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Neolamarckia cadamba (Roxb.), a close relative of Coffea canephora and Ophiorrhiza pumila, is an important traditional medicine in Southeast Asia. Three major glycosidic monoterpenoid indole alkaloids (MIAs), cadambine and its derivatives 3β-isodihydrocadambine and 3β-dihydrocadambine, accumulate in the bark and leaves, and exhibit antimalarial, antiproliferative, antioxidant, anticancer and anti-inflammatory activities. Here, we report a chromosome-scale N. cadamba genome, with 744.5 Mb assembled into 22 pseudochromosomes with contig N50 and scaffold N50 of 824.14 Kb and 29.20 Mb, respectively. Comparative genomic analysis of N. cadamba with Co. canephora revealed that N. cadamba underwent a relatively recent whole-genome duplication (WGD) event after diverging from Co. canephora, which contributed to the evolution of the MIA biosynthetic pathway. We determined the key intermediates of the cadambine biosynthetic pathway and further showed that NcSTR1 catalyzed the synthesis of strictosidine in N. cadamba. A new component, epoxystrictosidine (C27H34N2O10, m/z 547.2285), was identified in the cadambine biosynthetic pathway. Combining genome-wide association study (GWAS), population analysis, multi-omics analysis and metabolic gene cluster prediction, this study will shed light on the evolution of MIA biosynthetic pathway genes. This N. cadamba reference sequence will accelerate the understanding of the evolutionary history of specific metabolic pathways and facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants.

This study investigated the effects of illumination time and soil moisture on seed germination and seedling establishment of Magnolia sprengeri Pamp. to improve the seed germination percentage and seedling survival percentage of M. sprengeri. It is of great significance for rapid propagation, seedling regeneration, field management, and artificial high-efficiency cultivation of M. sprengeri. In this study, the seeds of natural M. sprengeri populations from original habitat were used as test materials. Seed germination and seedling establishment of M. sprengeri were performed under different illumination time and soil moisture treatments in artificial climate incubator. The study found that there were significant differences among various key parameters related to seed germination and seedling establishment under different treatments (P < 0.05). Germination percentage, germination potential, germination index, vigor index, germination rate, plant height, number of leaves, base diameter, taproot length, number of lateral roots, maximum lateral root length, single plant leaf area, fresh weight, and seedling survival rate reached the maximum at continuous illumination and 13% of soil moisture, respectively. By the integrative evaluation for the influence of these two factors on seed germination and seedling establishment, soil moisture is a dominant factor affecting seed germination and seedling establishment, whereas illumination is an important promoting factor for seedling establishment of M. sprengeri. Continuous illumination and 13% of soil moisture content is suitable for seed germination and seedling establishment of M. sprengeri.

A massive depletion of CD4+ T lymphocytes has been described in early and acute human immunodeficiency virus (HIV) infection, leading to an imbalance between the human microbiome and immune responses. In recent years, a growing interest in the alterations in gut microbiota in HIV infection has led to many studies; however, only few studies have been conducted to explore the importance of oral microbiome in HIV-infected individuals. Evidence has indicated the dysbiosis of oral microbiota in people living with HIV (PLWH). Potential mechanisms might be related to the immunodeficiency in the oral cavity of HIV-infected individuals, including changes in secretory components such as reduced levels of enzymes and proteins in saliva and altered cellular components involved in the reduction and dysfunction of innate and adaptive immune cells. As a result, disrupted oral immunity in HIV-infected individuals leads to an imbalance between the oral microbiome and local immune responses, which may contribute to the development of HIV-related diseases and HIV-associated non-acquired immunodeficiency syndrome comorbidities. Although the introduction of antiretroviral therapy (ART) has led to a significant decrease in occurrence of the opportunistic oral infections in HIV-infected individuals, the dysbiosis in oral microbiome persists. Furthermore, several studies with the aim to investigate the ability of probiotics to regulate the dysbiosis of oral microbiota in HIV-infected individuals are ongoing. However, the effects of ART and probiotics on oral microbiome in HIV-infected individuals remain unclear. In this article, we review the composition of the oral microbiome in healthy and HIV-infected individuals and the possible effect of oral microbiome on HIV-associated oral diseases. We also discuss how ART and probiotics influence the oral microbiome in HIV infection. We believe that a deeper understanding of composition and function of the oral microbiome is critical for the development of effective preventive and therapeutic strategies for HIV infection.

Type 2 diabetes is the most common type of diabetes and causes a decline in muscle quality. In this study, we investigated the effects of the root extract of Morinda officinalis (MORE) on skeletal muscle damage in mice with high-fat-diet (HFD)/streptozotocin (STZ)-induced diabetes and the expression of myogenic and biogenesis regulatory proteins in C2C12 myoblast differentiation. An in vivo model comprised C57BL/6N mice fed HFD for 8 weeks, followed by a single injection of STZ at 120 mg/kg. MORE was administered at 100 and 200 mg/kg once daily (p.o.) for 4 weeks. The changes in body weight, calorie intake, and serum levels of glucose, insulin, total cholesterol (TCHO), HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C), aspartate transaminase (AST), and alanine aminotransferase (ALT) were investigated in diabetic mice. The histological changes in the gastrocnemius muscle were observed by H&E staining, and then the myofiber size was measured. The expression of the myogenic (MHC, myogenin, and MyoD) and biogenesis (PGC-1α, SIRT1, NRF1, and TFAM) regulatory proteins was examined in the muscle tissues and differentiated C2C12 myoblasts by Western blot, respectively. The administration of MORE at 200 mg/kg in mice with HFD/STZ-induced diabetes significantly reduced weight gains, calorie intake, insulin resistance, and serum levels of glucose, TCHO, LDL-C, AST, and ALT. MORE administration at 100 and 200 mg/kg significantly increased serum insulin and HDL-C levels in diabetic mice. In addition, MORE significantly increased the expression of MHC, myogenin, MyoD, PGC-1α, SIRT1, NRF1, and TFAM in muscle tissues as well as increased the myofiber size in diabetic mice. In C2C12 myoblast differentiation, MORE treatment at 0.5, 1, and 2 mg/mL significantly increased the expression of myogenic and biogenesis regulatory proteins in a dose-dependent manner. MORE improves diabetes symptoms in mice with HFD/STZ-induced diabetes by improving muscle function. This suggests that MORE could be used to prevent or treat diabetes along with muscle disorders.

Background Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems. Results Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs. Conclusion Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into “complete metagenomics”. The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment.

