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Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis, has latently infected about one-third of the world’s population and may lead to severe clinical symptoms and death. The WhiB4 protein, a transcription factor, plays a crucial role in the survival and pathology of Mtb. WhiB4 leads to the condensation of mycobacterial nucleoids and regulates the expression of genes involved in central metabolism, respiration, and maintaining redox homeostasis. Here, we report the solution structure of reduced apo-WhiB4 monomer, which consists of an unstructured N-terminal domain with four cysteine residues and a helix-turn-helix C-terminal domain that plays a major role in DNA binding. The C-terminal domain of WhiB4 binds DNA at the minor groove, with five positively charged lysine/arginine residues contacting DNA sugar-phosphate backbones through electrostatic interactions. AT-rich DNA sequences with narrower minor grooves are more preferred by WhiB4. The binding affinity of a single C-terminal domain of WhiB4 is weak. When oxidized, WhiB4 can form dimers and oligomers in different forms through disulfide bonds, which should significantly enhance its DNA binding ability through multivalent effect and change the local structure of target genes and influence their transcription. These structural features form the basis for WhiB4 to function as a redox-sensitive transcription factor in Mtb.

Thirty-one species of Paraclius Loew were known to occur in China. In this paper, two species are described as new to science: Paraclius ventralis sp. nov. and Paraclius wutongshanus sp. nov. A key to the Chinese species of Paraclius is provided. www.zoobank.org/urn:lsid:zoobank.org:pub:3E803E27-5E44-4A55-91D5-DA088F986485.

Identifying motifs in promoter regions is crucial to our understanding of transcription regulation. Researchers commonly use known promoter features in a variety of species to predict promoter motifs. However the results are not particularly useful. Different species rarely have similar features in promoter binding sites. In this study, we adopt sequence analysis techniques to find the possible promoter binding sites among different species. We sought to improve the existing algorithm to suit the task of mining sequential patterns with specific number of gaps. Moreover, we discuss the implementation of proposed method in a distributed environment. The proposed method finds the transcription start sites (TSS) and extracts possible promoter regions from DNA sequences according to TSS. We derived the motifs in the possible promoter regions, while taking into account the number of gaps in the motifs to deal with unimportant nucleotides. The motifs generated from promoter regions using the proposed methodology were shown to tolerate unimportant nucleotides. A comparison with known promoter motifs verified the efficacy of the proposed method.

Knowledge of the fundamental aspects of ecology such as the patterns of fish species distribution and biodiversity in the forest streams is the first and basic step to develop effective conservation strategies. Yet, studies on altitudinal changes of fish composition and assemblages in Bornean forest streams are scarce despite being one of the hotspots of biodiversity conservation. Hence, surveys on freshwater fish composition along the altitudinal gradients of the Baleh River Basin in Sarawak, Borneo were conducted from April 2014 to August 2015. The Baleh River Basin was divided into seven altitudinal groups with a total of 72 stations. Group elevation ranged from 53 to 269 m above sea level. The fish samples and environmental parameters were taken concurrently during samplings. A total of 3565 specimens belonging to six orders, 14 families, and 76 species were found in the present study. The most dominant family in the Baleh River Basin was Cyprinidae (74.4%), followed by Gastromyzontidae (16.2%) while the most dominant species was Tor tambra (12.9%), followed by Lobocheilos ovalis (12.3%). Fish abundance significantly higher at high altitude sites than those at low altitude sites except for Mengiong River which has the lowest fish abundance despite with high elevation. Species richness was found significantly lower in midstream segment. Noticeable altitudinal gradient of fish assemblages was observed along the Baleh River except a discontinuity at the midstream segment which is attributable to the poorer quality inflow from the Mengiong River coupled with the meandering feature of the segment. Fish abundance was significantly and positively correlated with elevation, water pH and conductivity while negatively correlated with turbidity. Anthropogenic activities in the Baleh River Basin had altered the environmental variables thus disrupted the altitudinal gradient of fish assemblages. This phenomenon is apparent when the Canonical Correspondence Analysis (CCA) revealed that the first axis (CCA1) explained 42.5% of the variation and has positive loading on dissolved oxygen (DO) and negative loading on water conductivity; whereas CCA2 explained 37.5% of the variation and positively loaded on elevation, water pH, and DO. The results demonstrated that Gastromyzon fasciatus preferred more oxygenated water than Protomyzon sp., G. sp 1, and G. punctulatus although they are all from Gastromyzontidae family that inhabiting high altitude sites. Barbonymus schwanenfeldii was also found most abundant with elevated dissolved oxygen value. On the other hand, Rasbora volzii and R. hosii inhabiting lower altitude sites with less oxygenated and more acidic water.

Drug–target interaction prediction is important for drug development and drug repurposing. Many computational methods have been proposed for drug–target interaction prediction due to their potential to the time and cost reduction. In this review, we introduce the molecular docking and machine learning-based methods, which have been widely applied to drug–target interaction prediction. Particularly, machine learning-based methods are divided into different types according to the data processing form and task type. For each type of method, we provide a specific description and propose some solutions to improve its capability. The knowledge of heterogeneous network and learning to rank are also summarized in this review. As far as we know, this is the first comprehensive review that summarizes the knowledge of heterogeneous network and learning to rank in the drug–target interaction prediction. Moreover, we propose three aspects that can be explored in depth for future research.

This study tested the hypothesis that combined therapy with human umbilical cord‐derived mesenchymal stem cells (HUCDMSCs) and hyperbaric oxygen (HBO) was superior to either one on preserving neurological function and reducing brain haemorrhagic volume (BHV) in rat after acute intracerebral haemorrhage (ICH) induced by intracranial injection of collagenase. Adult male SD rats (n = 30) were equally divided into group 1 (sham‐operated control), group 2 (ICH), group 3 (ICH +HUCDMSCs/1.2 × 106 cells/intravenous injection at 3h and days 1 and 2 after ICH), group 4 (ICH +HBO/at 3 hours and days 1 and 2 after ICH) and group 5 (ICH +HUCDMSCs‐HBO), and killed by day 28 after ICH. By day 1, the neurological function was significantly impaired in groups 2‐5 than in group 1 (P

Gram-positive (GP) pathogens are less accounted for in pediatric urinary tract infection (UTI), and their clinical impact is underrecognized. This study aimed to identify predictors of GP uropathogens in pediatric UTI. In this 14-year retrospective cohort of pediatric patients with UTI, we classified first-time UTIs cases into those caused by GP or Gram-negative (GN) bacteria. We constructed a multivariable logistic regression model to predict GP UTI. We evaluated model performance through calibration and discrimination plots. We developed a nomogram to predict GP UTI that is clinically feasible. Of 3783 children with first-time UTI, 166 (4.4%) were infected by GP and 3617 (95.6%) by GN bacteria. Among children with GP UTI, the most common uropathogens were vancomycin-resistant Enterococcus faecalis (VRE) (27.1%), Staphylococcus saprophyticus (26.5%), and coagulase-negative Staphylococci (12.7%). Eight independent risk factors were associated with GP UTI: Age ≥ 24 months (odds ratio [OR]: 3.21), no prior antibiotic use (OR: 3.13), serum white blood cell (WBC) count 3/μL (OR: 2.19), high sensitivity C-reactive protein (hsCRP) E. faecalis, the leading GP uropathogen causing pediatric UTI, requires early detection for infection control. Our model for predicting GP UTI can help clinicians detect GP uropathogens and administer antibiotic regimen early.

