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Genetic recombination produces new allelic combinations, thereby introducing variation for domestication. Allopolyploidization has increased the evolutionary potential of hexaploid common wheat by conferring the advantages of heterosis and gene redundancy, but whether a relationship exists between allopolyploidization and genetic recombination is currently unknown. To study the impact of allopolyploidization on genetic recombination in the ancestral D genome of wheat, we generated new synthetic hexaploid wheats by crossing tetraploid Triticum turgidum with multiple diploid Aegilops tauschii accessions, with subsequent chromosome doubling, to simulate the evolutionary hexaploidization process. Using the DArT-Seq approach, we determined the genotypes of two new synthetic hexaploid wheats with their parents, F2 plants in a diploid population (2x, D1D1 × D2D2) and its new synthetic hexaploid wheat-derived population (6x, AABBD1D1 × AABBD2D2). About 11% of detected SNP loci spanning the D genome of Ae. tauschii were eliminated after allohexaploidization, and the degree of segregation distortion was increased in their hexaploid offspring from the F2 generation. Based on codominant genotypes, the mean genetic interval length and recombination frequency between pairs of adjacent and linked SNPs on D genome of the hexaploid F2 population were 2.3 fold greater than those in the diploid F2 population, and the recombination frequency of Ae. tauschii was increased by their hexaploidization with T. turgidum. In conclusion, allopolyploidization increases genetic recombination of the ancestral diploid D genome of wheat, and DNA elimination and increased segregation distortion also occur after allopolyploidization. Increased genetic recombination could have produced more new allelic combinations subject to natural or artificial selection, helping wheat to spread rapidly to become a major global crop and thereby accelerating the evolution of wheat via hexaploidization.

Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.

Point mutations can be used as biomarkers to perform diagnosis for diseases. In this study, a nanorobot for low-abundance point mutation enrichment was constructed using DNA origami. The novel design achieved limits of detection of 0.1% and 1% for synthesized DNA samples and clinical gene samples, respectively. Resettability was a key property of this method, which also involved a simpler process, lower cost and shorter detection duration than traditional enrichment methods. This novel DNA nanorobot may enable the detection of tumor markers, potentially facilitating early cancer diagnosis.

This study aimed to assess the changes of small intestinal morphology, progenitors, differentiated epithelial cells, and potential mechanisms in neonatal piglets. Hematoxylin and eosin staining of samples from 36 piglets suggested that dramatic changes were observed in the jejunum crypts depth and crypt fission index of neonatal piglets (P

The proteasome has been validated as an anticancer drug target, while the role of a subunit of proteasome, PSMC6, in lung adenocarcinoma (LUAD) has not been fully unveiled. In this study, we observed that both the RNA and protein of PSMC6 were highly upregulated in LUAD compared with the adjacent normal tissues. Moreover, a high PSMC6 expression was associated with poor prognosis. In accordance with this finding, PSMC6 was associated with poor tumor differentiation. Furthermore, the silence of PSMC6 by small interference RNAs (siRNAs) could significantly inhibit cell growth, migration, and invasion in lung cancer cell lines, suggesting that PSMC6 might serve as a promising therapeutic target in LUAD. To further explore the molecular mechanism of PSMC6 in LUAD, we observed that the proteasome subunits, such as PSMD10, PSMD6, PSMD9, PSMD13, PSMB3, PSMB1, PSMA4, PSMC1, PSMC2, PSMD7, and PSMD14, were highly correlated with PSMC6 expression. Based on the gene set enrichment analysis, we observed that these proteasome subunits were involved in the degradation of AXIN protein. The correlation analysis revealed that the positively correlated genes with PSMC6 were highly enriched in WNT signaling-related pathways, demonstrating that the PSMC6 overexpression may activate WNT signaling via degrading the AXIN protein, thereby promoting tumor progression. In summary, we systematically evaluated the differential expression levels and prognostic values of PSMC6 and predicted its biological function in LUAD, which suggested that PSMC6 might act as a promising therapeutic target in LUAD.

Five new iridoid glucosides, cannabifolisides A–E (1 – 5), together with nine analogues (6 – 14), were isolated from the leaves of Vitex negundo var. cannabifolia. Their structures were elucidated by spectroscopic data (NMR, UV, IR, and MS) analyses and comparison of their spectroscopic and physical data with the literature values. The protective effect of isolated compounds on human gastric epithelial cells were evaluated by measuring the enhanced cell viability of GES-1 cell insulted by TCA. Among these, compounds 4, 6, 8, 10, 12, and 14 remarkably increased the cell viability in a concentration-depend manner.

Epidermal growth factor receptor (EGFR) is an efficient target for cancer therapy. In this study, a high-affinity EGFR-antagonistic affibody (ZEGFR) molecule coupled with cisplatin-loaded PEGylated liposomes (LS-DDP) was applied to actively target EGFR+ A431 tumor cells in vitro and in vivo. The LS-DDP coupled with ZEGFR (AS-DDP) had an average size of 140.01 ± 0.84 nm, low polydispersity, a zeta potential of -13.40 ± 0.8 mV, an acceptable encapsulation efficiency of 17.30 ± 1.35%, and released cisplatin in a slow-controlled manner. In vitro, AS-DDP demonstrated a higher amount of platinum intracellular uptake by A431 cells than LS-DDP. The IC50 value of AS-DDP (9.02 ± 1.55 μg/ml) was much lower than that of LS-DDP (16.44 ± 0.87 μg/ml), indicating that the anti-tumor effects of AS-DDP were remarkable due to the modification of ZEGFR. In vivo, the concentration of AS-DDP in the tumor site increased more than 1.76-fold, while an increase in apoptotic cells at 48 h compared to the LS-DDP was also observed, illustrating that AS-DDP possessed excellent tumor-targeting efficiency. As a result, the targeted nano-liposomes achieved greater tumor suppression. Therefore, selective targeting of LS-DDP coupled with ZEGFR enhanced the anti-tumor effects and appeared to be a promising strategy for the treatment of EGFR+ tumors.

Heat stress not only affects the physical condition but also affects reproductive performance in sheep. A thorough understanding of the molecular and physiological mechanisms underlying heat stress would certainly improve livestock productivity and provide genetic evaluation ways for heat resistant breeds selection. In this study, 85 Turpan Black sheep, a breed exhibited excellent heat resistance from long-term artificial selection, and 85 heat sensitive Kazakh sheep in Turpan basin were tested for physiological and reproductive performance from July to August in summer. The results showed that the estrus rate was significantly higher in Turpan Black sheep (P 0.05), while the heart rate and respiratory rate of Turpan Black sheep are significantly lower than that of Kazakh sheep (P 0.05). Furthermore, to clarify genes participated in heat stress response, the pituitary, ovarian and hepatic tissues from three Turpan Black sheep and three Kazakh sheep were subjected to RNA-seq. The results indicated that 32, 49 and 69 genes were up-regulated, and 39, 60 and 145 genes were down-regulated in pituitary, ovarian and hepatic tissues in Turpan Black sheep compared with that of the Kazakh sheep, respectively. KEGG and gene set enrichment analysis showed that the differentially expressed genes were mainly involved in signal transduction pathways. In particular, the differentially expressed genes in hepar were enriched in the energy metabolism pathway, while the differentially expressed genes in ovarian tissue were enriched in the ovarium steroidogenesis pathway. In conclusion, our results implied that the pituitary-ovary axis might include hepar as downstream targeted organism in heat resistant regulation. Under heat stress, the signals released from pituitary would impact steroidogenesis in ovary, and further alter energy metabolism in hepar. As we know, this is the first comparative study to investigate the gene expression in multi-tissue in sheep under heat stress.