Paeonia ostii is recognized as an important oilseed tree peony species with potential as a raw material source for cosmetic and health care products, strong seed setting capacity, high seed oil yield, and abundant omega-3 polyunsaturated fatty acids. P. ostii, commonly called Fengdan, is widely cultivated in China. The cultivation method difference has an important influence on the oil-use feature, which is a key index for evaluating the quality of oilseed crops. This study aimed to select an optimal cultivation method to provide the first reference data for high-yield and high-quality seed oil harvesting and to facilitate the understanding of the quality difference in the formation mechanism of seed oil in cultivated P. ostii. This study selected five representative cultivation methods, open field cultivation, sunny slope cultivation, shady slope cultivation, understory intercropping cultivation, and high-altitude cultivation, and investigated the influence of cultivation method differences on the oil-use feature based on the three aspects of seed yield traits, oil yield, and fatty acid compositions. Six seed yield traits (fruit pod length, fruit pod width, fruit pod thickness, number of fruit pods per plant, 1000-grain weight, and seed yield per plant) and oil yield reached the maximum values of 7.75 cm, 6.99 cm, 1.57 cm, 11.33, 290.45 g, 85.8 g, and 30.41%, respectively, using the understory intercropping cultivation method. Fatty acid compositions were mainly identified as α-linolenic acid, linoleic acid, oleic acid, stearic acid, and palmitic acid, with significant content differences among different cultivation methods (P < 0.05). Functional component α-linolenic acid and total amounts of unsaturated fatty acids reached the maximum values of 46.85% and 65.23%, respectively, with high-altitude cultivation and understory intercropping cultivation. The seed yield traits, oil yield, and total amounts of unsaturated fatty acids were optimal with the understory intercropping cultivation method, whereas high-altitude cultivation was conducive to the accumulation of α-linolenic acid. Understory intercropping cultivation with appropriate altitude increases is recommended as a preponderant cultivation method for high-yield and high-quality seed oil harvesting for this crop.

Drought stress severely limits plant growth and production in apple (Malus domestica Borkh.). To breed water-deficit-tolerant apple cultivars that maintain high yields under slight or moderate drought stress, it is important to uncover the mechanisms underlying the transcriptional regulation of chlorophyll metabolism in apple. To explore this mechanism, we generated transgenic 'Gala3' apple plants with overexpression or knockdown of MdWRKY17, which encodes a transcription factor whose expression is significantly induced by water deficit. Under moderate drought stress, we observed significantly higher chlorophyll contents and photosynthesis rates in overexpression transgenic plants than in controls, whereas these were dramatically lower in the knockdown lines. MdWRKY17 directly regulates MdSUFB expression, as demonstrated by in vitro and in vivo experiments. MdSUFB, a key component of the sulfur mobilization (SUF) system that assembles Fe-S clusters, is essential for inhibiting chlorophyll degradation and stabilizing electron transport during photosynthesis, leading to higher chlorophyll levels in transgenic apple plants overexpressing MdWRKY17. The activated MdMEK2-MdMPK6 cascade by water-deficit stress fine-tunes the MdWRKY17-MdSUFB pathway by phosphorylating MdWRKY17 under water-deficit stress. This fine-tuning of the MdWRKY17-MdSUFB regulatory pathway is important for balancing plant survival and yield losses (chlorophyll degradation and reduced photosynthesis) under slight or moderate drought stress. The phosphorylation by MdMEK2-MdMPK6 activates the MdWRKY17-MdSUFB pathway at S66 (identified by LC-MS), as demonstrated by in vitro and in vivo experiments. Our findings reveal that the MdMEK2-MdMPK6-MdWRKY17-MdSUFB pathway stabilizes chlorophyll levels under moderate drought stress, which could facilitate the breeding of apple varieties that maintain high yields under drought stress.

Carbonyl compounds play a critical role in the pathogenesis of diabetic nephropathy (DN). Pueraria lobata (PL), also known as "Kudzu", is a widely consumed functional food or nutraceutical and has shown promise in the prevention of diabetes and complications such as DN. To explore the beneficial effects and the underlying mechanisms of PL against DN, a new strategy for in-depth metabolic profiling of carbonyl compounds in DN mice plasma by chemical derivatization combined with UPLC-Q-Orbitrap high-resolution mass spectrometry (HRMS)/MS analysis was developed for the first time. Pharmacological evaluation revealed that PL extracts containing a total of 73 identified compounds could ameliorate kidney injury and regulate abnormal glycolipid metabolism. In metabolomics analysis, 19 carbonyl compounds with significant differences were identified between DN mice and normal mice. Moreover, 12 metabolites had a tendency to return to normal levels after PL treatment. Overall, PL exerts beneficial effects on DN by regulating abnormal glycolipid metabolism and carbonyl stress, and endogenous carbonyl compounds might serve as potential biomarkers for DN.

Currently available therapies for hepatocellular carcinoma (HCC), with a high morbidity and high mortality, are only marginally effective and with sharp adverse side effects, which makes it compulsory to explore novel and more effective anticancer molecules. Chinese medicinal herbs exhibited prominent anticancer effects and were applied to supplement clinical cancer treatment. Here, we reported a compound, trilobolide-6-O-isobutyrate (TBB), isolated from the flowers of Wedelia trilobata with a markedly cytotoxic effect on HCC cells. We found that TBB time- and dose-dependently inhibited HCC cells' growth and colony formation in vitro. Moreover, TBB induced cell cycle arrest at the G2/M phase, mitochondrial caspase-dependent apoptosis, and suppressed migration and invasion, as well as the glycolysis of HCC cells. Mechanistically, our data indicated that TBB inhibited the STAT3 pathway activation by directly interacting with the TYR 640/657 sites of the STAT3 protein and decreasing the level of p-STAT3. TBB also regulated the expression of PCNA, Ki67, Cyclin B1, Cyclin E, Bax, Bcl2, MMP2/9, and PGK1 through the inhibition of the IL-6/STAT3 signaling pathway. Lastly, we confirmed that TBB effectively eliminated tumor growth without causing overt toxicity to healthy tissues in the xenograft tumor model. The exploration of anticancer activity and the underlying mechanism of TBB suggested its usage as a promising chemotherapeutic agent for HCC.

A novel actinobacterial strain, designated SYSU K10008T, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008T was most closely related to Streptomyces cyaneus CGMCC 4.1671T, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, ll-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H6), while the major fatty acids (>10 %) were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008T was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008T represents a novel species of the genus Streptomyces , for which the name Streptomyces cavernae sp. nov. is proposed. The type strain is SYSU K10008T (=KCTC 39850T=DSM 104115T).

