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Minias A, Żukowska L, Lechowicz E, Gąsior F, Knast A, Podlewska S, Zygała D, Dziadek J. Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. Front Microbiol 2021; 11:618168. [PMID: 33603720 PMCID: PMC7884339 DOI: 10.3389/fmicb.2020.618168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, the disease is one of the top 10 causes of death of people worldwide. Mycobacterium tuberculosis is an intracellular pathogen with an unusually thick, waxy cell wall and a complex life cycle. These factors, combined with M. tuberculosis ability to enter prolonged periods of latency, make the bacterium very difficult to eradicate. The standard treatment of TB requires 6-20months, depending on the drug susceptibility of the infecting strain. The need to take cocktails of antibiotics to treat tuberculosis effectively and the emergence of drug-resistant strains prompts the need to search for new antitubercular compounds. This review provides a perspective on how modern -omic technologies facilitate the drug discovery process for tuberculosis treatment. We discuss how methods of DNA and RNA sequencing, proteomics, and genetic manipulation of organisms increase our understanding of mechanisms of action of antibiotics and allow the evaluation of drugs. We explore the utility of mathematical modeling and modern computational analysis for the drug discovery process. Finally, we summarize how -omic technologies contribute to our understanding of the emergence of drug resistance.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Lidia Żukowska
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Ewelina Lechowicz
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Filip Gąsior
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Agnieszka Knast
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Krakow, Poland
- Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - Daria Zygała
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Manicheva OA, Dogonadze MZ, Melnikova NN, Vishnevskiy BI, Manichev SA. THE GROWTH RATE PHENOTYPIC PROPERTY OF MYCOBACTERIUM TUBERCULOSIS CLINICAL STRAINS: DEPENDENCE ON TUBERCULOSIS LOCALIZATION, TREATMENT, DRUG SUSCEPTIBILITY. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2018. [DOI: 10.15789/2220-7619-2018-2-175-186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phenotypic properties of the M. tuberculosis strains obtained from patients with pulmonary or extra-pulmonary tuberculosis are determined by a complex set of factors: the genetic characteristics of the pathogen, its ability to adapt in vivo and in vitro, the influence of the host’s immune system and chemotherapy. The growth rate as the phenotypic property is the most accessible for the study of the host-pathogen relationships at the level of host/strain population interactions. The aim of the study is to assess in vitro of the growth rate of M. tuberculosis strains isolated from patients with pulmonary and extra-pulmonary tuberculosis: untreated and treated (with surgical and non-surgical treatment) and also sensitive and resistant isolates in comparison with the reference strain H37Rv. To estimate the growth rate of 116 clinical isolates we have used the modified method originally developed by von Groll and co-authors: to get the bacteria growth curve the fluorescence intensity of growing strains (with indicator resazurin) has been measured daily for 8 days in 96- well plate. The growth rate is determined as the slope of the growth curve. The mean values of the growth rate have been calculated in the following groups of patients: 1 — untreated patients with pulmonary tuberculosis (PT), respiratory material; 2 — non-surgical treated PT patients, respiratory material; 3 — surgical treated PT patients (mainly with chronic and hyperchronic process), respiratory material; 4 — patients like in 3rd group, surgical material; 5 — bone and joint tuberculosis (BJT), surgical material. In addition, groups of sensitive and resistant strains have been examined, but there are no significant differences in growth rates. It has been obtained that the growth rate of strains isolated from the PT patients is higher than in BJT patients: it can be explained less favorable conditions for the pathogen vegetation in the BJT. In the case of a closed tuberculous lesion where the pathogen transmission to another host is impossible, then the selection of strains with the property to survive in the tissues of the osteoarticular system is impossible too, therefor it should be observed only an adaptation of the pathogen strain population to the individual host. The growth rate of isolates from untreated PT patients is higher than that of the treated ones. Comparison of the growth parameters of only MDR strains 1–5 groups to eliminate the influence of the sensitivity/resistance has resulted in the same conclusions. We suggest that the decrease in the growth rate of strains from the treated PT patients is in not only result of the treatment, but also is conditioned by adaptation of the pathogen to its external environment, which is the internal environment of the macroorganism. To confirm this assumption, the bacterial load of 1,083 diagnostic specimens grouped in a similar manner has been estimated, taking into account only MDR/XDR strains. In the group of treated patients the frequency of high bacterial load (CFU ≥ 100) reached 52.5–63.8% that shows the conserved fitness of bacteria in such patients. The mean values of the growth rate of the strain H37Rv non-adapted to the macroorganism (due to numerous passages on artificial media) are higher than in all groups of clinical strains. Thus, heterogeneity of phenotypic properties of M. tuberculosis clinical strains on the basis of growth rate has been obtained. The growth rate of M. tuberculosis clinical strains is depended on the tuberculosis localization (PT, BJT) and on the joint effect of patient treatment and pathogen adaptation to the host.
