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Golovko G, Khanipov K, Reyes V, Pinchuk I, Fofanov Y. Identification of multivariable Boolean patterns in microbiome and microbial gene composition data. Biosystems 2023; 233:105007. [PMID: 37619924 DOI: 10.1016/j.biosystems.2023.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Virtually every biological system is governed by complex relations among its components. Identifying such relations requires a rigorous or heuristics-based search for patterns among variables/features of a system. Various algorithms have been developed to identify two-dimensional (involving two variables) patterns employing correlation, covariation, mutual information, etc. It seems obvious, however, that comprehensive descriptions of complex biological systems need also to include more complicated multivariable relations, which can only be described using patterns that simultaneously embrace 3, 4, and more variables. The goal of this manuscript is to (a) introduce a novel type of associations (multivariable Boolean patterns) that can be manifested between features of complex systems but cannot be identified (described) by traditional pair-vise metrics; (b) propose patterns classification method, and (c) provide a novel definition of the pattern's strength (pattern's score) able to accommodate heterogeneous multi-omics data. To demonstrate the presence of such patterns, we performed a search for all possible 2-, 3-, and 4-dimensional patterns in historical data from the Human Microbiome Project (15 body sites) and collection of H. pylori genomes associated with gastric ulcers, gastritis, and duodenal ulcers. In all datasets under consideration, we were able to identify hundreds of statistically significant multivariable patterns. These results suggest that such patterns can be common in microbial genomics/microbiomics systems.
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Affiliation(s)
- George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Victor Reyes
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Irina Pinchuk
- Department of Medicine, Penn State Health Milton Hershey Medical Center, Hershey, PA, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Glass Bottom Analytics Inc, League City, TX, USA.
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Grim C, Noble R, Uribe G, Khanipov K, Johnson P, Koltun WA, Watts T, Fofanov Y, Yochum GS, Powell DW, Beswick EJ, Pinchuk IV. Impairment of Tissue-Resident Mesenchymal Stem Cells in Chronic Ulcerative Colitis and Crohn's Disease. J Crohns Colitis 2021; 15:1362-1375. [PMID: 33506258 PMCID: PMC8328298 DOI: 10.1093/ecco-jcc/jjab001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Little is known about the presence and function of tissue-resident mesenchymal stem cells [MtSCs] within the gastrointestinal mucosa in health and inflammatory bowel disease [IBD]. The contribution of MtSCs to the generation of inflammatory fibroblasts during IBD is also poorly understood. We hypothesized that IBD-MtSCs are impaired and contribute to the generation of the pathological myofibroblasts in IBD. METHODS In a cohort of clinically and endoscopically active IBD patients and normal controls, we used quantitative RT-PCR and stem cell differentiation assays, as well as confocal microscopy, to characterize MtSCs. RESULTS Expression of two stem cell markers, Oct4 and ALDH1A, was increased in the inflamed IBD colonic mucosa and correlated with an increase of the mesenchymal lineage marker Grem1 in ulcerative colitis [UC], but not Crohn's disease [CD]. Increased proliferation and aberrant differentiation of Oct4+Grem1+ MtSC-like cells was observed in UC, but not in CD colonic mucosa. In contrast to normal and UC-derived MtSCs, CD-MtSCs lose their clonogenic and most of their differentiation capacities. Our data also suggest that severe damage to these cells in CD may account for the pathological PD-L1low phenotype of CD myofibroblasts. In contrast, aberrant differentiation of MtSCs appears to be involved in the appearance of pathological partially differentiated PD-L1high myofibroblasts within the inflammed colonic mucosa in UC. CONCLUSION Our data show, for the first time, that the progenitor functions of MtSCs are differentially impaired in CD vs UC, providing a scientific rationale for the use of allogeneic MSC therapy in IBD, and particularly in CD.
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Affiliation(s)
- Carl Grim
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert Noble
- Department of Medicine, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Gabriela Uribe
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA,Department of Medicine, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Kamil Khanipov
- Department of Pharmacology & Toxicology, at the University of Texas Medical Branch, Galveston, TX, USA
| | - Paul Johnson
- Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA,Department of Pharmacology & Toxicology, at the University of Texas Medical Branch, Galveston, TX, USA
| | - Walter A Koltun
- Department of Colorectal Surgery, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Tammara Watts
- Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA,Department of Head and Neck Surgery and Communication Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Yuriy Fofanov
- Department of Pharmacology & Toxicology, at the University of Texas Medical Branch, Galveston, TX, USA
| | - Gregory S Yochum
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Don W Powell
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Ellen J Beswick
- Department of Biochemistry and Molecular Biology, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Irina V Pinchuk
- Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA,Department of Medicine, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA,Corresponding author: Iryna V. Pinchuk, PhD, PennState Health Milton S. Hershey Medical Center 500, University Dr., Hershey, PA 17033, USA. E-mail:
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Narra HP, Sahni A, Alsing J, Schroeder CLC, Golovko G, Nia AM, Fofanov Y, Khanipov K, Sahni SK. Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells. BMC Genomics 2020; 21:665. [PMID: 32977742 PMCID: PMC7519539 DOI: 10.1186/s12864-020-07077-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts, resulting in disease manifestations attributed primarily to endothelial damage or dysfunction. Although rickettsiae are known to undergo evolution through genomic reduction, the mechanisms by which these pathogens regulate their transcriptome to ensure survival in tick vectors and maintenance by transovarial/transstadial transmission, in contrast to their ability to cause debilitating infections in human hosts remain unknown. In this study, we compare the expression profiles of rickettsial sRNAome/transcriptome and determine the transcriptional start sites (TSSs) of R. conorii transcripts during in vitro infection of human and tick host cells. RESULTS We performed deep sequencing on total RNA from Amblyomma americanum AAE2 cells and human microvascular endothelial cells (HMECs) infected with R. conorii. Strand-specific RNA sequencing of R. conorii transcripts revealed the expression 32 small RNAs (Rc_sR's), which were preferentially expressed above the limit of detection during tick cell infection, and confirmed the expression of Rc_sR61, sR71, and sR74 by quantitative RT-PCR. Intriguingly, a total of 305 and 132 R. conorii coding genes were differentially upregulated (> 2-fold) in AAE2 cells and HMECs, respectively. Further, enrichment for primary transcripts by treatment with Terminator 5'-Phosphate-dependent Exonuclease resulted in the identification of 3903 and 2555 transcription start sites (TSSs), including 214 and 181 primary TSSs in R. conorii during the infection to tick and human host cells, respectively. Seventy-five coding genes exhibited different TSSs depending on the host environment. Finally, we also observed differential expression of 6S RNA during host-pathogen and vector-pathogen interactions in vitro, implicating an important role for this noncoding RNA in the regulation of rickettsial transcriptome depending on the supportive host niche. CONCLUSIONS In sum, the findings of this study authenticate the presence of novel Rc_sR's in R. conorii, reveal the first evidence for differential expression of coding transcripts and utilization of alternate transcriptional start sites depending on the host niche, and implicate a role for 6S RNA in the regulation of coding transcriptome during tripartite host-pathogen-vector interactions.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jessica Alsing
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna M Nia
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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Golovko G, Kamil K, Albayrak L, Nia AM, Duarte RSA, Chumakov S, Fofanov Y. Identification of multidimensional Boolean patterns in microbial communities. Microbiome 2020; 8:131. [PMID: 32917276 PMCID: PMC7488411 DOI: 10.1186/s40168-020-00853-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 05/04/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction patterns for such microorganisms are expected to exhibit a visually uninterrupted pattern. As a result, such relations cannot be detected using traditional correlation, mutual information, principal coordinate analysis, or covariation-based network inference approaches. RESULTS We present a novel pattern-specific method to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relation patterns between abundance profiles of two organisms as well as extend this approach to allow search and visualize three-, four-, and higher dimensional patterns. The proposed approach has been tested using 2380 microbiome samples from the Human Microbiome Project resulting in body site-specific networks of statistically significant 2D patterns as well as revealed the presence of 3D patterns in the Human Microbiome Project data. CONCLUSIONS The presented study suggested that search for Boolean patterns in the microbial abundance data needs to be pattern specific. The reported presence of multidimensional patterns (which cannot be reduced to a combination of two-dimensional patterns) suggests that multidimensional (multi-organism) relations may play important roles in the organization of microbial communities, and their detection (and appropriate visualization) may lead to a deeper understanding of the organization and dynamics of microbial communities. Video Abstract.
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Affiliation(s)
- George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
| | - Khanipov Kamil
- Department of Pharmacology and Toxicology, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
| | - Anna M. Nia
- Department of Molecular Biophysics, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
| | | | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Revolucion, 1500 Guadalajara, Jalisco Mexico
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch–Galveston, Galveston, TX 77555-0144 USA
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Aguirre JE, Beswick EJ, Grim C, Uribe G, Tafoya M, Chacon Palma G, Samedi V, McKee R, Villeger R, Fofanov Y, Cong Y, Yochum G, Koltun W, Powell D, Pinchuk IV. Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn's disease and regulate Th1/Th17 cell responses. Int Immunol 2020; 32:57-68. [PMID: 31633754 DOI: 10.1093/intimm/dxz060] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/30/2019] [Indexed: 01/01/2023] Open
Abstract
Increased T helper (Th)1/Th17 immune responses are a hallmark of Crohn's disease (CD) immunopathogenesis. CD90+ (myo-)fibroblasts (MFs) are abundant cells in the normal (N) intestinal mucosa contributing to mucosal tolerance via suppression of Th1 cell activity through cell surface membrane-bound PD-L1 (mPD-L1). CD-MFs have a decreased level of mPD-L1. Consequently, mPD-L1-mediated suppression of Th1 cells by CD-MFs is decreased, yet the mechanism responsible for the reduction in mPDL-1 is unknown. Increased expression of matrix metalloproteinases (MMPs) has been reported in CD. Herein we observed that when compared to N- and ulcerative colitis (UC)-MFs, CD-MFs increase in LPS-inducible levels of MMP-7 and -9 with a significant increase in both basal and inducible MMP-10. A similar pattern of MMP expression was observed in the CD-inflamed mucosa. Treatment of N-MFs with a combination of recombinant human MMP-7, -9 and -10 significantly decreased mPD-L1. In contrast, inhibition of MMP activity with MMP inhibitors or anti-MMP-10 neutralizing antibodies restores mPD-L1 on CD-MFs. CD-MFs demonstrated reduced capacity to suppress Th1 and Th17 responses from activated CD4+ T cells. By contrast, supplementation of the CD-MF:T-cell co-cultures with MMP inhibitors or anti-MMP neutralizing antibodies restored the CD-MF-mediated suppression. Our data suggest that (i) increased MMP-10 expression by CD-MFs and concomitant cleavage of PD-L1 from the surface of CD-MFs are likely to be one of the factors contributing to the decrease of mPD-L1-mediated suppression of Th1/Th17 cells in CD; and (ii) MMPs are likely to have a significant role in the intestinal mucosal immune responses.
