Developing a fluorescent probe containing benzofuranone moiety for imaging sulphite in living hypoxia pulmonary cells.

In this work, a benzofuranone-derived fluorescent probe BFSF was developed for imaging the sulphite level in living hypoxia pulmonary cells. Under the excitation of 510 nm, BFSF showed a strong fluorescence response at 570 nm when reacted with sulphite. In the solution system, the constructed hypercapnia and serious hypercapnia conditions did not affect the fluorescence response. In comparison with the recently reported probes, BFSF suggested the advantages including rapid response, steady signal reporting, high specificity and low cytotoxicity upon living lung cells. Under a normal incubation atmosphere, BFSF realized the imaging of both exogenous and endogenous sulphite in living pulmonary cells. In particular, BFSF achieved imaging the decrease of the sulphite level under severe hypoxia as well as the recovery of the sulphite level with urgent oxygen supplement. With the imaging capability for the sulphite level in living pulmonary cells under hypoxia conditions, BFSF together with the information herein was meaningful for investigating the anaesthesia-related biological indexes.

Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing.

DNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most important methylation in mammals is 5-methylcytosine mostly occurring in the context of CpG dinucleotides. Sequencing methods such as whole-genome bisulfite sequencing successfully detect 5-methylcytosine DNA modifications. However, they suffer from the serious drawbacks of short read lengths and might introduce an amplification bias. Here we present Rockfish, a deep learning algorithm that significantly improves read-level 5-methylcytosine detection by using Nanopore sequencing. Rockfish is compared with other methods based on Nanopore sequencing on R9.4.1 and R10.4.1 datasets. There is an increase in the single-base accuracy and the F1 measure of up to 5 percentage points on R.9.4.1 datasets, and up to 0.82 percentage points on R10.4.1 datasets. Moreover, Rockfish shows a high correlation with whole-genome bisulfite sequencing, requires lower read depth, and achieves higher confidence in biologically important regions such as CpG-rich promoters while being computationally efficient. Its superior performance in human and mouse samples highlights its versatility for studying 5-methylcytosine methylation across varied organisms and diseases. Finally, its adaptable architecture ensures compatibility with new versions of pores and chemistry as well as modification types.

Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform.

This study describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module is designed to facilitate interactive learning of whole-genome bisulfite sequencing (WGBS) data analysis utilizing cloud-based tools in Google Cloud Platform, such as Cloud Storage, Vertex AI notebooks and Google Batch. WGBS is a powerful technique that can provide comprehensive insights into DNA methylation patterns at single cytosine resolution, essential for understanding epigenetic regulation across the genome. The designed learning module first provides step-by-step tutorials that guide learners through two main stages of WGBS data analysis, preprocessing and the identification of differentially methylated regions. And then, it provides a streamlined workflow and demonstrates how to effectively use it for large datasets given the power of cloud infrastructure. The integration of these interconnected submodules progressively deepens the user's understanding of the WGBS analysis process along with the use of cloud resources. Through this module, we can enhance the accessibility and adoption of cloud computing in epigenomic research, speeding up the advancements in the related field and beyond. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and clinical questions. DNA methylation analysis bears the particular promise to supplement or replace biochemical and imaging-based tests for the next generation of personalized medicine. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here, we provide a detailed protocol based on a commercial kit for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. The protocol is based on the construction of sequencing libraries from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For analyses requiring a quantitative distinction between 5-methylcytosine and 5-hydroxymethylcytosines levels, an oxidation step is included in the same workflow to perform oxidative bisulfite sequencing (OxBs-Seq). In this case, two sequencing libraries will be generated and sequenced: a classic methylome following bisulfite conversion and analyzing modified cytosines (not distinguishing between methylated and hydroxymethylated cytosines) and a methylome analyzing only methylated cytosines, respectively. Hydroxymethylation levels are deduced from the differences between the two reactions. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human and plant samples and yields robust and reproducible results.

Generation of Whole-Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis.

Whole-genome bisulfite sequencing (WGBS) enables the detection of DNA methylation at a single base-pair resolution. The treatment of DNA with sodium bisulfite allows the discrimination of methylated and unmethylated cytosines, but the power of this technology can be limited by the input amounts of DNA and the length of DNA fragments due to DNA damage caused by the desulfonation process. Here, we describe a WGBS library preparation protocol that minimizes the loss and damage of DNA, generating high-quality libraries amplified with fewer polymerase chain reaction (PCR) cycles, and hence data with fewer PCR duplicates, from lower amounts of input material. Briefly, genomic DNA is sheared, end-repaired, 3'-adenylated, and ligated to adaptors with fewer clean-up steps in between, minimizing DNA loss. The adapter-ligated DNA is then treated with sodium bisulfite and amplified with a few PCR cycles to reach the yield needed for sequencing.

Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data.

DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole-genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for the analysis of DNA methylation. However, the computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required. Here, we outline step-by-step an approach for the analysis and interpretation of WGBS data. First, sequencing reads must be trimmed, quality-checked, and aligned to the genome. Second, DNA methylation levels are estimated at each cytosine position using the aligned sequence reads of the bisulfite-treated DNA. Third, regions of differential cytosine methylation between samples can be identified. Finally, these data need to be visualized and interpreted in the context of the biological question at hand.

Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.

DNA methylation is an important epigenetic modification that regulates chromatin structure and the cell-type-specific expression of genes. The association of aberrant DNA methylation with many diseases, as well as the increasing interest in modifying the methylation mark in a directed manner at genomic sites using epigenome editing for research and therapeutic purposes, increases the need for easy and efficient DNA methylation analysis methods. The standard approach to analyze DNA methylation with a single-cytosine resolution is bisulfite conversion of DNA followed by next-generation sequencing (NGS). In this chapter, we describe a robust, powerful, and cost-efficient protocol for the amplification of target regions from bisulfite-converted DNA, followed by a second PCR step to generate libraries for Illumina NGS. In the two consecutive PCR steps, first, barcodes are added to individual amplicons, and in the second PCR, indices and Illumina adapters are added to the samples. Finally, we describe a detailed bioinformatics approach to extract DNA methylation levels of the target regions from the sequencing data. Combining barcodes with indices enables a high level of multiplexing allowing to sequence multiple pooled samples in the same sequencing run. Therefore, this method is a robust, accurate, quantitative, and cheap approach for the readout of DNA methylation patterns at defined genomic regions.

Preparation of a high-performance conductive lignocellulose hydrogel by directly using non-detoxified bisulfite-pretreated corncob.

Biomass-based hydrogels have become a research hotspot because of their better biocompatibility. However, the preparation of biomass hydrogels is complicated, and they often need to be modified by introducing other substances. In this study, corncob pretreated with bisulfite (125-185 °C) was used as a raw material to prepare lignocellulose hydrogels. The results showed that directly using the pretreated sample without the washing step lowered the total hydrogel costs while preserving the lignosulfonate (LS) produced during pretreatment. The best tensile (54.1 kPa) and compressive (177.7 kPa) stresses were obtained for the hydrogel prepared from non-detoxified pretreated corncob at 165 °C (NCH-165). The sulfonic acid groups in LS could enhance the interaction between plant cellulose, thus improving its mechanical properties. The capacitor assembled from NCH-165 achieved an energy density of 236.1 Wh/kg at a power density of 499.7 W/kg and a high coulombic efficiency of more than 99 % after 2000 charge/discharge cycles. In conclusion, the present study simplifies the pathway for the preparation of flexible, conductive, and anti-freezing hydrogels by directly utilizing a non-detoxified bisulfite-pretreated corncob.

Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach.

5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.

Phenanthroimidazole-based fluorescence probe for discriminative detecting of hydrazine and bisulfite and its applications in environmental samples.

Hydrazine (N2H4) and bisulfite (HSO3-) detection methods are urgently needed due to its harmful to the human health and environment safety. Herein, we reported a dual-response fluorescence probe EPC, which is capable of sequential detection of N2H4 and HSO3- by two different fluorescence signals. The probe EPC itself showed yellow florescence. In presence of N2H4, probe EPC exhibited an obviously fluorescence change (from yellow to green). However, a new addition product came into being after probe EPC mixed with HSO3-, followed with weak yellow emission. More important, probe EPC exhibited excellent fluorescence response properties for N2H4 and HSO3-, such as high sensitivity (0.182 µM for N2H4, 0.093 µM for HSO3-), rapid response (55 s for N2H4, 45 s for HSO3-), excellent selectivity and anti-interference performance. The sensing mechanisms for N2H4 and HSO3- were proved by 1H NMR and MS spectra. Practical applications were studied. EPC based test paper can be utilized for quantitative detecting N2H4 in actual water samples. And, probe EPC has been successfully applied to recognize N2H4 contaminant in soil samples. Moreover, EPC has great potential to be used to detect HSO3- in real food samples.

A highly sensitive ratiometric fluorescence probe for sensing and imaging sulfite in food samples and living cells.

In this work, a ratiometric and chromogenic fluorescent probe 1 was synthesized for the detection of SO32-. The probe 1 at PBS (10 mM, pH = 7.4) presented a marked emission band at 661 nm. Upon addition of SO32- ions, a highly emissive adduct with a marked fluorescence at 471 nm were obtained through a Michael addition. The probe 1 displayed a noticeable fluorescence ratiometric response with a large shift (190 nm) in emission wavelength. The probe can quantitatively detect SO32- with high specificity, fast response (within 130 s) as well as low detection limit (13 nM), and a large Stokes shift (139 nm). Fluorescence imaging of HeLa cells indicated that 1 could be used for monitoring the intrinsically generated intracellular SO32- in living cells by ratiometric fluorescence imaging. Furthermore, 1 could be application in real water and sugar samples with high sensitivity and good recoveries.

