The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice.

A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.

R-loops: emerging key regulators in plants.

The biological implications of R-loops are increasingly receiving attention in plant biology. Compared with recent progresses in humans, the studies of R-loops in plants are lagging behind. Massive efforts must be invested by the plant community to better harness the possible regulatory functions of R-loops. Pioneering studies indicate that R-loops might act as key regulators of plant growth and development, and stress responses. This review thus timely updates the biological implications of R-loops and proposes a series of future lines of investigations to further decipher R-loop biology in plants. The following three aspects are included: the interplay between R-loops and epigenetic modifications at DNA, RNA, and chromatin levels; their regulatory roles in genome integrity, centromere functions, and DNA replication; and how they likely control plant growth and development as well as stress responses and RNA processing. Altogether, the wealth of information provided here portrays R-loop biology in plants accurately, and makes these new regulators interesting genetic levers in developing plants with new and beneficial agronomical traits.

In-situ synthesis of magnetic iron-chitosan-derived biochar as an efficient persulfate activator for phenol degradation.

Persulfate activation is a forceful method for eliminating organic pollutants from coal chemical wastewater. In this study, an in-situ synthesis method was used to fabricate an iron-chitosan-derived biochar (Fe-CS@BC) nanocomposite catalyst using chitosan as a template. Fe was successfully imprinted into the newly synthesized catalyst. The Fe-CS@BC can activate persulfate to effectively degrade phenol. This point was confirmed by scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The impact of various parameters on the removal rate was investigated in a single factor experiment. In Fe-CS@BC/PDS system, 95.96% of phenol (significantly higher than the original biochar of 34.33%) was removed within 45 min and 54.39% TOC within 2 h. The system showed superior efficiency over a broad pH value band from 3 to 9 and has a high degradation rate at ambient temperature. Free radical quenching experiment, EPR experiment and LSV experiment confirmed that multiple free radicals (including 1O2, SO4•-, O2•- and •OH) and electron transfer pathway combined to enhance phenol decomposition. Finally, the activation mechanism of persulfate by Fe-CS@BC was proposed to provide logical guidance on the treatment of organic pollutants in coal chemical wastewater.

Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice.

DNA G-quadruplexes (G4s) are non-canonical four-stranded DNA structures involved in various biological processes in eukaryotes. Molecularly crowded solutions and monovalent cations have been reported to stabilize in vitro and in vivo G4 formation. However, how K+ and Na+ affect G4 formation genome-wide is still unclear in plants. Here, we conducted BG4-DNA-IP-seq, DNA immunoprecipitation with anti-BG4 antibody coupled with sequencing, under K+ and Na+ + PEG conditions in vitro. We found that K+-specific IP-G4s had a longer peak size, more GC and PQS content, and distinct AT and GC skews compared to Na+-specific IP-G4s. Moreover, K+- and Na+-specific IP-G4s exhibited differential subgenomic enrichment and distinct putative functional motifs for the binding of certain trans-factors. More importantly, we found that K+-specific IP-G4s were more associated with active marks, such as active histone marks, and low DNA methylation levels, as compared to Na+-specific IP-G4s; thus, K+-specific IP-G4s in combination with active chromatin features facilitate the expression of overlapping genes. In addition, K+- and Na+-specific IP-G4 overlapping genes exhibited differential GO (gene ontology) terms, suggesting they may have distinct biological relevance in rice. Thus, our study, for the first time, explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.

Metabolic Reconfiguration Activates Stemness and Immunomodulation of PDLSCs.