The aim of this study was to investigate the clinical features, distribution and antimicrobial susceptibility of Nocardia species isolated from pulmonary nocardiosis cases in tertiary hospital in China. The species were collected from January 1, 2018 to May 31, 2019 and identified using MALDI-TOF MS or PCR. Antimicrobial susceptibility testing was performed using the broth microdilution method. Within the 44 Nocardia species, N. farcinica was the most frequently identified species (n = 36), followed by N. nova (n = 5), N. otitidiscaviarum (n = 1), N. cyriacigeorgica (n = 1), and N. transvalensis (n = 1). The top three predisposing factors of pulmonary nocardiosis were chronic obstructive pulmonary disease (45.5%), hypertension (34.1%), and tuberculosis (31.8%). All 44 Nocardia strains were susceptible to amikacin, trimethoprim / sulfamethoxazole, and linezolid. The resistance rates of Nocardia to amoxicillin-clavulanic acid, ciprofloxacin, clarithromycin, ceftriaxone, tobramycin, and imipenem were 4.5%, 9.1%, 79.5%, 72.7%, 63.6%, and 38.6%, respectively. Two Nocardia strains had decreased sensitivity to trimethoprim / sulfamethoxazole. In conclusion, N. farcinica was the most frequently isolated Nocardia species in the First Hospital of Changsha. All isolated clinical Nocardia strains showed susceptible to amikacin, trimethoprim / sulfamethoxazole, and linezolid, suggesting that these drugs can be primary therapeutic choices for treating Nocardia infections.

Background Lysine succinylation (Ksu) exists in both eukaryotes and prokaryotes, and influences a variety of metabolism processes. However, little attention has been paid to Ksu in insects, especially the notorious invasive pest Solenopsis invicta. Results In this study, the first analyses of Ksu proteome and overlap between Ksu and lysine acetylation (Kac) in S. invicta were presented. 3753 succinylated sites in 893 succinylated proteins were tested. The dihydrolipoyl dehydrogenase, V-type proton ATPase subunit G, and tubulin alpha chain all had evolutionary conservatism among diverse ant or bee species. Immunoblotting validation showed that there were many Ksu protein bands with a wide range of molecular mass. In addition, 1230 sites in 439 proteins were highly overlapped between Ksu and Kac. 54.05% of Ksu proteins in cytoplasm were acetylated. The results demonstrated that Ksu may play a vital part in the allergization, redox metabolism, sugar, fat, and protein metabolism, energy production, immune response, and biosynthesis of various secondary metabolites. Conclusions Ksu and Kac were two ubiquitous protein post-translational modifications participated in a variety of biological processes. Our results may supply rich resources and a starting point for the molecular basic research of regulation on metabolic pathways and other biological processes by succinylation and acetylation.

Transcription factors (TFs), key regulators for gene expression, play varied yet crucial roles throughout cellular polarization, migration, proliferation, differentiation and apoptosis. An important function of TFs is acting in embryogenesis and organogenesis. To identify the candidate TFs in the progression of lamprey early embryogenesis, datasetGSE76037 was downloaded from the Gene Expression Omnibus (GEO) database and an integrated bioinformatic analysis was performed. Our findings revealed a total of 152 TFs in the dataset. The function enrichment analysis showed that these genes were mainly enriched in transcription from RNA polymerase II promoter, cell differentiation, embryonic digestive tract morphogenesis and so on. Hierarchical clustering analysis suggested the expression of TFs was significantly different during early embryogenesis. Moreover, volcano plots and Venn diagrams analysis identified 36 key TFs, which were considered to play an important role during embryogenesis. The weighted correlation network analysis (WGCNA) was constructed and the Pearson correlation coefficient was performed, indicating these TFs might involve in early development of lamprey germline by synergistically regulating each other. The result was confirmed by real-time polymerase chain reaction and Western blotting analysis. In conclusion, differentially expressed genes identified in the present study help us understand the molecular mechanisms underlying the lamprey embryogenesis and provide candidate TFs for further study of vertebrate embryonic development.

During acute reperfusion, the expression profiles of long noncoding RNAs in adult rats with focal cerebral ischemia undergo broad changes. However, whether long noncoding RNAs are involved in neuroprotective effects following focal ischemic stroke in rats remains unclear. In this study, RNA isolation and library preparation was performed for long noncoding RNA sequencing, followed by determining the coding potential of identified long noncoding RNAs and target gene prediction. Differential expression analysis, long noncoding RNA functional enrichment analysis, and co-expression network analysis were performed comparing ischemic rats with and without ischemic postconditioning rats. Rats were subjected to ischemic postconditioning via the brief and repeated occlusion of the middle cerebral artery or femoral artery. Quantitative real-time reverse transcription-polymerase chain reaction was used to detect the expression levels of differentially expressed long noncoding RNAs after ischemic postconditioning in a rat model of ischemic stroke. The results showed that ischemic postconditioning greatly affected the expression profile of long noncoding RNAs and mRNAs in the brains of rats that underwent ischemic stroke. The predicted target genes of some of the identified long noncoding RNAs (cis targets) were related to the cellular response to ischemia and stress, cytokine signal transduction, inflammation, and apoptosis signal transduction pathways. In addition, 15 significantly differentially expressed long noncoding RNAs were identified in the brains of rats subjected to ischemic postconditioning. Nine candidate long noncoding RNAs that may be related to ischemic postconditioning were identified by a long noncoding RNA expression profile and long noncoding RNA-mRNA co-expression network analysis. Expression levels were verified by quantitative real-time reverse transcription-polymerase chain reaction. These results suggested that the identified long noncoding RNAs may be involved in the neuroprotective effects associated with ischemic postconditioning following ischemic stroke. The experimental animal procedures were approved by the Animal Experiment Ethics Committee of Kunming Medical University (approval No. KMMU2018018) in January 2018.

The conditions for sex reversal in vertebrate species have been extensively studied, and the results highlighted numerous key factors involved in sex differentiation. However, the transcriptomes in hypothalamic and pituitary tissues from intersex goats have rarely been studied. The aim of this study was to screen candidate genes and signalling pathways related to sex reversal in Huai goats by analyzing gene expression in hypothalamic and pituitary tissues via transcriptome sequencing and bioinformatics analyses. In total, 612 and 139 differentially expressed genes (DEGs) were identified between the intersex and non‐intersex groups in the hypothalamus and pituitary, respectively. The DEGs in the hypothalamus and pituitary were significantly enriched in 41 and 16 signalling pathways, respectively, including the calcium signalling pathway, neuroactive ligand‐receptor interaction signalling pathway, and oestrogen signalling pathway, which might be related to intersex sex development disorders. A candidate gene from the tachykinin family (TACR1) was significantly enriched in the calcium signalling pathway. Thirty‐one DEGs were shared between these two comparisons and were enriched in several acetyl‐CoA‐related processes and the oestrogen signalling pathway. The results of the real‐time PCR analysis show that the transcriptome sequencing results were reliable. The transcriptome data indicate that the regulation of various physiological systems is involved in intersex goat development. Therefore, these results provide helpful data enhancing our understanding of the molecular mechanisms underlying intersex syndrome in goats., Our study compared the gene expression profiles of hypothalamus and pituitary tissues from intersex and normal goats. And 31 genes were shared between these two sets of comparisons. These genes were enriched in the oestrogen signalling pathway and acetyl‐CoA biosynthetic process, suggesting that they might exhibit important functions in the regulation of hormone biosynthesis related to gonad development.

