Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta

5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.

A practical chromogenic and fluorogenic dual-mode sensing platform for rapid quantification of sulfite in food

Sulfur dioxide (SO2) and its derivatives (HSO3- and SO32-) are widely used in food-processing. Whereas excessive consumption of sulfur dioxide and its derivatives (>0.70 mg·kg-1day-1) severely endangers human health. In this work, we rationally constructed a practical dual-mode probe (dicyanomethylene)-1-methyl-1,4-dihydroquinolin-2-yl)vinyl)-1-methylquinolinium (QMN), which underwent a specific 1, 4-Michael addition with sulfite to afford a noticeable color change from pale yellow to red along with a high-contrast fluorescence turn-on response at 598 nm. QMN has the advantages of rapid response, high signal-to-noise ratio, excellent selectivity, good water-solubility, large Stokes shift and low detection limit (LOD = 31.9 nM). QMN has been successfully used to on-site visually determine sulfite in a diversity of foods with satisfactory recoveries (91.33-111.33 %) and high accuracy (93.74-98.71 %). Furthermore, a portable smartphone-based fluorescence sensing platform was fabricated for on-site determination of sulfite in food with good performance.

Addressing raw material variability: In-line FTIR sugar composition analysis of lignocellulosic process streams

For a sustainable economy, biorefineries that use second-generation feedstocks to produce biochemicals and biofuels are essential. However, the exact composition of renewable feedstocks depends on the natural raw materials used and is therefore highly variable. In this contribution, a process analytical technique (PAT) strategy for determining the sugar composition of lignocellulosic process streams in real-time to enable better control of bioprocesses is presented. An in-line mid-IR probe was used to acquire spectra of ultra-filtered spent sulfite liquor (UF-SSL). Independent partial least squares models were developed for the most abundant sugars in the UF-SSL. Up to 5 sugars were quantified simultaneously to determine the sugar concentration and composition of the UF-SSL. The lowest root mean square errors of the predicted values obtained per analyte were 1.02 g/L arabinose, 1.25 g/L galactose, 0.50 g/L glucose, 1.60 g/L mannose, and 0.85 g/L xylose. Equipped with this novel PAT tool, new bioprocessing strategies can be developed for UF-SSL.

Successful treatment approaches for tumoral calcinosis in children and young people: A condition of diverse pathogenesis

BACKGROUND

Ectopic calcification is inappropriate biomineralization of soft tissues occurring due to genetic or acquired causes of hyperphosphataemia and rarely in normophosphataemic individuals. Tumoral Calcinosis (TC) is a rare metabolic bone disorder commonly presenting in childhood and adolescence with periarticular extra-capsular calcinosis. Three subtypes of TC have been recognised: primary hyperphosphataemic familial TC (HFTC), primary normophosphataemic familial TC and secondary TC most commonly seen in chronic renal failure. In the absence of established treatment, management is challenging due to variable success rates with medical therapies and recurrence following surgery.

AIM

We outline the successful treatment approaches in four children with TC (2 normophosphatemic TC, 2 HFTC) aged 2.5-10 years at initial presentation.

CASES

Patient 1 (P1) presented at 10 years with a painless lump behind the right knee, P2 with swelling of the right knee anteriorly at 9 years, P3 and P4 with pain and swelling over the right elbow at 5 and 2.5 years respectively. All patients were of Black African-Caribbean origin and were previously reported to be fit and well with no family history of TC.

RESULTS

P1, P2 had normophosphataemic TC and P3, P4 had HFTC with genetically confirmed GALNT3 mutation. All four patients had initial surgical resection with TC confirmed on histology. P1 had complete surgical resection with no recurrence at 27 months post-operatively. P2 had significant overgrowth of the tumour following surgery and was subsequently successfully managed with 25 % topical sodium metabisulphite (total duration of 8 months with a 4 month gap during which there was recurrence). P3 had post-surgical recurrence of TC on the right elbow and a new lesion on left elbow which resolved with oral acetazolamide monotherapy (15-20 mg/kg/day). P4 had recurrence of right elbow lesion following surgery and developed an extensive new hip lesion on sevelamer therapy which resolved completely with additional acetazolamide therapy (18-33 mg/kg/day). Acetazolamide was well tolerated with normal growth for 5 years in P3 and 6.5 years in P4 and no recurrence of lesions.

CONCLUSION

The frequent post-surgical recurrence in TC and successful medical therapy on the other hand indicates that medical management as first line therapy should be adopted. Monotherapies with topical 25 % sodium metabisulphite in normophosphataemic and oral acetazolamide in HFTC are effective treatment strategies which are well tolerated.

Methylation‑sensitive restriction enzyme‑droplet digital PCR assay for the one‑step highly sensitive analysis of DNA methylation hotspots

DNA methylation is an epigenetic modification that plays a key role in several cellular processes mediating the fine regulation of gene expression. Aberrant DNA methylation is observed in a wide range of pathologies, including cancer. Since these DNA modifications are transferred to the cell progenies and are stable over the time, the analysis of DNA methylation status has been proposed for diagnostic and prognostic purposes in cancer. Currently, DNA bisulfite conversion is the gold standard method for the high‑throughput analysis of DNA methylation alterations. However, bisulfite treatment induces DNA fragmentation affecting its quality for the downstream analyses. In this field, it is mandatory to identify novel methods to overcome the limits of conventional approaches. In the present study, the Methylation‑Sensitive Restriction Enzyme‑droplet digital PCR (MSRE‑ddPCR) assay was developed as a novel sensitive method for the analysis of DNA methylation of short genomic regions, combining the MSRE assay with the high‑sensitivity ddPCR and using an exogenous methylation sequence as control. Setup and validation experiments were performed analyzing a methylation hotspot of the Solute Carrier Family 22 Member 17 in DNA samples derived from melanoma cell lines as well as from tissues and serum samples obtained from patients with melanoma and healthy controls. Compared with the standard MSRE approaches, the MSRE‑ddPCR assay is more appropriate for the analysis of DNA methylation (methDNA) in samples with low amounts of DNA (up to 0.651 ng) showing a greater sensitivity. These findings suggested the potential clinical application of MSRE‑ddPCR paving the way to the analysis of other methDNA hotspots in different tumors.

Design and application of a novel "turn-on" fluorescent probe for imaging sulfite in living cells and inflammation models

Sulfite is one of the main existing forms of sulfur dioxide (SO2) in living system, which has been recognized as an endogenous mediator in inflammation. Evidence has accumulated to show that abnormal level of sulfite is associated with many inflammatory diseases, including neurological diseases and cancers. Herein, a novel fluorescent probe named QX-OA was designed and synthesized to detect sulfite. QX-OA was constructed by choosing quinolinium-xanthene as the fluorophore and levulinate as the specific and relatively steady recognition reaction. The probe showed remarkable green turn-on signal at 550 nm, together with high sensitivity (90-fold) and excellent selectivity to sulfite over other possible interfering species. In the meantime, QX-OA was successfully applied to visualize endogenous and exogenous sulfite in Hela cells. In the LPS-induced inflammation model, QX-OA could visualize the dose-dependent increase of sulfite level (0-2 mg/mL). Consequently, QX-OA was determined to be a potential method for detecting sulfite in pre-clinical diagnosis.

NBD-based colorimetric and ratiometric fluorescent probe in NIR for bisulfite

This work presented a FRET-ICT based fluorescent probe (named NTC) composed of coumarin-benzothiazole as the acceptor and 4-nitrobenzo[c][1,2,5] oxadiazole (NBD) as the donor for the detection of SO2 derivatives in NIR. Probe NTC possessed superior performance including selectivity, quickly response toward SO32-/HSO3- and high energy transfer efficiency (94 %). The test strips provided a simple and effective tool in detecting the presence of bisulfite. Besides, NTC was applied to test the sulfur dioxide derivatives in food samples and cells.

