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Liquiritin (LQ), a kind of flavonoid isolated from licorice, was proven to have great potential in treating heart failure. Pharmacokinetic evaluation is important for demonstrating clinical efficacy and mechanisms, and the prototype drug and its metabolite profiling are important for drug discovery and development. However, the metabolism of LQ in acute myocardial infarction (AMI) model rats still needs to be studied in depth. An information‐dependent acquisition (IDA)‐ultra‐high‐performance liquid chromatography‐tandem mass spectrometry (UHPLC‐MS/MS) method was applied to profile LQ metabolites in AMI model rat plasma. Protein precipitation and extraction were used for sample preparation. Chromatographic separation was achieved using an XSelect BEH C18 column (2.1 × 150 mm, 2.5 μm) using gradient elution method combining 0.1% formic acid and acetonitrile with a flow rate of 0.3 mL/min. Twelve metabolites were identified in IDA mode, sulfation, glucuronidation, methylation, methyl esterification, glutamine conjugation, and valine conjugation, and their composite reactions were presumed as the primary pathways of LQ metabolism. The variation in the peak areas showed that the time to reach the peak drug concentration of LQ and 12 metabolites was within 5 h. In summary, IDA‐bridged UHPLC‐MS/MS from characteristic fragment ions toward confidence‐enhanced identification could effectively screen and profile metabolites. [ABSTRACT FROM AUTHOR]

Rapid and accurate detection of pathogens and antimicrobial-resistant (AMR) genes of the pathogens are crucial for the clinical diagnosis and effective treatment of infectious diseases. However, the time-consuming steps of conventional culture-based methods inhibit the precise and early application of anti-infection therapy. For the prompt treatment of pathogen-infected patients, we have proposed a novel tube array strategy based on our previously reported FARPA (FEN1-aided recombinase polymerase amplification) principle for the ultra-fast detection of antibiotic-resistant pathogens on site. The entire process from "sample to result" can be completed in 25 min by combining quick DNA extraction from a urine sample with FARPA to avoid the usually complicated DNA extraction step. Furthermore, a 36-tube array made from commercial 384-well titre plates was efficiently introduced to perform FARPA in a portable analyser, achieving an increase in the loading sample throughput (from several to several tens), which is quite suitable for the point-of-care testing (POCT) of multiple pathogens and multiple samples. Finally, we tested 92 urine samples to verify the performance of our proposed method. The sensitivities for the detection of E. coli, K. pneumoniae, E. faecium, and E. faecalis were 92.7%, 93.8%, 100% and 88.9%, respectively. The specificities for the detection of the four pathogens were 100%. Consequently, our rapid, low-cost and user-friendly POCT method holds great potential for guiding the rational use of antibiotics and reducing bacterial resistance. [ABSTRACT FROM AUTHOR]

Circularly polarized luminescence (CPL) active materials have attracted widespread attention because of their potential applications. Nonetheless, it is still a great challenge to fabricate CPL materials with both high fluorescence quantum efficiency (Φ) and high luminescent asymmetry factor (glum). According to the unique structure characteristics of chiral layered metal–organic frameworks (CLMOFs), herein a novel strategy to construct high‐performance CPL materials, by utilizing the confinement effect of CLMOFs is developed. Conjugate dye molecules, such as fluorescent brighteners, fluorescein, and rhodamine B, which are readily subjected to aggregation‐caused quenching (ACQ) effect, are successfully intercalated into CLMOF matrix, affording blue, yellow–green, and red CPL, respectively. Both high Φ and glum values of up to 91% and 0.069 are obtained, owing to the distinct confinement effect of CLMOFs. After confining dye molecules within CLMOF, the ACQ effect is effectively inhibited, which is beneficial for fluorescence enhancement; simultaneously, the chirality transfer from CLMOF matrix to dyes by controlling their arrangement in the chiral confinement microenvironment, leading to the high glum values. Based on the full‐color and strong CPL, a multi‐dimensional code system is proposed. This work paves a new avenue to design and assemble CPL materials with high Φ and glum, which can be widely adopted. [ABSTRACT FROM AUTHOR]

Human disturbance stands as a prominent factor influencing the ecological environment within natural protected areas. Presently, the issue of balancing human activities and ecological preservation has emerged as a critical concern in the construction of China's natural protected area system. Functional zoning serves as the cornerstone of natural protected area management and represents a pivotal tool in achieving this equilibrium. This study endeavors to introduce a set of functional zoning methods for natural protected areas based on human disturbance assessments. Utilizing Dalingshan Forest Park in Dongguan city which is known for its significant human disturbances as a case study, field surveys were conducted to identify various types of small-scale and understory-hidden human disturbances, such as residential areas, roads, tourist areas, forestry areas, and energy facilities. Subsequently, a microcosmic human disturbance model tailored to forested areas was developed using the analytic hierarchy process. By integrating the findings of macrocosmic human disturbance assessments conducted concurrently by the research group, a functional zoning plan for Dalingshan Forest Park was proposed. The results show that ecological conservation zones within the park should be established in three specific areas, primarily in regions with low-level microcosmic human disturbance (levels 1 and 2) and terrain fluctuations ≥110 m. In contrast, the rational use zone is notably influenced by tourist infrastructure and road networks, predominantly located in regions with high human activity, such as popular tourist destinations and areas with road classifications and vehicular traffic. The microcosmic human disturbance assessment method proposed in this study enhances the rationality and accuracy of natural protected area functional zoning. It provides a more scientifically grounded research approach for similar studies concerning natural protected area functional zoning and contributes valuable insights for the further advancement of China's efforts in the integration and optimization of natural protected areas. [ABSTRACT FROM AUTHOR]

