An omics-based characterization of Wolfiporia cocos reveals three CYP450 members involved in the biosynthetic pathway of pachymic acid.

Wolfiporia cocos is a medicinal mushroom used in China. It biosynthesizes pachymic acid (PA), a main therapeutic triterpene associated with therapies. Nowadays, the unknown PA biosynthesis leads to difficulties in increasing its content in W. cocos. Herein, we report sequencing, assembling, and characterization of the genome and several transcriptomes of W. cocos. Sequence mining determined candidate genes that encode lanosterol synthase, sterol O-acyltransferase, and sterol C-24 methyltransferase likely involved in the steps from lanosterol to PA. Gene cluster analysis identified four CYP450 cDNAs likely involved in the biosynthesis of PA, namely WcCYP64-1, WcCYP64-2, WcCYP52, and WcCYP_FUM15, which were subjected to both overexpression and silencing in mycelia. The overexpression of each of WcCYP64-1, WcCYP52 and WcCYP_FUM15 increased the content of PA, 16α-hydroxytrametenolic acid, eburicoic acid, and tumulosic acid, while the silencing of each gene either significantly or slightly decreased the contents of these four compounds, indicating their involvement in the PA biosynthesis. In addition, different temperatures affected the expression of these genes and the formation of PA. By contrast, the overexpression and silencing of WcCYP64-2 did not alter the formation of these compounds. Taken together, these findings determine more potential steps in the biosynthetic pathway of PA for metabolic engineering.

A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa.

Chaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

Effects of the spatial patterns of urban parks on public satisfaction: evidence from Shanghai, China.

Context: Urban parks need to meet the growing demand for activities vital to residents' well-being and urban development. A holistic understanding of public satisfaction with urban parks is a prerequisite for improving management. Objective: The spatial patterns and composition of urban parks vary greatly, and the objective of this study is to comprehensively investigate public satisfaction with urban parks and the impact of their structure. Methods: With the metropolis of Shanghai, China, as an example, we employed 111,814 social media data sets for 50 urban park sites to quantify public satisfaction via the long short-term memory model. We analyzed the internal, boundary and external dimensions of spatial patterns and described the internal landscape patterns from the perspectives of size, heterogeneity, aggregation, shape, diversity and landscape elements. Moreover, we used all-subset regression and hierarchical partitioning to quantify the relationship and mechanism of action between spatial patterns and public satisfaction. Results: The results indicate that the mean value of public satisfaction with urban parks was 0.716 (ranging from 0 to 1), which is generally positive or neutral. Satisfaction was influenced by the internal, boundary, and external spatial patterns of urban parks. The independent contribution rates of external transportation facility density (51.49%) and internal edge density (48.51%) to satisfaction. Conclusions: We highlight the roles of spatial patterns, especially the degree of external transportation convenience and the edge density of urban parks at the landscape level. The findings provide guidance and recommendations for the planning and design of public satisfaction-oriented urban parks. Supplementary Information: The online version contains supplementary material available at 10.1007/s10980-023-01615-z.

Molecular cloning and characterization of an alpha-amylase inhibitor (TkAAI) gene from Trichosanthes kirilowii Maxim.

Trichosanthes kirilowii Maxim taxonomically belongs to the Cucurbitaceae family and Trichosanthes genus. Its whole fruit, fruit peel, seed and root are widely used in traditional Chinese medicines. A ribosome-inactivating protein with RNA N-glycosidase activity called Trichosanthrip was isolated and purified from the seeds of T. kirilowii in our recent previous research. To further explore the biological functions of Trichosanthrip, the cDNA of T. kirilowii alpha-amylase inhibitor (TkAAI) was cloned through rapid-amplification of cDNA ends and its sequence was analyzed. Also, the heterologous protein was expressed in Escherichia coli and its alpha-amylase activity was further measured under optimized conditions. The full-length cDNA of TkAAI was 613 bp. The speculated open reading frame sequence encoded 141 amino acids with a molecular weight of 16.14 kDa. Phylogenetic analysis demonstrated that the Alpha-Amylase Inhibitors Seed Storage domain sequence of TkAAI revealed significant evolutionary homology with the 2S albumin derived from the other plants in the Cucurbitaceae group. In addition, TkAAI was assembled into pET28a with eGFP to generate a prokaryotic expression vector and was induced to express in E. coli. The TkAAI-eGFP infusion protein was proven to exhibit alpha-amylase inhibitory activity against porcine pancreatic amylase in a suitable reaction system. Analysis of gene expression patterns proved that the relative expression level of TkAAI in seeds is highest. The results presented here forecasted that the TkAAI might play a crucial role during the development of T. kirilowii seeds and provided fundamental insights into the possibility of T. kirilowii derived medicine to treat diabetes related diseases.