OBJECTIVES To investigate the role of polymorphism rs11200638 of high-temperature requirement factor A-1 (HtrA1) gene in the pathogenesis of age-related macular degeneration (AMD). METHODS Cultured adult retinal pigment epithelial cells (ARPE-19) expressing HtrA1 gene were treated with H2O2 or lipopolysaccharides (LPS) and analysed using western blot and quantitative polymerase chain reaction to illustrate the effects of oxidative and inflammatory stress on HtrA1 gene expression. Luciferase reporter plasmid driven by HtrA1 promoter with either normal allele G or risk allele A at SNP rs11200638 was transfected to ARPE-19 cells to investigate the effect of the G/A variation on HtrA1 promoter activity. The effects of HtrA1 overexpression on ARPE-19 cells were analysed with respect to percentage of cell proliferation inhibition and cell apoptosis. RESULTS HtrA1 expression was significantly increased with LPS or H2O2 stimulations (p

C-type lectins are a family of pattern recognition receptors that recognize microbial components and subsequently activate the signaling cascade to induce the production of proinflammatory cytokines. In the current study, the homologs of ERK (named as CgERK) and GSK3β (named as CgGSK3β) and a novel C-type lectin with a transmembrane domain (named as CgCLec-TM1) were identified from oyster Crassostrea gigas. CgCLec-TM1 was able to bind Escherichia coli and Vibrio splendidus through its carbohydrate recognition domain and then activated CgERK by inducing its phosphorylation. The activated CgERK interacted with CgGSK3β to phosphorylate it at Ser9, which eventually induced the expressions of CgIL-17-1 and CgIL-17-5. The interaction between CgERK and CgGSK3β, as well as the phosphorylation of CgGSK3β, could be inhibited by ERK inhibitor (PD98059) to reduce the expressions of CgIL-17-1 and CgIL-17-5. CgGSK3β in oyster was proposed as a new substrate of CgERK. The results defined a CLec-TM1–ERK–GSK3β signaling pathway in oyster, which was activated by V. splendidus and then induced CgIL-17 productions.

Urokinase-type plasminogen activator (uPA) is a cell-secreted serine protease and plays a significant role in numerous biological processes. Overexpression of uPA has been proved to be relevant to some malignant tumors as well as poor prognosis. However, bioluminescence (BL) probes for selectively sensing uPA activity have not been reported up to now. Herein, we designed a BL probe, GGR-AmLuc, to detect uPA in vitro and sense uPA both inside cells and in tumors. In vitro studies demonstrated that GGR-AmLuc was able to selectively detect uPA with a limit of detection (LOD) of 1.37 μg/L. Moreover, GGR-AmLuc was successfully applied to image uPA in living subjects with excellent sensitivity. We anticipate that probe GGR-AmLuc could be applied for highly sensitive diagnosis of cancers overexpressing uPA and provide guidance for cancer treatment in the near future.

Application of the clustered regularly interspaced short palindromic repeats associated 9 (CRISPR-Cas9) technology has revolutionized biology by greatly enhancing the ability to introduce mutations into DNA for research and prospective therapeutic purposes. However, the understanding of Cas9 editing outcomes is still limited. Previously, it was considered that Cas9 introduces stochastic insertions or deletions (indels) at the target site. In the current study, we performed in vivo multiplex editing, deep sequencing, and comprehensive analysis of its editing outcomes in Bombyx mori (B. mori). A total of 31161 editing events from 9 single-guide RNA (sgRNA) sites in 16 individuals were generated and analyzed, and we found that Cas9 introduces mutations with some regularity rather than via stochastic indels. The editing efficiency varies with sgRNA sequences, individuals, and orientation. Small deletions account for the vast majority of mutated sequences, followed by a small fraction of substitutions and insertions. The most likely mutations are deletions between two microhomologous sequences or single-base deletions at the cleavage site in the absence of microhomologous pairs. Insertions are formed by diverse mechanisms, including direct acquisition of free genomic fragments, duplication of broken ends, replication of adjacent sequences, or random addition of free nucleotides. The above results indicate that the Cas9 editing spectrum is reproducible and predictable. Thus, our findings enable a deeper understanding of Cas9-mediated mutagenesis and better design of genome editing experiments, as well as elucidate the DNA double-strand break repair processes in B. mori.

Alzheimer’s disease (AD) is the most common form of neurodegeneration and cognitive dysfunction in the elderly. Identifying molecular signals that mitigate and reverse neurodegeneration in AD may be exploited therapeutically. Transgenic AD mice (PSAPP) exhibit learning and memory deficits at 9 and 11 months, respectively, with associated decreased expression of caveolin-1 (Cav-1), a membrane/lipid raft (MLR) scaffolding protein necessary for synaptic and neuroplasticity. Neuronal-targeted gene therapy using synapsin-Cav-1 cDNA (SynCav1) was delivered to the hippocampus of PSAPP mice at 3 months using adeno-associated virus serotype 9 (AAV9). Bilateral SynCav1 gene therapy was able to preserve MLRs profile, learning and memory, hippocampal dendritic arbor, synaptic ultrastructure, and axonal myelin content in 9- and 11-month PSAPP mice, independent of reducing toxic amyloid deposits and astrogliosis. Our data indicate that SynCav1 gene therapy may be an option for AD and potentially in other forms of neurodegeneration of unknown etiology., Graphical abstract, The findings demonstrate that regardless of the etiology of the neuropathology, SynCav1 may be exploited to treat sporadic conditions or to be used in combination with already existing drugs or biologics designed to target known monogenic candidates linked to other neurodegenerative conditions (AD, ALS, MS).

Dysregulation of transcriptome expression has been reported to play an increasingly significant role in AD. In this study, we firstly identified a vital gene module associated with the accumulation of β-amyloid (Aβ) and phosphorylated tau (p-tau) using the WGCNA method. The vital module, named target module, was then employed for the identification of key transcriptome biomarkers. For coding RNA, GNA13 and GJA1 were identified as key biomarkers based on ROC analysis. As for non-coding RNA, MEG3, miR-106a-3p, and miR-24-3p were determined as key biomarkers based on analysis of a ceRNA network and ROC analysis. Experimental analyses firstly confirmed that GNA13, GJA1, and ROCK2, a downstream effector of GNA13, were all increased in 5XFAD mice, compared to littermate mice. Moreover, their expression was increased with aging in 5XFAD mice, as Aβ and p-tau pathology developed. Besides, the expression of key ncRNA biomarkers was verified to be decreased in 5XFAD mice. GSEA results indicated that GNA13 and GJA1 were respectively involved in ribosome and spliceosome dysfunction. MEG3, miR-106a-3p, and miR-24-3p were identified to be involved in MAPK pathway and PI3K-Akt pathway based on enrichment analysis. In summary, we identified several key transcriptome biomarkers, which promoted the prediction and diagnosis of AD.

