Browsing by Author "Li H"

Now showing 1 - 6 of 6
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    Clustering by Search in Descending Order and Automatic Find of Density Peaks
    (IEEE, 2019-01-01) Liu T; Li H; Zhao X; Liang Q
    Clustering by fast search and find of density peaks published on journal Science in 2014 is a density-based clustering technique, which is not only unnecessary to determine the number of clusters in advance, but also able to recognize the clusters of arbitrary shapes. Due to a manual selection of clustering centers on a decision graph, samples which belong to one cluster may be assigned to two or more clusters and vice versa. On assumption that boundary points which keep comparable densities with cluster centers should be regarded as inner points, we make a new method which not only can find all possible clusters automatically but also can combine those with similarities simultaneously to obtain the final clusters. Unlike clustering by fast search and find of density peaks, we only focus on densities with discarding the relative metric which measures the minimum distance between a cluster center and a point with a higher density. Qualitative and quantitative experimental results on sufficient datasets demonstrate the effectiveness of our method.
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    Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses.
    (MDPI (Basel, Switzerland), 2024-05-26) Wang J; Meng Z; He H; Du P; Dijkwel PP; Shi S; Li H; Xie Q; Igamberdiev AU
    BBX protein is a class of zinc finger transcription factors that have B-box domains at the N-terminus, and some of these proteins contain a CCT domain at the C-terminus. It plays an important role in plant growth, development, and metabolism. However, the expression pattern of BBX genes in alfalfa under hormonal and salt stresses is still unclear. In this study, we identified a total of 125 BBX gene family members by the available Medicago reference genome in diploid alfalfa (Medicago sativa spp. Caerulea), a model plant (M. truncatula), and tetraploid alfalfa (M. sativa), and divided these members into five subfamilies. We found that the conserved motifs of BBXs of the same subfamily reveal similarities. We analyzed the collinearity relationship and duplication mode of these BBX genes and found that the expression pattern of BBX genes is specific in different tissues. Analysis of the available transcriptome data suggests that some members of the BBX gene family are involved in multiple abiotic stress responses, and the highly expressed genes are often clustered together. Furthermore, we identified different expression patterns of some BBX genes under salt, ethylene, salt and ethylene, salicylic acid, and salt and salicylic acid treatments, verified by qRT-PCR, and analyzed the subcellular localization of MsBBX2, MsBBX17, and MsBBX32 using transient expression in tobacco. The results showed that BBX genes were localized in the nucleus. This study systematically analyzed the BBX gene family in Medicago plants, which provides a basis for the study of BBX gene family tolerance to abiotic stresses.
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    Genome-Wide Analysis of the SRPP/REF Gene Family in Taraxacum kok-saghyz Provides Insights into Its Expression Patterns in Response to Ethylene and Methyl Jasmonate Treatments.
    (MDPI (Basel, Switzerland), 2024-07-07) He H; Wang J; Meng Z; Dijkwel PP; Du P; Shi S; Dong Y; Li H; Xie Q; Pollmann S
    Taraxacum kok-saghyz (TKS) is a model plant and a potential rubber-producing crop for the study of natural rubber (NR) biosynthesis. The precise analysis of the NR biosynthesis mechanism is an important theoretical basis for improving rubber yield. The small rubber particle protein (SRPP) and rubber elongation factor (REF) are located in the membrane of rubber particles and play crucial roles in rubber biosynthesis. However, the specific functions of the SRPP/REF gene family in the rubber biosynthesis mechanism have not been fully resolved. In this study, we performed a genome-wide identification of the 10 TkSRPP and 2 TkREF genes' family members of Russian dandelion and a comprehensive investigation on the evolution of the ethylene/methyl jasmonate-induced expression of the SRPP/REF gene family in TKS. Based on phylogenetic analysis, 12 TkSRPP/REFs proteins were divided into five subclades. Our study revealed one functional domain and 10 motifs in these proteins. The SRPP/REF protein sequences all contain typical REF structural domains and belong to the same superfamily. Members of this family are most closely related to the orthologous species T. mongolicum and share the same distribution pattern of SRPP/REF genes in T. mongolicum and L. sativa, both of which belong to the family Asteraceae. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the TkSRPP/REFs gene family. The expression levels of most TkSRPP/REF members were significantly increased in different tissues of T. kok-saghyz after induction with ethylene and methyl jasmonate. These results will provide a theoretical basis for the selection of candidate genes for the molecular breeding of T. kok-saghyz and the precise resolution of the mechanism of natural rubber production.
