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Thapliyal P, Sah V, Rautela I, Joshi M, Tyagi S, Verma R, Sharma MD. Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks. Pathol Res Pract 2024; 263:155606. [PMID: 39357183 DOI: 10.1016/j.prp.2024.155606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/03/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.
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Affiliation(s)
- Priya Thapliyal
- Department of Biochemistry, H.N.B. Garhwal (A Central) University, Srinagar, Uttarakhand 246174, India
| | - Vijayalaxmi Sah
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, Uttarakhand 248001, India
| | - Indra Rautela
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, Uttarakhand 248001, India
| | - Mallika Joshi
- Department of Biotechnology, Chandigarh University, Gharaun, Mohali, Punjab 140413, India
| | - Sheetal Tyagi
- Department of Chemistry, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India
| | - Rashmi Verma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India.
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Sharma GK, Sharma R, Joshi K, Qureshi S, Mathur S, Sinha S, Chatterjee S, Nunia V. Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection. Brief Bioinform 2024; 25:bbae545. [PMID: 39441245 PMCID: PMC11497845 DOI: 10.1093/bib/bbae545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 09/21/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024] Open
Abstract
Sequences derived from organisms sharing common evolutionary origins exhibit similarity, while unique sequences, absent in related organisms, act as good diagnostic marker candidates. However, the approach focused on identifying dissimilar regions among closely-related organisms poses challenges as it requires complex multiple sequence alignments, making computation and parsing difficult. To address this, we have developed a biologically inspired universal NAUniSeq algorithm to find the unique sequences for microorganism diagnosis by traveling through the phylogeny of life. Mapping through a phylogenetic tree ensures a low number of cross-contamination and false positives. We have downloaded complete taxonomy data from Taxadb database and sequence data from National Center for Biotechnology Information Reference Sequence Database (NCBI-Refseq) and, with the help of NetworkX, created a phylogenetic tree. Sequences were assigned over the graph nodes, k-mers were created for target and non-target nodes and search was performed over the graph using the depth first search algorithm. In a memory efficient alternative NoSQL approach, we created a collection of Refseq sequences in MongoDB database using tax-id and path of FASTA files. We queried the MongoDB collection for the target and non-target sequences. In both the approaches, we used an alignment free sliding window k-mer-based procedure that quickly compares k-mers of target and non-target sequences and returns unique sequences that are not present in the non-target. We have validated our algorithm with target nodes Mycobacterium tuberculosis, Neisseria gonorrhoeae, and Monkeypox and generated unique sequences. This universal algorithm is a powerful tool for generating diagnostic sequences, enabling the accurate identification of microbial strains with high phylogenetic precision.
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Affiliation(s)
- Gulshan Kumar Sharma
- Malaviya National Institute of Technology, Jawahar Lal Nehru Marg, Jhalana Gram, Malviya Nagar, Jaipur, Rajasthan 302017, India
| | - Rakesh Sharma
- Centre for Converging Technologies, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Kavita Joshi
- Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Sameer Qureshi
- Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Shubhita Mathur
- Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Sharad Sinha
- Department of Mathematics, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Samit Chatterjee
- Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
| | - Vandana Nunia
- Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India
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Hashemi Shahraki A, Vahed M, Mirsaeidi M. Genome sequencing of Pseudomonas aeruginosa phages; UF_RH7 and UF_RH9. Microbiol Resour Announc 2024; 13:e0105023. [PMID: 38483455 PMCID: PMC11008205 DOI: 10.1128/mra.01050-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/03/2024] [Indexed: 04/12/2024] Open
Abstract
We have sequenced the genomes of two lytic phages, UF_RH7 and UF_RH9, which infect Pseudomonas aeruginosa. UF_RH7 belongs to Casjensviridae family and has a genome length of 58,217 bp and encodes 82 proteins. UF_RH9 belongs to Caudoviricetes class and has a genome length of 42,609 bp and encodes 55 proteins.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
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Khamnuan S, Phrutivorapongkul A, Pitchakarn P, Buacheen P, Karinchai J, Chittasupho C, Na Takuathung M, Theansungnoen T, Thongkhao K, Intharuksa A. The Identification and Cytotoxic Evaluation of Nutmeg ( Myristica fragrans Houtt.) and Its Substituents. Foods 2023; 12:4211. [PMID: 38231602 DOI: 10.3390/foods12234211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The aril and seed of nutmeg, Myristica fragrans Houtt. (Myristicaceae), hold significant value in various industries globally. Our preliminary research found two morphological variations: a globose shape and an oval shape. Due to these different characteristics, the safety of consumers is of primary concern. Thus, authentication and comparative pharmacological and toxicity analyses are necessary. In this study, pharmacognostic and advanced phytochemical analyses, DNA barcoding, cytotoxicity, and the anti-nitric oxide production of commercial Thai nutmeg were examined. Via morphologic examinations and TLC fingerprinting, all the sampled aril and seed were categorized into globose and oval-shaped groups. The results of HPLC, GC-MS, and LC-MS/MS experiments revealed distinct differences between these groups. The DNA barcoding of the trnH-psbA region using the BLAST method and neighbor-joining tree analyses confirmed the globose nutmeg as M. fragrans and the oval-shaped variant as M. argentea. A comparison was then carried out between the potential toxicity and anti-inflammatory capabilities of M. fragrans and M. argentea. Cytotoxicity tests on HaCaT, 3T3-L1, Caco-2, HEK293, and RAW264.7 were performed using both methanolic extracts and volatile oil from the arils and seeds of both species. This study concludes that blending or substituting these two species maintains their therapeutic integrity without posing safety concerns.
