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Article ; Online: Discovery of novel inhibition site centered on 114-bit tryptophan of Thioredoxin reductase 1 through computer-aided drug design

Haoyi Yang / Hengyu Wang / Jia Feng / Jianmin Liao / Yuanyuan Lu

Arabian Journal of Chemistry, Vol 16, Iss 4, Pp 104642- (2023)

2023

Abstract: Thioredoxin reductase 1 (TrxR1) is an oxidoreductase playing the important role in the tumor cells. It is a new type of drug therapy target. Most of the existing TrxR1 inhibitors act directly covalently on the active sites. Herein, molecular docking- ... ...

Abstract	Thioredoxin reductase 1 (TrxR1) is an oxidoreductase playing the important role in the tumor cells. It is a new type of drug therapy target. Most of the existing TrxR1 inhibitors act directly covalently on the active sites. Herein, molecular docking-based virtual screening approach was used to screen inhibitors with new binding site of TrxR1 from the SPECS database. After experimental test, compound 22 was identified as the reversibility inhibitor of TrxR1 U498C mutant (It has similar structure and function to replace the wild-type TrxR1 which is difficult to express) with IC50 value of 15.31 ± 0.57 μM. The molecular docking results showed that the interaction between compound 22 and TrxR1 was centered on inactive site Trp114. Furthermore, phenazine compounds 24–30 with similar structures as 22 were also screened out from our phenazine database. Compounds 24–27 had longer chain structures and better inhibitory activity than compound 22, while compounds 28–30 were the opposite. Compounds 24–27 can be more stably bound in the protein cavity on Trp114 than compounds 28–30. Then we verified amino acids centered on Trp114 can regulate TrxR1 activity by amino acids mutation. Taken together, A new inhibition site are found that can regulate TrxR1 U498C mutant activity by acting on amino acids sequence at inactive sites centered on Trp114 and can provide ideas for the discovery and research of new TrxR1 inhibitors.
Keywords	Thioredoxin reductase 1 ; Computer-aided drug design ; Virtual screening ; Molecular docking ; Trp114 ; Chemistry ; QD1-999
Subject code	540 ; 500
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: PENet

Zhengyu Zhao / Yuanyuan Lu / Yijie Tong / Xin Chen / Ming Bai

Methods in Ecology and Evolution, Vol 14, Iss 12, Pp 3035-

A phenotype encoding network for automatic extraction and representation of morphological discriminative features

2023 Volume 3046

Abstract: Abstract Digitalized natural history collections serve as vital ecological and evolutionary research resources. Specimen retrieval based on morphological features allows for the rapid acquisition of similar specimens from these collections, aiding in ... ...

Abstract	Abstract Digitalized natural history collections serve as vital ecological and evolutionary research resources. Specimen retrieval based on morphological features allows for the rapid acquisition of similar specimens from these collections, aiding in maximizing the utilization of their resources and catering to the requirements of related research. However, achieving this objective requires effective feature extraction and representation techniques. We developed a phenotype encoding network (PENet), a deep learning‐based model that combines hashing methods to automatically extract and encode discriminative features into hash codes. We evaluated the performance of PENet on six data sets, including a newly constructed beetle data set (6566 images), which covers over 60% of the genera within the six subfamilies of Scarabaeidae. Phenotype encoding network showed high performance in feature extraction and image retrieval, allowing users to input an image of a specimen and efficiently retrieve all specimens with similar morphology. Two visualization methods, t‐SNE and Grad‐CAM, were used to evaluate the representation ability of the hash codes. Additionally, by using the hash codes generated from PENet, a phenetic distance tree was constructed based on the beetle data set. The result indicated that the hash codes could reveal the phenetic distances and relationships among categories to a certain extent. PENet provides an automatic and efficient method to extract and represent morphological discriminative features. The generated hash code can be used as a low‐dimensional carrier of these features, enabling efficient specimen retrieval. Moreover, the distance information carried by these hash codes suggests their potential in systematics, deserving further exploration.
Keywords	deep learning ; discriminative features ; encoding ; feature‐based retrieval ; hash ; Ecology ; QH540-549.5 ; Evolution ; QH359-425
Subject code	005
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of the Sustainable Use of Land Resources in the Cities along the Jiangsu Section of the Beijing–Hangzhou Grand Canal

