Genome-wide identification and expression analysis of the trihelix transcription factor family in sesame (Sesamum indicum L.) under abiotic stress.

BACKGROUND: The plant trihelix gene family is among the earliest discovered transcription factor families, and it is vital in modulating light, plant growth, and stress responses. METHODS: The identification and characterization of trihelix family members in the sesame genome were analyzed by bioinformatics methods, and the expression patterns of sesame trihelix genes were assessed by quantitative real-time PCR. RESULTS: There were 34 trihelix genes discovered in the genome of sesame, which were irregularly distributed among 10 linkage groups. Also, the genome contained 5 duplicate gene pairs. The 34 trihelix genes were divided into six sub-families through a phylogenetic study. A tissue-specific expression revealed that SiTH genes exhibited spatial expression patterns distinct from other trihelix genes in the same subfamily. The cis-element showed that the SiTHs gene promoter contained various elements associated with responses to hormones and multiple abiotic stresses. Additionally, the expression patterns of 8 SiTH genes in leaves under abiotic stresses demonstrated that all selected genes were significantly upregulated or downregulated at least once in the stress period. Furthermore, the SiTH4 gene was significantly induced in response to drought and salt stress, showing that SiTH genes may be engaged in the stress response mechanisms of sesame. CONCLUSION: These findings establish a foundation for further investigation of the trihelix gene-mediated response to abiotic stress in sesame.

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement.

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.

Recognition of Freezing of Gait in Parkinson's Disease Based on Machine Vision.

Background: Freezing of gait (FOG) is a common clinical manifestation of Parkinson's disease (PD), mostly occurring in the intermediate and advanced stages. FOG is likely to cause patients to fall, resulting in fractures, disabilities and even death. Currently, the pathogenesis of FOG is unclear, and FOG detection and screening methods have various defects, including subjectivity, inconvenience, and high cost. Due to limited public healthcare and transportation resources during the COVID-19 pandemic, there are greater inconveniences for PD patients who need diagnosis and treatment. Objective: A method was established to automatically recognize FOG in PD patients through videos taken by mobile phone, which is time-saving, labor-saving, and low-cost for daily use, which may overcome the above defects. In the future, PD patients can undergo FOG assessment at any time in the home rather than in the hospital. Methods: In this study, motion features were extracted from timed up and go (TUG) test and the narrow TUG (Narrow) test videos of 50 FOG-PD subjects through a machine learning method; then a motion recognition model to distinguish between walking and turning stages and a model to recognize FOG in these stages were constructed using the XGBoost algorithm. Finally, we combined these three models to form a multi-stage FOG recognition model. Results: We adopted the leave-one-subject-out (LOSO) method to evaluate model performance, and the multi-stage FOG recognition model achieved a sensitivity of 87.5% sensitivity and a specificity of 79.82%. Conclusion: A method to realize remote PD patient FOG recognition based on mobile phone video is presented in this paper. This method is convenient with high recognition accuracy and can be used to rapidly evaluate FOG in the home environment and remotely manage FOG-PD, or screen patients in large-scale communities.

Dual role of interleukin-33 in tumors. / ç™½ç»†èƒžä»‹ç´ -33在肿瘤中的双重作用.

Interleukin-33 (IL-33) is a new member of the IL-1 cytokine family which plays roles in the nucleus as a nuclear factor and is released by damaged or necrotic cells to act as a cytokine. It can be released via damaged or necrotic cells and functions as a cytokine. The released IL-33 activates the downstream NF-κB and MAPKs signaling pathways through the isomers of the specific receptor ST2 and the interleukin-1 receptor accessory protein (IL-1RAcP), resulting in danger signals and the activated multiple immune responses. IL-33 is abnormally expressed in various tumors and involves in tumorigenesis, development, and metastasis. Moreover, IL-33 can play both pro-tumor and anti-tumor roles in the same type of tumor.

QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing.

Improvement in sesame drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. In this study, three traits and their relative values, including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and osmotic conditions in a recombinant inbred line (RIL) population derived from cross of Zhushanbai and Jinhuangma. Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through whole genome re-sequencing (WGS) strategy. Quantitative trait loci (QTL) mapping was performed for all the traits. A total of 34 QTLs were detected on 10 chromosomes. Among them, 13 stable QTLs were revealed in two independent experiments, eight of them were associated with traits under water stress condition. One region on chromosome 12 related to RL under osmotic condition and relative RL had the highest LOD value and explained the largest phenotypic variation among all the QTLs detected under water stress condition. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

Inhibition of endoplasmic reticulum stress alleviates secondary injury after traumatic brain injury.