8-methylene-tert-butylamine-3',5,7-trihydroxy-4'-methoxyflavanone (MTBH), a novel hesperidin derivative, has potential in the prevention of hepatic disease, however, its effects on cytochrome P450 isoforms (P450s) remains unexplored. The purpose was to investigate the effects of MTBH on the mRNA, protein levels and activities of six P450s (1A2, 2C11/9, 2D2/6, 3A1/4, 2C13/19 and 2E1) in vitro and in vivo.In vitro study, rat and human liver microsomes were adopted to elucidate the inhibitory effect of MTBH on six P450s using probe drugs. In vivo study, Sprague-Dawley male rats were treated with MTBH (25, 50 or 100 mg/kg for 28 consecutive days), phenobarbital (80 mg/kg for 12 consecutive days) or 0.5% CMC-Na solution (control group) by intragastric administration, then, the mRNA, protein levels and activities of liver P450s were analyzed by real-time PCR, western blotting and probe-drug incubation systems, respectively.The in vitro study indicated that MTBH inhibits the activities of CYP3A1/4 and CYP2E1 in rat and human liver microsomes. In vivo data showed that MTBH inhibits mRNA, protein levels and activities of CYP3A1 and CYP2E1 in medium- and high-dose MTBH groups.MTBH has the potential to cause drug-drug interactions when co-administered with drugs that are metabolized by CYP3A1/4 and CYP2E1.

The present study aimed to investigate whether inflammation-associated responses in piglets are induced by high protein (HP) through activating nuclear factor kappa B (NF-κB) signaling. Sixteen piglets (35 d of age, Duroc × [Landrace × Yorkshire], weaned at d 21, initial BW = 9.70 ± 0.11 kg) were allocated to 18% and 26% CP (HP group) at random, comprising 8 replicate pens per treatment. The piglets were slaughtered to collect intestinal tissues when apparent, persistent, and stable diarrhea syndromes happened (on d 12). No significant differences were observed in their growth performance (P > 0.05), but reduction by 19.11%, 25.31%, 23.64% of ADFI, ADG, and G:F, respectively was detected in the HP group. The HP group had greater (P = 0.002) diarrhea rates. Furthermore, dietary HP had lower ileal villus height (VH; P = 0.048), ratio of villus height to crypt depth (VH/CD ratio; P = 0.016), and colonic CD (P = 0.034), as well as had the trend (P = 0.075) to reduce the ileal villus absorptive area. Moreover, HP diets significantly elevated the goblet cell numbers in the ileal villi (P = 0.016) and colonic crypts (P

A growing body of evidence suggests the pivotal role of long non-coding RNA (lncRNA) in influenza virus infection. Based on next-generation sequencing, we previously demonstrated that Lnc45 was distinctively stimulated by H5N1 influenza virus in mice. In this study, we systematically investigated the specific role of Lnc45 during influenza A virus (IAV) infection. Through qRT-PCR, we first demonstrated that Lnc45 is highly up-regulated by different subtypes of IAV strains, including H5N1, H7N9, and H1N1 viruses. Using RNA-FISH and qRT-PCR, we then found that Lnc45 can translocate from nuclear to cytoplasm during H5N1 virus infection. In addition, forced Lnc45 expression dramatically impeded viral replication of H1N1, H5N1, and H7N9 virus, while abolish of Lnc45 expression by RNA interference favored replication of these viruses, highlighting the potential broad antiviral activity of Lnc45 to IAV. Correspondingly, overexpression of Lnc45 inhibited viral polymerase activity and suppressed IAV-induced cell apoptosis. Moreover, Lnc45 significantly restrained nuclear aggregation of viral NP and PA proteins during H5N1 virus infection. Further functional study revealed that the stem ring arms of Lnc45 mainly mediated the antiviral effect. Therefore, we here demonstrated that Lnc45 functions as a broad-spectrum antiviral factor to inhibit influenza virus replication probably through inhibiting polymerase activity and NP and PA nuclear accumulation via its stem ring arms. Our study not only advances our understanding of the complexity of the IAV pathogenesis but also lays the foundation for developing novel anti-IAV therapeutics targeting the host lncRNA.

Objectives Stenotrophomonas maltophilia MER1, a multidrug resistant (MDR) bacterium was isolated from the wastewater from a hospital, Shandong province, China. We attempted to reveal the genetic determinants related to its striking MDR features for effective treatment to S. maltophilia. Methods Antibiotic susceptibility testing of strain MER1 was performed by using the disk diffusion method on the Mueller-Hinton agar plates, and the minimum inhibitory concentrations (MICs) were determined according to the Clinical Laboratory Standard Institute protocols. The genome of MER1 was sequenced and assembled with a PacBio RS II and a BGISEQ-500 platform. Antibiotic resistance agents together with other transferability or adaptability determinants were identified by comparative genomics. Phylogenetic and contextual assays for these identified elements were conducted to assess the spread risk of MER1. Results Susceptibility testing reveals that strain MER1 is strikingly resistant to nine different antibiotics, including ampicillin, meropenem, amikacin, erythromycin, vancomycin, tetracycline, tigecycline, polymyxin E and ceftazidime. Several genes were identified to encode efflux pumps and inactivation agents accounting for MER1 resistance to above antibiotics, including meropenem, tigecycline and colistin regarded as the last-line therapy for infections caused by multidrug-resistant Gram-negative bacteria. MER1 co-harbors two non-mobile mcr homologs. A novel genomic region of variability was demonstrated to confer bacterial robustness and adaptability upon strain MER1. Conclusion Collective efforts revealed the multiple drug resistance properties and potential genetic determinants of S. maltophilia MER1 isolated from the hospital sewage. Comparative genomic analysis of S. maltophilia MER1 may provide insights into prevention and treatment of its antimicrobial resistance. Our findings would prompt public concern that the MDR genes in the reservoir of S. maltophilia may further spread into various ecological niches or medically high-risk pathogens.

Three undescribed dammarane-type triterpenoids with rare carbon skeletons (1-3), together with one unreported gypenoside (4), were isolated from a acid hydrolysis product of Gynostemma pentaphyllum (Thunb.) Makino. Their molecular structures were elucidated via a combination of spectroscopic and spectrometric data, while the absolute configurations of compounds 1, 2 and 4 were determined by electronic circular dichroism (ECD) analyse. Notably, compounds 1-3 possess a 19(10→1)abeo structural moiety in the A ring. Saponin 4 possesses an unusual cyclopentenone side chain. Compounds 1, 2 and 4 were screened for their antiproliferative effects against HepG2, MCF-7 and DU145 cell lines.