RNA-binding proteins (RBPs) are critical regulators of transcription and translation that are often dysregulated in cancer. Although RBPs are increasingly recognized as being important for normal hematopoiesis and for hematologic malignancies as oncogenes or tumor suppressors, RBPs that are essential for the maintenance and survival of leukemia remain elusive. Here we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival in an N6-methyladenosine (m6A)-dependent manner. We found that expression of YBX1 is significantly upregulated in myeloid leukemia cells, and deletion of YBX1 dramatically induces apoptosis and promotes differentiation coupled with reduced proliferation and impaired leukemic capacity of primary human and mouse acute myeloid leukemia cells in vitro and in vivo. Loss of YBX1 has no obvious effect on normal hematopoiesis. Mechanistically, YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. Moreover, YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1. Thus, our findings have uncovered a selective and critical role of YBX1 in maintaining myeloid leukemia survival, which might provide a rationale for the therapeutic targeting of YBX1 in myeloid leukemia.

Food-borne illnesses caused by pathogenic bacteria are prominent issues in food safety. Rapid and sensitive detection of pathogenic bacteria is significantly essential for food safety. In this work, an aptamer biosensor (aptasensor) based on aldehyde magnetic beads (Mbs), rolling circle amplification (RCA) and DNA hydrogel was developed for visualized, simple and rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). Firstly, the Mbs@double-stranded DNA (dsDNA) complexes were prepared. In the presence of target, the aptamer combined with E. coli O157:H7, releasing E. coli aptamer-initiator (EA-I). The supernatant collected by magnetic separation and those released primers were hybridized with circular sequence to form padlock probe. Then, RCA reaction was initiated by adding T4 DNA ligase, phi29 DNA polymerase, and deoxynucleotides (dNTPs), while RCA cannot be triggered in the absence of target. Two circular sequences were designed to contain partially complementary bases. After RCA, two long single-stranded DNA (ssDNA) products were generated using those two circular sequences. They hybridized with each other and formed the naked-eye visible DNA hydrogel. The method showed high sensitivity and specificity with a detection limit of 4 × 103 CFU/mL for E. coli O157:H7 within 1 h, and the detection time could be finished within 30 min. The aptasensor offers many advantages such as high specificity, easy operation, efficient amplification, rapid and visualized readout, which has potential applications in food safety detection

Objective The objective of this study was to investigate the effects of inverted photoperiods on the blood pressure and carotid arteries in spontaneously hypertensive rats (SHRs) and Wistar-Kyoto (WKY) rats (homologous control group). Methods and results This study used two inverted photoperiods [inverted light:dark (ILD)16 : 8 and ILD12 : 12] to create the model. A total of 27 male SHR and 27 male WKY rats were randomly divided into six groups (nine rats per group): SHR (LD12 : 12), SHR (ILD16 : 8), SHR (ILD12 : 12), WKY (LD12 : 12), WKY (ILD16 : 8) and WKY (ILD12 : 12). We recorded the trajectory of the activity rhythm of the rats and performed carotid vascular ultrasound examination, MRI (arterial spin labelling) analysis and carotid biopsy. The results showed that inverted photoperiods increased the blood pressure, carotid intima-media thickness, resistance index and blood flow velocity. In addition, inverted photoperiods led to the development of carotid arterial thrombosis, significantly reduced cerebral blood flow and increased the number of collagen fibres. Moreover, it increased the expression of angiotensin receptor and low-density lipoprotein receptor in the carotid arteries, leading to decreased expression of 3-hydroxy-3-methylglutaryl-Coenzyme A reductase and nitric oxide synthase. Inverted photoperiods induced the formation of atherosclerotic plaque. Multiple results of SHR were worse than those of WKY rats. Conclusion Taken together, inverted photoperiods can produce a series of adverse consequences on blood pressure and carotid arteries. Hypertension can aggravate the adverse effects of inverted photoperiods.

Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.

Lysine metabolism plays an important role in the formation of the insecticidal crystal proteins of Bacillus thuringiensis (Bt). The genes lam, gabD and sucA encode three key enzymes of the lysine metabolic pathway in Bt4.0718. The lam gene mainly affects the cell growth at stable period, negligibly affected sporulation and insecticidal crystal protein (ICP) production. While, the deletion mutant strains of the gabD and sucA genes showed that the growth, sporulation and crystal protein formation were inhibited, cells became slender, and insecticidal activity was significantly reduced. iTRAQ proteomics and qRT-PCR used to analyse the differentially expressed protein (DEP) between the two mutant strains and the wild type strain. The functions of DEPs were visualized and statistically classified, which affect bacterial growth and metabolism by regulating biological metabolism pathways: the major carbon metabolism pathways, amino acid metabolism, oxidative phosphorylation pathways, nucleic acid metabolism, fatty acid synthesis and peptidoglycan synthesis. The gabD and sucA genes in lysine metabolic pathway are closely related to the sporulation and crystal proteins formation. The effects of DEPs and functional genes on basic cellular metabolic pathways were studied to provide new strategies for the construction of highly virulent insecticidal strains, the targeted transformation of functional genes.

PURPOSE Plasma detection of EGFR T790M mutations is an emerging alternative to tumor rebiopsy in acquired epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor resistance. Validation of analytical sensitivity and clinical utility is required before routine diagnostic use in clinical laboratories. PATIENTS AND METHODS Sixty-three patients with advanced EGFR-mutant lung cancer at 7 Canadian centers, who were being screened for the ASTRIS trial (ClinicalTrials.gov identifier: NCT02474355 ), participated in this companion study. Plasma T790M mutation was detected using droplet digital polymerase chain reaction, Cobas (Roche Diagnostics, Indianapolis, IN), or next-generation sequencing in 4 laboratories. T790M concordance was assessed between plasma and tumor samples. RESULTS Assessment of T790M in tumor biopsy tissue was successful in 81% of patients; 49% had confirmed T790M results (tumor or plasma) for ASTRIS. Plasma testing in this companion study yielded T790M results in 97% of patients; 62% had T790M-positive results, 36% had negative results, and 2% had indeterminate results. Of 38 patients with negative or indeterminate biopsy results, 55% had positive plasma T790M results, increasing the proportion with T790M-positive results to 73%. Sensitivity of plasma T790M testing was 75%. Overall concordance between tissue and plasma was 64%, and concordance among laboratories was 90.3%. Response to osimertinib and duration of therapy were similar irrespective of testing method (overall response rate, 62.5% for tissue, 66.7% for plasma, and 70.6% for both). CONCLUSION This multicenter validation study demonstrates that plasma EGFR T790M testing can identify significantly more patients than biopsy alone who may benefit from targeted therapy.