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Affiliation(s)
- Jose E Aguirre
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA.,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Ellen J Beswick
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Carl Grim
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Gabriela Uribe
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA.,Department of Medicine at PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Marissa Tafoya
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | | | - Von Samedi
- School of Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Rohini McKee
- Department of Surgery at the University of New Mexico, Albuquerque, NM, USA
| | - Romain Villeger
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yingzi Cong
- Microbiology and Immunology at the University of Texas Medical Branch, Galveston, TX, USA
| | - Gregory Yochum
- Department of Biochemistry and Molecular Biology, PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Walter Koltun
- Department of Colorectal Surgery at PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Don Powell
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA.,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Irina V Pinchuk
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA.,Institute of Translational Science, University of Texas Medical Branch, Galveston, TX, USA.,Department of Medicine at PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA.,Microbiology and Immunology at the University of Texas Medical Branch, Galveston, TX, USA
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Patterson EI, Khanipov K, Swetnam DM, Walsdorf S, Kautz TF, Thangamani S, Fofanov Y, Forrester NL. Measuring Alphavirus Fidelity Using Non-Infectious Virus Particles. Viruses 2020; 12:v12050546. [PMID: 32429270 PMCID: PMC7291308 DOI: 10.3390/v12050546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/17/2023] Open
Abstract
Mutations are incorporated into the genomes of RNA viruses at an optimal frequency and altering this precise frequency has been proposed as a strategy to create live-attenuated vaccines. However, determining the effect of specific mutations that alter fidelity has been difficult because of the rapid selection of the virus population during replication. By deleting residues of the structural polyprotein PE2 cleavage site, E3Δ56-59, in Venezuelan equine encephalitis virus (VEEV) TC-83 vaccine strain, non-infectious virus particles were used to assess the effect of single mutations on mutation frequency without the interference of selection that results from multiple replication cycles. Next-generation sequencing analysis revealed a significantly lower frequency of transversion mutations and overall mutation frequency for the fidelity mutants compared to VEEV TC-83 E3Δ56-59. We demonstrate that deletion of the PE2 cleavage site halts virus infection while making the virus particles available for downstream sequencing. The conservation of the site will allow the evaluation of suspected fidelity mutants across alphaviruses of medical importance.
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Affiliation(s)
- Edward I. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Correspondence:
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; (K.K.); (Y.F.)
| | - Daniele M. Swetnam
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA;
| | - Samantha Walsdorf
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
| | - Tiffany F. Kautz
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Saravanan Thangamani
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; (K.K.); (Y.F.)
| | - Naomi L. Forrester
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (S.W.); (S.T.); (N.L.F.)
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Martinez-Martinez YB, Huante MB, Chauhan S, Golovko G, Fofanov Y, Gelman B, Endsley J. Disturbances in Chemokine Pathways as a Mechanism for Poor Immune Containment of MTB in the setting of HIV Co-infection. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.60.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Tuberculosis (TB) is one of the ten top causes of death worldwide and the leading cause in people living with Human Immunodeficiency Virus (HIV). The loss of function by diverse leukocyte populations and poor organization of the protective granuloma structure due to HIV infection is associated with poor immunity and increased proliferation of Mtb bacilli in co-infection. We employed our humanized mouse model of Mtb and HIV co-infection to investigate the HIV-mediated disturbances in the chemokines and chemokine receptors that regulate the recruitment, activation, and localization of inflammatory leukocytes at sites of pulmonary infection. Lung tissue of mice that were non-infected or infected with Mtb, HIV, or Mtb/HIV was used for multiplex ELISA of chemokine profiles in supernatants and for high throughput RNA sequencing to identify differential transcription of chemokine and chemokine receptor genes. Our results show that Mtb infection of humanized mouse lung activates human chemokine pathways important for recruitment and effector function of leukocytes at sites of infection such as CXCL1, CXCL5, and CCL2. Co-infection with HIV, however, activated differential transcription of several chemokines and chemokine receptor families, compared to Mtb mono-infection. These outcomes were associated with greater bacterial and viral burden in co-infected animals and may identify candidate mechanisms for host directed therapies to reduce aggressive TB in those living with HIV.
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Albayrak L, Khanipov K, Golovko G, Fofanov Y. Broom: application for non-redundant storage of high throughput sequencing data. Bioinformatics 2019; 35:143-145. [PMID: 30010786 DOI: 10.1093/bioinformatics/bty580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation The data generation capabilities of high throughput sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage strategies. Results We present Broom, a stand-alone application designed to select and store only high-quality sequencing reads at extremely high compression rates. Written in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompresses data in FASTA format. Availability and implementation C++ code available at https://scsb.utmb.edu/labgroups/fofanov/broom.asp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch - Galveston, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch - Galveston, Galveston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch - Galveston, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch - Galveston, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch - Galveston, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch - Galveston, Galveston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch - Galveston, Galveston, TX, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch - Galveston, Galveston, TX, USA
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Albayrak L, Khanipov K, Golovko G, Fofanov Y. Detection of multi-dimensional co-exclusion patterns in microbial communities. Bioinformatics 2019; 34:3695-3701. [PMID: 29878050 DOI: 10.1093/bioinformatics/bty414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 06/01/2018] [Indexed: 01/08/2023] Open
Abstract
Motivation Identification of complex relationships among members of microbial communities is key to understand and control the microbiota. Co-exclusion is arguably one of the most important patterns reflecting micro-organisms' intolerance to each other's presence. Knowing these relations opens an opportunity to manipulate microbiotas, personalize anti-microbial and probiotic treatments as well as guide microbiota transplantation. The co-exclusion pattern however, cannot be appropriately described by a linear function nor its strength be estimated using covariance or (negative) Pearson and Spearman correlation coefficients. This manuscript proposes a way to quantify the strength and evaluate the statistical significance of co-exclusion patterns between two, three or more variables describing a microbiota and allows one to extend analysis beyond micro-organism abundance by including other microbiome associated measurements such as, pH, temperature etc., as well as estimate the expected numbers of false positive co-exclusion patterns in a co-exclusion network. Results The implemented computational pipeline (CoEx) tested against 2380 microbial profiles (samples) from The Human Microbiome Project resulted in body-site specific pairwise co-exclusion patterns. Availability and implementation C++ source code for calculation of the score and P-value for two, three and four dimensional co-exclusion patterns as well as source code and executable files for the CoEx pipeline are available at https://scsb.utmb.edu/labgroups/fofanov/co-exclusion_in_microbial_communities.asp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch-Galveston, Galveston, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch-Galveston, Galveston, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch-Galveston, Galveston, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch-Galveston, Galveston, USA.,Department of Computer Science, University of Houston, Houston, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch-Galveston, Galveston, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch-Galveston, Galveston, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch-Galveston, Galveston, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch-Galveston, Galveston, USA
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10
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Hancock K, Hsu W, Khanipov K, Fofanov Y, Suzanne Klimberg VS, Sowers L. Era of Error in Next Generation Sequencing: Examining a Hot Spot of p53 in Colorectal Cancer. J Am Coll Surg 2019. [DOI: 10.1016/j.jamcollsurg.2019.08.1283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Malania L, Bai Y, Khanipov K, Tsereteli M, Metreveli M, Tsereteli D, Sidamonidze K, Imnadze P, Fofanov Y, Kosoy M. Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis. Infect Dis Rep 2019; 11:8132. [PMID: 31579471 PMCID: PMC6761468 DOI: 10.4081/idr.2019.8132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022] Open
Abstract
The authors report isolation and identification of two strains of bacteria belonging to the genus Janibacter from a human patient with aortic stenosis from a rural area of the country of Georgia. The microorganisms were isolated from aortic heart valve. Two isolates with slightly distinct colony morphologies were harvested after sub-culturing from an original agar plate. Preliminary identification of the isolates is based on amplification and sequencing of a fragment of 16SrRNA. Whole genome sequencing was performed using the Illumina MiSeq instrument. Both isolates were identified as undistinguished strains of the genus Janibacter. Characterization of whole genome sequences of each culture has revealed a 15% difference in gene profile between the cultures and confirmed that both strains belong to the genus Janibacter with the closest match to J. terrae. Genomic comparison of cultures of Janibacter obtained from human cases and from environmental sources presents a promising direction for evaluating a role of these bacteria as human pathogens.
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Affiliation(s)
- Lile Malania
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Ying Bai
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Mikheil Metreveli
- Department of Cardiology, High Technology Medical Center, University Clinic, Tbilisi, Georgia
| | - David Tsereteli
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | | | - Paata Imnadze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael Kosoy
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
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12
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Warmbrod KL, Patterson EI, Kautz TF, Stanton A, Rockx-Brouwer D, Kalveram BK, Khanipov K, Thangamani S, Fofanov Y, Forrester NL. Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts. PLoS Pathog 2019; 15:e1007610. [PMID: 30947291 PMCID: PMC6467425 DOI: 10.1371/journal.ppat.1007610] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 04/16/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023] Open
Abstract
The presence of bottlenecks in the transmission cycle of many RNA viruses leads to a severe reduction of number of virus particles and this occurs multiple times throughout the viral transmission cycle. Viral replication is then necessary for regeneration of a diverse mutant swarm. It is now understood that any perturbation of the mutation frequency either by increasing or decreasing the accumulation of mutations in an RNA virus results in attenuation of the virus. To determine if altering the rate at which a virus accumulates mutations decreases the probability of a successful virus infection due to issues traversing host bottlenecks, a series of mutations in the RNA-dependent RNA polymerase of Venezuelan equine encephalitis virus (VEEV), strain 68U201, were tested for mutation rate changes. All RdRp mutants were attenuated in both the mosquito and vertebrate hosts, while showing no attenuation during in vitro infections. The rescued viruses containing these mutations showed some evidence of change in fidelity, but the phenotype was not sustained following passaging. However, these mutants did exhibit changes in the frequency of specific types of mutations. Using a model of mutation production, these changes were shown to decrease the number of stop codons generated during virus replication. This suggests that the observed mutant attenuation in vivo may be due to an increase in the number of unfit genomes, which may be normally selected against by the accumulation of stop codons. Lastly, the ability of these attenuated viruses to transition through a bottleneck in vivo was measured using marked virus clones. The attenuated viruses showed an overall reduction in the number of marked clones for both the mosquito and vertebrate hosts, as well as a reduced ability to overcome the known bottlenecks in the mosquito. This study demonstrates that any perturbation of the optimal mutation frequency whether through changes in fidelity or by alterations in the mutation frequency of specific nucleotides, has significant deleterious effects on the virus, especially in the presence of host bottlenecks.