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    Immobilization of Horseradish Peroxidase and Myoglobin Using Sodium Alginate for Treating Organic Pollutants
    (MDPI (Basel, Switzerland), 2024-03-15) Wang X; Ghanizadeh H; Khan S; Wu X; Li H; Sadiq S; Liu J; Liu H; Yue Q; Hung Y-T
    Removing organic pollutants from wastewater is crucial to prevent environmental contamination and protect human health. Immobilized enzymes are increasingly being explored for wastewater treatment due to their specific catalytic activities, reusability, and stability under various environmental conditions. Peroxidases, such as horseradish peroxidase (HRP) and myoglobin (Mb), are promising candidates for immobilized enzymes utilized in wastewater treatment due to their ability to facilitate the oxidation process of a wide range of organic molecules. However, the properties of the carrier and support materials greatly influence the stability and activity of immobilized HRP and Mb. In this research, we developed immobilized HRP and Mb using support material composed of sodium alginate and CaCl2 as carriers and glutaraldehyde as a crosslinking agent. Following this, the efficacy of immobilized HRP and Mb in removing aniline, phenol, and p-nitrophenol was assessed. Both immobilized enzymes removed all three organic pollutants from an aqueous solution, but Mb was more effective than HRP. After being immobilized, both enzymes became more resilient to changes in temperature and pH. Both immobilized enzymes retained their ability to eliminate organic pollutants through eight treatment cycles. Our study uncovered novel immobilized enzyme microspheres and demonstrated their successful application in wastewater treatment, paving the way for future research.
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    Prediction of seasonal population dynamics of Grapholita molesta (Busck) and Adoxophyes orana (Fischer von Röslerstamm) in peach orchards using sex pheromone trap and degree-days and its implications in pest management
    (2023-10-04) Ma A; Zhang H; Ran H; Yang X; J Hao J; Zhang J; Li H; Yu Z; Wang X; He X; Li J
    The successful management of lepidopteran moths in orchards usually depends on the precise forecast of adult activity. However, the seasonal phenology of moths varies between crop cultivars and years, making it difficult to schedule the control measures. Here, we monitored male flight activity of oriental fruit moth Grapholita molesta and summer fruit tortrix moth Adoxophyes orana by using sex pheromone traps in peach orchards of three different cultivars for three successive years. We developed a logistic multiple-peaks model to fit data and then calculated degree-days (DD) required for male activity and neonate emergency. Results show that G. molesta and A. orana males had 4–5 and 3 flight peaks per year, respectively. The seasonal phenology of G. molesta or A. orana was quite stable with an identical timing of each flight peak between cultivars in a year. The flight activity was usually higher in the second and third peaks for both moths, with a higher cumulative number of G. molesta males captured than that of A. orana. Compared to A. orana, G. molesta emerged early in spring and required lower degree-days to reach the subsequent flight peaks and for neonate emergency. Our results suggest that to decline the possibility of outbreaks of moths during the growing seasons, pheromone traps should be scheduled in April with a cumulative DD between 49.6 and 207.1 for G. molesta and in mid-May–early June with a cumulative DD between 450.4 and 866.7 for A. orana, aiming to trap the newly emerged male adults or disrupting female mating success of overwintered moths in orchards. Based on the thermal requirement for egg hatching (i.e., 79.4 DD for G. molesta and 90.0 DD for A. orana), insecticide treatments would be applied in late-April–early May and late May–early June to reduce the field population density of neonates of G. molesta and A. orana, respectively, to reduce fruit damage in orchards. Furthermore, pheromone traps set up in late July–early August (573.8–1025.2 DD) for G. molesta and in mid-September (1539.7–1788.9 DD) for A. orana may suppress overwintering populations and thus decrease pest infestation in next year.
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    Rapid Spread of Severe Fever with Thrombocytopenia Syndrome Virus by Parthenogenetic Asian Longhorned Ticks.
    (2022-02) Zhang X; Zhao C; Cheng C; Zhang G; Yu T; Lawrence K; Li H; Sun J; Yang Z; Ye L; Chu H; Wang Y; Han X; Jia Y; Fan S; Kanuka H; Tanaka T; Jenkins C; Gedye K; Chandra S; Price DC; Liu Q; Choi YK; Zhan X; Zhang Z; Zheng A
    Severe fever with thrombocytopenia syndrome virus (SFTSV) is spreading rapidly in Asia. This virus is transmitted by the Asian longhorned tick (Haemaphysalis longicornis), which has parthenogenetically and sexually reproducing populations. Parthenogenetic populations were found in ≥15 provinces in China and strongly correlated with the distribution of severe fever with thrombocytopenia syndrome cases. However, distribution of these cases was poorly correlated with the distribution of populations of bisexual ticks. Phylogeographic analysis suggested that the parthenogenetic population spread much faster than bisexual population because colonization is independent of sexual reproduction. A higher proportion of parthenogenetic ticks was collected from migratory birds captured at an SFTSV-endemic area, implicating the contribution to the long-range movement of these ticks in China. The SFTSV susceptibility of parthenogenetic females was similar to that of bisexual females under laboratory conditions. These results suggest that parthenogenetic Asian longhorned ticks, probably transported by migratory birds, play a major role in the rapid spread of SFTSV.