Antimicrobial resistance to existing antibiotics represents one of the greatest threats to human health and is growing at an alarming rate. To further complicate treatment of bacterial infections, many chronic infections are the result of bacterial biofilms that are tolerant to treatment with antibiotics because of the presence of metabolically dormant persister cell populations. Together these threats are creating an increasing burden on the healthcare system, and a “preantibiotic” age is on the horizon if significant action is not taken by the scientific and medical communities. While the golden era of antibiotic discovery (1940s–1960s) produced most of the antibiotic classes in clinical use today, followed by several decades of limited development, there has been a resurgence in antibiotic drug discovery in recent years fueled by the academic and biotech sectors. Historically, great success has been achieved by developing next-generation variants of existing classes of antibiotics, but there remains a dire need for the identification of novel scaffolds and/or antimicrobial targets to drive future efforts to overcome resistance and tolerance. In this regard, there has been no more valuable source for the identification of antibiotics than natural products, with 69–77% of approved antibiotics either being such compounds or being derived from them. Our group has developed a program centered on the chemical synthesis and chemical microbiology of marine natural products with unusual structures and promising levels of activity against multidrug-resistant (MDR) bacterial pathogens. As we are motivated by preparing and studying the biological effects of these molecules, we are not initially pursuing a biological question but instead are allowing the observed phenotypes and activities to guide the ultimate project direction. In this Account, our recent efforts on the synoxazolidinone, lipoxazolidinone, and batzelladine natural products will be discussed and placed in the context of the field’s greatest challenges and opportunities. Specifically, the synoxazolidinone family of 4-oxazolidinone-containing natural products has led to the development of several chemical methods to prepare antimicrobial scaffolds and has revealed compounds with potent activity as adjuvants to treat bacterial biofilms. Bearing the same 4-oxazolidinone core, the lipoxazolidinones have proven to be potent single-agent antibiotics. Finally, our synthetic efforts toward the batzelladines revealed analogues with activity against a number of MDR pathogens, highlighted by non-natural stereochemical isomers with superior activity and simplified synthetic access. Taken together, these studies provide several distinct platforms for the development of novel therapeutics that can add to our arsenal of scaffolds for preclinical development and can provide insight into the biochemical processes and pathways that can be targeted by small molecules in the fight against antimicrobial-resistant and -tolerant infections. We hope that this work will serve as inspiration for increased efforts by the scientific community to leverage synthetic chemistry and chemical microbiology toward novel antibiotics that can combat the growing crisis of MDR and tolerant bacterial infections.

Anaerobic digestion (AD) was employed to utilize fresh vinegar residue (FVR) in this study. The performance and microbial community structure at increasing organic loading rates (OLRs) were evaluated. The results showed that the mono-fermentation of FVR was unstable at high OLRs due to the high acidity and the high cellulose content of the raw material. The optimum OLR was 2.0 g VS/(L·d), with the maximum average methane yield at 216 mL /g VS. High OLRs (2.5 g VS/(L·d)) led to the irreversible inhibition of AD process, although digester ceased feeding during the recovering stage. The diversity of microbial community decreased at high OLRs. The relative abundance of major bacterial community at different OLRs also varied. The syntrophic volatile fatty acids (VFAs) oxidizing bacteria declined while the acid-producing bacteria became dominant. The close correlation between the AD process stability and the microbial community structure suggested that maintaining a rich and diverse microbial community was essential for the practical application of AD on vinegar residue (VR) utilization.

Hodgkin lymphoma (HL) is composed of neoplastic Hodgkin and Reed‐Sternberg cells in an inflammatory background. The neoplastic cells are derived from germinal center B cells that, in most cases, are infected by Epstein‐Barr virus (EBV), which may play a role in tumorigenesis. Given that EBV‐latent membrane protein 1 (LMP1) regulates autophagy in B cells, we explored the role of autophagy mediated by EBV or LMP1 in HL. We found that EBV‐LMP1 transfection in HL cells induced a modest increase in autophagy signals, attenuated starvation‐induced autophagic stress, and alleviated autophagy inhibition‐ or doxorubicin‐induced cell death. LMP1 knockdown leads to decreased autophagy LC3 signals. A xenograft mouse model further showed that EBV infection significantly increased expression of the autophagy marker LC3 in HL cells. Clinically, LC3 was expressed in 15% (19/127) of HL samples, but was absent in all cases of nodular lymphocyte‐predominant and lymphocyte‐rich classic HL cases. Although expression of LC3 was not correlated with EBV status or clinical outcome, autophagic blockade effectively eradicated LMP1‐positive HL xenografts with better efficacy than LMP1‐negative HL xenografts. Collectively, these results suggest that EBV‐LMP1 enhances autophagy and promotes the viability of HL cells. Autophagic inhibition may be a potential therapeutic strategy for treating patients with HL, especially EBV‐positive cases., EBV‐LMP1 enhances autophagy and promotes viability of Hodgkin lymphoma cells. Autophagic inhibition may be a potential therapeutic strategy for treating patients with Hodgkin lymphoma, especially EBV‐positive cases.

Pericarpium Citri Reticulatae (PCR), the mature fruit peel of Citrus reticulata Blanco and its different cultivars, is an important citrus by‐product with beneficial health and nutritive properties. However, due to the lack of value‐added methods for its development and utilization, a large amount of PCR is discarded or wasted. To explore a possibly more effective method to utilize PCR, we compared the chemical and biological differences before (CK) and after (CP) microbial transformation of PCR by Aspergillus niger. UPLC‐ESI‐MS/MS, HPLC, and LC‐MS methods were used to compare the chemical profiles of CK and CP. The results demonstrated that microbial biotransformation by A. niger could transform flavonoid compounds by utilizing the carbohydrate and amino acid nutrients in PCR. This could also promote the accumulation of polyhydroxyflavones compounds in CP. The antioxidant assay demonstrated that CP had significantly greater free radical‐scavenging activity than CK. The higher antioxidant activity of CP may result from the high level of flavonoids with associated phenolic hydroxyl groups. Microbial biotransformation is an effective method for improving the antioxidant capacity of PCR and may be effective and useful in other natural product situations., Microbial biotransformation is an effective method for improving the antioxidant capacity of PCR and may be effective and useful in other natural product situations.