Apoptosis after traumatic brain injury has been shown to be a major factor influencing prognosis and outcome. Endoplasmic reticulum stress may be involved in mitochondrial mediated neuronal apoptosis. Therefore, endoplasmic reticulum stress has become an important mechanism of secondary injury after traumatic brain injury. In this study, a rat model of traumatic brain injury was established by lateral fluid percussion injury. Fluorescence assays were used to measure reactive oxygen species content in the cerebral cortex. Western blot assays were used to determine expression of endoplasmic reticulum stress-related proteins. Hematoxylin-eosin staining was used to detect pathological changes in the cerebral cortex. Transmission electron microscopy was used to measure ultrastructural changes in the endoplasmic reticulum and mitochondria. Our results showed activation of the endoplasmic reticulum stress-related unfolded protein response. Meanwhile, both the endoplasmic reticulum stress response and mitochondrial apoptotic pathway were activated at different stages post-traumatic brain injury. Furthermore, pretreatment with the endoplasmic reticulum stress inhibitor, salubrinal (1 mg/kg), by intraperitoneal injection 30 minutes before injury significantly inhibited the endoplasmic reticulum stress response and reduced apoptosis. Moreover, salubrinal promoted recovery of mitochondrial function and inhibited activation of the mitochondrial apoptotic pathway post-traumatic brain injury. These results suggest that endoplasmic reticulum stress might be a key factor for secondary brain injury post-traumatic brain injury.

Fine Mapping of Two Wheat Powdery Mildew Resistance Genes Located at the Cluster.

Powdery mildew caused by (DC.) f. sp. () is a globally devastating foliar disease of wheat ( L.). More than a dozen genes against this disease, identified from wheat germplasms of different ploidy levels, have been mapped to the region surrounding the locus on the long arm of chromosome 7A, which forms a resistance ()-gene cluster. and from einkorn wheat ( L.) were two of the genes belonging to this cluster. This study was initiated to fine map these two genes toward map-based cloning. Comparative genomics study showed that macrocolinearity exists between L. chromosome 1 (Bd1) and the - region, which allowed us to develop markers based on the wheat sequences orthologous to genes contained in the Bd1 region. With these and other newly developed and published markers, high-resolution maps were constructed for both and using large F populations. Moreover, a physical map of was constructed through chromosome walking with bacterial artificial chromosome (BAC) clones and comparative mapping. Eventually, and were restricted to a 0.12- and 0.86-cM interval, respectively. Based on the closely linked common markers, , , and (another powdery mildew resistance gene in the cluster) were not allelic to one another. Severe recombination suppression and disruption of synteny were noted in the region encompassing . These results provided useful information for map-based cloning of the genes in the cluster and interpretation of their evolution.

Synergistic Activity of Econazole-Nitrate and Chelerythrine against Clinical Isolates of Candida albicans.

The aim of this investigation was to assess the in-vitro interaction of two antifungal agents, econazole-nitrate and chelerythrine, against ten fluconazole-resistant clinical isolates and one ATCC type strain 10231 of Candida albicans. The checkerboard microdilution method was performed according to the recommendations of the National Committee for Clinical Laboratory Standards, and the results were determined by visual examination. The interaction intensity was tested in all isolates using the fractional inhibitory concentration index (FICI). These experiments showed synergism between econazole-nitrate and chelerythrine in antifungal activity against C. albicans, and no antagonistic activity was observed in any of the strains tested. Moreover, time-kill curves were performed with selected strains to confirm the positive interactions. The similarity between the results of the FICI values and the time-kill curves revealed that chelerythrine greatly enhances the antifungal effects of econazole-nitrate against isolates of C. albicans. This synergistic effect may markedly reduce the dose of econazole-nitrate required to treat candidiasis, thereby decreasing the econazole-nitrate toxic side effects. This novel synergism might provide a potential combination treatment against fungal infections.

[Establishment of an allele-specific PCR method for direct screening of CYP21A2 gene mutation].