Background Recent years, multi drug resistant pathogens and their pathogenicity were increased worldwide due to unauthorized consumption of antibiotics. In addition, correlation between multi drug resistant bacteria and biofilm formation is heightened due to the production of more virulence behavior. There is no better identification methods are available for detection of biofilm producing gram negative bacteria. Materials and methods In this research work, multi drug resistant strains of Pseudomonas aeruginosa (P. aeruginosa) and Klebsiella pneumoniae (K. pneumoniae) were identified based on the specific antibiotics and third generation cephalosporin discs by disc diffusion assay. Subsequently, biofilm forming ability of selected pathogens were identified tissue culture plate and tube test. Based on the multi-drug resistant ability and biofilm production, the molecular identification of P. aeruginosa and K. pneumoniae were confirmed by PCR using universal primers. Results and conclusions No zone of inhibition present around the discs of muller hinton agar plates were confirm, selected P. aeruginosa and K. pneumoniae strains were multi drug resistant pathogens. Performed third generation cephalosporin antibiotics were also highly sensitive to selected pathogens of P. aeruginosa and K. pneumoniae. Further, biofilm forming ability of selected P. aeruginosa and K. pneumoniae was confirmed by tissue culture plate and tube methods. Finally, molecular identification of P. aeruginosa and K. pneumoniae was named as P. aeruginosa and K. pneumoniae. Our result was conclude, selected P. aeruginosa and K. pneumoniae as biofilm producing pathogens and also highly resistant to current antibiotics.

OBJECTIVES: The genus Pseudomonas comprised of Gram-negative strains with a variety of prospective industrial applications plus a growing pathogen that reported to produce nosocomial infections worldwide. The current study describes the first draft genome sequence analysis of a CRISPR-carrying, multidrug resistant, candidate novel Pseudomonas sp. NCCP-436T that was isolated from fecal sample of a neonatal calf and endowed with zoonotic potential. METHODS: 16S rRNA gene was used to identify Pseudomonas strain NCCP-436T. The disk diffusion technique was applied to assess antimicrobial susceptibility as per the Clinical and Laboratory Standards Institute (CLSI) recommendations (M100). The genome of strain NCCP-436T was sequenced using an Illumina NovaSeq PE150 platform and analyzed using various bioinformatic tools. The virulence factors and resistome were identified using the Pathosystems Resource Integration Center (PATRIC) and Comprehensive Antibiotic Resistance Database (CARD) servers, while the CGView Server was used to set up a circular map of the strain NCCP-436T genome. RESULTS: The draft genome of Pseudomonas strain NCCP-436T contained 43 contigs with a total genome size of 3,683,517 bp (61.4% GC content). There were 3,452 predicted genes, including 60 tRNA, 7 rRNA (five copies of 5S and single copies each of 16S and 23S) and 12 sRNA, as well as three genomic islands. CRISPR analyses revealed two CRISPR arrays with lengths of 1103 and 867 bp on the positive strand of scaffold 1, while functional annotation demonstrated the absence of prophage-related genes. Repetitive DNA analysis confirmed the existence of 57 tandemly repetitive DNA sequences, while minisatellite DNA and microsatellite DNA were located in numbers of 41 and 5, respectively. A total of 72 genes that encode the carbohydrate active enzymes were identified, whereas determination of secondary metabolites revealed 65 secondary metabolites genes distributed on 2 gene clusters i.e., non-ribosomal peptide synthetase cluster (NRPS) and s-lactone cluster. Antibiotic susceptibility showed that strain NCCP-436T was highly resistant to fluoroquinolones, beta lactams, cephalosporins, aminoglycosides, penicillins, rifamycins, macrolides, glycopeptides and trimethoprim-sulfonamide antibiotic classes. Additionally, 22 antibiotic resistance genes (ARGs), 313 virulence genes and 253 pathogen-host interactor genes were predicted in Pseudomonas sp. NCCP-436T genome. The comparison of average nucleotide identity (ANI) and digital DNA-DNA hybridization (digi-DDH) values with the closely related strain Pseudomonas khazarica (TBZ2) was found to be 82.08 and 34.90 %, respectively. These findings depict that strain NCCP-436T could potentially be a new species of Pseudomonas genus. CONCLUSION: In conclusion, the draft genome of a candidate novel strain of Pseudomonas sp. NCCP-436T was successfully sequenced and assembled. Substantial numbers of antibiotic resistance and virulence genes and homology to human pathogens were predicted, exposing its pathogenic and zoonotic ability to public health. All of these data could be used to conduct more research into multidrug resistance mechanisms, leading to a better understanding of the genomic epidemiological features and drug resistance mechanisms of pathogenic Pseudomonas species in Pakistan.

Puberty is the gateway to adult reproductive competence, encompassing a suite of complex, integrative, and coordinated changes in neuroendocrine functions. However, the regulatory mechanisms of transcriptional reprogramming in the arcuate nucleus (ARC) during onset of puberty are still not fully understood. To understand the role of epigenetics in regulating gene expression, mouse hypothalamic ARCs were isolated at 4 and 8 weeks, and the transcriptome, DNA hydroxymethylation, DNA methylation, and chromatin accessibility were assessed via RNA sequencing (RNA-seq), reduced representation bisulfite sequencing (RRBS-seq), reduced representation hydroxymethylation profiling (RRHP)-seq, and assay for transposase-accessible chromatin (ATAC-seq), respectively. The overall DNA hydroxymethylation and DNA methylation changes in retroelements (REs) were associated with gene expression modeling for puberty in the ARC. We focused on analyzing DNA hydroxymethylation and DNA methylation at two short interspersed nuclear elements (SINEs) located on the promoter of the 5-hydroxytryptamine receptor 6 (Htr6) gene and the enhancer of the KISS-1 metastasis suppressor (Kiss1) gene and investigated their regulatory roles in gene expression. Our data uncovered a novel epigenetic mechanism by which SINEs regulate gene expression during puberty., Graphical abstract, Shen et al. summarize genome-wide DNA (hydroxy)methylation of retroelements in the mouse arcuate nucleus and report novel epigenetic mechanisms of short interspersed nuclear elements for regulating gene expression across pubertal development.

Duplex polymerase chain reaction with lateral flow dipsticks (duplex PCR-LFD) was developed for the simultaneous detection of beta-lactamase Klebsiella pneumoniae carbapenemase (blaKPC ) and beta-lactamase New Dehli metallo-beta-lactamase (blaNDM ) genes in body fluid samples. This method was validated using well-characterized isolates. The assessment of the specificity of duplex PCR-LFD showed that there was no cross-reactivity with other targets. The detection limit of the duplex PCR-LFD assay was 20 CFU per ml for blaKPC and blaNDM . Among 177 sterile body fluid samples tested by the duplex PCR-LFD assay, 40 were blaKPC -positive and five were blaNDM -positive. The results obtained from 122 corresponding Gram-negative bacteria which were isolated from these clinical samples and tested by duplex PCR-LFD assay showed that there were 37 strains carrying blaKPC genes in 40 blaKPC -positive samples and three strains carrying blaNDM genes in five blaNDM -positive samples. Statistical analysis indicated that there was no significant difference between the direct detection of blaKPC and blaNDM genes in clinical sterile body fluid samples and their corresponding clinical isolates. Therefore, duplex PCR-LFD can be effective for the simultaneous detection of blaKPC and blaNDM in clinical isolates and directly from clinical samples, which may be helpful for the administration of appropriate antimicrobial treatment.