Patchoulol is a tricyclic sesquiterpene widely used in perfumes and cosmetics. Herein, comprehensive engineering strategies were employed to construct an efficient yeast strain for patchoulol production. First, a platform strain was constructed via pathway modification. Second, three off-pathway genes were deleted, which led to significant physiological changes in yeast. Further, strengthening of the ergosterol pathway, enhancement of the energy supply, and a decrease in intracellular reactive oxygen species were implemented to improve the physiological status of yeast, demonstrating a new promotive relationship between ergosterol biosynthesis and synthesis of patchoulol. Moreover, patchoulol synthase was improved through protein modification and Mg2+ addition, reaching a final titer of 141.5 mg/L in a shake flask. Finally, a two-stage fermentation with dodecane addition was employed to achieve the highest production (1632.0 mg/L, 87.0 mg/g dry cell weight, 233.1 mg/L/d) ever reported for patchoulol in a 5 L bioreactor. This work lays a foundation for green and efficient patchoulol production.

Super-enhancers (SEs) are congregated enhancer clusters with high level of loading of transcription factors (TFs), cofactors and epigenetic modifications. Through direct co-occupancy at their own SEs as well as each other's, a small set of so called "master" TFs form interconnected core regulatory circuitry (CRCs) to orchestrate transcriptional programs in both normal and malignant cells. These master TFs can be predicted mathematically using epigenomic methods. In this Review, we summarize the identification of SEs and CRCs in cancer cells, the mechanisms by which master TFs and SEs cooperatively regulate cancer-type-specific expression programs, and the cancer-type- and subtype-specificity of CRC and the significance in cancer biology.

Length weight relationships (LWRs) are presented for six loach species belonging to two families of Gastromyzontidae and Nemacheilidae captured in the Baleh River Basin, Sarawak, Malaysia. One time sampling was conducted at each station representing first- to fourth-order tributaries in the Baleh River Basin from April 2014 to November 2015. Loach samples were collected via electrofishing method and measured for total length to the nearest 0.1 cm and weighted to the nearest 0.1 g immediately after capture. The values of the equation parameter ‘b’ of the LWR falls within the range of 2.5 to 3.5 for six loach species in Sarawak, Malaysia.

The long-legged fly Lichtwardtia dentalis Zhang, Masunaga et Yang, 2009 belongs to the subfamily Dolichopodinae of Dolichopodidae. The newly sequenced mitogenome of L. dentalis is a new representative of the subfamily. The nearly complete mitogenome is 15,124 bp in length, consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). All genes have similar locations and encoding directions with that of other published mitogenomes of Dolichopodidae. The nucleotide composition biases toward A and T with the overall A + T % is 73.9%. All protein-coding genes initiate with standard start codon ATN except COI and NAD1, and TAA/TAG are conventionally used as stop codons. All tRNAs, ranging from 62 to 71 bp, have a clover-leaf structure. Based on the result of the phylogenetic analysis, Dolichopodidae and Empididae were monophyletic, and the relationships among subfamilies of Dolichopodidae were Diaphorinae + (Peloropeodinae + (Xanthochlorinae + (Medeterinae + Dolichopodinae))). The monophyly of the subfamily Dolichopodinae and the sister relationship between Dolichopus and Lichtwardtia were also strongly supported.

Background: Atrial fibrillation (AF) is related to a higher risk of thromboembolic events and mortality. Some studies have demonstrated that the inflammatory biomarker interleukin-6 (IL-6) is associated with a higher risk of higher thrombosis in AF patients, but the real effect of IL-6 remains a controversy. Methods: We conducted a systematic review and meta-analysis to investigate the association between IL-6 and thromboembolic events, as well as bleeding events, acute coronary syndrome (ACS) events and all-cause mortality in AF. Results: A total of five studies involving 22 928 patients met our inclusion criteria for the systematic review. The higher level of IL-6 in AF patients is related to long-term thromboembolic events including stroke (RR 1.44, CI 95% 1.09-1.90, p=0.01). IL-6 meant a higher risk of long-term bleeding risk (RR 1.36, CI 95% 1.06-1.74, p=0.02), ACS risk (RR 1.81, CI 95% 1.43-2.30, p

The complete Eclipophleps carinata mitogenome was sequenced through Illumina HiSeq 2500 platform and the resulting data were analyzed in this paper. The mitochondrial genome of E. carinata is a typ...

Many studies have reported a positive association between lower socioeconomic status (SES) and higher head and neck cancer (HNC) risk. Fewer studies have examined the impact of SES on the association between alcohol or cigarette use and HNC risk. The current case‐control study (1104 HNC cases and 1363 controls) investigated the influence of education, a SES indicator, on the association between HNC and the use of alcohol, cigarettes, or betel quids in Taiwan, a country with universal health care. Our results showed a larger increase in HNC risk associated with alcohol among those with lower educational level (odds ratio [OR] = 2.07; 95% confidence interval [CI], 1.53‐2.80) than those with higher educational level (OR = 1.38; 95% CI, 1.04‐1.85) (heterogeneity‐P = .03). Educational level had an influence on the association between alcohol use and HNC risk among those with genetic susceptibility (ALDH2‐deficient) to the carcinogenic effect of alcohol. The association between cigarette or betel quid use and HNC risk was similar between the high and low educational groups. National policies and social interventions have led to the decline in the prevalence of cigarette and betel quid users in Taiwan. In contrast, due to the lack of adequate alcohol control policies, alcohol consumption in Taiwan has continued to rise. A higher impact of alcohol on HNC risk among lower SES individuals even with universal health care could be the result of insufficient alcohol control policies in Taiwan.