Periodontal ligament derived stem cells (PDLSC) are adult multipotent mesenchymal-like stem cells (MSCs) that can induce a promising immunomodulation to interact with immune cells for disease treatment. Metabolic reconfiguration has been shown to be involved in the immunomodulatory activity of MSCs. However, the underlying mechanisms are largely unknown, and it remains a challenging to establish a therapeutic avenue to enhance immunomodulation of endogenous stem cells for disease management. In the present study, RNA-sequencing (RNA-seq) analysis explores that curcumin significantly promotes PDLSC function through activation of MSC-related markers and metabolic pathways. In vitro stem cell characterization further confirms that self-renewal and multipotent differentiation capabilities are largely elevated in curcumin treated PDLSCs. Mechanistically, RNA-seq reveals that curcumin activates ERK and mTOR cascades through upregulating growth factor pathways for metabolic reconfiguration toward glycolysis. Interestingly, PDLSCs immunomodulation is significantly increased after curcumin treatment through activation of prostaglandin E2-Indoleamine 2,3 dioxygenase (PGE2-IDO) signaling, whereas inhibition of glycolysis activity by 2-deoxyglucose (2-DG) largely blocked immunomodulatory capacity of PDLSCs. Taken together, this study provides a novel pharmacological approach to activate endogenous stem cells through metabolic reprogramming for immunomodulation and tissue regeneration.

RNA interference-mediated knockdown and virus-induced suppression of Troponin C gene adversely affect the behavior or fitness of the green rice leafhopper, Nephotettix cincticeps.

The green rice leafhopper, Nephotettix cincticeps, is a major rice pest in Southeast Asia and Southern China. Novel control strategies must be explored to control the rice pest. Behavior or fitness regulation of insect by modulating the Troponin C (TnC) may be a novel strategy in the comprehensive management of the insect pest. However, characterizations and functions of TnC, especially regarding effect of its RNA interference-mediated gene knockdown on the behavior or fitness of N. cincticeps remain unknown. Here, we successfully cloned and characterized TnC gene from N. cincticeps (Nc-TnC). We demonstrated that Nc-TnC ubiquitously transcribed at all development stages and special tissues in adult insects, with relative higher levels at the adult stage and in the intestinal canal. Microinjection- or oral membrane feeding-based transient knockdown of Nc-TnC adversely affected the performance or fitness, such as the decreased survival, feeding capacity, weight, and fecundity of N. cincticeps. Furthermore, we revealed that the expression of Nc-TnC was suppressed by its interaction with rice dwarf virus-encoded nonstructural protein 10, which ultimately affected detrimentally the corresponding parameters of the performance or fitness of N. cincticeps. In conclusion, our data deepen understanding of Nc-TnC functions during the development of and viral infection in N. cincticeps. It imply Nc-TnC may serve as a potential target for N. cincticeps control in future.

Nannochloropsis genomes reveal evolution of microalgal oleaginous traits.

Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains) and one time-series transcriptome dataset for triacylglycerol (TAG) synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2) in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.

Spatial working memory impairment in primary onset middle-age type 2 diabetes mellitus: An ethology and BOLD-fMRI study.

PURPOSE: To explore mild cognitive dysfunction and/or spatial working memory impairment in patients with primary onset middle-age type 2 diabetes mellitus (T2DM] using ethology (behavior tests) and blood oxygen level-dependent functional magnetic resonance imaging (BOLD-fMRI). MATERIALS AND METHODS: Eighteen primary onset T2DM patients and 18 matched subjects with normal blood glucose levels were all tested using the Montreal cognitive assessment scale test, the Wechsler Memory Scale Chinese-revised test, and scanned using BOLD-fMRI (1.5T, EPI sequence) while performing the n-back task to find the activation intensity of some cognition-related areas. RESULTS: The ethology results showed that T2DM patients had a mild cognitive impairment and memory dysfunction (P < 0.05). The fMRI scan identified a neural network consisting of bilateral dorsolateral prefrontal cortex (DLPFC), bilateral premotor area (PreMA), bilateral parietal lobe (PA), and anterior cingulate cortex (ACC) / supplementary motor area (SMA) that was activated during the n-back task, with right hemisphere dominance. However, only the right PA and ACC/SMA showed a load effect via quantitative analysis in the T2DM group; the activation intensity of most working memory-related brain areas for the T2DM group were lower than for the control group under three memory loads. Furthermore, we found that the activation intensity of some cognition-related areas, including the right insular lobe, left caudate nucleus, and bilateral hippocampus/parahippocampal gyrus were lower than the control group under the memory loads. CONCLUSION: Diabetes-related brain damage of primary onset middle-age T2DM patients with right DLPFC-posterior parietal lobe and parahippocampal gyrus default network causes impairment of spatial working memory and mild cognitive dysfunction.