Leaving no one behind: tracing every human thymocyte by single-cell RNA-sequencing.

The thymus is the primary organ for T-cell development, providing an essential microenvironment consisting of the appropriate cytokine milieu and specialized stromal cells. Thymus-seeding progenitors from circulation immigrate into the thymus and undergo the stepwise T-cell specification, commitment, and selection processes. The transcriptional factors, epigenetic regulators, and signaling pathways involved in the T-cell development have been intensively studied using mouse models. Despite our growing knowledge of T-cell development, major questions remain unanswered regarding the ontogeny and early events of T-cell development at the fetal stage, especially in humans. The recently developed single-cell RNA-sequencing technique provides an ideal tool to investigate the heterogeneity of T-cell precursors and the molecular mechanisms underlying the divergent fates of certain T-cell precursors at the single-cell level. In this review, we aim to summarize the current progress of the study on human thymus organogenesis and thymocyte and thymic epithelial cell development, which is to shed new lights on developing novel strategies for in vitro T-cell regeneration and thymus rejuvenation.

Vanadium exposure-induced striatal learning and memory alterations in rats.

Occupational and environmental exposure to vanadium has been associated with toxicities in reproductive, respiratory, and cardiovascular systems. The knowledge on whether and how vanadium exposure caused neurobehavioral changes remains incomplete. This study was designed to investigate the changes in learning and memory following drinking water exposure to vanadium, and to conduct the preliminary study on underlying mechanisms. Male Sprague-Dawley rats were exposed to vanadium dissolved in drinking water at the concentration of 0.0, 0.5, 1.0 and 2.0g/L, as the control, low-, medium-, and high- dose groups, respectively, for 12 weeks. The results by the Morris water maze test showed that the time for the testing animal to find the platform in the high exposed group was increased by 82.9% and 49.7%, as compared to animals in control and low-dose groups (p<0.05). There were significantly fewer rats in the medium- and high- dose groups than in the control group who were capable of crossing the platform (p<0.05). Quantitation of vanadium by atomic absorption spectrophotometry revealed a significant dose-dependent accumulation of vanadium in striatum (r=0.931, p<0.01). Histopathological examination further demonstrated a degenerative damage in vanadium-exposed striatum. Interestingly, with the increase of the dose of vanadium, the contents of neurotransmitter ACh, 5-HT and GABA in the striatum increased; however, the levels of Syn1 was significantly reduced in the exposed groups compared with controls (p<0.05). These data suggest that vanadium exposure apparently reduces the animals' learning ability. This could be due partly to vanadium's accumulation in striatum and the ensuing toxicity to striatal structure and synaptic plasticity. Further research is warranted for mechanistic understanding of vanadium-induced neurotoxicity.

Effects of lead and cadmium co-exposure on bone mineral density in a Chinese population.

It has been indicated that both cadmium (Cd) and lead (Pb) may have adverse effects on the bone. However, most studies have only focused on a single factor. The primary and main and interactive effects of Cd and Pb on bone mineral density (BMD) in a Chinese population were observed in this study. A total of 321 individuals (202 women and 119 men), aged 27 years and older, living in control and polluted areas, were recruited to participate in this study. The BMD was measured through dual energy X-ray absorptiometry (DXA) at the proximal radius and ulna. The samples of urine and blood were collected to determine the levels of Cd and Pb in the urine (UCd and UPb) and blood (BCd and BPb). The Cd and Pb levels of people living in the polluted area were significantly higher than those living in the control area (p<0.05). The BMD of women living in polluted area was significantly lower than that of women living in the control area (p<0.05). Furthermore, the BMD decreased with increasing of BCd (p<0.05), BPb and UPb in women. The likelihood of low BMD was associated with higher BCd in women (OR=2.5, 95% CI: 1.11-5.43) and BPb in men (OR=4.49, 95% CI: 1.37-14.6). The relative extra risk index of low BMD for female and male subjects with both high levels of BCd and BPb was 0.45 and 1.16, respectively. This study strengthens previous evidence that cadmium and lead may influence the bone and also demonstrates that cadmium and lead may have interactive effects on BMD.