Primulina silaniae X.X.Bai & F.Wen, a new species of Primulina Hance (Gesneriaceae) from the limestone area of Wangmo County, Guizhou Province, is described and illustrated. The new species is similar to P. spiradiclioides Z.B.Xin & F.Wen, but can be easily distinguished from the latter by a combination of characteristics, especially in the lateral veins of its leaf and floral shape and tube. At present, three populations in one locality of this new taxon were found, totaling about 600 mature individuals. According to the IUCN Red List Categories and Criteria (Version 3.1), the species is provisionally assessed as Vulnerable [VU D1].

Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections.

There is a growing appreciation that synonymous codon usage, although historically regarded as phenotypically silent, can instead alter a wide range of mechanisms related to functional protein production, a term we use here to describe the net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure. In particular, recent discoveries have highlighted the important role that sub-optimal codons can play in modifying co-translational protein folding. These results have drawn increased attention to the patterns of synonymous codon usage within coding sequences, particularly in light of the discovery that these patterns can be conserved across evolution for homologous proteins. Because synonymous codon usage differs between organisms, for heterologous gene expression it can be desirable to make synonymous codon substitutions to match the codon usage pattern from the original organism in the heterologous expression host. Here we present CHARMING (for Codon HARMonizING), a robust and versatile algorithm to design mRNA sequences for heterologous gene expression and other related codon harmonization tasks. CHARMING can be run as a downloadable Python script or via a web portal at http://www.codons.org. This article is protected by copyright. All rights reserved.

Two novel species of the genus Deinococcus, designated SYSU M49105T and SYSU M42101T, were isolated from freshwater samples of the Pearl River estuary in Guangdong, China. Phylogenetic analysis using 16S rRNA gene sequence indicated that strains SYSU M49105T and SYSU M42101T showed the highest sequence similarities to Deinococcus aetherius JCM 11751 T (93.6%) and Deinococcus multiflagellatus NBRC 112888 T (97.3%), respectively. Cells of both strains were Gram-staining positive, aerobic, coccus-shaped, oxidase-negative and non-motile. The cell wall contained meso-diaminopimelic acid as their diagnostic diamino acid. MK-8 was the predominant respiratory quinone for both strains. The polar lipid profile of SYSU M49105T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, and five unidentified polar lipids. SYSU M42101T had one unidentified phosphoglycolipid, nine unidentified glycolipids, one unidentified aminophospholipid and four unidentified polar lipids. The major fatty acids of strains SYSU M49105T and SYSU M42101T were summed feature 3 (C16:1 ω7c and/ or C16:1 ω6c) and C16:0. The G + C contents of the novel isolates based on genomic DNAs were 69.6% and 67.4%, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU M49105T and SYSU M42101T should be considered to represent two novel species in the genus Deinococcus, for which the names Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov. were proposed with the type strains SYSU M49105T (= KCTC 43258 T = CGMCC 1.18609 T) and SYSU M42101T (= KCTC 43257 T = CGMCC 1.18614 T), respectively.

OBJECTIVE To investigate a previously uncharacterized function of Sijunzi Decoction (SJZD) in inhibition of gastric cancer stem cells (GCSCs). METHODS MKN74 and MKN45, two CD44 positive gastric cancer cell lines with stem cell properties were used. The cells were divided into 2 groups. Treatment group was treated with SJZD (1-5 mg/mL) for indicated time (48 h-14 days). The control group was treated with equal volume of phosphate buffered saline. Cell Counting Assay Kit-8 were used to measure cell viability. Spheroid colony formation and GCSCs marker expression were performed to determine GCSCs stemness. Cell fractionation and chromatin immunoprecipitation assays were used to assess the distribution and DNA-binding activity of β-catenin after SJZD treatment, respectively. RESULTS SJZD treatment repressed cell growth and induced apoptosis in MKN74 and MKN45 cell lines (P

Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC., Small-cell lung cancer (SCLC) is an aggressive disease with limited therapeutic options. Here the authors perform an immunogenomic analysis of limited-stage SCLC, revealing a homogeneous mutational landscape, but limited T-cell infiltration and a cold and heterogeneous T cell repertoire.

Interferon regulatory factor 3 (IRF3) is activated by IκB kinase ε (IKKε) and Tank-binding kinase 1 (TBK1), which plays a crucial role in the interferon signaling in vertebrates. However, the regulation of teleost IRF3 by IKKε remains largely unknown. In this study, the IRF3 homologue (bcIRF3) of black carp (Mylopharyngodon piceus) has been cloned and characterized. The transcription of bcIRF3 was detected to increase in host cells in response to different stimuli. bcIRF3 distributed predominantly in the cytosolic area; however, translocated into nuclei after virus infection. bcIRF3 showed IFN-inducing ability in reporter assay and EPC cells expressing bcIRF3 showed enhanced antiviral ability against both grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV). Moreover, knockdown of bcIRF3 reduced the antiviral ability of the host cells, and the transcription of antiviral-related cytokines was obviously lower in bcIRF3-deficient host cells than that of control cells. The data of reporter assay and plaque assay demonstrated that bcIKKε obviously enhanced bcIRF3-mediated IFN production and antiviral activity. Immunofluorescent staining and co-immunoprecipitation assay revealed that bcIKKε interacted with bcIRF3. It was interesting that the nuclear translocation of bcIRF3 and bcIKKε was enhanced by each other when these two molecules were co-expressed in the cells, however, the protein levels of bcIRF3 and bcIKKε were decreased mutually. Thus, our data support the conclusion that bcIKKε interacts with bcIRF3 and enhances bcIRF3-mediated antiviral signaling during host innate immune activation.

Alternaria alternata is a critical plant pathogen, and the black spot caused by this fungus is the main cause of crop loss. In this study, four monoterpenes commonly found in plant essential oils, β-lonone, citral, γ-terpinene and myrcene, were found to possess a two-way interaction relationship with A. alternata. Four monoterpenes exhibited moderate inhibitory activities against A. alternata with MIC values of 128, 256, 512 and 256 μg/mL, respectively. However, when the concentration of monoterpenes in the culture medium was reduced to 1/4 MIC, A. alternata could facilitate the biotransformation of the aforementioned four monoterpenes by hydroxylation, dihydroxylation or carboxylation. These biotransformations were verified to be promoted by the P450 enzyme. Considering that none of the converted products showed inhibitory activity against A. alternata, these transformations were hypothesized to be self-protective mechanism of A. alternata. Expectedly, the combined use of P450 enzyme inhibitors and monoterpenes exhibited stronger antifungal activities, and could significantly inhibited black spot development in tomatoes. This work provides a reference for the development of effective antifungal agents.

