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Carbonation has been proven to be a promising way to improve the mechanism properties and durability of steel slag products. Carbonic anhydrase (CA) bacteria can promote the early-age carbonation process of γ-dicalcium silicate (γ-C2S), which is one of the main mineral phases of steel slag. In this study, one kind of alkali-resistant CA bacteria was chosen to investigate its effects on the carbonation process of γ-C2S. Results showed that the bacteria could increase the compressive strength of carbonated γ-C2S by 19.0% when compared with carbonated samples without bacteria. The main products of carbonated γ-C2S were vaterite, calcite and silicon dioxide gel. The addition of bacteria could only accelerate the deposition of calcium carbonate, while hardly changing the types and properties of the carbonation products. The accelerated carbonation was found to reduce the inward diffusion of carbon dioxide. In addition, reasons for the decline of the accelerating carbonation effect were explained by X-ray computed tomography testing results. However, CA bacteria could change the morphology of calcium carbonated during the carbonation process of β-C2S and further accelerate the hydration process of β-C2S. The pore structure could also be refined with the incorporation of bacteria.

The mechanism of melatonin (MT) induced chilling tolerance in harvested cucumber fruit was investigated at commercial maturity. In this study, cucumber fruits were treated with 100 µmol L–1 MT at 4°C and 90% relative humidity for 15 d of storage. In comparison with the control, cucumber treatment with MT resulted in reduced chilling injury (CI), decreased electrolyte leakage and enhanced firmness. The fruits treated with MT showed higher chlorophyll contents in storage conditions with suppressed chlorophyllase enzyme activity. MT treatment increased arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) enzyme activities. Moreover, enhanced expression of the Cucumis sativus ADC (CsADC) and C. sativus ODC (CsODC) genes resulted in the accumulation of polyamine contents. Similarly, proline levels exhibited higher levels among treated fruits. Meanwhile, the proline synthesizing enzymes △1-pyrroline-5-carboxylate syntheses (P5CS) and ornithine aminotransferase (OAT) were significantly increased, while a catabolic enzyme of proline dehydrogenase (PDH) activity was inhibited by treatment. In addition, MT induced expression of C. sativus OAT (CsOAT) and C. sativus P5CS (CsP5CS) genes. Cucumber fruits treated with MT also exhibited higher γ-aminobutyric acid (GABA) content by enhanced GABA transaminase (GABA-T) and glutamate decarboxylase (GAD) enzyme activities and a higher C. sativus GAD (CsGAD) gene expression. To sum up, the results show that MT treatment enhanced chilling tolerance, which was associated with the regulation of polyamines, as well as proline and γ-aminobutyric acid.

Long noncoding RNAs (lncRNAs) play roles in the development and progression of many cancers; however, the contributions of lncRNAs to human gallbladder cancer (GBC) remain largely unknown. In this study, we identify a group of differentially expressed lncRNAs in human GBC tissues, including prognosis‐associated gallbladder cancer lncRNA (lncRNA‐PAGBC), which we find to be an independent prognostic marker in GBC. Functional analysis indicates that lncRNA‐PAGBC promotes tumour growth and metastasis of GBC cells. More importantly, as a competitive endogenous RNA (ceRNA), lncRNA‐PAGBC competitively binds to the tumour suppressive microRNAs miR‐133b and miR‐511. This competitive role of lncRNA‐PAGBC is required for its ability to promote tumour growth and metastasis and to activate the AKT/mTOR pathway. Moreover, lncRNA‐PAGBC interacts with polyadenylate binding protein cytoplasmic 1 (PABPC1) and is stabilized by this interaction. This work provides novel insight on the molecular pathogenesis of GBC.

Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), an RNA-binding protein that can regulate the translation of specific mRNAs. In this study, we developed an FXS human forebrain organoid model and observed that the loss of FMRP led to dysregulated neurogenesis, neuronal maturation and neuronal excitability. Bulk and single-cell gene expression analyses of FXS forebrain organoids revealed that the loss of FMRP altered gene expression in a cell-type-specific manner. The developmental deficits in FXS forebrain organoids could be rescued by inhibiting the phosphoinositide 3-kinase pathway but not the metabotropic glutamate pathway disrupted in the FXS mouse model. We identified a large number of human-specific mRNAs bound by FMRP. One of these human-specific FMRP targets, CHD2, contributed to the altered gene expression in FXS organoids. Collectively, our study revealed molecular, cellular and electrophysiological abnormalities associated with the loss of FMRP during human brain development.

Background Heat shock transcription factors (Hsfs) play pivotal roles in plant response to stress. Although glycine betaine (GB) and hot water (HW) treatments are effective in reducing chilling injury (CI), little is known about characterization of Hsfs gene family and their potential roles in alleviating CI by regulating antioxidant system in peach fruit. Results In this study, 17 PpHsfs were identified in peach genome and investigated by using bioinformatics, including chromosomal locations, phylogenetic relationships, gene structure, motifs and promoter analyses. Furthermore, the expression patterns of PpHsfs under GB and HW treatments were investigated. PpHsfs showed different expression patterns in GB- and HW-treated fruit, while most of them were significantly up-regulated by both treatments, especially PpHsfA1a/b, PpHsfA2a, PpHsfA9a and PpHsfB2a/b. Meanwhile, GB and HW treatments induced the higher levels of genes expressions and antioxidant enzymes activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) compared to control, contributing to inhibiting hydrogen peroxide (H2 O2 ) accumulation and superoxide anion (O2 .- ) production. Moreover, the correlation analysis between PpHsfs and antioxidant-related genes showed that three PpAPXs were significantly correlated with ten PpHsfs, while PpCAT and PpSOD had no significant correlations with PpHsfs, which indicated that PpAPX might be regulated by PpHsfs. Conclusions Results indicated that GB and HW treatments induced different PpHsfs transcript levels to regulate the antioxidant genes expressions, which might be beneficial to inhibit the accumulation of reactive oxygen species and protect the integrity of cell structure, thus alleviating the development of CI in peach fruit during cold storage. This article is protected by copyright. All rights reserved.

Alzheimer’s disease (AD) is influenced by both genetic and environmental factors; thus, brain epigenomic alterations may provide insights into AD pathogenesis. Multiple array-based Epigenome-Wide Association Studies (EWASs) have identified robust brain methylation changes in AD; however, array-based assays only test about 2% of all CpG sites in the genome. Here, we develop EWASplus, a computational method that uses a supervised machine learning strategy to extend EWAS coverage to the entire genome. Application to six AD-related traits predicts hundreds of new significant brain CpGs associated with AD, some of which are further validated experimentally. EWASplus also performs well on data collected from independent cohorts and different brain regions. Genes found near top EWASplus loci are enriched for kinases and for genes with evidence for physical interactions with known AD genes. In this work, we show that EWASplus implicates additional epigenetic loci for AD that are not found using array-based AD EWASs., Array-based epigenome-wide association studies only test about 2% of the CpG sites in the genome. Here, the authors describe EWASplus, a supervised machine learning strategy that extends EWAS coverage to the entire genome, and use it to identify novel brain CpGs associated with Alzheimer’s disease.

