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• No single laboratory method could independently diagnose tuberculous meningitis. • Polymerase-chain-reaction is highly sensitive and specific for the diagnosis of tuberculous meningitis. • Metagenomic next-generation sequencing does not offer much strength in diagnosing tuberculous meningitis. The aim of this study was to comprehensively evaluate metagenomic next-generation sequencing (mNGS), Acid-fast bacillus stain (AFB), MGIT960 culture, polymerase-chain-reaction (PCR), and Xpert MTB/RIF in the diagnosis of tuberculous meningitis (TBM). A cohort of 280 patients who presented with suspected TBM (ie, headache or altered mental status with clinical signs of meningism) were analyzed. The sensitivities of the 5 assays for the diagnosis of TBM ranged from 10.0% to 70.0%. The AFB had the lowest sensitivity of 10.0% (0.5-45.9), while mNGS and PCR had the highest sensitivity, both at 70.0% (35.4-91.9). mNGS demonstrated a distinct advantage in identifying a wider array of pathogens, including viruses, in CSF samples. PCR was a cost-effective option with excellent sensitivity and specificity. However, no single method was statistically significantly better than any other in the diagnosis of TBM. New diagnostic techniques are urgently needed for the independent, rapid and accurate detection of Mycobacterium tuberculosis to guide the diagnosis of TBM. [ABSTRACT FROM AUTHOR]

Ras-related nuclear protein (Ran) GTPase plays an important role in nucleo-cytoplasmic transportation of proteins and RNA, mitotic spindle assembly, microtubule assembly and nuclear envelope (NE) assembly. We previously identified the full-length cDNAs and a DNA of DlRan3A from longan ( Dimocarpus longan Lour.) somatic embryos and demonstrated its possible roles in cell activities during longan somatic embryogenesis (SE). However, thus far little is known of how Ran functions in the signaling pathways in plant embryos in response to changing environmental stimuli. To discover more biological roles of DlRan3A , we observed DlRan3A located in the nucleus and detected abundant accumulation of DlRan3A s in globular and cotyledon embryos during longan SE, which suggested its involvement in auxin signal pathways in longan early SE. The transcript level of the DlRan3A gene were also determined in longan embryogenic callus (EC) in response to different levels of exogenous phytohormones (indoleacetic acid (IAA), gibberellin A3 (GA 3 ), salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Eth)), salt, sucrose, prolonged culturing period and light quality treatments. IAA (1 mg/L), GA 3 (12 mg/L), SA (75 μm), MeJA (50 and 100 μm), and Eth (50 mg/L) modulate expression of DlRan3A to 1.3–1.4 folds, and the expression of DlRan3A was significantly affected by light quality, significantly induced to 2-fold by salt (10 g/L), 2.7-fold by sucrose (90 g/L) and was completely suppressed by prolonged cultivation (> 40 days). Deletion analysis suggested that both activation and repression regulatory elements co-exist in the DlRan3A promoter sequence and that the key cis-acting elements included ones in response to auxin, SA, MeJA, and stress. Promoter activities were induced to the highest level by IAA followed by SA, GA 3 and MeJA, while suppressed by ABA and Eth. Together, these results showed DlRan3A close involvement in phytohormones, light, and abiotic stress responsiveness during longan SE. [ABSTRACT FROM AUTHOR]

The efficient removal of uranium from aqueous solution remains of great challenge in securing water environment safety. In this paper, we reported a high temperature electrochemical method for the preparation of EuVO 4 with different morphologies from rare earth oxides and vanadate, which solved the problems of rare earth and vanadium recovery. The effects of pH, ionic strength, contact time, initial concentration and reaction temperature on the adsorption of U(VI) by prepared adsorbent were studied by static batch experiments. When the concentration of U(VI) standard is 100 mg g−1, the maximum adsorption capacity of EuVO 4 is 276.16 mg g−1. The adsorption mechanism was elucidated with zeta potential and XPS: 1) negatively charged EuVO 4 attracted UO 2 2+ by electrostatic attraction; 2) exposed Eu, V, and O atoms complexed with U(VI) through coordination; 3) the hybrid of Eu was complex, which accommodated different electrons to interact. In the multi-ion system with Al3+, Zn2+, Cu2+, Ni2+, Cr2+ and Mn2+, EuVO 4 also showed good selective adsorption properties for U(VI). Five adsorption and desorption cycle experiments demonstrated that EuVO 4 possessed good renewable performance. • Different morphologies of EuVO 4 were synthesized by high-temperature electrochemical method. • U(VI) sorption on EuVO 4 was studied using batch and spectroscopies. • The maximum adsorption capacity of EuVO 4 reached at 276.16 mg g−1. • EuVO 4 showed good selective adsorption property for U(Ⅵ) in the multi-ion system. [ABSTRACT FROM AUTHOR]