Ganodermataceae was introduced by Donk (1948) which belongs to Polyporales and the latest studies indicated that it is a monophyletic group (Costa-Rezende et al. 2020). Currently, eleven genera viz. Amauroderma Murril, Amaurodermellus Costa-Rezende, Cristataspora Costa-Rezende, Foraminispora Robledo, Costa-Rezende & Drechsler-Santos, Furtadoa Costa-Rezende, Robledo & Drechsler-Santos, Ganoderma P. Karst., Haddowia Steyaert, Humphreya Steyaert, Magoderna (Murrill) Steyaert, Sanguinoderma Y.F. Sun, D.H. Costa & B.K. Cui and Tomophagus Murrill are accepted in Ganodermataceae and supported by morphology and phylogeny (Steyaert 1972; Furtado 1981; C orner 1983; Zhao and Zhang 2000; Ryvarden 2004; Thametal 2012; Costa-Rezende et al. 2017; Costa-Rezende et al. 2020; Sun et al. 2020). Ganoderma P. Karst (Ganodermataceae, Polyporales) was introduced to accommodate a laccate and stipitate fungus, Ganodermalucidum (Curtis) P. Karst (Karsten 1881). Ganoderma is characterized by double-walled basidiospores with inter-wall protuberances (Karsten 1881; Moncalvo and Ryvarden 1997). There are 462 records in the Index Fungorum (http://www.Indexfungorum.org/; accessed date: 7 October 2021) and 506 records in MycoBank (http://www.mycobank.org/; accessed date: 7 October 2021). Ganoderma is one of the most taxonomically scrutinized genera among the Ganodermataceae and even in Polyporales (Richter et al. 2015; Costa-Rezende et al. 2020). Most Ganoderma species are wood decomposers, found in all temperate and tropical regions (Pilotti et al. 2004; Cao et al. 2012; Zhou et al. 2015). Ganoderma has long been regarded as one of the most important medicinal fungi in the world (Paterson 2006); they have been used as medicine for over two millennia in China (Dai et al. 2009). Several Ganoderma species are known to be prolific sources of highly active bioactive compounds, especially polysaccharides, protein, sterols, and triterpenoids (Ahmadi and Riazipour 2007; Chan et al. 2007). These compounds are known to possess extensive therapeutic properties, such as antioxidant, antitumor, and antiviral agents, and improve sleep function (De Silva et al. 2013). Species diversity of Ganoderma is abundant in China and more than 30 species have been described (Zhao and Zhang 2000; Wang et al. 2009; Cao et al. 2012; Li et al. 2015; Xing et al. 2016; Hapuarachchi et al. 2018; Liu et al. 2019; He et al. 2019; Wu et al. 2020). Yunnan province is considered as one of the hot-spots for studying biodiversity of polypores, and some new Ganoderma species have been described (Zhao 1989; Wang et Wu 2010; Cao and Yuan 2013). During our investigation into the diversity of Ganoderma in Yunnan province, several specimens of Ganoderma were collected from central and southern Yunnan. Phylogenetic analysis showed that the seven collections formed two distinct lineages and can be recognized as new species, hence two new species, namely G.dianzhongense and G.esculentum are introduced based on morphology and phylogeny.

Male infertility may be caused by genetic and/or environmental factors that impair spermatogenesis and sperm maturation. High-altitude (HA) hypoxic environments represent one of the most serious challenges faced by humans that reside in these areas. To assess the influence of the plateau environment on semen parameters, 2,798 males, including 1,111 native Tibetans and 1,687 Han Chinese individuals living in the plains (HCILP) who underwent pre-pregnancy checkups, were enrolled in this study. The semen samples of males were evaluated to determine conventional sperm parameters, sperm morphology, and sperm movement. Reproductive endocrine hormones (REHs) were detected in 474 males, including 221 Tibetans and 253 HCILP. Due to recurrent abortions in partners, the DNA fragmentation index (DFI) of 133 native Tibetans and 393 HCILP individuals was further compared. Luteinizing hormone (LH) (4.94 ± 2.12 vs. 3.29 ± 1.43 U/L), prolactin (11.34 ± 3.87 vs. 8.97 ± 3.48 nmol/L), E2/T (0.22 ± 0.11 vs 0.11 ± 0.05), median total sperm motility (61.20% vs. 51.56%), and DFI (23.11% vs. 7.22%) were higher in males from plateau areas while median progressive motility (PR) (35.60% vs. 41.12%), total number of PR sperms (51.61 vs. 59.63 mil/ejaculate), percentage of normal form sperms (3.70% vs. 6.00%), curvilinear velocity (36.10 vs. 48.97 μm/s), straight-line (rectilinear) velocity (14.70 vs. 31.52 μm/s), estradiol (103.82 ± 45.92 vs. 146.01 ± 39.73 pmol/L), progesterone (0.29 ± 0.27 vs. 2.22 ± 0.84 nmol/L), testosterone (4.90 ± 1.96 vs. 14.36 ± 5.24 nmol/L), and testosterone secretion index (ratio of testosterone to LH) (33.45 ± 22.86 vs 145.78 ± 73.41) were lower than those in males from the plains. There was no difference in median total sperm number (157.76 vs. 151.65 mil/mL), sperm concentration (52.40 vs. 51.79 mil/mL), volume (3.10 vs. 3.10 mL), total normal form sperms (5.91 vs. 6.58 mil/ejaculate, p50), and follicle-stimulating hormone (FSH) levels (4.13 ± 2.55 U/L vs 3.82 ± 2.35 U/L) between the two groups of males. The REH and sperm parameters of males from HA hypoxic environments were adaptively altered. Although the total number of PR sperm decreased and DFI increased, the Tibetan population that lives at HAs has been found to grown continuously and rapidly. These results supplement prior findings regarding the impact of HA on male reproductive function.

The development of transcriptome-wide association studies (TWAS) has enabled researchers to better identify and interpret causal genes in many diseases. However, there are currently no resources providing a comprehensive listing of gene-disease associations discovered by TWAS from published GWAS summary statistics. TWAS analyses are also difficult to conduct due to the complexity of TWAS software pipelines. To address these issues, we introduce a new resource called webTWAS, which integrates a database of the most comprehensive disease GWAS datasets currently available with credible sets of potential causal genes identified by multiple TWAS software packages. Specifically, a total of 235 064 gene-diseases associations for a wide range of human diseases are prioritized from 1298 high-quality downloadable European GWAS summary statistics. Associations are calculated with seven different statistical models based on three popular and representative TWAS software packages. Users can explore associations at the gene or disease level, and easily search for related studies or diseases using the MeSH disease tree. Since the effects of diseases are highly tissue-specific, webTWAS applies tissue-specific enrichment analysis to identify significant tissues. A user-friendly web server is also available to run custom TWAS analyses on user-provided GWAS summary statistics data. webTWAS is freely available at http://www.webtwas.net.

Postoperative cognitive dysfunction (POCD) affects the outcome of millions of patients each year. Aging is a risk factor for POCD. Here, we showed that surgery induced learning and memory dysfunction in adult mice. Transplantation of feces from surgery mice but not from control mice led to learning and memory impairment in non-surgery mice. Low intensity exercise improved learning and memory in surgery mice. Exercise attenuated surgery-induced neuroinflammation and decrease of gut microbiota diversity. These exercise effects were present in non-exercise mice receiving feces from exercise mice. Exercise reduced valeric acid, a gut microbiota product, in the blood. Valeric acid worsened neuroinflammation, learning and memory in exercise mice with surgery. The downstream effects of exercise included attenuating growth factor decrease, maintaining astrocytes in the A2 phenotypical form possibly via decreasing C3 signaling and improving neuroplasticity. Similar to these results from adult mice, exercise attenuated learning and memory impairment in old mice with surgery. Old mice receiving feces from old exercise mice had better learning and memory than those receiving control old mouse feces. Surgery increased blood valeric acid. Valeric acid blocked exercise effects on learning and memory in old surgery mice. Exercise stabilized gut microbiota, reduced neuroinflammation, attenuated growth factor decrease and preserved neuroplasticity in old mice with surgery. These results provide direct evidence that gut microbiota alteration contributes to POCD development. Valeric acid is a mediator for this effect and a potential target for brain health. Low intensity exercise stabilizes gut microbiota in the presence of insult, such as surgery.