Development of a novel panel for blood identification based on blood-specific CpG-linked SNP markers

Blood-containing mixtures often appear in murder and robbery cases, and their identification plays a significant role in solving crimes. In recent years, the co-detection of DNA methylation markers (CpG) and single nucleotide polymorphism (SNP) markers has been shown to be a promising tool for the identification of semen and its donor. However, similar research on blood stains that are frequently found at crime scenes has not yet been reported. In this study, we employed blood-specific CpG-linked SNP markers (CpG-SNP) for blood-specific genotyping and the linking of blood and its donor. The tissue-specific CpG markers were screened from the literature and further verified by combining bisulfite conversion with amplification-refractory mutation system (ARMS) technology. Meanwhile, adjacent SNP markers with a minor allele frequency (MAF) greater than 0.1 were selected within 400 bp upstream and downstream of the CpG markers. SNP genotyping was performed using SNaPshot technology on a capillary electrophoresis (CE) platform. Finally, a multiplex panel, including 19 blood-specific CpG linked to 23 SNP markers, as well as 1 semen-specific CpG, 1 vaginal secretion-specific CpG, and 1 saliva-specific CpG marker, was constructed successfully. The panel showed good tissue specificity and blood stains stored at room temperature for up to nine months and moderately degraded (4 < DI < 10) could be effectively identified. Moreover, it could also be detected when blood content in the mixed stains was as low as 1%. In addition, 15 ng of DNA used for bisulfite conversion was required for obtaining a complete profile. The cumulative discrimination power of the panel among the Han population of northern China could reach 0.999983. This is the first investigation conducted for the simultaneous identification of blood and its donor regardless of other body fluids included in mixed stains. The successful construction of the panel will play a vital role in the comprehensive analysis of blood-containing mixtures in forensic practice.

Construction of a glycosylation-mediated fluorescent biosensor for label-free measurement of site-specific 5-hydroxymethylcytosine in cancer cells with zero background signal

BACKGROUND

5-hydroxymethylcytosine (5hmC) as an epigenetic modification can regulate gene expression, and its abnormal level is related with various tumor invasiveness and poor prognosis. Nevertheless, the current methods for 5hmC assay usually involve expensive instruments/antibodies, radioactive risk, high background, laborious bisulfite treatment procedures, and non-specific/long amplification time.

RESULTS

We develop a glycosylation-mediated fluorescent biosensor based on helicase-dependent amplification (HDA) for label-free detection of site-specific 5hmC in cancer cells with zero background signal. The glycosylated 5hmC-DNA (5ghmC) catalyzed by β-glucosyltransferase (β-GT) can be cleaved by AbaSI restriction endonuclease to generate two dsDNA fragments with sticky ends. The resultant dsDNA fragments are complementary to the biotinylated probes and ligated by DNA ligases, followed by being captured by magnetic beads. After magnetic separation, the eluted ligation products act as the templates to initiate HDA reaction, generating abundant double-stranded DNA (dsDNA) products within 20 min. The dsDNA products are measured in a label-free manner with SYBR Green I as an indicator. This biosensor can measure 5hmC with a detection limit of 2.75 fM and a wide linear range from 1 × 10-14 to 1 × 10-8 M, and it can discriminate as low as 0.001% 5hmC level in complex mixture. Moreover, this biosensor can measure site-specific 5hmC in cancer cells, and distinguish tumor cells from normal cells.

SIGNIFICANCE

This biosensor can achieve a zero-background signal without the need of either 5hmC specific antibody or bisulfite treatment, and it holds potential applications in biological research and disease diagnosis.

A colorimetric and NIR fluorescent probe for ultrafast detecting bisulfite and organic amines and its applications in food, imaging, and monitoring fish freshness

Herein, for the first time, we have successfully constructed a novel near-infrared (NIR) emission fluorescent probe Dpyt for ultrafast detecting (within 5 s) bisulfate and organic amines based on a 1,2-dihydrocyclopenta[b]chromene-barbiturate conjugation system. Upon addition of bisulfate or organic amines, Dpyt displayed a distinct color change from blue to colorless or from purple to blue, respectively, suggesting that the Dpyt can be used to detect two analytes by the naked eye. Based on quantum chemistry calculations, the fluorescence quenching of Dpyt after the addition of HSO3- is caused by the photoinduced electron transfer (PET) process of the adduct Dpyt-HSO3-. The fluorescence enhancement of Dpyt caused by most organic amines is due to the enhanced intramolecular charge transfer (ICT) process of deprotonated Dpyt. Notably, Dpyt can be applied for detecting HSO3- in actual food samples such as red wine and sugar, as well as for imaging of HSO3- and representative propylamine in living cells. And more importantly, indicator labels constructed by filter paper loaded with Dpyt can visually monitor the freshness of salmon in real-time by daylight and fluorescence dual-mode. The comparison with national standard method of China manifests that indicator labels are a valid tool to assess the freshness of seafood.

BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies

Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT's performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing.

Sodium sulfite triggered hepatic apoptosis, necroptosis, and pyroptosis by inducing mitochondrial damage in mice and AML-12 cells

Sodium sulfite (SS) is a biological derivative of the air pollutant sulfur dioxide, and is often used as a food and pharmaceutical additive. Improper or excessive SS exposure in liver cell death. The phenomenon of simultaneous regulation of apoptosis, necroptosis, and pyroptosis is defined as PANoptosis. However, the specific types of programmed cell death (PCD) caused by SS and their interconnections remain unclear. In the present study, C57BL/6 mice were orally administered SS for 30 d, consecutively, to establish an in vivo mouse exposure model. AML-12 cells were treated with SS for 24 h to establish an in vitro exposure model. The results showed that SS-induced mitochondrial reactive oxygen species (mtROS) accumulation activated the BAX/Bcl-2/caspase 3 pathway to trigger apoptosis and RIPK1/RIPK3/p-MLKL to trigger necroptosis. Interestingly, ROS-activated p-MLKL perforated not the cell membrane as well as the lysosomal membrane. We determined that p-MLKL mediates lysosomal membrane permeabilization (LMP), resulting in cathepsin B (CTSB) release. Furthermore, knockdown of MLKL, a CTSB inhibitor (CA074-ME) and an NLRP3 inhibitor (MCC950) alleviated SS-induced pyroptosis. In summary, our study showed that SS induced apoptosis and necroptosis though mtROS accumulation, whereas the activation of p-MLKL mediated NLRP3-dependent pyroptosis by causing CTSB leakage through LMP. This study comprehensively explored the mechanism unerlying SS-induced PCD and provided an experimental basis for p-MLKL as a potential regulatory protein in PANoptosis.

Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting

Allele-specific methylation (ASM) is an epigenetic modification whereby one parental allele becomes methylated and the other unmethylated at a specific locus. ASM is most often driven by the presence of nearby heterozygous variants that influence methylation, but also occurs somatically in the context of genomic imprinting. In this study, we investigate ASM using publicly available single-cell reduced representation bisulfite sequencing (scRRBS) data on 608 B cells sampled from six healthy B cell samples and 1,230 cells from 11 chronic lymphocytic leukemia (CLL) samples. We developed a likelihood-based criterion to test whether a CpG exhibited ASM, based on the distributions of methylated and unmethylated reads both within and across cells. Applying our likelihood ratio test, 65,998 CpG sites exhibited ASM in healthy B cell samples according to a Bonferroni criterion (p < 8.4 × 10-9), and 32,862 CpG sites exhibited ASM in CLL samples (p < 8.5 × 10-9). We also called ASM at the sample level. To evaluate the accuracy of our method, we called heterozygous variants from the scRRBS data, which enabled variant-based calls of ASM within each cell. Comparing sample-level ASM calls to the variant-based measures of ASM, we observed a positive predictive value of 76%-100% across samples. We observed high concordance of ASM across samples and an overrepresentation of ASM in previously reported imprinted genes and genes with imprinting binding motifs. Our study demonstrates that single-cell bisulfite sequencing is a potentially powerful tool to investigate ASM, especially as studies expand to increase the number of samples and cells sequenced.

Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes

DNA methylation is an essential epigenetic mechanism that regulates cellular reprogramming and development. Studies using whole-genome bisulfite sequencing have revealed distinct DNA methylome landscapes in human and mouse cells and tissues. However, the factors responsible for the differences in megabase-scale methylome patterns between cell types remain poorly understood. By analyzing publicly available 258 human and 301 mouse whole-genome bisulfite sequencing datasets, we reveal that genomic regions rich in guanine and cytosine, when located near the nuclear center, are highly susceptible to both global DNA demethylation and methylation events during embryonic and germline reprogramming. Furthermore, we found that regions that generate partially methylated domains during global DNA methylation are more likely to resist global DNA demethylation, contain high levels of adenine and thymine, and are adjacent to the nuclear lamina. The spatial properties of genomic regions, influenced by their guanine-cytosine content, are likely to affect the accessibility of molecules involved in DNA (de)methylation. These properties shape megabase-scale DNA methylation patterns and change as cells differentiate, leading to the emergence of different megabase-scale methylome patterns across cell types.

How to achieve adequate quenching for DBP analysis in drinking water?

Quenching is an important step to terminate disinfection during preparation of disinfected water samples for the analysis of disinfection byproducts (DBPs). However, an incomplete quenching might result in continued reactions of residual chlorine, whereas an excessive quenching might decompose target DBPs. Therefore, an adequate quenching to achieve simultaneous disinfection termination and DBP preservation is of particular importance. In this study, the two-stage reaction kinetics of chlorine and three commonly used quenching agents (i.e., ascorbic acid, sodium thiosulfate, and sodium sulfite) were determined. Stopping quenching during the first stage prevented interactions of residual chlorine with natural organic matter. Complete quenching was achieved by minimizing the quenching time for ascorbic acid and sodium sulfite, while limiting the quenching time to less than 3 min for sodium thiosulfate. At the optimized quenching times, the molar ratios (MRs) of quenching agent to chlorine were 1.05, 1.10, and 0.75 for ascorbic acid, sodium sulfite, and sodium thiosulfate, respectively. The destructive effects of the three quenching agents on total organic halogen (TOX) followed the rank order of ascorbic acid (33.7-64.8 %) < sodium sulfite (41.6-72.8 %) < sodium thiosulfate (43.3-73.2 %), and the destructive effects on aliphatic DBPs also followed the rank order of ascorbic acid (29.5-44.5 %) < sodium sulfite (34.9-51.9 %) < sodium thiosulfate (46.9-53.2 %). For total organic chlorine (TOCl) and aliphatic DBPs, the quenching behavior itself had more significant destructive effect than the quenching agent type/dose and quenching time, but for total organic bromine (TOBr), the destructive effect caused by quenching agent type/dose and quenching time was more significant. High-dose, long-duration quenching enhanced the reduction of TOX, but had little effect on aliphatic DBPs. Additionally, the three quenching agents reduced the levels of halophenols (except for tribromophenol), while maintained or increased the levels of tribromophenol, halobenzoic/salicylic acids, and halobenzaldehydes/salicylaldehydes. To achieve adequate quenching for overall DBP analysis in chlorinated water samples, it is recommended to use ascorbic acid at a quenching agent-to-chlorine MR of 1.0 for a quenching time of < 0.5 h.

A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models

Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.

Modelling energy-harvesting processes in primitive cells: Proton transport across bilayers driven by the oxidation of sulfite

A frequently debated topic related to the origin of life centers around the question of how complex forms of life on today's Earth may have evolved over time from simpler predecessors. For example, the question of how proton concentration gradients across cellular membranes developed in ancestral protocells remains unanswered. This process, which is indispensable for the generation of chemical energy in modern organisms, is driven by energy derived from redox processes in the respiratory chain. Since it is highly unlikely that the complex machinery of the respiratory chain was available on early Earth, we provide an example of how proton gradients can be established in less complex systems. Utilizing liposomes as models of primitive cells, we were able to generate proton gradients of about two pH units across the liposome bilayers using redox reactions as the driving force. Electrons were transferred from sodium sulfite present on the outside of the liposomes to ferricyanide, which was trapped on the inside. A lipid-soluble phenazine derivative served as a shuttle that transferred both electrons and protons across the lipid bilayer. Because sulfite would have been an abundant reduced solute available to the earliest cells, we propose that it may have been a primary source of redox energy for primitive chemiosmotic energy transduction.

Biochar and surfactant synergistically enhanced PFAS destruction in UV/sulfite system at neutral pH

The UV/sulfite-based advanced reduction process (ARP) emerges as an effective strategy to combat per- and polyfluoroalkyl substances (PFAS) pollution in water. Yet, the UV/sulfite-ARP typically operates at highly alkaline conditions (e.g., pH > 9 or even higher) since the generated reductive radicals for PFAS degradation can be quickly sequestered by protons (H+). To overcome the associated challenges, we prototyped a biochar-surfactant-system (BSS) to synergistically enhance PFAS sorption and degradation by UV/sulfite-ARP. The degradation and defluorination efficiencies of perfluorooctanoic acid (PFOA) depended on solution pH, and concentrations of surfactant (cetyltrimethylammonium bromide; CTAB), sulfite, and biochar. At high pH (8-10), adding biochar and BSS showed no or even small inhibitory effect on PFOA degradation, since the degradation efficiencies were already high enough that cannot be differentiated. However, at acidic and neutral pH (6-7), an evident enhancement of PFOA degradation and defluorination efficiencies occurred. This is due to the synergies between biochar and CTAB that create favorable microenvironments for enhanced PFOA sorption and deeper destruction by prolonging the longevity of reductive radicals (e.g., SO3•-), which is less affected by ambient pH conditions. The performance of UV/sulfite/BSS was further optimized and used for the degradation of four PFAS. At the optimal experimental condition, the UV/sulfite/BSS system can completely degrade PFOA with >30% defluorination efficiency for up to five continuous cycles (n = 5). Overall, our BSS provides a cost-effective and sustainable technique to effectively degrade PFAS in water under environmentally relevant pH conditions. The BSS-enabled ARP technique can be easily tied into PFAS treatment train technology (e.g., advanced oxidation process) for more efficient and deeper defluorination of various PFAS in water.