Fei Shi / Yuanyuan Lu / Longgao Chen / Wei-Ling Hsu

Land, Vol 12, Iss 1173, p

2023 Volume 1173

Abstract: Sustainable development is an important topic of urban research. The rational use of land resources is of great significance for urban development and is conducive to promoting regional governance and coordinated development. The purpose of this study ... ...

Abstract	Sustainable development is an important topic of urban research. The rational use of land resources is of great significance for urban development and is conducive to promoting regional governance and coordinated development. The purpose of this study was to construct an effective evaluation framework for urban land resources to maintain sustainable urban development. Taking the cities along the Jiangsu Section of the Beijing–Hangzhou Grand Canal as the research object, this study constructed an evaluation system for the sustainable use of land resources including the dimensions of economic level, social development, and environmental resources. The statistical data for 2010, 2015, and 2020 were selected to comprehensively calculate and evaluate the level of sustainable use of land resources in the study area via the analytic hierarchy process (AHP)-entropy combined weight method, which combines the analytic hierarchy process and the entropy weight method. According to the research results, the sustainable use of land resources in the study area presented an overall upward trend from 2010 to 2015, and an overall downward trend from 2015 to 2020. Overall, the study area was in a critically sustainable stage, although the annual change rate of the level of sustainable use of land resources showed significant fluctuations and exhibited a spatial pattern of progressive increase from north to south. The cities in southern Jiangsu were in the initially sustainable and basically sustainable stages; those in central Jiangsu were in the critically sustainable and initially sustainable stages; and those in northern Jiangsu were in the unsustainable and critically sustainable stages. This study proposed a scientific and effective evaluation method for cities along the Grand Canal to explore the efficient, sustainable use of land resources in the future. The evaluation framework constructed on this basis can serve as an important reference for urban governance and is expected to guide the sustainable use and development of ...
Keywords	analytic hierarchy process ; entropy weight method ; decision-making analysis ; Agriculture ; S
Subject code	710 ; 910
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Notes on Paratrichius Janson, 1881 inhabiting Hainan Island, with description of a new species and the definition of two new junior synonyms (Coleoptera

Enrico Ricchiardi / Yuanyuan Lu / Sha Li / Bai Ming

Fragmenta entomologica, Vol 54, Iss

Scarabaeidae, Cetoniinae)

2022 Volume 1

Abstract: Nearly three decades ago two new species belonging to the genus Paratrichius Janson, 1881 were described from Hainan Island (SW China): Paratrichius papilionaceus Ma, 1990 and P. rufescens Ma, 1990. The present paper increases the number of Paratrichius ... ...

Abstract	Nearly three decades ago two new species belonging to the genus Paratrichius Janson, 1881 were described from Hainan Island (SW China): Paratrichius papilionaceus Ma, 1990 and P. rufescens Ma, 1990. The present paper increases the number of Paratrichius species known from Hainan Island to four, with the description of a new species (P. pilosus Ricchiardi and Lu, n. sp.), and a new regional record for P. elegantulus (Moser, 1902), thus far known from N Indochina and continental SW China only. Additionally, Paratrichius papilionaceus Ma, 1990 is here proposed as junior synonym of Paratrichius marmoreus (Moser, 1902), described from northern Vietnam (n. syn.), and Paratrichius brevifolius Kobayashi and Fujioka, 2013, described from northern Vietnam, is here proposed as junior synonym of the above cited Paratrichius elegantulus (Moser, 1902) (n. syn.). Among the four Paratrichius species now listed from Hainan, two (P. pilous and P. rufescens) are very likely endemic to the island’s highlands, while other two inhabit the highlands of northern Vietnam, too.
Keywords	Scarabaeidae ; Cetoniinae ; Paratrichius ; new species ; new synonymy ; Oriental Region ; Zoology ; QL1-991
Subject code	590
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	University La Sapienza of Rome
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Editorial