Dia1, which belongs to the diaphanous-related formin family, influences a variety of cellular processes through straight actin elongation activity. Recently, novel DIA1 mutants such as p.R1213X (p.R1204X) and p.A265S, have been reported to cause an autosomal dominant sensorineural hearing loss (DFNA1). Additionally, active DIA1 mutants induce progressive hearing loss in a gain-of-function manner. However, the subcellular localization and pathological function of DIA1(R1213X/R1204X) remains unknown. In the present study, we demonstrated the localization of endogenous Dia1 and the constitutively active DIA1 mutant in the cochlea, using transgenic mice expressing FLAG-tagged DIA1(R1204X) (DIA1-TG). Endogenous Dia1 and the DIA1 mutant were regionally expressed at the organ of Corti and the spiral ganglion from early life; alongside cochlear maturation, they became localized at the apical junctional complexes (AJCs) between hair cells (HCs) and supporting cells (SCs). To investigate HC vulnerability in the DIA1-TG mice, we exposed 4-week-old mice to moderate noise, which induced temporary threshold shifts with cochlear synaptopathy and ultrastructural changes in stereocilia 4 weeks post noise exposure. Furthermore, we established a knock-in (KI) mouse line expressing AcGFP-tagged DIA1(R1213X) (DIA1-KI) and confirmed mutant localization at AJCs and the tips of stereocilia in HCs. In MDCKAcGFP-DIA1(R1213X) cells with stable expression of AcGFP-DIA1(R1213X), AcGFP-DIA1(R1213X) revealed marked localization at microvilli on the apical surface of cells and decreased localization at cell-cell junctions. The DIA1-TG mice demonstrated hazy and ruffled circumferential actin belts at AJCs and abnormal stereocilia accompanied with HC loss at 5 months of age. In conclusion, Dia1 plays a pivotal role in the development and maintenance of AJCs and stereocilia, ensuring cochlear and HC integrity. Subclinical/latent vulnerability of HCs may be the cause of progressive hearing loss in DFNA1 patients, thus suggesting new therapeutic targets for preventing HC degeneration and progressive hearing loss associated with DFNA1.

Regulation of Nuclear Pre-mRNA Domain Containing 1B (RPRD1B) has been of great interest in the field of oncology in recent years. The relationship between miRNAs and RPRD1B in gastric cancer (GC) has not been adequately reported. This study was designed to screen RPRD1B-targeted miRNAs and investigate its regulatory mechanism in GC cells. Quantitative RT-PCR and in situ hybridization were used to detect miRNA expression in GC tissues. Colony formation, EdU cell proliferation assay, and flow cytometry were used to analyze the cell cycle. Database-assisted gene expression analysis revealed that RPRD1B was targeted and regulated by miRNA-139-5p in GC. miRNA-139-5p expression was higher in GC tissue than in normal tissues and significantly correlated with tumor size, pathological stage, and disease-free survival of GC (p 0.05). MiRNA-139-5p regulates GC cell proliferation and affects the transition from G1 to S phase. It binds explicitly to the 2013-2019 sites of the 3'UTR of RPRD1B and negatively regulates RPRD1B expression. We demonstrated that the ability of miR-139-5p to regulate GC cell proliferation depends on RPRD1B. This process is accompanied by changes in Cyclin D1 protein expression. We established a miR-139-5p/RPRD1B/tumor proliferation axis in GC, which may serve as novel biomarkers and drug targets for GC.

Long noncoding RNAs (lncRNAs) have important regulatory roles in cancer biology. Although some lncRNAs have well‐characterized functions, the vast majority of this class of molecules remains functionally uncharacterized. To systematically pinpoint functional lncRNAs, a computational approach was proposed for identification of lncRNA‐mediated competing endogenous RNAs (ceRNAs) through combining global and local regulatory direction consistency of expression. Using esophageal squamous cell carcinoma (ESCC) as model, we further identified many known and novel functional lncRNAs acting as ceRNAs (ce‐lncRNAs). We found that most of them significantly regulated the expression of cancer‐related hallmark genes. These ce‐lncRNAs were significantly regulated by enhancers, especially super‐enhancers (SEs). Landscape analyses for lncRNAs further identified SE‐associated functional ce‐lncRNAs in ESCC, such as HOTAIR, XIST, SNHG5, and LINC00094. THZ1, a specific CDK7 inhibitor, can result in global transcriptional downregulation of SE‐associated ce‐lncRNAs. We further demonstrate that a SE‐associated ce‐lncRNA, LINC00094 can be activated by transcription factors TCF3 and KLF5 through binding to SE regions and promoted ESCC cancer cell growth. THZ1 downregulated expression of LINC00094 through inhibiting TCF3 and KLF5. Our data demonstrated the important roles of SE‐associated ce‐lncRNAs in ESCC oncogenesis and might serve as targets for ESCC diagnosis and therapy., We developed the GloceRNA method for the identification of functional ce‐lncRNAs based on merging global and local regulatory direction consistency of expression associated with ceRNAs. GloceRNA identified many known and novel functional ce‐lncRNAs, which regulated the expression of a large number of cancer hallmark genes. We further identified novel SE‐associated ce‐lncRNAs and demonstrated their important roles in ESCC.

This study aimed to investigate the protective mechanism of common buckwheat (Fagopyrum esculentum Moench.) against nonalcoholic fatty liver disease (NAFLD) associated with dyslipidemia in mice that were fed a high-fat and high-cholesterol diet (HFD). Results showed that oral supplementation of common buckwheat significantly improved physiological indexes and biochemical parameters related to dyslipidemia and NAFLD in mice fed with HFD. Furthermore, the HFD-induced reductions in fecal short-chain fatty acids were reversed by common buckwheat intervention, which also increased the fecal bile acid (BA) abundance compared with HFD-induced hyperlipidemic mice. Liver metabolomics based on ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry demonstrated that common buckwheat supplementation made significant regulatory effects on the pentose phosphate pathway, starch and sucrose metabolism, primary BA biosynthesis, and so forth. The results of high-throughput sequencing revealed that common buckwheat supplementation significantly altered the structure of the intestinal microbiota in mice fed with HFD. The correlations between lipid metabolic parameters and intestinal microbial phylotypes were also revealed by the heatmap and network. Additionally, common buckwheat intervention regulated the mRNA expressions of genes responsible for liver lipid metabolism and BA homeostasis, thus promoting BA synthesis and excretion. These findings confirmed that common buckwheat has the outstanding ability of improving lipid metabolism and could be used as a potential functional food for the prevention of NAFLD and hyperlipidemia.

We developed a multiplex ligation-dependent probe amplification (MLPA) assay for the simultaneous detection of 6 clinically relevant viral pathogens causing porcine reproductive failure, that is porcine reproductive and respiratory syndrome virus (PRRSV), Japanese encephalitis virus (JEV), classical swine fever virus (CSFV), porcine circovirus type 2 (PCV2), pseudorabies virus (PRV) and porcine parvovirus (PPV). The limits of detection for the assay varied among the 6 target organisms from 1 to 8 copies per MLPA assay. The MLPA assay was evaluated with 346 heparinized porcine umbilical cord blood specimens, and the results of the assay were compared to those of real-time PCR. The MLPA assay showed specificities and sensitivities of 99.2% and 100%, respectively, for PRRSV; 100% and 100%, respectively, for CSFV, PCV2, PRV and PPV. No sample was found to be positive for JEV by either the MLPA assay or the real-time PCR. In conclusion, the MLPA assay has comparable clinical sensitivity to that of real-time PCR assay and provides a useful tool for fast screening porcine reproductive failure-associated viruses.