Rationale: Ling‐Gui‐Zhu‐Gan decoction (LGZGD), one of the 100 herbal classic formulas, is clinically used to treat chronic heart failure with remarkable curative effect. However, LGZGD pharmacokinetic parameters in pathological model rats are poorly understood, in particular for special components. As physicochemical properties are specific to each representative component, no standard sample preparation is available for absolute quantification of representative components of LGZGD in rat plasma. Methods: A specific, sensitive and high‐throughput ultrahigh‐performance liquid chromatography–tandem mass spectrometry (UHPLC/MS/MS) method capturing 24 representative components was developed and applied to evaluate the pharmacokinetic parameters of LGZGD in acute myocardial infarction (AMI) rat plasma after intragastric administration (2.4, 4.8 and 9.6 g/kg). Precipitation and extraction were selected and optimized for plasma preparation, and isopropanol precipitation could offer higher recovery and broader coverage. Results: It was expected that AMI could cause less absorption and slower elimination of most of active components of LGZGD. Most of newly reported special components absorbed quickly and eliminated slowly. The average elimination half‐life of the 24 representative components was 10.09 h, which is consistent with the dosage of LGZGD (twice daily). Conclusions: The specificity, linearity, precision and accuracy, recovery, matrix effect and stability were validated according to Food and Drug Administration guidance. The validation results demonstrated that the method could be applied to evaluate the pharmacokinetic parameters of LGZGD in AMI rats. The pharmacokinetic parameters showed substantial improvement in quality research of LGZGD, thereby laying the groundwork for preclinical and clinical trials in chronic heart failure clinical efficacy. [ABSTRACT FROM AUTHOR]

The original 'Green Revolution' genes are associated with gibberellin deficiency. However, in some species, mutations in these genes cause pleiotropic phenotypes, preventing their application in dwarf breeding. The development of novel genotypes with reduced plant height will resolve this problem. In a previous study, we obtained two dwarf lines, L28 and L30, by introducing the Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. C-repeat-binding factor 1 (AmCBF1) into the upland cotton variety R15. We found that Gossypium hirsutum Tubulin beta-1 (GhTUBB1) was downregulated in L28 and L30, which suggested that this gene may have contributed to the dwarf phenotype of L28 and L30. Here, we tested this hypothesis by silencing GhTUBB1 expression in R15 and found that decreased expression resulted in a dwarf phenotype. Interestingly, we found that repressing AmCBF1 expression in L28 and L30 partly recovered the expression of GhTUBB1. Thus, AmCBF1 expression presented a negative relationship with GhTUBB1 expression in L28 and L30. Moreover, yeast one-hybrid and dual-luciferase assays suggest that AmCBF1 negatively regulates GhTUBB1 expression by directly binding to C-repeat/dehydration-responsive (CRT/DRE) elements in the GhTUBB1 promoter, potentially explaining the dwarf phenotypes of L28 and L30. This study elucidates the regulation of GhTUBB1 expression by AmCBF1 and suggests that GhTUBB1 may be a new target gene for breeding dwarf and compact cultivars. [ABSTRACT FROM AUTHOR]

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein‐coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high‐altitude adaptation in alpine plants. Our results detected convergent contractions of disease‐resistance genes in alpine genomes, which might be an energy‐saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self‐incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high‐taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments. [ABSTRACT FROM AUTHOR]

Background: Cytoplasmic male sterility (CMS) is the basis of heterosis exploitation. CMS has been used to hybrid production in cotton, but its molecular mechanism remains unclear. CMS is associated with advanced or delayed tapetal programmed cell death (PCD), and reactive oxygen species (ROS) may mediate this process. In this study, we obtained Jin A and Yamian A, two CMS lines with different cytoplasmic sources. Results: Compared with maintainer Jin B, Jin A anthers showed advanced tapetal PCD with DNA fragmentation, producing excessive ROS which accumulated around the cell membrane, intercellular space and mitochondrial membrane. The activities of peroxidase (POD) and catalase (CAT) enzymes which can scavenge ROS were significantly decreased. However, Yamian A tapetal PCD was delayed with lower ROS content, and the activities of superoxide dismutase (SOD) and POD were higher than its maintainer. These differences in ROS scavenging enzyme activities may be caused by isoenzyme gene expressions. In addition, we found the excess ROS generated in Jin A mitochondria and ROS overflow from complex III might be the source in parallel with the reduction of ATP content. Conclusion: ROS accumulation or abrogation were mainly caused by the joint action of ROS generation and scavenging enzyme activities transformation, which led to the abnormal progression of tapetal PCD, affected the development of microspores, and eventually contributed to male sterility. In Jin A, tapetal PCD in advance might be caused by mitochondrial ROS overproduction, accompanied by energy deficiency. The above studies will provide new insights into the cotton CMS and guide the follow-up research ideas. [ABSTRACT FROM AUTHOR]

