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Article ; Online: Diurnal retinal and choroidal gene expression patterns support a role for circadian biology in myopia pathogenesis

Richard A. Stone / John W. Tobias / Wenjie Wei / Jonathan Schug / Xia Wang / Lixin Zhang / P. Michael Iuvone / Debora L. Nickla

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 13

Abstract: Abstract The prevalence of myopia (nearsightedness) is increasing to alarming levels, but its etiology remains poorly understood. Because both laboratory and clinical findings suggest an etiologic role for circadian rhythms in myopia development, we ... ...

Abstract	Abstract The prevalence of myopia (nearsightedness) is increasing to alarming levels, but its etiology remains poorly understood. Because both laboratory and clinical findings suggest an etiologic role for circadian rhythms in myopia development, we assayed gene expression by RNA-Seq in retina and choroid at the onset of unilateral experimental myopia in chick, isolating tissues every 4 h during a single 24-h period from myopic and contralateral control eyes. Occluded versus open eye gene expression differences varied considerably over the 24-h sampling period, with some occurring at multiple times of day but with others showing differences at only a single investigated timepoint. Some of the genes identified in retina or choroid of chick myopia were previously identified as candidate genes for common human myopia. Like differentially expressed genes, pathways identified by Gene Set Enrichment Analysis also varied dramatically by sampling time. Considered with other laboratory data, human genetic and epidemiology data, these findings further implicate circadian events in myopia pathogenesis. The present results emphasize a need to include time of day in mechanistic studies of myopia and to assess circadian biology directly in trying to understand better the origin of myopia and to develop more effective therapies.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Incomplete neighbourhood multi-granulation decision-theoretic rough set in the hybrid-valued decision system

Jiajun Chen / Shuhao Yu / Wenjie Wei / Zhongrong Shi

The Journal of Engineering (2019)

2019

Abstract: It is an important subject to mine valuable knowledge from complex and massive data in the era of big data. Rough set theory is a new mathematical tool for dealing with uncertain and inaccurate data, decision-theoretic rough set model (DTRS), as an ... ...

Abstract	It is an important subject to mine valuable knowledge from complex and massive data in the era of big data. Rough set theory is a new mathematical tool for dealing with uncertain and inaccurate data, decision-theoretic rough set model (DTRS), as an extension of classical rough set model, is used to analyze decision information systems and multi-granulation decision-theoretic rough set model (MG-DTRS) can analyze and process target concepts from different angles and levels. However, the classical DTRS model exists some limitations in dealing numerical or hybrid-valued data. Considering the different influence of numerical features and symbolic features on decision-making, the paper proposes an incomplete neighborhood multi-granulation decision-theoretic rough set model in hybrid-valued decision system through integrating MG-DTRS with neighbourhood rough sets, and two types of neighborhood multi-granulation decision-theoretic set models are emphatically analysed. Furthermore, taking pessimistic and optimistic neighborhood multi-granulation decision-theoretic rough sets as examples, the implementation algorithms and related properties of the two type of models are studied. Finally, the relationship between the proposed model and other models is analyzed through formula derivation. The model proposed in this paper can effectively solve the decision-making problem of hybrid-valued incomplete information system through multi-angle and multi-level analysis.
Keywords	decision making ; fuzzy set theory ; rough set theory ; information systems ; decision theory ; probability ; granular computing ; data mining ; incomplete neighbourhood multigranulation decision-theoretic rough set ; hybrid-valued decision system ; data science ; uncertainty ; complex data ; massive data ; big data ; uncertain data ; inaccurate data ; decision-theoretic rough set model ; classical rough set model ; analyse decision information systems ; multigranulation dtrs ; classical dtrs model ; decision systems ; hybrid-valued incomplete decision information systems ; neighbourhood rough sets ; numerical feature granularity ; symbolic feature granularity ; incomplete neighbourhood mg-dtrs model ; neighbourhood granularity ; incomplete neighbourhood systems ; traditional dtrs model ; neighbourhood multigranulation decision-theoretic set models ; pessimistic neighbourhood mg-dtrss ; optimistic neighbourhood mg-dtrss ; decision-making problem ; hybrid-valued incomplete information systems ; Engineering (General). Civil engineering (General) ; TA1-2040
Subject code	006
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Capping protein regulates endosomal trafficking by controlling F-actin density around endocytic vesicles and recruiting RAB5 effectors

Dawei Wang / Zuodong Ye / Wenjie Wei / Jingting Yu / Lihong Huang / Hongmin Zhang / Jianbo Yue

eLife, Vol

2021 Volume 10

Abstract: Actin filaments (F-actin) have been implicated in various steps of endosomal trafficking, and the length of F-actin is controlled by actin capping proteins, such as CapZ, which is a stable heterodimeric protein complex consisting of α and β subunits. ... ...

