FUS reads histone H3K36me3 to regulate alternative polyadenylation.

Complex organisms generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates cellular behavior in tissues. However, little is known about how chromatin, especially histone modifications, regulates RNA polyadenylation. In this study, we found that FUS was recruited to chromatin by H3K36me3 at gene bodies. The H3K36me3 recognition of FUS was mediated by the proline residues in the ZNF domain. After these proline residues were mutated or H3K36me3 was abolished, FUS dissociated from chromatin and bound more to RNA, resulting in an increase in polyadenylation sites far from stop codons genome-wide. A proline mutation corresponding to a mutation in amyotrophic lateral sclerosis contributed to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal that FUS is an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.

Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing.

Tn5 transposon tagments double-stranded DNA and RNA/DNA hybrids to generate nucleic acids that are ready to be amplified for high-throughput sequencing. The nucleic acid substrates for the Tn5 transposon must be explored to increase the applications of Tn5. Here, we found that the Tn5 transposon can transpose oligos into the 5' end of single-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA sequencing, starting with as little as 30 pg of total RNA. Moreover, compared with traditional dUTP-based strand-specific RNA sequencing, this method detects more genes, has a higher strand specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.

Bioprinting EphrinB2-Modified Dental Pulp Stem Cells with Enhanced Osteogenic Capacity for Alveolar Bone Engineering.

Bioprinting, a technology that allows depositing living cells and biomaterials together into a complex tissue architecture with desired pattern, becomes a revolutionary technology for fabrication of engineered constructs. Previously, we have demonstrated that EphrinB2-modified dental pulp stem cells (DPSCs) are expected to be promising seed cells with enhanced osteogenic differentiation capability for alveolar bone regeneration. In this study, we aimed to bioprint EphrinB2-overexpressing DPSCs with low-concentrated Gelatin methacrylate (GelMA) hydrogels into three-dimensional (3D) constructs. The printability of GelMA (5% w/v) and the structural fidelity of bioprinted constructs were examined. Then, viability, proliferation, morphology, and osteogenic differentiation of DPSCs in bioprinted constructs were measured. Finally, the effect of EphrinB2 overexpression on osteogenic differentiation of DPSCs in bioprinted constructs was evaluated. Our results demonstrated that GelMA (5% w/v) in a physical gel form was successfully bioprinted into constructs with various shapes and patterns using optimized printing parameters. Embedded DPSCs showed round-like morphology, and had a high viability (91.93% ± 8.38%) and obvious proliferation (∼1.9-fold increase) 1 day after printing. They also showed excellent osteogenic potential in bioprinted constructs. In bioprinted 3D constructs, EphrinB2-overexpressing DPSCs expressed upregulated osteogenic markers, including ALP, BMP2, RUNX2, and SP7, and generated more mineralized nodules, as compared with Vector-DPSCs. Taken together, this study indicated that fabrication of bioprinted EphrinB2-DPSCs-laden constructs with enhanced osteogenic potential was possible, and 3D bioprinting strategy combined with EphrinB2 gene modification was a promising way to create bioengineered constructs for alveolar bone regeneration.

SMYD5 catalyzes histone H3 lysine 36 trimethylation at promoters.

Histone marks, carriers of epigenetic information, regulate gene expression. In mammalian cells, H3K36me3 is mainly catalyzed by SETD2 at gene body regions. Here, we find that in addition to gene body regions, H3K36me3 is enriched at promoters in primary cells. Through screening, we identify SMYD5, which is recruited to chromatin by RNA polymerase II, as a methyltransferase catalyzing H3K36me3 at promoters. The enzymatic activity of SMYD5 is dependent on its C-terminal glutamic acid-rich domain. Overexpression of full-length Smyd5, but not the C-terminal domain-truncated Smyd5, restores H3K36me3 at promoters in Smyd5 knockout cells. Furthermore, elevated Smyd5 expression contributes to tumorigenesis in liver hepatocellular carcinoma. Together, our findings identify SMYD5 as the H3K36me3 methyltransferase at promoters that regulates gene expression, providing insights into the localization and function of H3K36me3.

Degradation of 2,6-dichloro-1,4-benzoquinone by UV/H2O2/O3 treatment: Effectiveness, water matrix effects, and degradation mechanism.