Lutao Du / Yuanyuan Lu / Jiayi Wang

Frontiers in Cell and Developmental Biology, Vol

The role of interplay between metabolism and chromosomes in tumorigenesis

2022 Volume 10

Keywords	non-coding RNA ; post-translational modification ; epigenetic regulation ; glycolysis ; m6A modification ; cancer ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Experimental investigation of pore structure and its influencing factors of marine-continental transitional shales in southern Yan’an area, ordos basin, China

Hui Xiao / Nan Xie / Yuanyuan Lu / Tianyue Cheng / Wei Dang

Frontiers in Earth Science, Vol

2022 Volume 10

Abstract: The intensive study of the pore structure and its controlling factors of shale reservoir has important guiding significance for further exploration and exploitation of shale gas. This work investigated the effects of organic and inorganic compositions on ...

Abstract	The intensive study of the pore structure and its controlling factors of shale reservoir has important guiding significance for further exploration and exploitation of shale gas. This work investigated the effects of organic and inorganic compositions on the development of pore structures of the Upper Permian Shanxi shale in the southern Yan’an area, Ordos Basin. Based on the results of high-pressure mercury intrusion, low-pressure N2 and CO2 adsorption and organic geochemical experiments, X-ray diffraction and scanning electron microscope observations, the mineral composition, pore structure and its influencing factors of the transitional shale were studied systematically. The results indicate that the total organic carbon (TOC) content of the shale is between 0.12% and 5.43%, with an average of 1.40%. The type of the organic matter (OM) belongs to Type III and has over maturity degree with an average Ro of 2.54%. An important character of this kind of shale is the large proportion of clay mineral content, which ranges from 40.70% to 87.00%, and with an average of 60.05%. Among them, illite and kaolinite are the main components, and they account for 36.6% and 36.7% of the total clay minerals respectively, followed by chlorite and illite/smectite (I/S) mixed layer. The quartz content is between 10.6% and 54.5%, with an average of 35.49%. OM (organic matter) pores are mostly circular bubble-shaped pores, and most of them are micropores, while inorganic pores are well developed and mainly contributed by clay mineral pores and have slit-type, plate-like and irregular polygon forms. Mesopores are the major contributor to pore volume (PV), while micropores contribute the least to PV. The contribution of micropores to the specific surface area (SSA) is greater than 61%, followed by mesopores. Macropores have almost no contribution to the development of SSA. OM pores are the main contributor to the total specific surface area of the shale, with an average contribution rate of 61.05%, but clay mineral pores contribute ...
Keywords	clay-rich shale ; transitional shale ; pore structure ; controlling factors ; ordos basin ; Science ; Q
Subject code	550
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic and Chemical Profiling of B9, a Unique Penicillium Fungus Derived from Sponge

Chaoyi Chen / Jiangfeng Qi / Yajing He / Yuanyuan Lu / Ying Wang

Journal of Fungi, Vol 8, Iss 7, p

2022 Volume 686

Abstract: This study presented the first insights into the genomic and chemical profiles of B9, a specific Penicillium strain derived from sponges of the South China Sea that demonstrated the closest morphological and phylogenetic affinity to P. paxillin . Via the ...