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Chinsembu KC. Tuberculosis and nature's pharmacy of putative anti-tuberculosis agents. Acta Trop 2016; 153:46-56. [PMID: 26464047 DOI: 10.1016/j.actatropica.2015.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 01/13/2023]
Abstract
Due to the growing problem of drug resistant Mycobacterium tuberculosis strains, coupled with the twinning of tuberculosis (TB) to human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), the burden of TB is now difficult to manage. Therefore, new antimycobacterial agents are being sought from natural sources. This review focuses on natural antimycobacterial agents from endophytes and medicinal plants of Africa, Europe, Asia, South America and Canada. In the countries mentioned in this review, numerous plant species display putative anti-TB activity. Several antimycobacterial chemical compounds have also been isolated, including: ellagitannin punicalagin, allicin, anthraquinone glycosides, iridoids, phenylpropanoids, beta-sitosterol, galanthimine, crinine, friedelin, gallic acid, ellagic acids, anthocyanidin, taraxerol, termilignan B, arjunic acid, glucopyranosides, 1-epicatechol, leucopelargonidol, hydroxybenzoic acids, benzophenanthridine alkaloids, neolignans, and decarine. These compounds may provide leads to novel and more efficacious drugs to lessen the global burden of TB and drug-resistant M. tuberculosis strains. If there is a long-term remedy for TB, it must lie in nature's pharmacy of putative antimycobacterial agents.
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Affiliation(s)
- Kazhila C Chinsembu
- University of Namibia, Faculty of Science, Department of Biological Sciences, Private Bag 13301, Windhoek, Namibia.
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4
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Architectural plan of transcriptional regulation in Mycobacterium tuberculosis. Trends Microbiol 2015; 23:123-5. [PMID: 25701110 DOI: 10.1016/j.tim.2015.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 11/22/2022]
Abstract
Transcriptional regulation enables adaptation in bacteria. Typically, only a few transcriptional events are well understood, leaving many others unidentified. The recent genome-wide identification of transcription factor binding sites in Mycobacterium tuberculosis has changed this by deciphering a molecular road-map of transcriptional control, indicating active events and their immediate downstream effects.
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Gupta S, Chavan S, Deobagkar DN, Deobagkar DD. Bio/chemoinformatics in India: an outlook. Brief Bioinform 2014; 16:710-31. [PMID: 25159593 DOI: 10.1093/bib/bbu028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/28/2014] [Indexed: 12/25/2022] Open
Abstract
With the advent of significant establishment and development of Internet facilities and computational infrastructure, an overview on bio/chemoinformatics is presented along with its multidisciplinary facts, promises and challenges. The Government of India has paved the way for more profound research in biological field with the use of computational facilities and schemes/projects to collaborate with scientists from different disciplines. Simultaneously, the growth of available biomedical data has provided fresh insight into the nature of redundant and compensatory data. Today, bioinformatics research in India is characterized by a powerful grid computing systems, great variety of biological questions addressed and the close collaborations between scientists and clinicians, with a full spectrum of focuses ranging from database building and methods development to biological discoveries. In fact, this outlook provides a resourceful platform highlighting the funding agencies, institutes and industries working in this direction, which would certainly be of great help to students seeking their career in bioinformatics. Thus, in short, this review highlights the current bio/chemoinformatics trend, educations, status, diverse applicability and demands for further development.