Microorganisms in the gastrointestinal tract of animals play vital roles in food digestion, homeostasis and immune response regulation. Globally, there are 33,700 fish species, representing almost half of all vertebrate diversity and a wide range of physiologies, ecologies and life histories. To investigate gut microbiomes with high coverage, we performed 16S rRNA gene amplicon sequencing with 115 samples of 20 common marine fish species. The fish gut microbiome is a remarkably simple community with low microbial diversity (a maximum of 300 amplicon sequence variants only) and has up to 70% of unknown species in some fish species. The gut microbial community structure was significantly shaped by the combined influence of host‐associated factors, including the fish taxon (p

The CRISPR/Cas (clustered regularly interspaced short palindromic repeat technology/CRISPR-associated protein) is a widely used and powerful research tool in biosciences and a promising therapeutic agent for treating genetic diseases. Mutations induced by Cas9 are generally considered stochastic and unpredictable, thus hindering its applications where precise genetic alternations are required. Here, through deep sequencing and analysis of genome editing outcomes of multiple sites in four distinct species, we found that Cas9-induced mutations are coincident in mutation types but are significantly different in indel patterns among species. In human and mouse cells, indels were almost evenly distributed at both ends of the cleavage sites. However, the indels mainly appeared at the upstream of cleavage sites in Bombyx mori, while they predominantly occurred downstream of the cleavage sites in the zebrafish Danio rerio. We also found that within a species, indel patterns are sequence dependent, wherein deletions between two adjacent micro-homology sequences were the most frequently observed mutations in the repair spectrum. These results suggested the species differences in DNA repair processes during Cas9-induced gene editing, and the important role of sequence structure at the target site in predicting the gene editing outcome.

The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) gene. Overall, 83 haplotypes were detected in 1253 mtDNA COI sequences. High levels of genetic variability (Hd = 0.756 ± 0.009, π = 0.00416 ± 0.00011) and genetic differentiation (FST = 0.262, p

Background Zeaxanthin, a carotenoid commonly found in plants, has a variety of biological functions including anti-cancer activity. Purpose This study aimed to investigate the potential mechanisms of zeaxanthin in human gastric cancer cells. Methods CCK-8 assay was used to examine the cytotoxic effect of zeaxanthin on human gastric cancer cells. Flow cytometry was used to analyse AGS cell cycle distribution and apoptosis status. Western blot analysis was used to detect the expression levels of cycle-related proteins (Cyclin A, Cyclin B1, CDK1/2, p21, and p27), apoptosis-related proteins (Bcl-2, Bad, caspase-3, PARP), MAPK, AKT, STAT3, and NF-κB. Results CCK-8 assay showed that zeaxanthin has obvious cytotoxic effects on 12 types of human gastric cancer cells, but no obvious toxic effect on normal cells. In addition, flow cytometry and Western blotting results showed that zeaxanthin induces apoptosis by reducing mitochondrial membrane potential; increasing Cytochrome C, Bax, cleaved-caspase-3 (cle-cas-3), and cleaved-PARP (cle-PARP) expression levels; and decreasing Bcl-2, pro-caspase-3 (pro-cas-3), and pro-PARP expression levels. Additionally, zeaxanthin caused cell cycle arrest at the G2/M phase by increasing the levels of p21 and p27 and reduced the levels of AKT, Cyclin A, Cyclin B1, and Cyclin-dependent kinase 1/2 (CDK1/2). Furthermore, after zeaxanthin treatment, the expression levels of reactive oxygen species (ROS), p-JNK, p-p38, and I-κB increased, and the expression levels of p-ERK, p-AKT, STAT3, and NF-κB decreased. However, the ROS scavenger N-acetylcysteine (NAC) and MAPK inhibitors inhibited zeaxanthin-induced apoptosis, and under the action of zeaxanthin, MAPK regulated NF-κB and STAT3, and reduced their protein expression levels. Conclusion Zeaxanthin has a potential effect against gastric cancer cells through the ROS-mediated MAPK, AKT, NF-κB, and STAT3 signaling pathways, and it is expected to become a new drug for the treatment of human gastric cancer.

The impact of commensal bacteria on the host arises from complex microbial-diet-host interactions. Mapping metabolic interactions in gut microbial communities is therefore key to understand how the microbiome influences the host. Here we use an interdisciplinary approach including isotope-resolved metabolomics to show that in Drosophila melanogaster, Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) a syntrophic relationship is established to overcome detrimental host diets and identify Ap as the bacterium altering the host’s feeding decisions. Specifically, we show that Ap uses the lactate produced by Lp to supply amino acids that are essential to Lp, allowing it to grow in imbalanced diets. Lactate is also necessary and sufficient for Ap to alter the fly’s protein appetite. Our data show that gut bacterial communities use metabolic interactions to become resilient to detrimental host diets. These interactions also ensure the constant flow of metabolites used by the microbiome to alter reproduction and host behaviour., In the fly Drosophila melanogaster commensal bacteria and dietary essential amino acids control food choice behavior. Here, by using chemically defined diets and metabolomics, the authors show that Acetobacter pomorum (Ap) and Lactobacilli plantarum (Lp) engage in a mutualistic metabolic relationship to overcome detrimental diets, and identify Ap as the bacterium altering the host’s feeding decisions.

Seed germination plays an important role in mediating plant species composition of grassland communities under nitrogen (N) enrichment. Shifts of plant community structure with N‐enhanced deposition in terrestrial ecosystems have occurred globally. Despite numerous studies about the effects of enhanced N deposition on mature plant communities, few studies have focused on seed germination. Using a laboratory experiment, we report the effects of five N concentrations, including 0, 5, 10, 20, and 40 mM N (NH4NO3) on seed germination of eight semi‐arid grassland species. Results showed that low N concentrations (5‐ and 20‐mM N) promoted mean final germination proportion of all eight species by 4.4% and 6.4%, but high concentrations (40 mM N) had no effect. The mean germination rate was decreased 2.1% and 5.1% by higher N concentration (20‐ and 40‐mM N) levels, but germination start time showed the opposite trend, delayed by 0.7, 0.9, and 1.8 d for the 10, 20, and 40 mM N treatments. Final germination proportion, mean germination rate, and germination start time were significantly different among species in response to N concentration treatments. The final germination proportion of Allium tenuissimum and Chenopodium glaucum were suppressed by increased N concentration, whereas it increased for Potentilla bifurca, Plantago asiatica, and Setaria viridis. Our findings provide novel insights into N deposition‐induced species loss based on seed germination factors in semi‐arid grassland communities., Low N concentrations promoted mean final germination proportion of all species. The responses of eight species to N addition were differences. Mean germination rate was lower at higher N concentration levels.

