Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant.

BACKGROUND: Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. RESULTS: The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. CONCLUSIONS: In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

Probing the occurrence, sources and cancer risk assessment of polycyclic aromatic hydrocarbons in PM2.5 in a humid metropolitan city in China.

Fifty-two consecutive PM2.5 samples from December 2021 to February 2022 (the whole winter) were collected in the center of Chongqing, a humid metropolitan city in China. These samples were analysed for the 16 USEPA priority polycyclic aromatic hydrocarbons (16 PAHs) to explore their composition and sources, and to assess their cancer risks to humans. The total concentrations of the 16 PAHs (ng m-3) ranged from 16.45 to 174.15, with an average of 59.35 ± 21.45. Positive matrix factorization (PMF) indicated that traffic emissions were the major source (42.4%), followed by coal combustion/industrial emission (31.3%) and petroleum leakage/evaporation (26.3%). The contribution from traffic emission to the 16 PAHs increased from 40.0% in the non-episode days to as high as 46.2% in the air quality episode during the sampling period. The population attributable fraction (PAF) indicates that when the unit relative risk (URR) is 4.49, the number of lung cancer cases per million individuals under PAH exposure is 27 for adults and 38 for seniors, respectively. It was 5 for adults and 7 for seniors, when the URR is 1.3. The average incremental lifetime cancer risk (ILCR) for children, adolescents, adults and seniors was 0.25 × 10-6, 0.23 × 10-6, 0.71 × 10-6, and 1.26 × 10-6, respectively. The results of these two models complemented each other well, and both implied acceptable PAH exposure levels. Individual genetic susceptibility and exposure time were identified as the most sensitive parameters. The selection and use of parameters in risk assessment should be further deepened in subsequent studies to enhance the reliability of the assessment results.

The callus formation capacity of strawberry leaf explant is modulated by DNA methylation.

Shoot regeneration from leaf tissue requires de-differentiation of cells from a highly differentiated state into an active dividing state, but how this physiological transition occurs and is regulated especially at epigenetic level remains obscure. Here we have characterized the DNA methylome represented by 5-methylcytosine (5mC) in leaf and the callus tissue derived from the leaf explant of woodland strawberry Fragaria vesca. We detected an overall increase of DNA methylation and distinct 5mC enrichment patterns in the CG, CHG and CHH sequence contexts in genetic and transposable elements. Our analyses revealed an intricate relation between DNA methylation and gene expression levels in leaf or leaf-derived callus. However, when considering the genes involved in callus formation and shoot regeneration, e.g. FvePLT3/7, FveWIND3, FveWIND4, FveLOG4 and FveIAA14, their dynamic transcription levels were associated with the differentially methylated regions located in the promoters or gene bodies, indicating a regulatory role of DNA methylation in the transcriptional regulation of pluripotency acquisition in strawberry. Furthermore, application of a DNA methyltransferase inhibitor 5'-azacytidine (5'-Aza) hampered both callus formation and shoot regeneration from the leaf explant. We further showed that 5'-Aza down-regulated the genes involved in cell wall integrity, such as expansin, pectin lyase and pectin methylesterase genes, suggesting an essential role of cell wall metabolism during callus formation. This study reveals the contribution of DNA methylation in callus formation capacity and will provide a basis for developing a strategy to improve shoot regeneration for basic and applied research applications.

The complete chloroplast genome sequence of Persicaria perfoliata (L.) H. Gross: a medicinal plant.

Persicaria perfoliata (L.) H. Gross is an herbal medicine with a long history of common use in China. In this study, we sequenced and assembled the complete chloroplast genome sequence of P. perfoliata and investigated its phylogenetic relationship in the family Polygonaceae. The total genome size is 160,585 bp in length with 37.96% GC content, consisting of a small single-copy (SSC) of 12,876 bp, a large single-copy (LSC) of 85,439 bp, and two inverted repeats (IRs) of 31,135 bp. The cp genome contains 128 genes, including 35 tRNA genes, eight rRNA genes, and 85 protein-coding genes. The phylogenetic tree showed that P. perfoliata was closely related to P. maackiana, and Persicaria exhibited a closer relationship with Bistorta in the family Polygonaceae. This work provides a molecular basis for investigating the evolutionary status, phylogenetic relationships, and population genetics of this species.