Eco-friendly shrink-resist finishing of wool through synergistic effect of disulfide bond reducing agent and papain.

The environmental benefits of utilizing protease as a biocatalyst for wool shrink-resist finishing have been widely recognized. However, the efficacy of individual protease treatment is unsatisfactory due to its incapability towards the outermost cuticle layer of wool fibers that contains hydrophobic fatty acids. In order to weaken the structural integrity of the highly cross-linked scales and promote the enzymatic anti-felting, sodium sulfite and tris (2-carboxyethyl) phosphine hydrochloride (TCEP) were employed in combination with papain, respectively, aiming at obtaining a low shrinkage without unacceptable fiber damages. Based on the synergistic effect of papain and TCEP, the edges of wool scales were slightly destroyed by the reduction of disulfide bonds, accompanied by enzymatic hydrolysis of the keratin component. Through the controlled reduction and hydrolysis of wool scales, satisfactory anti-felting result was achieved without causing severe damage to the fiber interiors. In the presence of 0.25 g/L TCEP and 25 U/mL papain, the area shrinkage of wool fabric decreased to approximately 6 %, with a low strength loss of less than 8 %. Meanwhile, the dyeing behavior of the wool fabric under low-temperature conditions was dramatically improved, leading to decreased energy consumption during production. The present work provides an alternative for eco-friendly finishing of wool fabrics, which can be applied commercially.

LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA.

Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here, we report linear amplification-based bisulfite sequencing (LABS), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.

Robust, fully quantifiable and scalable bioprocess utilizing spent sulfite liquor with Corynebacterium glutamicum.

In this study, a bioprocessing strategy was designed to valorize ultra-filtered spent sulfite liquor (UF-SSL) without prior detoxification steps as well as using it purely as a carbon source supplement to defined or complex media. Hence, a minimal medium for the bioconversion of UF-SSL with Corynebacterium glutamicum was developed and process robustness and reproducibility were validated. Process quantifiability was ensured by development of a biomass measurement technique for matrices with high water-insoluble solids and verified using elemental balancing. Mechanistic modeling based on Monod equations was used to identify batch kinetics. In a final step, scale-up of the developed process was performed to showcase process maturity towards commercialisation.

bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data.

BACKGROUND: Bisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from bisulfite-converted BS-Seq data allows allele-specific methylation analysis and the concurrent exploration of genetic and epigenetic profiles. Despite various methods have been proposed, single nucleotide polymorphisms (SNPs) calling from BS-Seq data, particularly for SNPs on chromosome X and in the presence of contaminative data, poses ongoing challenges. RESULTS: We introduce bsgenova, a novel SNP caller tailored for bisulfite sequencing data, employing a Bayesian multinomial model. The performance of bsgenova is assessed by comparing SNPs called from real-world BS-Seq data with those from corresponding whole-genome sequencing (WGS) data across three human cell lines. bsgenova is both sensitive and precise, especially for chromosome X, compared with three existing methods. Moreover, in the presence of low-quality reads, bsgenova outperforms other methods notably. In addition, bsgenova is meticulously implemented, leveraging matrix imputation and multi-process parallelization. Compared to existing methods, bsgenova stands out for its speed and efficiency in memory and disk usage. Furthermore, bsgenova integrates bsextractor, a methylation extractor, enhancing its flexibility and expanding its utility. CONCLUSIONS: We introduce bsgenova for SNP calling from bisulfite-sequencing data. The source code is available at https://github.com/hippo-yf/bsgenova under license GPL-3.0.

A rapid near-infrared turn on fluorescence probe for the detection of sulfite in food and its application in biological imaging.

A near-infrared fluorescent "turn on" probe DTMI featuring simple skeleton was constructed easily. It undergoes a structure transformation from an A-π-A to a D-π-A framework towards SO32-. Besides, DTMI is capable of distinctive sensing sulfite with a fast response and a significant Stokes shift as well as with high sensitivity, excellent selectivity, long-term stability of fluorescence signals, and good anti-interference ability. The detection limit (LOD) of DTMI for sulfite within the linear concentration range of 0.5-10 µM is 27.39 nM. More importantly, DTMI has been favorably utilized for detecting sulfite in food samples such as red wine and vermicelli. Based on its low biotoxicity, DTMI has been successfully applied in imaging experiments involving HeLa cells, onion inner epidermal cells, and zebrafish. Therefore, the results show that the presented probe possesses potential sensing activity towards sulfite in complex biological system and food samples.

