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Koh D, Sonker M, Arriaga EA, Ros A. Numerical modeling reveals improved organelle separation for dielectrophoretic ratchet migration. Electrophoresis 2023; 44:1826-1836. [PMID: 37622551 PMCID: PMC10905386 DOI: 10.1002/elps.202300091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Organelle size varies with normal and abnormal cell function. Thus, size-based particle separation techniques are key to assessing the properties of organelle subpopulations differing in size. Recently, insulator-based dielectrophoresis (iDEP) has gained significant interest as a technique to manipulate sub-micrometer-sized particles enabling the assessment of organelle subpopulations. Based on iDEP, we recently reported a ratchet device that successfully demonstrated size-based particle fractionation in combination with continuous flow sample injection. Here, we used a numerical model to optimize the performance with flow rates a factor of three higher than previously and increased the channel volume to improve throughput. We evaluated the amplitude and duration of applied low-frequency DC-biased AC potentials improving separation efficiency. A separation efficiency of nearly 0.99 was achieved with the optimization of key parameters-improved from 0.80 in previous studies (Ortiz et al. Electrophoresis, 2022;43;1283-1296)-demonstrating that fine-tuning the periodical driving forces initiating the ratchet migration under continuous flow conditions can significantly improve the fractionation of organelles of different sizes.
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Affiliation(s)
- Domin Koh
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Edgar A Arriaga
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Ortiz R, Koh D, Kim DH, Rabbani MT, Anguaya Velasquez C, Sonker M, Arriaga EA, Ros A. Continuous organelle separation in an insulator-based dielectrophoretic device. Electrophoresis 2022; 43:1283-1296. [PMID: 34964147 PMCID: PMC10905415 DOI: 10.1002/elps.202100326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 11/06/2022]
Abstract
Heterogeneity in organelle size has been associated with devastating human maladies such as neurodegenerative diseases or cancer. Therefore, assessing the size-based subpopulation of organelles is imperative to understand the biomolecular foundations of these diseases. Here, we demonstrated a ratchet migration mechanism using insulator-based dielectrophoresis in conjunction with a continuous flow component that allows the size-based separation of submicrometer particles. The ratchet mechanism was realized in a microfluidic device exhibiting an array of insulating posts, tailoring electrokinetic and dielectrophoretic transport. A numerical model was developed to elucidate the particle migration and the size-based separation in various conditions. Experimentally, the size-based separation of a mixture of polystyrene beads (0.28 and 0.87 μ $\umu $ m) was accomplished demonstrating good agreement with the numerical model. Furthermore, the size-based separation of mitochondria was investigated using a mitochondria mixture isolated from HepG2 cells and HepG2 cells carrying the gene Mfn-1 knocked out, indicating distinct size-related migration behavior. With the presented continuous flow separation device, larger amounts of fractionated organelles can be collected in the future allowing access to the biomolecular signature of mitochondria subpopulations differing in size.
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Affiliation(s)
- Ricardo Ortiz
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Domin Koh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Mohammad Towshif Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Cesar Anguaya Velasquez
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Edgar A Arriaga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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Huang X, Liufu Q, Xu R, Chen X, Liu M, Han J, Guan H, Ma C. Integrating lncRNAs and mRNAs Expression Profiles in Penicillin-Induced Persistent Chlamydial Infection in HeLa Cells. Front Mol Biosci 2022; 9:744901. [PMID: 35252346 PMCID: PMC8890745 DOI: 10.3389/fmolb.2022.744901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia trachomatis (C. trachomatis) is a major etiological agent of sexually transmitted infection. Some stressing conditions can result in persistent chlamydial infection, which is thought to be associated with severe complications including ectopic pregnancy and tubal factor infertility. Long noncoding RNAs (lncRNAs) have been identified as key modulators in many biological processes. Nevertheless, the role of lncRNAs in persistent chlamydial infection is still unclear. In this study, we used lncRNA and mRNA microarray to identify the global lncRNAs and mRNAs expression in penicillin-induced persistent chlamydial infection in HeLa cells as well as the control group (HeLa cells without C. trachomatis infection). Among 1005 differentially expressed lncRNAs, 585 lncRNAs were upregulated and 420 downregulated in persistent chlamydial infection, while 410 mRNAs were identified to express differentially, of which 113 mRNAs were upregulated and 297 downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with differentially expressed genes were performed. We then constructed the lncRNA-miRNA-mRNA competing endogenous RNAs (ceRNAs) network. Four mRNAs were validated to be changed by quantitative real-time PCR which were correlated with the microarray result. Integration of protein-protein interaction network was constructed and hub genes were identified. These findings provide a new perspective on the molecular mechanisms of penicillin-induced persistent chlamydial infection.