Time-series analysis of the association between air pollution exposure and outpatient visits for dry eye disease: a case study in Zhengzhou, China.

Background: Dry eye disease (DED) is a prevalent ocular surface disease that significantly impacts patients' quality of life. The association between air pollution and the risk of dry eye disease remains uncertain. Methods: Data on outdoor air pollutants, meteorological information, and outpatient visits for DED were collected from July 1, 2014, to December 31, 2019. The relationship between ambient air pollutants and DED outpatient visits was analyzed using a generalized additive model with a Poisson distribution. Results: Among the 5,204 DED patients included in the study, 63.76% were female and 36.24% were male. The single-pollutant model revealed a significant association between a 10 µg/m3 increase in concentrations of fine-particulate matter with a median aerometric diameter of less than 10 µm (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), and carbon monoxide (CO) and outpatient visits for DED. Fine-particulate matter with a median aerometric diameter of less than 2.5 µm (PM2.5) showed a significant association with DED outpatient visits in males and the 19-59 years age group. The strongest associations between air pollutants and outpatient visits were observed in male patients and during the cold season. Conclusion: The noteworthy correlation between air pollutants and DED outpatient visits can offer evidence for policy makers and underscore the significance of reinforcing environmental protection.

Alterations of the cerebral microstructure in patients with noise-induced hearing loss: A diffusion tensor imaging study.

OBJECTIVE: To explore the changes in the cerebral microstructure of patients with noise-induced hearing loss (NIHL) using diffusion tensor imaging (DTI). METHOD: Overall, 122 patients with NIHL (mild [MP, n = 79], relatively severe patients [including moderate and severe; RSP, n = 32], and undetermined [lost to follow-up, n = 11]) and 84 healthy controls (HCs) were enrolled. All clinical data, including age, education level, hearing threshold, occupation type, noise exposure time, and some scale scores (including the Mini-Mental State Examination [MMSE], tinnitus handicap inventory [THI], and Hamilton Anxiety Scale [HAMA]), were collected and analyzed. All participants underwent T1WI3DFSPGR and DTI, and tract-based spatial statistics and region of interest (ROI) analysis were used for assessment. RESULTS: The final sample included 71 MP, 28 RSP, and 75 HCs. The HAMA scores of the three groups were significantly different (p < .05). The noise exposure times, hearing thresholds, and HAMA scores of the MP and RSP were significantly different (p < .05). The noise exposure time was positively correlated with the hearing threshold and negatively correlated with the HAMA scores (p < .05), whereas the THI scores were positively correlated with the hearing threshold (p < .05). DTI analysis showed that all DTI parameters (fractional anisotropy [FA], axial diffusivity [AD], mean diffusivity [MD], and radial diffusivity [RD]) were significantly different in the left inferior longitudinal fasciculus (ILF) and left inferior fronto-occipital fasciculus (IFOF) for the three groups (p < .05). In addition, the FA values were significantly lower in the bilateral corticospinal tract (CST), right fronto-pontine tract (FPT), right forceps major, left superior longitudinal fasciculus (temporal part) (SLF), and left cingulum (hippocampus) (C-H) of the MP and RSP than in those of the HCs (p < .05); the AD values showed diverse changes in the bilateral CST, left IFOF, right anterior thalamic radiation, right external capsule (EC), right SLF, and right superior cerebellar peduncle (SCP) of the MP and RSP relative to those of the HC (p < .05). However, there were no significant differences among the bilateral auditory cortex ROIs of the three groups (p > .05). There was a significant negative correlation between the FA and HAMA scores for the left IFOF/ILF, right FPT, left SLF, and left C-H for the three groups (p < .05). There was a significant positive correlation between the AD and HAMA scores for the left IFOF/ILF and right EC of the three groups (p < .05). There were significantly positive correlations between the RD/MD and HAMA scores in the left IFOF/ILF of the three groups (p < .05). There was a significant negative correlation between the AD in the right SCP and noise exposure time of the MP and RSP groups (p < .05). The AD, MD, and RD in the left ROI were significantly positively correlated with hearing threshold in the MP and RSP groups (p < .05), whereas FA in the right ROI was significantly positively correlated with the HAMA scores for the three groups (p < .05). CONCLUSION: The changes in the white matter (WM) microstructure may be related to hearing loss caused by noise exposure, and the WM structural abnormalities in patients with NIHL were mainly located in the syndesmotic fibers of the temporooccipital region, which affected the auditory and language pathways. This confirmed that the auditory pathways have abnormal structural connectivity in patients with NIHL.