Summary: The phytohormones abscisic acid (ABA) and gibberellic acid (GA) antagonistically control the shift between seed dormancy and its alleviation. DELAY OF GERMINATION1 (DOG1) is a critical regulator that determines the intensity of primary seed dormancy, but its underlying regulatory mechanism is unclear.In this study, we combined physiological, biochemical, and genetic approaches to reveal that a bHLH transcriptional factor WRKY36 progressively silenced DOG1 expression to break seed dormancy through ABI5‐BINDING PROTEIN 2 (AFP2) as the negative regulator of ABA signal.AFP2 interacted with WRKY36, which recognizes the W‐BOX in the DOG1 promoter to suppress its expression; Overexpressing WRKY36 broke primary seed dormancy, whereas wrky36 mutants showed strong primary seed dormancy. In addition, AFP2 recruited the transcriptional corepressor TOPLESS‐RELATED PROTEIN2 (TPR2) to reduce histone acetylation at the DOG1 locus, ultimately mediating WRKY36‐dependent inhibition of DOG1 expression to break primary seed dormancy.Our result proposes that the WRKY36‐AFP2‐TPR2 module progressively silences DOG1 expression epigenetically, thereby fine‐tuning primary seed dormancy. [ABSTRACT FROM AUTHOR]

A two-dimensional (2D) layered metal–organic framework (MOF), [Cd(hsb-2)(bdc)·5H2O]n (HSB-W10), was constructed from Cd(II) and the mixed ligands of bdc (1,4-benzendicarboxylate) and hydrogenated Schiff base hsb-2 (1,2-bis(4′-pyridylmethylamino)-ethane) under mild conditions. The self-assembly of HSB-W10 was predicted with the help of a dimension expansion strategy. By slowly diffusing Cd(II) into the bdc solution, one dimensional (1D) zigzag [Cd(bdc)]n chains arranged in a staggered manner were formed, which can be knitted to a 2D two-fold interpenetrated network if a suitable second ligand was employed. When hsb-2 was added as the second ligand, the staggered zigzag Cd-bdc chains were linked together respectively, resulting in the formation of HSB-W10 with a 2D layered structure. Due to its interpenetrated structural features, HSB-W10 exhibited good thermodynamic and chemical stability. HSB-W10 can serve as a host matrix to encapsulate Tb3+ and Eu3+ for tunable fluorescence emission. White-light emission was also obtained by finely tuning the inclusion amounts of Tb3+ and Eu3+. 0.064Tb(H2O)x3+/0.012Eu(H2O)x3+@HSB-W10 was obtained with the corresponding CIE coordinate of (0.33, 0.29). This work provided a new strategy to fabricate MOFs with the interpenetrated network, which is also beneficial to enhancing the performance of MOFs. [ABSTRACT FROM AUTHOR]

A simple, cost-effective and reliable diagnosis of pathogen nucleic acids assay is much required for controlling a pandemic of a virus disease, such as COVID-19. Our previously developed visualized detection of pathogen DNA in a single closed tube is very suitable for POCT. However, virus RNA could not be detected directly and should be reverse-transcribed into cDNA in advance. To enable this visualized assay to detect virus RNA directly, various types of reverse transcriptase were investigated, and finally we found that HiScript II reverse transcriptase could keep active and be well adapted to the one-pot visualized assay in optimized conditions. Reverse transcription, template amplification and amplicon identification by PCR coupled with invasive reaction, as well as visualization by self-assembling of AuNP probes could be automatically and sequentially performed in a closed tube under different temperature conditions, achieving "sample (RNA)-in-result (red color)-out" only by a simple PCR engine plus the naked eye. The visualized RT-PCR is sensitive to unambiguous detection of 5 copies of the N and ORFlab genes of SARS-CoV-2 RNA comparing favourably with qPCR methods (commercialized kit), is specific to genotype 3 variants (Alpha, Beta and Omicron) of SARS-CoV-2, and is very accurate for picking up 0.01% Omicron variant from a large amount of sequence-similar backgrounds. The method is employed in detecting 50 clinical samples, and 10 of them were detected as SARS-CoV-2 positive samples, identical to those by conventional RT-PCR, indicating that the method is cost-effective and labor-saving for pathogen RNA screening in resource-limited regions. [ABSTRACT FROM AUTHOR]