At present, there are 31 species of Rhaphium Meigen recorded in China. In this paper, two species from Qinghai Province of China are described as new to science: Rhaphium huzhuensesp. nov., Rhaphium minhensesp. nov. A key to the Chinese species of Rhaphium is provided.

Two lactic acid bacteria (LAB) designated J02 and J13 were recovered from fermented vegetables based on their ability to suppress soft rot disease caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) on radish. J02 and J13 were identified as Lactobacillus pentosus and Leuconostoc fallax, respectively. The ability of J02 and J13 to suppress plant diseases is highly dependent on chitosan. LAB alone has no effect and chitosan alone has only a moderate effect on disease reduction. However, J02 or J13 broth cultures plus chitosan display a strong inhibitory effect against plant pathogens and significantly reduces disease severity. LAB strains after being cultured in fish surimi (agricultural waste) and glycerol or sucrose-containing medium and mixed with chitosan, reduce three cruciferous vegetable diseases, including cabbage black spot caused by Alternaria brassicicola, black rot caused by Xanthomonas campestris pv. campestris, and soft rot caused by Pcc. Experimental trials reveal that multiple applications are more effective than a single application. In-vitro assays also reveal the J02/chitosan mixture is antagonistic against Colletotrichum higginsianum, Sclerotium rolfsii, and Fusarium oxysporum f. sp. rapae, indicating a broad-spectrum activity of LAB/chitosan. Overall, our results indicate that a synergistic combination of LAB and chitosan offers a promising approach to biocontrol.

Purpose: To investigate the antioxidative properties of Lycium barbarum (LB) fruits in the eyes and to study whether LB fruits prepared with new nanotechnology have stronger antioxidative effects. Methods: Fourteen days post-supplementation with milled or blended LB fruits, intravitreal paraquat (PQ) was injected into Wistar rats to create oxidative stress. After an additional 14-day supplementation with LB fruits, the rats were sacrificed. An electroretinogram (ERG) was performed to evaluate retinal function before and after the PQ injection. Expression levels of antioxidative responders' mRNA in retina were detected by reverse transcription-polymerase chain reaction. Superoxide dismutase (SOD) and glutathione reductase activity in the aqueous humor (AqH) were analyzed by ELISA. Immunohistochemistry was conducted to evaluate the morphological changes of retina and the levels of oxidative biomarkers. The levels of cell apoptosis were assessed by the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. The reactive oxygen species (ROS) levels in AqH were measured by chemiluminescence methods. Results: The murine eyes supplemented with LB fruits exhibited several changes compared with the control group. The ERGs revealed significant improvement in retinal function. The mRNA expression levels of oxidative responders were downregulated in the retinas. The ROS was significantly reduced in the retinas, but the SOD meaningfully increased in the AqH. Immunohistochemistry staining and TUNEL assays showed decreased incidences of oxidative biomarkers and apoptosis in the retinas. Milled LB fruits exhibited better antioxidative effects than blended fruits. Conclusions: Milled LB fruits demonstrated superior protection against oxidative threats than blended fruits. Thus, these fruits could be an inexpensive supplement for many oxidative stress-related ocular diseases.

Phosphatidylcholine and phosphatidylethanolamine are two major phospholipid classes in eukaryotes. Each biosynthesis pathway starts with the phosphorylation of choline (Cho) or ethanolamine (Etn) catalyzed by either choline or ethanolamine kinase (CEK). Arabidopsis contains four CEK isoforms, but their isozyme-specific roles in metabolism and development are poorly described. Here, we showed that these four CEKs have distinct substrate specificities in vitro. While CEK1 and CEK2 showed substrate preference for Cho over Etn, CEK3 and CEK4 had clear substrate specificity for Cho and Etn, respectively. In vivo, CEK1, CEK2, and CEK3 exhibited kinase activity for Cho but not Etn, although the latter two isoforms showed rather minor contributions to total Cho kinase activity in both shoots and roots. The knockout mutants of CEK2 and CEK3 both affected root growth, and these isoforms had nonoverlapping cell-type-specific expression patterns in the root meristematic zone. In-depth phenotype analysis, as well as chemical and genetic complementation, revealed that CEK3, a Cho-specific kinase, is involved in cell elongation during root development. Phylogenetic analysis of CEK orthologs in Brassicaceae species showed evolutionary divergence between Etn kinases and Cho kinases. Collectively, our results demonstrate the distinct roles of the four CEK isoforms in Cho/Etn metabolism and plant development.

Drought and flooding are environmental extremes and major threats to crop production. Water uptake is achieved by plant roots which have to explore new soil spaces to alleviate water deficit during drought or to cope with water excess during flooding. Adaptation of the root system architecture helps plants cope with such extreme conditions and is crucial for plant health and survival. While for dicot plants the well studied model plant Arabidopsis thaliana has provided insight into the genetic and molecular regulation of the root system, less information is available for monocot species, which include the agronomically important cereal crops. Rice (Oryza sativa L.) is a semi-aquatic monocot plant that develops strong tolerance to flooding. Flooding tolerance of rice is closely linked to its adaptive root system. The functional root system of rice is mainly composed of crown roots and is shifted to nodal adventitious roots during flooding which allows rice to maintain oxygen supply to the roots and to survive longer periods of partial submergence as compared with other crops. Likewise, a number of drought-tolerance traits of rice are the result of an altered root system architecture. Hence, the structure of the root system adapts to, both, flooding and drought. Understanding the regulatory mechanisms that control root system adaptation to extreme environments is a key task for scientists to accelerate the breeding efforts for stress-tolerant crops. This review summarizes recently identified genes and molecular mechanisms that regulate root system architecture in rice in response to drought and flooding.