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Affiliation(s)
- Suthiwat Khamnuan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Suthep, Mueang, Chiang Mai 50200, Thailand
| | - Ampai Phrutivorapongkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Suthep, Mueang, Chiang Mai 50200, Thailand
| | - Pornsiri Pitchakarn
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pensiri Buacheen
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jirarat Karinchai
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chuda Chittasupho
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Suthep, Mueang, Chiang Mai 50200, Thailand
| | - Mingkwan Na Takuathung
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Clinical Research Center for Food and Herbal Product Trials and Development (CR-FAH), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Tinnakorn Theansungnoen
- Green Cosmetic Technology Research Group, School of Cosmetic Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Kannika Thongkhao
- School of Languages and General Education, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Aekkhaluck Intharuksa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Suthep, Mueang, Chiang Mai 50200, Thailand
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Hashemi Shahraki A, Vahed M, Dinparastisaleh R, Mirsaeidi M. Complete Genome Sequencing of a Novel Pseudomonas aeruginosa Phage, UF_RH5. Microbiol Resour Announc 2023:e0039623. [PMID: 37338387 DOI: 10.1128/mra.00396-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Here, we introduce UF_RH5, a novel lytic phage targeting clinically isolated Pseudomonas aeruginosa. It belongs to the Siphovirus morphology family, Septimatrevirus genus, with a 42,566-bp genome with a GC content of 53.60%, encoding 58 proteins. Under electron microscopy, UF_RH5 exhibits a length of 121 nm and a capsid size of 45 nm.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Roshan Dinparastisaleh
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
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Adenaike O, Olabanjo OE, Adedeji AA. Integrating computational skills in undergraduate Microbiology curricula in developing countries. Biol Methods Protoc 2023; 8:bpad008. [PMID: 37396465 PMCID: PMC10310463 DOI: 10.1093/biomethods/bpad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
The employability of young graduates has gained increasing significance in the labour market of the 21st century. Universities turn out millions of graduates annually, but at the same time, employers highlight their lack of the requisite skills for sustainable employment. We live today in a world of data, and therefore courses that feature numerical and computational tools to gather and analyse data are to be sourced for and integrated into life sciences' curricula as they provide a number of benefits for both the students and faculty members that are engaged in teaching the courses. The lack of this teaching in undergraduate Microbiology curricula is devastating and leaves a knowledge gap in the graduates that are turned out. This results in an inability of the emerging graduates to compete favourably with their counterparts from other parts of the world. There is a necessity on the part of life science educators to adapt their teaching strategies to best support students' curricula that prepare them for careers in science. Bioinformatics, Statistics and Programming are key computational skills to embrace by life scientists and the need for training beginning at undergraduate level cannot be overemphasized. This article reviews the need to integrate computational skills in undergraduate Microbiology curricula in developing countries with emphasis on Nigeria.