SUMMARY: The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4‐1 and PpKP4‐2) exist in P. patens. Knockout mutants ppkp4‐1 and ppkp4‐2 showed cell death at the protonemal stage, and ppkp4‐2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4‐1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution. Significance Statement: Plants are intimately associated with fungi. However, it remains largely unclear how fungi may have affected the biology of plant partners through genetic integration (e.g. horizontal gene transfer) following organismal interaction. In the present study, we show that KP4 genes in mosses were acquired from fungi through at least three independent horizontal gene transfer events and that the acquired KP4 genes affect the protonemal development of mosses. [ABSTRACT FROM AUTHOR]

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Light and ambient high temperature (HT) have opposite effects on seed germination. Light induces seed germination through activating the photoreceptor phytochrome B (phyB), resulting in the stabilization of the transcription factor HFR1, which in turn sequesters the suppressor PIF1. HT suppresses seed germination and triggers protein S‐nitrosylation. Here, we find that HT suppresses seed germination by inducing the S‐nitrosylation of HFR1 at C164, resulting in its degradation, the release of PIF1, and the activation of PIF1‐targeted SOMNUS (SOM) expression to alter gibberellin (GA) and abscisic acid (ABA) metabolism. Active phyB (phyBY276H) antagonizes HFR1 S‐nitrosylation and degradation by increasing S‐nitrosoglutathione reductase (GSNOR) activity. In line with this, substituting cysteine‐164 of HFR1 with serine (HFR1C164S) abolishes the S‐nitrosylation of HFR1 and decreases the HT‐induced degradation of HFR1. Taken together, our study suggests that HT and phyB antagonistically modulate the S‐nitrosylation level of HFR1 to coordinate seed germination, and provides the possibility to enhance seed thermotolerance through gene‐editing of HFR1. Synopsis: High temperature and photoreceptor phytochrome B antagonistically modulate the S‐nitrosylation level of HFR1 to coordinate seed germination. High temperature (HT) stimulates the S‐nitrosylation of HFR1 at C164 and its degradation, thereby releasing PIF1 to induce SOMNUS (SOM) expression and seed dormancy. Active phyB antagonizes HT‐induced S‐nitrosylation and degradation of HFR1 by increasing S‐nitrosoglutathione reductase (GSNOR) activity. Substituting cysteine‐164 of HFR1 with serine (HFR1C164S) abolishes the HT‐induced S‐nitrosylation of HFR1 and decreases its degradation, ultimately suppressing SOM expression to enhance seed thermotolerance. [ABSTRACT FROM AUTHOR]

How horizontal gene transfer (HGT) has contributed to the evolution of animals and plants remains a major puzzle. Despite recent progress, defining the overall scale and pattern of HGT events in land plants has been largely elusive. In this study, we performed systematic analyses for acquired genes in different plant groups and throughout land plant evolution. We found that relatively recent HGT events occurred in charophytes and all major land plant groups, but their frequency declined rapidly in seed plants. Two major episodes of HGT events occurred in land plant evolution, corresponding to the early evolution of streptophytes and the origin of land plants, respectively. Importantly, a vast majority of the genes acquired in the two episodes have been retained in descendant groups, affecting numerous activities and processes of land plants. We analyzed some of the acquired genes involved in stress responses, ion and metabolite transport, growth and development, and specialized metabolism, and further assessed the cumulative effects of HGT in land plants. The role of horizontal gene transfer in the evolution of multicellular eukaryotes such as plants and animals has long been elusive. This study identifies two major episodes of horizontal gene transfer in the evolution of land plants. Genes acquired from environmental organisms have fundamentally shaped the structure, physiology, and development of land plants. [ABSTRACT FROM AUTHOR]

In order to solve the problem that the blurred image of a moving object decreases accuracy in the process of detecting the payload swing angle of an overhead crane based on vision, and the tracking failure caused by the drastic change of grey targets, a robust real-time detection method of the load swing angle of a bridge crane is proposed. This method uses a spherical marker attached to the load, which is insensitive to rotation and tilt when it is detected. First, it uses the mean shift algorithm combined with Kalman filter to track the moving objects in the image plane continuously, and then integrates the method of minimum area circle to detect the spherical marker image in the region of interest accurately and quickly. Finally, combined with the geometric method, the real-time swing angle is calculated. In addition, the angle diagram method is used to increase the speed of calculating the swing angle. The experimental results show that the method is effective for detecting the load target swing angle of different trolley motion speed. [ABSTRACT FROM AUTHOR]