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Affiliation(s)
- Xiaobao Huang
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qian Liufu
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Xu
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Chen
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingna Liu
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiande Han
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hongyu Guan
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chunguang Ma, ; Hongyu Guan,
| | - Chunguang Ma
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chunguang Ma, ; Hongyu Guan,
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Huang X, Tan J, Chen X, Liu M, Zhu H, Li W, He Z, Han J, Ma C. Akt Phosphorylation Influences Persistent Chlamydial Infection and Chlamydia-Induced Golgi Fragmentation Without Involving Rab14. Front Cell Infect Microbiol 2021; 11:675890. [PMID: 34169005 PMCID: PMC8218875 DOI: 10.3389/fcimb.2021.675890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/29/2021] [Indexed: 11/30/2022] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium that causes multiple diseases involving the eyes, gastrointestinal tract, and genitourinary system. Previous studies have identified that in acute chlamydial infection, C. trachomatis requires Akt pathway phosphorylation and Rab14-positive vesicles to transmit essential lipids from the Golgi apparatus in survival and replication. However, the roles that Akt phosphorylation and Rab14 play in persistent chlamydial infection remain unclear. Here, we discovered that the level of Akt phosphorylation was lower in persistent chlamydial infection, and positively correlated with the effect of activating the development of Chlamydia but did not change the infectivity and 16s rRNA gene expression. Rab14 was found to exert a limited effect on persistent infection. Akt phosphorylation might regulate Chlamydia development and Chlamydia-induced Golgi fragmentation in persistent infection without involving Rab14. Our results provide a new insight regarding the potential of synergistic repressive effects of an Akt inhibitor with antibiotics in the treatment of persistent chlamydial infection induced by penicillin.
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Affiliation(s)
- Xiaobao Huang
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinfeng Tan
- Department of Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Chen
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingna Liu
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huiling Zhu
- Department of Dermatology, The First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Wenjing Li
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhenjian He
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiande Han
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunguang Ma
- Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Liu J, Huang Y, Li T, Jiang Z, Zeng L, Hu Z. The role of the Golgi apparatus in disease (Review). Int J Mol Med 2021; 47:38. [PMID: 33537825 PMCID: PMC7891830 DOI: 10.3892/ijmm.2021.4871] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The Golgi apparatus is known to underpin many important cellular homeostatic functions, including trafficking, sorting and modifications of proteins or lipids. These functions are dysregulated in neurodegenerative diseases, cancer, infectious diseases and cardiovascular diseases, and the number of disease-related genes associated with Golgi apparatus is on the increase. Recently, many studies have suggested that the mutations in the genes encoding Golgi resident proteins can trigger the occurrence of diseases. By summarizing the pathogenesis of these genetic diseases, it was found that most of these diseases have defects in membrane trafficking. Such defects typically result in mislocalization of proteins, impaired glycosylation of proteins, and the accumulation of undegraded proteins. In the present review, we aim to understand the patterns of mutations in the genes encoding Golgi resident proteins and decipher the interplay between Golgi resident proteins and membrane trafficking pathway in cells. Furthermore, the detection of Golgi resident protein in human serum samples has the potential to be used as a diagnostic tool for diseases, and its central role in membrane trafficking pathways provides possible targets for disease therapy. Thus, we also introduced the clinical value of Golgi apparatus in the present review.
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Affiliation(s)
- Jianyang Liu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yan Huang
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ting Li
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zheng Jiang
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Liuwang Zeng
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhiping Hu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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Sun Y, Zhou P, Chen S, Hu C, Bai Q, Wu H, Chen Y, Zhou P, Zeng X, Liu Z, Chen L. The JAK/STAT3 signaling pathway mediates inhibition of host cell apoptosis by Chlamydia psittaci infection. Pathog Dis 2018; 75:4062151. [PMID: 28981630 DOI: 10.1093/femspd/ftx088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The JAK-STAT3 signaling pathway is a key regulator of cell growth, motility, migration, invasion and apoptosis in mammalian cells. Infection with intracellular pathogens of the genus Chlamydia can inhibit host cell apoptosis, and here we asked whether the JAK-STAT3 pathway participates in chlamydial anti-apoptotic activity. We found that, compared with uninfected cells, levels of JAK1 and STAT3 mRNA as well as total and phosphorylated JAK1 and STAT3 protein, were significantly increased in C. psittaci-infected HeLa cells. Moreover, the apoptosis rate of infected cells was higher after treatment with the tyrosine kinase inhibitor AG-490 (2-cyano-3-(3, 4-dihydroxyphenyl)-N-(phenylmethyl)-2-propenamide). Immunoblotting of apoptosis-related proteins showed that C. psittaci infection reduces Bax, but increases Bcl-2, protein levels, resulting in reduced activation of caspase-3, caspase-7, caspase-9 and PARP; AG490 attenuates these effects. Together, our data suggest that the JAK/STAT3 signaling pathway facilitates the anti-apoptotic effect of C. psittaci infection by reducing the Bax/Bcl-2 apoptotic switch ratio, and by inhibiting the intracellular activation of key pro-apoptotic enzymes.