Abstract	This study presented the first insights into the genomic and chemical profiles of B9, a specific Penicillium strain derived from sponges of the South China Sea that demonstrated the closest morphological and phylogenetic affinity to P. paxillin . Via the Illumina MiSeq sequencing platform, the draft genome was sequenced, along with structural assembly and functional annotation. There were 34 biosynthetic gene clusters (BGCs) predicted against the antiSMASH database, but only 4 gene clusters could be allocated to known BGCs (≥50% identities). Meanwhile, the comparison between B9 and P. paxillin ATCC 10480 demonstrated clear distinctions in morphology, which might be ascribed to the unique environmental adaptability of marine endosymbionts. In addition, two novel pyridinones, penicidihydropyridone A (2) and penicidihydropyridone B (3), were isolated from cultures of B9, and structurally characterized by nuclear magnetic resonance (NMR) and mass spectrometry (MS). The absolute configurations were confirmed by comparison of experimental and calculated electronic circular dichroism (ECD) curves. In addition, structure-based molecular docking indicated that both neo-pyridinones might block the programmed cell death protein 1(PD-1) pathway by competitively binding a programmed cell death 1 ligand 1(PD-L1) dimer. This was verified by the significant inhibition rates of the PD-1/L1 interaction. These indicated that Penicillium sp. B9 possessed a potential source of active secondary metabolites.
Keywords	Penicillium sp ; genome sequence ; BGCs ; secondary metabolites ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using MaxEnt Model to Predict the Potential Distribution of Three Potentially Invasive Scarab Beetles in China

Shuangyi Wang / Yuanyuan Lu / Mengyang Han / Lulu Li / Ping He / Aimin Shi / Ming Bai

Insects, Vol 14, Iss 239, p

2023 Volume 239

Abstract: A hot topic in recent years is the prediction of the potential distribution of possible invasive insects. China is facing a great challenge due to invasive insects. Scarab beetles are a highly diverse group, and many of them are well-known invasive ... ...

Abstract	A hot topic in recent years is the prediction of the potential distribution of possible invasive insects. China is facing a great challenge due to invasive insects. Scarab beetles are a highly diverse group, and many of them are well-known invasive insects. Here, in order to prevent the invasion of scarab beetles in China, we screened the invasive insects globally and obtained a preliminary database of quarantine or invasive scarab beetles. From the obtained database, we selected the top five species ( Popillia japonica , Heteronychus arator , Oryctes monoceros , Oryctes boas and Amphimallon majale ) to discuss and analyzed the potential distribution of three species that have not invaded China by using the MaxEnt model. The prediction results show that every continent has potential distribution areas for these species. Specifically within China, Popillia japonica and Amphimallon majale were mainly concentrated in east central regions and Heteronychus arator and Oryctes boas were mainly distributed in the southwest areas, while Oryctes monoceros has no suitable area. Notably, Yunnan, Hunan, Jiangxi and Zhejiang province had a high risk of invasion. In general, local agriculture, forestry and customs departments in China should pay more attention to monitoring for the prevention of infestation by invasive insects.
Keywords	quarantine ; invasive insect ; potential distribution ; MaxEnt model ; Science ; Q
Subject code	590
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification and validation of a novel survival prediction model based on the T-cell phenotype in the tumor immune microenvironment and peripheral blood for gastric cancer prognosis

Jing Ma / Jianhui Li / Nan He / Meirui Qian / Yuanyuan Lu / Xin Wang / Kaichun Wu

Journal of Translational Medicine, Vol 21, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract Background The correlation and difference in T-cell phenotypes between peripheral blood lymphocytes (PBLs) and the tumor immune microenvironment (TIME) in patients with gastric cancer (GC) is not clear. We aimed to characterize the phenotypes of ...