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Affiliation(s)
- K. Lane Warmbrod
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Edward I. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tiffany F. Kautz
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Adam Stanton
- School of Computing and Mathematics, University of Keele, Keele, United Kingdom
| | - Dedeke Rockx-Brouwer
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Birte K. Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Saravanan Thangamani
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yuriy Fofanov
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Naomi L. Forrester
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
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13
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Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN. 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. PLoS One 2019; 14:e0213869. [PMID: 30889210 PMCID: PMC6424447 DOI: 10.1371/journal.pone.0213869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/01/2019] [Indexed: 12/31/2022] Open
Abstract
The prebiotic potential of nervine herbal medicines has been scarcely studied. We therefore used anaerobic human fecal cultivation to investigate whether medicinal herbs commonly used as treatment in neurological health and disease in Ayurveda and other traditional systems of medicine modulate gut microbiota. Profiling of fecal cultures supplemented with either Kapikacchu, Gotu Kola, Bacopa/Brahmi, Shankhapushpi, Boswellia/Frankincense, Jatamansi, Bhringaraj, Guduchi, Ashwagandha or Shatavari by 16S rRNA sequencing revealed profound changes in diverse taxa. Principal coordinate analysis highlights that each herb drives the formation of unique microbial communities predicted to display unique metabolic potential. The relative abundance of approximately one-third of the 243 enumerated species was altered by all herbs. Additional species were impacted in an herb-specific manner. In this study, we combine genome reconstruction of sugar utilization and short chain fatty acid (SCFA) pathways encoded in the genomes of 216 profiled taxa with monosaccharide composition analysis of each medicinal herb by quantitative mass spectrometry to enhance the interpretation of resulting microbial communities and discern potential drivers of microbiota restructuring. Collectively, our results indicate that gut microbiota engage in both protein and glycan catabolism, providing amino acid and sugar substrates that are consumed by fermentative species. We identified taxa that are efficient amino acid fermenters and those capable of both amino acid and sugar fermentation. Herb-induced microbial communities are predicted to alter the relative abundance of taxa encoding SCFA (butyrate and propionate) pathways. Co-occurrence network analyses identified a large number of taxa pairs in medicinal herb cultures. Some of these pairs displayed related culture growth relationships in replicate cultures highlighting potential functional interactions among medicinal herb-induced taxa.
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Affiliation(s)
- Christine Tara Peterson
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
- * E-mail:
| | - Vandana Sharma
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
| | - Stanislav N. Iablokov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sasha Uchitel
- Washington University, Department of Biology, St. Louis, Missouri, United States of America
| | - Deepak Chopra
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
- Chopra Foundation, Department of Ayurveda and Yoga Research, Carlsbad, California, United States of America
| | - Paul J. Mills
- UC San Diego, School of Medicine, Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine and Public Health, La Jolla, California, United States of America
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Scott N. Peterson
- Sanford Burnham Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, California, United States of America
- Sanford Burnham Prebys Medical Discovery Institute, Tumor Microenvironment and Cancer Immunology Program, La Jolla, California, United States of America
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14
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Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Rickettsia conorii Infection. Genes (Basel) 2019; 10:genes10030204. [PMID: 30857242 PMCID: PMC6470625 DOI: 10.3390/genes10030204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 02/06/2023] Open
Abstract
Mediterranean spotted fever develops from an infection with Rickettsia conorii, an obligate intracellular, Gram-negative, endotheliotropic, and tick-transmitted bacterial pathogen, and is an acute, febrile illness that can progress to life-threatening complications if not diagnosed and treated early with effective antibiotics. Despite significant morbidity and mortality, little is known about changes in gene expression that determine the host responses during in vivo infection. We have investigated the transcriptional landscape of host lungs as a prominently affected organ system in an established murine model of infection by RNA-sequencing. Ingenuity pathway analysis resulted in the identification of 1332 differentially expressed genes and 292 upstream regulators. Notably, genes encoding for ubiquitin D, aconitate decarboxylase, antimicrobial peptides, calgranulins, cytokines and chemokines, and guanylate binding proteins were highly up-regulated, whereas those involved in hemoglobin biosynthesis and heme homeostasis were significantly down-regulated. Amongst response regulators, nucleotide-binding oligomerization domain-containing protein 2 and killer cell lectin-like receptors were differentially expressed, and gene clustering revealed eukaryotic initiation factor-2, oxidative phosphorylation, and ubiquitination as the predominantly activated biological pathways. Collectively, this first global transcriptomic profiling has identified R. conorii-induced regulation of novel genes and pathways in the host lungs, further in-depth investigation of which will strengthen our understanding of the pathogenesis of human rickettsioses.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Yuriy Fofanov
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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15
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Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK. Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection. Front Immunol 2019; 9:3014. [PMID: 30687302 PMCID: PMC6333757 DOI: 10.3389/fimmu.2018.03014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. Despite being implicated in the pathways of infection and inflammation, the roles of lncRNAs in host response to Rickettsia species have remained a mystery. We have profiled the expression of host lncRNAs during infection of susceptible mice with R. conorii as a model closely mimicking the pathogenesis of human spotted fever rickettsioses. RNA sequencing on the lungs of infected hosts yielded reads mapping to 74,964 non-coding RNAs, 206 and 277 of which were determined to be significantly up- and down-regulated, respectively, in comparison to uninfected controls. Following removal of short non-coding RNAs and ambiguous transcripts, remaining transcripts underwent in-depth analysis of mouse lung epigenetic signatures H3K4Me1 and H3K4Me3, active transcript markers (POLR2A, p300, CTCF), and DNaseI hypersensitivity sites to identify two potentially active and highly up-regulated elncRNAs NONMMUT013718 and NONMMUT024103. Using Hi-3C sequencing resource, we further determined that genomic loci of NONMMUT013718 and NONMMUT024103 might interact with and regulate the expression of nearby PCGs, namely Id2 (inhibitor of DNA binding 2) and Apol10b (apolipoprotein 10b), respectively. Heterologous reporter assays confirmed the activity of elncRNAs as the inducers of their predicted PCGs. In the lungs of infected mice, expression of both elncRNAs and their targets was significantly higher than mock-infected controls. Induced expression of NONMMUT013718/Id2 in murine macrophages and NONMMUT024103/Apol10b in endothelial cells was also clearly evident during R. conorii infection in vitro. Finally, shRNA mediated knock-down of NONMMUT013718 and NONMMUT024103 elncRNAs resulted in reduced expression of endogenous Id2 and Apl10b, demonstrating the regulatory roles of these elncRNAs on their target PCGs. Our results provide very first experimental evidence suggesting altered expression of pulmonary lncRNAs and elncRNA-mediated regulation of PCGs involved in immunity and during host interactions with pathogenic rickettsiae.
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Affiliation(s)
- Imran H Chowdhury
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Yuriy Fofanov
- Department of Pharmacology, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, University Boulevard, Galveston, TX, United States
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16
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Jeffries CL, Lawrence GG, Golovko G, Kristan M, Orsborne J, Spence K, Hurn E, Bandibabone J, Tantely LM, Raharimalala FN, Keita K, Camara D, Barry Y, Wat'senga F, Manzambi EZ, Afrane YA, Mohammed AR, Abeku TA, Hedge S, Khanipov K, Pimenova M, Fofanov Y, Boyer S, Irish SR, Hughes GL, Walker T. Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa. Wellcome Open Res 2018; 3:113. [PMID: 30483601 PMCID: PMC6234743 DOI: 10.12688/wellcomeopenres.14765.2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 12/31/2022] Open
Abstract
Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations in West Africa. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species A, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species A. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species A but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.
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Affiliation(s)
- Claire L Jeffries
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Gena G Lawrence
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, 30033, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Mojca Kristan
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - James Orsborne
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Kirstin Spence
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Eliot Hurn
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Janvier Bandibabone
- Laboratoire d'entomologie médicale et parasitologie, Centre de Recherche en Sciences Naturelles (CRSN/LWIRO), Sud-Kivu, Congo, Democratic Republic
| | - Luciano M Tantely
- Unité d'Entomologie Médicale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Fara N Raharimalala
- Unité d'Entomologie Médicale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Kalil Keita
- Nationale de Lutte contre le Paludisme, Ministere de la Sante, Conakry, Guinea
| | - Denka Camara
- Nationale de Lutte contre le Paludisme, Ministere de la Sante, Conakry, Guinea
| | - Yaya Barry
- Nationale de Lutte contre le Paludisme, Ministere de la Sante, Conakry, Guinea
| | - Francis Wat'senga
- National Institute of Biomedical Research, Kinshasa, Congo, Democratic Republic
| | - Emile Z Manzambi
- National Institute of Biomedical Research, Kinshasa, Congo, Democratic Republic
| | - Yaw A Afrane
- Department of Medical Microbiology, University of Ghana, Accra, Ghana
| | - Abdul R Mohammed
- Department of Medical Microbiology, University of Ghana, Accra, Ghana
| | | | - Shivanand Hedge
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Sebastien Boyer
- Unité d'Entomologie Médicale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Seth R Irish
- The US President's Malaria Initiative and Entomology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, 30329-4027, USA
| | - Grant L Hughes
- Department of Pathology, Institute for Human Infections and Immunity, Center for Tropical Diseases, Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, Texas, USA
| | - Thomas Walker
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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17
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Kalesinskas L, Cudone E, Fofanov Y, Putonti C. S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences. Evol Bioinform Online 2018; 14:1176934318797354. [PMID: 30245567 PMCID: PMC6144591 DOI: 10.1177/1176934318797354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022] Open
Abstract
With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool proved valuable in identifying genome rearrangements as well as exogenous sequences acquired via LGT in several bacterial species. Herein, we present the next generation of this tool, S-plot2. Similar to its predecessor, S-plot2 creates an interactive, 2-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). This new version, however, includes additional metrics for analysis, new reporting options, and integrated BLAST query functionality for the user to interrogate regions of interest. Furthermore, S-plot2 can evaluate larger sequences, including whole eukaryotic chromosomes. To illustrate some of the applications of the tool, 2 case studies are presented. The first examines strain-specific variation across the Pseudomonas aeruginosa genome and strain-specific LGT events. In the second case study, corresponding human, chimpanzee, and rhesus macaque autosomes were studied and lineage specific contributions to divergence were estimated. S-plot2 provides a means to both visually and quantitatively compare nucleotide sequences, from microbial genomes to eukaryotic chromosomes. The case studies presented illustrate just 2 potential applications of the tool, highlighting its capability to identify and investigate the variation in molecular divergence rates across sequences. S-plot2 is freely available through https://bitbucket.org/lkalesinskas/splot and is supported on the Linux and MS Windows operating systems.