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Affiliation(s)
- Omolara Adenaike
- Correspondence address. Department of Biological Sciences (Microbiology Unit), Oduduwa University, Ipetumodu, Nigeria. Tel: +2348061278100; E-mail:
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Recent Applications and Strategies to Enhance Performance of Electrochemical Reduction of CO2 Gas into Value-Added Chemicals Catalyzed by Whole-Cell Biocatalysts. Processes (Basel) 2023. [DOI: 10.3390/pr11030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Carbon dioxide (CO2) is one of the major greenhouse gases that has been shown to cause global warming. Decreasing CO2 emissions plays an important role to minimize the impact of climate change. The utilization of CO2 gas as a cheap and sustainable source to produce higher value-added chemicals such as formic acid, methanol, methane, and acetic acid has been attracting much attention. The electrochemical reduction of CO2 catalyzed by whole-cell biocatalysts is a promising process for the production of value-added chemicals because it does not require costly enzyme purification steps and the supply of exogenous cofactors such as NADH. This study covered the recent applications of the diversity of microorganisms (pure cultures such as Shewanella oneidensis MR1, Sporomusa species, and Clostridium species and mixed cultures) as whole-cell biocatalysts to produce a wide range of value-added chemicals including methane, carboxylates (e.g., formate, acetate, butyrate, caproate), alcohols (e.g., ethanol, butanol), and bioplastics (e.g., Polyhydroxy butyrate). Remarkably, this study provided insights into the molecular levels of the proteins/enzymes (e.g., formate hydrogenases for CO2 reduction into formate and electron-transporting proteins such as c-type cytochromes) of microorganisms which are involved in the electrochemical reduction of CO2 into value-added chemicals for the suitable application of the microorganism in the chemical reduction of CO2 and enhancing the catalytic efficiency of the microorganisms toward the reaction. Moreover, this study provided some strategies to enhance the performance of the reduction of CO2 to produce value-added chemicals catalyzed by whole-cell biocatalysts.
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8
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Balakrishnan S, Rahman RNZRA, Noor NDM, Latip W, Ali MSM. Molecular dynamics simulation and structural analysis of aquaporin Z from an Antarctic Pseudomonas sp. strain AMS3. J Biomol Struct Dyn 2023; 41:11498-11509. [PMID: 36598349 DOI: 10.1080/07391102.2022.2164519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 12/27/2022] [Indexed: 01/05/2023]
Abstract
Aquaporin is a water channel protein that facilitates the movement of water across the cell membrane. Aquaporin from the Antarctic region has been noted for its psychrophilic properties and its ability to perform at a lower temperature but there remains limited understanding of the water mechanism of Antarctic Pseudomonas sp. strain AMS3 However, studies regarding aquaporin isolated from psychrophilic Pseudomonas sp. are still scattered. Recently, the genome sequence of an Antarctic Pseudomonas sp. strain AMS3 revealed a gene sequence encoding for a putative aquaporin designated as AqpZ1 AMS3. In this study, structure analysis and a molecular dynamics (MD) simulation of a predicted model of a fully hydrated aquaporin tetramer embedded in a lipid bilayer was performed at different temperatures for structural flexibility and stability analysis. The MD simulation results revealed that the structures were able to remain stable at low to medium temperatures. The protein was observed to have high flexibility in the loop region as compared to the helices region throughout the simulated temperatures. The selectivity filter and NPA motifs play a major role in solute selectivity and the pore radius of the protein. The structural and functional characterization of this psychrophilic aquaporin provides new insights for the future applications of this protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Balakrishnan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - R N Z R A Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - N D M Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - W Latip
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - M S M Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Benslama Y, Dennouni-Medjati N, Dali-Sahi M, Meziane FZ, Harek Y. Childhood type 1 diabetes mellitus and risk factor of interactions between dietary cow's milk intake and HLA-DR3/DR4 genotype. J Biomol Struct Dyn 2022; 40:10931-10939. [PMID: 34282715 DOI: 10.1080/07391102.2021.1953599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Short-term breastfeeding and early exposure to dairy products into infant diets, may be critical factors for development of type 1 diabetes. In this study, we investigate whether cow's milk proteins are risk factors for type 1 diabetes in genetically susceptible individuals (HLA DR3/DR4) by using statistical analysis and in silico approach. In order to verify the potential risk of the early introduction of cow's milk, we conducted this study to validate the veracity of this hypothesis in our population. We included 121 subjects, 55 type 1 diabetics and 74 controls from the region of Tlemcen (Algeria). Thus, the in silico approach was performed to determine the molecular mimicry region between Bovine serum albumin and beta-lactoglobulin with self-Islet antigen 2 and glutamate decarboxylase 65 by determining their sequences and their 3D structures. The risk factors associated with type 1 diabetes in a genetically predisposed individual (HLA DR3/DR4) retained by the logistic model are: type 1 and type 2 diabetes inheritance, the early introduction of cow's milk before 6 months and breastfeeding less than 9 months. Besides, the epitopes of cow's milk proteins have the capacity to bind to predisposing HLA class II molecules (HLA DR3/DR4) and induce an immune reaction by the secretion of Interleukin 4 (Th2) and Interferon (Th1) which lead to the destruction of pancreatic beta cells. The early introduction of cow's milk proteins in susceptible individuals is considered as risk factors for the pathogenesis of T1DM. The in silico approach confirm that BSA and BLG share sequence and structure homology with IA2 and GAD65.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmine Benslama