Six major QTLs for wheat grain size and weight were identified on chromosomes 4A, 4B, 5A and 6A across multiple environments, and were validated in different genetic backgrounds. Grain size and weight are crucial components of wheat yield. Dissection of their genetic control is thus essential for the improvement of yield potential in wheat breeding. We used a doubled haploid (DH) population to detect quantitative trait loci (QTLs) for grain width (GW), grain length (GL), and thousand grain weight (TGW) in five environments. Six major QTLs, QGw.cib-4B.2, QGl.cib-4A, QGl.cib-5A.1, QGl.cib-6A, QTgw.cib-4B, and QTgw.cib-5A, were consistently identified in at least three individual environments and in best linear unbiased prediction (BLUP) datasets, and explained 5.65–34.06% of phenotypic variation. QGw.cib-4B.2, QTgw.cib-4B, QGl.cib-5A.1 and QGl.cib-6A had no effect on grain number per spike (GNS). In addition to QGl.cib-4A, the other major QTLs were further validated by using Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. Moreover, significant interactions between the three major GL QTLs and two major TGW QTLs were observed. Comparison analysis showed that QGl.cib-5A.1 and QGl.cib-6A are likely new loci. Notably, QGw.cib-4B.2 and QTgw.cib-4B were co-located on chromosome 4B and improved TGW by increasing only GW, unlike nearby or overlapped loci reported previously. Three genes associated with grain development within the QGw.cib-4B.2/QTgw.cib-4B interval were identified by searches on sequence similarity, spatial expression patterns, and orthologs. The major QTLs and KASP markers reported here will be useful for elucidating the genetic architecture of grain size and weight and for developing new wheat cultivars with high and stable yield.

T7 expression system (T7 RNA polymerase / T7 promoter), derived from T7 bacteriophage, is one of the most extensively used protein expression systems, which is also an enabling tool in synthetic biology. However, in eukaryote, most of T7 expression system is transient expression system. This is mainly due to the absence of post-transcriptional processing of mRNAs transcribed by T7RNAP in eukaryotic cells, so they cannot effectively pass through nuclear membrane and enter cytoplasm. In this study, Saccharomyces cerevisiae was selected as host to construct stable T7 expression system, in which HIV-1 viroporin (Vpu) was used to improve the permeability of nuclear membrane. Results of NanoLuc® (Nluc) luciferase expression indicated that Vpu could effectively promote the transport of T7 transcripts and increase the amount of protein synthesized. The method of using viroporin to improve permeability of the nuclear membrane provides an effective tool for constructing a stable T7 expression system in eukaryote. Supplementary Information The online version contains supplementary material available at 10.1007/s12010-021-03665-y.

This study aims to explore the potential mechanisms of Xinnaokang in atherosclerosis treatment. Firstly, the active components of Xinnaokang were analysed by HPLC, which contains ginsenoside Rg1, puerarin, tanshinone, notoginsenoside R1, ammonium glycyrrhizate and glycyrrhizin. Network pharmacology analysis showed there were 145 common targets of Xinnaokang, including the chemical stress, lipid metabolite, lipopolysaccharide, molecules of bacterial origin, nuclear receptor and fluid shear stress pathways. Then, the animal experiment showed that Xinnaokang reduced the body weight and blood lipid levels of atherosclerotic mice. Vascular plaque formation was increased in atherosclerotic mice, which was markedly reversed by Xinnaokang. In addition, Xinnaokang reduced CAV-1 expression and increased ABCA1, SREBP-1 and LXR expressions in the vasculature. Xinnaokang promoted SREBP-2 and LDLR expressions in the liver but decreased IDOL and PCSK9 expressions, indicating that Xinnaokang regulated lipid transport-related protein expression. Cecal microbiota diversity was reduced in atherosclerotic mice but increased after Xinnaokang treatment. Xinnaokang treatment also improved gut microbiota communities by enriching Actinobacteria, Bifidobacteriales and Bifidobacteriaceae abundances. Metabolic profile showed that Xinnaokang significantly reduced homogentisate, phenylacetylglycine, alanine and methionine expressions in the liver of atherosclerotic mice. Xinnaokang effectively alleviated atherosclerosis, and this effect might be linked with the altered features of the liver metabolite profiles and cecal microbiota.

Three Gram-staining negative, facultatively anaerobic, rod-shaped and motile strains, FJAT-51800T, FJAT-52962T and FJAT-54481T were isolated from the sediment samples of Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequencing results indicated they could be novel members of the genus Shewanella. The optimum temperature for growth was 30 °C. The respiratory quinones of the strains were ubiquinone Q-7 or Q-8, and menaquinone MK-7. Polar lipids of the strains FJAT-52962T and FJAT-51800T were phosphatidyl glycerol, phosphatidyl ethanolamine, and unidentified aminophospholipids while strain FJAT-54481 consist of phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipids, two unidentified aminolipids and four unidentified lipids. The major fatty acid of the three strains was iso-C15:0. The genomic DNA G + C contents of strains FJAT-51800T, FJAT-52962T and FJAT-54481T were 48.2, 55.3 and 48.1%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strains FJAT-51800T, FJAT-52962T and FJAT-54481T and other closely related Shewanella members were below the cut-off level (95–96%) for species identification. Genome analysis showed that these strains encode genes for osmo-regulation. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains FJAT-51800T, FJAT-52962T and FJAT-54481T represent three novel species of the genus Shewanella, for which the names Shewanella avicenniae sp. nov., Shewanella sedimentimangrovi sp. nov., and Shewanella yunxiaonensis sp. nov., are proposed. The type strains are FJAT-51800T (= GDMCC 1.2204T = KCTC 82448T), FJAT-52962T (= MCCC 1K05496T = KCTC 82445T) and FJAT-54481T (= GDMCC 1.2348T = KCTC 82646T).

This study aims to investigate the utilization status of nitrogen (N), potassium (K) and phosphorus (P) fertilizers at molecular level in field conditions. Maize cultivar Luyu 16 was planted in 41-year-old plots treated with different fertilizer combinations: unfertilized (control), N fertilizer (N), N fertilizer with P (NP), N fertilizer with K (NK), and N fertilizer with P and K (NPK). The ear leaves at grain filling stage were harvested for transcriptome analysis using RNA-Seq techniques. Results showed that NPK enhanced the contents of chlorophyll, soluble sugar, and protein, and improved the activities of antioxidant enzymes but reduced malondialdehyde (MDA) content much, relative to other treatments. There were 1258, 4438, 5177, and 4505 differentially expressed genes (DEGs) identified from the paired comparisons of NvsCK, NKvsCK, NPvsCK and NPKvsCK, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DEGs identified from different paired comparisons but involved in the same biological or metabolic process were having significant differences in numbers, transcript levels, and expression pattern. Many promising genes related to absorption, transport, and metabolism of N, P and K were identified. The combination of N together with K and/or P fertilizers induced more differential genes than sole N fertilizer application. This study would deepen our understanding of macronutrient utilization efficiency in crops.

