1
|
Veldsman WP, Yang C, Zhang Z, Huang Y, Chowdhury D, Zhang L. Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection. Viruses 2024; 16:134. [PMID: 38257834 PMCID: PMC10820185 DOI: 10.3390/v16010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.
Collapse
Affiliation(s)
- Werner P. Veldsman
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | | | - Debajyoti Chowdhury
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China;
- Computational Medicine Laboratory, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen 518057, China
| |
Collapse
|
2
|
Abstract
Abstract
This review reports the progress on the recent development of molecular dynamics simulation of nanofluidics. Molecular dynamics simulations of nanofluidics in nanochannel structure, surface roughness of nanochannel, carbon nanotubes, electrically charged, thermal transport in nanochannels and gases in nanochannels are illustrated and discussed. This paper will provide an expedient and valuable reference to designers who intend to research molecular dynamics simulation of nanofluidic devices.
Collapse
Affiliation(s)
- Xueye Chen
- Faculty of Mechanical Engineering and Automation , Liaoning University of Technology , Jinzhou 121001 , China
| |
Collapse
|
3
|
Ziebarth JD, Gardiner AA, Wang Y, Jeong Y, Ahn J, Jin Y, Chang T. Comparison of Critical Adsorption Points of Ring Polymers with Linear Polymers. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01925] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jesse D. Ziebarth
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee 38154, United States
| | - Abigail Anne Gardiner
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee 38154, United States
| | - Yongmei Wang
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee 38154, United States
| | - Youncheol Jeong
- Division of Advanced Materials
Science and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Junyoung Ahn
- Division of Advanced Materials
Science and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ye Jin
- Division of Advanced Materials
Science and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Taihyun Chang
- Division of Advanced Materials
Science and Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| |
Collapse
|
4
|
A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root. PLoS Genet 2016; 12:e1006175. [PMID: 27583367 PMCID: PMC5008728 DOI: 10.1371/journal.pgen.1006175] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/15/2016] [Indexed: 01/03/2023] Open
Abstract
Reactive oxygen species (ROS) are recognized as important regulators of cell division and differentiation. The Arabidopsis thaliana P-loop NTPase encoded by APP1 affects root stem cell niche identity through its control of local ROS homeostasis. The disruption of APP1 is accompanied by a reduction in ROS level, a rise in the rate of cell division in the quiescent center (QC) and the promotion of root distal stem cell (DSC) differentiation. Both the higher level of ROS induced in the app1 mutant by exposure to methyl viologen (MV), and treatment with hydrogen peroxide (H2O2) rescued the mutant phenotype, implying that both the increased rate of cell division in the QC and the enhancement in root DSC differentiation can be attributed to a low level of ROS. APP1 is expressed in the root apical meristem cell mitochondria, and its product is associated with ATP hydrolase activity. The key transcription factors, which are defining root distal stem niche, such as SCARECROW (SCR) and SHORT ROOT (SHR) are both significantly down-regulated at both the transcriptional and protein level in the app1 mutant, indicating that SHR and SCR are important downstream targets of APP1-regulated ROS signaling to control the identity of root QC and DSCs. Reactive oxygen species (ROS) are recognized as important regulators of cell division and differentiation. In this study, we characterized an Arabidopsis thaliana P-loop NTPase encoded by APP1 regulates root stem cell niche identity through its control of local ROS homeostasis. The app1 mutant shows a reduction in ROS level, a rise in the rate of cell division in the quiescent center (QC) and the promotion of root distal stem cell (DSC) differentiation. The increased rate of cell division in the QC and the enhancement in root DSC differentiation in app1 can be attributed to a low level of ROS since both the exposure to methyl viologen (MV), and treatment with hydrogen peroxide (H2O2) rescued the mutant phenotype. APP1 is expressed in the root apical meristem cell mitochondria, and its product is associated with ATP hydrolase activity. The key transcription factors such as SCARECROW (SCR) and SHORT ROOT (SHR), which are defining root distal stem niche, are both greatly down-regulated at both the transcriptional and protein level in app1, indicating that SHR and SCR are important downstream targets of APP1-regulated ROS signaling to control the identity of root QC and DSCs.
Collapse
|
5
|
Yu Q, Liu J, Zheng H, Jia Y, Tian H, Ding Z. Topoisomerase II-associated protein PAT1H1 is involved in the root stem cell niche maintenance in Arabidopsis thaliana. PLANT CELL REPORTS 2016; 35:1297-307. [PMID: 26956135 DOI: 10.1007/s00299-016-1961-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/21/2016] [Indexed: 05/15/2023]
Abstract
PAT1H1, one of the homologues of Topoisomerase II-associated protein, is involved in the maintenance of root stem cell niche through the interaction with NINJA. The root stem cell niche, which possesses four mitotically inactive quiescent cells (QC) and the surrounding mitotically active stem cells, is critical for root development in Arabidopsis thaliana. However, the molecular regulation of the maintenance of root stem cell niche identity is still not fully understood. Here we show that one of the homologues of Topoisomerase II-associated protein, here named as PAT1H1, could regulate root stem cell niche identity. The pat1h1 mutant showed higher frequency of QC cell division and root distal stem cell (DSC) differentiation. With a high expression in roots, PAT1H1 was found to interact with the jasmonic acid (JA) signalling negative regulator Novel Interactor of JAZ (NINJA) and thus regulate root DSC niche identity. Consistent with the active QC cell division, which rarely occurs in wild-type controls, the pat1h1 mutant displayed higher expression of CYCB1 in the root stem cell niche. Together our data reveals that PAT1H1 maintains root stem cell niche stability through the interaction with NINJA and the regulation of cell division.
Collapse
Affiliation(s)
- Qianqian Yu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Jiajia Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Huihui Zheng
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Yuebin Jia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Huiyu Tian
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China.
| | - Zhaojun Ding
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| |
Collapse
|
6
|
Smithe TSC, Iarko V, Muralidhar A, Werner E, Dorfman KD, Mehlig B. Finite-size corrections for confined polymers in the extended de Gennes regime. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062601. [PMID: 26764718 PMCID: PMC4714778 DOI: 10.1103/physreve.92.062601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 06/01/2023]
Abstract
Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favorably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear λ-DNA confined to nanochannels at the high ionic strengths used in many experiments.
Collapse
Affiliation(s)
- T. St Clere Smithe
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - V. Iarko
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - A. Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - E. Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - K. D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| |
Collapse
|
7
|
Abstract
The Topological Aspects of DNA Function and Protein Folding international meeting provided an interdisciplinary forum for biological scientists, physicists and mathematicians to discuss recent developments in the application of topology to the study of DNA and protein structure. It had 111 invited participants, 48 talks and 21 posters. The present article discusses the importance of topology and introduces the articles from the meeting's speakers.
Collapse
|