiazole/hemicyanine as an acceptor has good selectivity and high sensitivity to bisulfite (HSO₃^-) in aqueous solution. Besides one-photon fluorescence properties, the probe possesses excellent two-photon fluorescence properties and is successfully utilized for fluorescence imaging of HSO₃^- in MCF-7 cells and rat liver tissues. More importantly, the probe also has practical application potential for measuring the HSO₃^- content of real food samples.

A Novel Fluorescence Probe for the Reversible Detection of Bisulfite and Hydrogen Peroxide Pair in Vitro and in Vivo

The detection of changes in the reactive oxygen species (ROS)/reactive sulfur species (RSS) couple is important for studying the cellular redox state. Herein, we developed a 1,8-naphthalimide-based fluorescence probe (NI) for the reversible detection of bisulfite (HSO₃ ^- ) and hydrogen peroxide (H₂ O₂ ) in vitro and in vivo. NI has been designed with a reactive ethylene unit which specifically reacts with HSO₃ ^- by a Michael addition reaction mechanism, resulting in the quenching of yellow fluorescence at 580 nm and the appearing of green fluorescence at 510 nm upon excitation at 500 nm and 430 nm, respectively. The addition product (NI-HSO₃ ) could be specifically oxidized to form the original C=C bond of NI, recovering the fluorescence emission and color. The detection limits of NI for HSO₃ ^- and NI-HSO₃ for H₂ O₂ were calculated to be 2.05 μM and 4.23 μM, respectively. The reversible fluorescence response of NI towards HSO₃ ^- /H₂ O₂ couple can be repeated for at least five times. NI is reliable at a broad pH range (pH 3.0-11.5) and features outstanding selectivity, which enabled its practical applications in biological and food samples. Monitoring the reversible and dynamic inter-conversion between HSO₃ ^- and H₂ O₂ in vitro and in vivo has been verified by fluorescence imaging in live HeLa cells, adult zebrafish and nude mice. Moreover, NI has been successfully applied to detect of HSO₃ ^- levels in food samples.

Rational Development of a New Reaction-Based Ratiometric Fluorescent Probe with a Large Stokes Shift for Selective Detection of Bisulfite in Tap Water, Real Food Samples, Onion Tissues, and Zebrafish

Bisulfite (HSO₃^-) is usually widely added to tap water and food because it has antibacterial, bleaching, and antioxidant effects. However, its abnormal addition would cause a series of serious diseases related to it. Therefore, development of an effective method for HSO₃^- detection was of great significance to human health. In this work, a new reaction-based ratiometric fluorescent probe KQ-SO₂ was rationally designed, which could be used for the highly selective detection of HSO3^- in tap water, real food samples, onion tissues, and zebrafish. Specifically, a positively charged benzo[e]indolium moiety and a carbazole group through a condensation reaction resulted in KQ-SO₂, which displayed two well-resolved emission bands separated by 225 nm, fast response (1 min), and high selectivity and sensitivity toward HSO3^- upon undergoing the Michael addition reaction, as well as low cytotoxicity in vitro. In addition, KQ-SO₂ has been successfully applied for the detection of HSO₃^- in tap water, real food samples, onion tissues, and zebrafish with satisfactory results. We predict that KQ-SO₂ could be used as a powerful tool to reveal the relationship between HSO3^- and the human health.

Reaction-Based Ratiometric and Colorimetric Chemosensor for Bioimaging of Biosulfite in Live Cells, Zebrafish, and Food Samples

In this work, a reaction-based ratiometric and colorimetric sensor was designed and synthesized for probing bisulfite (HSO₃^-) by coupling coumarin (CM) with barbituric (BA) moiety. Further tests have shown that CM-BA has high selectivity and sensitivity for the recognition of HSO₃^-, which can be applied for the detection of HSO₃^- in environmental and biological systems very effectively. The fluorescence intensity ratios (F₄₆₂/F₅₆₈) exhibited an outstanding HSO₃^--dependent response with ultrafast response time (within 20 s) and a lower detection limit (105 nM). Meanwhile, the color of the CM-BA solution changed from green to colorless during the recognition process, and its fluorescence changed from green to blue. The mechanism of response is confirmed by the density functional theory (DFT) model. In summary, CM-BA has demonstrated low toxicity and good permeability, which can be applied for imaging HSO₃^- in cells and zebrafish safely and effectively. Besides, this novel sensor CM-BA successfully realized the quantification of the concentration of HSO₃^- in paper strips and food samples.