OBJECTIVE: To establish an allele-specific PCR method for detect screening of CYP21A2 gene mutation. METHODS: Allele-specific PCR primers and analogy primers were designed based on the sequence alignment of CYP21A2 and CYP21AP genes. Genomic DNA was extracted from blood specimens of 4 patients with 21-hydroxylase deficiency and 5 healthy controls and respectively amplified with allele-specific PCR primers and analogy primers and sequenced. RESULTS: Mutations of CYP21A2 including IVS2-13A/C>G, Arg356Trp and Arg149Pro were found with the established method in all of the 4 patients but not in the healthy controls. When detected with the analogy primers set, IVS2-13A/C>G and Arg356Trp were observed in both patients and healthy controls. CONCLUSION: The allele-specific PCR-based method is a simple, effective and reliable method for the detection of CYP21A2 gene mutation.

Genome-wide transcription analyses in Mycobacterium tuberculosis treated with lupulone.

Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, still causes higher mortality than any other bacterial pathogen until now. With the emergence and spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR-TB) strains, it becomes more important to search for alternative targets to develop new antimycobacterial drugs. Lupulone is a compound extracted from Hops (Hurnulus lupulus), which exhibits a good antimicrobial activity against M. tuberculosis with minimal inhibitory concentration (MIC) value of 10 µg/mL, but the response mechanisms of lupulone against M. tuberculosis are still poorly understood. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of M. tuberculosis H37Rv triggered by exposure to MIC of lupulone. A total of 540 genes were found to be differentially regulated by lupulone. Of these, 254 genes were upregulated, and 286 genes were downregulated. A number of important genes were significantly regulated which are involved in various pathways, such as surface-exposed lipids, cytochrome P450 enzymes, PE/PPE multigene families, ABC transporters, and protein synthesis. Real-time quantitative RT-PCR was performed for choosed genes to verified the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of M. tuberculosis to a lupulone challenge.

Genome-wide transcription analyses in Mycobacterium tuberculosis treated with lupulone

Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, still causes higher mortality than any other bacterial pathogen until now. With the emergence and spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR-TB) strains, it becomes more important to search for alternative targets to develop new antimycobacterial drugs. Lupulone is a compound extracted from Hops (Hurnulus lupulus), which exhibits a good antimicrobial activity against M. tuberculosis with minimal inhibitory concentration (MIC) value of 10 µg/mL, but the response mechanisms of lupulone against M. tuberculosis are still poorly understood. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of M. tuberculosis H37Rv triggered by exposure to MIC of lupulone. A total of 540 genes were found to be differentially regulated by lupulone. Of these, 254 genes were upregulated, and 286 genes were downregulated. A number of important genes were significantly regulated which are involved in various pathways, such as surface-exposed lipids, cytochrome P450 enzymes, PE/PPE multigene families, ABC transporters, and protein synthesis. Real-time quantitative RT-PCR was performed for choosed genes to verified the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of M. tuberculosis to a lupulone challenge.

DNA microarray gene expression profile of Mycobacterium tuberculosis when exposed to osthole.

Tuberculosis (TB), affecting one-third of the global population, kills an estimated two to three million people every year. The development of drug resistance is becoming a serious threat to any attempt to control this disease, which underscores the need for new agents targeting Mycobacterium tuberculosis (M. tuberculosis). Osthole (7-methoxy-8-isopentenoxycoumarin) is a coumarin derivative present in many medicinal plants. Previous studies have shown that osthole possesses antimycobacterial effects, however, the action mechanism of osthole is unclear. In the study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of M. tuberculosis H37Rv triggered by exposure to osthole. Analysis of the microarray data revealed that a total of 478 genes were differentially regulated by osthole. Of these, 241 genes were upregulated, and 237 genes were downregulated. Some of the important genes that were significantly regulated are related to different pathways such as fumarate reductase, class I peroxidase, cell wall, nitrate respiration, and protein synthesis. Real-time quantitative RT-PCR was performed for chosen genes to validate the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of M. tuberculosis when exposed to osthole.

Genome-wide expression profiling of the response to linezolid in Mycobacterium tuberculosis.