Women heterozygous for an expansion of CGG repeats in the 5’UTR of FMR1 risk developing fragile X-associated primary ovarian insufficiency (FXPOI) and/or tremor and ataxia syndrome (FXTAS). We show that expanded CGGs, independent of FMR1, are sufficient to drive ovarian insufficiency and that expression of CGG-containing mRNAs alone or in conjunction with a polyglycine-containing peptide translated from these RNAs contribute to dysfunction. Heterozygous females from two mouse lines expressing either CGG RNA-only (RNA-only) or CGG RNA and the polyglycine product FMRpolyG (FMRpolyG+RNA) were used to assess ovarian function in aging animals. The expression of FMRpolyG+RNA led to early cessation of breeding, ovulation and transcriptomic changes affecting cholesterol and steroid hormone biosynthesis. Females expressing CGG RNA-only did not exhibit decreased progeny during natural breeding, but their ovarian transcriptomes were enriched for alterations in cholesterol and lipid biosynthesis. The enrichment of CGG RNA-only ovaries for differentially expressed genes related to cholesterol processing provided a link to the ovarian cysts observed in both CGG-expressing lines. Early changes in transcriptome profiles led us to measure ovarian function in prepubertal females that revealed deficiencies in ovulatory responses to gonadotropins. These include impairments in cumulus expansion and resumption of oocyte meiosis, as well as reduced ovulated oocyte number. Cumulatively, we demonstrated the sufficiency of ectopically expressed CGG repeats to lead to ovarian insufficiency and that co-expression of CGG-RNA and FMRpolyG lead to premature cessation of breeding. However, the expression of CGG RNA-alone was sufficient to lead to ovarian dysfunction by impairing responses to hormonal stimulation.

GGGGCC repeats in a non-coding region of the C9orf72 gene have been identified as a major genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We previously showed that the GGGGCC expanded repeats alone were sufficient to cause neurodegeneration in Drosophila. Recent evidence indicates that GGGGCC expanded repeats can modify various gene transcriptomes. To determine the role of these genes in GGGGCC-mediated neurotoxicity, we screened an established Drosophila model expressing GGGGCC expanded repeats in this study. Our results showed that knockdown of the DNA topoisomerase II (Top2) gene can specifically modulate GGGGCC-associated neurodegeneration of the eye. Furthermore, chemical inhibition of Top2 or siRNA-induced Top2 downregulation could alleviate the GGGGCC-mediated neurotoxicity in Drosophila assessed by eye neurodegeneration and locomotion impairment. By contrast, upregulated Top2 levels were detected in Drosophila strains, and moreover, TOP2A level was also upregulated in Neuro-2a cells expressing GGGGCC expanded repeats, as well as in the brains of Sod1G93A model mice. This indicated that elevated levels of TOP2A may be involved in a pathway common to the pathophysiology of distinct ALS forms. Moreover, through RNA-sequencing, a total of 67 genes, involved in the pathways of intracellular signaling cascades, peripheral nervous system development, and others, were identified as potential targets of TOP2A to modulate GGGGCC-mediated neurodegeneration.

Purpose Using a quick electroretinography (ERG) protocol for rapid assessment of the retinal function of wild giant pandas (Ailuropoda melanoleuca) performed in field conditions to demonstrate the range of ERG recordings in giant pandas of unknown retinal status. Animals studied Nine free range giant pandas. Procedure All the giant pandas were anesthetized using an intramuscular dexMTZ injection, which is a combination of dexmedetomidine and tiletamine-zolazepam. After 20 mins of dark adaptation, scotopic ERGs were obtained by using three flash intensities: -25 dB (0.0087 cd·s/m2 ), 0 dB (2.75 cd·s/m2 ), and +5 dB (8.7 cd·s/m2 ). Next, photopic ERGs were acquired using a single flash protocol with a flash intensity of 3.0 cd·s/m2 after 10 minutes of light adaptation. Results In scotopic ERG at 0.0087 cd·s/m2 , mean b-wave amplitude and peak time were 82.26 µV (SD ± 16.65 and 95% CI 68.33-96.18) and 66.97 ms (SD ± 10.86 and 95% CI 57.90-76.05), respectively. This flash intensity was below a-wave threshold and resulted in b waves with greater peak times compared to those with higher intensities. At 2.75 cd·s/m2 , the mean a-wave amplitude and peak time were 53.95 µV (SD ± 11.63 and 95% CI 44.23-63.67) and 16.13 ms (SD ± 2.62 and 95% CI 13.94-18.31), and mean b-wave amplitude and peak time were 119.57 µV (SD ± 15.54 and 95% CI 106.57-132.56) and 32.00 ms (SD ± 6.47 and 95% CI 26.59-37.41). At 8.7 cd·s/m2 , the mean a-wave amplitude and peak time were 58.85 µV (SD ± 14.90 and 95% CI 46.39-71.31) and 15.59 ms (SD ± 2.63 and 95% CI 13.40-17.79), and the mean b-wave amplitude and peak time were 132.97 µV (SD ± 22.11 and 95% CI 114.48-151.46) and 32.66 ms (SD ± 6.87 and 95% CI 26.91-38.40). In photopic ERG at 2.75 cd·s/m2 , the mean a-wave amplitude and peak time were 62.08 µV (SD ± 16.61 and 95% CI 48.19-75.97) and 16.28 ms (SD ± 0.90 and 95% CI 15.53-17.03), and the mean b-wave amplitude and peak time were 214.93 µV (SD ± 70.41 and 95% CI 156.07-273.80) and 33.09 ms (SD ± 1.27 and 95% CI 32.03-34.15). Conclusion Using a portable ERG system with a brief ERG protocol to perform electroretinographies in wild giant pandas is a practical, useful, and reliable method for the rapid assessment of their retinal function.

The aim of this study was to improve the stability of eugenol–casein nanoparticles (EL–CS-NPs) through polyethylene glycol (PEG) modification. The results show that modifying the EL–CS-NPs with PEG after loading with eugenol (EL) gives PEG–EL–CS-NPs, with increased stability. The NPs modified with higher-molecular-weight PEG showed better stability. A CS/PEG ratio of 200 : 1 (w/w) yielded the NPs with the best stability. A PEG20 K–EL–CS-NP dispersion remained stable in cold storage for over one year, and also exhibited stronger inhibitory effects against Colletotrichum musae inoculated on bananas than an EL–CS-NP dispersion, since it showed more prolonged sustained release of EL than the EL–CS-NP dispersion. Lyophilized PEG20 K–EL–CS-NP powder showed better effectiveness against mold on bread than lyophilized EL–CS-NPs powder. Using PEG to modify CS-NPs shows potential for improving the stability of CS-NPs loaded with hydrophobic substances for delivery in the fields of food and agriculture.

Background Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene transcription and thereby playing a crucial regulatory role in plant development. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana, Oryza sativa, barley, grapes, tomato, litchi and Zea mays, but comparable identification and analyses have not been conducted in wheat (Triticum aestivum). Results In this study, 31 TaHATs were identified and divided into six groups with conserved gene structures and motif compositions. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa and Triticum aestivum HAT genes. The TaHATs appeared to be regulated by cis-acting elements such as LTR and TC-rich repeats. The qRT–PCR analysis showed that the TaHATs were differentially expressed in multiple tissues. The TaHATs in expression also responded to temperature changes, and were all significantly upregulated after being infected by barley streak mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV). Conclusions These results suggest that TaHATs may have specific roles in the response to viral infection and provide a basis for further study of TaHAT functions in T. aestivum plant immunity.

