The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant.

BACKGROUND: Hemerocallis citrina Baroni (Huang hua cai in Chinese) is a perennial herbaceous plant grown for its flower buds that are eaten fresh or dried and is known as the vegetarian three treasures. The nuclear genome of H. citrina has been reported, but the intraspecific variation of the plastome (plastid genome) has not yet been studied. Therefore, the panplastome of this species collected from diverse locations is reported here for the first time. RESULTS: In this study, 65 H. citrina samples were resequenced, de novo assembled, and aligned with the published plastome of H. citrina to resolve the H. citrina panplastome. The sizes of the 65 newly assembled complete plastomes of H. citrina ranged from 156,048 bp to 156,263 bp, and the total GC content ranged from 37.31 to 37.34%. The structure of the complete plastomes showed a typical tetrameric structure, including a large single copy (LSC), a small single copy (SSC), and a pair of inverted repeat regions (IRA and IRB). Many nucleotide variants were identified between plastomes, among which the variants in the intergenic spacer region were the most abundant, with the highest number of variants concentrated in the LSC region. Based on the phylogenetic tree constructed using the ML method, population structure analysis, and principal component analysis (PCA), the panplastome data were subdivided into five genetic clusters. The C5 genetic cluster was mostly represented by samples from Qidong, Hunan Province, while samples from Shanxi and Shaanxi Provinces were classified into the C4 genetic cluster. The greatest genetic diversity was found in the C1 genetic cluster, and the greatest genetic distance between any two clusters was found between the C4 and C5 clusters. CONCLUSION: The resolution of the panplastome and the analysis of the population structure of H. citrina plastomes provide important data for future breeding projects and germplasm preservation.

Modelling and forecasting non-renewable energy consumption and carbon dioxide emissions in China using a PSO algorithm-based fractional non-linear grey Bernoulli model.

In China, the consumption of non-renewable energy increases not only in general economic growth but also in large amounts of carbon dioxide (CO2) emissions which cause disasters and catastrophic damages to the environment. To alleviate environmental pressure, it is neccessary to forecast and model the relationship between energy consumption and CO2 emissions. In this study, a fractional non-linear grey Bernoulli (FANGBM(1,1)) model based on particle swarm optimization is proposed to forecast and model non-renewable energy consumption and CO2 emissions in China. Firstly, based on the FANGBM(1,1) model, non-renewable energy consumption in China is predicted. The comparison results of several competitive models show that the FANGBM(1,1) model has the best predictive performance. Then, the relationship between non-renewable energy consumption and CO2 emissions is modeled. On this basis, China's future CO2 emissions are effectively predicted based on the established model. The forecast results show that the growth trend of China's CO2 emissions will continue to grow to 2035, while the prediction results in different scenarios also show that that the different growth rates of renewable energy share lead to different times to peak CO2 emissions. In the end, relevant suggestions are proposed to support China's dual carbon goals.

Molecular Characterization Analysis of Prevalent Infectious Bronchitis Virus and Pathogenicity Assessment of Recombination Strain in China.

Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.

Pharmacokinetic Characteristics, Tissue Bioaccumulation and Toxicity Profiles of Oral Arsenic Trioxide in Rats: Implications for the Treatment and Risk Assessment of Acute Promyelocytic Leukemia.