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Affiliation(s)
- Laurynas Kalesinskas
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Evan Cudone
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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18
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Jeffries CL, Lawrence GG, Golovko G, Kristan M, Orsborne J, Spence K, Hurn E, Bandibabone J, Tantely LM, Raharimalala FN, Keita K, Camara D, Barry Y, Wat’senga F, Manzambi EZ, Afrane YA, Mohammed AR, Abeku TA, Hedge S, Khanipov K, Pimenova M, Fofanov Y, Boyer S, Irish SR, Hughes GL, Walker T. Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa. Wellcome Open Res 2018; 3:113. [DOI: 10.12688/wellcomeopenres.14765.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2018] [Indexed: 01/09/2023] Open
Abstract
Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing endosymbiotic bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis of samples was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species ‘A’, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species ‘A’. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species ‘A’, but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were also shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.
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Hegde S, Khanipov K, Albayrak L, Golovko G, Pimenova M, Saldaña MA, Rojas MM, Hornett EA, Motl GC, Fredregill CL, Dennett JA, Debboun M, Fofanov Y, Hughes GL. Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus Mosquito Vectors. Front Microbiol 2018; 9:2160. [PMID: 30250462 PMCID: PMC6140713 DOI: 10.3389/fmicb.2018.02160] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Microbial interactions are an underappreciated force in shaping insect microbiome communities. Although pairwise patterns of symbiont interactions have been identified, we have a poor understanding regarding the scale and the nature of co-occurrence and co-exclusion interactions within the microbiome. To characterize these patterns in mosquitoes, we sequenced the bacterial microbiome of Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus caught in the field or reared in the laboratory and used these data to generate interaction networks. For collections, we used traps that attracted host-seeking or ovipositing female mosquitoes to determine how physiological state affects the microbiome under field conditions. Interestingly, we saw few differences in species richness or microbiome community structure in mosquitoes caught in either trap. Co-occurrence and co-exclusion analysis identified 116 pairwise interactions substantially increasing the list of bacterial interactions observed in mosquitoes. Networks generated from the microbiome of Ae. aegypti often included highly interconnected hub bacteria. There were several instances where co-occurring bacteria co-excluded a third taxa, suggesting the existence of tripartite relationships. Several associations were observed in multiple species or in field and laboratory-reared mosquitoes indicating these associations are robust and not influenced by environmental or host factors. To demonstrate that microbial interactions can influence colonization of the host, we administered symbionts to Ae. aegypti larvae that either possessed or lacked their resident microbiota. We found that the presence of resident microbiota can inhibit colonization of particular bacterial taxa. Our results highlight that microbial interactions in mosquitoes are complex and influence microbiome composition.
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Affiliation(s)
- Shivanand Hegde
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
- Department of Computer Science, University of Houston, Houston, TX, United States
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - George Golovko
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Miguel A. Saldaña
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Mark M. Rojas
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Emily A. Hornett
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Greg C. Motl
- Harris County Public Health, Mosquito & Vector Control Division, Houston, TX, United States
| | - Chris L. Fredregill
- Harris County Public Health, Mosquito & Vector Control Division, Houston, TX, United States
| | - James A. Dennett
- Harris County Public Health, Mosquito & Vector Control Division, Houston, TX, United States
| | - Mustapha Debboun
- Harris County Public Health, Mosquito & Vector Control Division, Houston, TX, United States
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Grant L. Hughes
- Department of Pathology, Institute for Human Infections and Immunity, Center for Tropical Diseases, Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, TX, United States
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Webb MS, Miller AL, Howard TL, Johnson BH, Chumakov S, Fofanov Y, Nguyen-Vu T, Lin CY, Thompson EB. Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways. Mol Cell Endocrinol 2018; 471:118-130. [PMID: 29596968 PMCID: PMC6075652 DOI: 10.1016/j.mce.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 02/13/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
Abstract
Gene expression responses to glucocorticoid (GC) in the hours preceding onset of apoptosis were compared in three clones of human acute lymphoblastic leukemia CEM cells. Between 2 and 20h, all three clones showed increasing numbers of responding genes. Each clone had many unique responses, but the two responsive clones showed a group of responding genes in common, different from the resistant clone. MYC levels and the balance of activities between the three major groups of MAPKs are known important regulators of glucocorticoid-driven apoptosis in several lymphoid cell systems. Common to the two sensitive clones were changed transcript levels from genes that decrease amounts or activity of anti-apoptotic ERK/MAPK1 and JNK2/MAPK9, or of genes that increase activity of pro-apoptotic p38/MAPK14. Down-regulation of MYC and several MYC-regulated genes relevant to MAPKs also occurred in both sensitive clones. Transcriptomine comparisons revealed probable NOTCH-GC crosstalk in these cells.
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Affiliation(s)
- M S Webb
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - A L Miller
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - T L Howard
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - B H Johnson
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - S Chumakov
- Dept. of Computer Science, Dept. of Physics, University of Guadalahara, Gaudalahara, Jalisco, Mexico
| | - Y Fofanov
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - T Nguyen-Vu
- Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA
| | - C Y Lin
- Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA
| | - E B Thompson
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA; Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA.
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Uribe G, Rourke R, Villeger R, Golovko G, Khanipov K, Liu Z, Pimenova M, Fofanov Y, Zhou J, Brasier AR, Pinchuk IV. Abstract 5065: Cancer derived Escherichia coli induces tumor-promoting inflammatory cytokine IL-6 in cancer associated fibroblasts (CAFs) in a NF-κB/BRD4 dependent manner. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Chronic inflammatory responses within the colonic environment are critical to colorectal cancer (CRC) tumor development. While the exact causes of CRC development are unknown, recent data suggest that dysbiosis in the colonic microbiome results in the overgrowth of bacteria from Enterebacteriaceae, Fusobacteriaceae and Bacteroidaceae taxonomic families, contributing to CRC development. Among bacteria of the Enterebacteriaceae family, adherent invasive Esherichia coli has been shown to promote tumor cell growth via production of colibactin. However, the contribution of E.coli to the tumor promoting inflammatory microenvironment (TME) during sporadic CRC development remains unknown. Cancer associated fibroblasts (CAFs) are a major component of TME and contribute to tumor-promoting inflammatory responses via NF-κB dependent production of IL-6. Herein we investigate the effect of E. coli on CAFs. We hypothesize that stimulation of CAFs by cancer derived E.coli is a key processes in supporting tumor-promoting inflammation in CRC. Methods: Bacterial DNA was extracted from tumor and adjacent normal tissue of 28 CRC patients. High throughput sequencing was done using metabarcoding of 16S rDNA for bacteria and analyzed using CLC Genomics Workbench 8.0.5 Microbial Genomics Module, SILVA v119 database for 16S. E.coli PS092717 strain, isolated from CRC tumor site, was used in co-culture experiments. Real time RT-PCR and multiplex cytokine array was used to analyze fibroblasts gene expression and secretion, respectively. Results: We observed a reduction in microbial diversity in tumor vs adjacent normal tissue, with an increased prevalence of Fusobacteria, and Enterobactereacea, but not Bacteroidacea. We then tested the effect of E.coli PS092717 on colonic primary normal fibroblasts and CAFs. Exposure of N-CMFs to E.coli for 24 h only moderately increased IL-6, while CAF responded with a greater increase in IL-6 production. Analysis of the signaling mechanism demonstrated that this process was NF-κB dependent, and was abrogated in the presence of NF-kB specific inhibitor, triptolide (20 ng/mL). Bromodomain containing protein 4 (Brd4) is an epigenetic regulator that can recruit canonical NF-κB transcription factor RelA. Therefore, we analyzed its involvement in the above processes. NF-κB mediated increase in IL-6 expression and secretion induced by E.coli PS092717 was strongly reduced in CAFs than N-CMFs in the presence of BRD4 specific inhibitor (1 µM ZL0590). A similar observation was made when a major components of the E.coli cell wall, lipopolysaccharide (LPS), was used. Conclusion Taken together our data suggests that, E.coli derived from cancer tissue and its cell wall component LPS can contribute to the tumor promoting inflammation via stimulation of IL-6 production by CAFs and this process is BRD4/NF-κB-dependent.
Citation Format: Gabriela Uribe, Russel Rourke, Romain Villeger, George Golovko, Kamil Khanipov, Zhiqing Liu, Maria Pimenova, Yuriy Fofanov, Jia Zhou, Allen R. Brasier, Irina V. Pinchuk. Cancer derived Escherichia coli induces tumor-promoting inflammatory cytokine IL-6 in cancer associated fibroblasts (CAFs) in a NF-κB/BRD4 dependent manner [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5065.
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Affiliation(s)
| | | | | | | | | | - Zhiqing Liu
- University of Texas Medical Branch, Galveston, TX
| | | | | | - Jia Zhou
- University of Texas Medical Branch, Galveston, TX
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Zhao Y, Chen F, Wu W, Sun M, Bilotta AJ, Yao S, Xiao Y, Huang X, Eaves-Pyles TD, Golovko G, Fofanov Y, D’Souza W, Zhao Q, Liu Z, Cong Y. GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3. Mucosal Immunol 2018; 11:752-762. [PMID: 29411774 PMCID: PMC5976519 DOI: 10.1038/mi.2017.118] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/06/2017] [Indexed: 02/04/2023]
Abstract
The antimicrobial peptides (AMP) produced by intestinal epithelial cells (IEC) play crucial roles in the regulation of intestinal homeostasis by controlling microbiota. Gut microbiota has been shown to promote IEC expression of RegIIIγ and certain defensins. However, the mechanisms involved are still not completely understood. In this report, we found that IEC expression levels of RegIIIγ and β-defensins 1, 3, and 4 were lower in G protein-coupled receptor (GPR)43-/- mice compared to that of wild-type (WT) mice. Oral feeding with short-chain fatty acids (SCFA) promoted IEC production of RegIIIγ and defensins in mice. Furthermore, SCFA induced RegIIIγ and β-defensins in intestinal epithelial enteroids generated from WT but not GPR43-/- mice. Mechanistically, SCFA activated mTOR and STAT3 in IEC, and knockdown of mTOR and STAT3 impaired SCFA induction of AMP production. Our studies thus demonstrated that microbiota metabolites SCFA promoted IEC RegIIIγ and β-defensins in a GPR43-dependent manner. The data thereby provide a novel pathway by which microbiota regulates IEC expression of AMP and intestinal homeostasis.