A Novel Anion Exchange Membrane for Bisulfite Anion Separation by Grafting a Quaternized Moiety through BPPO via Thermal-Induced Phase Separation

Ion-exchange membranes are the core elements for an electrodialysis (ED) separation process. Phase inversion is an effective method, particularly for commercial membrane production. It introduces two different mechanisms, i.e., thermal induced phase separation (TIPS) and diffusion induced phase separation (DIPS). In this study, anion exchange membranes (AEMs) were prepared by grafting a quaternized moiety (QM,2-[dimethylaminomethyl]naphthalen-1-ol) through brominated poly (2,6-dimethyl-1,4-phenylene oxide) (BPPO) via the TIPS method. Those membranes were applied for selective bisulfite (HSO₃^-) anion separation using ED. The membrane surface morphology was characterized by SEM, and the compositions were magnified using a high-resolution transmission electron microscope (HRTEM). Notably, the membranes showed excellent substance stability in an alkali medium and in grafting tests performed in a QM-soluble solvent. The ED experiment indicated that the as-prepared membrane exhibited better HSO₃^- separation performance than the state-of-the-art commercial Neosepta AMX (ASTOM, Japan) membrane.

Discrimination of CpG Methylation Status and Nucleotide Differences in Tissue Specimen DNA by Oligoribonucleotide Interference-PCR

Oligoribonucleotide (ORN) interference-PCR (ORNi-PCR) is a method in which PCR amplification of a target sequence is inhibited in a sequence-specific manner by the hybridization of an ORN with the target sequence. Previously, we reported that ORNi-PCR could detect nucleotide mutations in DNA purified from cultured cancer cell lines or genome-edited cells. In this study, we investigated whether ORNi-PCR can discriminate nucleotide differences and CpG methylation status in damaged DNA, such as tissue specimen DNA and bisulfite-treated DNA. First, we showed that ORNi-PCR could discriminate nucleotide differences in DNA extracted from acetone-fixed paraffin-embedded rat liver specimens or formalin-fixed paraffin-embedded human specimens. Rat whole blood specimens were compatible with ORNi-PCR for the same purpose. Next, we showed that ORNi-PCR could discriminate CpG methylation status in bisulfite-treated DNA. These results demonstrate that ORNi-PCR can discriminate nucleotide differences and CpG methylation status in multiple types of DNA samples. Thus, ORNi-PCR is potentially useful in a wide range of fields, including molecular biology and medical diagnosis.

Simple workflow for genome and methylation analyses of ejaculated bovine spermatozoa with low sperm input

We developed a simplified workflow of gDNA extraction from ejaculated bovine sperm using a low total number of sperm and a short time frame that yields high-quality DNA suitable for downstream methylation and genome analyses. These techniques have broad implications in human biomedical sciences and agriculture, including clinical diagnoses of infertility, the identification of single-nucleotide polymorphisms and aberrant methylation patterns that can impact fertility, lower embryo development and contribute to heritable disease. The methods described here provide a reliable, simplistic approach for analyzing both the genomic and epigenomic status of whole sperm ejaculates that can be adapted for laboratory diagnostics, clinical reproductive practice and basic research.