2,6-dichloro-1,4-benzoquinone (DCBQ), a typical representative of Halobenzoquinones, is an emerging aromatic disinfection by-product (DBP) with high toxicity and carcinogenicity, generated commonly through the chlorination in the drinking water disinfection process while there is still a lack of research on its removal. In this study, the effects of ultraviolet-based advanced oxidation processes (UV-AOPs) on the degradation of DCBQ were evaluated. The results showed that UV-AOPs are effective in degrading DCBQ. The removal of DCBQ by UV/H2O2/O3 was more significant than by UV/H2O2 or UV/O3, achieving a 96.7% removal rate at both the O3 and H2O2 doses of 1 mg/L. The results also indicated the alkaline and weakly acidic environments could facilitate the degradation of DCBQ, inorganic anions could inhibit DCBQ degradation and the degree of inhibition increased as the matrix concentration increased. The degradation of DCBQ was inhibited more by the CO32- than the other matrix components, such as Cl- and NO3-. It was shown by the density functional theory simulations and the ultrahigh-performance liquid chromatography (UPLC) - Orbitrap mass spectra that the electrons in DCBQ are mainly on the chlorine atom connected to the carboatomic ring and that OH• can attack the chlorine atom to cause de-chlorination. The DCBQ degradation pathway may involve the oxidation of DCBQ to 3-hydroxy-2,6-DCBQ (HO-DCBQ) and 3,5-dichloro-1,2,4-pyrogallol, the further degradation of intermediate products by OH• to dechlorinated forms of HO-DCBQ and DCBQ.

Analysis of volatile compounds and flavor fingerprint in hairtail (Trichiurus lepturus) during air-drying using headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS).

In the present study, changes in volatile compounds during processing were analyzed using the headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), to investigate the generation of aroma in hairtails (Trichiurus lepturus) during air-drying. Physicochemical indices, such as moisture content and thiobarbituric acid reactive substances (TBARS), were also detected. Flavor fingerprints were studied and developed to distinguish the samples of fresh hairtails (0 day) from air-dried hairtails (2 and 4 days). A total of 75 volatile organic compounds (VOCs) were identified in hairtails, in which alcohols, aldehydes, ketones, and esters were the principal contributors to the formation of the overall flavor of hairtails during air-drying. Seven flavor compounds (ethanol, 3-methyl-1-butanol, 1-pentanol, hexanal, octanal, benzaldehyde, and 3-methylbutanal), two flavor compounds (acetoin and dimethyl sulfide), and eight flavor compounds (1-hexanol, 1-octen-3-ol, nonanal, heptanal, 2-heptanone, ethyl acetate, trimethylamine, and ammonia) were identified in 0, 2, and 4 air-dried hairtails as biomarkers, respectively. The results showed that HS-GC-IMS could detect VOCs in different air-dried hairtails rapidly and comprehensively.

[Composition and histopathological features of prostatic calculi in patients with benign prostatic hyperplasia].

OBJECTIVE: To analyze the composition of prostatic calculus in patients with BPH and explore its pathogenic factors and histopathological characteristics. METHODS: Strictly following the inclusion and exclusion criteria, we included in this retrospective study 580 cases of bipolar transurethral plasma kinetic prostatectomy (TUPKP) performed in our hospital from May 2015 to May 2019, analyzed the histopathological and calculus-composition features of the patients with BPH complicated by prostatic calculi (the BPH+PC group) and the histopathological data of those with BPH only (the BPH group). We compared the related factors between the two groups of patients and performed uni- and multivariate logistic regression analyses of the data on those in the BPH+PC group. RESULTS: The incidence rate of chronic inflammation was significantly higher in the BPH+PC than in the BPH group (83.1% vs 61.1%, P < 0.05), 90% of the cases moderate to severe and 81% with inflammatory cells mainly distributed in the prostate gland in the BPH+PC group, and 74% with inflammatory cells chiefly distributed in the prostate gland and stroma in the BPH group, with statistically significant difference between the two groups (P < 0.05). Prostatic calculi were found in 302 (52.1%) of the patients, including 71 cases of simple calculi (23.5%) and 231 cases of mixed calculi (76.5%). As for the chemical composition, calcium oxalate was detected in 212 cases (70.2%), carbonate apatite in 206 (68.2%), magnesium ammonium phosphate in 158 (52.3%), and uric acid calculi in 19 (6.3%). The calculus composition was not correlated with the age of the patients. There were statistically significant differences between the two groups of patients in age, prostate volume and IPSS (P < 0.05), but not in the PSA level, postvoid residual urine volume (PRV) or maximum urinary flow rate (Qmax) (P > 0.05). Logistic regression analyses showed that prostatic calculus was significantly correlated with chronic inflammation of the prostate, the patient's age and IPSS (P < 0.05) but not with the PSA level, PRV or Qmax (P > 0.05). CONCLUSIONS: Prostatic calculus has a high incidence in BPH patients and varies widely in composition, chiefly consisting of calcium oxalate and carbonate apatite. The major factors contributing to prostatic calculi include chronic inflammation of the prostate (primarily the severe type), age and BPH. Prostate calculi may aggravate lower urinary tract symptoms, especially urinary storage symptoms, in patients with BPH, but not significantly affect the PSA level.？.