Spatial working memory impairment in subclinical hypothyroidism: an FMRI study.

OBJECTIVE: Using a block-designed BOLD-fMRI to explore the neural basis of spatial working memory impairment in patients with subclinical hypothyroidism (SCH) performing an n-back task. METHODS: Sixteen patients with SCH before and after being treated with levothyroxine (LT4) for 6 months and 16 matched euthyroid subjects were scanned by fMRI under the n-back task. RESULTS: The fMRI scan found that a neural network consisting of bilateral dorsolateral prefrontal cortex (DLPFC), bilateral premotor area (PreMA), supplementary motor area/anterior cingulate cortex, bilateral parietal lobe (PA) and right caudate nucleus/thalamus was activated, with right hemisphere dominance. In euthyroid subjects, all these regions of interest (ROIs) showed load effect; however, only left DLPFC, left PA, bilateral PreMA and right caudate nucleus/thalamus showed the same effect in Pre-SCH patients. Furthermore, activation intensities of most ROIs (especially DLPFC and right PA) for Pre-SCH patients were lower than those in the euthyroid subjects (F <3.046, p > 0.062). Importantly, after a 6-month treatment with LT4, the load effect in SCH patients appeared the same as in the euthyroid subjects in all the ROIs (F >13.176, p < 0.0001). CONCLUSION: Our previous study shows that verbal working memory of SCH patients is impaired with abnormal activity in bilateral frontal areas. In this study, the results indicated that SCH patients may also have spatial working memory impairments, and the altered activities of right DLPFC and right posterior parietal lobe may be one of the underlying neural mechanisms. Most importantly, this study shows that LT4 replacement therapy can improve the memory impairment and reverse the altered neural activity network.

EVMP: enhancing machine learning models for synthetic promoter strength prediction by Extended Vision Mutant Priority framework.

Introduction: In metabolic engineering and synthetic biology applications, promoters with appropriate strengths are critical. However, it is time-consuming and laborious to annotate promoter strength by experiments. Nowadays, constructing mutation-based synthetic promoter libraries that span multiple orders of magnitude of promoter strength is receiving increasing attention. A number of machine learning (ML) methods are applied to synthetic promoter strength prediction, but existing models are limited by the excessive proximity between synthetic promoters. Methods: In order to enhance ML models to better predict the synthetic promoter strength, we propose EVMP(Extended Vision Mutant Priority), a universal framework which utilize mutation information more effectively. In EVMP, synthetic promoters are equivalently transformed into base promoter and corresponding k-mer mutations, which are input into BaseEncoder and VarEncoder, respectively. EVMP also provides optional data augmentation, which generates multiple copies of the data by selecting different base promoters for the same synthetic promoter. Results: In Trc synthetic promoter library, EVMP was applied to multiple ML models and the model effect was enhanced to varying extents, up to 61.30% (MAE), while the SOTA(state-of-the-art) record was improved by 15.25% (MAE) and 4.03% (R2). Data augmentation based on multiple base promoters further improved the model performance by 17.95% (MAE) and 7.25% (R2) compared with non-EVMP SOTA record. Discussion: In further study, extended vision (or k-mer) is shown to be essential for EVMP. We also found that EVMP can alleviate the over-smoothing phenomenon, which may contributes to its effectiveness. Our work suggests that EVMP can highlight the mutation information of synthetic promoters and significantly improve the prediction accuracy of strength. The source code is publicly available on GitHub: https://github.com/Tiny-Snow/EVMP.

Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.

Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other biotechnological processes. The retrieval of full-length BGC (biosynthetic gene cluster) sequences from uncultivated bacteria is difficult due to the technical constraints of short-read sequencing, making it impossible to determine BGC diversity. Using long-read sequencing and genome mining, 339 mainly full-length BGCs were recovered in this study, illuminating the wide range of BGCs from uncultivated lineages discovered in seawater from Aoshan Bay, Yellow Sea, China. Many extremely diverse BGCs were discovered in bacterial phyla such as Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota as well as the previously uncultured archaeal phylum "Candidatus Thermoplasmatota." The data from metatranscriptomics showed that 30.1% of secondary metabolic genes were being expressed, and they also revealed the expression pattern of BGC core biosynthetic genes and tailoring enzymes. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional expression of BGCs in environmental processes. IMPORTANCE Genome mining of metagenomic data has become the preferred method for the bioprospecting of novel compounds by cataloguing secondary metabolite potential. However, the accurate detection of BGCs requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until recently with new long-read technologies. We used high-quality metagenome-assembled genomes generated from long-read data to determine the biosynthetic potential of microbes found in the surface water of the Yellow Sea. We recovered 339 highly diverse and mostly full-length BGCs from largely uncultured and underexplored bacterial and archaeal phyla. Additionally, we present long-read metagenomic sequencing combined with metatranscriptomic analysis as a potential method for gaining access to the largely underutilized genetic reservoir of specialized metabolite gene clusters in the majority of microbes that are not cultured. The combination of long-read metagenomic and metatranscriptomic analyses is significant because it can more accurately assess the mechanisms of microbial adaptation to the environment through BGC expression based on metatranscriptomic data.

Selective RNA Processing and Stabilization are Multi-Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli.

Selective RNA processing and stabilization (SRPS) facilitates the differential expression of multiple genes in polycistronic operons. However, how the coordinated actions of SRPS-related enzymes affect stoichiometric regulation remains unclear. In the present study, the first genome-wide targetome analysis is reported of these enzymes in Escherichia coli, at a single-nucleotide resolution. A strictly linear relationship is observed between the RNA pyrophosphohydrolase processing ratio and scores assigned to the first three nucleotides of the primary transcript. Stem-loops associated with PNPase targetomes exhibit a folding free energy that is negatively correlated with the termination ratio of PNPase at the 3' end. More than one-tenth of the RNase E processing sites in the 5'-untranslated regions（UTR） form different stem-loops that affect ribosome-binding and translation efficiency. The effectiveness of the SRPS elements is validated using a dual-fluorescence reporter system. The findings highlight a multi-layer and quantitative regulatory method for optimizing the stoichiometric expression of genes in bacteria and promoting the application of SRPS in synthetic biology.

The Transcriptional Repressor PerR Senses Sulfane Sulfur by Cysteine Persulfidation at the Structural Zn2+ Site in Synechococcus sp. PCC7002.

Cyanobacteria can perform both anoxygenic and oxygenic photosynthesis, a characteristic which ensured that these organisms were crucial in the evolution of the early Earth and the biosphere. Reactive oxygen species (ROS) produced in oxygenic photosynthesis and reactive sulfur species (RSS) produced in anoxygenic photosynthesis are closely related to intracellular redox equilibrium. ROS comprise superoxide anion (O2●-), hydrogen peroxide (H2O2), and hydroxyl radicals (●OH). RSS comprise H2S and sulfane sulfur (persulfide, polysulfide, and S8). Although the sensing mechanism for ROS in cyanobacteria has been explored, that of RSS has not been elucidated. Here, we studied the function of the transcriptional repressor PerR in RSS sensing in Synechococcus sp. PCC7002 (PCC7002). PerR was previously reported to sense ROS; however, our results revealed that it also participated in RSS sensing. PerR repressed the expression of prxI and downregulated the tolerance of PCC7002 to polysulfide (H2Sn). The reporter system indicated that PerR sensed H2Sn. Cys121 of the Cys4:Zn2+ site, which contains four cysteines (Cys121, Cys124, Cys160, and Cys163) bound to one zinc atom, could be modified by H2Sn to Cys121-SSH, as a result of which the zinc atom was released from the site. Moreover, Cys19 could also be modified by polysulfide to Cys19-SSH. Thus, our results reveal that PerR, a representative of the Cys4 zinc finger proteins, senses H2Sn. Our findings provide a new perspective to explore the adaptation strategy of cyanobacteria in Proterozoic and contemporary sulfurization oceans.