Sodium sulfite-driven Helicobacter pylori eradication: Unraveling oxygen dynamics through multi-omics investigation

Due to the emergence and spread of multidrug resistance in Helicobacter pylori (H. pylori), its eradication has become difficult. Sodium sulfite (SS), a widely used food additive for ensuring food safety and storage, has been recognized as an effective nonbactericidal agent for H. pylori eradication. However, the mechanism by which H. pylori adapts and eventually succumbs under low- or no-oxygen conditions remains unknown. In this study, we aimed to evaluate the anti-H. pylori effect of SS and investigated the multiomics mechanism by which SS kills H. pylori. The results demonstrated that SS effectively eradicated H. pylori both in vitro and in vivo. H. pylori responds to the oxygen changes regulated by SS, downregulates the HcpE gene, which is responsible for redox homeostasis in bacteria, decreases the activities of enzymes related to oxidative stress, and disrupts the outer membrane structure, increasing susceptibility to oxidative stress. Furthermore, SS downregulates the content of cytochrome C in the microaerobic respiratory chain, leading to a sharp decrease in ATP synthesis. Consequently, the accumulation of triglycerides (TGs) in bacteria due to oxidative stress supports anaerobic respiration, meeting their energy requirements. The multifaceted death of H. pylori caused by SS does not result in drug resistance. Thus, screening of the redox homeostasis of HcpE as a new target for H. pylori infection treatment could lead to the development of a novel approach for H. pylori eradication therapy.

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.

Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis

BACKGROUND

Patients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of extracellular matrix (ECM) proteins. While ECM accumulation can prevent liver infection and injury, it can destroy normal liver function and architecture. miRNA's own regulation was involved in DNA methylation change. The purpose of this study is to detect DNA methylation landscape of miRNAs genes in mice liver fibrosis tissues.

METHODS

Male mice (10-12 weeks) were injected CCl4 from abdominal cavity to induced liver fibrosis. 850 K BeadChips were used to examine DNA methylation change in whole genome. The methylation change of 16 CpG dinucleotides located in promoter regions of 4 miRNA genes were detected by bisulfite sequencing polymerase chain reaction (BSP) to verify chip data accuracy, and these 4 miRNA genes' expressions were detected by RT-qPCR methods.

RESULTS

There are 769 differential methylation sites (DMS) in total between fibrotic liver tissue and normal mice liver tissue, which were related with 148 different miRNA genes. Chips array data were confirmed by bisulfite sequencing polymerase chain reaction (R = 0.953; P < 0.01). GO analysis of the target genes of 2 miRNA revealed that protein binding, cytoplasm and chromatin binding activity were commonly enriched; KEGG pathway enrichment analysis displayed that TGF-beta signaling pathway was commonly enriched.

CONCLUSION

The DNA of 148 miRNA genes was found to have methylation change in liver fibrosis tissue. These discoveries in miRNA genes are beneficial to future miRNA function research in liver fibrosis.

Sperm DNA methylation defects in a new mouse model of the 5,10-methylenetetrahydrofolate reductase 677C>T variant and correction with moderate dose folic acid supplementation

5,10-Methylenetetrahydrofolate reductase (MTHFR) is an enzyme that plays a key role in providing methyl groups for DNA methylation, including during spermatogenesis. A common genetic variant in humans (MTHFR 677C>T) results in reduced enzyme activity and has been linked to various disorders, including male infertility. A new animal model has been created by reproducing the human equivalent of the polymorphism in mice using CRISPR/Cas9. Biochemical parameters in the Mthfr 677TT mice recapitulate alterations found in MTHFR 677TT men. Our aims were to characterize the sperm DNA methylome of the Mthfr 677CC and TT mice on a control diet (2 mg folic acid/kg diet) and assess the effects of folic acid supplementation (10 mg/kg diet) on the sperm DNA methylome. Body and reproductive organ weights, testicular sperm counts, and histology were examined. DNA methylation in sperm was assessed using bisulfite pyrosequencing and whole-genome bisulfite sequencing (WGBS). Reproductive parameters and locus-specific imprinted gene methylation were unaffected by genotype or diet. Using WGBS, sperm from 677TT mice had 360 differentially methylated tiles as compared to 677CC mice, predominantly hypomethylation (60% of tiles). Folic acid supplementation mostly caused hypermethylation in sperm of males of both genotypes and was found to partially correct the DNA methylation alterations in sperm associated with the TT genotype. The new mouse model will be useful in understanding the role of MTHFR deficiency in male fertility and in designing folate supplementation regimens for the clinic.

Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing

Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.

Identifying and validating MMP family members (MMP2, MMP9, MMP12, and MMP16) as therapeutic targets and biomarkers in kidney renal clear cell carcinoma (KIRC)

Kidney Renal Clear Cell Carcinoma (KIRC) is a malignant tumor that carries a substantial risk of morbidity and mortality. The MMP family assumes a crucial role in tumor invasion and metastasis. This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma (KIRC) through a comprehensive approach encompassing both computational and molecular analyses. STRING, Cytoscape, UALCAN, GEPIA, OncoDB, HPA, cBioPortal, GSEA, TIMER, ENCORI, DrugBank, targeted bisulfite sequencing (bisulfite-seq), conventional PCR, Sanger sequencing, and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC. By performing STRING and Cytohubba analyses of the 24 MMP gene family members, MMP2 (matrix metallopeptidase 2), MMP9 (matrix metallopeptidase 9), MMP12 (matrix metallopeptidase 12), and MMP16 (matrix metallopeptidase 16) genes were denoted as hub genes having highest degree scores. After analyzing MMP2, MMP9, MMP12, and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines, interestingly, all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls. The notable effect of the up-regulated MMP2, MMP9, MMP12, and MMP16 was also documented on the overall survival (OS) of the KIRC patients. Moreover, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes (MMP2, MMP9, MMP12, and MMP16). In addition to this, hub genes were involved in various diverse oncogenic pathways. The MMP gene family members (MMP2, MMP9, MMP12, and MMP16) may serve as therapeutic targets and prognostic biomarkers in KIRC.

Iodide and sulfite synergistically accelerate the photo-reduction and recovery of As(V) and As(III) in sulfite/iodide/UV process: Efficiency and mechanism

Photo-reduction of arsenic (As) by hydrated electron (eaq-) and recovery of elemental arsenic (As(0)) is a promising pathway to treat As-bearing wastewater. However, previously reported sulfite/UV system needs large amounts of sulfite as the source of eaq-. This work suggests a sulfite/iodide/UV approach that is more efficient and consumes much less chemical reagents to remove As(III) and As(V) and recover valuable As(0) from wastewater, hence preventing the production of large amounts of As-containing hazardous wastes. Our results showed that more than 99.9% of As in the aqueous phase was reduced to highly pure solid As(0) (>99.5 wt%) by sulfite/iodide/UV process under alkaline conditions. Sulfite and iodide worked synergistically to enhance reductive removal of As. Compared with sulfite/UV, the addition of iodide had a substantially greater effect on As(III) (over 200 times) and As(V) (approximately 30 times) removals because of its higher absorptivity and quantum yield of eaq-. Furthermore, more than 90% of the sulfite consumption was decreased by adding a small amount of iodide while maintaining similar reduction efficiency. Hydrated electron (eaq-) was mainly responsible for As(III) and As(V) reductions and removals under alkaline conditions, while both SO3•- and reactive iodine species (e.g., I•, I2, I2•-, and I3-) may oxidize As(0) to As(III) or As(V). Acidic circumstances caused sulfite protonation and the scavenging of eaq- by competing processes. Dissolved oxygen (O2) and CO32- prevented As reduction by light blocking or eaq- scavenging actions, but Cl-, Ca2+, and Mg2+ showed negligible impacts. This study presented an efficient method for removing and recovering As from wastewater.