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Nouria Dennouni-Medjati
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Majda Dali-Sahi
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Fatima Zahra Meziane
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Yahia Harek
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
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Vij S, Thakur R, Rishi P. Reverse engineering approach: a step towards a new era of vaccinology with special reference to Salmonella. Expert Rev Vaccines 2022; 21:1763-1785. [PMID: 36408592 DOI: 10.1080/14760584.2022.2148661] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Salmonella is responsible for causing enteric fever, septicemia, and gastroenteritis in humans. Due to high disease burden and emergence of multi- and extensively drug-resistant Salmonella strains, it is becoming difficult to treat the infection with existing battery of antibiotics as we are not able to discover newer antibiotics at the same pace at which the pathogens are acquiring resistance. Though vaccines against Salmonella are available commercially, they have limited efficacy. Advancements in genome sequencing technologies and immunoinformatics approaches have solved the problem significantly by giving rise to a new era of vaccine designing, i.e. 'Reverse engineering.' Reverse engineering/vaccinology has expedited the vaccine identification process. Using this approach, multiple potential proteins/epitopes can be identified and constructed as a single entity to tackle enteric fever. AREAS COVERED This review provides details of reverse engineering approach and discusses various protein and epitope-based vaccine candidates identified using this approach against typhoidal Salmonella. EXPERT OPINION Reverse engineering approach holds great promise for developing strategies to tackle the pathogen(s) by overcoming the limitations posed by existing vaccines. Progressive advancements in the arena of reverse vaccinology, structural biology, and systems biology combined with an improved understanding of host-pathogen interactions are essential components to design new-generation vaccines.
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Affiliation(s)
- Shania Vij
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Reena Thakur
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Praveen Rishi
- Department of Microbiology, Panjab University, Chandigarh, India
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11
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Shekhawat U, Roy Chowdhury (Chakravarty) A. Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV. J Biol Phys 2022; 48:399-414. [PMID: 36422744 PMCID: PMC9686260 DOI: 10.1007/s10867-022-09615-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022] Open
Abstract
The hydrophobic force is one of the most dominant factors in protein folding. A protein becomes functional only when it achieves its three-dimensional structure and stability upon folding. For a better understanding of the hydrophobic effects and their function in protein folding, quantitative measurement of the hydrophobicity of amino acid side chains is crucial. Spike protein is the primary structural protein in SARS-CoV-2 and SARS-CoV. This study explores how protein sequences in SARS-CoV-2 and SARS-CoV spike proteins encode hydrophobic interactions. Computational tools/techniques have been utilized to investigate the protein sequences of the spike proteins of SARS-CoV-2 and SARS-CoV. Investigations provided an estimate of hydrophobic distribution and its relative strength, indicating a hydrophobic pattern. Analysis of the spike protein's hydrophobic profile may help identify and treat the virus-caused disease; additionally, it can give an insight into the transmissibility and pathogenicity of the virus.
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Affiliation(s)
- Uma Shekhawat
- School of Engineering and Sciences, G.D. Goenka University, Gurugram, Haryana 122103 India ,Department of Physics, Pt. Jawaharlal Nehru Govt. College, Faridabad, Haryana 121002 India
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12
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Hoque MN, Talukder AK, Saha O, Hasan MM, Sultana M, Rahman ANMA, Das ZC. Antibiogram and virulence profiling reveals multidrug resistant
Staphylococcus aureus
as the predominant aetiology of subclinical mastitis in riverine buffaloes. Vet Med Sci 2022; 8:2631-2645. [DOI: 10.1002/vms3.942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Anup Kumar Talukder
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Otun Saha
- Department of Microbiology Noakhali Science and Technology University Noakhali Bangladesh
- Department of Microbiology University of Dhaka Dhaka Bangladesh
| | - Mehedi Mahmudul Hasan
- Department of Fisheries and Marine Science Noakhali Science and Technology University Noakhali Bangladesh
| | - Munawar Sultana
- Department of Microbiology University of Dhaka Dhaka Bangladesh
| | - ANM Aminoor Rahman
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
| | - Ziban Chandra Das
- Department of Gynecology Obstetrics and Reproductive Health Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) Gazipur Bangladesh