Chitin-derived biochar with nitrogen doping to activate persulfate for phenol degradation: Application potential and electron transfer pathway in system.

The fast and efficient removal of organic pollutants (e.g., phenolics) remains one of the focus problems in environment pollution. Thus, a chitin-derived biochar with nitrogen doping (N-BC) was successfully prepared at a lower calcination temperature of 600 °C, which is environmentally friendly and energy saving. The N-BC was analyzed by SEM, FTIR, BET, XRD, XPS and Raman spectroscopy to confirm that the doping of nitrogen element provided sufficient defect sites to promote the activation of persulfate (PDS). Quenching experiments and EPR results revealed the presence of •OH and •O2- contributed to phenol degradation in N-BC 600/PDS system. In addition, the linear sweep voltammogram experiments also demonstrated the existence of electron transfer pathway. The electrons were donated from phenol and shifted to PDS through N-BC. The graphitic N and carbon defects in N-BC served as the active sites of the reaction and involved absorption and transfer of electrons as the key character. Moreover, the removal rates of phenol and TOC reached 98.8% and 58.2% within 2 h, indicating that N-BC effectively activated the persulfate to degrade phenol. This study provides the theoretical support and potential applications for the activation of persulfate by nitrogen-doped biochar to degrade other phenolic compounds.

mTOR Signaling in the Regulation of CD4+ T Cell Subsets in Periodontal Diseases.

Periodontal disease results from the inflammatory infiltration by the microbial community which is marked through tooth mobility and alveolar bone resorption. The inflammation in periodontal disease is mediated by CD4+ T cells through cytokine secretion and osteoclastogenetic activity. Historically, the inflammatory model in periodontal disease is described through disruption of the balance between two subsets of T helper cells which are T-helper type 1 (Th1) and T-helper type 2 (Th2). However, more and more studies have found that apart from subsets of helper T cells, regulatory T-cells and Th17 cells are also involved in the pathogenesis of periodontal diseases. Growing evidence proves that helper T cells differentiation, activation, and subset determination are under the strong impact of mTOR signaling. mTOR signaling could promote Th1 and Th17 cell differentiation and inhibit Treg commitment through different mTOR complexes, therefore we anticipate a regulation effect of mTOR signaling on periodontal diseases by regulating CD4+ T cell subsets. This review aims to integrate the topical researches about the role of different types of Th cells in the pathogenesis of periodontal diseases, as well as the regulation of mTOR signaling in the specification and selection of Th cell commitment.

Efficacy of artificial intelligence-based screening for diabetic retinopathy in type 2 diabetes mellitus patients.

AIM: To explore the efficacy of artificial intelligence (AI)-based screening for diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) patients. METHODS: Data were obtained from 549 T2DM patients who visited the Fundus Disease Center at Henan Provincial People's Hospital from 2018/10-2020/09. DR identification and grading were conducted by two retina specialists, EyeWisdom®DSS and EyeWisdom®MCS, with ophthalmologist grading as reference standard, efficacy of EyeWisdom was evaluated according to sensitivity, specificity, positive predictive value, and negative predictive value. RESULTS: Ophthalmologists detected 324 DR cases. Among them, there were 43 of mild non-proliferative DR (NPDR), 79 of moderate NPDR, 61 of severe NPDR, and 141 of proliferative DR (PDR). EyeWisdom®DSS detected 337 DR and EyeWisdom®MCS detected 264 DR. Sensitivity and specificity of EyeWisdom®DSS were 91.0%(95 %CI: 87.3%-93.8%) and 81.3% (95 %CI: 75.5%-86.1%), while EyeWisdom®MCS correctly identified 76.2%(95 %CI: 71.1%-80.7%) of patients with DR and 92.4%(95 %CI: 87.9%-95.4%) of patients without DR. EyeWisdom®DSS showed 76.5%(95 %CI: 69.6%-82.3%) sensitivity and 78.4%(95 %CI: 73.7%-82.5%) specificity for detecting NPDR and 64.5%(95 %CI: 56.0%-72.3%) sensitivity and 93.1%(95 %CI: 90.1%-95.3%) specificity for diagnosing PDR. CONCLUSION: EyeWisdom®DSS is effective in screening for DR, and the accuracy of EyeWisdom®MCS was higher for identifying patients without DR. It is valuable to carry out AI-based DR screening in poorer regions.