Digital Droplet PCR for Monitoring Tissue-Specific Cell Death Using DNA Methylation Patterns of Circulating Cell-Free DNA

Cell death involves the release of short DNA fragments into blood, termed circulating cell-free DNA (cfDNA). Sequencing of cfDNA in the plasma has recently emerged as a liquid biopsy for detecting fetal chromosomal aberrations, tumor DNA, and graft rejection. However, in cases where cfDNA is derived from tissues with a normal genome, its primary sequence is not informative regarding the tissue of origin. We developed a method of determining the tissue origins of cfDNA, allowing inference of tissue-specific cell death, based on tissue-specific methylation patterns. We have previously described a version of the method that uses next generation sequencing (NGS) to determine methylation patterns in specific marker loci. Here we describe a rapid and simple procedure for cfDNA methylation analysis using droplet digital PCR (ddPCR) on bisulfite treated cfDNA to accurately count the number of molecules carrying a specific methylation signature. Specificity and sensitivity of the assay increases by simultaneously interrogating four to six cytosines in the same molecule using two fluorescent probes. cfDNA methylation analysis using ddPCR can find multiple applications in the non-invasive study of human tissue dynamics in health and disease. © 2019 by John Wiley & Sons, Inc.

Latest techniques to study DNA methylation

Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and animals. Meanwhile, research on other base modifications, including 6-methyladenine and 4-methylcytosine that are frequent in prokaryotes, has been impeded by the lack of a comparable technique. Bisulfite sequencing also suffers from a number of drawbacks that are difficult to surmount, among which DNA degradation, lack of specificity, or short reads with low sequence diversity. In this review, we explore the recent refinements to bisulfite sequencing protocols that enable targeting genomic regions of interest, detecting derivatives of 5-methylcytosine, and mapping single-cell methylomes. We then present the unique advantage of long-read sequencing in detecting base modifications in native DNA and highlight the respective strengths and weaknesses of PacBio and Nanopore sequencing for this application. Although analysing epigenetic data from long-read platforms remains challenging, the ability to detect various modified bases from a universal sample preparation, in addition to the mapping and phasing advantages of the longer read lengths, provide long-read sequencing with a decisive edge over short-read bisulfite sequencing for an expanding number of applications across kingdoms.

Cyclometalated Iridium Complex as Off-On-Off Reversible Photoluminescence Probe for Redox Cycle HSO3-/H2O2 in Living Cells

The development of new methods for the detection of redox cycle is important for biological and clinical diagnoses. Here, a new cyclometalated iridium complex, (4-(2-pyridyl) benzaldehyde)₂Ir (5-chloro-1,10-phenanthroline) ([(4-pba)₂Ir(5-Cl-phen)]PF₆, probe 1), has been synthesized and applied to rapid, sensitive, and reversible detection and imaging of redox cycle HSO3-/H₂O₂ in living cells. The probe 1 is synthesized by using 4-(2-pyridyl) benzaldehyde as main ligand and 5-chloro-1,10-phenanthroline as ancillary ligand. Probe 1 exhibited "off-on-off" photoluminescence (PL) signal change in response to HSO3- and H₂O₂ in aqueous solution within 1 min. The change of PL intensity is proportional to HSO3- concentration from 40 μM to 300 μM and to H₂O₂ concentration from 40 μM to 260 μM. The detection limit is 10 μM for HSO3- and 20 μM for H₂O₂. Additionally, probe 1 was applied to detect HSO3- in food samples with satisfactory results. More importantly, PL imaging of HeLa cells indicates that probe 1 is able to image redox cycle HSO3-/H₂O₂ in living cells.

A New Red-Emitting Fluorescence Probe for Rapid and Effective Visualization of Bisulfite in Food Samples and Live Animals

The development of new methods for rapid and effective detection of bisulfite (HSO₃^-) in food samples and imaging of HSO₃^- intake in animals is of significant importance due to the key roles of HSO₃^- in food quality assurance and community health. In this work, a new responsive fluorescence probe, EQC, is reported for the quantitative detection of HSO₃^- in food samples and visualization of HSO₃^- intake in animals. Upon addition of HSO₃^-, the UV-vis absorption and red emission of EQC were significantly decreased within 120 s. The changes in absorption and emission spectra of EQC were rationalized by theoretical computations. The proposed reaction mechanism of EQC with HSO₃^- was confirmed by high-resolution mass spectrometry (HRMS) and spectroscopic titration measurements. EQC has the advantages of high sensitivity, selectivity (a detection limit of 18.1 nM), and fast response toward HSO₃^-, which enable rapid and effective HSO₃^- detection in buffer solution. The practical applications of EQC were demonstrated by the detection of HSO₃^- in food samples and the imaging of HSO₃^- intake in live animals.