Objectives. Ling-Gui-Zhu-Gan decoction (LGZGD) is a potentially effective treatment for heart failure, and it showed significant anti-inflammatory potential in our previous studies. However, its ability to ameliorate heart failure through regulation of oxidative stress response is still unknown. This study was aimed to investigate the protective effect of LGZGD-containing serum on H2O2-induced oxidative injury in H9c2 cells and explore the underlying mechanism. Methods. Eighteen rats were randomly divided into two groups: the blank control group and LGZGD group. The LGZGD group rats were administrated with 8.4 g/kg/d LGZGD for seven consecutive days through gavage, while the blank control group rats were given an equal volume of saline. The serum was extracted from all the rats. To investigate the efficacy and the underlying mechanism of LGZGD, we categorized the H9c2 cells into groups: the control group, model group, normal serum control (NSC) group, LGZGD group, LGZGD + all-trans-retinoic acid (ATRA) group, and ATRA group. Malonedialdehyde (MDA) and superoxide dismutase (SOD) were used as markers for oxidative stress. Dichlorodihydrofluorescin diacetate (DCFH-DA) staining was used to measure the levels of reactive oxygen species (ROS). The apoptosis rate was detected using flow cytometry. The expression levels of pro-caspase-3, cleaved-caspase-3, Bcl-2, Bax, Keap1, Nrf2, and HO-1 were measured using western blotting. The mRNA levels of Keap1, Nrf2, and HO-1 were measured using RT-qPCR. Results. The LGZGD attenuated injury to H9c2 cells and reduced the apoptosis rate. It was also found to upregulate the SOD activity and suppress the formation of MDA and ROS. The expression levels of pro-caspase-3 and Bcl-2 were significantly increased, while those of cleaved-caspase-3 and Bax were decreased in the LGZGD group compared with the model group. As compared with the model group, the LGZGD group demonstrated decreased Keap1 protein expression and significantly increased Nrf2 nuclear expression and Nrf2-mediated transcriptional activity. ATRA was found to reverse the LGZGD-mediated antioxidative and antiapoptotic effect on injured H9c2 cells induced by H2O2. Conclusion. Our results demonstrated that LGZGD attenuated the H2O2-induced injury to H9c2 cells by inhibiting oxidative stress and apoptosis via the Nrf2/Keap1/HO-1 pathway. These observations suggest that LGZGD might prevent and treat heart failure through regulation of the oxidative stress response. [ABSTRACT FROM AUTHOR]

Purpose: Photodynamic therapy (PDT) schedules are based on sensitiser dose, light dose, and drug-light interval. The aim of the phase Ι study was to choose optimal dose and drug-light interval for PDT with photocyanine using pharmacokinetics (PK) and pharmacodynamics (PD). Methods: Twenty-eight cancer patients were enrolled. In trial A, 12 patients received one of four ascending doses of photocyanine intravenously 24 h prior to 180–270 J/cm2 illumination. 0.2 mg/kg dose was infused to ten patients 12–48 h prior to 120 J/cm2 illumination in trial B. In trial C, 0.1 mg/kg dose was infused to six patients 6 or 12 h prior to 180–270 J/cm2 illumination. Serum concentrations of photocyanine were measured, and simulations were performed to assess the effect of drug exposure in tissue on responses. Results: Analysis of photocyanine levels of patients indicated that the two-compartment model best fit the data. Simulations showed that the rates of the drug entering tissues and leaving tissues were equal at 8–12 h after injection. Patients experienced pain which was related to photocyanine serum levels, especially with serum levels above 2500 ng/ml. Fewer non-responders were observed at serum levels higher than 1000 ng/ml for illumination at least 12 h after administration. Conclusion: It is the first report of human trials of photocyanine, and the results suggested that patients receive 180 J/cm2 illumination about 20–30 min at serum concentrations of photocyanine between 1000 and 2500 ng/ml at least 10 h after administration. [ABSTRACT FROM AUTHOR]

Ligustilide (LIG), a main lipophilic component isolated from Cnidii Rhizoma (Cnidium officinale, rhizome) and Angelicae Gigantis Radix (Angelica gigas Nakai, root), has been shown to alleviate cerebral ischemia injury and paly a neuroprotective role. We investigated mechanisms underlying the antiapoptotic effects of LIG in vitro and in vivo , respectively, using cultured primary hippocampal neurons under oxygen-glucose deprivation/reperfusion (OGD/R) and rats under cerebral ischemia reperfusion(I/R) conditions. In vitro studies revealed that the suppressed apoptosis in hippocampal neurons upon LIG treatment was associated with reduced calcium influx and generation of reactive oxygen species. The LIG-treated hippocampal neurons exhibited decreased the ratio of Bax/Bcl-2, and the release of CytC from mitochondria as well as the expression of cleaved caspase-3, which were accompanied with enhanced the phosphorylation of Akt protein, in a PI3K-dependent manner. In vivo studies demonstrated a neuroprotective role of LIG in attenuating cerebral infarction volume, neurological injury and hippocampal neuron injury, suggesting that LIG could reverse ischemia reperfusion(I/R)-induced apoptosis of hippocampal neurons. These results together suggest that LIG may be considered as a neuroprotectant in the treatment of ischemia stroke. [ABSTRACT FROM AUTHOR]

The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella. Our results indicated that the mutation frequency ranged from 3.39 × 10–4 to 5.46 × 10–2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes (mut S, mut T, mut L, and uvr D) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mut S, mut T, and mut L. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella. [ABSTRACT FROM AUTHOR]