Abstract	Actin filaments (F-actin) have been implicated in various steps of endosomal trafficking, and the length of F-actin is controlled by actin capping proteins, such as CapZ, which is a stable heterodimeric protein complex consisting of α and β subunits. However, the role of these capping proteins in endosomal trafficking remains elusive. Here, we found that CapZ docks to endocytic vesicles via its C-terminal actin-binding motif. CapZ knockout significantly increases the F-actin density around immature early endosomes, and this impedes fusion between these vesicles, manifested by the accumulation of small endocytic vesicles in CapZ-knockout cells. CapZ also recruits several RAB5 effectors, such as Rabaptin-5 and Rabex-5, to RAB5-positive early endosomes via its N-terminal domain, and this further activates RAB5. Collectively, our results indicate that CapZ regulates endosomal trafficking by controlling actin density around early endosomes and recruiting RAB5 effectors.
Keywords	CapZ ; F-actin ; endosome ; RAB5 ; endosomal trafficking ; Rabaptin-5 ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Xixi Li / Wenjie Wei / Fangfang Li / Lin Zhang / Xia Deng / Ying Liu / Shushen Yang

International Journal of Molecular Sciences, Vol 21, Iss 4499, p

Xixi, Li., et al. The Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Is Critical for Abiotic Stress Response in Wheat. Int. J. Mol. Sci. 2019, 20 , 1104

2020 Volume 4499

Abstract: The author wishes to make the following correction to this paper [.] ...

Abstract	The author wishes to make the following correction to this paper [.]
Keywords	n/a ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pre-transplant Transcriptional Signature in Peripheral Blood Mononuclear Cells of Acute Renal Allograft Rejection

Wenyu Xiang / Shuai Han / Cuili Wang / Hongjun Chen / Lingling Shen / Tingting Zhu / Kai Wang / Wenjie Wei / Jing Qin / Nelli Shushakova / Song Rong / Hermann Haller / Hong Jiang / Jianghua Chen

Frontiers in Medicine, Vol

2022 Volume 8

Abstract: Acute rejection (AR) is closely associated with renal allograft dysfunction. Here, we utilised RNA sequencing (RNA-Seq) and bioinformatic methods to characterise the peripheral blood mononuclear cells (PBMCs) of patients with acute renal allograft ... ...

Abstract	Acute rejection (AR) is closely associated with renal allograft dysfunction. Here, we utilised RNA sequencing (RNA-Seq) and bioinformatic methods to characterise the peripheral blood mononuclear cells (PBMCs) of patients with acute renal allograft rejection. Pretransplant blood samples were collected from 32 kidney allograft donors and 42 corresponding recipients with biopsies classified as T cell-mediated rejection (TCMR, n = 18), antibody-mediated rejection (ABMR, n = 5), and normal/non-specific changes (non-AR, n = 19). The patients with TCMR and ABMR were assigned to the AR group, and the patients with normal/non-specific changes (n = 19) were assigned to the non-AR group. We analysed RNA-Seq data for identifying differentially expressed genes (DEGs), and then gene ontology (GO) analysis, Reactome, and ingenuity pathway analysis (IPA), protein—protein interaction (PPI) network, and cell-type enrichment analysis were utilised for bioinformatics analysis. We identified DEGs in the PBMCs of the non-AR group when compared with the AR, ABMR, and TCMR groups. Pathway and GO analysis showed significant inflammatory responses, complement activation, interleukin-10 (IL-10) signalling pathways, classical antibody-mediated complement activation pathways, etc., which were significantly enriched in the DEGs. PPI analysis showed that IL-10, VEGFA, CXCL8, MMP9, and several histone-related genes were the hub genes with the highest degree scores. Moreover, IPA analysis showed that several proinflammatory pathways were upregulated, whereas antiinflammatory pathways were downregulated. The combination of NFSF14+TANK+ANKRD 33 B +HSPA1B was able to discriminate between AR and non-AR with an AUC of 92.3% (95% CI 82.8–100). Characterisation of PBMCs by RNA-Seq and bioinformatics analysis demonstrated gene signatures and biological pathways associated with AR. Our study may provide the foundation for the discovery of biomarkers and an in-depth understanding of acute renal allograft rejection.
Keywords	actue renal allograft rejection ; RNA-Seq ; bioinformatics ; biomarker ; PBMCs ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A pan-Zea genome map for enhancing maize improvement