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Vasakova M. Challenges of antituberculosis treatment in patients with difficult clinical conditions. CLINICAL RESPIRATORY JOURNAL 2014; 9:143-52. [DOI: 10.1111/crj.12119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/30/2014] [Accepted: 02/06/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Martina Vasakova
- Department of Respiratory Medicine; Thomayer Hospital Prague; Prague Czech Republic
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Shahine AE, Chan PY, Littler D, Vivian J, Brammananth R, Crellin PK, Coppel RL, Rossjohn J, Beddoe T. Cloning, expression, purification and preliminary X-ray diffraction studies of a mycobacterial protein implicated in bacterial survival in macrophages. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:566-9. [PMID: 23695579 PMCID: PMC3660903 DOI: 10.1107/s1744309113010427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 04/16/2013] [Indexed: 11/10/2022]
Abstract
Mycobacterium species have developed numerous strategies to avoid the antimycobacterial actions of macrophages, enabling them to survive within the generally inhospitable environment of the cell. The recently identified MSMEG_5817 protein from M. smegmatis is highly conserved in Mycobacterium spp. and is required for bacterial survival in macrophages. Here, the cloning, expression, purification and crystallization of MSMEG_5817 is reported. Crystals of MSMEG_5817 were grown in 1.42 M Li2SO4, 0.1 M Tris-HCl pH 7.7, 0.1 M sodium citrate tribasic dihydrate. Native and multiple-wavelength anomalous dispersion (MAD) data sets have been collected and structure determination is in progress.
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Affiliation(s)
- Adam E. Shahine
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - Phooi Y. Chan
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dene Littler
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - Julian Vivian
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - Rajini Brammananth
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Paul K. Crellin
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Ross L. Coppel
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
| | - Travis Beddoe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Australian Research Council (ARC) Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, Australia
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Affiliation(s)
- Nagasuma Chandra
- Indian Institute of Science, Department of Biochemistry,
Bangalore – 560012, India ,
| | - Jyothi Padiadpu
- Indian Institute of Science, Department of Biochemistry,
Bangalore – 560012, India
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9
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Vashisht R, Mondal AK, Jain A, Shah A, Vishnoi P, Priyadarshini P, Bhattacharyya K, Rohira H, Bhat AG, Passi A, Mukherjee K, Choudhary KS, Kumar V, Arora A, Munusamy P, Subramanian A, Venkatachalam A, S G, Raj S, Chitra V, Verma K, Zaheer S, J B, Gurusamy M, Razeeth M, Raja I, Thandapani M, Mevada V, Soni R, Rana S, Ramanna GM, Raghavan S, Subramanya SN, Kholia T, Patel R, Bhavnani V, Chiranjeevi L, Sengupta S, Singh PK, Atray N, Gandhi S, Avasthi TS, Nisthar S, Anurag M, Sharma P, Hasija Y, Dash D, Sharma A, Scaria V, Thomas Z, Chandra N, Brahmachari SK, Bhardwaj A. Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PLoS One 2012; 7:e39808. [PMID: 22808064 PMCID: PMC3395720 DOI: 10.1371/journal.pone.0039808] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 05/30/2012] [Indexed: 11/18/2022] Open
Abstract
A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.
