SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress.

Alternative splicing (AS) regulates gene expression and increases proteomic diversity for the fine tuning of stress responses in plants, but the exact mechanism through which AS functions in plant stress responses is not thoroughly understood. Here, we investigated how AS functions in poplar (Populus trichocarpa), a popular plant for bioremediation, in response to lead (Pb) stress. Using a proteogenomic analysis, we determine that Pb stress induced alterations in AS patterns that are characterized by an increased use of nonconventional splice sites and a higher abundance of Pb-responsive splicing factors (SFs) associated with Pb-responsive transcription factors. A strong Pb(II)-inducible chaperone protein, PtHSP70, that undergoes AS was further characterized. Overexpression of its two spliced isoforms, PtHSP70-AS1 and PtHSP70-AS2, in poplar and Arabidopsis significantly enhances the tolerance to Pb. Further characterization shows that both isoforms can directly bind to Pb(II), and PtHSP70-AS2 exhibits 10-fold higher binding capacities and a greater increase in expression under Pb stress, thereby reducing cellular toxicity through Pb(II) extrusion and conferring Pb tolerance. AS of PtHSP70 is found to be regulated by PtU1-70K, a Pb(II)-inducible core SF involved in 5'-splice site recognition. Because the same splicing pattern is also found in HSP70 orthologs in other plant species, AS of HSP70 may be a common regulatory mechanism to cope with Pb(II) toxicity. Overall, we have revealed a novel post-transcriptional machinery that mediates heavy metal tolerance in diverse plant species. Our findings offer new molecular targets and bioengineering strategies for phytoremediation and provide new insight for future directions in AS research.

Evaluation of the Chemical Composition and Antioxidant Activity of Mulberry (Morus alba L.) Fruits from Different Varieties in China.

Mulberry (Morus alba L.) fruit is a fruit with nutritional and medicinal value. It is widely cultivated in different regions of China, which may result in differences in its chemical composition. In this research, 25 mulberry fruit samples from six provinces in China were investigated. The contents of anthocyanins were evaluated by high-performance liquid chromatography (HPLC). The contents of two main anthocyanins, cyanidin-3-O-glucoside (C3G) and cyanidin-3-O-rutinoside (C3R), ranged from 0.656 ± 0.006 mg/g to 4.367 ± 0.243 mg/g and from 0.226 ± 0.007 mg/g to 1.649 ± 0.013 mg/g, respectively. Additionally, the contents of total phenolic, total flavonoid, vitamin C, titratable acids, reducing sugars and antioxidant capacity (FRAP, DPPH, scavenging and hydroxyl radical scavenging activity) were also assessed. The results and principal component analysis showed that the Zhongsang 5801 variety from Sichuan, Dechang had the greatest health value with the highest active compound contents. Based on our analysis, the variety from Sichuan, Dechang is a high-quality plant source for mulberry fruit cultivation. This research provides a basis for the rational development and utilization of mulberry fruit resources in China.

The reference genome of camellia chekiangoleosa provides insights into camellia evolution and tea oil biosynthesis.

Camellia oil extracted from Camellia seeds is rich in unsaturated fatty acids (UFAs) and secondary metabolites beneficial to human health. However, no oil-tea tree genome has yet been published, which is a major obstacle to investigating the heredity improvement of oil-tea trees. Here, using both Illumina and PicBio sequencing technologies, we present the first chromosome-level genome sequence of the oil-tea tree species Camellia chekiangoleosa Hu. (CCH). The assembled genome consists of 15 pseudochromosomes with a genome size of 2.73 Gb and a scaffold N50 of 185.30 Mb. At least 2.16 Gb of the genome assembly consists of repetitive sequences, and the rest involves a high-confidence set of 64 608 protein-coding gene models. Comparative genomic analysis revealed that the CCH genome underwent a whole-genome duplication (WGD) event shared across the Camellia genus at ~57.48 MYA and a γ-WGT event shared across all core eudicot plants at ~120 MYA. Gene family clustering revealed that the genes involved in terpenoid biosynthesis have undergone rapid expansion. Furthermore, we determined the expression patterns of oleic acid accumulation- and terpenoid biosynthesis-associated genes in six tissues. We found that these genes tend to be highly expressed in leaves, pericarp tissues, roots, and seeds. The first chromosome-level genome of oil-tea trees will provide valuable resources for determining Camellia evolution and utilizing the germplasm of this taxon.

