Molecular evolution and phylogeographic analysis of wheat dwarf virus

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10−4 substitutions/site/year (95% credibility interval, 2.828 × 10−4–5.723 × 10−4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517–1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China

Neuropeptide Localization in Lymnaea stagnalis: From the Central Nervous System to Subcellular Compartments

Due to the relatively small number of neurons (few tens of thousands), the well-established multipurpose model organism Lymnaea stagnalis, great pond snail, has been extensively used to study the functioning of the nervous system. Unlike the more complex brains of higher organisms, L. stagnalis has a relatively simple central nervous system (CNS) with well-defined circuits (e.g., feeding, locomotion, learning, and memory) and identified individual neurons (e.g., cerebral giant cell, CGC), which generate behavioral patterns. Accumulating information from electrophysiological experiments maps the network of neuronal connections and the neuronal circuits responsible for basic life functions. Chemical signaling between synaptic-coupled neurons is underpinned by neurotransmitters and neuropeptides. This review looks at the rapidly expanding contributions of mass spectrometry (MS) to neuropeptide discovery and identification at different granularity of CNS organization. Abundances and distributions of neuropeptides in the whole CNS, eleven interconnected ganglia, neuronal clusters, single neurons, and subcellular compartments are captured by MS imaging and single cell analysis techniques. Combining neuropeptide expression and electrophysiological data, and aided by genomic and transcriptomic information, the molecular basis of CNS-controlled biological functions is increasingly revealed

Anew Chinese bayberry cultivar Dingkui

Dingkui is a new Chinese bayberry variety selected from a single variant found in the growing orchard of Ding'ao. After more than 20 years of observation and identification on the mother tree and offsprings, it is believed that the characteristics of the variety are stable and consistent. When the fruit fully matures, the flesh column is round and blunt, the average fruit weight is 22.6 g, the fruit hardness is 2.89 N, the fruit shape index is 0.97, the solid soluble content is 10.8%, the titratable acid content is 10.57 g·kg-1, the total sugar content is 73.3 mg·g-1, the flavone content is 0.74 mg·g-1, the polyphenol contentis 1.77 mg·g-1, the amino acid content is 7.76 mg·100 g-1, and the vitamin C contentis 33.3 mg·100 g-1. The tree is strong in vigour and round or semicircular in shape, and the trunk and branches are short. The leaves are lanceolate-inverted, dark-green, 11.1 cm long and 2.7 cm wide, and have a short petiole. The flower is pure pistil, the female flower inflorescence is cylindrical, 0.76 cm long and 0.31 cm thick, and the flower is “V”-shaped. The budbreak period of Dingkui flower buds is in late February, the initial flowering period is in early March, the peak flowering period is in early March, and the final flowering period and young fruit period are in mid-March. The fruit ripening period is in early June, and the fruit development period is 55-60 days. The top flower buds on short fruit branches in spring and summer mainly bear fruits, with a natural fruit setting rate of about 15%, significantly lower than that of Ding'ao. The artificial thinning amount during fruit setting is small and it is easy to manage. Generally, it enters the peak production period 5-7 years after high grafting, with an average yield of 660 kg·666.7 m-2. We used SNP molecular marker technology to conduct molecular identification on 18 Chinese bayberry samples collected in 2023. The clustering analysis results confirmed that Dingkui did not have any homonyms with other varieties. 18 materials were divided into 2 groups, with Dingkui located in Group Ⅰ and showing differences from the other 17 materials. Among them, Dingkui and Ding'ao had the closest genetic relationship with a coefficient of 0.92, indicating that Dingkui is a new germplasm. It is suitable for cultivation in the south of Yangtze River and areas with similar climate, especially in southern Zhejiang. We suggest choosing gravelly red and yellow soil with deep depth, sufficient moisture, and pH between 4.5-6.5 for orchard establishment, and adopting natural sod system for orchard soil management. The recommended spacing for cultivation is 5 m × 5 m or 5 m × 6 m, with 20-30 plants per acre. For dwarfing and dense planting, a spacing of 4 m × 4 m can be used, with 42 plants per acre and planting holes of 0.8 m × 0.8 m × 0.6 m. There is no special requirement for the configuration mode for male plants in the orchard, which is the same as that of Ding'ao. In production, some bare branches should be pressed and hung, and thin and weak branches, overlapping branches, crossed branches and dead branches with diseases and pests should be cut off. In the fruiting period, fertilizer should be applied three times in spring, summer and autumn every year, about 1-2 kg of pure potassium sulfate should be applied to each plant for each time, and the ratio of nitrogen, phosphorus and potassium for adult trees is 1∶0.3∶4. Strengthen routine cultivation management, maintain reasonable ventilation and light transmission for tree crown, and pay attention to clearing the orchard in winter. There are few diseases and insect pests