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Nurliana N, Siregar BH, Sari WE, Helmi TZ, Sugito S. Identification of cellulolytic lactic acid bacteria from the intestines of laying hens given AKBISprob based on 16S ribosomal ribonucleic acid gene analysis. Vet World 2022; 15:1650-1656. [PMID: 36185519 PMCID: PMC9394149 DOI: 10.14202/vetworld.2022.1650-1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background and Aim: Supplementation of AKBISprob (developed in a previous study) in feed can improve production efficiency and poultry health, especially laying hens. In addition, it can also increase cellulolytic lactic acid bacteria (LAB) in chicken intestines, but these bacteria are still unknown; thus, they need to be identified. This study aimed to identify cellulolytic LAB in the intestines of laying hens administered AKBISprob based on 16S ribosomal ribonucleic acid (16S rRNA) gene analysis. Materials and Methods: The samples used in this study were 13 LAB isolates from the intestines of laying hens that were given AKBISprob 4%. Cellulolytic LAB DNA was isolated and 16S rRNA gene was amplified by polymerase chain reaction, followed by sequencing, bioinformatics analysis, and phylogenetic tree construction. Results: From 10 cellulolytic LAB isolates with a clear zone of >6 mm, four were selected and their DNA was amplified with BaCF and UniB primers ~1500 bp DNA fragments. Of these, the P31H62 isolate was genetically close to Enterococcus hirae strain 1-1X-16 with 92.90% maximum identity, the P33S52 isolate had homology with Enterococcus mundtii strain ZU 26 with 96.76% maximum identity, and the P33S62 isolate was closely related to E. hirae strain SJ3 with 72.96% maximum identity. The phylogenetic tree revealed that the cellulolytic LAB isolates P31H62 and P33S52 were in one cluster closely related to the genus Enterococcus. Conclusion: This study suggests that the isolates P31H62, P33S62, and P33S52 from the intestines of laying hens administered 4% AKBISprob are cellulolytic LAB belonging to the genus Enterococcus.
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Affiliation(s)
- Nurliana Nurliana
- Laboratory of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Baharuddin Halim Siregar
- Study Program of Veterinary Education, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Wahyu Eka Sari
- Laboratory of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia; Laboratory of Research, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Teuku Zahrial Helmi
- Laboratory of Biochemical, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Sugito Sugito
- Laboratory of Clinic, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
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Jeyaraj A, Subramanian S. Synthesis, optimization, and characterization of biogenic manganese oxide (BioMnOx) by bacterial isolates from mangrove soils with sorbents property towards different toxic metals. Biometals 2022; 35:429-449. [PMID: 35357611 DOI: 10.1007/s10534-022-00378-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/17/2021] [Indexed: 11/02/2022]
Abstract
Manganese oxidizing bacteria, Bacillus mycoides and Bacillus subtilis were isolated from mangrove soils and optimized for the removal of Mn(II) with simultaneous production of biogenic manganese oxide (BioMnOx). The removal rate of Mn(II) was 90% in 48 h for B. mycoides and 72 h for B. subtilis under the optimized conditions at pH 7, temperature 37 °C, 120 rpm, with 1% inoculum containing 10 mM MnCl2. Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), Energy dispersive X-Ray analysis (EDAX), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to characterize the synthesized biogenic manganese oxide. BioMnOx by Bacillus mycoides and Bacillus subtilis were identified as Bixbyite (Mn2O3) and Hausmannite (Mn3O4), respectively, with nano-sized monocrystalline nature. BioMnOx of Bacillus subtilis strain was more efficient in the removal of metals Zn and Co than BioMnOx of Bacillus mycoides except for mercury. The removal property of synthesized BioMnOx could be applied to treat multi-metal containing wastewater.
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Affiliation(s)
- Anitha Jeyaraj
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Sangeetha Subramanian
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India.
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15
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Casas A, Bultelle M, Motraghi C, Kitney R. Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology. Front Bioeng Biotechnol 2022; 9:785131. [PMID: 35083201 PMCID: PMC8784771 DOI: 10.3389/fbioe.2021.785131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences—based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and when it is not the case, to locate the discrepancies and estimate their severity. In terms of reproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps. When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called “construct-matching” and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across the whole construct. Two algorithms (called CM_1 and CM_2) are presented. They differ according to the nature of their inputs. CM_1 is the core algorithm for construct-matching and is to be used when input sequences are long enough to cover constructs in their entirety (e.g., obtained with methods such as next generation sequencing). CM_2 is an extension designed to deal with shorter data (e.g., obtained with Sanger sequencing), and that need recombining. Both algorithms are shown to yield accurate construct-matching in a few minutes (even on hardware with limited processing power), together with a set of metrics that can be used to improve the robustness of the decision-making process. To ensure reliability and reproducibility, cMatch builds on the highly validated pairwise-matching Smith-Waterman algorithm. All the tests presented have been conducted on synthetic data for challenging, yet realistic constructs - and on real data gathered during studies on a metabolic engineering example (lycopene production).