Songtao Gui / Wenjie Wei / Chenglin Jiang / Jingyun Luo / Lu Chen / Shenshen Wu / Wenqiang Li / Yuebin Wang / Shuyan Li / Ning Yang / Qing Li / Alisdair R. Fernie / Jianbing Yan

Genome Biology, Vol 23, Iss 1, Pp 1-

2022 Volume 22

Abstract: Abstract Background Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking. Results Here, we ... ...

Abstract	Abstract Background Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking. Results Here, we construct an approximately 6.71-Gb pan-Zea genome that contains around 4.57-Gb non-B73 reference sequences from fragmented de novo assemblies of 721 pan-Zea individuals. We annotate a total of 58,944 pan-Zea genes and find around 44.34% of them are dispensable in the pan-Zea population. Moreover, 255,821 common structural variations are identified and genotyped in a maize association mapping panel. Further analyses reveal gene presence/absence variants and their potential roles during domestication of maize. Combining genetic analyses with multi-omics data, we demonstrate how structural variants are associated with complex agronomic traits. Conclusions Our results highlight the underexplored role of the pan-Zea genome and structural variations to further understand domestication of maize and explore their potential utilization in crop improvement.
Keywords	Pan-Zea genome ; Gene presence/absence variation (gPAV) ; Structural variation (SV) ; Narrow-sense heritability ; GWAS ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Subject code	572
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeting polarized phenotype of microglia via IL6/JAK2/STAT3 signaling to reduce NSCLC brain metastasis

Yu Jin / Yalin Kang / Minghuan Wang / Bili Wu / Beibei Su / Han Yin / Yang Tang / Qianxia Li / Wenjie Wei / Qi Mei / Guangyuan Hu / Veronika Lukacs-Kornek / Jian Li / Kongming Wu / Xianglin Yuan / Wei Wang

Signal Transduction and Targeted Therapy, Vol 7, Iss 1, Pp 1-

2022 Volume 12

Abstract: Abstract Tumor-associated macrophages have emerged as crucial factors for metastases. Microglia are indispensable components of the brain microenvironment and play vital roles in brain metastasis (BM). However, the underlying mechanism of how activated ... ...

Abstract	Abstract Tumor-associated macrophages have emerged as crucial factors for metastases. Microglia are indispensable components of the brain microenvironment and play vital roles in brain metastasis (BM). However, the underlying mechanism of how activated microglia promote brain metastasis of non-small cell lung cancer (NSCLC) remains elusive. Here, we purified cell lines with brain-metastatic tropism and employed a co-culture system to reveal their communication with microglia. By single-cell RNA-sequencing and transcriptome difference analysis, we identified IL6 as the key regulator in brain-metastatic cells (A549-F3) to induce anti-inflammatory microglia via JAK2/STAT3 signaling, which in turn promoted the colonization process in metastatic A549-F3 cells. In our clinical samples, patients with higher levels of IL6 in serum showed higher propensity for brain metastasis. Additionally, the TCGA (The Cancer Genome Atlas) data revealed that NSCLC patients with a lower level of IL6 had a longer overall survival time compared to those with a higher level of IL6. Overall, our data indicate that the targeting of IL6/JAK2/STAT3 signaling in activated microglia may be a promising new approach for inhibiting brain metastasis in NSCLC patients.
Keywords	Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Therapeutic Effect of Berberine on Huntington's Disease Transgenic Mouse Model.

Wenxiao Jiang / Wenjie Wei / Marta A Gaertig / Shihua Li / Xiao-Jiang Li

PLoS ONE, Vol 10, Iss 7, p e

2015 Volume 0134142

Abstract: Huntington disease (HD) represents a family of neurodegenerative diseases that are caused by misfolded proteins. The misfolded proteins accumulate in the affected brain regions in an age-dependent manner to cause late-onset neurodegeneration. Transgenic ... ...