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Affiliation(s)
- Ye Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, China
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Feidi Chen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
| | - Wei Wu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital, Shanghai, China
| | - Mingming Sun
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital, Shanghai, China
| | - Anthony J. Bilotta
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Suxia Yao
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Yi Xiao
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Institute of Animal Nutrition, Sichuan Agricultural University, China
| | - Xiangsheng Huang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Tonyia D. Eaves-Pyles
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | | | | | - Zhanju Liu
- Department of Gastroenterology, The Shanghai Tenth People’s Hospital, Shanghai, China
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Department of Pathology, University of Texas Medical Branch, Galveston, TX
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Kautz TF, Guerbois M, Khanipov K, Patterson EI, Langsjoen RM, Yun R, Warmbrod KL, Fofanov Y, Weaver SC, Forrester NL. Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy. Virus Evol 2018; 4:vey004. [PMID: 29593882 PMCID: PMC5841381 DOI: 10.1093/ve/vey004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During RNA virus replication, there is the potential to incorporate mutations that affect virulence or pathogenesis. For live-attenuated vaccines, this has implications for stability, as replication may result in mutations that either restore the wild-type phenotype via reversion or compensate for the attenuating mutations by increasing virulence (pseudoreversion). Recent studies have demonstrated that altering the mutation rate of an RNA virus is an effective attenuation tool. To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Next generation sequencing after passage in the presence of mutagens revealed a mutant containing three mutations in the RdRp, TC-83 3x, to have decreased replication fidelity, while a second mutant, TC-83 4x displayed no change in fidelity, but shared many phenotypic characteristics with TC-83 3x. Both mutants exhibited increased, albeit inconsistent attenuation in an infant mouse model, as well as increased immunogenicity and complete protection against lethal challenge of an adult murine model compared with the parent TC-83. During serial passaging in a highly permissive model, the mutants increased in virulence but remained less virulent than the parent TC-83. These results suggest that the incorporation of low-fidelity mutations into the RdRp of live-attenuated vaccines for RNA viruses can confer increased immunogenicity whilst showing some evidence of increased attenuation. However, while in theory such constructs may result in more effective vaccines, the instability of the vaccine phenotype decreases the likelihood of this being an effective vaccine strategy.
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Affiliation(s)
- Tiffany F Kautz
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mathilde Guerbois
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Edward I Patterson
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Rose M Langsjoen
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Ruimei Yun
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kelsey L Warmbrod
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Naomi L Forrester
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL. Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity. Virus Evol 2018; 4:vey001. [PMID: 29479479 PMCID: PMC5814806 DOI: 10.1093/ve/vey001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viral diversity is theorized to play a significant role during virus infections, particularly for arthropod-borne viruses (arboviruses) that must infect both vertebrate and invertebrate hosts. To determine how viral diversity influences mosquito infection and dissemination Culex taeniopus mosquitoes were infected with the Venezuelan equine encephalitis virus endemic strain 68U201. Bodies and legs/wings of the mosquitoes were collected individually and subjected to multi-parallel sequencing. Virus sequence diversity was calculated for each tissue. Greater diversity was seen in mosquitoes with successful dissemination versus those with no dissemination. Diversity across time revealed that bottlenecks influence diversity following dissemination to the legs/wings, but levels of diversity are restored by Day 12 post-dissemination. Specific minority variants were repeatedly identified across the mosquito cohort, some in nearly every tissue and time point, suggesting that certain variants are important in mosquito infection and dissemination. This study demonstrates that the interaction between the mosquito and the virus results in changes in diversity and the mutational spectrum and may be essential for successful transition of the bottlenecks associated with arbovirus infection.
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Affiliation(s)
- Edward I Patterson
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Mark M Rojas
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Tiffany F Kautz
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Dedeke Rockx-Brouwer
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Georgiy Golovko
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Naomi L Forrester
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
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Robeson MS, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ. Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig ( Sus scrofa). Ecol Evol 2017; 8:185-196. [PMID: 29321862 PMCID: PMC5756863 DOI: 10.1002/ece3.3638] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.
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Affiliation(s)
- Michael S Robeson
- Fish and Wildlife Conservation Biology Colorado State University Fort Collins CO USA.,USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA.,Present address: Department of Biomedical Informatics College of Medicine University of Arkansas for Medical Sciences Little Rock AR USA
| | - Kamil Khanipov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - George Golovko
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Samantha M Wisely
- Department of Wildlife Ecology and Conservation USA 5 USDA, Wildlife Services University of Florida Gainesville FL USA
| | | | | | - Timothy J Smyser
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
| | - Yuriy Fofanov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
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Chonmaitree T, Jennings K, Golovko G, Khanipov K, Pimenova M, Patel JA, McCormick DP, Loeffelholz MJ, Fofanov Y. Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media. PLoS One 2017; 12:e0180630. [PMID: 28708872 PMCID: PMC5510840 DOI: 10.1371/journal.pone.0180630] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants. Methods We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform. Results Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium. Bacterial diversity was lower in culture-positive samples for Streptococcus pneumoniae, and Haemophilus influenzae, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in Micrococcus colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in Pseudomonas, Myroides, Yersinia, and Sphingomonas. Otopathogen abundance was increased during symptomatic viral infection, but not during asymptomatic infection. The risk for AOM complicating URI was reduced by increased abundance of Staphylococcus and Sphingobium. Conclusion Otopathogen genera played the key roles in URI and AOM occurrences. Staphylococcus counteracts otopathogens thus Staphylococcal colonization may be beneficial, rather than harmful. While Sphingobium may play a role in preventing AOM complicating URI, the commonly used probiotic Bifidobacterium did not play a significant role during URI or AOM. The role of less common commensals in counteracting the deleterious effects of otopathogens requires further studies.
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Affiliation(s)
- Tasnee Chonmaitree
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- * E-mail:
| | - Kristofer Jennings
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Georgiy Golovko
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Kamil Khanipov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Maria Pimenova
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Janak A. Patel
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - David P. McCormick
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Michael J. Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Yuriy Fofanov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
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Schroeder CLC, Narra HP, Sahni A, Khanipov K, Patel J, Fofanov Y, Sahni SK. Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions. Ticks Tick Borne Dis 2017; 8:827-836. [PMID: 28709615 DOI: 10.1016/j.ttbdis.2017.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 01/09/2023]
Abstract
Natural pathogen transmission of Rickettsia prowazekii, the etiologic agent of epidemic typhus, to humans is associated with arthropods, including human body lice, ticks, and ectoparasites of eastern flying squirrel. Recently, we have documented the presence of small RNAs in Rickettsia species and expression of R. prowazekii sRNAs during infection of cultured human microvascular endothelial cells (HMECs), which represent the primary target cells during human infections. Bacterial noncoding transcripts are now well established as critical post-transcriptional regulators of virulence and adaptation mechanisms in varying host environments. Despite their importance, little is known about the expression profile and regulatory activities of R. prowazekii sRNAs (Rp_sRs) in different host cells encountered as part of the natural life-cycle. To investigate the sRNA expression profile of R. prowazekii during infection of arthropod host cells, we employed an approach combining in vitro infection, bioinformatics, RNA sequencing, and PCR-based quantitation. Global analysis of R. prowazekii transcriptome by strand-specific RNA sequencing enabled us to identify 67 cis-acting (antisense) and 26 trans-acting (intergenic) Rp_sRs expressed during the infection of Amblyomma americanum (AAE2) cells. Comparative evaluation of expression during R. prowazekii infection of HMECs and AAE2 cells by quantitative RT-PCR demonstrated significantly higher expression of four selected Rp_sRs in tick AAE2 cells. Examination of the coding transcriptome revealed differential up-regulation of >150 rickettsial genes in either HMECs or AAE2 cells and yielded evidence for host cell-dependent utilization of alternative transcription start sites by 18 rickettsial genes. Our results thus suggest noticeable differences in the expression of both Rp_sRs as well as the coding transcriptome and the exploitation of multiple transcription initiation sites for select genes during the infection of human endothelium and tick vector cells as the host and yield new insights into rickettsial virulence and transmission mechanisms.
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Affiliation(s)
- Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard Galveston, TX 77555, USA.
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard Galveston, TX 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard Galveston, TX 77555, USA.
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Jignesh Patel
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard Galveston, TX 77555, USA.
| | - Yuriy Fofanov
- Department of Pharmacology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard Galveston, TX 77555, USA.
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Albayrak L, Khanipov K, Pimenova M, Golovko G, Rojas M, Pavlidis I, Chumakov S, Aguilar G, Chávez A, Widger WR, Fofanov Y. The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. BMC Genomics 2016; 17:1017. [PMID: 27955616 PMCID: PMC5153897 DOI: 10.1186/s12864-016-3375-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 12/05/2016] [Indexed: 02/03/2023] Open
Abstract
Background Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput sequencing technology has significantly improved the heteroplasmy identification process, the ability of this technology to detect low-abundance mutations can be affected by the presence of similar sequences originating from nuclear DNA (nDNA). To determine to what extent nDNA can cause false positive low-abundance heteroplasmy calls, we have identified mitochondrial locations of all subsequences that are common or similar (one mismatch allowed) between nDNA and mitochondrial DNA (mtDNA). Results Performed analysis revealed up to a 25-fold variation in the lengths of longest common and longest similar (one mismatch allowed) subsequences across the mitochondrial genome. The size of the longest subsequences shared between nDNA and mtDNA in several regions of the mitochondrial genome were found to be as low as 11 bases, which not only allows using these regions to design new, very specific PCR primers, but also supports the hypothesis of the non-random introduction of mtDNA into the human nuclear DNA. Conclusion Analysis of the mitochondrial locations of the subsequences shared between nDNA and mtDNA suggested that even very short (36 bases) single-end sequencing reads can be used to identify low-abundance variation in 20.4% of the mitochondrial genome. For longer (76 and 150 bases) reads, the proportion of the mitochondrial genome where nDNA presence will not interfere found to be 44.5 and 67.9%, when low-abundance mutations at 100% of locations can be identified using 417 bases long single reads. This observation suggests that the analysis of low-abundance variations in mitochondria population can be extended to a variety of large data collections such as NCBI Sequence Read Archive, European Nucleotide Archive, The Cancer Genome Atlas, and International Cancer Genome Consortium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3375-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark Rojas
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Ioannis Pavlidis
- Department of Computer Science, University of Houston, Houston, TX, USA
| | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Gerardo Aguilar
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Arturo Chávez
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - William R Widger
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA. .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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Schroeder CLC, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R, Fofanov Y, Sahni SK. Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii. Front Microbiol 2016; 7:859. [PMID: 27375581 PMCID: PMC4896933 DOI: 10.3389/fmicb.2016.00859] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 12/12/2022] Open
Abstract
Emerging evidence implicates a critically important role for bacterial small RNAs (sRNAs) as post-transcriptional regulators of physiology, metabolism, stress/adaptive responses, and virulence, but the roles of sRNAs in pathogenic Rickettsia species remain poorly understood. Here, we report on the identification of both novel and well-known bacterial sRNAs in Rickettsia prowazekii, known to cause epidemic typhus in humans. RNA sequencing of human microvascular endothelial cells (HMECs), the preferred targets during human rickettsioses, infected with R. prowazekii revealed the presence of 35 trans-acting and 23 cis-acting sRNAs, respectively. Of these, expression of two trans-acting (Rp_sR17 and Rp_sR60) and one cis-acting (Rp_sR47) novel sRNAs and four well-characterized bacterial sRNAs (RNaseP_bact_a, α-tmRNA, 4.5S RNA, 6S RNA) was further confirmed by Northern blot or RT-PCR analyses. The transcriptional start sites of five novel rickettsial sRNAs and 6S RNA were next determined using 5′ RLM-RACE yielding evidence for their independent biogenesis in R. prowazekii. Finally, computational approaches were employed to determine the secondary structures and potential mRNA targets of novel sRNAs. Together, these results establish the presence and expression of sRNAs in R. prowazekii during host cell infection and suggest potential functional roles for these important post-transcriptional regulators in rickettsial biology and pathogenesis.