Deposition kinetics of bacteriophage MS2 on Microcystis aeruginosa and kaolin surface.

Waterborne virus contamination might easily adsorb on the organic or inorganic surface in the complex aquatic environment. A quartz crystal microbalance coupled with dissipation monitoring was used to investigate the effects of the ionic strength of monovalent cation and divalent cation and pH on the deposition kinetics of bacteriophage MS2 on silica surface coated with Microcystis aeruginosa or kaolin, which represents organic or inorganic particle, respectively. Derjaguin-Landau-Verwey-Overbeek theory was used to illustrate the deposition mechanisms of MS2. The increased concentration of Na+ significantly enhanced the deposition rates of MS2 on both coated silica surfaces due to the reduction of repulsive electrostatic interactions. However, the MS2 deposition rates decreased at higher ionic strength of Ca2+, which accounted for the steric and hydrophobic interactions. And the higher MS2 deposition rates on both surfaces occurred at pH 3. In addition, the deposition rates of MS2 on kaolin-coated silica surfaces were higher than on the Microcystis-coated surface under all studied conditions. Furthermore, the Derjaguin-Landau-Verwey-Overbeek theory could elucidate the deposition mechanism in Na+ solution, whereas the steric and hydrophobic interactions should be considered for the presence of high concentration of Ca2+.

Inactivation and genome damage of rotavirus and a human norovirus surrogate by monochloramine treatment and sequential application with UV.

The inactivation efficacy by monochloramine for disinfecting gastroenteritis-causing rotaviruses (RV) and Tulane viruses (TV), a surrogate for noroviruses, were evaluated in this study. In addition, the strategies for improving the disinfection efficiency of monochloramine by raising the temperature and sequentially implementing UV irradiation were investigated. The results showed that monochloramine was more effective in the inactivation of TV than RV. Additionally, the inactivation rate constants of RV and TV by monochloramine at 35 °C were improved approximately by 46% and 100%, respectively, compared to those at 25 °C. Moreover, applying UV irradiation before monochloramine enhanced the inactivation efficacy of RV and TV by 63% and 72% compared to monochloramine alone (UV: 6 mJ/cm2, NH2Cl: 60 ppm × min). Furthermore, the synergistic effect was observed during the RV inactivation by the sequential process. Especially, higher than 0.5 log10 reductions of RV VP1 genome contributed to the synergistic effect in sequential treatment, while less than 0.1 log10 reductions of RV VP1 genome were observed during UV alone (13 mJ/cm2) or monochloramine alone (94 ppm × min). The genome damage might be the primary mechanism of generating synergy in sequential treatment for the inactivation of RV. By comparison, no synergistic effect was discovered for the inactivation of TV due to high susceptibility to monochloramine and UV. The findings on the inactivation efficacy and mechanism for improvement will contribute to a wide application of monochloramine for virus inactivation in water treatment and distribution systems.

Eliminate the hardware: Mobile terminals-oriented food recognition and weight estimation system.

Food recognition and weight estimation based on image methods have always been hotspots in the field of computer vision and medical nutrition, and have good application prospects in digital nutrition therapy and health detection. With the development of deep learning technology, image-based recognition technology has also rapidly extended to various fields, such as agricultural pests, disease identification, tumor marker recognition, wound severity judgment, road wear recognition, and food safety detection. This article proposes a non-wearable food recognition and weight estimation system (nWFWS) to identify the food type and food weight in the target recognition area via smartphones, so to assist clinical patients and physicians in monitoring diet-related health conditions. In addition, the system is mainly designed for mobile terminals; it can be installed on a mobile phone with an Android system or an iOS system. This can lower the cost and burden of additional wearable health monitoring equipment while also greatly simplifying the automatic estimation of food intake via mobile phone photography and image collection. Based on the system's ability to accurately identify 1,455 food pictures with an accuracy rate of 89.60%, we used a deep convolutional neural network and visual-inertial system to collect image pixels, and 612 high-resolution food images with different traits after systematic training, to obtain a preliminary relationship model between the area of food pixels and the measured weight was obtained, and the weight of untested food images was successfully determined. There was a high correlation between the predicted and actual values. In a word, this system is feasible and relatively accurate for one automated dietary monitoring and nutritional assessment.