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Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, London, United Kingdom
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16
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Abdel-Kafy ESM, Ramadan SI, Ali WH, Youssef SF, Shabaan HA, El-Deighadi A, Inoue-Murayama M. Genetic and Phenotypic Characterization of Domestic Geese ( Anser anser) in Egypt. Animals (Basel) 2021; 11:3106. [PMID: 34827838 PMCID: PMC8614349 DOI: 10.3390/ani11113106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022] Open
Abstract
The objectives of this study were to achieve phenotypic characterization of three domestic Egyptian goose populations collected from three different geographical zones (Kafr El-Sheikh, Fayoum and Luxor) and to perform genetic characterization of these three populations based on mtDNA D-loop and 12 microsatellite markers. The body measurements of 402 domestic mature geese belonging to these three governorates showed that the lengths of the head, culmen and tarsus and the live body weight varied significantly among the three studied Egyptian goose populations. After alignment of a 710-base-pair segment of the goose mtDNA control region, there was a single haplotype in the three Egyptian goose populations, indicating the same maternal origins. The genotyping of the 12 microsatellite markers showed low diversity indices, including average observed (NA) and effective (NE) number of alleles and observed (HO) and expected heterozygosity (HE) (3.333, 1.760, 0.277 and 0.352, respectively), and a high inbreeding coefficient (FIS = 0.203) across the three Egyptian goose populations. The high inbreeding and low genetic and morphological differentiation of Egyptian geese could be corrected by establishing a large base population through capturing small populations with the highest genetic variation. The findings of the current study can therefore serve as an initial guide to design further investigations for developing conservation programs of Egyptian geese genetic resources.
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Affiliation(s)
- El-Sayed M. Abdel-Kafy
- Agricultural Research Center (ARC), Animal Production Research Institute (APRI), Dokki, Giza 12651, Egypt; (E.-S.M.A.-K.); (W.H.A.); (S.F.Y.); (H.A.S.); (A.E.-D.)
| | - Sherif I. Ramadan
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Weal H. Ali
- Agricultural Research Center (ARC), Animal Production Research Institute (APRI), Dokki, Giza 12651, Egypt; (E.-S.M.A.-K.); (W.H.A.); (S.F.Y.); (H.A.S.); (A.E.-D.)
| | - Sabbah F. Youssef
- Agricultural Research Center (ARC), Animal Production Research Institute (APRI), Dokki, Giza 12651, Egypt; (E.-S.M.A.-K.); (W.H.A.); (S.F.Y.); (H.A.S.); (A.E.-D.)
| | - Hoda A. Shabaan
- Agricultural Research Center (ARC), Animal Production Research Institute (APRI), Dokki, Giza 12651, Egypt; (E.-S.M.A.-K.); (W.H.A.); (S.F.Y.); (H.A.S.); (A.E.-D.)
| | - Amira El-Deighadi
- Agricultural Research Center (ARC), Animal Production Research Institute (APRI), Dokki, Giza 12651, Egypt; (E.-S.M.A.-K.); (W.H.A.); (S.F.Y.); (H.A.S.); (A.E.-D.)
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Rahman SIA, Nguyen TNT, Khanam F, Thomson NR, Dyson ZA, Taylor-Brown A, Chowdhury EK, Dougan G, Baker S, Qadri F. Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018. PLoS Negl Trop Dis 2021; 15:e0009748. [PMID: 34648506 PMCID: PMC8516307 DOI: 10.1371/journal.pntd.0009748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/22/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The proportion of enteric fever cases caused by Salmonella Paratyphi A is increasing and may increase further as we begin to introduce typhoid conjugate vaccines (TCVs). While numerous epidemiological and genomic studies have been conducted for S. Typhi, there are limited data describing the genomic epidemiology of S. Paratyphi A in especially in endemic settings, such as Bangladesh. PRINCIPAL FINDINGS We conducted whole genome sequencing (WGS) of 67 S. Paratyphi A isolated between 2008 and 2018 from eight enteric disease surveillance sites across Bangladesh. We performed a detailed phylogenetic analysis of these sequence data incorporating sequences from 242 previously sequenced S. Paratyphi A isolates from a global collection and provided evidence of lineage migration from neighboring countries in South Asia. The data revealed that the majority of the Bangladeshi S. Paratyphi A isolates belonged to the dominant global lineage A (67.2%), while the remainder were either lineage C (19.4%) or F (13.4%). The population structure was relatively homogenous across the country as we did not find any significant lineage distributions between study sites inside or outside Dhaka. Our genomic data showed presence of single point mutations in gyrA gene either at codon 83 or 87 associated with decreased fluoroquinolone susceptibility in all Bangladeshi S. Paratyphi A isolates. Notably, we identified the pHCM2- like cryptic plasmid which was highly similar to S. Typhi plasmids circulating in Bangladesh and has not been previously identified in S. Paratyphi A organisms. SIGNIFICANCE This study demonstrates the utility of WGS to monitor the ongoing evolution of this emerging enteric pathogen. Novel insights into the genetic structure of S. Paratyphi A will aid the understanding of both regional and global circulation patterns of this emerging pathogen and provide a framework for future genomic surveillance studies.