• Xylo-oligosaccharides reduced plasma total cholesterol levels. • Xylo-oligosaccharides increased fecal outputs of neutral and acidic sterols. • Xylo-oligosaccharides increased fecal outputs of short chain fatty acids. • Xylo-oligosaccharides influenced gut microbiota composition. The present study investigated the cholesterol-lowering activity of xylo- oligosaccharides and its associated underlying mechanisms in hamsters. Twenty-four hamsters were randomly divided into three groups and fed one of three diets, namely a low cholesterol diet, a high cholesterol diet (HCD), and an HCD diet with supplementation of 5% xylo -oligosaccharides for 6 weeks. The changes in gut microbiota, fecal neutral and acidic sterols were examined. Results exhibited that xylo- oligosaccharides could significantly reduce plasma total cholesterol, non-high-density lipoprotein cholesterol and total triacylglycerol by 11.24%, 24.89% and 38.72%, respectively (p < 0.05). Such benefits were associated with an increase in fecal outputs of neutral and acidic sterols as well as SCFAs. Furthermore, dietary supplementation with xylo -oligosaccharides could change the composition of gut microbiota. It was therefore concluded that xylo -oligosaccharides supplementation could reduce plasma cholesterol levels, enhance the excretion of neutral and acidic sterols, and promote the production of SCFAs via changing the gut microbiota composition. [ABSTRACT FROM AUTHOR]

Atomic Force Microscopy (AFM) is one of the most popular and advanced tools for ultra high-resolution imaging and nanomanipulation of nano-scale matter. But AFM imaging typically takes a long time. High-speed and high-precision AFM measurement has attracted wide attention in recent several years. In traditional AFM, simple reduction in the number of measurement points may lose essential sample topography information. To resolve such problems, an AFM image reconstruction method based on Compressed Sensing (CS) theory is applied to reduce image acquisition time without cutting down the image quality. The benefit of using CS approach in AFM is shortening the imaging time, minimizing the interaction with the sample, and finally avoiding sample damage in AFM. Three kinds of testing samples with high and low frequency components were examined by a scanning electron microscope (SEM) and by AFM. An orthogonal Matching Pursuit (OMP) algorithm is employed to reconstruct an AFM image with different sampling rates. Subsequently the reconstruction results of sample topography images are analyzed and evaluated. Using the CS approach in AFM can greatly improve the AFM imaging process. Experimental results show that the obtained reconstructed images have different resolution and quality, depending on the surface morphology of the sample and sampling rates. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan) is a precious subtropical fruit with high nutritional value. The somatic embryogenesis (SE) affects the quality and yield of fruit. Apart from clonal propagation, SE has extensive applications in genetic improvement and mutation. Thus, understanding the molecular basis of embryogenesis in longan will help to develop strategies for mass production of quality planting material. Lysine acetylation (Kac) plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in plant early SE. In this study, the proteome and acetylome of longan embryogenic callus (ECs) and globular embryos (GEs) were investigated. In total, 7232 proteins and 14,597 Kac sites were identified, and this resulted in the discovery of 1178 differentially expressed proteins and 669 differentially expressed acetylated proteins. KEGG and GO analysis showed that glucose metabolism, carbon metabolism, fatty acid degradation, and oxidative phosphorylation pathways were influenced by Kac modification. Furthermore, sodium butyrate (Sb, a deacetylase inhibitor) led to reduced the proliferation and delayed the differentiation of ECs by regulating the homeostasis of reactive oxygen species (ROS) andindole-3-acetic acid (IAA). Our study provides a comprehensive proteomic and acetylomic analysis to aid in understanding the molecular mechanisms involved in early SE, representing a potential tool for genetic improvement of longan. • Kac is involved in the early regulation of longan embryogenesis with various regulatory pathways. • Sodium butyrate led to reduced the proliferation and delayed the differentiation of ECs by regulating the homeostasis of ROS and IAA. • Carbon metabolism, fatty acid degradation, and oxidative phosphorylation pathways were mainly influenced by Kac. [ABSTRACT FROM AUTHOR]