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Affiliation(s)
- Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch Galveston, TX, USA
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch Galveston, TX, USA
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch Galveston, TX, USA
| | - Mark Rojas
- Department of Pharmacology, University of Texas Medical Branch Galveston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch Galveston, TX, USA
| | - Jignesh Patel
- Department of Pathology, University of Texas Medical Branch Galveston, TX, USA
| | - Riya Shah
- Department of Neuroscience, University of Texas at Dallas Dallas, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology, University of Texas Medical Branch Galveston, TX, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch Galveston, TX, USA
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Kosoy M, Bai Y, Enscore R, Rizzo MR, Bender S, Popov V, Albayrak L, Fofanov Y, Chomel B. Bartonella melophagi in blood of domestic sheep (Ovis aries) and sheep keds (Melophagus ovinus) from the southwestern US: Cultures, genetic characterization, and ecological connections. Vet Microbiol 2016; 190:43-49. [PMID: 27283855 DOI: 10.1016/j.vetmic.2016.05.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Bartonella melophagi sp. nov. was isolated from domestic sheep blood and from sheep keds (Melophagus ovinus) from the southwestern United States. The sequence analyses of the reference strain performed by six molecular markers consistently demonstrated that B. melophagi relates to but differ from other Bartonella species isolated from domestic and wild ruminants. Presence of 183 genes specific for B. melophagi, being absent in genomes of other Bartonella species associated with ruminants also supports the separation of this bacterial species from species of other ruminants. Bartonella DNA was detected in all investigated sheep keds; however, culturing of these bacteria from sheep blood rejects a speculation that B. melophagi is an obligatory endosymbiont. Instead, the results support the hypothesis that the domestic sheep is a natural host reservoir for B. melophagi and the sheep ked its main vector. This bacterium was not isolated from the blood of bighorn sheep and domestic goats belonging to the same subfamily Caprinae. B. melophagi has also been shown to be zoonotic and needs to be investigated further.
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Affiliation(s)
- Michael Kosoy
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 90521, USA.
| | - Ying Bai
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 90521, USA
| | - Russell Enscore
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 90521, USA
| | - Maria Rosales Rizzo
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 90521, USA
| | - Scott Bender
- Navajo Nation Veterinary Program, Department of Agriculture, The Navajo Nation, P.O. Box 1450, Window Rock, AZ 86515, USA
| | - Vsevolod Popov
- University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Levent Albayrak
- University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Yuriy Fofanov
- University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0609, USA
| | - Bruno Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Schroeder CLC, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK. Bacterial small RNAs in the Genus Rickettsia. BMC Genomics 2015; 16:1075. [PMID: 26679185 PMCID: PMC4683814 DOI: 10.1186/s12864-015-2293-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/14/2015] [Indexed: 01/02/2023] Open
Abstract
Background Rickettsia species are obligate intracellular Gram-negative pathogenic bacteria and the etiologic agents of diseases such as Rocky Mountain spotted fever (RMSF), Mediterranean spotted fever, epidemic typhus, and murine typhus. Genome sequencing revealed that R. prowazekii has ~25 % non-coding DNA, the majority of which is thought to be either “junk DNA” or pseudogenes resulting from genomic reduction. These characteristics also define other Rickettsia genomes. Bacterial small RNAs, whose biogenesis is predominantly attributed to either the intergenic regions (trans-acting) or to the antisense strand of an open reading frame (cis-acting), are now appreciated to be among the most important post-transcriptional regulators of bacterial virulence and growth. We hypothesize that intergenic regions in rickettsial species encode for small, non-coding RNAs (sRNAs) involved in the regulation of its transcriptome, leading to altered virulence and adaptation depending on the host niche. Results We employed a combination of bioinformatics and in vitro approaches to explore the presence of sRNAs in a number of species within Genus Rickettsia. Using the sRNA Identification Protocol using High-throughput Technology (SIPHT) web interface, we predicted over 1,700 small RNAs present in the intergenic regions of 16 different strains representing 13 rickettsial species. We further characterized novel sRNAs from typhus (R. prowazekii and R. typhi) and spotted fever (R. rickettsii and R. conorii) groups for their promoters and Rho-independent terminators using Bacterial Promoter Prediction Program (BPROM) and TransTermHP prediction algorithms, respectively. Strong σ70 promoters were predicted upstream of all novel small RNAs, indicating the potential for transcriptional activity. Next, we infected human microvascular endothelial cells (HMECs) with R. prowazekii for 3 h and 24 h and performed Next Generation Sequencing to experimentally validate the expression of 26 sRNA candidates predicted in R. prowazekii. Reverse transcriptase PCR was also used to further verify the expression of six putative novel sRNA candidates in R. prowazekii. Conclusions Our results yield clear evidence for the expression of novel R. prowazekii sRNA candidates during infection of HMECs. This is the first description of novel small RNAs for a highly pathogenic species of Rickettsia, which should lead to new insights into rickettsial virulence and adaptation mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2293-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Casey L C Schroeder
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Hema P Narra
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Mark Rojas
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Jignesh Patel
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Kamil Khanipov
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Yuriy Fofanov
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Sanjeev K Sahni
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
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Loeffelholz M, Fofanov Y. The main challenges that remain in applying high-throughput sequencing to clinical diagnostics. Expert Rev Mol Diagn 2015; 15:1405-8. [DOI: 10.1586/14737159.2015.1088385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sible E, Cooper A, Malki K, Bruder K, Watkins SC, Fofanov Y, Putonti C. Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches. Data Brief 2015; 5:9-12. [PMID: 26380839 PMCID: PMC4556746 DOI: 10.1016/j.dib.2015.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 12/02/2022] Open
Abstract
In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141–151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31–45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97–141; Wilhelm and Suttle, Bioscience 49 (1999) 781–788; Bratback et al., Microb. Ecol. 28 (1994) 209–221. Despite their prevalence and likely critical role in freshwater environments, very few viral species have been characterized. Metagenomic approaches, however, have allowed for a glimpse into phage diversity. We collected surface water samples from four Chicago area beaches – Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach – every two weeks from May 13 through August 5, 2014. Sampling was conducted with four biological replicates for each sampling date and location, resulting in 112 samples. DNA isolated from each of the individual samples for a given collection date/location was pooled together, with one exception – Calumet Beach on August 5, 2014 – in which each biological replicate was sequenced individually. Raw sequence data is available via NCBI’s SRA database (part of BioProject PRJNA248239).
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Affiliation(s)
- Emily Sible
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Alexandria Cooper
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Kema Malki
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Katherine Bruder
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Siobhan C. Watkins
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 5.112 BSB, Galveston, TX 77555, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
- Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
- Department of Computer Science, Loyola University Chicago, 820 N Michigan Ave, Chicago, IL 60611, USA
- Correspondence to: 1032 W Sheridan Rd, Chicago, IL 60660, USA.
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Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y. Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines. PLoS One 2015; 10:e0127799. [PMID: 26039084 PMCID: PMC4454691 DOI: 10.1371/journal.pone.0127799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/18/2015] [Indexed: 11/25/2022] Open
Abstract
The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data.
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Affiliation(s)
- Mark Rojas
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
| | - Georgiy Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - B. Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Chernov AV, Reyes L, Xu Z, Gonzalez B, Golovko G, Peterson S, Perucho M, Fofanov Y, Strongin AY. Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells. Epigenetics 2015; 10:303-18. [PMID: 25695131 DOI: 10.1080/15592294.2015.1020000] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. Mycoplasmas spp., including Mycoplasma hyorhinis, efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the M. hyorhinis CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼ 11% of GATC sites overlap with CGs (e.g., CGAT(m)CG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
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Affiliation(s)
- Andrei V Chernov
- a Infectious & Inflammatory Disease Center ; Sanford-Burnham Medical Research Institute ; La Jolla , CA USA
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Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Metagenomic analysis of the airborne environment in urban spaces. Microb Ecol 2015; 69:346-55. [PMID: 25351142 PMCID: PMC4312561 DOI: 10.1007/s00248-014-0517-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/09/2014] [Indexed: 05/04/2023]
Abstract
The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.
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Affiliation(s)
- Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | | | - Jonathan E. Allen
- Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Mark Rojas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - George Golovko
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - Yuriy Fofanov
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | | | - Crystal J. Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
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Stepanov VG, Xiao Y, Tran Q, Rojas M, Willson RC, Fofanov Y, Fox GE, Roberts DJ. The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions. BMC Microbiol 2014; 14:225. [PMID: 25194715 PMCID: PMC4174249 DOI: 10.1186/s12866-014-0225-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/18/2014] [Indexed: 11/16/2022] Open
Abstract
Background Perchlorate contamination has been detected in both ground water and drinking water. An attractive treatment option is the use of ion-exchange to remove and concentrate perchlorate in brine. Biological treatment can subsequently remove the perchlorate from the brine. When nitrate is present, it will also be concentrated in the brine and must also be removed by biological treatment. The primary objective was to obtain an in-depth characterization of the microbial populations of two salt-tolerant cultures each of which is capable of metabolizing perchlorate. The cultures were derived from a single ancestral culture and have been maintained in the laboratory for more than 10 years. One culture was fed perchlorate only, while the other was fed both perchlorate and nitrate. Results A metagenomic characterization was performed using Illumina DNA sequencing technology, and the 16S rDNA of several pure strains isolated from the mixed cultures were sequenced. In the absence of nitrate, members of the Rhodobacteraceae constituted the prevailing taxonomic group. Second in abundance were the Rhodocyclaceae. In the nitrate fed culture, the Rhodobacteraceae are essentially absent. They are replaced by a major expansion of the Rhodocyclaceae and the emergence of the Alteromonadaceae as a significant community member. Gene sequences exhibiting significant homology to known perchlorate and nitrate reduction enzymes were found in both cultures. Conclusions The structure of the two microbial ecosystems of interest has been established and some representative strains obtained in pure culture. The results illustrate that under favorable conditions a group of organisms can readily dominate an ecosystem and yet be effectively eliminated when their advantage is lost. Almost all known perchlorate-reducing organisms can also effectively reduce nitrate. This is certainly not the case for the Rhodobacteraceae that were found to dominate in the absence of nitrate, but effectively disappeared in its presence. This study is significant in that it reveals the existence of a novel group of organisms that play a role in the reduction of perchlorate under saline conditions. These Rhodobacteraceae especially, as well as other organisms present in these communities may be a promising source of unique salt-tolerant enzymes for perchlorate reduction. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0225-3) contains supplementary material, which is available to authorized users.