Oral arsenic trioxide (ATO) has demonstrated a favorable clinical efficiency in the treatment of acute promyelocytic leukemia (APL). However, the pharmacokinetic characteristics, tissue bioaccumulation, and toxicity profiles of arsenic metabolites in vivo following oral administration of ATO have not yet been characterized. The present study uses high performance liquid chromatography-hydride generation-atomic fluorescence spectrometry (HPLC-HG-AFS) to assess the pharmacokinetics of arsenic metabolites in rat plasma after oral and intravenous administration of 1 mg kg-1 ATO. In addition, the bioaccumulation of arsenic metabolites in blood and selected tissues were evaluated after 28 days oral administration of ATO in rats at a dose of 0, 2, 8, and 20 mg kg-1 d-1. The HPLC-HG-AFS analysis was complemented by a biochemical, hematological, and histopathological evaluation conducted upon completion of ATO treatment. Pharmacokinetic results showed that arsenite (AsIII) reached a maximum plasma concentration rapidly after initial dosing, and the absolute bioavailability of AsIII was 81.03%. Toxicological results showed that the levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and white blood cells (WBC) in the 20 mg kg-1 d-1 ATO group were significantly increased compared to the control group (p < 0.05). The distribution trend of total arsenic in the rat was as follows: whole blood > kidney > liver > heart. Dimethylated arsenic (DMA) was the predominant bioaccumulative metabolite in the whole blood, liver, and heart, while monomethylated arsenic (MMA) was the predominant one in the kidney. Collectively, these results revealed that oral ATO was rapidly absorbed, well-tolerated, and showed organ-specific and dose-specific bioaccumulation of arsenic metabolites. The present study provides preliminary evidence for clinical applications and the long-term safety evaluation of oral ATO in the treatment of APL.

Occurrence, distribution, and health risk assessment of quinolone antibiotics in water, sediment, and fish species of Qingshitan reservoir, South China.

The residual antibiotics in the environment have lately caused widespread concerns. However, little information is available on the antibiotic bioaccumulation and its health risk in drinking water resources of South China. Therefore, the occurrence, distribution, and health risk of four quinolone antibiotics including ofloxacin (OFX), norfloxacin (NOR), ciprofloxacin (CIP), and enrofloxacin (ENR) in the Qingshitan reservoir using high-performance liquid chromatography were investigated. Results revealed that the concentrations in water, sediment, and edible fish ranged from 3.49-660.13 ng/L, 1.03-722.18 µg/kg, and 6.73-968.66 µg/kg, respectively. The ecological risk assessment via the risk quotient (RQ) method showed that the values in sediment were all greater than 1, posing a high risk to the environment. The health risk index of water samples was at the maximum acceptable level, with OFX at the top while the rest were at the medium risk level. The main edible fish kinds of the reservoir had high dietary safety and the highest contaminations were found in carnivorous feeding habits and demersal habitat fishes with OFX as the highest magnitude. Source identification and correlation analysis using SPSS showed significant relationships between NOR with pH and turbidity (in water), as well as total phosphor (TP) and total organic carbon (TOC) in sediment. NOR was the highest in sediment which mostly sourced from livestock wastewater, croplands irrigation drain water, and stormwater. Correlations between CIP and ENR with TP were significant, while OFX was positively associated with total nitrogen (TN) which mainly originated from urban sewage as well as directly dosed drugs in fish farms. In conclusion, our results are of great significance for ensuring the safety of drinking water and aquatic products in this region.

Spatial distribution, source identification, and risk assessment of organochlorines in wild tilapia from Guangxi, South China.

Seventy-five wild tilapia samples from six rivers (ten sites) in Guangxi province were collected and analyzed for 53 organochlorine compounds. DDTs, endosulfan, and PCBs were the most dominant compounds found in this study. Tiandong County (TD) and Guigang City (GG) sites were found to be heavily contaminated with high levels of endosulfan (385-925 ng/g lw) and/or DDTs (20.1-422 ng/g lw). The diagnostic ratios indicated that the residues of DDTs and endosulfan in wild tilapia are associated with historical applications as well as the recent introduction of technical DDTs and endosulfan at some sampling sites. The correlation between total length, body mass, and organochlorines (OCs) was higher than the correlation between age and lipid content. There was no significant correlation between organochlorine pesticides (OCPs) and lipid content. Therefore, for organisms, the feeding intensity (related to length and mass) of fish could better reflect degree of pollution than exposure time (age) of fish. The hazardous ratios for the 50th and 95th percentile data of OCPs and PCBs in fish were both below 1, suggesting that daily exposure to OCPs and PCBs yields a lifetime cancer risk lower than 1 in 10,000.

DRodVir: A resource for exploring the virome diversity in rodents.