Edwardsiella piscicida causes edwardsiellosis in a variety of fish species and leads to tremendous economic losses in the global aquaculture industries. Thus, effective and safe prevention and control of this bacterium are urgently needed to combat the related infections. Live attenuated vaccines (LAVs) effectively prevent infectious diseases. However, most of the existing E. piscicida LAVs are based on the deletion of genes encoding the translocon components of the type III secretion system (T3SS), the core virulence system, which is the most prominent protective bacterial antigen with the strongest immunogenicity. In this study, we systematically deleted all of the 9 established T3SS effectors in E. piscicida (aka 9Δ) and the rpoS gene encoding the alternative sigma factor, the esrB repressor (10Δ), then we overexpressed esrB and T3SS in E. piscicida to obtain the recombinant strain 10Δ/esrBOE. The modified strains 10Δ and 10Δ/esrBOE exhibited severe attenuation and in vivo colonization defects. Additionally, vaccination by intraperitoneal injection with 10Δ and 10Δ/esrBOE could significantly upregulate the expression of the antigen recognition related gene (TLR5) and the adaptive immune response-related gene (MHC II) in the spleen/kidney of turbot fish, and it also enhanced the hosts' serum bactericidal capacity. Finally, vaccination with 10Δ/esrBOE led to increased immune protection against the challenge of wild type E. piscicida EIB202 in turbot fish. Collectively, these findings demonstrated that 10Δ/esrBOE was a novel LAV strain and therefore a potential novel strategy for the construction of LAVs against bacterial pathogens.

Purpose The use of Aspergillus ochraceus TCCC41060 for synthesis of 11α-OH-ethylgonendione, an important intermediate for synthesis of desogestrel-a major ingredient of the “third-generation” oral contraceptives, is hampered by its low regioselectivity of hydroxylation. In the present study, we sought to characterize gene(s) involved in steroid hydroxylation specificity in strain TCCC41060. Methods Taking advantage of the fact that expression of the 11α-hydroxylase, a member of the cytochrome P450 family, is highly induced by steroid substrates, we combined RNA-seq, qRT-PCR, and yeast functional expression to search for responsible steroid hydroxylase gene(s). Results Two highly inducible P450 genes (CYP68L8 and CYP68J5) were isolated and recombinant yeast cells expressing CYP68J5 were capable of 11α-hydroxylating both 16,17α-epoxyprogesterone and D-ethylgonendione. Disruption of CYP68J5 in strain TCCC41060 resulted in complete loss of hydroxylation activities towards D-ethylgonendione, indicating that CYP68J5 was solely responsible for hydroxylation activity on D-ethylgonendione in TCCC41060. Conclusion The above results demonstrated that low hydroxylation specificity of CYP68J5 on D-ethylgonendione fully accounted for high by-product contents in TCCC41060, thus pointing to a strategy to engineer 11α-hydroxylase variants with higher hydroxylation specificity.

Inactivated vaccines are often applied with adjuvants in commercial fish farming. Although some mineral or non-mineral oil adjuvants show efficient improvement with inactivated vaccines, but sometimes bring side effects such as tissue adhesion and granulomatous lesion at the injection site. CpG ODN is a novel type of soluble adjuvant which has been proved to possess excellent advantages in fish vaccine development. In this study, we designed a tandem sequence of CpG ODN synthesized in plasmid pcDNA 3.1, and an inactivated Vibrio anguillarum vaccine developed in our previous work was chosen for determining the efficiency of the CpG-riched plasmids (pCpG) as an adjuvant. Results showed that pCpG we designed can offer higher immunoprotection with the vaccine. Interestingly, even below the minimum immune dosage of the vaccine, a high RPS of 84% was observed once the vaccine was administrated with the pCpG. Serum specific antibody titer, superoxide dismutase and total protein were enhanced and some immune genes related to both innate and adaptive immune response were upregulated, implying an effective auxiliary function of the pCpG. Totally, our study suggested that the pCpG is a potential and available adjuvant for turbot vaccine development.

N6-methyladenosine (m6A) is a dynamic RNA modification that regulates various aspects of RNA metabolism and has been implicated in many biological processes and transitions. m6A is highly abundant in the brain; however, only recently has the role of m6A in brain development been a focus. The machinery that controls m6A is critically important for proper neurodevelopment, and the precise mechanisms by which m6A regulates these processes are starting to emerge. However, the role of m6A in neurodegenerative and neuropsychiatric diseases still requires much elucidation. This review discusses and summarizes the current body of knowledge surrounding the function of the m6A modification in regulating normal brain development, neurodegenerative diseases and outlines possible future directions.

Protein S-palmitoylation is a powerful post-translational modification that regulates protein trafficking, localization, turnover, and signal transduction. Palmitoylation controls several important cellular processes, and, if dysregulated, can lead to cancer, cardiovascular disease, and neurological disorders. The role of protein palmitoylation in mediating resistance to systemic cisplatin-based chemotherapies in cancer is currently unknown. This is of particular interest because cisplatin is currently the gold standard of treatment for bladder cancer (BC), and there are no feasible options after resistance is acquired. Using unbiased global proteomic profiling of purified S-palmitoylated peptides combined with intensive bioinformatics analyses, we identified 506 candidate palmitoylated proteins significantly enriched in cisplatin-resistant BC cells. One of these proteins included PD-L1, which is highly palmitoylated in resistant cells. Pharmacological inhibition of fatty acid synthase (FASN) suppressed PD-L1 palmitoylation and expression, which suggests the potential use of FASN-PD-L1-targeted therapeutic strategies in BC patients. Taken together, these results highlight the role of protein palmitoylation in mediating BC chemoresistance.

Increasing the active site density of single atom catalysts (SACs) is expected to generate closely neighboring atomic sites with potential synergetic interaction. However, the synthesis of SACs with high active site density still remains a great challenge due to the easy aggregation of high density metal atoms during the synthesis. In the present work, we develop a stepwise anchoring strategy for the large-scale preparation of carbon-supported high-density Pt SACs (denoted as PtSA@BP). The Pt loading of PtSA@BP is as high as 2.5 wt%, leading to the observation of abundant closely distanced single Pt sites. The produced PtSA@BP catalyst exhibits ultrahigh catalytic activity for the alkaline hydrogen evolution reaction with a low overpotential of 26 mV at 10 mA cm−2 in 1.0 M KOH under ultralow Pt loadings of 0.0009 mgPt cm−2 on the electrode, much superior to commercial Pt/C (20 wt%). Mechanistic studies suggest the main contribution of the coordination of closely distanced three-coordinated PtC2N1 moieties to the excellent catalytic activities towards the conversion of water to H2, due to their close-to-zero metal–hydrogen binding value and intense adsorption capability to H2O molecules as well as their low water-dissociation energy barrier. More importantly, this strategy has been verified to be feasible for preparing other noble-metal based SACs, for example, Rh and Pd. The present result provides an enabling and versatile platform for facile access of SACs with technological importance in various areas.