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Miller AL, Geng C, Golovko G, Sharma M, Schwartz JR, Yan J, Sowers L, Widger WR, Fofanov Y, Vedeckis WV, Thompson EB. Epigenetic alteration by DNA-demethylating treatment restores apoptotic response to glucocorticoids in dexamethasone-resistant human malignant lymphoid cells. Cancer Cell Int 2014; 14:35. [PMID: 24795534 PMCID: PMC4008436 DOI: 10.1186/1475-2867-14-35] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/01/2014] [Indexed: 11/17/2022] Open
Abstract
Background Glucocorticoids (GCs) are often included in the therapy of lymphoid malignancies because they kill several types of malignant lymphoid cells. GCs activate the glucocorticoid receptor (GR), to regulate a complex genetic network, culminating in apoptosis. Normal lymphoblasts and many lymphoid malignancies are sensitive to GC-driven apoptosis. Resistance to GCs can be a significant clinical problem, however, and correlates with resistance to several other major chemotherapeutic agents. Methods We analyzed the effect of treatment with the cytosine analogue 5 aza-2’ deoxycytidine (AZA) on GC resistance in two acute lymphoblastic leukemia (T or pre-T ALL) cell lines- CEM and Molt-4- and a (B-cell) myeloma cell line, RPMI 8226. Methods employed included tissue culture, flow cytometry, and assays for clonogenicity, cytosine extension, immunochemical identification of proteins, and gene transactivation. High throughput DNA sequencing was used to confirm DNA methylation status. Conclusions Treatment of these cells with AZA resulted in altered DNA methylation and restored GC-evoked apoptosis in all 3 cell lines. In CEM cells the altered epigenetic state resulted in site-specific phosphorylation of the GR, increased GR potency, and GC-driven induction of the GR from promoters that lie in CpG islands. In RPMI 8226 cells, expression of relevant coregulators of GR function was altered. Activation of p38 mitogen-activated protein kinase (MAPK), which is central to a feed-forward mechanism of site-specific GR phosphorylation and ultimately, apoptosis, occurred in all 3 cell lines. These data show that in certain malignant hematologic B- and T-cell types, epigenetically controlled GC resistance can be reversed by cell exposure to a compound that causes DNA demethylation. The results encourage studies of application to in vivo systems, looking towards eventual clinical applications.
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Affiliation(s)
- Aaron L Miller
- Department of Biochemistry & Molecular Biology, (ALM present address, Department. of Pediatrics, & Assay Devel. Service Division Galveston National Lab.), University of Texas Medical Branch, Galveston, TX, USA
| | - Chuandong Geng
- Department of Biochemistry & Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA CG present address, Depts. of Medicine and of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Georgiy Golovko
- Department of Biology & Biochemistry, Centers for Biomedical & Environmental Genomics and/or Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX, USA ; Department of Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, Univ. of Texas Medical Branch, Galveston, TX, USA
| | - Meenakshi Sharma
- Department of Biology & Biochemistry, Centers for Biomedical & Environmental Genomics and/or Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX, USA
| | - Jason R Schwartz
- Department of Biochemistry & Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA CG present address, Depts. of Medicine and of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA ; Present address St. Jude Children's Hospital, Memphis, TN, USA
| | - Jiabin Yan
- Department of Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, Univ. of Texas Medical Branch, Galveston, TX, USA
| | - Lawrence Sowers
- Department of Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, Univ. of Texas Medical Branch, Galveston, TX, USA
| | - William R Widger
- Department of Biology & Biochemistry, Centers for Biomedical & Environmental Genomics and/or Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX, USA
| | - Yuriy Fofanov
- Department of Biology & Biochemistry, Centers for Biomedical & Environmental Genomics and/or Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX, USA ; Department of Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, Univ. of Texas Medical Branch, Galveston, TX, USA
| | - Wayne V Vedeckis
- Department of Biochemistry & Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA CG present address, Depts. of Medicine and of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - E Brad Thompson
- Department of Biochemistry & Molecular Biology, (ALM present address, Department. of Pediatrics, & Assay Devel. Service Division Galveston National Lab.), University of Texas Medical Branch, Galveston, TX, USA ; Department of Biology & Biochemistry, Centers for Biomedical & Environmental Genomics and/or Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX, USA
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Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. BMC Evol Biol 2013; 13:184. [PMID: 24007216 PMCID: PMC3848584 DOI: 10.1186/1471-2148-13-184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/28/2013] [Indexed: 02/03/2023] Open
Abstract
Background Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organism’s pathogenicity within its host. Previously we introduced a tool called S-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. Utilizing S-plot and new functionality developed here, we examined 18 publicly available Neisseria genomes, including strains of both pathogenic and non-pathogenic species, in order to identify regions of unusual compositional properties (RUCPs) using both a sliding window as well as a gene-by-gene approach. Results Numerous GEIs and PAIs were identified including virulence genes previously found within the pathogenic Neisseria species. While some genes were conserved amongst all species, only pathogenic species, or an individual species, a number of genes were detected that are unique to an individual strain. While the majority of such genes have an origin unknown, a number of putative sources including pathogenic and capsule-containing bacteria were determined, indicative of gene exchange between Neisseria spp. and other bacteria within their microhabitat. Furthermore, we uncovered evidence that both N. meningitidis and N. gonorrhoeae have separately acquired DNA from their human host. Data suggests that all three Neisseria species have received horizontally transferred elements post-speciation. Conclusions Using this approach, we were able to not only find previously identified regions of virulence but also new regions which may be contributing to the virulence of the species. This comparative analysis provides a means for tracing the evolutionary history of the acquisition of foreign DNA within this genus. Looking specifically at the RUCPs present within the 18 genomes considered, a stronger similarity between N. meningitidis and N. lactamica is observed, suggesting that N. meningitidis arose before N. gonorrhoeae.
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Affiliation(s)
- Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W, Sheridan Rd, Chicago, IL 60660, USA.
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Saxer G, Havlak P, Fox SA, Quance MA, Gupta S, Fofanov Y, Strassmann JE, Queller DC. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum. PLoS One 2012; 7:e46759. [PMID: 23056439 PMCID: PMC3466296 DOI: 10.1371/journal.pone.0046759] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval of 4.1×10(-9) - 9.5×10(-9), per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10(-11), with a Poisson confidence interval ranging from 7.4×10(-13) to 1.6×10(-10), is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.
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Affiliation(s)
- Gerda Saxer
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America.
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Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, Howard JJ, Ballesteros E, Gupta S, Widger W, Fofanov Y. Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. BMC Bioinformatics 2012; 13:166. [PMID: 22800377 PMCID: PMC3505481 DOI: 10.1186/1471-2105-13-166] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 06/18/2012] [Indexed: 11/10/2022] Open
Abstract
Background The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data is limited due to large file sizes, so even simple tasks such as data filtration and quality assessment have to be performed in several steps. This requires (potentially problematic) interaction between the investigator and a bioinformatics/computational service provider. Furthermore, such services are often performed using specialized computational facilities. Results We present a Windows-based application, Slim-Filter designed to interactively examine the statistical properties of sequencing reads produced by Illumina Genome Analyzer and to perform a broad spectrum of data manipulation tasks including: filtration of low quality and low complexity reads; filtration of reads containing undesired subsequences (such as parts of adapters and PCR primers used during the sample and sequencing libraries preparation steps); excluding duplicated reads (while keeping each read’s copy number information in a specialized data format); and sorting reads by copy numbers allowing for easy access and manual editing of the resulting files. Slim-Filter is organized as a sequence of windows summarizing the statistical properties of the reads. Each data manipulation step has roll-back abilities, allowing for return to previous steps of the data analysis process. Slim-Filter is written in C++ and is compatible with fasta, fastq, and specialized AS file formats presented in this manuscript. Setup files and a user’s manual are available for download at the supplementary web site (
https://www.bioinfo.uh.edu/Slim_Filter/). Conclusion The presented Windows-based application has been developed with the goal of providing individual investigators with integrated sequencing reads analysis, curation, and manipulation capabilities.
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Affiliation(s)
- Georgiy Golovko
- Center for BioMedical and Environmental Genomics, University of Houston, Houston, TX, USA.
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Gijavanekar C, Drabek R, Soni M, Jackson GW, Strych U, Fox GE, Fofanov Y, Willson RC. Detection and typing of viruses using broadly sensitive cocktail-PCR and mass spectrometric cataloging: demonstration with dengue virus. J Mol Diagn 2012; 14:402-7. [PMID: 22579629 DOI: 10.1016/j.jmoldx.2012.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 01/19/2012] [Accepted: 02/03/2012] [Indexed: 10/28/2022] Open
Abstract
Virus detection and taxonomic identification of serotypes, strains, or genotypes provide important information relevant for diagnosis, and for the epidemiological characterization and tracking of new strains in an endemic region. In the specific case of dengue virus, rapid serotype identification can also be useful in the treatment of secondary infections that may cause the more severe dengue hemorrhagic fever and dengue shock syndrome. In this work, dengue virus was used as a model to test a new approach of combining broadly sensitive RT-PCR amplification of nearly any virus strain with subsequent serotype- and finer-level identification by mass spectrometry. PCR primers were appended with promoter sequences, such that the resulting PCR products could be transcribed into RNA. RNA fragments generated by guanosine-specific RNase T(1) digestion were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Viral serotypes were identified by comparing the pattern of observed fragment masses to a mass database. The database was created by computationally fragmenting 2517 dengue strains after each guanosine residue using the same primers. Computationally, all 2517 strains in the mass database were correctly identified at the serotype level from the predicted PCR product. The methodology was successfully demonstrated experimentally by identifying the serotypes of eight test strains using mosquito cell cultures infected with strains of all four serotypes and with full-length cDNA clones.