Comparison of the formation of N-nitrosodimethylamine (NDMA) from algae organic matter by chlor(am)ination and UV irradiation.

Microcystis aeruginosa (M. aeruginosa, blue-green algae) blooms frequently in drinking water reservoirs and subsequently causes the formation of disinfection by-products (DBPs) after disinfection, which may pose a potential health risk. In this study, the formation of N-nitrosodimethylamine (NDMA) was evaluated from algal organic matter (AOM) including extracellular organic matter (EOM) and intracellular organic matter (IOM) during the disinfection process of chlorination, chloramination, or ultraviolet (UV) irradiation. The effects of a variety of factors, including reaction times, disinfectant dosages and pH, on the NDMA formation by three different disinfection methods were investigated. Additionally, this study evaluated the nitrogen sources involved in NDMA formation during chloramination of EOM and IOM using 15N-labeled monochloramine. The results showed that the NDMA formation by three different disinfection methods were ranked in the order of chlorination > UV irradiation ≈ chloramination and the specific yield from EOM was greater than that from IOM regardless of disinfection method. The yields of NDMA firstly increased and then plateaued as time prolonged during the chlorination and chloramination of AOM. Similarly, the NDMA formation from EOM was firstly increased and then remained constant with the increase of the disinfectant dosage, while it was gradually increased for IOM. The solution pH highly influenced the NDMA formation during chlorination and chloramination, while exhibited a little impact under UV irradiation. Moreover, fluorescence excitation-emission (EEM) analysis confirmed that soluble microbial by-product-like (SMPs) in EOM and IOM were the major precursors in algal-derived organic matter that contributed to the NDMA formation. Chloramination of EOM and IOM using isotope 15N-labeled monochloramine indicated that the nitroso group of the formed NDMA originates mainly from EOM and IOM of algal cells.

Life-threatening complications after microvascular decompression procedure: Lessons from a consecutive series of 596 patients.

The microvascular decompression procedure (MVD) is widely utilized on patients with neurovascular compression syndromes, such as trigeminal neuralgia, hemifacial spasm and glossopharyngeal neuralgia, which have failed medical therapy. However, surgical complications are an ongoing problem. We retrospectively reviewed a total of 596 patients undergoing MVD in the Affiliated Hospital of Qingdao University from January 2008 to December 2018. Furthermore, we discussed the cases with life-threatening complications to determine the potential causes, aiming to achieve the goal of safer microvascular decompression. There were seven cases with life-threatening complications. Of those complications, one was cerebellar infarction with acute hydrocephalus, one was infarction of the cerebellum and the brain stem with acute hydrocephalus and serious intracranial infection, two were cerebellar haematoma, one was multiple haemorrhage with acute hydrocephalus, one was supratentorial subdural haematoma, and one was cerebellar swelling with acute hydrocephalus. After therapy, one patient died, one was in a persistent vegetative state, and five were discharged from the hospital upon recovery. In brief, MVD is a safe operation, and life-threatening complications accompanying MVD are rare, but require attention. The causes of some life-threatening complications are still not completely clear. Surgeons should continuously improve surgical techniques and perioperative care to reduce potential risks.

Evolution and roles of cytokinin genes in angiosperms 1: Do ancient IPTs play housekeeping while non-ancient IPTs play regulatory roles?