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Affiliation(s)
- Yuanbin Sun
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Peng Zhou
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Shenghua Chen
- Medical college, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Chunsheng Hu
- Outpatient Department, Hunan Provincial Center for Disease Control and Provention, Changsha 421000, China
| | - Qinqin Bai
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Haiying Wu
- The second Affiliated Hospital, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Yuyu Chen
- Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 421000, China
| | - Pufan Zhou
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Xindian Zeng
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Ziqing Liu
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
| | - Lili Chen
- College of Public Health, University of South China, 28 West Changsheng Rd., Hengyang, Hunan 421001, China
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Zhang W, Chen K, Zhang X, Guo C, Chen Y, Liu X. An integrated analysis of membrane remodeling during porcine reproductive and respiratory syndrome virus replication and assembly. PLoS One 2018; 13:e0200919. [PMID: 30040832 PMCID: PMC6057628 DOI: 10.1371/journal.pone.0200919] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/27/2018] [Indexed: 01/20/2023] Open
Abstract
Background Recently, three-dimensional (3D) imaging techniques have been used to detect viral invasion and the appearance of specialized structures established in virus-infected cells. These methods have had a positive impact in the field of virology and helped to further our knowledge of how viruses invade cells. Nearly all positive-strand RNA viruses propagate their viral genomes in part through intracellular membranes. Porcine reproductive and respiratory syndrome virus (PRRSV), an Arterivirus, accumulates viral RNA that forms replication complexes (RCs) in infected cells. In this study, using immunofluorescence and electron microscopy (EM), we dissected PRRSV-induced membrane structures in infected cells and determined the correlations between PRRSV particles and vesicles stimulated by PRRSV to understand the structural and dynamic aspects of PRRSV infection. Methods We identified the appropriate time point by determining the 50% tissue culture infectious dose (TCID50) and using qRT-PCR and Western blotting. The co-localization of viruses and organelles was determined by immunofluorescence and immune-electron microscopy (IEM). The ultrastructure of cells infected by PRRSV was observed using EM and electron tomography (ET). Results In our study, we found that PRRSV dsRNA was located at the endoplasmic reticulum (ER) and autophagosomes; in addition, the N protein was located at the mitochondria, ER and autophagosomes. Vesicles induced by PRRSV appeared at 16 hours post-infection (h.p.i.) and increased in size with time during the infection period. In addition, our findings demonstrated that the virus vesicles originated from the ER, and these two organelle structures connected with each other to form a reticulovesicular network (RVN) that provided a site for virus replication and assembly. Conclusion Our results revealed that membrane vesicles induced by PRRSV were derived from the ER. The vesicles may provide a location for PRRSV replication and assembly.
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Affiliation(s)
- Wei Zhang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Keren Chen
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xueqing Zhang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Chunhe Guo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Yaosheng Chen
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaohong Liu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- * E-mail:
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Shi Y, Li K, Tang P, Li Y, Zhou Q, Yang K, Zhang Q. Three-dimensional visualization of the Autographa californica multiple nucleopolyhedrovirus occlusion-derived virion envelopment process gives new clues as to its mechanism. Virology 2015; 476:298-303. [PMID: 25569457 DOI: 10.1016/j.virol.2014.11.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/02/2014] [Accepted: 11/28/2014] [Indexed: 11/25/2022]
Abstract
Baculoviruses produce two virion phenotypes, occlusion-derived virion (ODV) and budded virion (BV). ODV envelopment occurs in the nucleus. Morphogenesis of the ODV has been studied extensively; however, the mechanisms underlying microvesicle formation and ODV envelopment in nuclei remain unclear. In this study, we used electron tomography (ET) together with the conventional electron microscopy to study the envelopment of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ODV. Our results demonstrate that not only the inner but also the outer nuclear membrane can invaginate and vesiculate into microvesicles and that intranuclear microvesicles are the direct source of the ODV membrane. Five main events in the ODV envelopment process are summarized, from which we propose a model to explain this process.
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Affiliation(s)
- Yang Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kunpeng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiping Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yinyin Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiang Zhou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kai Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qinfen Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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