Plant colonization of land has been intimately associated with mycorrhizae or mycorrhizae-like fungi. Despite the pivotal role of fungi in plant adaptation, it remains unclear whether and how gene acquisition following fungal interaction might have affected the development of land plants. Here we report a macro2 domain gene in bryophytes that is likely derived from Mucoromycota, a group that includes some mycorrhizae-like fungi found in the earliest land plants. Experimental and transcriptomic evidence suggests that this macro2 domain gene in the moss Physcomitrella patens, PpMACRO2, is important in epigenetic modification, stem cell function, cell reprogramming and other processes. Gene knockout and over-expression of PpMACRO2 significantly change the number and size of gametophores. These findings provide insights into the role of fungal association and the ancestral gene repertoire in the early evolution of land plants. Plant evolution is intimately associated with fungal partners. Here the authors provide evidence that Physcomitrella patens MACRO2, a gene likely derived from early mycorrhizae-like fungi, was transferred to early land plants and plays an important role in regulating stem cell growth and gametophore development in moss. [ABSTRACT FROM AUTHOR]

Cytokinin oxidase/dehydrogenase (CKX) is a key enzyme responsible for the degradation of endogenous cytokinins. However, the origins and roles of CKX genes in angiosperm evolution remain unclear. Based on comprehensive bioinformatic and transgenic plant analyses, we demonstrate that the CKXs of land plants most likely originated from an ancient chlamydial endosymbiont during primary endosymbiosis. We refer to the CKXs retaining evolutionarily ancient characteristics as "ancient CKXs" and those that have expanded and functionally diverged in angiosperms as "non-ancient CKXs". We show that the expression of some non-ancient CKXs is rapidly inducible within 15 min upon the dehydration of Arabidopsis, while the ancient CKX (AtCKX7) is not drought responsive. Tobacco plants overexpressing a non-ancient CKX display improved oxidative and drought tolerance and root growth. Previous mutant studies have shown that non-ancient CKXs regulate organ development, particularly that of flowers. Furthermore, ancient CKXs preferentially degrade cis-zeatin (cZ)-type cytokinins, while non-ancient CKXs preferentially target N6-(Δ2-isopentenyl) adenines (iPs) and trans-zeatins (tZs). Based on the results of this work, an accompanying study (Wang et al. 10.1038/s41438-019-0211-x) and previous studies, we hypothesize that non-ancient CKXs and their preferred substrates of iP/tZ-type cytokinins regulate angiosperm organ development and environmental stress responses, while ancient CKXs and their preferred substrates of cZs play a housekeeping role, which echoes the conclusions and hypothesis described in the accompanying report (Wang, X. et al. Evolution and roles of cytokinin genes in angiosperms 1: Doancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? Hortic Res7, (2020). 10.1038/s41438-019-0211-x). [ABSTRACT FROM AUTHOR]

This study aims to figure out the methylation of long non‐coding RNA GAS5 promoter in cervical cancer and the mechanism of GAS5 on the progression of cervical cancer cells. The expression of GAS5 and methylation state of GAS5 in cervical cancer tissues and cells were determined. With the aim to to explore the ability of GAS5 in the proliferation, cell cycle progression, apoptosis, invasion, migration as well as the tumor growth, and metastasis in nude mice were determined. The expression of GAS5 was decreased and methylation state of GAS5 was elevated in cervical cancer. Overexpression of GAS5 inhibited proliferation, cell cycle progression, invasion, migration while inducing apoptosis of cervical cancer cells as well as suppressed tumor growth and metastasis in nude mice. Our study demonstrates that abnormal methylation of GAS5 contributes to poor expression of GAS5 in cervical cancer. In addition, upregulation of GAS5 inhibits the cervical cancer development. [ABSTRACT FROM AUTHOR]

Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered 'ready to eat', once it is contaminated by foodborne pathogens such as Salmonella , the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015–2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of antibiotic resistance genes and amino acid mutations in 219 Salmonella isolates, followed by subtyping of 115 representative isolates. The average detection rate of Salmonella -positive PRTEM was 58.9%, and the average most probable number (MPN) of Salmonella in positive samples was 2.27 logMPN per gram of sample (range: 2.10–2.43). Ten serotypes were identified from the 219 Salmonella isolates, with S. Thompson (37.9%) and S. Indiana (20.5%) being predominant. The remaining serotypes were S. Typhi (7.8%), S. Typhimurium (7.3%), S. Mbandaka (6.9%), S. Albany (6.4%), S. Blockley (5.5%), S. Infantis (4.1%), S. Escanaba (3.2%), and S. Dusseldorf (0.5%). All isolates were resistant to ceftiofur (100%), while most of them were resistant to ciprofloxacin (99.1%), amoxicillin-clavulanic acid (97.7%), trimethoprim-sulfamethoxazole (96.4%), ampicillin (92.3%), sulfisoxazole (92.2%), tetracyclines (90.4%), and nalidixic acid (90.4%), respectively. A single mutation of Ser83Phe (27.1%) and double mutations of Ser83Phe-Asp87Gly (25.9%) in GyrA were detected in 85 isolates, whereas mutations of Thr57Ser (63.9%) and Ser80Arg (36.1%) in ParC were detected in 122 isolates. qnr B, oqx AB, aac(6′)-Ib , and qnr A were present in 50 (22.8%), 48 (21.9%), 26 (11.9%), and 1 (0.5%) isolate(s), respectively. Pulse field gel electrophoresis results revealed that those isolates recovered from the same type of PRTEM or the same sampling place shared identical or similar DNA profiles, antibiotic resistance phenotypes, and even plasmid-mediated quinolone resistance encoding genes. The findings indicate that Salmonella is commonly prevalent in PRTEMs at high concentrations in Shaanxi, China. More attention should be paid to the processing and storage of this ready-to-eat food to prevent bacterial contamination and foodborne outbreaks. [ABSTRACT FROM AUTHOR]

Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula , we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies. [ABSTRACT FROM AUTHOR]

FRIGIDA (FRI), as the major regulator of flowering time in Arabidopsis accessions, can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. In addition to FLC , other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatio-temporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets, MADS AFFECTING FLOWERING4 (MAF4) and MAF5 , in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as the pro-embryo stage is enough to up-regulate FLC expression to delay flowering. Together, our findings demonstrate the spatio-temporal effect of FRI on delaying flowering, and we propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI. [ABSTRACT FROM AUTHOR]

Salinity levels and drought status of coastal wetlands may be strongly affected by climate change, and changes in the nitrogen cycle of mangrove wetlands may also be affected. We established combinations of three salinity and water levels with applied stable isotope15N to study the δ15N distributions in the sediment and plants of a greenhouse-based simulated mangroveAegiceras corniculatumwetland system. The stable isotope13C and15N, C and N contents and the C:N ratio were determined. Results showed that increasing in salinity significantly increased the δ13C value in plant organs. The δ15N value of plant organs increased with increasing water level in low salinity (10‰) and medium salinity (20‰) treatment groups but not in the high salinity (30‰) treatment group. This may attributed toA. corniculatumadjusting the δ15N distribution in different organs in response to high salinity stress. Compared to the δ13C, the δ15N values of plant were strongly affected by salinity and water level treatments, indicating that the behavior of N cycle was somewhat different than the C cycle, and affected by the combined effects of both salinity and water level. Most of15N absorbed by plant tissues were in leaves except for the highest salinity and high water level treatment, showing at increasing water level, the proportion of15N increased in root. Overall, the measured indicators exhibited different responses to salinity level and water level, suggesting that the changes in salinity and water levels have an impact on N cycling processes of wetland systems. [ABSTRACT FROM PUBLISHER]

Iron (Fe) is an essential micronutrient for humans, and iron deficiency is the most common micronutrient deficiency worldwide. Research on the genetic basis of iron concentration in maize kernels will provide guidance for the development of iron-rich crops, a major breeding goal to address iron deficiency. The maize Yellow Stripe 1 ( ZmYS1) gene encodes a specific transporter that takes up Fe(III)-phytosiderophore complexes into roots. Here, we re-sequenced ZmYS1 gene in 88 elite maize inbred lines and detected the association between the nucleotide polymorphisms and micronutrient concentrations in maize kernels. Our analyses detected a total of 71 sequence variants in ZmYS1, including 61 single nucleotide polymorphisms (SNPs) and 10 insertions and deletions (indels), from the tested population. Fourteen haplotypes, which encode 13 different ZmYS1 proteins, are classified based on the polymorphism in the coding region. Numerous polymorphic sites in maize ZmYS1 locus were found in linkage disequilibrium (LD) that decay with increasing physical distance, and at least 14 recombination events have contributed to the LD and haplotype diversity of this gene. Additionally, our data show that a non-synonymous site in the ZmYS1 gene is associated with the maize kernel Fe concentration, and two other non-synonymous sites with Zinc (Zn) concentration. These findings suggest that the polymorphism in maize ZmYS1 locus may be used for biofortifying kernel mineral concentrations in maize breeding programs. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome. [ABSTRACT FROM AUTHOR]

A major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. However, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown., Here, we investigate the evolution of the land plant TAL-type transaldolase ( TAL) gene and its potential function in rice ( Oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively., TAL genes are only present in land plants and bacteria. Phylogenetic analyses suggest that land plant TAL genes are derived from Actinobacteria through an ancient horizontal gene transfer (HGT) event. Further evidence reveals that land plant TAL genes have undergone positive selection and gained several introns following its acquisition by the most recent common ancestor of land plants. Transgenic plant experiments show that rice TAL is specifically expressed in vascular tissues and that knockdown of TAL expression leads to changes in both the number and pattern of vascular bundles., Our findings show that the ancient HGT of TAL from bacteria probably plays an important role in plant vascular development and adaptation to land environments. [ABSTRACT FROM AUTHOR]