Decay of Electric Charge on Corona Charged Polyethylene

In this paper, the surface potential decay of corona-charged low density polyethylene (LDPE) films has been investigated. It has been found that for the same sample thickness the faster decay occurs in the sample with a higher charging voltage. For the same charging voltage, the surface potential in the thinner sample shows rapid decay. Our new evidence from both the surface potential measurement on multilayer samples and space charge measurement suggests the surface potential decay is a bulk limited process. More importantly, space charge measurement indicates double injection has taken place during corona charging process

Study on the Historical Dynamics of the Medicine Buddha Sutra Illustrations based on Medicine Buddha Beliefs

A substantial portion of the murals and manuscripts housed in the Sutra Caves of Dunhuang is intimately tied to the cult of the Medicine Buddha. An examination of the Catalogue of Dunhuang Mogao Caves compiled by the Dunhuang Academy, alongside the New Catalogue of the Dunhuang Manuscripts edited by Huang Yongwu, reveals the presence of 295 texts pertaining to the Medicine Buddha, underscoring the prevalence of this belief system in Dunhuang. The popularity of the Medicine Buddha belief in the region emerged as a pivotal factor influencing the evolution of sutra illustrations’ content and form. The Medicine Buddha’s attributes of averting calamities, curing illnesses, and prolonging life—all catering to worldly aspirations—resonated deeply with people’s pursuit of immediate benefits in this life. This paper employs a multifaceted approach, encompassing documentary research, iconographic analysis, and comparative studies, to trace the historical trajectory and graphical transformations of the “Medicine Buddha Sutra Illustrations” (Yaoshijing Biantu), culminating in a comprehensive synthesis. Furthermore, by delving into the societal backdrop, the underlying economic underpinnings, and the evolving “compositional strategies” of these illustrations across various eras, we aim to present a holistic view of the dynamic development of the Medicine Buddha Sutra illustrations throughout time

Emerging Methods for Single Cell Metabolomics

Single cell metabolomics provides new insights into understanding cellular heterogeneity of small molecules, and individual cell response to environmental perturbations. With high sensitivity and specificity, mass spectrometry (MS) has become an important tool for analyzing metabolites, lipids, and peptides in individual cells. Facing significant challenges, single cell and subcellular analysis by MS requires technical advances to answer fundamental biological questions, for example the phenotypic variations of genetically identical cells. The work presented in this dissertation describes my efforts to develop and apply capillary microsampling MS with ion mobility separation (IMS) for the analysis of single cells and subcellular compartments. Chapter 1 introduces MS based analytical techniques for single cell and subcellular analysis. Recent advances of sampling and ionization methods for MS analysis of volume-limited samples are reviewed with emphasis on ambient ionization techniques, cell micromanipulation methods, and rapid gas phase separations. In Chapter 2, the application of capillary microsampling electrospray ionization (ESI)-IMS-MS for metabolic and lipidomic analysis of single Arabidopsis thaliana epidermal cells is presented. Distinct metabolite compositions and metabolic pathways are identified among basal and pavement cells, and trichomes. These three specialized epidermal cells serve different functions in the plant leaf, and our single cell MS data reveals the corresponding metabolic pathways. In Chapter 3, it describes the utilization of capillary microsampling ESI-IMS-MS for the analysis of metabolites and lipids in single human hepatocellular carcinoma cells. Cellular physiological states and their heterogeneity in response to xenobiotics treatment, and lipid turnover rates are explored. Here, IMS helps to enhance molecular coverage, facilitate metabolite and lipid identification, resolve isobaric ions, and minimize background interference. Comparing cells affected by metabolic modulators to unaffected counterparts reveals dramatic reduction in the availability of energy in the former. In Chapter 4, the combination of fluorescence microscopy with capillary microsampling ESI-IMS-MS for selective analysis of identified cell subpopulations at a single cell level is demonstrated. Molecular differences and heterogeneity corresponding to cells in distinct mitotic stages are explored. Pairwise correlations between relative metabolite levels among individual mitotic cells are also studied. In Chapter 5, the subcellular distributions of neuropeptides in individual identified neurons are explored by capillary microsampling ESI-IMS-MS. Distinct peptide distributions between the cytoplasm and nucleus are revealed. Mass spectra provide direct evidence for high abundance of these peptides in the nucleus despite the scarcity of immunostaining results supporting their presence there. A new neuropeptide is discovered and sequenced by MS in a single cell. In Chapter 6, the current state of single cell and subcellular metabolomics is discussed. Major challenges include the low-throughput of current sampling techniques, low molecular coverage of metabolites, lipids and peptides, and external perturbations introduced by the sampling and ionization processes. In addition to exploring new solutions to these challenges, future advances will lead to the development of systems biology at the single cell level, to nano- and micro-fabricated tools to study perturbations in a lab-in-a-cell framework, and to coupling with optical manipulations and microfluidic techniques to investigate subcellular heterogeneity