The early auxin responsive small auxin up-regulated RNA (SAUR) family is an important gene family in the auxin signal transduction pathway. This study focused on the regulatory mechanism of DlSAUR genes during early somatic embryogenesis (SE) and its response to hormone treatment and abiotic stress. Mining of the available Dimocarpus longan Lour. (D. longan) genome sequence yielded 68 putative SAUR genes. Transcript profiles based on RNA-seq data showed that most of the 24 detected DlSAUR genes were highly expressed in the globular embryos (GE) (10) and most of them responded to heat stress and 2,4-D treatment. The results of qRT-PCR showed that most of DlSAUR genes were up-regulated under auxin inhibitor N-1-naphthylphthalamic acid (NPA) and auxin indole-3-acetic acid (IAA) treatments. Moreover, NPA could promote longan SE. The assay for ATAC-seq data analysis showed that chromatin accessibility of 19 of the 24 DlSAUR genes were open during early SE, and most DlSAUR genes differentially expressed during early SE were not associated with H3K4me1 signal enrichment. The DlSAUR32 was selected for subcellular localization and RNA-seq analysis, which encode a cell nuclear-localized protein. Dual-luciferase assays and transient transformation showed that the transcription factors (TFs) DlWRKY75-1 and DlWRKY75-2 might bind to the DlSAUR32 promoters to inhibition gene transcription. Transient overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content in N. benthamiana leaves. Thus, the regulatory network composed of DlSAUR32 and its related TFs may regulate the early longan SE and be involved in the auxin response regulatory pathway of longan. • DlSAUR genes were sensitive to IAA and NPA treatments. • The regulatory network of transcription factors and DlSAUR genes was predicted. • DlWRKY75-1 and DlWRKY75-2 can significantly reduce the expression of DlSAUR32. • Overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content. [ABSTRACT FROM AUTHOR]

• Fifty-three LysM gene family members were found in banana (Musa L.) genomes, and there were more members in Musa acuminata than in both Musa balbisiana and Musa itinerans. • Banana LysMs were expressed under low-temperature stresses, high-temperature stresses and root infestation by pathogens. • LysMs were highly conserved in the evolution of bananas, but they also show some differences among the genomes of three banana species. LysM (Lysin motif), in response to pathogenic molecular stresses, is a crucial signal recognition gene. To understand the molecular characteristics of banana LysM gene family members, we used a series of bioinformatics methods. Based on the genomic databases of Musa acuminata , Musa balbisiana and Musa itinerans , a total of 53 genes and 55 proteins were identified, with 21 genes and 23 proteins in the M.acuminata , 16 genes and 16 proteins in each of M.balbisiana and M.itinerans , respectively. According to the conserved structural domains, LysM can be divided into five classes, namely LysM&MltD , LYK , LYP , LysMn , and LysMe. The LysM gene was relatively highly conserved in the evolution of the three genomes of banana, and some differences occurred. Expression analysis revealed that MaLysM4-5 was relatively highly expressed under high-temperature stress, low-temperature stress and pathogen infection; at the same time, about one-third of the members were down-regulated under low-temperature stress and high-temperature stress, while the expression of MaLysM10-1 and MaLysM4-5 were up-regulated. After the banana wilt fungus Foc TR4 infected the banana roots, MaLysM1 was down-regulated and MaLysM11-1 was up-regulated. In conclusion, our study suggests that MaLysMs may be necessary in the response to high- and low-temperature stresses, as well as the banana wilt fungus infestation. Overall, this paper found that LysM genes may be involved in biotic and abiotic stresses in banana, and provided helpful information about LysM 's evolution, expression and properties, which will provide theoretical references for further studies on the functions of LysM genes and resistance breeding in the future. [ABSTRACT FROM AUTHOR]