Tuberculosis (TB) is still one of the most common causes of death in the world. The emergence of multidrug-resistant and extensively drug-resistant (XDR-TB) Mycobacterium tuberculosis (M. tuberculosis) strains has increased the importance of searching for alternative targets to develop new antimycobacterial drugs. Linezolid, the first of oxazolidinones, is active in vitro against M. tuberculosis, but the response mechanisms of M. tuberculosis to linezolid are still poorly understood. To reveal the possible mechanism of action of linezolid against M. tuberculosis, commercial oligonucleotide microarrays were used to analyze the genome-wide transcriptional changes triggered by treatment with subinhibitory concentrations of linezolid. Quantitative real-time RT-PCR was performed for selected genes to verify the microarray results. A total of 729 genes were found to be differentially regulated by linezolid. Among these, 318 genes were upregulated, and 411 genes were downregulated. A number of important genes were significantly regulated that are involved in various pathways, such as protein synthesis, sulfite metabolism, and genes involved in the cell envelope and virulence. This genome-wide transcriptomics approach produced the first insights into the response of M. tuberculosis to a linezolid challenge.

In-vitro Antimycoplasmal Activity of Triclosan in Combination with Fluoroquinolones against Five mycoplasma Species.

Mycoplasmosis caused by mycoplasma has immensely reduced the performance of commercial animal husbandry, along with prevalence and increase of drug resistance in mycoplasma, thus new agents and therapies are urgently needed. Triclosan is a broad spectrum antimicrobial agent with a favorable safety profile. In the present study, we tested the antimycoplasmal activity of triclosan alone, as well as the in-vitro interaction of triclosan and the fluoroquinolones, gatifloxacin (GAT), moxifloxacin (MXF), levofloxacin (LVX), sparfloxacin (SPX), ciprofloxacin (CIP), enrofloxacin (EFX), and norfloxacin (NOR), against five mycoplasma species. This study demonstrated that triclosan had antimycoplasmal activity against both fluoroquinolones-sensitive species and a fluoroquinolones-resistant species isolated from clinic, with minimum inhibitory concentrations (MICs) of 16.0-64.0 µg/mL and 64.0 µg/ mL, respectively. A synergistic antimycoplasmal effect between triclosan and GAT, MFX or EFX against the five mycoplasma species was observed, with modulation factors (MFs) of 4-8, 4-16, 8-32, respectively, and fractional inhibitory concentration indexes (FICIs) of 0.375- 0.500, 0.350-0.500, 0.281-0.375, respectively. The combination of triclosan with LVX, SPX, CIP or NOR displayed either synergistic activity or indifference against the same mycoplasma species with MFs of 2-64, 4-16, 2-16, 2-64, respectively, while FICI values range from 0.516- 0.750, 0.500-0.625, 0.306-0.750, and 0.615-0.750, respectively. No antagonism was observed for any drug combination against any of the species tested. To the best of our knowledge, this is the first report that triclosan has synergistic activity with fluoroquinolones against mycoplasma species.

Transcriptional and functional analysis of the effects of magnolol: inhibition of autolysis and biofilms in Staphylococcus aureus.

BACKGROUND: The targeting of Staphylococcus aureus biofilm structures are now gaining interest as an alternative strategy for developing new types of antimicrobial agents. Magnolol (MOL) shows inhibitory activity against S. aureus biofilms and Triton X-100-induced autolysis in vitro, although there are no data regarding the molecular mechanisms of MOL action in bacteria. METHODOLOGY/PRINCIPAL FINDINGS: The molecular basis of the markedly reduced autolytic phenotype and biofilm inhibition triggered by MOL were explored using transcriptomic analysis, and the transcription of important genes were verified by real-time RT-PCR. The inhibition of autolysis by MOL was evaluated using quantitative bacteriolytic assays and zymographic analysis, and antibiofilm activity assays and confocal laser scanning microscopy were used to elucidate the inhibition of biofilm formation caused by MOL in 20 clinical isolates or standard strains. The reduction in cidA, atl, sle1, and lytN transcript levels following MOL treatment was consistent with the induced expression of their autolytic repressors lrgA, lrgB, arlR, and sarA. MOL generally inhibited or reversed the expression of most of the genes involved in biofilm production. The growth of S. aureus strain ATCC 25923 in the presence of MOL dose-dependently led to decreases in Triton X-100-induced autolysis, extracellular murein hydrolase activity, and the amount of extracellular DNA (eDNA). MOL may impede biofilm formation by reducing the expression of cidA, a murein hydrolase regulator, to inhibit autolysis and eDNA release, or MOL may directly repress biofilm formation. CONCLUSIONS/SIGNIFICANCE: MOL shows in vitro antimicrobial activity against clinical and standard S. aureus strains grown in planktonic and biofilm cultures, suggesting that the structure of MOL may potentially be used as a basis for the development of drugs targeting biofilms.

Microarray analysis of the chelerythrine-induced transcriptome of Mycobacterium tuberculosis.