Abstract	Huntington disease (HD) represents a family of neurodegenerative diseases that are caused by misfolded proteins. The misfolded proteins accumulate in the affected brain regions in an age-dependent manner to cause late-onset neurodegeneration. Transgenic mouse models expressing the HD protein, huntingtin, have been widely used to identify therapeutics that may retard disease progression. Here we report that Berberine (BBR), an organic small molecule isolated from plants, has protective effects on transgenic HD (N171-82Q) mice. We found that BBR can reduce the accumulation of mutant huntingtin in cultured cells. More importantly, when given orally, BBR could effectively alleviate motor dysfunction and prolong the survival of transgenic N171-82Q HD mice. We found that BBR could promote the degradation of mutant huntingtin by enhancing autophagic function. Since BBR is an orally-taken drug that has been safely used to treat a number of diseases, our findings suggest that BBR can be tested on different HD animal models and HD patients to further evaluate its therapeutic effects.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: W3 Is a New Wax Locus That Is Essential for Biosynthesis of β-Diketone, Development of Glaucousness, and Reduction of Cuticle Permeability in Common Wheat.

Zhengzhi Zhang / Wenjie Wei / Huilan Zhu / Ghana S Challa / Caili Bi / Harold N Trick / Wanlong Li

PLoS ONE, Vol 10, Iss 10, p e

2015 Volume 0140524

Abstract: W3 is essential for β-diketone biosynthesis but suppresses its hydroxylation. Loss-of-function mutation w3 significantly increased cuticle permeability in terms of water loss and chlorophyll efflux. ...

Abstract	W3 is essential for β-diketone biosynthesis but suppresses its hydroxylation. Loss-of-function mutation w3 significantly increased cuticle permeability in terms of water loss and chlorophyll efflux.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antimicrobial susceptibility of hospital acquired Stenotrophomonas maltophilia isolate biofilms

Erlin Sun / Gehong Liang / Lining Wang / Wenjie Wei / Mingde Lei / Shiduo Song / Ruifa Han / Yubao Wang / Wei Qi

Brazilian Journal of Infectious Diseases, Vol 20, Iss 4, Pp 365-373

Abstract: Abstract Aims We sought to characterize the antibiotic susceptibility of strains of Stenotrophomonas maltophilia isolated from clinical samples, and the role of Stenotrophomonas maltophilia biofilm in antibiotic resistance. Methods Fifty-one clinical ... ...

Abstract	Abstract Aims We sought to characterize the antibiotic susceptibility of strains of Stenotrophomonas maltophilia isolated from clinical samples, and the role of Stenotrophomonas maltophilia biofilm in antibiotic resistance. Methods Fifty-one clinical Stenotrophomonas maltophilia isolates were obtained from patients with nosocomial infection in the surgical wards and ICUs of six general hospitals in Tianjin, China. In vitro models of Stenotrophomonas maltophilia biofilms were established and confirmed by scanning electron microscopy and fluorescence microscopy with silver staining. The minimal inhibitory concentrations and biofilm inhibitory concentrations of commonly used antibiotics were determined. Results 47 of 51 strains were resistant to three or more antibiotics. 42 of 51 strains formed Stenotrophomonas maltophilia biofilms in vitro. Stenotrophomonas maltophilia biofilm formation greatly reduced sensitivity to most tested antibiotics, but not to levofloxacin. However, in the presence of erythromycin scanning electron microscopy revealed that levofloxacin inhibited Stenotrophomonas maltophilia biofilm formation. Factorial ANOVA revealed that erythromycin enhanced susceptibility to levofloxacin, cefoperazone/sulbactam, and piperacillin (p < 0.05), and an ΔE model revealed that levofloxacin and erythromycin acted synergistically in biofilms, suggesting specific use of combined macrolide therapy may represent an effective treatment for Stenotrophomonas maltophilia infection. Conclusions Antibiotics could act synergistically to combat the protection conferred to clinical isolates of Stenotrophomonas maltophilia by biofilms. Macrolide antibiotics may be effective where used in combination.
Keywords	Stenotrophomonas maltophilia ; Biofilm ; Antibiotic resistance ; Nosocomial ; Infectious and parasitic diseases ; RC109-216 ; Internal medicine ; RC31-1245 ; Medicine ; R
Subject code	610
Language	English
Publisher	Brazilian Society of Infectious Diseases
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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