Objectives Osseointegration of oral implants has a low success rate in patients with type 2 diabetes. This is because of the inhibition of osteogenic differentiation in the jawbone marrow mesenchymal stem cells, in which the expression of microRNA(miR)-491-5p is significantly downregulated, as ascertained through gene chip screening. However, the underlying mechanisms are unclear. Here, we aimed to clarify the mechanisms involved in the influence of miR-491-5p on osteogenic differentiation. Subjects and methods Jawbone marrow mesenchymal stem cells were isolated from jawbones of patients with type 2 diabetes and subjected to bioinformatics and functional analyses. Osteogenesis experiments were conducted using the isolated cells and an in vivo model. Results Knockdown and overexpression experiments revealed the positive effects of miR-491-5p expression on osteogenic differentiation in vivo and in vitro. Additionally, a dual-luciferase assay revealed that miR-491-5p targeted the SMAD/RUNX2 pathway by inhibiting the expression of epidermal growth factor receptor. Conclusions miR-491-5p is vital in osteogenic differentiation of jawbone mesenchymal stem cells; its downregulation in type 2 diabetes could be a major cause of decreased osteogenic differentiation. Regulation of miR-491-5p expression could improve osteogenic differentiation of jawbone mesenchymal stem cells in patients with type 2 diabetes.

Objective To determine the potent and broad neutralizing monoclonal antibody (mAb) against enterovirus A (EV-A) in vitro and in vivo induced by enterovirus A71(EVA71) and coxsackievirus 16 (CVA16) co-immunization. Methods The mAb was Generated by co-immunization with EVA71 and CVA16 through hybridomas technology. The characteristics and neutralizing ability of mAb were analysed in vitro and in mice. Results We screened three mAb, the IgM antibody M20 and IgG antibody B1 and C31. All three antibodies showed cross-reactivity against tetra-EV-As. However, M20 showed potent and broad neutralizing ability against tetra-EV-As than B1 and C31. Meanwhile, M20 provided cross-antiviral efficacy in tetra-EV-As orally infected mice. Moreover, M20 binds to a conserved neutralizing epitope within the GH loop of tetra-EV-As VP1. Conclusions M20 and its property exhibited potent and broad antiviral activity against tetra-EV-As, and that is expected to be a potential preventive and therapeutic candidate against EV-As.

BACKGROUND Recent studies demonstrate that fish byproducts can be used as sources of bioactive peptides for functional foods. Sturgeon skin contains abundant proteins but it has commonly been discarded during sturgeon processing. The objective of the present work was to identify and characterize the bioactive peptides from protein hydrolysates of sturgeon skin. RESULTS Sturgeon skin protein extract (SKPE) hydrolyzed by flavourzyme for 60 min exhibited high antioxidant activity, dipeptidyl peptidase IV (DPP-IV) and angiotensin converting enzyme (ACE) inhibitory activity. The sequences of peptides from flavourzyme hydrolysates were identified using high-performance liquid chromatography-tandem mass spectrometry. Gly-Asp-Arg-Gly-Glu-Ser-Gly-Pro-Ala (P1) showed the highest DPPH radical scavenging activity (DPPH IC50 = 1.93 mmol L-1 ). Gly-Pro-Ala-Gly-Glu-Arg-Gly-Glu-Gly-Gly-Pro-Arg (P11) (DPP-IV IC50 = 2.14 mmol L-1 ) and Ser-Pro-Gly-Pro-Asp-Gly-Lys-Thr-Gly-Pro-Arg (P12) (DPP-IV IC50 = 2.61 mmol L-1 ) exhibited the strongest DPP-IV inhibitory activity. Gly-Pro-Pro-Gly-Ala-Asp-Gly-Gln-Ala-Gly-Ala-Lys (P6) displayed the highest ACE inhibitory activity (ACE IC50 = 3.77 mmol L-1 ). The molecular docking analysis revealed that DPP-IV inhibition of P11 and P12 are mainly attributed to hydrogen bonds and hydrophobic interactions, whereas ACE inhibition of P6 is mainly attributed to strong hydrogen bonds. CONCLUSIONS These results indicate that SKPE hydrolysates generated by flavourzyme are potential sources of bioactive peptides that could be used in the health food industry. © 2021 Society of Chemical Industry.

Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.

Background Antibody-mediated rejection (AMR) induced by donor-specific anti-human leukocyte antigen (HLA) antibodies (DSA) remains a major cause of long-term graft loss after kidney transplantation. Currently, the presence of DSA cannot always be determined at a specific allele level, because existing donor HLA typing is low resolution and often incomplete, lacking HLA-DP, and occasionally HLA-C and HLA-DQ information and historical donor DNA samples are not available for HLA retyping. Here we present a novel, non-invasive technique for obtaining donor DNA from selectively expanded donor cells from urine of renal transplant recipients. Methods Urine-derived cells were successfully expanded ex vivo from 31 of 32 enrolled renal transplant recipients, and with DNA obtained from these cells, donor HLA typing was unambiguously determined for HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1 and -DPB1 loci by next-generation sequencing. Results Our results showed 100% concordance of HLA typing data between donor peripheral blood and recipient urine-derived cells. In comparison, HLA typing showed that DNA derived from urine sediments mainly contained recipient-derived DNA. We also present the successful application of our novel technique in a clinical case of AMR in a renal transplant recipient. Conclusions Urine-derived donor cells can be isolated from kidney transplant recipients and serve as a suitable source of donor material for reliable high-resolution HLA genotyping. Thus, this approach can aid the assessment of DSA specificity to support the diagnosis of AMR as well as the evaluation of treatment efficacy in kidney transplant recipients when complete donor HLA information and donor DNA are unavailable. This article is protected by copyright. All rights reserved.

Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.

Two new α-pyrones, micropyrones A (1) and B (2), along with four known γ-pyrones, nocapyrone D (3), nocapyrone A (4), marinactinone A (5), and nocapyrone H (6), were isolated from the culture extract of actinomycete Microbacterium sp. GJ312, which was isolated from Glycyrrhiza uralensis. The structures of these compounds were identified by analysis of spectral data. They are the first α- and γ-pyrones reported from the genus Microbacterium. The antibacterial activity of all compounds against Staphylococcus aureus and methicillin resistant S. aureus was evaluated. However, none of them showed significant activity. This study represents the first phytochemical example of a Glycyrrhiza-derived actinomycete.

In modern agricultural production, straw return (SR) plus nitrogen (N) fertilizer (SR-N) input has been considered a better practical mode to improve soil fertility and crop yield. Here, we investigate the underlying mechanisms of long-term SR-N application on wheat growth, yield, and quality. Wheat seeds were cultivated in 11-year-old plots treated with different N fertilizer levels under corn SR and non-straw return (NSR) conditions. Five levels of N fertilizer were set: N0 (0), N1 (90 kg ha−1), N2 (180 kg ha−1), N3 (270 kg ha−1), and N4 (360 kg ha−1). The wheat plants in SR-N2 exhibited the best growth status, the highest yield, and yield components. Physiological indicators exhibited that wheat plants in SR-N2 also had the maximum chlorophyll, soluble sugars, and protein contents, the highest antioxidant enzyme activities, and the lowest malondialdehyde (MDA) content. Wheat grains in SR-N2 had the highest protein content, which might be attributed to the highest glutamine synthetase activity during filling stage. qRT-PCR analysis showed that six genes related to N uptake and assimilation were significantly upregulated in SR-N2 treatment. Taken together, SR-N2 might be the effective mode that decrease the N fertilizer usage but maintain the maximize crop yield and grain quality by reducing oxidative stress and upregulating the expression of N metabolism-related genes.