Rapidly Responsive and Highly Selective Fluorescent Probe for Bisulfite Detection in Food

The new fluorescent probe 4-hydroxy-3-((2E,4E)-5-phenylpenta-2,4-dienoyl)-2H-chromen-2-one (probe 1) was designed and synthesized for selective detection of sulfite. The fluorescence intensity of the probe was decreased only in the presence of HSO₃^-; all other anions assessed resulted in an increased fluorescence response. Hence, probe 1 acts as a highly selective sensor for HSO₃^-. This sulfite sensitivity can also be readily monitored visually, as once treated with sulfite the solution shows a marked color change from yellow to colorless. Moreover, probe 1 can be conveniently used as a signal tool to determine the HSO₃^- levels in various sugar samples.

Methylenetetrahydrofolate Reductase CpG Islands: Epigenotyping

BACKGROUND

Determination of the differential DNA methylation patterns of methylenetetrahydrofolate reductase (MTHFR) that are associated with differential MTHFR activity is important to understand the pathogenesis of ischemic stroke. However, to date, no data are available on the differential DNA methylation profiles of Kelantanese Malays. Therefore, we developed a rapid and efficient serial pyrosequencing assay to determine differential DNA methylation profiles of MTHFR, which help to further our understanding of the pathogenesis of ischemic stroke. The developed assay also served as the validation platform for our previous computational epigenetic research on MTHFR.

METHODS

Polymerase chain reaction primers were designed and validated to specifically amplify the cytosine that is followed by guanine residues (CpGs) A and B regions. Prior epigenotyping on 110 Kelantanese Malays, the serial pyrosequencing assays for the CpGs A and B regions were validated using five validation controls. The mean values of the DNA methylation profiles of CpGs A and B were calculated.

RESULTS

The mean DNA methylation levels for CpGs A and B were 0.984 ± 0.582 and 2.456 ± 1.406, respectively. The CpGs 8 and 20 showed the highest (5.581 ± 4.497) and the lowest (0.414 ± 2.814) levels of DNA methylation at a single-base resolution.

CONCLUSION

We have successfully developed and validated a pyrosequencing assay that is fast and can yield high-quality pyrograms for DNA methylation analysis and is therefore applicable to high throughput study. Using this newly developed pyrosequencing assay, the MTHFR DNA methylation profiles of 110 Kelantanese Malays were successfully determined. It also validated our computational epigenetic research on MTHFR.

Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER

EpiTYPER® is a mass spectrometry-based bisulfite sequencing method that enables region-specific DNA methylation analysis in a quantitative and high-throughput fashion. The technology targets genomic regions of 100–600 base pairs and results in the quantitative measurement of DNA methylation levels largely at single-nucleotide resolution. It is particularly suitable for larger scale efforts to study candidate regions or to validate regions from genome-wide DNA methylation studies. Here, we describe in detail how to design and perform EpiTYPER measurements and preprocess the data, providing details for high quality measurements not provided in the standard EpiTYPER protocol.

Properties of wine polymeric pigments formed from anthocyanin and tannins differing in size distribution and subunit composition

To explore the effect of tannin composition on pigment formation, model ferments of purified 3-O-monoglucoside anthocyanins (ACN) were conducted either alone or in the presence of two different tannins. Tannins were isolated from grape seeds (Sd) or skins (Sk) following exhaustive extraction in 70% v/v acetone. The Sd and Sk tannin fractions had a mean degree of polymerization of 5.2 and 25.6, respectively. The Sd fraction was highly galloylated, at 22%, but galloylation was <2% in the Sk fraction. The Sk fraction was distinguished by a high proportion of prodelphinidin, at 58%. After a 6 month aging period, polymeric pigments were quantified and their color properties determined following isolation by solid-phase extraction. Wine color and polymeric pigment were highest in the treatment containing ACN+Sd and similar in the ACN+Sk and ACN treatments. The same trend between treatments was observed for total and polymeric nonbleachable pigments. Only minor changes in tannin subunit composition were found following ACN incorporation, but the size distribution of polymeric pigments determined by gel permeation chromatography decreased, in particular for the ACN+Sk treatment. Color incorporation in the higher molecular mass range was lower for ACN+Sk wines than for ACN+Sd wines. Compositional differences between the two tannin fractions may therefore limit the incorporation of ACNs in the colored form. The results suggest that in the ACN+Sk and ACN treatments, the formation of lower molecular mass oligomeric pigments was favored. In polymeric pigments derived from ACNs, the presence of ethyl- and vinyl-linked ACNs to the level of trimers was identified using mass spectrometry.