Targeted bisulfite sequencing of Scots pine adaptation-related genes.

During environmental changes, epigenetic processes can enable adaptive responses faster than natural selection. In plants, very little is known about the role of DNA methylation during long-term adaptation. Scots pine is a widely distributed coniferous species which must adapt to different environmental conditions throughout its long lifespan. Thus, epigenetic modifications may contribute towards this direction. We provide bisulfite next-generation sequencing data from the putative promoters and exons of eight adaptation-related genes (A3IP2, CCA1, COL1, COL2, FTL2, MFT1, PHYO, and ZTL) in three Scots pine populations located in northern and southern parts of Finland. DNA methylation levels were studied in the two seed tissues: the maternal megagametophyte which contributes to embryo viability, and the biparental embryo which represents the next generation. In most genes, differentially methylated cytosines (DMCs) were in line with our previously demonstrated gene expression differences found in the same Scots pine populations. In addition, we found a strong correlation of total methylation levels between the embryo and megagametophyte tissues of a given individual tree, which indicates that DNA methylation can be inherited from the maternal parent. In conclusion, our results imply that DNA methylation differences may contribute to the adaptation of Scots pine populations in different climatic conditions.

Synergistic enhancement of pulsed light-induced H2 photoproduction in Chlamydomonas cells by optimal sulfite concentration and light waveform.

Pulsed light illumination stands out as a noteworthy technique for photosynthetic H2 production, playing a crucial role in eliminating O2 and activating hydrogenase enzymes. However, further improvements are essential to make H2 photoproduction suitable for future commercial applications. In our study, we observed a distinct enhancement in pulsed light-induced H2 photoproduction in the unicellular green alga Chlamydomonas reinhardtii when treated with the optimal concentration of the mild O2 scavenger Na2SO3. This improvement was a result of reduced O2 content, increased hydrogenase enzyme activity, and suppressed H2-uptake activity. Furthermore, our findings indicate that exposing Na2SO3-treated C. reinhardtii to optimal light waveform continues to significantly boost pulsed light-induced H2 photoproduction, attributed to the alleviation of impaired photosystem II activity. Altogether, the combined application of optimal sulfite concentration and light waveform effectively enhances pulsed light-induced photosynthetic H2 production in the green alga C. reinhardtii.

Untargeted metabolomics combined with vitro antioxidant to comprehensively evaluate the effect of sodium sulfite immersion on the holistic quality of mung bean sprouts.

Mung bean sprouts are widely consumed as a seasonal fresh vegetable, renowned for their affordability and richness in antioxidants and bioactive compounds. This study employed ultra-high-performance liquid chromatogram-Q-Exactive HF mass spectrometry (UHPLC-QE-MS) and multivariate statistical analysis to comprehensively evaluate the chemical profile of mung bean sprouts following sulfite immersion. The findings revealed a significant alteration in the overall chemical composition of mung bean sprouts following sodium sulfite immersion. Eleven components, including four sulfur-containing compounds, were identified as characteristic markers distinguishing between non-immersed and sodium sulfite-immersed mung bean sprouts. Esterification and addition reactions were inferred to occur during sodium sulfite immersion, leading to the transformation of flavonoid and saponin sulfates. Commercial samples analysis indicated that sulfur-containing compounds were detectable in 9 of 11 commercial mung bean sprouts. Meanwhile, when sodium sulfite concentration exceeded 3.00 mg/mL and immersion time exceeded 360 min, the contents of total polyphenol and flavonoid were significantly reduced and the antioxidant activity was adversely influenced.

Effect of sodium metabisulfite-mediated self-assembly on the quality of silver carp myofibrillar protein-EGCG composite gels.

Myofibrillar protein (MP) gels are susceptible to oxidation, which can be prevented by complexing with hydrophilic polyphenols, but may cause gel deterioration. Sodium metabisulfite (Na2S2O5) has been used to induce self-assembly of MP and analyze the impact of self-assembly on the quality of composite gels containing high amounts of (-)-epigallocatechin gallate (EGCG). Hydrophobic forces were confirmed as the main driver of self-assembly. Self-assembly reduced the size of the MP-EGCG complex to approximately 670 nm and increased the gel's hydrophobic force by approximately 3.6-fold. The maximum hardness of the Na2S2O5-treated MP-EGCG composite gel was 52.43 g/kg, which was approximately 49% greater than pure MP gel. After oxidative treatment, the Na2S2O5-treated MP-EGCG composite gel had considerably lower carbonyl and dityrosine levels (2.47-µmol/g protein and 450 a.u.) than the control (8.37-µmol/g protein and 964 a.u.). Therefore, Na2S2O5 shows potential as a cost-effective additive for alleviating MP limitations in the food industry.