The genetic events occurring in recurrent nasopharyngeal carcinoma (rNPC) are poorly understood. Here, we performed whole-genome and whole-exome sequencing in 55 patients with rNPC and 44 primarily diagnosed NPC (pNPC), with 7 patients having paired rNPC and pNPC samples. Previously published pNPC exome data were integrated for analysis. rNPC and pNPC tissues had similar mutational burdens, however, the number of clonal mutations was increased in rNPC samples. TP53 and three NF-κB pathway components (TRAF3, CYLD, and NFKBIA) were significantly mutated in both pNPC and rNPC. Notably, mutations in TRAF3, CYLD, and NFKBIA were all clonal in rNPC, however, 55.6% to 57.9% of them were clonal in pNPC. In general, the number of clonal mutations in NF-κB pathway–associated genes was significantly higher in rNPC than in pNPC. The NF-κB mutational clonality was selected and/or enriched during NPC recurrence. The amount of NF-κB translocated to the nucleus in samples with clonal NF-κB mutants was significantly higher than that in samples with subclonal NF-κB mutants. Moreover, the nuclear abundance of NF-κB protein was significantly greater in pNPC samples with locoregional relapse than in those without relapse. Furthermore, high nuclear NF-κB levels were an independent negative prognostic marker for locoregional relapse-free survival in pNPC. Finally, inhibition of NF-κB enhanced both radiosensitivity and chemosensitivity in vitro and in vivo. In conclusion, NF-κB pathway activation by clonal mutations plays an important role in promoting the recurrence of NPC. Moreover, nuclear accumulation of NF-κB is a prominent biomarker for predicting locoregional relapse-free survival. Significance: This study uncovers genetic events that promote the progression and recurrence of nasopharyngeal carcinoma and has potential prognostic and therapeutic implications. See related commentary by Sehgal and Barbie, p. 5915

Nuclear import, mediated in part by karyopherin-α (KPNA)/importin-α subtypes, regulates transcription factor access to the genome and determines cell fate. However, the cancer-specific changes of KPNA subtypes and the relevancy in cancer biology remain largely unknown. Here, we report that KPNA4, encoding karyopherin-α4 (KPNA4), is exclusively amplified and overexpressed in head and neck of squamous cell carcinoma (HNSCC). Depletion of KPNA4 attenuated nuclear localization signal-dependent transport activity and suppressed malignant phenotypes and induced epidermal differentiation. Mechanistically, KPNA4-mediated nuclear transport of Ras-responsive element-binding protein (RREB1), which sustains Ras/ERK pathway signaling through repressing miR-143/145 expression. Notably, MAPK signaling enhanced trafficking activity of KPNA4 via phosphorylation of KPNA4 at Ser60. These data reveal that KPNA4 establishes a feed-forward cascade that potentiates Ras/ERK signaling in HNSCC.

Summary Arabidopsis FLOWERING LOCUS T (FT) is a pivotal component of florigen, a long-range mobile flowering signal. Here, we determined the 1.0 Å-resolution crystal structure of FT, a significantly higher-resolution crystal structure of FT than previously reported one (2.6 Å). The present crystallographic studies revealed 4 alternative configurations with the precise location of the surrounding water molecules. Using this structural data, computational docking simulation predicted the putative binding sites for phosphatidylcholine (PC), an endogenous ligand that interacts with FT to modulate flowering time. In vitro reconstitution of the lipid–protein interaction showed that mutations at two of the predicted sites significantly compromised the lipid binding ability of FT. In planta, one of the mutant FT proteins significantly affected FT function in flowering, emphasizing the involvement of PC binding in modulating FT function. Our structural, biochemical, and transgenic analyses reveal the molecular mechanism of PC binding in FT-mediated flowering time control., Graphical Abstract, Highlights • The crystal structure of FT is determined at 1.0 Å resolution • A phospholipid-binding site is identified in FT protein • Phospholipid-binding is demonstrated to modulate FT function • Molecular basis for FT-mediated flowering time control is proposed, Biological Sciences; Plant Biochemistry; Structural Biology; Plant Biology

This study tested the hypothesis that preactivated and disaggregated shape-changed platelet (PreD-SCP) therapy significantly protected rat kidney from ischemia-reperfusion (IR) injury. Adult-male Sprague-Dawley rats (n = 24) were equally categorized into Groups 1 (sham-operated control [SC]), 2 (SC + PreD-SCP), 3 (IR only), and 4 (IR + PreD-SCP). By 72 hr after IR procedure, the circulatory levels of creatinine, blood urine nitrogen and inflammatory biomarkers (interleukin [IL]-6/tumor necrosis factor [TNF]-α), and ratio of urine protein to urine creatinine were significantly higher in Group 3 than in other groups and significantly higher in Group 4 than in Groups 1 and 2, but they showed no different between Groups 1 and 2 (all p < .001). The microscopic findings showed that the expressions of kidney injury score, cellular inflammation (MMP-9/CD14//F4/80), and fibrotic area were identical to the circulatory inflammation, whereas the integrity of podocyte components (ZO-1/synaptopodin/podocin) exhibited an opposite to circulatory inflammation among the four groups (all p < .0001). The protein expressions of inflammatory (TNF-α/IL-1s/NF-κB/iNOS/TRAF6/MyD88/TLR-4), apoptotic/cell death (mitochondrial Bax/cleaved caspase-3/p-53), oxidized protein, mitogen-activated protein kinase family (p-38/p-JNK/p-c-JUN), and mitochondrial-damaged biomarkers displayed a similar pattern, whereas the antiapoptotic (Bcl-2/Bcl-XL) and integrity of mitochondrial biomarkers followed an opposite trend to circulatory inflammation among the four groups (all p < .001). PreD-SCP therapy effectively protected the kidney against IR injury.

Description, The CaCTS algorithm nominates cancer cell master transcription factors and guides a model of ovarian cancer regulatory circuitry., Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.

Phytoplasmas are uncultivated plant-pathogenic bacteria with agricultural importance. Those belonging to the 16SrII group, represented by ‘Candidatus P. aurantifolia’, have a wide range of plant hosts and cause significant yield losses in valuable crops, such as pear, sweet potato, peanut, and soybean. In this study, a method that combines immunoprecipitation-based enrichment and MinION long-read DNA sequencing was developed to solve the challenge of phytoplasma genome studies. This approach produced long reads with high mapping rates and high genomic coverage that can be combined with Illumina reads to produce complete genome assemblies with high accuracy. We applied this method to strain NCHU2014 and determined its complete genome sequence, which consists of one circular chromosome with 635,584 bp and one plasmid with 4,224 bp. Although ‘Ca. P. aurantifolia’ NCHU2014 has a small chromosome with only 471 protein-coding genes, it contains 33 transporter genes and 27 putative effector genes, which may contribute to obtaining nutrients from hosts and manipulating host developments for their survival and multiplication. Two effectors, the homologs of SAP11 and SAP54/PHYL1 identified in ‘Ca. P. aurantifolia’ NCHU2014, have the biochemical activities in destabilizing host transcription factors, which can explain the disease symptoms observed in infected plants. Taken together, this study provides the first complete genome available for the 16SrII phytoplasmas and contributes to the understanding of phytoplasma pathogenicity.