Changes in human sirtuin 6 gene promoter methylation during aging

Aging is a natural process during which changes at the cellular level increase death risk by developing susceptibility to a variety of diseases. Sirtuins have been shown to regulate lifespan in various organisms by deacetylating a number of important transcription factors. Of the 7 identified mammalian sirtuins (SIRT1-7), SIRT6 depletion is associated with severe symptoms of premature aging. In this study, we investigated the association between human longevity and SIRT6 promoter methylation. Genomic DNA from blood samples of 55 individuals (34 females and 21 males) was examined to detect methylation levels by quantitative polymerase chain reaction analysis following bisulfite treatment. While the results indicated 43.21% methylation in the 9-19 age group, this ratio was found to be increased up to 65.63% in the 20-79 age group and decreased to 52.15% in the 80-95 age group. Our results demonstrated that the SIRT6 gene is more active between 9-19 and 80-95 years compared to 20-79 years.

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers.

DNA methylation: a timeline of methods and applications

DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation is of paramount importance to biological health and disease. Recently, the quest to unravel the Human Epigenome commenced, calling for a modernization of previous DNA methylation profiling techniques. Here, we describe the major developments in the methodologies used over the past three decades to examine the elusive epigenome (or methylome). The earliest techniques were based on the separation of methylated and unmethylated cytosines via chromatography. The following years would see molecular techniques being employed to indirectly examine DNA methylation levels at both a genome-wide and locus-specific context, notably immunoprecipitation via anti-5'methylcytosine and selective digestion with methylation-sensitive restriction endonucleases. With the advent of sodium bisulfite treatment of DNA, a deamination reaction that converts cytosine to uracil only when unmethylated, the epigenetic modification can now be identified in the same manner as a DNA base-pair change. More recently, these three techniques have been applied to more technically advanced systems such as DNA microarrays and next-generation sequencing platforms, bringing us closer to unveiling a complete human epigenetic profile.

Growth of microorganisms in total parenteral nutrition solutions containing lipid

BACKGROUND

To identify the microorganisms that can grow rapidly in total parenteral nutrition (TPN) solutions, we investigated the growth of the major causes of catheter-related blood stream infection (Staphylococcus aureus, Serratia marcescens, Bacillus cereus, and Candida albicans) in TPN solutions containing lipid.

METHODS

The pH value of a TPN solution containing lipid (pH 6.0, containing 20 ppm of NaHSO(3)) was adjusted by the addition of HCl to 5.7, 5.4, or 4.9. The pH value of another TPN solution (pH5.5, containing 400 ppm of NaHSO(3)) was adjusted by the addition of NaOH to 5.9, 6.3, or 6.8. A specific number of each microorganism was added to 10 mL of each test solution and incubated at room temperature. The number of microorganisms was counted as colony forming units at 0, 24, and 48 hrs later.

RESULTS

C albicans increased similarly at any pH values in the TPN solution. The bacterial species also increased rapidly at pH6.0 in the solution containing 20 ppm of NaHSO(3), but growth was suppressed as the pH value was reduced, with growth halted at pH4.9. However, these bacterial species did not increase, even at pH5.9, in the other solution containing 400 ppm of NaHSO(3).

CONCLUSIONS

These results suggest that Candida species can grow rapidly in almost all TPN solutions regardless of the acidity, lipid, and NaHSO(3); also, some bacterial species may grow in TPN solutions containing lipid unless the pH value is 5.0 or less. Therefore, each TPN solution should be examined whether or not the bacterial species can proliferate.

Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis--a personal account

Methylation at position 5 of cytosine in DNA is being intensively studied in many areas of biological sciences, as the methylation is intimately associated with the control of gene functions. The principal analytical method for determining the sites of 5-methylcytosine in genome at the sequence level involves bisulfite modification of DNA. The utility of this chemical treatment is based on the property of bisulfite to selectively deaminate cytosine residues. The bisulfite-mediated cytosine deamination was discovered in 1970 by us in the University of Tokyo. At the same time, Shapiro and his coworkers in New York University found the same reaction independently. We also reported that 5-methylcytosine was deaminated by bisulfite only very slowly. These findings were later utilized by a group of Australian scientists to devise a means to analyze 5-methylcytosine in DNA; thus, a method called 'bisulfite genomic sequencing' was invented by these researchers in 1992. This review describes the author's reflection of the discovery of bisulfite reactions with pyrimidine bases. The author's recent work that has resulted in an improvement of the procedure of analysis by use of a newly devised high concentration bisulfite solution is also described.

Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis--a personal account

Methylation at position 5 of cytosine in DNA is being intensively studied in many areas of biological sciences, as the methylation is intimately associated with the control of gene functions. The principal analytical method for determining the sites of 5-methylcytosine in genome at the sequence level involves bisulfite modification of DNA. The utility of this chemical treatment is based on the property of bisulfite to selectively deaminate cytosine residues. The bisulfite-mediated cytosine deamination was discovered in 1970 by us in the University of Tokyo. At the same time, Shapiro and his coworkers in New York University found the same reaction independently. We also reported that 5-methylcytosine was deaminated by bisulfite only very slowly. These findings were later utilized by a group of Australian scientists to devise a means to analyze 5-methylcytosine in DNA; thus, a method called 'bisulfite genomic sequencing' was invented by these researchers in 1992. This review describes the author's reflection of the discovery of bisulfite reactions with pyrimidine bases. The author's recent work that has resulted in an improvement of the procedure of analysis by use of a newly devised high concentration bisulfite solution is also described.

Single-molecule and population probing of chromatin structure using DNA methyltransferases

Probing chromatin structure with DNA methyltransferases offers advantages over more commonly used nuclease-based and chromatin immunoprecipitation methods for detection of nucleosomes and non-histone protein-DNA interactions. Here, we describe two related methods in which the readout of MTase accessibility is obtained by assaying 5-methylcytosine in DNA through the PCR-based technique of bisulfite genomic sequencing. The methyltransferase accessibility protocol (MAP) determines the relative frequency at which the enzyme accesses each of its target sites over an entire population of PCR amplified product. While MAP yields much quantitative information about relative accessibility of a region of chromatin, a complementary single-molecule view of methyltransferase accessibility, termed MAP for individual templates (MAP-IT), is provided by analysis of cloned PCR products. Absolute rather than relative methylation frequencies in a region are obtained by summing the methylation status at each site over a cohort of clones. Moreover, as the integrity of individual molecules is maintained in MAP-IT, unique information about the distribution of multiple footprints along continuous regions is gleaned. In principle, the population MAP and single-molecule MAP-IT strategies can be used to analyze chromatin structure in a variety of model systems. Here, we describe the application of MAP in living Saccharomyces cerevisiae cells and MAP-IT in the analysis of a mammalian tumor suppressor gene in nuclei. This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule.

Detoxification of dissolved SO2 (bisulfite) by terricolous mosses

BACKGROUND AND AIMS

The widespread calcifuge moss Pleurozium schreberi is moderately tolerant of SO2, whereas Rhytidiadelphus triquetrus is limited to calcareous soils in regions of the UK that were strongly affected by SO2 pollution in the 20th century. The proposition that tolerance of SO2 by these terricolous mosses depends on metabolic detoxification of dissolved bisulfite was investigated.

METHODS

The capacities of the two mosses to accelerate loss of bisulfite from aqueous solutions of NaHSO3 were studied using DTNB [5, 5-dithio-(2-nitrobenzoic acid)] to assay bisulfite, and HPLC to assay sulfate in the incubation solutions. Incubations were performed for different durations, in the presence and absence of light, at a range of solution pH values, in the presence of metabolic inhibitors and with altered moss apoplastic Ca2+ and Fe3+ levels.