Physical impediment to sodium houttuyfonate conversely reinforces β-glucan exposure stimulated innate immune response to Candida albicans

Candida albicans is a dimorphic opportunistic pathogen in immunocompromised individuals. We have previously demonstrated that sodium houttuyfonate (SH), a derivative of medicinal herb Houttuynia cordata Thunb, was effective for antifungal purposes. However, the physical impediment of SH by C. albicans β-glucan may weaken the antifungal activity of SH. In this study, the interactions of SH with cell wall (CW), extracellular matrix (EM), CW β-glucan, and a commercial β-glucan zymosan A (ZY) were inspected by XTT assay and total plate count in a standard reference C. albicans SC5314 as well as two clinical fluconazole-resistant strains Z4935 and Z5172. After treatment with SH, the content and exposure of CW β-glucan, chitin, and mannan were detected, the fungal clearance by phagocytosis of RAW264.7 and THP-1 was examined, and the gene expressions and levels of cytokines TNF-ɑ and IL-10 were also monitored. The results showed that SH could be physically impeded by β-glucan in CW, EM, and ZY. This impediment subsequently triggered the exposure of CW β-glucan and chitin with mannan masked in a time-dependent manner. SH-induced β-glucan exposure could significantly enhance the phagocytosis and inhibit the growth of C. albicans. Meanwhile, the SH-pretreated fungal cells could greatly stimulate the cytokine gene expressions and levels of TNF-ɑ and IL-10 in the macrophages. In sum, the strategy that the instant physical impediment of C. albicans CW to SH, which can induce the exposure of CW β-glucan may be universal for C. albicans in response to physical deterrent by antifungal drugs.

Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling

BACKGROUND

The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples.

RESULTS

We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding.

CONCLUSIONS

Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.

BSXplorer: analytical framework for exploratory analysis of BS-seq data

BACKGROUND

Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily.

RESULTS

BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication.

CONCLUSIONS

BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.

Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences

MOTIVATION

Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented.

RESULTS

Here, we introduce Lambda3, a new version of the local alignment application Lambda. Lambda3 is the first solution that enables the search of protein, nucleotide as well as bisulfite-converted nucleotide query sequences. Its protein mode achieves comparable performance to that of the highly optimized protein alignment application Diamond, while the nucleotide mode consistently outperforms established local nucleotide aligners. Combined, Lambda3 presents a universal local alignment framework that enables fast and sensitive homology searches for a wide range of use-cases.

AVAILABILITY AND IMPLEMENTATION

Lambda3 is free and open-source software publicly available at https://github.com/seqan/lambda/.

DNA methylation-based age estimation and quantification of the degradation levels of bisulfite-converted DNA

DNA methylation modifications are known to influence epigenetic phenomena and have been a focus of forensic science research for some time. Degraded DNA after bisulfite treatment is widely used in DNA methylation analysis. In this study, we analyzed methylation levels at 12 CpG sites of four selected genomic regions by pyrosequencing after bisulfite treatment. DNA was extracted from buccal swab samples collected from 102 Japanese individuals who were 21-77 years old. We also developed a simple method to quantify the degradation levels of bisulfite-converted DNA by real-time PCR, and evaluated the effect of DNA degradation on age estimation. We found that the methylation levels and chronological ages were highly correlated in the four selected regions, and the mean absolute deviation (MAD) between chronological and estimated ages was low at 3.88 years. These results indicated that pyrosequencing analysis at the 12 CpGs was useful for age estimation in the Japanese population. To develop a sensitive quantification method, we analyzed the amplification efficiency of short and long fragments from 10 regions by real-time PCR. The amplification efficiency was highest for CCDC102B, and the degradation levels of bisulfite-converted DNA for the 102 samples were categorized as moderately or heavily degraded. For the younger age groups (20-49 years), the MADs were lower for moderately degraded DNA than they were for heavily degraded DNA. This finding indicates that degradation levels affected the accuracy of age estimation in most of the samples; the exception was the samples from the 50-77 years age group.

Computing Sickle Erythrocyte Health Index on quantitative phase imaging and machine learning

Sickle cell disease (SCD) is a genetic disorder characterized by abnormal hemoglobin and deformation of red blood cells (RBCs), leading to complications and reduced life expectancy. This study developed an in vitro assessment, the Sickle Erythrocyte Health Index, using quantitative phase imaging (QPI) and machine learning to model the health of RBCs in people with SCD. The health index combines assessment of cell deformation, sickle-shaped classification, and membrane flexibility to evaluate erythrocyte health. Using QPI and image processing, the percentage of sickle-shaped cells and membrane flexibility were quantified. Statistically significant differences were observed between individuals with and without SCD, indicating the impact of underlying pathophysiology on erythrocyte health. Additionally, sodium metabisulfite led to an increase in sickle-shaped cells and a decrease in flexibility in the sickle cell blood samples. Based on these findings, two approaches were used to calculate the Sickle Erythrocyte Health Index: one using hand-crafted features and one using learned features from deep learning models. Both indices showed significant differences between non-SCD and SCD groups and sensitivity to changes induced by sodium metabisulfite. The Sickle Erythrocyte Health Index has important clinical implications for SCD management and could be used by providers when making treatment decisions. Further research is warranted to evaluate the clinical utility and applicability of the Sickle Erythrocyte Health Index in diverse patient populations.

Sodium Sulfite as a Novel Hypoxia Revulsant Involved in Hypoxic Regulation in Escherichia coli

As a reducing salt, sodium sulfite could deprive oxygen in solution, which could mimic hypoxic stress in Caenorhabditis elegans. In this study, the wild-type Escherichia coli strain MG1655 was used to examine the inhibition of sodium sulfite-induced hypoxia by observing the bacterial growth curves. We also analyzed the growth curves of mutant strains (for arcA/B, soxR/S, fnr, and oxyR) related to E. coli hypoxic pathways to reveal roles of the related genes during hypoxia. The ultrastructure of hypoxia-inhibited bacteria were also observed using transmission electron microscopy. Sodium sulfite could maintain hypoxic condition of bacterial culture for 8 h with concentrations over 40 mmol/L. Complete ultrastructure of the bacteria indicated sodium sulfite did inhibit bacterial growth and division. Among the hypoxia genes, fnr and arcB played key roles in sodium sulfite-induced hypoxia. This study showed that sodium sulfite could be used as a novel hypoxia revulsant for bacterial cultures.

Background-Free and Reversible Upconversion Hydrogel Sensing Platform for Visual Monitoring of Sulfite

Excessive sulfite usage in food and pharmaceutical production causes respiratory and neurological diseases, underscoring the need for a sensitive and rapid quantification strategy. The portable sensing platform based on a luminescent hydrogel sensor is a powerful tool for the on-site, real-time detection of sulfite ions. However, the lack of recyclability in almost all reaction-based hydrogel sensors increases the application cost. This study constructed a reversible and upconversion nanoprobe combining upconversion nanoparticles (UCNPs) and pararosaniline (PAR) for sulfite detection. The upconversion nanoprobe was further encapsulated in a three-dimensional polyacrylamide hydrogel matrix to create a background-free, reversible hydrogel sensor. The near-infrared excitation of UCNPs avoids the autofluorescence in the hydrogel and real samples. Meanwhile, PAR serves as a specific recognition unit for sulfite ions. After the addition of sulfites, a specific reaction occurs between PAR and sulfites, leading to the recovery of characteristic emission at 540 nm, achieving sensitive detection of sulfite ions. Importantly, this specific reaction is reversible under thermal treatment, allowing the hydrogel sensor to return to its initial state and thus enabling reversible detection of sulfite ions. Furthermore, a portable sensing platform is developed to realize point-of-care, real-time quantitative detection of sulfite ions. The proposed upconversion reversible hydrogel sensor provides a new sensing strategy for the detection of hazardous substances in food and offers new insights into the preparation of reversible, highly sensitive hydrogel sensors.