Acanthamoeba spp. are free-living parasites that can cause severe infections such as granulomatous amoebic encephalitis (GAE) and amoebic keratitis (AK). Polyhexamethylene biguanide (PHMB) is a topical application for AK treatment. However, PHMB is not entirely effective against all Acanthamoeba strains or isolates. The mechanisms by which Acanthamoeba protects itself against extreme drug conditions without encystation are still unknown. According to a previous study, cytochrome P450 monooxygenase (CYP450MO) plays an important role in the oxidative biotransformation of numerous drugs related to metabolism. In this study, a CYP450MO fragment was inserted into the pGAPDH-EGFP vector and transfected into Acanthamoeba castellanii. We found that CYP450MO-overexpressing Acanthamoeba had higher survival rates than those of the control cells after PHMB treatment. Moreover, we also found that encystation-related genes such as cellulose synthase I (CSI), encystation-mediating serine proteinase (EMSP), and autophagy-related protein 8 (ATG8) expression levels were not significantly different between Acanthamoeba transfected by pGAPDH-EGFP or pGAPDH-EGFP-CYP450MO. We suggest that Acanthamoeba transfected by pGAPDH-EGFP-CYP450MO may not induce encystation-related genes to resist PHMB treatment. In conclusion, these findings indicate that CYP450MO may be an additional target when PHMB is used for treatment of amoebic keratitis.La monooxygénase du cytochrome P450 d’Acanthamoeba castellanii participe à la résistance au traitement par le polyhexaméthylène biguanide.Les Acanthamoeba spp. sont des parasites libres qui peuvent provoquer des infections graves telles que l’encéphalite amibienne granulomateuse (EAG) et la kératite amibienne (KA). Le polyhexaméthylène biguanide (PHMB) est une application topique pour le traitement de la KA. Cependant, le PHMB n’est pas entièrement efficace contre toutes les souches ou isolats d’Acanthamoeba. Les mécanismes par lesquels Acanthamoeba se protège contre des conditions médicamenteuses extrêmes sans enkystation sont encore inconnus. Selon une étude précédente, la monooxygénase du cytochrome P450 (CYP450MO) joue un rôle important dans la biotransformation oxydative de nombreux médicaments liés au métabolisme. Dans cette étude, un fragment CYP450MO a été inséré dans le vecteur pGAPDH-EGFP et transfecté dans Acanthamoeba castellanii. Nous avons constaté que les Acanthamoeba surexprimant le CYP450MO avaient des taux de survie plus élevés que ceux des cellules témoins après un traitement au PHMB. De plus, nous avons également constaté que les gènes liés aux enkystations tels que la cellulose synthase I (CSI), la sérine protéinase médiatrice de l’enkystation (EMSP) et les niveaux d’expression de la protéine 8 liée à l’autophagie (ATG8) n’étaient pas significativement différents entre les Acanthamoeba transfectés par pGAPDH-EGFP ou par pGAPDH-EGFP-CYP450MO. Nous suggérons que les Acanthamoeba transfectés par pGAPDH-EGFP-CYP450MO ne peuvent pas induire les gènes liés à l’enkystation pour résister au traitement PHMB. En conclusion, ces résultats peuvent indiquer que la monooxygénase du cytochrome P450 peut être une cible potentielle pour le traitement par PHMB de la kératite amibienne.

The WhiB4 protein, a member of WhiB-like proteins, plays an important role in the survival and pathology of Mycobacterium tuberculosis (Mtb). As a transcription factor, WhiB4 regulates the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration. Furthermore, WhiB4 leads to the condensation of mycobacterial nucleoids and is capable of binding to DNA. WhiB4 contains four cysteine residues and exists in multiple forms under different redox environments, including a dimeric holo form with iron-sulfur cluster, multimeric disulfide-linked oxidized apo forms and monomeric reduced apo form. Here, we report the 1H, 13C, 15N chemical shifts of WhiB4 protein in its reduced apo state, providing a basis for the determination of its solution structure.

Phytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has an exceptionally repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ~25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for neofunctionalization or subfunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.

Cerebral ischemia is related to increased oxidative stress. Resveratrol displays anti-oxidant and anti-inflammatory properties. The transition elements iron (Fe) and copper (Cu) are indispensable for the brain but overload is deleterious to brain function. Aluminum (Al) and arsenic (As) are toxic metals that seriously threaten brain health. This study was conducted to elucidate the correlation of the neuroprotective mechanism of resveratrol to protect cerebral ischemic damage with modulation of the levels of lipid peroxidation, anti-oxidants, transition elements, and toxic metals. Experimentally, 20 mg/kg of resveratrol was given once daily for 10 days. The cerebral ischemic operation was performed via occlusion of the right common carotid artery together with the right middle cerebral artery for 60 min followed by homogenization of the brain cortex and collection of supernatants for biochemical analysis. In the ligation group, levels of malondialdehyde, Fe, Cu, Al, and As increased but those of the anti-oxidants superoxide dismutase and catalase decreased. Pretreating rats with resveratrol before ischemia significantly reversed these effects. Our findings highlight the association of overload of Fe, Cu, As, and Al with the pathophysiology of cerebral ischemia. In conclusion, resveratrol protects against cerebral ischemic injury via restraining lipid peroxidation, transition elements, and toxic metals, but increasing anti-oxidant activity.

This is the first study to discuss the effects of dark septate endophytes (DSE) on the growth promotion and berberine concentration in Mahonia oiwakensis, whose extract (MOE) has been suggested to have potential therapeutic effects against human lung cancer. First, as per phylogenetic analysis, the strains were divided into four groups: CkDB2, CkDB5, MoAL2 and MoAL5. All of these were DSEs, which could form microsclerotia in M. oiwakensis. The growth response experiment revealed that inoculation of the plant with MoAL5 and CkDB5 promoted an increase in the total fresh weight of the seedlings. Chemical composition analysis showed that seedlings inoculated with CkDB5 had the highest berberine concentration. These results showed that some DSEs have the ability to promote growth and induce phytochemical responses in the host plant.