Adhesion G protein–coupled receptors (aGPCRs) represent a distinct family of GPCRs that regulate several developmental and physiological processes. Most aGPCRs undergo GPCR autoproteolysis-inducing domain–mediated protein cleavage, which produces a cryptic tethered agonist (termed Stachel (stinger)), and cleavage-dependent and -independent aGPCR signaling mechanisms have been described. aGPCR G1 (ADGRG1 or G protein–coupled receptor 56 (GPR56)) has pleiotropic functions in the development of multiple organ systems, which has broad implications for human diseases. To date, two natural GPR56 ligands, collagen III and tissue transglutaminase (TG2), and one small-molecule agonist, 3-α-acetoxydihydrodeoxygedunin (3-α-DOG), have been identified, in addition to a synthetic peptide, P19, that contains seven amino acids of the native Stachel sequence. However, the mechanisms by which these natural and small-molecule agonists signal through GPR56 remain unknown. Here we engineered a noncleavable receptor variant that retains signaling competence via the P19 peptide. We demonstrate that both natural and small-molecule agonists can activate only cleaved GPR56. Interestingly, TG2 required both receptor cleavage and the presence of a matrix protein, laminin, to activate GPR56, whereas collagen III and 3-α-DOG signaled without any cofactors. On the other hand, both TG2/laminin and collagen III activate the receptor by dissociating the N-terminal fragment from its C-terminal fragment, enabling activation by the Stachel sequence, whereas P19 and 3-α-DOG initiate downstream signaling without disengaging the N-terminal fragment from its C-terminal fragment. These findings deepen our understanding of how GPR56 signals via natural ligands, and a small-molecule agonist may be broadly applicable to other aGPCR family members.

Aeromonas salmonicida is an aquatic pathogen that can infect a variety of fish. Phage therapy has been applied to treat bacterial infections. In this study, we obtained three A. salmonicida subsp. masoucida phage isolates from sewage, and one phage (vB_AsM_ZHF) exhibited the best antibacterial effect, based on in vitro kinetics experiments. Sequencing indicated that the vB_AsM_ZHF genome is 161,887 bp (41.24% C+G content) with 237 predicted open reading frames. No antibiotic resistance or virulence genes were detected in the complete genome, which is a requirement for phage therapy safety. Intraperitoneal injection of phage vB_AsM_ZHF into turbot at 8 × 104 PFU/fish rescued turbot from A. salmonicida subsp. masoucida injection and reduced the bacterial burden by 1 order of magnitude. Injection of vB_AsM_ZHF also decreased levels of inflammatory cell infiltration in muscle tissue, cytokines interleukin-1β (IL-1β), tumor necrosis factor alpha (TNF-α), and gamma interferon (IFN-γ) in serum and the expression of the inflammatory factors IL-1β, IL-6, IFN-γ, transforming growth factor β, TNF-α, and hepcidin in the liver, spleen, and head kidney of turbot. Phage vB_AsM_ZHF demonstrated antibacterial ability in vitro and in vivo and significantly reduced mortality in turbot challenged by A. salmonicida subsp. masoucida. This study revealed that phage vB_AsM_ZHF can effectively treat the infection caused by A. salmonicida subsp. masoucida in turbot. IMPORTANCEA. salmonicida is an aquatic pathogen that can infect different fish and causes economic loss to the global aquaculture industry. Clinical strains of A. salmonicida have developed multidrug resistance, and phage therapy is being evaluated for controlling bacterial infections. Phages are biological antibacterial agents and have the potential to be therapeutic agents against multidrug-resistant bacteria. In this study, three A. salmonicida subsp. masoucida phages were isolated from sewage, and their biological behaviors were characterized. The newly isolated phage vB_AsM_ZHF could inhibit A. salmonicida subsp. masoucida infection in vitro and in vivo, suggesting that it may be an alternative strategy to antibiotics for protecting fish against multidrug-resistant A. salmonicida subsp. masoucida in the aquaculture industry.

Both low temperature and nitrogen starvation caused chlorosis of cyanobacteria. Here, in this study, for the first time, we compared the effects of low temperature, nitrogen starvation, and their combination on the photosynthesis and metabolites of a thermophilic cyanobacterium strain, Thermosynechococcus E542. Under various culture conditions, the growth rates, pigment contents, and chlorophyll fluorescence were monitored, and the composition of alkanes, lipidomes, and carbohydrates were determined. It was found that low temperature (35 °C) significantly suppressed the growth of Thermosynechococcus E542. Nitrogen starvation at 45 °C and 55 °C did not affect the growth, however, combined treatment of low temperature and nitrogen starvation led to the lowest growth rate and biomass productivity. Both low temperature and nitrogen starvation caused significantly declined contents of pigments, but they resulted in a different effect on the OJIP curves, and their combination led to the lowest pigment contents. The composition of fatty acids and alkanes was altered upon low-temperature cultivation, while nitrogen starvation caused reduced contents of all lipids. The low temperature did not affect carbohydrate contents, while nitrogen starvation greatly enhanced carbohydrate content, and their combination did not enhance carbohydrate content, but led to reduced productivity. These results revealed the influence of low temperature, nitrogen starvation, and their combined treatment for the accumulation of phycobiliproteins, lipids, and carbohydrates of a thermophilic cyanobacterium strain, Thermosynechococcus E542.

Background The study aimed to measure the expression of translocator protein (TSPO) in brain tissue following traumatic brain injury (TBI) and to determine whether TSPO can predict outcomes. Methods TBI patients requiring emergent craniectomy and removing of intracranial hematoma were recruited from Wujin Hospital Affiliated with Jiangsu University between January 2018 and May 2020. TBI patients were divided into unfavorable and favorable groups according to GOS score. The TSPO in brain samples was analyzed by western blot and immunocytochemistry. Results The western blot and immunocytochemistry showed that the TSPO in the unfavorable group was higher than that in the favorable group. Double immunofluorescence staining exhibited that the percentage of TSPO positive cells in IBA1 and GFAP positive cells was 45.2 ± 3.1% and 3.5 ± 0.6% respectively. After adjusting for age, sex, CT, ICP and GCS, we found each 1-unit increase in TSPO was associated with 40% higher occurrence of unfavorable outcome (OR = 1.4, 95% CI 0.4–5.6). The area under the receiver operating characteristic curve (AUC), specificity, and sensitivity of TSPO was 0.87, 76.7%, 88.2% respectively. Conclusion Our study demonstrated that higher TSPO was associated with higher occurrence of unfavorable outcomes.

Given most tissues are consist of abundant and diverse sub cell-types, an important yet unaddressed problem in bulk RNA-seq analysis is to identify at which sub cell-type(s) the differential expression occur. Single-cell RNA-sequencing (scRNA-seq) technologies can answer the question, but they are often labor-intensive and cost-prohibitive. Here, we present LRcell, a computational method aiming to identify specific sub-cell type(s) that drives the changes observed in a bulk RNA-seq experiment. In addition, LRcell provides pre-embedded marker genes computed from putative single-cell RNA-seq experiments as options to execute the analyses. Using three different real datasets, we show that LRcell successfully identifies known cell types involved in psychiatric disorders and LRcell is more sensitive than even the leading deconvolution methods.

Understanding the impact of non-coding sequence variants on complex diseases is an essential problem. We present a novel ensemble learning framework—CASAVA, to predict genomic loci in terms of disease category-specific risk. Using disease-associated variants identified by GWAS as training data, and diverse sequencing-based genomics and epigenomics profiles as features, CASAVA provides risk prediction of 24 major categories of diseases throughout the human genome. Our studies showed that CASAVA scores at a genomic locus provide a reasonable prediction of the disease-specific and disease category-specific risk prediction for non-coding variants located within the locus. Taking MHC2TA and immune system diseases as an example, we demonstrate the potential of CASAVA in revealing variant-disease associations. A website (http://zhanglabtools.org/CASAVA) has been built to facilitate easily access to CASAVA scores.