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Affiliation(s)
- Rohit Vashisht
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Akanksha Jain
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Anup Shah
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Priti Vishnoi
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | | | - Harsha Rohira
- Acharya Narendra Dev College, University of Delhi, India
| | - Ashwini G. Bhat
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Anurag Passi
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Keya Mukherjee
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | | | - Anshula Arora
- Acharya Narendra Dev College, University of Delhi, India
| | | | | | | | | | - Sweety Raj
- Acharya Narendra Dev College, University of Delhi, India
| | - Vijaya Chitra
- Sree Narayan Guru College, Coimbatore, Tamil Nadu, India
| | - Kaveri Verma
- Maharshi Dayanand University, Rohtak, Haryana, India
| | - Salman Zaheer
- Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, India
| | - Balaganesh J
- Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Mohammed Razeeth
- Bharathidasan University, Palkalaiperur, Tiruchirappall, Tamil Nadu, India
| | - Ilamathi Raja
- Bharathidasan University, Palkalaiperur, Tiruchirappall, Tamil Nadu, India
| | | | - Vishal Mevada
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | - Raviraj Soni
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | - Shruti Rana
- Bitvirtual patan Node, Hem. North Gujarat University, Patan, Gujarat, India
| | | | - Swetha Raghavan
- Business Intelligence Technologies India Pvt Ltd., Bangalore, Karnataka, India
| | - Sunil N. Subramanya
- Business Intelligence Technologies India Pvt Ltd., Bangalore, Karnataka, India
| | - Trupti Kholia
- Christ College, Vidya Niketan, Saurashtra University, Rajkot, Gujarat, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Varsha Bhavnani
- Department of Biotechnology, University of Pune, Maharashtra State, India
| | | | - Soumi Sengupta
- Indian Statistical Institute, Kolkata, West Bengal, India
| | - Pankaj Kumar Singh
- Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh, India
| | - Naresh Atray
- Shri Ram College of Pharmacy, Karnal, Haryana, India
| | - Swati Gandhi
- The Maharaj Sayajirao University of Baroda, Gujarat, India
| | - Tiruvayipati Suma Avasthi
- Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, Andhra Pradesh, India
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Meenakshi Anurag
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | | | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - Debasis Dash
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Arun Sharma
- Bioinformatics Centre, Institute of Microbial Technology, CSIR, Chandigarh, India
| | - Vinod Scaria
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Zakir Thomas
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - OSDD Consortium
- Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail: (SKB); (NC); (AB)
| | - Samir K. Brahmachari
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
- * E-mail: (SKB); (NC); (AB)
| | - Anshu Bhardwaj
- Council of Scientific and Industrial Research (CSIR), Delhi, India
- * E-mail: (SKB); (NC); (AB)
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Bothamley G. Supporting health systems for tuberculosis through research. Tuberculosis (Edinb) 2012; 92:289; athor reply 290. [PMID: 22687424 DOI: 10.1016/j.tube.2012.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/13/2012] [Indexed: 11/18/2022]
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Abstract
The remarkable advances in TB vaccinology over the last decade have been driven by a pragmatic approach to moving candidates along the development pipeline to clinical trials, fuelled by encouraging data on protection in animal models. Efficacy data from Phase IIb trials of the first generation of new candidates are anticipated over the next 1-2 years. As outlined in the TB Vaccines Strategic Blueprint, to exploit this information and to inspire design of next generation candidates, it is important that this empirical approach is complemented by progress in understanding of fundamental immune mechanisms and improved translational modalities. Current trends towards improved experimental and computational approaches for studying biological complexity will be an important element in the developing science of TB vaccinology.
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Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M. Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. MICROBIAL INFORMATICS AND EXPERIMENTATION 2012; 2:4. [PMID: 22587966 PMCID: PMC3353838 DOI: 10.1186/2042-5783-2-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 03/21/2012] [Indexed: 11/30/2022]
Abstract
Background Protein-protein interaction (PPI) networks (interactomes) of most organisms, except for some model organisms, are largely unknown. Experimental methods including high-throughput techniques are highly resource intensive. Therefore, computational discovery of PPIs can accelerate biological discovery by presenting "most-promising" pairs of proteins that are likely to interact. For many bacteria, genome sequence, and thereby genomic context of proteomes, is readily available; additionally, for some of these proteomes, localization and functional annotations are also available, but interactomes are not available. We present here a method for rapid development of computational system to predict interactome of bacterial proteomes. While other studies have presented methods to transfer interologs across species, here, we propose transfer of