Quality assessment of enzymatic methyl-seq library constructed using crude cell lysate

Enzymatic methyl-seq (EM-seq), an enzyme-based method, identifies genome-wide DNA methylation, which enables us to obtain reliable methylome data from purified genomic DNA by avoiding bisulfite-induced DNA damage. However, the loss of DNA during purification hinders the methylome analysis of limited samples. The crude DNA extraction method is the quickest and minimal sample loss approach for obtaining useable DNA without requiring additional dissolution and purification. However, it remains unclear whether crude DNA can be used directly for EM-seq library construction. In this study, we aimed to assess the quality of EM-seq libraries prepared directly using crude DNA. The crude DNA-derived libraries provided appropriate fragment sizes and concentrations for sequencing similar to those of the purified DNA-derived libraries. However, the sequencing results of crude samples exhibited lower reference sequence mapping efficiencies than those of the purified samples. Additionally, the lower-input crude DNA-derived sample exhibited a marginally lower cytosine-to-thymine conversion efficiency and hypermethylated pattern around gene regulatory elements than the higher-input crude DNA- or purified DNA-derived samples. In contrast, the methylation profiles of the crude and purified samples exhibited a significant correlation. Our findings indicate that crude DNA can be used as a raw material for EM-seq library construction.

Unveiling the Chemical Composition of Sulfur-Fumigated Herbs: A Triple Synthesis Approach Using UHPLC-LTQ-Orbitrap MS-A Case Study on Steroidal Saponins in Ophiopogonis Radix

Ophiopogonis Radix (OR) is a traditional Chinese medicine. In recent years, in order to achieve the purpose of drying, bleaching, sterilizing and being antiseptic, improving appearance, and easy storage, people often use sulfur fumigation for its processing. However, changes in the chemical composition of medicinal herbs caused by sulfur fumigation can lead to the transformation and loss of potent substances. Therefore, the development of methods to rapidly reveal the chemical transformation of medicinal herbs induced by sulfur fumigation can guarantee the safe clinical use of medicines. In this study, a combined full scan-parent ions list-dynamic exclusion acquisition-diagnostic product ions analysis strategy based on UHPLC-LTQ-Orbitrap MS was proposed for the analysis of steroidal saponins and their transformed components in sulfur-fumigated Ophiopogonis Radix (SF-OR). Based on precise mass measurements, chromatographic behavior, neutral loss ions, and diagnostic product ions, 286 constituents were screened and identified from SF-OR, including 191 steroidal saponins and 95 sulfur-containing derivatives (sulfates or sulfites). The results indicated that the established strategy was a valuable and effective analytical tool for comprehensively characterizing the material basis of SF-OR, and also provided a basis for potential chemical changes in other sulfur-fumigated herbs.

In-situ sulfite treatment promotes solid reduction during aerobic digestion of waste activated sludge: Feasibility for small-scale wastewater treatment plants

Aerobic digestion remains the preferred choice for small-scale wastewater treatment plants (WWTPs) in some developing countries, largely due to economic viability and operational simplicity. The escalating production of waste activated sludge (WAS) has prompted small-scale WWTPs to improve efficiency. To address this issue, this study employed an in-situ sulfite treatment as a non-intrusive method to augment aerobic digestion. With sulfite-enhanced solubilization and hydrolysis, a 3.6-fold increase in degradation was achieved. Both sludge dewatering properties and pathogens inactivation were improved. Microbial community analysis revealed a preferential enrichment of Actinobacteriota and Firmicutes during sulfite treatment. The desktop scaling-up estimation suggests that implementing this treatment yielded operational cost savings exceeding 40 %. In summary, in-situ sulfite treatment offers a cost-effective strategy for WAS management in small-scale WWTPs.

SERS-based pH-Dependent detection of sulfites in wine by hydrogel nanocomposites

Sulfur dioxide (SO2) and sulfites are well-known additives in winemaking due to their preservative properties. Although they can prevent oxidation and inhibit microbial growth, they pose health risks and require limitations on their use. Consequently, the total level of SO2 is regulated and several quantification strategies have been proposed. The approved detection methods require the extraction of SO2 by heating and/or acid treatment. Then, iodine or acid/base titrations are conducted for the detection of liberated SO2. Although these methods can provide sensitive detection of SO2, they are complex, time-consuming, and require sample preparation steps and skilled operators. Thus, to overcome these disadvantages, an easy-to-use method, involving simple sample preparation steps, and offering high sensitivity and selectivity, is desirable. Herein, we introduce a SERS-based strategy for SO2 detection in liquids using hydrogel nanocomposites. The hydrogels are prepared by poly(ethylene glycol) diacrylate (PEGDA) in the presence of gold nanoparticles (AuNPs), acting as the SERS substrate. The use of hydrogels ensures a homogenous signal distribution and an efficient collection of SO2, and drying the hydrogels enhances and stabilizes the obtained SO2 signal. The detection strategy is based on the pH-dependent dissociation of SO2. By adjusting the pH value of wine to 10 through simple dilutions, SO2 can be directly detected in wine, down to 0.4 ppm, well below the regulatory limits. The proposed method allows for sensitive, direct, cost-effective detection of SO2 by eliminating the loss of the gaseous form of the sample and avoids titration-based detection methods.

Highly efficient reduction of bromate by vacuum UV/sulfite system

Bromate (BrO3-), a worldwide regulated by-product after ozone disinfection, is often detected in bromide-containing water, and has a strict limit of 10 μg L-1 in potable water. BrO3- degradation by advanced reduction processes (ARPs) has gained much attention because of efficient removal and easy integration with ultraviolet disinfection (UV at 254 nm). In the vacuum UV (VUV, 185/254 nm)/sulfite system, the elimination kinetics of BrO3- increased by 9-fold and 15-fold comparing with VUV alone and UV/sulfite system. This study further demonstrated the hydrated electron (eaq-) works as the dominant species in BrO3- degradation in alkaline solution, while in the acidic solution the H• became a secondary reactive species besides eaq-. Hence, the influences of pH, sulfite concentration, dissolved gas and water matrix on effectiveness of degradation kinetics of BrO3- was explored in details. With increasing pH, the proportion of SO32- species increased and even became the major ones, which also correlated well with the kobs (min-1) of BrO3- degradation. The stability of eaq- also climbs with increasing pH, while that of H• drops significantly. Higher sulfite dosage favored a more rapid degradation of BrO3-. The presence of dissolved oxygen inhibited BrO3- removal due to the scavenging effect of O2 toward eaq- and transformed VUV/sulfite-based ARP to an advanced oxidation process (AOP), which was ineffective for BrO3- removal. BrO3- removal was inhibited to varying degrees after anions (e.g., bicarbonate (HCO3-), chloride (Cl-), nitrate (NO3-)) and humic acid (HA) being added.