Paeonol, a major ingredient isolated from Moutan Cort, has various pharmacological effects. Our previous studies have shown that paeonol can exert antioxidant and anti-inflammatory therapeutic effects on ethanol-induced experimental gastric ulcer (GU). Therefore, in this study, we designed two GU models in rats induced by pyloric ligation (PL) and acetic acid and evaluated the protective effects of paeonol and gastroretention tablets of paeonol (GRT-Ps; 24, 48, and 96 mg/kg) on GU in rats and the effect of paeonol (48 mg/kg) on the intestinal flora. In vivo experiments showed that paeonol or GRT-Ps remarkably reduced gastric mucosal damage in a dose-dependent manner in the different types of models and improved the superoxide dismutase (SOD) activity and the malondialdehyde (MDA) content. And in fact, the sustained-release effect of GRT-Ps is more conducive to the improvement of GU compared with the rapid clearance of free drugs. In the PL-induced model, gastric secretion parameters, that is, pH and total acid, showed significant differences compared with the model group. In addition, paeonol treatment can improve the richness and diversity of the intestinal flora and increase the amount of beneficial bacteria, such as Lactobacillus. Paeonol and its stable sustained-release tablet GRT-Ps can promote ulcer healing by inhibiting oxidative stress and regulating the intestinal flora. This study can provide basis for the clinical treatment of GU with paeonol. Graphical Abstract.

Wood processing waste, poplar wood shavings, were used for fiberboard production, and the pretreatment conditions using cellulase were studied using response surface methodology (RSM). After single factors optimization, central level of temperature, dosage, and liquid/solid ratio (LSR) of cellulase pretreatment conditions were obtained. Further optimization to study the influence of the factors was carried out using Box-Behnken design of experiments. A second-order polynomial equation was obtained, and the low p-value (

Dryopteris crassirhizoma dryocrassin ABBA is a kind of phloroglucinol compound isolated from the whole plants of Dryopteris crassirhizoma. While previous studies have shown that dryocrassin ABBA induces various defence responses in potato tubers, limited information is known about the mechanism of dryocrassin ABBA-induced plant responses. The transcriptome profiles in potato tubers after treatment with dryocrassin ABBA or distilled water were analysed using RNA-Seq. The profiling analysis revealed a total of 37 million clean reads and 3252 differentially expressed genes (DEGs). The data were further confirmed by real-time PCR. The results suggest that dryocrassin ABBA treatment enhances resistance in potatoes, which may be primarily mediated by the salicylic acid (SA) signal pathway, while the jasmonic acid (JA), the ethylene (ET) and the abscisic acid (ABA) signal pathways effectively induce resistance in potatoes. Moreover, the transcripts related to flavonoid metabolism were also up-regulated in potatoes after dryocrassin ABBA treatment, demonstrating that secondary metabolites are related to the constitutive activation of the defence response in dryocrassin ABBA-treated potatoes. These findings reveal that the induced resistance of dryocrassin ABBA is related tomultiple signaling pathways and defence components to enhance host defence responses in potato tubers.

Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.

Objective Plasmablasts play important roles in autoimmune diseases, including systemic lupus erythematosus (SLE). Activation of mechanistic target of rapamycin complex 1 (mTORC1) is regulated by amino acid levels. In patients with SLE, mTORC1 is activated in B cells and modulates plasmablast differentiation. However, the detailed mechanisms of amino acid metabolism in plasmablast differentiation remain elusive. We undertook this study to evaluate the effects of methionine in human B cells. Methods Purified CD19+ cells from healthy donors (n = 21) or patients with SLE (n = 35) were cultured with Toll-like receptor 7/9 ligand, interferon-α (IFNα), and B cell receptor crosslinking, and we determined the types of amino acids that were important for plasmablast differentiation and amino acid metabolism. We also identified the transcriptional regulatory mechanisms induced by amino acid metabolism, and we assessed B cell metabolism and its relevance to SLE. Results The essential amino acid methionine strongly committed cells to plasmablast differentiation. In the presence of methionine, Syk and mTORC1 activation synergistically induced methyltransferase EZH2 expression. EZH2 induced H3K27me3 at BTB and CNC homolog 2 (Bach2) loci and suppressed Bach2 expression, leading to induction of B lymphocyte-induced maturation protein 1 and X-box binding protein 1 expression and plasmablast differentiation. CD19+ cells from patients with SLE overexpressed EZH2, which was correlated with disease activity and autoantibody production. Conclusion Our findings show that methionine activated signaling by controlling immunologic metabolism in B cells and played an important role in the differentiation of B cells into plasmablasts through epigenome modification of Bach2 by the methyltransferase EZH2.

Gecko’s amazing ability to adhere to almost any kind of surface has stirred significantly research interests over the last decade. There have been a series of researches in the field of Gecko-inspi...

The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida , Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2–94.9 %) and in silico DNA–DNA hybridization (52.5–62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strain.

HIV has remarkable genetic diversity among populations. The diversity has critical impacts on transmission, immune escape, pathogenesis, and clinical management. HIV-1 diversity originates from frequent mutation and recombination during reverse transcription. This work focuses on the quasispecies genetic dynamics within individuals with primary infections. Eleven men who have sex with men from the Beijing PRIMO Clinical Cohort were identified as primary infection and had three or four series of their anticoagulant blood samples collected. Viral RNA was extracted and amplified using single-genome amplification. Products of the gp120 gene that met single-genome amplification requirements were sequenced. Subtype assortment of all collected sequences was performed using both the jumping profile hidden Markov model (jpHMM) and REGA. Quasispecies diversity at each time was estimated using Mega 6. Intrapatient recombination was analyzed using RDP4. According to the Fiebig classification system, YA-81 belongs to stage III and YA-113 belongs to stage IV. The other samples are all associated with the infection stage of V/VI. YA113 had a dual infection with subtype B and a new unique recombinant form involving CRF01_AE and C. The other eight were infected with CRF01_AE, one was infected with B/C recombinant, and the last one with B. Of the 10 single infections, 8 were caused by 1 founder virus. They all displayed a sharp increase of quasispecies diversity during the sampling times. Two were caused by at least two founder viruses. The diversity of these strains starts at a significantly high level and is followed by a relatively steady trend. Critically, the separate subtypes YA113-B and YA113-CRF01_AE/C both showed a similar trend to those infected by a single founder virus. Recombination analysis revealed that 5 of 11 cases underwent detectable intrapatient recombination. These findings indicate that tracing the dynamics of HIV-1 quasispecies during early infection may be relevant and valuable for understanding pathways of viral diversification and immune escape.