Ocean acidification is recognized as a major anthropogenic perturbation of the modern ocean. While extensive studies have been carried out to explore the short-term physiological responses of phytoplankton to ocean acidification, little is known about their lipidomic responses after a long-term ocean acidification adaptation. Here we perform the lipidomic analysis of a marine diatom Phaeodactylum tricornutum following long-term (∼400 days) selection to ocean acidification conditions. We identified a total of 476 lipid metabolites in long-term high CO2 (i.e., ocean acidification condition) and low CO2 (i.e., ambient condition) selected P. tricornutum cells. Our results further show that long-term high CO2 selection triggered substantial changes in lipid metabolites by down- and up-regulating 33 and 42 lipid metabolites. While monogalactosyldiacylglycerol (MGDG) was significantly down-regulated in the long-term high CO2 selected conditions, the majority (∼80%) of phosphatidylglycerol (PG) was up-regulated. The tightly coupled regulations (positively or negatively correlated) of significantly regulated lipid metabolites suggest that the lipid remodeling is an organismal adaptation strategy of marine diatoms to ongoing ocean acidification. Since the composition and content of lipids are crucial for marine food quality, and these changes can be transferred to high trophic levels, our results highlight the importance of determining the long-term adaptation of lipids in marine producers in predicting the ecological consequences of climate change.

The effects of calcium chloride (CaCl2) treatment on chilling injury (CI), reactive oxygen species (ROS) metabolism, and ascorbate-glutathione (AsA-GSH) cycle in loquat fruit at 1 °C storage for 35 d were investigated. The results indicated that CaCl2 treatment remarkably suppressed the increase in browning index and firmness as well as the decrease in extractable juice rate. CaCl2 treatment also decreased the production of superoxide radical (O2•−), hydrogen peroxide (H2O2) content, but increased the 1,1-diphenyl-2-picrylhydrazyl (DPPH), hydroxyl radical (OH•) scavenging ability, the activities of superoxide dismutase (SOD), catalase (CAT), and their gene expressions. Moreover, compared to the control loquat fruit, CaCl2-treated fruit maintained higher contents of AsA, GSH, higher levels of activities of ascorbate peroxidase (APX), glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR) and expressions of EjAPX, EjGR, EjMDHAR, and EjDHAR, but exhibited lower glutathione disulfide (GSSG) content. These results suggested that CaCl2 treatment alleviated CI in loquat fruit through enhancing antioxidant enzymes activities and AsA-GSH cycle system to quench ROS.

Background Hypoxic–ischemic encephalopathy (HIE) is a severe anoxic brain injury that leads to premature mortality or long-term disabilities in infants. Neuroinflammation is a vital contributor to the pathogenic cascade post-HIE and a mediator to secondary neuronal death. As a plasma membrane G-protein-coupled receptor, GPR39, exhibits anti-inflammatory activity in several diseases. This study aimed to explore the neuroprotective function of GPR39 through inhibition of inflammation post-hypoxic–ischemic (HI) injury and to elaborate the contribution of sirtuin 1(SIRT1)/peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α)/nuclear factor, erythroid 2 like 2(Nrf2) in G-protein-coupled receptor 39 (GPR39)-mediated protection. Methods A total of 206 10-day-old Sprague Dawley rat pups were subjected to HIE or sham surgery. TC-G 1008 was administered intranasally at 1 h, 25 h, 49 h, and 73 h post-HIE induction. SIRT1 inhibitor EX527, GPR39 CRISPR, and PGC-1α CRISPR were administered to elucidate the underlying mechanisms. Brain infarct area, short-term and long-term neurobehavioral tests, Nissl staining, western blot, and immunofluorescence staining were performed post-HIE. Results The expression of GPR39 and pathway-related proteins, SIRT1, PGC-1α and Nrf2 were increased in a time-dependent manner, peaking at 24 h or 48-h post-HIE. Intranasal administration of TC-G 1008 reduced the percent infarcted area and improved short-term and long-term neurological deficits. Moreover, TC-G 1008 treatment significantly increased the expression of SIRT1, PGC-1α and Nrf2, but downregulated the expressions of IL-6, IL-1β, and TNF-α. GPR39 CRISPR EX527 and PGC-1α CRISPR abolished GPR39’s neuroprotective effects post-HIE. Conclusions TC-G 1008 attenuated neuroinflammation in part via the SIRT1/PGC-1α/Nrf2 pathway in a neonatal rat model of HIE. TC-G 1008 may be a novel therapeutic target for treatment post-neonatal HIE injury.

Thermophilic cyanobacteria are a low-carbon environmental resource with high potential thanks to their innate temperature tolerance and thermostable pigment, phycocyanin, which enhances light utilisation efficiency and generates a high-value product. However, large-scale cultivation and harvesting have always been bottlenecks in unicellular cyanobacteria cultivation due to their micrometric size. In this study, a 40-litre inner-light photobioreactor (PBR) was designed for scaled-up cultivation of Thermosynechococcus elongatus E542. By analysing light transmission and attenuation in the PBR and describing it via mathematical models, the supply of light energy to the reactor was optimised. It was found that the hyperbolic model describes the light attenuation characteristics of the cyanobacterial culture more accurately than the Lambert–Beer model. The internal illumination mode was applied for strain cultivation and showed a two-fold better growth rate and four-fold higher biomass concentration than the same strain grown in an externally illuminated photobioreactor. Finally, the downstream harvesting process was explored. A mixture of chitosan solutions was used as a flocculant to facilitate biomass collection. The effect of the following parameters on biomass harvesting was analysed: solution concentration, flocculation time and flocculant concentration. The analysis revealed that a 4 mg L−1 chitosan solution is optimal for harvesting the strain. The proposed solutions can improve large-scale cyanobacterial biomass cultivation and processing.

BackgroundPatients with severe acute pancreatitis (SAP) have a high mortality, thus early diagnosis and interventions are critical for improving survival. However, conventional tests are limited in acute pancreatitis (AP) stratification. We aimed to assess AP severity by integrating the informative clinical measurements with cell free DNA (cfDNA) methylation markers.MethodsOne hundred and seventy-five blood samples were collected from 61 AP patients at multiple time points, plus 24 samples from healthy individuals. Genome-wide cfDNA methylation profiles of all samples were characterized with reduced representative bisulfite sequencing. Clinical blood tests covering 93 biomarkers were performed on AP patients within 24 hours. SAP predication models were built based on cfDNA methylation and conventional blood biomarkers separately and in combination. ResultsWe identified 565 and 59 cfDNA methylation markers informative for acute pancreatitis and its severity. These markers were used to develop prediction models for AP and SAP with area under the receiver operating characteristic of 0.92 and 0.81, respectively. Twelve blood biomarkers were systematically screened for a predictor of SAP with a sensitivity of 87.5% for SAP, and a specificity of 100% in mild acute pancreatitis, significantly higher than existing blood tests. An expanded model integrating 12 conventional blood biomarkers with 59 cfDNA methylation markers further improved the SAP prediction sensitivity to 92.2%.ConclusionsWe have demonstrated accurate prediction of SAP by the integration of conventional and novel blood molecular markers, paving the way for early and effective SAP intervention through a non-invasive rapid diagnostic test.