computational models to benefit from cross-species annotations, thereby predicting many more novel interactions even in the absence of interologs. Mycobacterium tuberculosis (Mtb) and Clostridium difficile (CD) have been used to demonstrate the work. Results We developed a random forest classifier over features derived from Gene Ontology annotations and genetic context scores provided by STRING database for predicting Mtb and CD interactions independently. The Mtb classifier gave a precision of 94% and a recall of 23% on a held out test set. The Mtb model was then run on all the 8 million protein pairs of the Mtb proteome, resulting in 708 new interactions (at 94% expected precision) or 1,595 new interactions at 80% expected precision. The CD classifier gave a precision of 90% and a recall of 16% on a held out test set. The CD model was run on all the 8 million protein pairs of the CD proteome, resulting in 143 new interactions (at 90% expected precision) or 580 new interactions (at 80% expected precision). We also compared the overlap of predictions of our method with STRING database interactions for CD and Mtb and also with interactions identified recently by a bacterial 2-hybrid system for Mtb. To demonstrate the utility of transfer of computational models, we made use of the developed Mtb model and used it to predict CD protein-pairs. The cross species model thus developed yielded a precision of 88% at a recall of 8%. To demonstrate transfer of features from other organisms in the absence of feature-based and interaction-based information, we transferred missing feature values from Mtb orthologs into the CD data. In transferring this data from orthologs (not interologs), we showed that a large number of interactions can be predicted. Conclusions Rapid discovery of (partial) bacterial interactome can be made by using existing set of GO and STRING features associated with the organisms. We can make use of cross-species interactome development, when there are not even sufficient known interactions to develop a computational prediction system. Computational model of well-studied organism(s) can be employed to make the initial interactome prediction for the target organism. We have also demonstrated successfully, that annotations can be transferred from orthologs in well-studied organisms enabling accurate predictions for organisms with no annotations. These approaches can serve as building blocks to address the challenges associated with feature coverage, missing interactions towards rapid interactome discovery for bacterial organisms. Availability The predictions for all Mtb and CD proteins are made available at: http://severus.dbmi.pitt.edu/TB and http://severus.dbmi.pitt.edu/CD respectively for browsing as well as for download.
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Affiliation(s)
- Seshan Ananthasubramanian
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh 15260, USA.,Intelligent Systems Program, University of Pittsburgh, Pittsburgh 15260, USA
| | - Rahul Metri
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Aman Gupta
- Birla Institute of Technology and Science, Pilani, India
| | - Adam Handen
- Rochester Institute of Technology, Henrietta, USA
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Madhavi Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh 15260, USA.,Intelligent Systems Program, University of Pittsburgh, Pittsburgh 15260, USA
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Finlay EK, Berry DP, Wickham B, Gormley EP, Bradley DG. A genome wide association scan of bovine tuberculosis susceptibility in Holstein-Friesian dairy cattle. PLoS One 2012; 7:e30545. [PMID: 22355315 PMCID: PMC3280253 DOI: 10.1371/journal.pone.0030545] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 12/19/2011] [Indexed: 11/25/2022] Open
Abstract
Background Bovine tuberculosis is a significant veterinary and financial problem in many parts of the world. Although many factors influence infection and progression of the disease, there is a host genetic component and dissection of this may enlighten on the wider biology of host response to tuberculosis. However, a binary phenotype of presence/absence of infection presents a noisy signal for genomewide association study. Methodology/Principal Findings We calculated a composite phenotype of genetic merit for TB susceptibility based on disease incidence in daughters of elite sires used for artificial insemination in the Irish dairy herd. This robust measure was compared with 44,426 SNP genotypes in the most informative 307 subjects in a genome wide association analysis. Three SNPs in a 65 kb genomic region on BTA 22 were associated (i.e. p<10−5, peaking at position 59588069, p = 4.02×10−6) with tuberculosis susceptibility. Conclusions/Significance A genomic region on BTA 22 was suggestively associated with tuberculosis susceptibility; it contains the taurine transporter gene SLC6A6, or TauT, which is known to function in the immune system but has not previously been investigated for its role in tuberculosis infection.
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Affiliation(s)
- Emma K. Finlay
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
| | - Donagh P. Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, County Cork, Ireland
| | - Brian Wickham
- Irish Cattle Breeding Federation, Shinagh House, Bandon, County Cork, Ireland
| | - Eamonn P. Gormley
- School of Agriculture, Food Science and Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Daniel G. Bradley
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
- * E-mail:
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