Viciamingyueshanensis (Fabeae, Papilionoideae, Fabaceae), a new species from western Jiangxi, China.

Viciamingyueshanensis, a new species from the Mingyue Mountain Region of western Jiangxi, China, is described and illustrated. It is a perennial climbing liana that always links to riparian woods. A morphological comparison indicated that the new species is closely similar to Viciataipaica K. T. Fu and Viciadichroantha Diels; however, it differs from the other two species by several salient characters, such as plant indumentum, stipule shape, corolla colour, bractlet shape and calyx shape. Photographs, a preliminary conservation assessment, table of morphological characters and distribution map comparing this new species to two morphologically-similar species are also provided.

Accuracy of endoscopic ultrasound-guided needle aspiration specimens for molecular diagnosis of non-small-cell lung carcinoma.

BACKGROUND: Endoscopic ultrasonography-guided fine-needle aspiration (EUS-FNA) and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) are highly sensitive for diagnosing and staging lung cancer. In recent years, targeted therapy has shown great significance in the treatment of non-small cell lung carcinoma (NSCLC). Using these minimally invasive techniques to obtain specimens for molecular testing will provide patients with a more convenient diagnostic approach. AIM: To evaluate the feasibility and accuracy of tissue samples obtained using EUS-FNA and EBUS-TBNA for molecular diagnosis of NSCLC. METHODS: A total of 83 patients with NSCLC underwent molecular testing using tissues obtained from EUS-FNA or EBUS-TBNA at the Tianjin Medical University Cancer Hospital from January 2017 to June 2019. All enrolled patients underwent chest computed tomography or positron emission tomography/computed tomography prior to puncture. We detected abnormal expression of EGFR, KRAS, MET, HER2, ROS1 and anaplastic lymphoma kinase protein. Two patients failed to complete molecular testing due to insufficient tumor tissue. The clinical features, puncture records, molecular testing results and targeted treatment in the remaining 81 patients were summarized. RESULTS: In a total of 99 tissue samples obtained from 83 patients, molecular testing was successfully completed in 93 samples with a sample adequacy ratio of 93.9% (93/99). Biopsy samples from two patients failed to provide test results due to insufficient tumor tissue. In the remaining 81 patients, 62 cases (76.5%) were found to have adenocarcinoma, 11 cases (13.6%) had squamous cell carcinoma, 3 cases (3.7%) had adenosquamous carcinoma and 5 cases (6.2%) had NSCLC-not otherwise specified. The results of molecular testing showed EGFR mutations in 21 cases (25.9%), KRAS mutations in 9 cases (11.1%), ROS-1 rearrangement in 1 case (1.2%) and anaplastic lymphoma kinase-positive in 5 cases (6.2%). Twenty-four patients with positive results received targeted therapy. The total effectiveness rate of targeted therapy was 66.7% (16/24), and the disease control rate was 83.3% (20/24). CONCLUSION: Tissue samples obtained by EUS-FNA or EBUS-TBNA are feasible for the molecular diagnosis of NSCLC and can provide reliable evidence for clinical diagnosis and treatment.

Bronchogenic cyst of the stomach: A case report.

BACKGROUND: Gastric bronchogenic cysts (BCs) are extremely rare cystic masses caused by abnormal development of the respiratory system during the embryonic period. Gastric bronchial cysts are rare lesions first reported in 1956; as of 2019, only 37 cases are available in the MEDLINE/PubMed online databases. BCs usually have no clinical symptoms in the early stage, and their imaging findings also lack specificity. Therefore, they are difficult to diagnose before histopathological examination. CASE SUMMARY: A 55-year-old woman presented at our hospital with intermittent epigastric pain. She had a slightly high level of serum carbohydrate antigen 72-4 (CA 72-4). Endoscopic ultrasound found that a cystic mass originated from the submucosa of the posterior gastric wall near the cardia, indicating a diagnosis of cystic hygroma of the stomach. Furthermore, a computed tomography scan demonstrated a quasi-circular cystic mass closely related to the lesser curvature of the gastric fundus with a low density. Because the imaging examinations did not suggest a malignancy and the patient required complete resection, she underwent laparoscopic surgery. As an intraoperative finding, this cystic lesion was located in the posterior wall of the fundus and contained some yellow viscous liquid. Finally, the pathologists verified that the cyst in the fundus was a gastric BC. The patient recovered well with normal CA 72-4 levels, and her course was uneventful at 10 mo. CONCLUSION: This is a valuable report as it describes an extremely rare case of gastric BC. Moreover, this is the first case of BC to present with elevated CA 72-4 levels.

Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis.

BACKGROUND: Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. FINDINGS: To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. CONCLUSIONS: We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

Study on relationship between pollen exine ornamentation pattern and germplasm evolution in flowering crabapple.

Pollen ornamentation patterns are important in the study of plant genetic evolution and systematic taxonomy. However, they are normally difficult to quantify. Based on observations of pollen exine ornamentation characteristics of 128 flowering crabapple germplasms (44 natural species and 84 varieties), three qualitative variables with binary properties (Xi: regularity of pollen exine ornamentation; Yi: scope of ornamentation arrangement regularity; Zi: ornamentation arrangement patterns) were extracted to establish a binary three-dimensional data matrix (Xi Yi Zi) and the matrix data were converted to decimal data through weight assignment, which facilitated the unification of qualitative analysis and quantitative analysis. The result indicates that from species population to variety population and from parent population to variety population, the exine ornamentation of all three dimensions present the evolutionary trend of regular → irregular, wholly regular → partially regular, and single pattern → multiple patterns. Regarding the evolutionary degree, the regularity of ornamentation was significantly lower in both the variety population and progeny population, with a degree of decrease 0.82-1.27 times that of the regularity range of R-type ornamentation. In addition, the evolutionary degree significantly increased along Xi → Yi → Zi. The result also has certain reference values for defining the taxonomic status of Malus species.

[A Quercetin-Based Fluorescent Probe for the Recognition of Fluorid Ions].

Quercetin (Q) is one of the most common flavonoids present in roots, stems, leaves, flowers and fruits of most plants. In this study, a quercetin-based fluorescent probe for detecting fluorid ions had been proposed. With good selectivity and sensitivity for fluorid ions, Q-based fluorescent probe was easier to prepare, more eco-friendly and more innoxious compared with traditional fluorescent probe obtained by organic chemistry synthesis operation. There was a major fluorescence emission peak at 500 nm for Q in dimethyl sulfoxide (DMSO) when the excitation wavelength was 390 nm. The changes of fluorescence spectra were investigated before and after adding different anions into Q solution. The fluorescence emission intensity of Q even had no change when adding Cl-，Br-，I-，ClO-4，H2PO-4, respectively. While adding fluorid ions, the fluorescence emission intensity of Q was decreased obviously, which suggested fluorid ions could induce fluorescence quenching of Q in DMSO. And the fluorescence emission intensity of Q-F- system had almost no significant change when adding other anions (Cl-，Br-，I-，ClO-4，H2PO-4), which meant the progress for detecting fluorid ions didn't be affected by other anions, and Q showed a good selectivity for fluorid ions. The fluorescence titration spectra showed that the fluorescence emission intensity of Q was decreased with the increase of concentration of fluorid ions, and they were in concentration-dependent manner. The fluorescence titration curve exhibited that the Q as fluorescent probe can be applied to the quantification of fluorid ions with a good linearity (R2=0.991), linear range of 1.0～8.0×10-6 mol·L-1 and the detection limit of 1.0×10-7 mol·L-1. Not only the changes appeared in fluorescence spectra, but also the changes appeared in UV-visible spectra, compared with Q absorption spectrum, the location of band at 375 nm had no change after adding Cl-，Br-，I-，ClO-4，H2PO-4, respectively. However, when adding fluorid ions, the band at 375 nm was shifted to 394 nm, and the color of the solution was changed into dark yellow, which revealed the interactions between Q and fluorid ions. The probable mechanism of fluorid ions inducing fluorescence quenching of Q was obtained with 1H NMR spectrum and the changes of fluorescence emission intensity of Q-F- system in different polar solvents (DMSO containing different concentration of water). The interaction mode about Q and fluorid ions in DMSO was related with hydrogen bond. Both experiments suggested that the possible recognition mechanism on fluorid ions was: fluorid ions were destroyed or weakened by original hydrogen bonds, and were promoted charge transfer within quercetin molecule, which resulted in fluorescence intensity decreasing of quercetin. This method was successfully applied in detecting fluorid ions of samples in DMSO with good recovery.

Allergic identification for ginkgo kernel protein in guinea pigs.