Ubiquitination is essential for plant growth and development. Deubiquitination cooperates with ubiquitination to regulate the ubiquitination levels of target proteins. The ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases (DUBs), which perform extensive and significant roles in eukaryotic organisms. However, the UBP genes in wheat (TaUBPs) are not identified, and the functions of TaUBPs are unknown. The present study identified 97 UBP genes in the whole genome of T. aestivum. These genes were divided into 15 groups and non-randomly distributed on chromosomes of T. aestivum. Analyses of evolutionary patterns revealed that TaUBPs mainly underwent purification selection. The studies of cis-acting regulatory elements indicated that they might be involved in response to hormones. Quantitative real-time PCR (qRT-PCR) results showed that TaUBPs were differentially expressed in different tissues. Besides, several TaUBPs were significantly up-regulated when plants were treated with salicylic acid (SA), implying that these DUBs may play a role in abiotic stress responses in plants and few TaUBPs displayed differential expression after viral infection. Furthermore, TaUBP1A.1 (TraesCS1A02G432600.1) silenced by virus-induced gene silencing (VIGS) facilitates Chinese wheat mosaic virus (CWMV) infection in wheat, indicating that TaUBP1A.1 may be involved in a defense mechanism against viruses. This study comprehensively analyzed the UBP gene family in wheat and provided a basis for further research of TaUBPs functions in wheat plant response to viral infection.

The effect of glycine betaine (GB) treatment on chilling injury (CI), cell membrane integrity and membrane fatty acid metabolism in peach fruit during storage were investigated using biochemical and transcriptomic analysis in this study. The results showed that GB treatment alleviated the CI by suppressing lipoxygenase (LOX), phospholipase D (PLD) and lipase gene expression and enzyme activities, resulting in higher levels of unsaturated fatty acids and degree of unsaturation. In addition, this study suggested that GB treatment could inhibit the release of cytochrome C and caspase-3 activity, thus suppressing cell breakdown and contributing to membrane function. Moreover, transcriptome analysis revealed that genes related to fatty acid biosynthesis and desaturation were enhanced, while genes related to fatty acid degradation and activation of caspases were suppressed by GB treatment. Therefore, GB treatment could maintain normal cell membrane structure and function through upregulating membrane fatty acid biosynthesis and desaturation metabolism and downregulating caspase activation to alleviate CI in peaches.

The pace of genetic discovery in complex disease has accelerated exponentially over the last decade. Our fund of knowledge of the foundational genetics in disease has never been as great. There is a clear path forward to the resolution of the genetic architecture toward a point at which we will saturate the biological understanding of disease through genetics. This understanding continues to provide fundamental insights into disease biology and, with the advent of new data and methodologies, the path from gene to function is becoming clearer and cleaner. In this opinion piece, we discuss progress in the genetics of Parkinson disease. We explore what genetics has revealed thus far in the context of disease biology. We highlight mitophagy/autophagy, dopamine metabolism and the adaptive immune system. We try and link these findings together to give a holistic view of pathogenesis with the underlying theme that disease pathogenesis relates to a failure of damage response pathways. In the 1990s, Parkinson’s disease wa disorders and diseases. This review highlights recent advances in our understanding of the methylome's functionality and covers potential new roles for DNA methylation, their readers, writers, and erasers. Additionally, we examine novel insights into the relationship between the methylome, DNA–protein interactions, and their contribution to neurodegenerative diseases. Lastly, we outline the gaps in our knowledge that will likely be filled through the widespread use of newer technologies that provide greater resolution into how individual cell types are affected by disease and the contribution of each individual modification site to disease pathogenicity.

Background: Burdock (Arctium lappa L.) is a fructan-rich plant with prebiotic potential. The aim of this study was to develop an efficient enzymatic route to prepare fructooligosaccharides (FOS)-rich and highly antioxidative syrup using burdock root as a raw material. Results: Endo-inulinase significantly improved the yield of FOS 2.4-fold while tannase pretreatment further increased the yield of FOS 2.8-fold. Other enzymes, including endo-polygalacturonase, endo-glucanase and endo-xylanase, were able to increase the yield of total soluble sugar by 11.1% (w/w). By this process, a new enzymatic process for burdock syrup was developed and the yield of burdock syrup increased by 25% (w/w), whereas with FOS, total soluble sugars, total soluble protein and total soluble polyphenols were enhanced to 28.8%, 53.3%, 8.9% and 3.3% (w/w), respectively. Additionally, the scavenging abilities of DPPH and hydroxyl radicals, and total antioxidant capacity of the syrup were increased by 23.7%, 51.8% and 35.4%, respectively. Conclusions: Our results could be applied to the development of efficient extraction of valuable products from agricultural materials using enzyme-mediated methods.How to cite: Tian K, Wang J, Zhang Z, et al. Expression and purification of a transcription factor StMsn2 from Setosphaeria turcica in Escherichia coli. Electron J Biotechnol 2019;40. https://doi.org/10.1016/j.ejbt.2019.04.009 Keywords: Antioxidant activity, Arctium, Burdock, Endo-inulinase, Enzymatic process, Fructooligosaccharides, Functional food, Fungitetraose, Hydroxyl radical, Polygalacturonase, Polyphenols, Tannase

Ferrous ion (Fe2+) in a sulfate reducing bacteria (SRB) culture medium is known to enhance microbiologically influenced corrosion (MIC) of carbon steel, but the underlining mechanism is controversial. This work showed that it was due to better sessile cell growth that was likely attributed to Fe2+ detoxification of H2S. Two hundred ppm (w/w) initial Fe2+ in the ATCC 1249 medium achieved a 4.7 times higher Desulfovibrio vulgaris sessile cell count and 5.0 times higher C1018 carbon steel weight loss, compared to 20 ppm. Linear polarization resistance, electrochemical impedance spectroscopy and potentiodynamic polarization measurements corroborated weight loss and pitting data trends.

Nitrogen removal performance of a simultaneous heterotrophic nitrifying-aerobic denitrifying (SND) bacterium (KSND) in a purification tank bioreactor (PTBR) amended with two-stage dissolved oxygen (DO) control was investigated. NH4+–N and total nitrogen (TN) removal efficiencies under aerobic conditions for domestic wastewater treatment were 97.12% and 52.64%, respectively. Under serial aerobic (DO > 4.0 mg/L) and anaerobic (DO

Diatoms are experiencing striking fluctuations in seawater carbonate chemistry in the natural marine environment, especially in coastal seawaters. Here, we show that the diatoms Thalassiosira weissflogii and Phaeodactylum tricornutum, which utilize different carbon acquisition mechanisms, respond differently to short-term changes in seawater carbonate chemistry. Our results showed that T. weissflogii showed significantly higher photosynthetic oxygen evolution rates than that of P. tricornutum at low levels of CO2 or HCO3−. This suggests that T. weissflogii had higher affinities for CO2 or HCO3− when their concentrations were not sufficient to support saturated growth and photosynthesis. While the activity of Rubisco in P. tricornutum positively correlated with carbonic anhydrases (CA), we observed negative relationship between Rubisco and CA activity in the diatom T. weissflogii. These contrasting physiological responses of diatoms with varied carbon acquisition mechanisms indicate different abilities to cope up with abrupt changes in seawater carbonate chemistry. We propose that the ability to respond to varying carbonate chemistry may act as one determinant of the diatom distributions and phytoplankton community structures.