Isopentenyltransferase (IPT) genes, including those encoding ATP/ADP-IPTs and tRNA-IPTs, control the rate-limiting steps of the biosynthesis of N 6-(Δ2-isopentenyl)adenine (iP)-type and trans-zeatin (tZ)-type cytokinins and cis-zeatin (cZ)-type cytokinins, respectively. However, the evolution and roles of these IPTs in angiosperms are not well understood. Here, we report comprehensive analyses of the origins, evolution, expression patterns, and possible roles of ATP/ADP-IPTs and tRNA-IPTs in angiosperms. We found that Class I and II tRNA-IPTs likely coexisted in the last common ancestor of eukaryotes, while ATP/ADP-IPTs likely originated from a Class II tRNA-IPT before the divergence of angiosperms. tRNA-IPTs are conservatively retained as 2-3 copies, but ATP/ADP-IPTs exhibit considerable expansion and diversification. Additionally, tRNA-IPTs are constitutively expressed throughout the plant, whereas the expression of ATP/ADP-IPTs is tissue-specific and rapidly downregulated by abiotic stresses. Furthermore, previous studies and our present study indicate that ATP/ADP-IPTs and their products, iPs/tZs, may regulate responses to environmental stresses and organ development in angiosperms. We therefore hypothesize that tRNA-IPTs and the associated cZs play a housekeeping role, whereas ATP/ADP-IPTs and the associated iP/tZ-type cytokinins play regulatory roles in organ development and stress responses in angiosperms, which echoes the conclusions and hypothesis presented in the accompanying study by Wang, X. et al Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles? Hortic Res 10.1038/s41438-020-0246-z.

Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles?

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).

Characterization and Expression Analysis of ERF Genes in Fragaria vesca Suggest Different Divergences of Tandem ERF Duplicates.

Ethylene-responsive factors (ERFs) play important roles in plant growth and development and in responses to abiotic stresses. However, little information was available about the ERF genes in woodland strawberry (Fragaria vesca), a genetic model plant for the Fragaria genus and Rosaceae family. In this study, 91 FveERF genes were identified, including 35 arrayed in tandem, indicating that tandem duplication is a major mechanism for the expansion of the FveERF family. According to their phylogenetic relationships with AtERFs from Arabidopsis thaliana, the tandem FveERF genes could be grouped into ancestral and lineage-specific tandem ones. The ancestral tandem FveERFs are likely derived from tandem duplications that occurred in the common ancestor of F. vesca and A. thaliana, whereas the lineage-specific ones are specifically present in the F. vesca lineage. The lineage-specific tandem FveERF duplicates are more conserved than the ancestral ones in sequence and structure. However, their expression in flowers and fruits is similarly diversified, indicating that tandem FveERFs have diverged rapidly after duplication in this respect. The lineage-specific tandem FveERFs display the same response patterns with only one exception under drought or cold, whereas the ancestral tandem ones are largely differentially expressed, suggesting that divergence of tandem FveERF expression under stress may have occurred later in the reproductive development. Our results provide evidence that the retention of tandem FveERF duplicates soon after their duplication may be related to their divergence in the regulation of reproductive development. In contrast, their further divergence in expression pattern likely contributes to plant response to abiotic stress.

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development.

Gibberellins (GAs) play a crucial role in growth and development of the tomato fruit. Previously published studies focusing on the effect of GAs on tomato fruits used chemical treatments, constitutive overexpression or silencing of GA biosynthetic and catabolic genes globally throughout the plant. Fruit-specific overexpression of GA catabolic enzyme genes GA2-oxidases (GA2oxs), however, may provide an alternative method to study the role of endogenous GAs on the fruit development. In this study, we have identified 11 SlGA2ox proteins in tomato that are classified into three subgroups. Motif analysis and multiple sequence alignments have demonstrated that all SlGA2oxs, except SlGA2ox10, have similar motif compositions and high-sequence conservation. Quantitative reverse transcription-PCR analysis has showed that SlGA2oxs exhibit differential expression patterns in tomato fruits at different developmental stages. When the fruit-specific promoter TFM7 was used to control the expression of SlGA2ox1, we observed no changes in growth and development of vegetative organs. However, fruit weight, seed number and germination rate were significantly affected. We also treated tomato fruits with GA biosynthesis inhibitor and observed phenotypes similar to those of the transgenic fruits. Furthermore, we have demonstrated that expression of cell expansion and GA responsive genes were downregulated in transgenic tomato fruits, supporting that overexpression of the SlGA2ox1 leads to reduction in endogenous GAs. This study provides additional evidence that endogenous GAs and the SlGA2ox1 gene play an important role in controlling on fruit weight, seed development and germination in tomato plant.