Winter-annual accessions of Arabidopsis thaliana require either exposure to cold stress or vernalization to initiate flowering via FRIGIDA (FRI). FRI acts as a scaffold protein to recruit several chromatin modifiers that epigenetically modify flowering genes. Here, we report that proteasome-mediated FRI degradation regulates flowering during vernalization in Arabidopsis. Our genetic and biochemical experiments demonstrate that FRI directly interacts with the BTB (Bric-a-Brac/Tramtrack/Broad Complex) proteins LIGHT-RESPONSE BTB1 (LRB1) and LRB2 as well as the CULLIN3A (CUL3A) ubiquitin-E3 ligase in vitro and in vivo, leading to proteasomal degradation of FRI during vernalization. The degradation of FRI is accompanied by an increase in the levels of the long noncoding RNA ColdAIR , which reduces the level of histone H3Lys4 trimethylation (H3K4me3) in FLOWERING LOCUS C chromatin to promote flowering. Furthermore, we found that the cold-induced WRKY34 transcription factor binds to the W-box in the promoter region of CUL3A to modulate CUL3A expression. Deficiency of WRKY34 suppressed CUL3A transcription to enhance FRI protein stability and led to late flowering after vernalization. Conversely, overexpression of WRK34 promoted FRI degradation and early flowering through inducing CUL3A accumulation. Together, these data suggest that WRKY34-induced and CUL3A-dependent proteolysis of FRI modulate flowering in response to vernalization. [ABSTRACT FROM AUTHOR]

Cytoplasmic male sterility (CMS) is the failure to produce functional pollen, which is inherited maternally. And it is known that anther development is modulated through complicated interactions between nuclear and mitochondrial genes in sporophytic and gametophytic tissues. However, an unbiased transcriptome sequencing analysis of CMS in cotton is currently lacking in the literature. This study compared differentially expressed (DE) genes of floral buds at the sporogenous cells stage (SS) and microsporocyte stage (MS) (the two most important stages for pollen abortion in JA-CMS) between JA-CMS and its fertile maintainer line JB cotton plants, using the Illumina HiSeq 2000 sequencing platform. A total of 709 (1.8%) DE genes including 293 up-regulated and 416 down-regulated genes were identified in JA-CMS line comparing with its maintainer line at the SS stage, and 644 (1.6%) DE genes with 263 up-regulated and 381 down-regulated genes were detected at the MS stage. By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage. Quantitative RT-PCR was used to validate 7 randomly selected DE genes. Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages. All these four biological processes play important roles in reactive oxygen species (ROS) homeostasis, which may be an important factor contributing to the sterile trait of JA-CMS. Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS. [ABSTRACT FROM AUTHOR]

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. [ABSTRACT FROM AUTHOR]

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes. [ABSTRACT FROM AUTHOR]

The aim of this study was to develop homogeneous and stable plasmid DNA reference materials for detecting the mechanisms of resistance to quinolones and fluoroquinolones in foodborne pathogens. The DNA fragments of 11 target genes associated with quinolone and fluoroquinolone resistance were artificially synthesized, inserted into plasmid vectors, and transferred into recipient cells. PCR and sequencing of DNA were performed to assess the genetic stability of the target DNA in recombinant Escherichia coli DH5α cells during subculturing for 15 generations. The limit of detection (LOD) of the target DNA was determined using PCR and real-time qualitative PCR (qPCR). The homogeneity and storage stability of plasmid DNA reference materials were evaluated in terms of plasmid DNA quantity, PCR-measured gene expression, and qPCR threshold cycle. All 11 target DNAs were successfully synthesized and inserted into vectors to obtain recombinant plasmids. No nucleotide mutations were identified in the target DNA being stably inherited and detectable in the corresponding plasmids during subculturing of recombinant strains. When the target DNA was assessed using PCR and qPCR, the LOD was ≤1.77 × 105 and 3.26 × 104 copies/μL, respectively. Further, when the reference materials were stored at 37 °C for 13 days, 4 °C for 90 days, and −20 °C for 300 days, each target DNA was detectable by PCR, and no mutations were found. Although the threshold cycle values of qPCR varied with storage time, they were above the LOD, and no significant differences were found in the quantity of each plasmid DNA at different timepoints. Further, the homogeneity and stability of the materials were highly consistent with the requirements of standard reference materials. To summarize, considering that our plasmid DNA reference materials conformed to standard requirements, they can be used to detect the mechanisms of quinolone and fluoroquinolone resistance in foodborne pathogens. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer (HGT) may not only create genome mosaicism, but also introduce evolutionary novelties to recipient organisms. HGT in plastid genomes, though relatively rare, still exists. HGT-derived genes are particularly common in unicellular photosynthetic eukaryotes and they also occur in multicellular plants. In particular, ancient HGT events occurring during the early evolution of primary photosynthetic eukaryotes were probably frequent. There is clear evidence that anciently acquired genes played an important role in the establishment of primary plastids and in the transition of plants from aquatic to terrestrial environments. Although algal genes have often been used to infer historical plastids in plastid-lacking eukaryotes, reliable approaches are needed to distinguish endosymbionts-derived genes from those independently acquired from preferential feeding or other activities. [ABSTRACT FROM AUTHOR]

Background: Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results: Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions: Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution. [ABSTRACT FROM AUTHOR]