Ginkgo biloba L. can cause allergic reactions when consumed. In this paper, an allergy test to guinea pig was investigated. Guinea pigs were sensitized with 50 mg/mL of ginkgo kernel protein orally on days 1, 3, and 5, and intraperitoneally challenged with 100mg/mL of the protein on day 7 after the last sensitization. The volume of sensitization and challenge was 0.20mL/100 g weight. The results showed the average allergy grade for guinea pigs reached four and the allergy rate was 100%. The immunoglobulin G and E levels in sera were significantly higher than those in the controls. Footpads swelled distinctly, and the passive cutaneous allergy test manifested a positive response. There were inflammatory changes in the lungs and intestines. In conclusion, the present results may indicate that gingko kernel protein has an allergenic capacity.

[Effects of air temperature and soil moisture on flavonoids accumulation in Ginkgo biloba leaves].

Taking the 2-year old Ginkgo biloba seedlings as test materials, a pot experiment was conducted in an artificial climate chamber to study the effects of air temperature and soil moisture on the flavonoids accumulation in leaves. Three levels of air temperature (15/5 degrees C, 25/15 degrees C, and 35/25 degrees C day/night) and three levels of soil moisture (55%-60%, 40%-45%, and 30%-35% of field capacity) were installed, yielding nine temperature-soil moisture combinations. Under the three levels of soil moisture, the quercetin, kaempferol, isorhamnetin, and total flavonoids contents in the leaves were higher at 15/5 degrees C than at 25/15 degrees C and 35/25 degrees C. Soil moisture had minor effects on the flavonoids accumulation. The leaf kaempferol content was the highest, followed by quercetin and isorhamnetin. The total flavonoids yield per plant at 35/25 degrees C was higher than that at 15/5 degrees C and 25/15 degrees C. It was suggested that to adopt appropriate soil covering and watering before harvesting to decrease the ambient temperature could benefit the enhancement of leaf flavonoids content and the improvement of per unit area flavonoids production in G. biloba leaf-harvesting plantation.

[Effects of waterlogging on the growth and energy-metabolic enzyme activities of different tree species].

Aimed to understand the waterlogging tolerance and adaptation mechanisms of different tree species, a simulated field experiment was conducted to study the growth and energy-metabolic enzyme activities of one-year-old seedlings of Taxodium distichum, Carya illinoensis, and Sapium sebiferum. Three treatments were installed, i. e., CK, waterlogging, and flooding, with the treatment duration being 60 days. Under waterlogging and flooding, the relative growth of test tree species was in the order of T. distichum > C. illinoensis > S. sebiferum, indicating that T. distichum had the strongest tolerance against waterlogging and flooding, while S. sebiferum had the weakest one. Also under waterlogging and flooding, the root/crown ratio of the three tree species increased significantly, suggesting that more photosynthates were allocated in roots, and the lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH) activities of the tree species also had a significant increase. Among the test tree species, T. distichum had the lowest increment of LDH and ADH activities under waterlogging and flooding, but the increment could maintain at a higher level in the treatment duration, while for C. illinoensis and S. sebiferum, the increment was larger during the initial and medium period, but declined rapidly during the later period of treatment. The malate dehydrogenase (MDH), phosphohexose (HPI), and glucose-6-phosphate dehydrogenase (G6PDH) -6-phosphogluconate dehydrogenase (6PGDH) activities of the tree species under waterlogging and flooding had a significant decrease, and the decrement was the largest for T. distichum, being 35.6% for MDH, 21.0% for HPI, and 22.7% for G6PDH - 6PGDH under flooding. It was suggested that under waterlogging and flooding, the tree species with strong waterlogging tolerance had a higher ability to maintain energy-metabolic balance, and thus, its growth could be maintained at a certain level.

Progress in researches on the pharmaceutical mechanism and clinical application of Ginkgo Biloba extract on various kinds of diseases.

Progress made over the pharmaceutical mechanism and clinical application of Ginkgo Biloba extract (GBE) on various kinds of diseases were reviewed in this paper. The effective elements contained in GBE are mainly kinds of Ginkgo flavonoid and Ginkgolide, which have marked protective effects on cardio-cerebral vascular and central nerve systems. In clinical practice, it is applied mostly in treatment of cardio-cerebral vascular diseases. Also it shows apparent effects in the treatment processes of some other diseases as an adjuvant, and therefore, has been gradually accepted by the medical circle in the world, proving to be a medicine of wide prospect in development and application.