This study revealed the ABA-dependent signaling pathway and flavonoid synthesis pathway of sea buckthorn under drought conditions from plant physiology and gene expression levels. As climate changes and temperatures rise, sea buckthorn (Hippophae rhamnoides L.) is increasingly exposed to numerous challenges, particularly aridity. In this study, the leaves of sea buckthorn were harvested from plants in drought-recovery cycles and selected for RNA sequencing to uncover the underlying genetic basis of drought stress response through physiological and biochemical analyses. The results revealed that drought conditions significantly (p

A coccobacilli-shaped proteobacterium, designated strain SYSU XM001T, was isolated from an activated sludge sample collected from JiMei sewage treatment plant, Xiamen, PR China. Cells were Gram-stain-negative, catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain SYSU XM001T shared less than 92 % sequence identities with members of the class Alphaproteobacteria , with highest sequence similarity to Aquidulcibacter paucihalophilus TH1-2T (91.6 %; family Hyphomonadaceae , order Rhodobacterales ). The strain exhibited growth at 25–37 °C, pH 7.0–9.0 and in the presence of up to 1 % (w/v) NaCl. Its chemotaxonomic features included ubiquinone-10 as the respiratory isoprenologue, iso-C16 : 0, 10-methyl C16 : 0 TSBA and anteiso-C17 : 0 as major cellular fatty acids and monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids as the main polar lipids. The DNA G+C content was determined to be 62.9 % (draft genome). Analyses of the phylogenetic data and differences in the chemotaxonomic and biochemical features from related genera in the family Hyphomonadaceae indicated that strain SYSU XM001T merits representation of a novel species of a novel genus, for which the name Vitreimonas flagellata gen. nov., sp. nov. is proposed. The type strain of Vitreimonas flagellata is SYSU XM001T (=CGMCC 1.16661T=KCTC 62915T).

RIOK2 is a member of RIO (right open reading frame) kinase family. Recent studies have revealed the involvement of RIO kinases in glioma cell growth and expansion. However, the role and mechanism of RIOK2 in glioma cell migration and invasion remain unclear. Wound healing assay, Transwell assay and real‐time quantitative PCR (qRT‐PCR) detection of matrix metalloproteinases (MMPs) were used to evaluate the migration/invasion of glioma cells. Western blot and qRT‐PCR were employed to measure the expression of epithelial‐mesenchymal transition (EMT) markers. Dual luciferase reporter assay was performed to determine the binding between RIOK2 and miR‐4744. In addition, RIOK2 and miR‐4744 levels were quantified by qRT‐PCR and/or immunohistochemistry in glioma tissues. Transfection of RIOK2 siRNAs significantly inhibited glioma cell migration and invasion and down‐regulated the expression of MMPs (MMP2 and MMP9) and mesenchymal markers (N‐cadherin, β‐catenin, Twist1, fibronectin, ZEB‐1) in glioma cells. Overexpression of RIOK2 showed the opposite effects. MiR‐4744 directly bound to the 3'‐untranslated region of RIOK2 and negatively regulated the expression of RIOK2. Up‐regulation of miR‐4744 inhibited the migration and invasion of glioma cells. Overexpression of RIOK2 could reverse the effects of miR‐4744 up‐regulation on the migration, invasion and EMT process in glioma cells. Moreover, RIOK2 was high, while miR‐4744 was low in glioma tissues, and a negative correlation was found between them. These results suggest that RIOK2 is post‐transcriptionally targeted by miR‐4744, the low miR‐4744 and high RIOK2 levels in glioma may contribute to tumour cell infiltration through promoting the EMT.

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade’s works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum ‘ Actinobacteria ’, using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences. Based on the refined phylogeny of the 16S rRNA gene sequences, we could arrange all the members of the 425 genera of the phylum ‘ Actinobacteria ’ with validly published names currently in use into six classes, 46 orders and 79 families, including 16 new orders and 10 new families. The order Micrococcales Prévot 1940 (Approved Lists 1980) emend. Nouioui et al. 2018 is now split into 11 monophyletic orders: the emended order Micrococcales and ten proposed new orders Aquipuribacterales , Beutenbergiales , Bogoriellales , Brevibacteriales , Cellulomonadales , Demequinales , Dermabacterales , Dermatophilales , Microbacteriales and Ruaniales . Further, the class ‘ Actinobacteria ’ Stackebrandt et al. 1997 emend. Nouioui et al. 2018 was described without any nomenclature type, and therefore the name ‘ Actinobacteria ’ is deemed illegitimate. In accordance to Rule 8 of the International Code of Nomenclature of Prokaryotes, Parker et al. 2019, we proposed the name Actinomycetia which is formed by using the stem of the name Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009, to replace the name ‘ Actinobacteria ’. The nomenclature type of the proposed new class Actinomycetia is the order Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009.

A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).

The morbidity and mortality of HIV type‐1 (HIV‐1)‐related diseases were dramatically diminished by the grounds of the introduction of potent antiretroviral therapy, which induces persistent suppression of HIV‐1 replication and gradual recovery of CD4+ T‐cell counts. However, ∼10–40% of HIV‐1‐infected individuals fail to achieve normalization of CD4+ T‐cell counts despite persistent virological suppression. These patients are referred to as “inadequate immunological responders,” “immunodiscordant responders,” or “immunological non‐responders (INRs)” who show severe immunological dysfunction. Indeed, INRs are at an increased risk of clinical progression to AIDS and non‐AIDS events and present higher rates of mortality than HIV‐1‐infected individuals with adequate immune reconstitution. To date, the underlying mechanism of incomplete immune reconstitution in HIV‐1‐infected patients has not been fully elucidated. In light of this limitation, it is of substantial practical significance to deeply understand the mechanism of immune reconstitution and design effective individualized treatment strategies. Therefore, in this review, we aim to highlight the mechanism and risk factors of incomplete immune reconstitution and strategies to intervene., Highlights the mechanism and risk factors of incomplete immune reconstitution and strategies to intervene.