KEY RESULTS

Bisulfite disappearance was markedly stimulated in the light and twice as great for R. triquetrus as for P. schreberi. DCMU, an inhibitor of photosynthetic electron chain transport, significantly reduced bisulfite loss.

CONCLUSIONS

Bisulfite (SO2) tolerance in these terricolous mosses involves extracellular oxidation using metabolic (photo-oxidative) energy, passive oxidation by adsorbed Fe3+ (only available to the calcifuge) and probably also internal metabolic detoxification.

Soil cations influence bryophyte susceptibility to bisulfite

The hypothesis that metal ions absorbed by bryophytes from the underlying soil may ameliorate adverse effects of SO2 was investigated in the terricolous moss species Pleurozium schreberi (Brid.) Mitt. and Rhytidiadelphus triquetrus (Hedw.) Warnst. Dilute sodium bisulfite solutions (equivalent to dissolved SO2) were applied to shoots isolated from soil or in contact with artificial substrata. Marked inhibition of net photosynthesis was observed within 2 h of treatment with 0.3 mM bisulfite in both mosses. Progressive recovery of net photosynthesis occurred 2-8 h after bisulfite treatment, although the extent of this depended on the concentration and pH of the solution. When R. triquetrus and P. schreberi were grown on artificial substrata (calcareous, acid-mineral or acid-organic) with weekly bisulfite applications, the only significant effect was poorer growth of P. schreberi receiving bisulfite on the calcareous and acid-organic substrata. In both species, growth on the calcareous substratum led to increased concentrations of exchangeable Ca2+, whereas exchangeable Fe3+ concentrations increased following growth on the acid-mineral soil. In another experiment the two mosses were pre-treated with either Ca2+ or Fe3+ before incubation with bisulfite. In P. schreberi, the depression of net photosynthetic rate caused by bisulfite was ameliorated from 33 to 64% of the control by pre-treatment with Fe3+, but it was unaffected by Ca2+ pre-treatment. In R. triquetrus, the amelioration caused by Fe3+ pre-treatment was from 16 to 60% of the control, but pre-treatment with Ca2+ gave a greater amelioration, to 75% of the control value. The responses are discussed in terms of soil preferences of the mosses and possible underlying bisulfite amelioration mechanisms.

Thermodynamics of Solution of SO2(g) in Water and of Aqueous Sulfur Dioxide Solutions

A consistent set of thermochemical property values, Δ f H°, Δ f G°, S°, andC p o , at 298.15 K is given for the known constituents of aqueous sulfur dioxide (SO 2 0 ( aq ) ,HSO 3 - ( aq ) ,SO 3 2 - ( aq ) , H+(aq), andS 2 O 5 2 - ( aq ) ). Also tabulated are values of the mean ionic activity coefficients, osmotic coefficients, partial pressure of SO2(g), and the relative apparent molar enthalpy as a function of concentration of SO2(aq) at 298.15 K. The data analysis considered a wide variety of measurement techniques: calorimetric enthalpies of solution and reaction, heat capacities, equilibrium constants, solubilities, and vapor pressure measurements, both partial and total, over aqueous solutions of SO2 for the temperature range 278 to 393 K. All auxiliary data have been taken from the most recent set of CODATA values which were converted to a standard state pressure of one bar (0.1 MPa). For the processSO 2 ( g ) = SO 2 0 ( aq ) , the selected "best" values are: K = 1.23±0.05 mol kg-1 bar-1, ΔG° = -0.5±0.10 kJ mol-1, ΔH° = -26.97±0.30 kJ mol-1, and Δ C p o = 155 ± 10 J mol - 1 K - 1 . The standard state partial molar entropy ofSO 3 2 - ( aq ) , obtained by the analysis of data via two independent thermodynamic pathways is -15.40±0.80 J mol-1 K-l at 298.15 K. Parameters are given which extend the predictions to temperatures up to 373 K.