Joint single-cell multiomic analysis in Wnt3a induced asymmetric stem cell division.

Wnt signaling usually functions through a spatial gradient. Localized Wnt3a signaling can induce the asymmetric division of mouse embryonic stem cells, where proximal daughter cells maintain self-renewal and distal daughter cells acquire hallmarks of differentiation. Here, we develop an approach, same cell epigenome and transcriptome sequencing, to jointly profile the epigenome and transcriptome in the same single cell. Utilizing this method, we profiled H3K27me3 and H3K4me3 levels along with gene expression in mouse embryonic stem cells with localized Wnt3a signaling, revealing the cell type-specific maps of the epigenome and transcriptome in divided daughter cells. H3K27me3, but not H3K4me3, is correlated with gene expression changes during asymmetric cell division. Furthermore, cell clusters identified by H3K27me3 recapitulate the corresponding clusters defined by gene expression. Our study provides a convenient method to jointly profile the epigenome and transcriptome in the same cell and reveals mechanistic insights into the gene regulatory programs that maintain and reset stem cell fate during differentiation.

The H3K36me2 methyltransferase NSD1 modulates H3K27ac at active enhancers to safeguard gene expression.

Epigenetics, especially histone marks, functions beyond the DNA sequences to regulate gene expression. Depletion of NSD1, which catalyzes H3K36me2, leads to both up- and down-regulation of gene expression, indicating NSD1 is associated with both active and repressed gene expression. It's known that NSD1 regulates the deposition and expansion of H3K27me3, a repressive mark for gene expression, to keep active gene transcription. However, how NSD1 functions to repress gene expression is largely unknown. Here, we find that, when NSD1 is knocked out in mouse embryonic stem cells (mESCs), H3K27ac increases correlatively with the decrease of H3K36me2 at active enhancers, which is associated with mesoderm differentiation genes, leading to elevated gene expression. Mechanistically, NSD1 recruits HDAC1, the deacetylase of H3K27ac, to chromatin. Moreover, HDAC1 knockout (KO) recapitulates the increase of H3K27ac at active enhancers as the NSD1 depletion. Together, we propose that NSD1 deposits H3K36me2 and recruits HDAC1 at active enhancers to serve as a 'safeguard', preventing further activation of active enhancer-associated genes.

A retrospective study to compare the treatment outcomes with and without surgical navigation for fracture of the orbital wall.

PURPOSE: To evaluate the outcomes with and without aid of a computer-assisted surgical navigation system (CASNS) for treatment of unilateral orbital wall fracture (OWF). METHODS: Patients who came to our hospital for repairing unilateral traumatic OWF from 2014 to 2017 were included in this study. The patients were divided into the navigation group who accepted orbital wall reconstruction aided by CASNS and the conventional group. We evaluated the surgical precision in the navigation group by analyzing the difference between actual postoperative computed tomography data and preoperative virtual surgical plan through color order ratios. We also compared the duration of surgery, enophthalmos correction, restoration of orbital volumes, and improvement of clinical symptoms in both groups systemically. Quantitative data were presented as mean ± SD. Significance was determined by the two-sample t-test using SPSS Version 19.0 A p < 0.05 was considered statistically significant. RESULTS: Seventy patients with unilateral OWF were included in the study cohort. The mean difference between preoperative virtual planning and actual reconstruction outcome was (0.869 ± 0.472) mm, which means the reconstruction result could match the navigation planning accurately. The mean duration of surgery in the navigation group was shorter than it is in the control group, but not significantly. Discrepancies between the reconstructed and unaffected orbital-cavity volume and eyeball projection in the navigation group were significantly less than that in the conventional group. One patient had remnant diplopia and two patients had enophthalmos after surgery in the navigation group; two patients had postoperative diplopia and four patients had postoperative enophthalmos in the conventional group. CONCLUSION: Compare with the conventional treatment for OWF, the use of CASNS can provide a significantly better surgical precision, greater improvements in orbital-cavity volume and eyeball projection, and better clinical results, without increasing the duration of surgery.

Overview of Histone Modification.