Emerging zoonotic diseases have received tremendous interests in recent years, as they pose a significant threat to human health, animal welfare, and economic stability. A high proportion of zoonoses originate from wildlife reservoirs. Rodents are the most numerous, widespread, and diverse group of mammals on the earth and are reservoirs for many zoonotic viruses responsible for significant morbidity and mortality. A better understanding of virome diversity in rodents would be of importance for researchers and professionals in the field. Therefore, we developed the DRodVir database (http://www.mgc.ac.cn/DRodVir/), a comprehensive, up-to-date, and well-curated repository of rodent-associated animal viruses. The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. In addition to virus sequences, the database provides detailed information on related samples and host rodents, as well as a set of online analytical tools for text query, BLAST search and phylogenetic reconstruction. The DRodVir database will help virologists better understand the virome diversity of rodents. Moreover, it will be a valuable tool for epidemiologists and zoologists for easy monitoring and tracking of the current and future zoonotic diseases. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases.

[Influence of the river-lake relation change on the distribution of heavy metal and ecological risk assessment in the surface sediment of Poyang Lake].

Effects of river (Yangtze River)-lake (Poyang Lake) relation on the distribution and potential ecological risk of Cu, Pb, Zn, Cr and Cd were investigated in surface sediment of Poyang Lake under different waterregimens. The results indicated: (1) the sediments of Poyang Lake were polluted by various concentrations of heavy metals mainly originated from particulates of Yangtze River, and Cu and Pb were the main pollution factors. The pollution level of determined heavy metals followed the order of Cu > Pb > Zn > Cr >Cd. The concentration ranges of Cu, Pb, Zn, Cr and Cd in the sediment of Poyang Lake were 13.1-108.1 mg.kg-1 , 37-119.1 mg.kg-1, 29.9-129.9 mgkg-1, 13.3-98.6 mgkg-1 and 0. 19-2.77 mg.kg-1 during the wet period, and 3.05-69.7 mg.kg-1, 27.5-105 mgkg-1, 18.8-95.4 mg.kg-1, 7.34-70 mg.kg- and 0.033-0.406 mg.kg-1 during the dry period respectively. The region with the highest heavy metal concentrations was located in water input area of the " Five River" and water output area of " Hukou" ; (2)The regions with high risk of heavy metals in sediment were mainly located in the area of the trail of "Five Rivers" during the wet period; while during the dry period, the area with high risk of heavy metals in sediment enlarged, which was not only limited in the area of the trail of "Five Rivers", but also enlarged northwards. The potential ecological risk of "Hukou" was relatively high, however, the potential ecological risk of the sediment in the whole lake during the dry period was lower than that during the wet period. (3) With the change of river-lake relation, water level rose, the maintaining time was shortened during the wet period, the dry season appeared ahead of schedule, the transformation course of Poyang Lake from "Lake morphology" to " River morphology" increased, and the typical river properties were enhanced, which resulted in the decreased potential ecological risk of heavy metals in sediment of the whole lake, however, the area of high risk-region was enlarged northwards.

The evaluation of catechins that contain a galloyl moiety as potential HIV-1 integrase inhibitors.

Four catechins with the galloyl moiety, including catechin gallate (CG), epigallocatechin gallate (EGCG), gallocatechin gallate (GCG), and epicatechin gallate (ECG), were found to inhibit HIV-1 integrase effectively as determined by our ELISA method. In our docking study, it is proposed that when the HIV-1 integrase does not combine with virus DNA, the four catechins may bind to Tyr143 and Gln148, thus altering the flexibility of the loop (Gly140-Gly149), which could lead to an inhibition of HIV-1 integrase activity. In addition, after combining HIV-1 integrase with virus DNA, the four catechins may bind between the integrase and virus DNA, consequently, disrupt this interaction. Thus, the four catechins may reduce the activity of HIV-1 integrase by disrupting its interaction with virus DNA. The four catechins have a highly cooperative inhibitory effect (IC50=0.1 µmol/L). Our study suggests that catechins with the galloyl moiety could be a novel and effective class of HIV-1 integrase inhibitors.