BackgroundNF-κB is one of the most important inflammatory mediators in the tumour microenvironment promotes inflammation-induced cancer. Many studies report that NF-κB is activated in many kinds of leukaemia, so that some researchers by inhibiting NF-κB to treat leukaemia. The overexpression of BCL11B has been primarily reported in T cell malignancies. Some studies have reported that BCL11B is a potential transcriptional repressor which has several splice isoforms. MiR-21-5p promotes cell proliferation by targeting BCL11B in Thp-1 human monocytes. Both NF-κB and BCL11B transcription factors are related to inflammation and leukaemia. Whether there is correlation between NF-κB and BCL11B transcription factors? If BCL11B is a potential important transcription factor in treatment of T lymphocyte leukaemia? In this study, we stimulated Jurkat cells and normal peripheral blood T cells with staphylococcal enterotoxin A(SEA), and we detected the expression of both the BCL11B and NF-κB genes and their respective proteins at different stimulation times. Then, the BCL11B gene was suppressed by BCL11B-siRNA and detected at another stimulation time. ResultsWe found that the mRNA expression of BCL11B and NF-κB increased in two kinds of T cell lines over time which stimulated by SEA or PMA+IO. A similar result was confirmed for BCL11B and NF-κB protein expression. While the expression of the NF-κB protein did not increase on equal conditions in the BCL11B-knockdown group. ConclusionOur result suggested that the gene and protein expression levels of both BCL11B and NF-κB were related, and BCL11B regulates NF-κB expression in Jukat cells and healthy human peripheral blood through the TCR signalling pathway. This study reveals that BCL11B can be used as a new therapeutic target for chronic inflammation and T cell leukaemia pathogenesis.

Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism, which play an important role in a variety of biological activities. Viruses can encode circRNA, and viral circRNAs have been found in multiple single-stranded and double-stranded viruses. However, the characteristics and functions of viral circRNAs remain unknown. Sequence alignment showed that viral circRNAs are less conserved than circRNAs in animal, indicating that the viral circRNAs may evolve rapidly. Through the analysis of the sequence characteristics of viral circRNAs and circRNAs in animal, it was found that viral circRNAs and animals circRNAs are similar in nucleic acid composition, but have obvious differences in secondary structure and autocorrelation characteristics. Based on these characteristics of viral circRNAs, machine learning algorithms were employed to construct a prediction model to identify viral circRNA. Additionally, analysis of the interaction between viral circRNA and miRNAs showed that viral circRNA is expected to interact with 518 human miRNAs, and preliminary analysis of the role of viral circRNA. And it has been also found that viral circRNAs may be involved in many KEGG pathways related to nervous system and cancer. We curated an online server, and the data and code are available: http://server.malab.cn/viral-CircRNA/.

Cardiovascular disease (CVD) is strongly associated with the gut microbiota and its metabolites, including trimethylamine-N-oxide (TMAO), formed from metaorganismal metabolism of ʟ-carnitine. Raw garlic juice, with allicin as its primary compound, exhibits considerable effects on the gut microbiota. This study validated the benefits of raw garlic juice against CVD risk via modulation of the gut microbiota and its metabolites. Allicin supplementation significantly decreased serum TMAO in ʟ-carnitine-fed C57BL/6 J mice, reduced aortic lesions, and altered the fecal microbiota in carnitine-induced, atherosclerosis-prone, apolipoprotein E-deficient (ApoE−/−) mice. In human subjects exhibiting high-TMAO production, raw garlic juice intake for a week reduced TMAO formation, improved gut microbial diversity, and increased the relative abundances of beneficial bacteria. In in vitro and ex vivo studies, raw garlic juice and allicin inhibited γ-butyrobetaine (γBB) and trimethylamine production by the gut microbiota. Thus, raw garlic juice and allicin can potentially prevent cardiovascular disease by decreasing TMAO production via gut microbiota modulation.

Phosphorus (P) is an essential nutrient for plants. Membrane lipid remodeling is an adaptive mechanism for P-starved plants that replaces membrane phospholipids with non-P galactolipids, presumably to retrieve scarce P sources and maintain membrane integrity. Whereas metabolic pathways to convert phospholipids to galactolipids are well-established, the mechanism by which phospholipid biosynthesis is involved in this process remains elusive. Here, we report that phospho-base N-methyltransferases 1 and 2 (PMT1 and PMT2), which convert phosphoethanolamine to phosphocholine (PCho), are transcriptionally induced by P starvation. Shoots of seedlings of pmt1 pmt2 double mutant showed defective growth upon P starvation; however, membrane lipid profiles were unaffected. We found that P-starved pmt1 pmt2 with defective leaf growth had reduced PCho content, and the growth defect was rescued by exogenous supplementation of PCho. We propose that PMT1 and PMT2 are induced by P starvation to produce PCho mainly for leaf growth maintenance, rather than for phosphatidylcholine biosynthesis, in membrane lipid remodeling.

Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC., The relevance and underlying molecular mechanisms of epigenetic regulation in squamous cell carcinomas (SCC) await further characterization. Here, the authors show a transcriptional regulatory loop involving SREBF1, TP63 and KLF5 driving tumourigenesis in SCC through fatty acid, ERBB and mTOR pathway regulation.

CpG Island promoter genes make up more than half of human genes, and a subset regulated by Polycomb-Repressive Complex 2 (PRC2

Context The timing of early cumulus cell removal (ECCR) can be changed within a range. The change has an effect on the multiple pronuclei (MPN) rate and the exposure time of oocytes to sperm waste products. The timing of ECCR effects the outcomes of assisted reproductive technology, however, it is still unclear what time is best for ECCR. Aims To find the best time for ECCR based on clinical outcomes in order to increase the success rate of assisted reproductive technology. Methods A retrospective study was performed. Cycles were categorised into six groups according to the timing of ECCR. The clinical outcomes of these six groups were compared by Kruskal–Wallis test and Pearson X 2 test. Key results The timing of ECCR had a significant effect on the MPN rate, 0PN without cleavage rate and grade 1–2 embryo rate at Day 3. Among our six time groups of ECCR, the cumulus cell removal ≤4 h post-insemination group had the highest MPN rate and grade 1–2 embryo rate at Day 3, and the 5.5 h

Fermented meat products have a long history in China. These products exhibit a characteristic unique flavor, compact meat quality, clear color, long shelf life and wide variety and are easy to transport. During the processing and storage of fermented meat products, microorganisms are present and exhibit diverse characteristics. Microorganisms can accelerate the degradation of proteins and fats to produce flavor compounds, inhibit the growth and reproduction of heterozygous bacteria, and reduce the content of chemical pollutants. This paper reviews the microbial diversity of Chinese ham, sausage, preserved meat, pressed salted duck, preserved fish and air-dried meat and provides analyses of the microbial compositions of various products. Due to the differences in raw materials, technology, auxiliary materials, and fermentation technology, the microbial species found in various fermented meat products in China are different. However, most fermented meat products in China are subjected to pickling and fermentation, so their microbial compositions also have similarities. Microorganisms in fermented meat products mainly include staphylococci, lactobacilli, micrococci, yeasts, and molds. The study of microbial diversity is of great significance for the formation of quality flavor and the safety control of fermented meat products, and it provides some theoretical reference for the study of fermented meat products in China.