• 16 volatiles were identified as key odorants in postharvest jasmine flower (PJF). • A reference transcriptome of jasmine with 366,081 full-length isoforms was obtained. • Aroma formation of PJF depend on both de novo biosynthesis and glycoside hydrolysis. • HSPs may guarantee the normal fragrance release of PJF during flowering. Jasmine [ Jasminum sambac (L.) Aiton] flowers usually bloom and release their fragrance at night. However, the underlying regulatory mechanisms of aroma formation during flowering in postharvest jasmine are still poorly understood. Here, we profiled the volatile metabolome, multi-flux full-length sequencing, and transcriptome analysis to investigate volatile biosynthesis and global transcriptomic changes in postharvest flowering jasmine. A total of 102 volatiles were identified. Of these, 16 volatiles were considered key odorants of jasmine flowers. Linalool, α-farnesene, d -nerolidol, geraniol, α-cadinol, benyzl alcohol, benzaldehyde, benzyl acetate, benzyl benzoate, 3-hexen-1-ol benzoate, and (Z)-3-hexen-1-ol acetate play decisive roles in the typical jasmine fragrance, while benzeneacetaldehyde, benzoic acid, methyl anthranilate, methyl 2-(methylamino) benzoate, and (E)-2-hexenal modify the aroma of jasmine. Meanwhile, we built the first reference full-length transcriptome of postharvest jasmine flowers, which had 366,081 non-redundant isoforms. Among them, 280,326 (76.57 %) were annotated with at least one hit in the NT, NR, Swissprot, KEGG, KOG, Pfam, and GO databases. Combined with second-generation transcriptome analysis, we identified 52 differentially expressed transcripts (DETs) involved in terpenoid metabolic pathways and 28 DETs involved in phenylpropanoid/benzenoid metabolic pathway, and 31 β-glucosidase transcripts may be related to aroma formation of postharvest jasmine during flowering. In addition, the expression of 42 heat shock protein (HSP) transcripts was positively correlated with the content of 11 key odorants, as revealed by weighted gene co-expression network analysis (WGCNA). The present results advance the knowledge of the regulatory mechanism of aroma formation in postharvest jasmine during flowering and provide an abundant genetic resource for further studies on gene discovery in jasmine. [ABSTRACT FROM AUTHOR]

• A total of 18 CsZF-HDs were confirmed from tea plant genome. • CsZF-HD genes have spatio-temporal expression patterns in various tissues. • All the CsZF-HDs we detected differentially expressed under diverse treatments. • Some CsZF-HDs may be regulated by miRNAs under abiotic stresses and hormones stimuli. • The predicted eTM of csn-miR2673a may indirectly modulate CsZF-HD under SA treatment. In plants, zinc finger motif-associated homeodomain (ZF-HD) transcription factors (TFs) play indispensable roles in developmental processes and stress responses. However, the specific functions of members of the ZF-HD gene family in tea plants (Camellia sinensis) are poorly understood. We identified 18 CsZF-HD genes in tea at the whole-genome scale. These genes were phylogenetically classified into two major subfamilies: ZF-HD and MIF. Gene structural analyses showed that 13 of the 18 members have no introns. Analysis of transcriptome data revealed different spatio-temporal expression patterns of CsZF-HD genes in various tissues. On the basis of the cis -acting elements analysis, we detected the expression patterns of CsZF-HD genes under various abiotic and phytohormone treatments (drought, cold, exogenous SA, MeJA, ABA, and GA 3). Quantitative real time polymerase chain reaction (qRT-PCR) analyses confirmed the differential expression of CsZF-HDs under diverse stress and phytohormone treatments. The miRNAs that regulate CsZF-HD genes and their endogenous target mimics (eTMs) were predicted and investigated. The expression patterns of CsZF-HD10 and csn-miR172b-5p-3 were completely opposite under salicylic acid treatment. We also detected negative regulatory relationships between csn-miR2673a and CsZF-HD15 under salicylic acid treatment, between csn-miR399a-5 and CsZF-HD9 under abscisic acid treatment, and between csn-miR2673a and CsZF-HD3 under methyl jasmonate treatment during most sequential stages. The results indicate that the predicted eTM (LTCONS-00,013,981) of csn-miR2673a may indirectly modulate CsZF-HD expression by baiting relevant miRNAs under salicylic acid treatment. Together, these results lay the foundation for further research on the biological functions of CsZF-HDs. [ABSTRACT FROM AUTHOR]