Comparative study of Fe(II)/sulfite, Fe(II)/PDS and Fe(II)/PMS for p-arsanilic acid treatment: Efficient organic arsenic degradation and contrasting total arsenic removal

As a widely used feed additives, p-arsanilic acid (p-AsA) frequently detected in the environment poses serious threats to aquatic ecology and water security due to its potential in releasing more toxic inorganic arsenic. In this work, the efficiency of Fe(II)/sulfite, Fe(II)/PDS and Fe(II)/PMS systems in p-AsA degradation and simultaneous arsenic removal was comparatively investigated for the first time. Efficient p-AsA abatement was achieved in theses Fe-based systems, while notable discrepancy in total arsenic removal was observed under identical acidic condition. By using chemical probing method, quenching experiments, isotopically labeled water experiments, p-AsA degradation was ascribed to the combined contribution of high-valent Fe(IV) and SO4•-in these Fe(II)-based system. In particular, the relative contribution of Fe(IV) and SO4•- in the Fe(II)/sulfite system was highly dependent on the molar ratio of [Fe(II)] and [sulfite]. Negligible arsenic removal was observed in the Fe(II)/sulfite and Fe(II)/PDS systems, while ∼80% arsenic was removed in the Fe(II)/PMS system under identical acidic condition. This interesting phenomenon was due to that ferric precipitation only occurred in the Fe(II)/PMS system. As(V) was further removed via adsorption onto the iron precipitate or the formation of ferric arsenate-sulfate compounds, which was confirmed by particle diameter measurements, fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. Through tuning solution pH, complete removal of total arsenic could achieve in all three systems. Among these three Fe-based technologies, the hybrid oxidation-coagulation Fe(II)/PMS system demonstrated potential superiority for arsenic immobilization by not requiring pH adjustment for coagulation and facilitating the in-situ generation of ferric arsenate-sulfate compounds with comparably low solubility levels like scorodite. These findings would deepen the understanding of these three Fe-based Fenton-like technologies for decontamination in water treatment.

The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet

DNA methylation is widely found in higher plants and can control gene expression by regulation without changing the DNA sequence. In this study, the whole-genome methylation map of sugar beet was constructed by WGBS (whole-genome bisulfite sequencing) technology, and the results of WGBS were verified by bisulfite transformation, indicating that the results of WGBS technology were reliable. In addition, 12 differential methylation genes (DMGs) were identified, which were related to carbohydrate and energy metabolism, pollen wall development, and endogenous hormone regulation. Quantitative real-time PCR (qRT-PCR) showed that 75% of DMG expression levels showed negative feedback with methylation level, indicating that DNA methylation can affect gene expression to a certain extent. In addition, we found hypermethylation inhibited gene expression, which laid a foundation for further study on the molecular mechanism of DNA methylation at the epigenetic level in sugar beet male sterility.

An efficient dual-function fluorescent probe for sulfites and sulfides and its imaging application in cells

As gas signaling molecules in organisms, SO2 derivatives and H2S play crucial regulating roles in a series of physiological processes. Therefore, developing an assay that can accurately monitor the concentration of SO2 derivatives and H2S in cells is extremely important for the research and treatment of related illnesses. A bifunctional probe SN-F based on FRET mechanism for SO2 derivatives and H2S was designed. SN-F had a short response time to SO2 (2 min), excellent anti-interference capability and selectivity in the non-organic solvent system (pH = 7.4), which was suitable for the determination of SO2 derivatives in cells. SN-F had a wide linear range for H2S. Moreover, SN-F was applied in cell imaging successfully with high targeting ability to endoplasmic reticulum (ER) and could monitor endogenous and exogenous H2S in cells.

Interactions between Damaged Hair Keratin and Juglone as a Possible Restoring Agent: A Vibrational and Scanning Electron Microscopy Study

Juglone, a quinonic compound present in walnut extracts, was proposed as a restoring agent for hair keratin treated with permanent or discoloration processes. The proposed mechanism of restoration by juglone involves the formation of a Michael adduct between the quinone and the thiol moieties of cysteine residues. To this purpose, the first part of the present paper involved the spectroscopic study of the product of the reaction between juglone and N-acetyl-L-cysteine as a model compound. IR spectroscopy and Scanning Electron Microscopy (SEM) monitored the chemical and morphological variations induced by applying juglone to hair keratin. In order to simulate the most common hair treatments (i.e., permanent and discoloration), juglone was applied to hair that had been previously treated with a reducing agent, i.e., methyl thioglycolate (MT) or with bleaching agents (based on hydrogen peroxide and persulfates) followed by sodium hydrogen sulfite. IR spectroscopy allowed us to monitor the formation of Michael adducts between juglone and cysteine residues: the Michael adducts' content was related to the cysteine content of the samples. In fact, MT and sodium hydrogen sulfite favored the reduction of the disulfide bonds and increased the content of free cysteine residues, which can react with juglone. SEM analyses confirmed the trend observed by IR spectroscopy since hair samples treated with juglone adopted a more regular hair surface and more imbricated scales, thus supporting the possible use of juglone as a restoring agent for damaged hair keratins.

Design of mobile and website health application devices for drug tolerability in hereditary fructose intolerance

BACKGROUND

Hereditary fructose intolerance (HFI) is a rare metabolic disease caused by aldolase B deficiency. The aim of our study was to analyse excipient tolerability in patients with HFI and other related diseases and to design mobile and website health applications to facilitate the search for drugs according to their tolerance.

RESULTS

A total of 555 excipients listed in the Spanish Medicines Agency database (July 2023) were classified as suitable for HFI patients, suitable with considerations ((glucose and glucose syrup, intravenous sucrose, oral mannitol, polydextrose, gums and carrageenans, ethanol, sulfite caramel and vanilla), not recommended (intravenous mannitol) and contraindicated (fructose, oral sucrose, invert sugar, sorbitol, maltitol, lactitol, isomaltitol, fruit syrups, honey, sucrose esters and sorbitol esters). Glucose and glucose syrup were classified as suitable with considerations due to its possible fructose content and their potential endogenous fructose production. For other related intolerances, wheat starch was contraindicated and oatmeal was not recommended in celiac disease; oral lactose and lactose-based coprocessed excipient (Cellactose®) were not recommended in lactose intolerance; and glucose, invert sugar and oral sucrose were not recommended in diabetes mellitus. The applications were named IntoMed®. Results are listed in order of tolerability (suitable drugs appear first and contraindicated drugs at the end), and they are accompanied by a note detailing their classified excipients. If a drug contains excipients within different categories, the overall classification will be the most restrictive. The apps are also able to classify substances with the same criteria if they act as active ingredients. The tools exhibited good usability (82.07 ± 13.46 points on the System Usability Scale [range: 0-100]) on a sample of HFI patients, their families and health care professionals.

CONCLUSIONS

IntoMed® is a tool for finding information about the tolerability of drugs according to excipients for patients with HFI and other related intolerances, with good usability. It is a fast and reliable system that covers the current excipient legislation and expands on it with other specific information: HFI patients should be alert for excipients such as mannitol (especially in intravenous drugs), fruit syrups, honey, sulfite caramel or vanilla. Glucose might contain or produce fructose, and special precaution is needed because of potential errors in their composition.

Quantification of Total Sulfite in Shrimps by BIOFISH 300 SUL Method: First Action 2021.09

BACKGROUND

Sulfite is the oldest and most widely used additive in our food supply with antioxidant and preservative properties. Due to its allergenic-like reactions and other adverse health effects, its use is regulated by international regulatory bodies. Therefore, food industries as well as regulatory laboratories must ensure that the maximum concentration of sulfite permitted is not exceeded. The AOAC INTERNATIONAL-approved official method for the quantification of sulfites is the Optimized Monier-Williams Method (AOAC Official Method 990.28), which consists of a time-consuming titration.

OBJECTIVE

The present study aims to demonstrate the reliability of the BIOFISH 300 SUL, a simple, fast, and accurate method, as an alternative, for the quantification of total sulfites in shrimp, with a lower LOQ than that of the OMA 990.28, set at 10 mg/Kg.

METHODS

The BIOFISH 300 SUL method is a highly specific biosensor based on its proprietary enzyme-based electrode, for the rapid quantification of total sulfite. The test kit consists of an electrochemical reader (biosensor BIOFISH 300) and disposable electrodes (Biotest) that are capable of providing an electrical signal proportional to the amount of sulfite in the sample analyzed. The method mainly consists of the extraction of sulfite from the solid matrix in an aqueous solution, and its subsequent quantification by the device in less than 3 min.