Chelerythrine (a natural quaternary benzophenanthridine alkaloid) is an extract from the roots of Chelidonium majus with potential antimycobacterial activity. To reveal the possible mechanism of action of chelerythrine against Mycobacterium tuberculosis (M. tuberculosis), commercial oligonucleotide microarrays were used to analyze the genome-wide transcriptional changes triggered by treatment with subinhibitory concentrations of chelerythrine. Quantitative real-time RT-PCR was performed for selected genes to verify the microarray results. We interpreted our microarray data using Agilent software. Analysis of the microarray data revealed that a total of 759 genes were differentially regulated by chelerythrine. Of these, 372 genes were upregulated, and 387 genes were downregulated. Some of the important genes that were significantly regulated are related to different pathways (such as urease), methoxy-mycolic acid synthase, surface-exposed lipids, the heat shock response, and protein synthesis. This genome-wide transcriptomics approach produced the first insights into the response of M. tuberculosis to a chelerythrine challenge.

In Vitro Synergy of Biochanin A and Ciprofloxacin against Clinical Isolates of Staphylococcus aureus.

Many clinical isolates of Staphylococcus aureus (S. aureus) are resistant to numerous antimicrobials, including the fluoroquinolones (FQs). Flavonoids such as biochanin A (BCA) are compounds that are naturally present in fruits, vegetables, and plant-derived beverages. The goal of this investigation was to study the possible synergy between the antimicrobial agents BCA and ciprofloxacin (CPFX) when used in combination; CPFX was chosen as a representative FQ compound. We used S. aureus strain ATCC 25923 and 11 fluoroquinolone (FQ)-resistant methicillin-resistant S. aureus (MRSA) strains. Results from the drug susceptibility testing and checkerboard assays show that the minimum inhibitory concentration (MIC) of BCA ranged from 64 µg/mL to 512 µg/mL. When BCA was combined with CPFX, the fractional inhibitory concentration index (FICI) data showed that there was synergy in all 12 of the S. aureus strains tested. No antagonistic activity was observed in any of the strains tested. The results of time-kill tests and agar diffusion tests confirm that there was synergy between BCA and CPFX against S. aureus strains. These results suggest that BCA can be combined with FQs to produce a powerful antimicrobial agent.

The plant alkaloid piperine as a potential inhibitor of ethidium bromide efflux in Mycobacterium smegmatis.

Piperine, a major plant alkaloid found in black pepper (Piper nigrum) and long pepper (Piper longum), has shown potential for inhibiting the efflux pump (EP) of Staphylococcus aureus. In this study, a modulation assay showed that piperine could decrease the MIC of ethidium bromide (EtBr) twofold at 32 µg ml(-1) and fourfold at 64 µg ml(-1) against Mycobacterium smegmatis mc(2) 155 ATCC 700084. A real-time, 96-well plate fluorometric method was employed to evaluate the EP inhibition ability of piperine in M. smegmatis. Reserpine, chlorpromazine, verapamil and carbonyl cyanide m-chlorophenylhydrazone were used as positive controls. Piperine significantly enhanced accumulation and decreased the efflux of EtBr in M. smegmatis, which suggests that it has the ability to inhibit mycobacterial EPs.

Farnesol, a potential efflux pump inhibitor in Mycobacterium smegmatis.

The active multidrug efflux pump (EP) has been described as one of the mechanisms involved in the natural drug resistance of bacteria, such as mycobacteria. As a result, the development of efflux pumps inhibitors (EPIs) is an important topic. In this study, a checkerboard synergy assay indicated that farnesol both decreased the minimum inhibitory concentration (MIC) of ethidium bromide (EtBr) 8-fold against Mycobacterium smegmatis (M. smegmatis) mc²155 ATCC 700084 when incorporated at a concentration of 32 µg/mL (FICI = 0.625) and decreased MIC 4-fold at 16 µg/mL (FICI = 0.375). Farnesol also showed synergism when combined with rifampicin. A real-time 96-well plate fluorometric method was used to assess the ability of farnesol to inhibit EPs in comparison with four positive EPIs: chlorpromazine, reserpine, verapamil, and carbonyl cyanide m-chlorophenylhydrazone (CCCP). Farnesol significantly enhanced the accumulation of EtBr and decreased the efflux of EtBr in M. smegmatis; these results suggest that farnesol acts as an inhibitor of mycobacterial efflux pumps.