ADP-ribosylation modification considered as a model to study histone post-translational modification in chromatin modification. Despite it was reported in many plants, the study of ARFs gene family in longan was still unclear. In this study, 14 longan ARFs genes were identified using the longan genome (the third-generation genome) and further divided into two major groups, including the DlARF in the I-II group and the ARF-like (DlARL) in the III-V group, according to their structure and evolutionary characteristics. Whole-genome duplication (WGD) and segmental duplication events played a major role in the expansion of the DlARFs gene family, the synteny and phylogenetic analyses provided a deeper insight into the evolutionary characteristics of the DlARFs. Protein-protein interactions suggested that some DlARFs proteins may interact to participate in biological processes. Promoter analysis showed more stress response elements in DlARF5 , DlGB1 , DlARL1 , DlARL2, and DlARL8a , suggesting that they may participate in abiotic stress. Expression profiles of DlARFs by quantitative real-time PCR (qRT-PCR) showed that they were abundant accumulation during early somatic embryogenesis (SE). Expression pattern analysis of RNA-seq and qRT-PCR revealed that some ARFs members regulated early SE, and respond to exogenous hormones and abiotic stress such as abscisic acid (ABA), gibberellin A3 (GA3), salicylic acid (SA), methyl jasmonate (MeJA), cold, and heat. Our study provides new insights for further research on the potential function of DlARFs , which may be useful for the improvement of longan. [ABSTRACT FROM AUTHOR]

• 58 DlDDX family genes were identified during the early SE in longan genome. • DlDDX proteins appeared neofunctionalization in longan, and associated with abiotic stress during longan early SE. • Upregulation of 8 DlDDXs genes might promote abortion of in vitro and in vivo embryogenesis. • DlDDX3, 15, 28, 36 might be contribute to miRNA biosynthesis and DNA demethylation in longan early SE. DEAD-box (DDX) proteins belong to the largest subfamily of RNA helicase SF2, which contributes to all biological processes of RNA metabolism in the plant kingdom. Till now, no significant data are available regarding studies on DDX in Somatic Embryogenesis (SE) of woody plants. It is important to investigate the biological function of the DlDDX family in longan SE. Thus, a comprehensive analysis of 58 longan DEAD-box (DlDDX) genes characterization was performed by genome-wide identification and transcript abundance validation analysis. Homologous evolution has revealed that some DlDDXs in longan had high sequence similarity with Mus musculus , Citrus and Saccharomyces cerevisiae , indicating that DlDDXs were highly conservative in the animal, plant, and microorganism. Remarkably, gene duplication, purifying selection, and alternative splicing events, and new auxiliary domains have likely contributed to the functional evolution of DlDDX, indicating that DlDDX appeared neofunctionalization in longan. Besides, DlDDX3, 15, 28, 36 might interact with protein complex (MAC3A, MAC3B, CDC5, CBP20) of miRNA biosynthesis. Notably, DlDDX28 contained a novel auxiliary domain (CAF-1 p150), which might contribute to DNA demethylation in longan early SE. 4 DlDDX genes significantly expressed not only in early SE and zygotic embryogenesis (ZE) but also up-regulated at high levels in 'Honghezi' and 'Quanlongbaihe' with abortive seeds, which are of great significance. Moreover, some DlDDXs presented abiotic stress-response dynamic expression patterns by ABA, SA, JA, and NaCl treatments during early SE. Hence, DEAD-box is essential to SE development and seed abortive in longan. [ABSTRACT FROM AUTHOR]