RESULTS

Comparative studies between BIOFISH 300 SUL and OMA 990.28 were conducted for naturally contaminated and spiked samples of raw and boiled shrimp with sulfite levels covering the 7-150 mg/kg range in order to determine linearity, recovery, repeatability, intermediate reproducibility, and accuracy.

CONCLUSION

The BIOFISH 300 SUL method demonstrated high accuracy and precision for the whole range of quantification (7-150 mg/kg). Its ease of use and fast response make it the ideal technology to be implemented by the industry.

HIGHLIGHTS

BIOFISH 300 SUL was adopted as a First Action Official MethodSM by the AOAC Expert Review Panel for Sulfites in Seafood Methods in February 2021 after rigorous review.

scDMV: a zero-one inflated beta mixture model for DNA methylation variability with scBS-seq data

MOTIVATION

The utilization of single-cell bisulfite sequencing (scBS-seq) methods allows for precise analysis of DNA methylation patterns at the individual cell level, enabling the identification of rare populations, revealing cell-specific epigenetic changes, and improving differential methylation analysis. Nonetheless, the presence of sparse data and an overabundance of zeros and ones, attributed to limited sequencing depth and coverage, frequently results in reduced precision accuracy during the process of differential methylation detection using scBS-seq. Consequently, there is a pressing demand for an innovative differential methylation analysis approach that effectively tackles these data characteristics and enhances recognition accuracy.

RESULTS

We propose a novel beta mixture approach called scDMV for analyzing methylation differences in single-cell bisulfite sequencing data, which effectively handles excess zeros and ones and accommodates low-input sequencing. Our extensive simulation studies demonstrate that the scDMV approach outperforms several alternative methods in terms of sensitivity, precision, and controlling the false positive rate. Moreover, in real data applications, we observe that scDMV exhibits higher precision and sensitivity in identifying differentially methylated regions, even with low-input samples. In addition, scDMV reveals important information for GO enrichment analysis with single-cell whole-genome sequencing data that are often overlooked by other methods.

AVAILABILITY AND IMPLEMENTATION

The scDMV method, along with a comprehensive tutorial, can be accessed as an R package on the following GitHub repository: https://github.com/PLX-m/scDMV.

Reductive degradation mechanism of perfluorooctanoic acid (PFOA) during vacuum ultraviolet (VUV) reactions combining with sulfite and iodide

In this study, PFOA removal and defluorination were examined during vacuum ultraviolet (VUV) photolysis in the presence of sulfite and sulfite/iodide conditions. PFOA (24 μM) degradation rate constant (kobs) and defluorination amount in VUV photolysis, and VUV/sulfite, and VUV/sulfite/iodide reactions under nitrogen-purging condition were 5.50 × 10-3, 7.26 × 10-2, 1.60 × 10-1 min-1, and 34.6, 72.7, 73.9% in 6 h, respectively. When tert-butanol (t-BuOH), NO2-, and NO3- ions were added as radical scavengers, hydrated electrons (eaq-) was confirmed as the main species responsible for degrading PFOA and mediating defluorination in VUV-based reactions. While, during VUV photolysis, short-chain perfluoroalkyl carboxylic acids (PFCAs), such as PFHpA, PFHxA, PFPeA, and PFBA, were mainly produced as transformation products (TPs) by the chain-shortening mechanism, additional 14 and 15 TPs were identified in the VUV/sulfite and VUV/sulfite/iodide reactions by LC-QTOF/MS, respectively. The main degradation mechanisms in these reactions are H-F exchange (e.g., TP395 (m/z = 394.9739) and TP377 (m/z = 376.9838)), •SO3--F exchange (TP474, m/z = 474.9323), carbon double bond formation by defluorination (e.g., TP392 (m/z = 392.9455), TP410 (m/z = 410.9355), and TP436 (m/z = 436.9347)), and H-F exchange followed by hydration reaction (TP393, m/z = 392.9773), respectively. PFOA degradation pathways were proposed for these VUV-based reactions based on the identified TPs, their time profiles, and the density functional theory (DFT). Finally, the toxicity of PFOA and its TPs produced during three reactions were assessed using ECOSAR simulation.

Use of genome-wide DNA methylation analysis to identify prognostic CpG site markers associated with longer survival time in dogs with multicentric high-grade B-cell lymphoma

BACKGROUND

DNA methylation analysis might identify prognostic CpG sites in CHOP-treated dogs with multicentric high-grade B-cell lymphoma (MHGL) with heterogenous prognosis.

OBJECTIVE

To identify prognostic CpG sites of MHGL through genome-wide DNA methylation analysis with pyrosequencing validation.

ANIMALS

Test group: 24 dogs. Validation group: 100 dogs. All client-owned dogs were diagnosed with MHGL and treated with CHOP chemotherapy.

METHODS

Cohort study. DNA was extracted from lymph node samples obtained via FNA. Genome-wide DNA methylation analysis using Digital Restriction Enzyme Analysis of Methylation (DREAM) was performed on the test group to identify differentially methylated CpG sites (DMCs). Bisulfite pyrosequencing was used to measure methylation status of candidate DMCs in the validation group. Median survival times (MST) were analyzed using Kaplan-Meier (log-rank) product limit method.

RESULTS

DREAM analyzed 101 576 CpG sites. Hierarchical clustering of 16 262 CpG sites in test group identified group with better prognosis (MST = 55-477 days vs 10-301 days, P = .007). Volcano plot identified 1371 differentially methylated CpG sites (DMCs). DMC near the genes of FAM213A (DMC-F) and PHLPP1 (DMC-P) were selected as candidates. Bisulfite-pyrosequencing performed on validation group showed group with methylation level of DMC-F < 40% had favorable prognosis (MST = 11-1072 days vs 8-1792 days, P = .01), whereas group with the methylation level combination of DMC-F < 40% plus DMC-P < 10% had excellent prognosis (MST = 18-1072 days vs 8-1792 days, P = .009).

CONCLUSION AND CLINICAL IMPORTANCE

Methylation status of prognostic CpG sites delineate canine MGHL cases with longer MST, providing owners with information on expectations of potential improved treatment outcomes.

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.

Electrochemical sensor for sensitive nitrite and sulfite detection in milk based on acid-treated Fe3O4@SiO2 nanoparticles

In this work, a simple electrochemical sensing platform based on acid-treated Fe3O4@SiO2 nanoparticles was successfully prepared for nitrite and sulfite detection. Fe3O4@SiO2 nanoparticles were synthesized through the sol-gel and hydrothermal methods. Fe3O4@SiO2 presented positive charges after acid treatment, which could enhance the electrostatic attraction between Fe3O4@SiO2 and nitrite and sulfite. The Fe3O4@SiO2(acid-treated) modified magnetic glassy carbon electrode (MGCE) was applied to detect nitrite and sulfite using differential pulse voltammetry and cyclic voltammetry. Under optimized conditions, the developed electrochemical sensor presented good analytical properties for nitrite and sulfite detection with detection limits of 3.33 μmol/L and 31.57 μmol/L, respectively. The good recoveries varied from 85.18% to 111.02%, with a relative standard deviation of 0.23-4.80%. Furthermore, the Fe3O4@SiO2(acid-treated) modified MGCE showed better selectivity, reproducibility, and repeatability in nitrite and sulfite detection. Therefore, this proposed electrochemical sensor provides a new method for developing a nitrite and sulfite detection sensor.