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Affiliation(s)
- Charul Gijavanekar
- Department of Biology and Biochemistry, University of Houston, TX 77204, USA
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Gijavanekar C, Añez-Lingerfelt M, Feng C, Putonti C, Fox GE, Sabo A, Fofanov Y, Willson RC. PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'. FEBS J 2011; 278:1676-87. [PMID: 21410643 DOI: 10.1111/j.1742-4658.2011.08091.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PCR detection of viral pathogens is extremely useful, but suffers from the challenge of detecting the many variant strains of a given virus that arise over time. Here, we report the computational derivation and initial experimental testing of a combination of 10 PCR primers to be used in a single high-sensitivity mixed PCR reaction for the detection of dengue virus. Primer sequences were computed such that their probability of mispriming with human DNA is extremely low. A 'cocktail' of 10 primers was shown experimentally to be able to detect cDNA clones representing the four serotypes and dengue virus RNA spiked into total human whole blood RNA. Computationally, the primers are predicted to detect 95% of the 1688 dengue strains analyzed (with perfect primer match). Allowing up to one mismatch and one insertion per primer, the primer set detects 99% of strains. Primer sets from three previous studies have been compared with the present set of primers and their relative sensitivity for dengue virus is discussed. These results provide the formulation and demonstration of a mixed primer PCR reagent that may enable the detection of nearly any dengue strain irrespective of serotype, in a single PCR reaction, and illustrate an approach to the broad problem of detecting highly mutable RNA viruses.
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Affiliation(s)
- Charul Gijavanekar
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y. PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics 2009; 25:2438-9. [PMID: 19602525 PMCID: PMC2735671 DOI: 10.1093/bioinformatics/btp429] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Summary: PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and cycle-by-cycle graphical representation of clusters density, quality scores and nucleotide frequencies allow easy identification of various technical problems including defective tiles, mistakes in sample/library preparations and abnormalities in the frequencies of appearance of sequenced genomic reads. PIQA is written in the R statistical programming language and is compatible with bustard, fastq and scarf Illumina G1 Genome Analyzer data formats. Availability: The PIQA pipeline, installation instructions and examples are available at the supplementary web site (http://bioinfo.uh.edu/PIQA). Contact:yfofanov@bioinfo.uh.edu
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Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y. Ultraspecific probes for high throughput HLA typing. BMC Genomics 2009; 10:85. [PMID: 19232123 PMCID: PMC2661095 DOI: 10.1186/1471-2164-10-85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 02/20/2009] [Indexed: 11/23/2022] Open
Abstract
Background The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. Results We present a novel three-step approach for the design of high-throughput microarray assays for HLA typing. This approach first selects sequences containing the SNPs present in all alleles of the locus of interest and next calculates the number of base changes necessary to convert a candidate probe sequences to the closest subsequence within the set of sequences that are likely to be present in the sample including the remainder of the human genome in order to identify those candidate probes which are "ultraspecific" for the allele of interest. Due to the high specificity of these sequences, it is possible that preliminary steps such as PCR amplification are no longer necessary. Lastly, the minimum number of these ultraspecific probes is selected such that the highest resolution typing can be achieved for the minimal cost of production. As an example, an array was designed and in silico results were obtained for typing of the HLA-B locus. Conclusion The assay presented here provides a higher resolution than has previously been developed and includes more alleles than previously considered. Based upon the in silico and preliminary experimental results, we believe that the proposed approach can be readily applied to any highly polymorphic gene system.
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Affiliation(s)
- Chen Feng
- Department of Computer Science, University of Houston, Houston, TX, USA.
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Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y. Effect of the mutation rate and background size on the quality of pathogen identification. ACTA ACUST UNITED AC 2007; 23:2665-71. [PMID: 17881407 DOI: 10.1093/bioinformatics/btm420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Genomic-based methods have significant potential for fast and accurate identification of organisms or even genes of interest in complex environmental samples (air, water, soil, food, etc.), especially when isolation of the target organism cannot be performed by a variety of reasons. Despite this potential, the presence of the unknown, variable and usually large quantities of background DNA can cause interference resulting in false positive outcomes. RESULTS In order to estimate how the genomic diversity of the background (total length of all of the different genomes present in the background), target length and target mutation rate affect the probability of misidentifications, we introduce a mathematical definition for the quality of an individual signature in the presence of a background based on its length and number of mismatches needed to transform the signature into the closest subsequence present in the background. This definition, in conjunction with a probabilistic framework, allows one to predict the minimal signature length required to identify the target in the presence of different sizes of backgrounds and the effect of the target's mutation rate on the quality of its identification. The model assumptions and predictions were validated using both Monte Carlo simulations and real genomic data examples. The proposed model can be used to determine appropriate signature lengths for various combinations of target and background genome sizes. It also predicted that any genomic signatures will be unable to identify target if its mutation rate is >5%. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chris Reed
- Department of Computer Science, University of Houston, 501 Philip G. Hoffman Hall, Houston, TX 77204, USA
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Añez M, Putonti C, Fox GE, Fofanov Y, Willson RC. Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers. J Biotechnol 2007; 133:267-76. [PMID: 17996971 DOI: 10.1016/j.jbiotec.2007.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 08/23/2007] [Accepted: 09/05/2007] [Indexed: 01/19/2023]
Abstract
We recently developed novel algorithms for exhaustive identification of all nucleotide subsequences present in a pathogen genome which differ by at least a chosen number of mismatches from the sequences of host/background organisms. This type of exhaustive computational analysis will be useful in reducing false positives and cross-reactivity in PCR and hybridization assays. We present the first experimental test of the method by showing that the subsequences identified when used as 18-mer PCR primers can detect the presence of dengue virus (DENV) even in the presence of a large excess of complex human genomic DNA. From our computations, 715 serotype-specific primer pairs were identified for three different DENV serotypes in which each primer sequence lies at least two mismatches from the nearest human sequence. DNA clones of representative strains of DENV-1, DENV-2, and DENV-4 viruses were subjected to real-time PCR testing using eight primer pairs each. Efficiencies were uniformly very high (mean+/-S.D.=99.6+/-3%), and amplification of human DNA was never observed within 35 cycles, even at a 5.5-fold molar excess of human DNA. Exhaustive primer/probe screening can potentially produce more selective and sensitive diagnostic assays for pathogens, especially in the presence of complex backgrounds.
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Affiliation(s)
- Mariaclara Añez
- Department of Chemical and Biomolecular Engineering, University of Houston, 4800 Calhoun Road, Houston, TX 77204-4004, United States
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Putonti C, Pettitt B, Reid J, Fofanov Y. PIDA:A new algorithm for pattern identification. Online J Bioinform 2007; 8:30-40. [PMID: 19834570 PMCID: PMC2761635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Algorithms for motif identification in sequence space have predominately been focused on recognizing patterns of a fixed length containing regions of perfect conservation with possible regions of unconstrained sequence. Such motifs can be found in everything from proteins with distinct active sites to non-coding RNAs with specific structural elements that are necessary to maintain functionality. In the event that an insertion/deletion has occurred within an unconstrained portion of the pattern, it is possible that the pattern retains its functionality. In such a case the length of the pattern is now variable and may be overlooked when utilizing existing motif detection methods. The Pattern Island Detection Algorithm (PIDA) presented here has been developed to recognize patterns that have occurrences of varying length within sequences of any size alphabet. PIDA works by identifying all regions of perfect conservation (for lengths longer than a user-specified threshold), and then builds those conservation "islands" into fixed-length patterns. Next the algorithm modifies these fixed-length patterns by identifying additional (and different) islands that can be incorporated into each pattern through insertions/deletions within the "water" separating the islands. To provide some benchmarks for this analysis, PIDA was used to search for patterns within randomly generated sequences as well as sequences known to contain conserved patterns. For each of the patterns found, the statistical significance is calculated based upon the pattern's likelihood to appear by chance, thus providing a means to determine those patterns which are likely to have a functional role. The PIDA approach to motif finding is designed to perform best when searching for patterns of variable length although it is also able to identify patterns of a fixed length. PIDA has been created to be as generally applicable as possible since there are a variety of sequence problems of this type. The algorithm was implemented in C++ and is freely available upon request from the authors.
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Affiliation(s)
- C Putonti
- Department of Computer Science, University of Houston, Houston, Texas, USA
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Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol 2006; 23:1863-8. [PMID: 16829541 DOI: 10.1093/molbev/msl053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Similarity Plot (S-plot) is a Windows-based application for large-scale comparisons and 2-dimensional visualization of compositional similarities between genomic sequences. This application combines 2 approaches widely used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in identifying highly similar regions between genomes as well as regions with unusual compositional properties (RUCPs) within a single genome, which may be indicative of horizontal gene transfer or of locus-specific selective forces. We use S-plot to identify regions that may have originated through horizontal gene transfer through a 2-step approach, by first comparing a genomic sequence to itself and, subsequently, comparing it to the genomic sequence of a closely related taxon. Moreover, by comparing these suspect sequences to one another, we can estimate a minimum number of sources for these putative xenologous sequences. We illustrate the uses of S-plot in a comparison involving Escherichia coli K12 and E. coli O157:H7. In O157:H7, we found 145 regions that have most probably originated through horizontal gene transfer. By using S-plot to compare each of these regions with 277 completely sequenced prokaryotic genomes, 1 sequence was found to have similar compositional properties to the Yersinia pseudotuberculosis genome, indicating a transfer from a Yersinia or Yersinia relative. Based upon our analysis of RUCPs in O157:H7, we infer that there were at least 53 sources of horizontally transferred sequences.
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Chumakov S, Ballesteros E, Rodriguez Sanchez JE, Chavez A, Zhang M, Pettit BM, Fofanov Y. Using Mutual Information to Discover Temporal Patterns in Gene Expression Data. Med Phys Mex Symp Med Phys 2006; 854:25-30. [PMID: 20428481 PMCID: PMC2860312 DOI: 10.1063/1.2356392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Finding relations among gene expressions involves the definition of the similarity between experimental data. A simplest similarity measure is the Correlation Coefficient. It is able to identify linear dependences only; moreover, is sensitive to experimental errors. An alternative measure, the Shannon Mutual Information (MI), is free from the above mentioned weaknesses. However, the calculation of MI for continuous variables from the finite number of experimental points, N, involves an ambiguity arising when one divides the range of values of the continuous variable into boxes. Then the distribution of experimental points among the boxes (and, therefore, MI) depends on the box size. An algorithm for the calculation of MI for continuous variables is proposed. We find the optimum box sizes for a given N from the condition of minimum entropy variation with respect to the change of the box sizes. We have applied this technique to the gene expression dataset from Stanford, containing microarray data at 18 time points from yeast Saccharomyces cerevisiae cultures (Spellman et al.,[3]). We calculated MI for all of the pairs of time points. The MI analysis allowed us to identify time patterns related to different biological processes in the cell.
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Affiliation(s)
- Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco 44420, Mexico
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