Epigenetics is the epi-information beyond the DNA sequence that can be inherited from parents to offspring. From years of studies, people have found that histone modifications, DNA methylation, and RNA-based mechanism are the main means of epigenetic control. In this chapter, we will focus on the general introductions of epigenetics, which is important in the regulation of chromatin structure and gene expression. With the development and expansion of high-throughput sequencing, various mutations of epigenetic regulators have been identified and proven to be the drivers of tumorigenesis. Epigenetic alterations are used to diagnose individual patients more accurately and specifically. Several drugs, which are targeting epigenetic changes, have been developed to treat patients regarding the awareness of precision medicine. Emerging researches are connecting the epigenetics and cancers together in the molecular mechanism exploration and the development of druggable targets.

The mechanisms and safety of probiotics against toxigenic clostridium difficile.

INTRODUCTION: Toxigenic Clostridium difficile (C. difficile) is the main cause of antibiotic-associated diarrhea and can induce pseudomembranous colitis and infrequent toxic megacolon, which are potentially fatal. The standard antibiotic therapy for C. difficile infection (CDI) is limited by antibiotics' broad spectrum and further disruptive effects on indigenous microbiota. Probiotics may offer a prospective and alternative strategy for the prevention and treatment of CDI. AREAS COVERED: In this article, the mechanisms implying the probiotic effect against C. difficile and the safety profile highlighting the patient groups with inappropriate application of probiotics were reviewed from 2015 to 2020. EXPERT OPINION: Although many strains with ability against C. difficile have been reported, the usage of probiotics for CDI prevention and/or treatment is scarce since the number of clinical trials is not sufficient to prove probiotics' efficacy and safety in CDI treatment, especially for premature infant and immunocompromised patient. Especially, there are few well-defined clinical studies supporting safety of probiotics for CDI. A few strains from Lactobacillus and Saccharomyces genus have been studied more extensively than other probiotic strains through clinical trials for CDI. Thus, more clinical intervention studies regarding the benefit and the comprehensive safety assessments of probiotics for CDI are needed.

RETRACTED: The effect of combined application of pentoxifylline and vitamin E for the treatment of osteoradionecrosis of the jaws: a meta-analysis.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the corresponding author and following a translated comparative examination of the two articles for similarity. It has been concluded that duplicate publication has occurred. The significantly duplicated article of the same title by same research team is: The effect of combined application of pentoxifylline and vitamin E for the treatment of osteoradionecrosis of the jaws: A meta-analysis Chin J Stomatol Res (Electronic Edition). August 2017, Vol.11, No.4. Both articles report on a meta-analysis study and focus on the treatment of osteoradionecrosis of the jaws by pentoxifylline combined with vitamin E, with search timeframe extending 2 years later in the retracted article.

H3K36me3, message from chromatin to DNA damage repair.

Histone marks control many cellular processes including DNA damage repair. This review will focus primarily on the active histone mark H3K36me3 in the regulation of DNA damage repair and the maintenance of genomic stability after DNA damage. There are diverse clues showing H3K36me3 participates in DNA damage response by directly recruiting DNA repair machinery to set the chromatin at a "ready" status, leading to a quick response upon damage. Reduced H3K36me3 is associated with low DNA repair efficiency. This review will also place a main emphasis on the H3K36me3-mediated DNA damage repair in the tumorigenesis of the newly found oncohistone mutant tumors. Gaining an understanding of different aspects of H3K36me3 in DNA damage repair, especially in cancers, would share the knowledge of chromatin and DNA repair to serve to the drug discovery and patient care.

CALB Immobilized onto Magnetic Nanoparticles for Efficient Kinetic Resolution of Racemic Secondary Alcohols: Long-Term Stability and Reusability.

In this study, an immobilization strategy for magnetic cross-linking enzyme aggregates of lipase B from Candida antarctica (CALB) was developed and investigated. Magnetic particles were prepared by conventional co-precipitation. The magnetic nanoparticles were modified with 3-aminopropyltriethoxysilane (APTES) to obtain surface amino-functionalized magnetic nanoparticles (APTES⁻Fe3O4) as immobilization materials. Glutaraldehyde was used as a crosslinker to covalently bind CALB to APTES⁻Fe3O4. The optimal conditions of immobilization of lipase and resolution of racemic 1-phenylethanol were investigated. Under optimal conditions, esters could be obtained with conversion of 50%, enantiomeric excess of product (eep) > 99%, enantiomeric excess of substrate (ees) > 99%, and enantiomeric ratio (E) > 1000. The magnetic CALB CLEAs were successfully used for enzymatic kinetic resolution of fifteen secondary alcohols. Compared with Novozym 435, the magnetic CALB CLEAs exhibited a better enantioselectivity for most substrates. The conversion was still greater than 49% after the magnetic CALB CLEAs had been reused 10 times in a 48 h reaction cycle; both ees and eep were close to 99%. Furthermore, there was little decrease in catalytic activity and enantioselectivity after being stored at -20 °C for 90 days.