Amyotrophic lateral sclerosis (ALS) is a fatal neurological disorder characterized by progressive muscular atrophy and respiratory failure. The G4C2 repeat expansion in the C9orf72 gene is the most prevalent genetic risk for ALS. Mutation carriers (C9ALS) display variability in phenotypes such as age-at-onset and duration, suggesting the existence of additional genetic factors. Here we introduce a three-step gene discovery strategy to identify genetic factors modifying the risk of both C9ALS and sporadic ALS (sALS) using limited samples. We first identified 135 candidate genetic modifiers of C9ALS using whole-genome sequencing (WGS) of extreme C9ALS cases diagnosed ~30 years apart. We then performed an unbiased genetic screen using a Drosophila model of the G4C2 repeat expansion with the genes identified from WGS analysis. This genetic screen identified the novel genetic interaction between G4C2 repeat-associated toxicity and 18 genetic factors, suggesting their potential association with C9ALS risk. We went on to test if 14 out of the 18 genes, those which were not known to be risk factors for ALS previously, are also associated with ALS risk in sALS cases. Gene-based-statistical analyses of targeted resequencing and WGS were performed. These analyses together reveal that rare variants in MYH15 represent a likely genetic risk factor for ALS. Furthermore, we show that MYH15 could modulate the toxicity of dipeptides produced from expanded G4C2 repeat. Our study presented here demonstrates the power of combining WGS with fly genetics to facilitate the discovery of fundamental genetic components of complex traits with a limited number of samples.

Blockade of PD-1/PD-L1 interactions using PD-1/PD-L1 pathway modulators has shown unprecedented clinical efficacy in various cancer models. Current PD-1/PD-L1 modulators approved by FDA are exclusively dominated by therapeutic antibodies. Nevertheless, therapeutic antibodies also exhibit several disadvantages such as low tumor penetration, difficulty in crossing physiological barriers, lacking oral bioavailability, high manufacturing costs, inaccessible to intracellular targets, immunogenicity, immune-related adverse events (irAEs). Modulation of PD-1/PD-L1 pathway using small molecules may be an alternative approach to mobilize immune system to fight against cancers. In this review, we focus on summarizing the recently disclosed chemical structures and preliminary structure-activity relationships (SARs) of small molecules as PD-1/PD-L1 modulators for cancer immunotherapy.

Oral vaccination is the most convenient method for disease protection in aquaculture due to possibility of adding vaccines as part of fish diet. However, low protective efficiency is the major problem of oral vaccination owing to some reasons, especially for antigens degradation. In this study, we developed an oral inactivated vaccine based on a chitosan/aluminum adjuvant system, and investigated immune response induced by the vaccine. As a result, Th1 and Th2 cells mediated immune responses were observed after the vaccination according to the upregulation of IL-6, IL-12, IFNγ and IgM genes expression that were deemed as the driver cytokines for triggering the responses. Moreover, ratio of IgT+/IgM+ B cells was elevated in intestine after vaccination, while IgM antibodies were also observed in the sera of vaccinated fish, suggested that both local and systemic immune responses were induced by the inactivated vaccine. Totally, this oral vaccine can be used for V. anguillarum protection and this chitosan/aluminum system is an efficient candidate adjuvant for developing more vaccines in the future.

N6-methyladenosine (m6A) methylation is the most prevalent internal modification of post-transcriptional modifications in mRNA, tRNA, miRNA, and long non-coding RNA in eukaryotes. m6A methylation has been proven to be involved in plant resistance to pathogens. However, there are no reports on wheat (Triticum aestivum) m6A transcriptome-wide map and its potential biological function in wheat resistance to wheat yellow mosaic virus (WYMV). To the best of our knowledge, this study is the first to determine the transcriptome-wide m6A profile of two wheat varieties with different resistances to WYMV. By analyzing m6A-sequencing (m6A-seq) data, we identified 25,752 common m6A peaks and 30,582 common m6A genes in two groups [WYMV-infected resistant wheat variety (WRV) and WYMV-infected sensitive wheat variety (WSV)], and all these peaks were mainly enriched in 3′ untranslated regions and stop codons of coding sequences. Gene Ontology analysis of m6A-seq and RNA-sequencing data revealed that genes that showed significant changes in both m6A and mRNA levels were associated with plant defense responses. Kyoto Encyclopedia of Genes and Genomes analysis revealed that these selected genes were enriched in the plant–pathogen interaction pathway. We further verified these changes in m6A and mRNA levels through gene-specific m6A real-time quantitative PCR (RT-qPCR) and normal RT-qPCR. This study highlights the role of m6A methylation in wheat resistance to WYMV, providing a solid basis for the potential functional role of m6A RNA methylation in wheat resistance to infection by RNA viruses.

Idiopathic membranous nephropathy (IMN) is an organ-specific autoimmune disease of the kidney glomerulus. It may gradually progress to end-stage renal disease (ESRD) characterized by increased proteinuria, which leads to serious consequences. Although substantial advances have been made in the understanding of the molecular bases of IMN in the last 10 years, certain questions remain largely unanswered. To define the transcriptomic landscape at single-cell resolution, we analyzed kidney samples from 6 patients with anti-PLA2R positive IMN and 2 healthy control subjects using single-cell RNA sequencing. We then identified distinct cell clusters through unsupervised clustering analysis of kidney specimens. Identification of the differentially expressed genes (DEGs) and enrichment analysis as well as the interaction between cells were also performed. Based on transcriptional expression patterns, we identified all previously described cell types in the kidney. The DEGs in most kidney parenchymal cells were primarily enriched in genes involved in the regulation of inflammation and immune response including IL-17 signaling, TNF signaling, NOD-like receptor signaling, and MAPK signaling. Moreover, cell-cell crosstalk highlighted the extensive communication of mesangial cells, which infers great importance in IMN. IMN with massive proteinuria displayed elevated expression of genes participating in inflammatory signaling pathways that may be involved in the pathogenesis of the progression of IMN. Overall, we applied single-cell RNA sequencing to IMN to uncover intercellular interactions, elucidate key pathways underlying the pathogenesis, and identify novel therapeutic targets of anti-PLA2R positive IMN.

Non-coding repeat expansions, such as CGG, GGC, CUG, CCUG, and GGGGCC, have been shown to be involved in many human diseases, particularly neurological disorders. Of the diverse pathogenic mechanisms proposed in these neurodegenerative diseases, dysregulated RNA metabolism has emerged as an important contributor. Expanded repeat RNAs that form particular structures aggregate to form RNA foci, sequestering various RNA binding proteins and consequently altering RNA splicing, transport, and other downstream biological processes. One of these repeat expansion-associated diseases, fragile X-associated tremor/ataxia syndrome (FXTAS), is caused by a CGG repeat expansion in the 5’UTR region of the fragile X mental retardation 1 (FMR1) gene. Moreover, recent studies have revealed abnormal GGC repeat expansion within the 5’UTR region of the NOTCH2NLC gene in both essential tremor (ET) and neuronal intranuclear inclusion disease (NIID). These CGG repeat expansion-associated diseases share genetic, pathological, and clinical features. Identification of the similarities at the molecular level could lead to a better understanding of the disease mechanisms as well as developing novel therapeutic strategies. Here, we highlight our current understanding of the molecular pathogenesis of CGG repeat expansion-associated diseases and discuss potential therapeutic interventions for these neurological disorders.

BackgroundMedulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB highlight the substantial role of epigenetic alterations. 5-hydroxymethylcytosine (5hmC) is a highly abundant cytosine modification in the developing cerebellum and is regulated by ten-eleven translocation (TET) enzymes.ResultsWe investigate the alterations of 5hmC and TET enzymes in MB and their significance to cerebellar cancer formation. We show total abundance of 5hmC is reduced in MB, but identify significant enrichment of MB-specific 5hmC marks at regulatory regions of genes implicated in stem-like properties and Nanog-binding motifs. While TET1 and TET2 levels are high in MBs, only knockout ofTet1in the smoothened (SmoA1)mouse model attenuates uncontrolled proliferation, leading to a favorable prognosis. The pharmacologicalTet1inhibition reduces cell viability andplatelet-derived growth factorsignaling pathway-associated genes.ConclusionsThese results together suggest a potential key role of 5hmC and indicate an oncogenic nature for TET1 in MB tumorigenesis, suggesting it as a potential therapeutic target for MBs.