Protective effects of dietary fibre against manganese-induced neurobehavioral aberrations in rats.

We tested the hypothesis that dietary fibre (DF) has protective effects against manganese (Mn)-induced neurotoxicity. Forty-eight one-month old Sprague-Dawley rats were randomly divided into six groups: control, 16 % DF, Mn (50 mg kg-1 body weight), Mn+ 4 % DF, Mn+ 8 % DF, and Mn+ 16 % DF. After oral administration of Mn (as MnCl2) by intragastric tube during one month, we determined Mn concentrations in the blood, liver, cerebral cortex, and stool and tested neurobehavioral functions. Administration of Mn was associated with increased Mn concentration in the blood, liver, and cerebral cortex and increased Mn excretion in the stool. Aberrations in neurobehavioral performance included increases in escape latency and number of errors and decrease in step-down latency. Irrespective of the applied dose, the addition of DF in forage decreased tissue Mn concentrations and increased Mn excretion rate in the stool by 20 % to 35 %. All neurobehavioral aberrations were also improved. Our findings show that oral exposure to Mn may cause neurobehavioral abnormalities in adult rats that could be efficiently alleviated by concomitant supplementation of DF in animal feed.

[Effects of cadmium on zinc metabolism and its functions in rats].

OBJECTIVE: To explore the effects of cadmium on zinc metabolism and its function and the protective effects of pre-supplement zinc to it. METHODS: NS or different doses of CdCl(2) were injected to pregnant dams intraperitoneally at the 7th, 10th and 13th day of gestation respectively. At the 21st pregnant day embryos were taken out from the pregnant rats. Another rats of pre-supplement zinc or no pre-supplement zinc group were injected different doses of CdCl(2) or NS intraperitoneally after 6 days. After 24 hours the rats were killed. The contents of Cd, Zn and relative biomarkers of effect of liver, brain or serum were detected in both embryos and adult rats. RESULTS: Compared with control group, the contents of T-AOC and Ach were significantly reduced in the Cd treatment group in the embryonic brains, the activity of AKP in the embryonic liver tissues was decreased, and The Cd content was increased significantly in embryonic liver and was negatively correlated with the Zinc content in the embryonic brain. There were no differences in the activities of SOD and AKP and the contents of Cd and MDA between pre-supplement Zn control group and no supplement Zn control group, but higher content of Zn in liver and serum in the former. Compared with no supplement Zn control group, there were higher contents of Cd in liver and serum, Zn and MDA in liver, lower activities of SOD in liver and AKP in liver and serum, and lower content of Zn in serum in the Cd treatment groups. Pre-supplement Zn significantly increase the content of Zn and the activities of SOD in liver and AKP in serum, decrease the content of MDA in liver and Cd in serum resulted by Cd treatment only. The content of Zn and the activity of AKP in serum and the activities of SOD and AKP in liver were negatively correlated with the content of Cd in corresponding tissue significantly. CONCLUSION: Cadmium can enter embryo and enter brain by permeating the brain-blood barrier during the embryonic period. The decrease of AKP activity, some neural transmitter and capacity of anti-lipid peroxidation that are related with Zn in embryos are caused when the pregnant rats are administered with cadmium. Cd can inhibits the activities of AKP and SOD in liver, and the activity of AKP in serum respectively, and increase the content of MDA in liver dose-dependently. The effects induced by cadmium are related with zinc abnormal distribution. Pre-supplement zinc to rats can antagonize these effects in different degree.