Synechococcus sp. PCC7002 Uses Peroxiredoxin to Cope with Reactive Sulfur Species Stress.

Cyanobacteria are a widely distributed group of microorganisms in the ocean, and they often need to cope with the stress of reactive sulfur species, such as sulfide and sulfane sulfur. Sulfane sulfur refers to the various forms of zero-valent sulfur, including persulfide, polysulfide, and element sulfur (S8). Although sulfane sulfur participates in signaling transduction and resistance to reactive oxygen species in cyanobacteria, it is toxic at high concentrations and induces sulfur stress, which has similar effects to oxidative stress. In this study, we report that Synechococcus sp. PCC7002 uses peroxiredoxin to cope with the stress of cellular sulfane sulfur. Synechococcus sp. PCC7002 contains six peroxiredoxins, and all were induced by S8. Peroxiredoxin I (PrxI) reduced S8 to H2S by forming a disulfide bond between residues Cys53 and Cys153 of the enzyme. A partial deletion strain of Synechococcus sp. PCC7002 with decreased copy numbers of the prxI gene was more sensitive to S8 than was the wild type. Thus, peroxiredoxin is involved in maintaining the homeostasis of cellular sulfane sulfur in cyanobacteria. Given that peroxiredoxin evolved before the occurrence of O2 on Earth, its original function could have been to cope with reactive sulfur species stress, and that function has been preserved. IMPORTANCE Cyanobacteria are the earliest microorganisms that perform oxygenic photosynthesis, which has played a key role in the evolution of life on Earth, and they are the most important primary producers in the modern oceans. The cyanobacterium Synechococcus sp. PCC7002 uses peroxiredoxin to reduce high levels of sulfane sulfur. That function is possibly the original role of peroxiredoxin, as the enzyme evolved before the appearance of O2 on Earth. The preservation of the reduction of sulfane sulfur by peroxiredoxin5-type peroxiredoxins may offer cyanobacteria an advantage in the complex environment of the modern oceans.

Distribution of diabetic retinopathy in diabetes mellitus patients and its association rules with other eye diseases.

The study aims to explore the distribution characteristics and influencing factors of diabetic retinopathy (DR) in diabetes mellitus (DM) patients and association rules of eye diseases in these patients. Data were obtained from 1284 DM patients at Henan Provincial People's Hospital. Association rules were employed to calculate the probability of the common occurrence of eye-related diseases in DM patients. A web visualization network diagram was used to display the association rules of the eye-related diseases in DM patients. DR prevalence in people aged < 40 years (≥ 58.5%) was higher than that in those aged 50-60 years (≤ 43.7%). Patients with DM in rural areas were more likely to have DR than those in urban areas (56.2% vs. 35.6%, P < 0.001). DR prevalence in Pingdingshan City (68.4%) was significantly higher than in other cities. The prevalence of DR in patients who had DM for ≥ 5 years was higher than in other groups (P < 0.001). About 33.07% of DM patients had both diabetic maculopathy and DR, and 36.02% had both diabetic maculopathy and cataracts. The number of strong rules in patients ≥ 60 years old was more than those in people under 60 in age, and those in rural areas had more strong rules than those in urban areas. DM patients with one or more eye diseases are at higher risks of other eye diseases than general DM patients. These association rules are affected by factors such as age, region, disease duration, and DR severity.