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Affiliation(s)
- Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - To Nguyen Thi Nguyen
- Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Zoe A. Dyson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Alyce Taylor-Brown
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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18
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López-Ardila IY, Martínez-Pérez FJ, Rondón-González F. Aplicación del modelo de pérdida de ADN para el diseño de cebadores en Potamotrygon magdalenae (Potamotrygonidae). ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v27n1.87401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El diseño de cebadores es fundamental para amplificar regiones de genes debido a que la especificidad que mantienen cebador-secuencia de interés puede causar el éxito o fracaso en la reacción de PCR. En relación a Potamotrygon magdalenae (especie de interés de acuerdo al PAN Tiburones-Colombia), existe poca información disponible de aspectos relacionados con la genética poblacional de esta Raya. El objetivo del presente trabajo consistió en diseñar cebadores bajo los criterios del Modelo de Pérdida de ADN (DNA-LM), que permitan evaluar el estado genético de las poblaciones de P. magdalenae. Alineamos secuencias de la superfamilia Dayastoidea, disponibles en el NCBI, de los genes mitocondriales Citocromo C Oxidasa 1 (MT-CO1) y Citocromo b (MT-CYB). Se guimos los parámetros Gap open penalty (5), Gap extension penalti (0,2) y Terminal gap penalties (0,1) y seleccionamos dos pares de cebadores de acuerdo con el DNA-LM. Estimamos el producto amplificado del gen MT-CO1 en 916 pb y del gen MT-CYB en 774 pb, en muestras de P. magdalenae procedentes de diferentes ciénagas del Magdalena medio. Discutimos los resultados desde la perspectiva de validar la especificidad de los cebadores diseñados, teniendo en cuenta la correspondencia e identidad de las secuencias de los genes considerados. Los cebadores aquí reportados pueden contribuir a ampliar el conocimiento de la genética poblacional, biogeografía y filogenética de la raya de agua dulce P. magdalenae.
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Rahman SIA, Taylor-Brown A, Khanam F, Khan AI, Horesh G, Dyson ZA, Begum YA, Chowdhury EK, Qadri F, Dougan G, Thomson NR. Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh. Microb Genom 2021; 7. [PMID: 34550065 PMCID: PMC8715441 DOI: 10.1099/mgen.0.000617] [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] [Indexed: 11/29/2022] Open
Abstract
The Salmonella enterica serotype Paratyphi B complex causes a wide range of diseases, from gastroenteritis to paratyphoid fever, depending on the biotypes Java and sensu stricto. The burden of Paratyphi B biotypes in Bangladesh is still unknown, as these are indistinguishable by Salmonella serotyping. Here, we conducted the first whole-genome sequencing (WGS) study on 79 Salmonella isolates serotyped as Paratyphi B that were collected from 10 nationwide enteric disease surveillance sites in Bangladesh. Placing these in a global genetic context revealed that these are biotype Java, and the addition of these genomes expanded the previously described PG4 clade containing Bangladeshi and UK isolates. Importantly, antimicrobial resistance (AMR) genes were scarce amongst Bangladeshi S. Java isolates, somewhat surprisingly given the widespread availability of antibiotics without prescription. This genomic information provides important insights into the significance of S. Paratyphi B biotypes in enteric disease and their implications for public health.