Background:. Since 2019, a novel coronavirus named 2019 novel coronavirus (2019-nCoV) has emerged worldwide. Apart from fever and respiratory complications, acute kidney injury has been observed in a few patients with coronavirus disease 2019. Furthermore, according to recent findings, the virus has been detected in urine. Angiotensin-converting enzyme II (ACE2) has been proposed to serve as the receptor for the entry of 2019-nCoV, which is the same as that for the severe acute respiratory syndrome. This study aimed to investigate the possible cause of kidney damage and the potential route of 2019-nCoV infection in the urinary system. Methods:. We used both published kidney and bladder cell atlas data and new independent kidney single-cell RNA sequencing data generated in-house to evaluate ACE2 gene expression in all cell types in healthy kidneys and bladders. The Pearson correlation coefficients between ACE2 and all other genes were first generated. Then, genes with r values larger than 0.1 and P values smaller than 0.01 were deemed significant co-expression genes with ACE2. Results:. Our results showed the enriched expression of ACE2 in all subtypes of proximal tubule (PT) cells of the kidney. ACE2 expression was found in 5.12%, 5.80%, and 14.38% of the proximal convoluted tubule cells, PT cells, and proximal straight tubule cells, respectively, in three published kidney cell atlas datasets. In addition, ACE2 expression was also confirmed in 12.05%, 6.80%, and 10.20% of cells of the proximal convoluted tubule, PT, and proximal straight tubule, respectively, in our own two healthy kidney samples. For the analysis of public data from three bladder samples, ACE2 expression was low but detectable in bladder epithelial cells. Only 0.25% and 1.28% of intermediate cells and umbrella cells, respectively, had ACE2 expression. Conclusion:. This study has provided bioinformatics evidence of the potential route of 2019-nCoV infection in the urinary system.

The molecular mechanisms underlying renal damage of IgA nephropathy (IgAN) remain incompletely defined. Here, single-cell RNA sequencing (scRNA-seq) was applied to kidney biopsies from IgAN and control subjects to define the transcriptomic landscape at single-cell resolution. We presented a comprehensive scRNA-seq analysis of human renal biopsies from IgAN. We showed for the first time that IgAN mesangial cells displayed increased expression of several novel genes including MALAT1, GADD45B, SOX4, and EDIL3, which were related to cell proliferation and matrix accumulation. The overexpressed genes in tubule cells of IgAN were mainly enriched in inflammatory pathways including TNF signaling, IL-17 signaling, and NOD-like receptor signaling. Furthermore, we compared the results of 4 IgAN patients with the published scRNA-Seq data of healthy kidney tissues of three human donors in order to further validate the findings in our study. The results also verified that the overexpressed genes in tubule cells from IgAN patients were mainly enriched in inflammatory pathways including TNF signaling, IL-17 signaling, and NOD-like receptor signaling. The receptor-ligand crosstalk analysis revealed potential interactions between mesangial cells and other cells in IgAN. IgAN patients with overt proteinuria displayed elevated genes participating in several signaling pathways compared with microproteinuria group. It needs to be mentioned that based on number of mesangial cells and other kidney cells analyzed in this study, the results of our study are preliminary and needs to be confirmed on larger number of cells from larger number of patients and controls in future studies. Therefore, these results offer new insight into pathogenesis and identify new therapeutic targets for IgAN.

Major depression disorder is one of the most common psychiatric diseases. Recent evidence supports that environmental stress affects gene expression and promotes the pathological process of depression through epigenetic mechanisms. Three ten-eleven translocation (Tet) enzymes are epigenetic regulators of gene expression that promote 5-hydroxymethylcytosine (5hmC) modification of genes. Here, we show that the loss of Tet2 can induce depression-like phenotypes in mice. Paradoxically, using the paradigms of chronic stress, such as chronic mild stress and chronic social defeat stress, we found that depressive behaviors were associated with increased Tet2 expression but decreased global 5hmC level in hippocampus. We examined the genome-wide 5hmC profile in the hippocampus of Tet2 knockout mice and identified 651 dynamically hydroxymethylated regions, some of which overlapped with known depression-associated loci. We further showed that chronic stress could induce the abnormal nuclear translocation of Tet2 protein from cytosol. Through Tet2 immunoprecipitation and mass spectrum analyses, we identified a cellular trafficking protein, Abelson helper integration site-1 (Ahi1), which could interact with Tet2 protein. Ahi1 knockout or knockdown caused the accumulation of Tet2 in cytosol. The reduction of Ahi1 protein under chronic stress explained the abnormal Ahi1-dependent nuclear translocation of Tet2. These findings together provide the evidence for a critical role of modulating Tet2 nuclear translocation in regulating stress response.

SUMMARY Transcriptional silencing of the FMR1 gene in fragile X syndrome (FXS) leads to the loss of the RNA-binding protein FMRP. In addition to regulating mRNA translation and protein synthesis, emerging evidence suggests that FMRP acts to coordinate proliferation and differentiation during early neural development. However, whether loss of FMRP-mediated translational control is related to impaired cell fate specification in the developing human brain remains unknown. Here, we use human patient induced pluripotent stem cell (iPSC)-derived neural progenitor cells and organoids to model neurogenesis in FXS. We developed a high-throughput, in vitro assay that allows for the simultaneous quantification of protein synthesis and proliferation within defined neural subpopulations. We demonstrate that abnormal protein synthesis in FXS is coupled to altered cellular decisions to favor proliferative over neurogenic cell fates during early development. Furthermore, pharmacologic inhibition of elevated phosphoinositide 3-kinase (PI3K) signaling corrects both excess protein synthesis and cell proliferation in a subset of patient neural cells., In brief Raj et al. developed a multiparametric assay to measure cellular and molecular phenotypes during neurogenesis in fragile X syndrome iPSC-derived neural cells. Relative to controls, FXS patient cultures have more proliferative cells with increased protein synthesis. Defects in cell fate acquisition can be normalized by inhibiting overactive PI3K signaling., Graphical Abstract

The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA–DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA–DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a ‘hot-spot’ for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA.

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21726-y

Epigenetic modifications of DNA play important roles in many biological processes. Identifying readers of these epigenetic marks is a critical step towards understanding the underlying mechanisms. Here, we present an all-to-all approach, dubbed digital affinity profiling via proximity ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying different epigenetic modifications (i.e., 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine) on CpG dinucleotides. Many proteins that recognize consensus sequences carrying these modifications in symmetric and/or hemi-modified forms are identified. We further demonstrate that the modifications in different sequence contexts could either enhance or suppress TF binding activity. Moreover, many modifications can affect TF binding specificity. Furthermore, symmetric modifications show a stronger effect in either enhancing or suppressing TF-DNA interactions than hemi-modifications. Finally, in vivo evidence suggests that USF1 and USF2 might regulate transcription via hydroxymethylcytosine-binding activity in weak enhancers in human embryonic stem cells., Identifying readers of epigenetic marks is a critical step for understanding the role of epigenetic marks in biology. Here, the authors applied DAPPL, an all-to-all approach to profile the interactions between TFs and epigenetic modified DNA libraries.