A genome-based phylogeny of the publicly available genomes of the genus Nocardiopsis reveals that Nocardiopsis baichengensis YIM 90130T is closely related to Nocardiopsis halophila DSM 44494T. Overall genome relatedness indices between the genomes of the two species were above the threshold values necessary for defining a new species (dDDH, 82.9 %; ANIb, 97.8 %; ANIm, 98.3 %; AAI, 97.7 %). Both species showed a similar G+C content of 73.6 mol% in their genomes. Considering the high similarity between the genomes of the two species, we propose that Nocardiopsis baichengesis Li et al. 2006 should be reclassified as a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994.

Pistachio consumption has increased significantly, mostly due to their potential health effects and their good organoleptic properties. However, pistachio is also an important food allergen and therefore, it is necessary to develop an appropriate method to detect this nut in foodstuffs. In this work, a loop-mediated isothermal amplification (LAMP) assay targeting Pis V 1 allergen coding gene was developed. The developed LAMP assay performed high specificity for pistachio and had no cross-reactions with cashew, mango, walnut, almonds, macadamia nut, hazelnut, peanut, and soybean. The assay can detect at least 10 pg of purified pistachio genomic DNA and 10 mg kg−1 of pistachio nuts in binary mixtures. The autoclave treatment influenced the amplificability of pistachio; however, this impact was not found after boiling treatment. Practical applicability of the developed LAMP assay has been analyzed by testing different commercial foods and this method may be useful for rapid detection of pistachio in foodstuffs.

The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432T and Egibacter rhizosphaerae EGI 80759T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10T has a closer phylogenetic relationship to Euzebya rosea DSW09T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2T and E. halophilus EGI 80432T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K+ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.

The standardization of apiceutical products like as propolis extracts has been widely debated worldwide and variations in the propolis chemical composition are still very relevant topics for use-standardized of different propolis-type as medication by much of the world’s population. The present manuscript discuss important issues related to the climate effect and variations in propolis metabolite-profiling changes, antioxidant capacity and variations of the antibacterial activity of the Brazilian red propolis metabolites using comprehensive multivariate correlations. It was observed the increasing of guttiferones concentrations during the intense drought period and drastic decreasing in rainy period. The climate variation induced the high concentration of flavonoids in rainy period with pronounced dropped in some rainy months. The Pearson´s analysis demonstrated correlation between IC50 from DPPH and guttiferones and flavonoids concentrations. The PCA-X and Hotelling T2 test showed outliers during the months with lowest concentrations of formononetin and isoliquiritigenin was observed in antibacterial tests. The PLS-DA, OPLS-DA and VIP analysis demonstrate guttiferone E, guttiferone B, liquiritigenin, naringenin are considered important substances responsible by anti-staphylococcal activity in red propolis composition during the rainy season and drought period, but a synergistic effect with other flavonoids and isoflavonoids are not ruled out.

Background: Abnormal expression of long non-coding RNAs (lncRNAs) has been found in almost all tumors in humans, providing numerous potential diagnostic and prognostic biomarkers, and therapeutic targets. Materials and methods: The Cancer Genome Atlas (TCGA) database was used to screen potential LncRNAs, and 30 paired hepatocellular carcinoma (HCC) tissues were used to investigate RP11-307C12.11 expression levels by qRT-PCR and another 105 HCC tissues by in situ hybridizsation (ISH). RP11-307C12.11 overexpression and knockdown experiments were performed to investigate the effects of RP11-307C12.11 on HCC growth through in vitro and in vivo assays (MTT assay, colony formation assay, EdU assay, and xenograft model). The molecular mechanism underlying these effects was confirmed by MS2-RIP-assay, RIP assay, luciferase assay, and rescue experiments. Results: RP11-307C12.11 expression level was significantly higher in tumor tissues than in the adjacent normal tissues. Elevated RP11-307C12.11 expression level was associated with poor prognosis of HCC patients, and it may be represented as an independent prognostic biomarker in patients with HCC. Functionally, RP11-307C12.11 overexpression promoted HCC growth both in vitro and in vivo; however, its knockdown reversed these effects. Mechanistically, we found that RP11-307C12.11 expressed predominantly in the cytoplasm and sponged microRNA (miR)-138 to regulate its common target CCND1 and PDK1. Conclusions: Thus, we found that RP11-307C12.11 acts as an oncogene in HCC by binding to miR-138, which might provide a novel target for HCC therapy. Keywords: Long non-coding RNAs (lncRNAs), LncRNA RP11-307C12.11, Hepatocellular carcinoma (HCC), Growth, MicroRNA (MiR)-138

A novel actinobacterium, designated strain CFH 30434T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive, non-motile and coccoid or short rods. The strain was found to be oxidase-positive and weakly catalase-positive. Strain CFH 30434T grew optimally at 28 °C, pH 7.0–9.0 and in the presence of up to 0–1.5 % NaCl (w/v). The whole-cell sugars were glucose, mannose and rhamnose. The major isoprenoid quinone was MK-9(H8) and the major fatty acids (>10 % of the total fatty acids compositions) were anteiso-C15 : 0, iso-C15:0 and iso-C14 : 0. The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The genomic DNA G+C content was determined to be 72.3 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that CFH 30434T clustered within the family Promicromonosporaceae , and closely with the type strains of Xylanimicrobium pachnodae DSM 12657T, Myceligenerans crystallogenes DSM 17134T and Promicromonospora xylanilytica CCTCC AA 208046T (97.3 %, 96.2 and 95.9 % sequence similarities, respectively). Phylogenetic analysis showed that strain CFH 30434T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae . Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain CFH 30434T represents a novel genus of the family Promicromonosporaceae , for which the name Antribacter gilvus gen. nov., sp. nov. is proposed. The type strain is CFH 30434T (=CGMCC 1.13856T=KCTC 49093T).

Summary Viral diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant virus resistance is essential for sustainable agriculture. In the last decades, several modern technologies were applied in plant antiviral engineering. Here we summarized breakthroughs of the two major antiviral strategies, RNA silencing and genome editing. RNA silencing strategy has been used in antiviral breeding for more than thirty years, and many crops engineered to stably express small RNAs targeting various viruses have been approved for commercial release. Genome editing technology has emerged in the past decade, especially CRISPR/Cas, which provides new methods for genetic improvement of plant virus resistance and accelerates resistance breeding. Finally, we discuss the potential of these technologies for breeding crops, and the challenges and solutions they may face in the future.