Abstract	Abstract Background The correlation and difference in T-cell phenotypes between peripheral blood lymphocytes (PBLs) and the tumor immune microenvironment (TIME) in patients with gastric cancer (GC) is not clear. We aimed to characterize the phenotypes of CD8+ T cells in tumor infiltrating lymphocytes (TILs) and PBLs in patients with different outcomes and to establish a useful survival prediction model. Methods Multiplex immunofluorescence staining and flow cytometry were used to detect the expression of inhibitory molecules (IMs) and active markers (AMs) in CD8+TILs and PBLs, respectively. The role of these parameters in the 3-year prognosis was assessed by receiver operating characteristic analysis. Then, we divided patients into two TIME clusters (TIME-A/B) and two PBL clusters (PBL-A/B) by unsupervised hierarchical clustering based on the results of multivariate analysis, and used the Kaplan–Meier method to analyze the difference in prognosis between each group. Finally, we constructed and compared three survival prediction models based on Cox regression analysis, and further validated the efficiency and accuracy in the internal and external cohorts. Results The percentage of PD-1+CD8+TILs, TIM-3+CD8+TILs, PD-L1+CD8+TILs, and PD-L1+CD8+PBLs and the density of PD-L1+CD8+TILs were independent risk factors, while the percentage of TIM-3+CD8+PBLs was an independent protective factor. The patients in the TIME-B group showed a worse 3-year overall survival (OS) (HR: 3.256, 95% CI 1.318–8.043, P = 0.006), with a higher density of PD-L1+CD8+TILs (P < 0.001) and percentage of PD-1+CD8+TILs (P = 0.017) and PD-L1+CD8+TILs (P < 0.001) compared to the TIME-A group. The patients in the PBL-B group showed higher positivity for PD-L1+CD8+PBLs (P = 0.042), LAG-3+CD8+PBLs (P < 0.001), TIM-3+CD8+PBLs (P = 0.003), PD-L1+CD4+PBLs (P = 0.001), and LAG-3+CD4+PBLs (P < 0.001) and poorer 3-year OS (HR: 0.124, 95% CI 0.017–0.929, P = 0.015) than those in the PBL-A group. In our three survival prediction models, Model 3, ...
Keywords	Inhibitory molecule ; Tumor immune microenvironment ; Peripheral blood lymphocytes ; Survival prediction model ; Gastric cancer ; Medicine ; R
Subject code	616
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Improved multivariate modeling for soil organic matter content estimation using hyperspectral indexes and characteristic bands.

Ming-Song Zhao / Tao Wang / Yuanyuan Lu / Shihang Wang / Yunjin Wu

PLoS ONE, Vol 18, Iss 6, p e

2023 Volume 0286825

Abstract: Soil organic matter (SOM) is a key index of soil fertility. Calculating spectral index and screening characteristic band reduce redundancy information of hyperspectral data, and improve the accuracy of SOM prediction. This study aimed to compare the ... ...

Abstract	Soil organic matter (SOM) is a key index of soil fertility. Calculating spectral index and screening characteristic band reduce redundancy information of hyperspectral data, and improve the accuracy of SOM prediction. This study aimed to compare the improvement of model accuracy by spectral index and characteristic band. This study collected 178 samples of topsoil (0-20 cm) in the central plain of Jiangsu, East China. Firstly, visible and near-infrared (VNIR, 350-2500 nm) reflectance spectra were measured using ASD FieldSpec 4 Std-Res spectral radiometer in the laboratory, and inverse-log reflectance (LR), continuum removal (CR), first-order derivative reflectance (FDR) were applied to transform the original reflectance (R). Secondly, optimal spectral indexes (including deviation of arch, difference index, ratio index, and normalized difference index) were calculated from each type of VNIR spectra. Characteristic bands were selected from each type of spectra by the competitive adaptive reweighted sampling (CARS) algorithm, respectively. Thirdly, SOM prediction models were established based on random forest (RF), support vector regression (SVR), deep neural networks (DNN) and partial least squares regression (PLSR) methods using optimal spectral indexes, denoted here as SI-based models. Meanwhile, SOM prediction models were established using characteristic wavelengths, denoted here as CARS-based models. Finally, this research compared and assessed accuracy of SI-based models and CARS-based models, and selected optimal model. Results showed: (1) The correlation between optimal spectral indexes and SOM was enhanced, with absolute value of correlation coefficient between 0.66 and 0.83. The SI-based models predicted SOM content accurately, with the coefficient of determination (R2) and root mean square error (RMSE) values ranging from 0.80 to 0.87, 2.40 g/kg to 2.88 g/kg in validation sets, and relative percent deviation (RPD) value between 2.14 and 2.52. (2) The accuracy of CARS-based models differed with models and ...
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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