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Affiliation(s)
- Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Alyce Taylor-Brown
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Gal Horesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zoe A Dyson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK.,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Yasmin Ara Begum
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
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20
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Halim FS, Parmin NA, Hashim U, Gopinath SCB, Dahalan FA, Zakaria II, Ang WC, Jaapar NF. MicroRNA of N-region from SARS-CoV-2: Potential sensing components for biosensor development. Biotechnol Appl Biochem 2021; 69:1696-1711. [PMID: 34378814 PMCID: PMC8427135 DOI: 10.1002/bab.2239] [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: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/29/2022]
Abstract
An oligonucleotide DNA probe has been developed for the application in the DNA electrochemical biosensor for the early diagnosis of coronavirus disease (COVID-19). Here, the virus microRNA from the N-gene of severe acute respiratory syndrome-2 (SARS-CoV-2) was used for the first time as a specific target for detecting the virus and became a framework for developing the complementary DNA probe. The sequence analysis of the virus microRNA was carried out using bioinformatics tools including basic local alignment search tools, multiple sequence alignment from CLUSTLW, microRNA database (miRbase), microRNA target database, and gene analysis. Cross-validation of distinct strains of coronavirus and human microRNA sequences was completed to validate the percentage of identical and consent regions. The percent identity parameter from the bioinformatics tools revealed the virus microRNAs' sequence has a 100% match with the genome of SARS-CoV-2 compared with other coronavirus strains, hence improving the selectivity of the complementary DNA probe. The 30 mer with 53.0% GC content of complementary DNA probe 5' GCC TGA GTT GAG TCA GCA CTG CTC ATG GAT 3' was designed and could be used as a bioreceptor for the biosensor development in the clinical and environmental diagnosis of COVID-19.
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Affiliation(s)
- Fatin Syakirah Halim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - N A Parmin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Uda Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia.,Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - Farrah Aini Dahalan
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute (MGI), National Institute of Biotechnology (NIBM), Kajang, Selangor, Malaysia
| | - Wei Chern Ang
- Clinical Research Centre, Ministry of Health Malaysia, Hospital Tuanku Fauziah Perlis, Kangar, Perlis, 01000, Malaysia
| | - Nurfareezah Fareezah Jaapar
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
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21
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Gumaa MA, Idris AB, Bilal NE, Hassan MA. First insights into molecular basis identification of 16 s ribosomal RNA gene of Staphylococcus aureus isolated from Sudan. BMC Res Notes 2021; 14:240. [PMID: 34172074 PMCID: PMC8229275 DOI: 10.1186/s13104-021-05569-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/13/2021] [Indexed: 01/09/2023] Open
Abstract
Objective In this study, we analyzed the molecular evolution of Staphylococcus aureus isolates using 16S rRNA gene and phylogenetic analysis to detect the prevalence of S. aureus infections in Sudan. Results Molecular detection of S. aureus has shown that 20 (43.47%) of patients were positive for S. aureus. The phylogenetic tree of 16S rRNA sequences was divided into three lineages of S. aureus isolates detected from wound infections in Sudan. Nucleotides base-pair substitution was appeared at position 249. This mutation do not linked with Macrolides, Lincosamides and Streptogramines b resistant phenotype. Further studies should investigate the effect of that mutation on resistance to other antibiotics. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05569-w.
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Affiliation(s)
- Manal A Gumaa
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Abeer Babiker Idris
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - N E Bilal
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences and the Director of Central Research Laboratory, University of Khartoum, Khartoum, Sudan
| | - Mohamed A Hassan
- Department of Bioinformatics, DETAGEN Genetic Diagnostics Center, Kayseri, Turkey
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Ramharack P, Soliman MES. Bioinformatics-based tools in drug discovery: the cartography from single gene to integrative biological networks. Drug Discov Today 2018; 23:1658-1665. [PMID: 29864527 DOI: 10.1016/j.drudis.2018.05.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/12/2018] [Accepted: 05/29/2018] [Indexed: 02/02/2023]
Abstract
Originally developed for the analysis of biological sequences, bioinformatics has advanced into one of the most widely recognized domains in the scientific community. Despite this technological evolution, there is still an urgent need for nontoxic and efficient drugs. The onus now falls on the 'omics domain to meet this need by implementing bioinformatics techniques that will allow for the introduction of pioneering approaches in the rational drug design process. Here, we categorize an updated list of informatics tools and explore the capabilities of integrative bioinformatics in disease control. We believe that our review will serve as a comprehensive guide toward bioinformatics-oriented disease and drug discovery research.
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Affiliation(s)
- Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
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23
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Cloning, expression, and characterization of a four-component O-demethylase from human intestinal bacterium Eubacterium limosum ZL-II. Appl Microbiol Biotechnol 2016; 100:9111-9124. [DOI: 10.1007/s00253-016-7626-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/26/2016] [Accepted: 05/10/2016] [Indexed: 01/18/2023]
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