Research on CFD numerical simulation and flow field characteristics of countercurrent-cocurrent dissolved air flotation.

Countercurrent-cocurrent dissolved air flotation (CCDAF), the popular water purification device, which consists of collision and adhesion contact zones, showed favorable flotation conditions for micro-bubble adhesion and stability. In this study, computational fluid dynamics (CFD) numerical simulation was employed to confirm that the unique CCDAF configuration create reasonable and that the flow field characteristics were good no matter for single phase or gas-liquid two-phase conditions. In addition, the turbulence of the flow field was enhanced with the increasing influent load; the swirling was remarkably reduced with the increase of gas holdup. Meanwhile, a thick micro-bubble filter layer was formed in the separation zone, which favored bubble-flocs agglomerating and rising. The force analysis also showed that the cross section within the tank contribute to the uniformity of the bottom water collection as well as enlargement of the bottom outflow area, therefore improving the overall flotation performance. The simulation results revealed for the CCDAF process can provide technical guidance for engineering design and application.

Novel Magnetic Cross-Linked Cellulase Aggregates with a Potential Application in Lignocellulosic Biomass Bioconversion.

The utilization of renewable biomass resources to produce high-value chemicals by enzymatic processes is beneficial for alternative energy production, due to the accelerating depletion of fossil fuels. As immobilization techniques can improve enzyme stability and reusability, a novel magnetic cross-linked cellulase aggregate has been developed and applied for biomass bioconversion. The crosslinked aggregates could purify and immobilize enzymes in a single operation, and could then be combined with magnetic nanoparticles (MNPs), which provides easy separation of the materials. The immobilized cellulase showed a better activity at a wider temperature range and pH values than that of the free cellulase. After six cycles of consecutive reuse, the immobilized cellulase performed successful magnetic separation and retained 74% of its initial activity when carboxylmethyl cellulose (CMC) was used as the model substrate. Furthermore, the structure and morphology of the immobilized cellulase were studied by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). Moreover, the immobilized cellulase was shown to hydrolyze bamboo biomass with a yield of 21%, and was re-used in biomass conversion up to four cycles with 38% activity retention, which indicated that the immobilized enzyme has good potential for biomass applications.

Improved activity of lipase immobilized in microemulsion-based organogels for (R, S)-ketoprofen ester resolution: Long-term stability and reusability.

Microemulsion-based organogels (MBGs) were effectively employed for the immobilization of four commonly used lipases. During the asymmetric hydrolysis of ketoprofen vinyl ester at 30 °C for 24 h, lipase from Rhizomucor miehei and Mucor javanicus immobilized in microemulsion-based organogels (RML MBGs and MJL MBGs) maintained good enantioselectivities (eep were 86.2% and 99.2%, respectively), and their activities increased 12.8-fold and 7.8-fold, respectively, compared with their free forms. They gave higher yields compared with other lipase MBGs and exhibited better enantioselectivity than commercial immobilized lipases. Immobilization considerably increased the tolerance to organic solvents and high temperature. Both MJL MBGs and RML MBGs showed excellent reusability during 30 cycles of repeated 24 h reactions at 30 °C (over 40 days). The system maintained yields of greater than 50%, while the ees values of RML MBGs and MJL MBGs remained nearly constant at 95% and 88%, respectively.

Regulatory roles of KDR antisense oligonucleotide on the proliferation of human prostate cancer cell line PC-3.

PURPOSE: To explore the regulatory roles of antisense oligonucleotide (ASODN) of vascular endothelial growth factor receptor 2/ VEGFR2 (kinase insert domain-containing receptor, KDR) on the proliferation of PC-3 human prostate cancer cell line. METHODS: Different concentrations of synthetic sense and antisense KDR oligonucleotides were transfected into PC-3 human prostate cancer cell line. The inhibitory effects of oligonucleotides on tumor cell proliferation, KDR mRNA expression, cell cycle distribution and cell apoptosis were analyzed. RESULTS: The inhibitory effects of ASODN on tumor cell proliferation reached the peak 48 hrs after transfection, and its intensity was positively related to the ASODN concentration. The expression of KDR mRNA was reduced in different degrees after transfection with ASODN, with significant differences in different concentration groups. After transfection of ASODN, apoptosis took place in different degrees but the cell cycle distributions were not significantly different in different concentration groups. CONCLUSION: KDR gene plays a certain role in promotion of human prostate cancer PC-3 cells' proliferation. It is expected to become a molecular target for the treatment of androgen-independent prostate cancer.