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Liu S, Pang H, Wang C, Wang Z, Wang M, Zhang Y, Zhang W, Sui Z. Rapid and accurate quantification of viable Bifidobacterium cells in milk powder with a propidium monoazide - antibiotic fluorescence in situ hybridization - flow cytometry method. J Dairy Sci 2024:S0022-0302(24)00947-0. [PMID: 38908696 DOI: 10.3168/jds.2024-24876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/24/2024]
Abstract
Due to its beneficial effects on human health, Bifidobacterium is commonly added to milk powder. Accurate quantification of viable Bifidobacterium is essential for assessing the therapeutic efficacy of milk powder. In this study, we introduced a novel propidium monoazide (PMA) - antibiotic fluorescence in situ hybridization (AFISH) - flow cytometry (FCM) method to rapidly and accurately quantify viable Bifidobacterium cells in milk powder. Briefly, Bifidobacterium cells were treated with chloramphenicol (CM) to increase their rRNA content, followed by staining with RNA-binding oligonucleotide probes, based on the AFISH technique. Then, the DNA-binding dye PMA was used to differentiate between viable and non-viable cells. The PMA-AFISH-FCM method, including sample pretreatment, CM treatment, dual staining, and FCM analysis, required around 2 h and was found to be better than the current methods. This is the first study to implement FCM combined with PMA and oligonucleotide probe for detecting Bifidobacterium.
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Affiliation(s)
- Siyuan Liu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China; College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China
| | - Huimin Pang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China; College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China
| | - Chenglong Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Ziquan Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Meng Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Yunzhe Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China
| | - Wei Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiwei Sui
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Thapa R, Afzal M, Goyal A, Gupta G, Bhat AA, Almalki WH, Kazmi I, Alzarea SI, Shahwan M, Kukreti N, Ali H, Dureja H, Kumar P, Singh TG, Kuppusamy G, Singh SK, Dua K. Exploring ncRNA-mediated regulation of EGFR signalling in glioblastoma: From mechanisms to therapeutics. Life Sci 2024; 345:122613. [PMID: 38582393 DOI: 10.1016/j.lfs.2024.122613] [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: 02/15/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Glioblastoma (GBM) is the most prevalent and deadly primary brain tumor type, with a discouragingly low survival rate and few effective treatments. An important function of the EGFR signalling pathway in the development of GBM is to affect tumor proliferation, persistence, and treatment resistance. Advances in molecular biology in the last several years have shown how important ncRNAs are for controlling a wide range of biological activities, including cancer progression and development. NcRNAs have become important post-transcriptional regulators of gene expression, and they may affect the EGFR pathway by either directly targeting EGFR or by modifying important transcription factors and downstream signalling molecules. The EGFR pathway is aberrantly activated in response to the dysregulation of certain ncRNAs, which has been linked to GBM carcinogenesis, treatment resistance, and unfavourable patient outcomes. We review the literature on miRNAs, circRNAs and lncRNAs that are implicated in the regulation of EGFR signalling in GBM, discussing their mechanisms of action, interactions with the signalling pathway, and implications for GBM therapy. Furthermore, we explore the potential of ncRNA-based strategies to overcome resistance to EGFR-targeted therapies, including the use of ncRNA mimics or inhibitors to modulate the activity of key regulators within the pathway.
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Affiliation(s)
- Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, U.P., India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, 7, United Arab Emirates
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Punjab, India
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
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Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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Kang H, Lee J. Adipose tissue macrophage heterogeneity in the single-cell genomics era. Mol Cells 2024; 47:100031. [PMID: 38354858 PMCID: PMC10960114 DOI: 10.1016/j.mocell.2024.100031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
It is now well-accepted that obesity-induced inflammation plays an important role in the development of insulin resistance and type 2 diabetes. A key source of the inflammation is the murine epididymal and human visceral adipose tissue. The current paradigm is that obesity activates multiple proinflammatory immune cell types in adipose tissue, including adipose-tissue macrophages (ATMs), T Helper 1 (Th1) T cells, and natural killer (NK) cells, while concomitantly suppressing anti-inflammatory immune cells such as T Helper 2 (Th2) T cells and regulatory T cells (Tregs). A key feature of the current paradigm is that obesity induces the anti-inflammatory M2 ATMs in lean adipose tissue to polarize into proinflammatory M1 ATMs. However, recent single-cell transcriptomics studies suggest that the story is much more complex. Here we describe the single-cell genomics technologies that have been developed recently and the emerging results from studies using these technologies. While further studies are needed, it is clear that ATMs are highly heterogeneous. Moreover, while a variety of ATM clusters with quite distinct features have been found to be expanded by obesity, none truly resemble classical M1 ATMs. It is likely that single-cell transcriptomics technology will further revolutionize the field, thereby promoting our understanding of ATMs, adipose-tissue inflammation, and insulin resistance and accelerating the development of therapies for type 2 diabetes.
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Affiliation(s)
- Haneul Kang
- Soonchunhyang Institute of Medi-Bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, South Korea
| | - Jongsoon Lee
- Soonchunhyang Institute of Medi-Bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, South Korea.
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Colom G, Hernandez-Albors A, Barallat J, Galan A, Bayes-Genis A, Salvador JP, Marco MP. A multiplexed immunochemical microarray for the determination of cardiovascular disease biomarkers. Mikrochim Acta 2023; 191:53. [PMID: 38151630 PMCID: PMC10752916 DOI: 10.1007/s00604-023-06119-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023]
Abstract
A fluorescence antibody microarray has been developed for the determination of relevant cardiovascular disease biomarkers for the analysis of human plasma samples. Recording characteristic protein molecular fingerprints to assess individual's states of health could allow diagnosis to go beyond the simple identification of the disease, providing information on its stage or prognosis. Precisely, cardiovascular diseases (CVDs) are complex disorders which involve different degenerative processes encompassing a collection of biomarkers related to disease progression or stage. The novel approach that we propose is a fluorescent microarray chip has been developed accomplishing simultaneous determination of the most significant cardiac biomarkers in plasma aiming to determine the CVD status stage of the patient. As proof of concept, we have chosen five relevant biomarkers, C-reactive protein (CRP) as biomarker of inflammation, cystatin C (CysC) as biomarker of renal failure that is directly related with heart failure, cardiac troponin I (cTnI) as already established biomarker for cardiac damage, heart fatty acid binding protein as biomarker of ischemia (H-FABP), and finally, NT-proBNP (N-terminal pro-brain natriuretic peptide), a well-established heart failure biomarker. After the optimization of the multiplexed microarray, the assay allowed the simultaneous determination of 5 biomarkers in a buffer solution reaching LODs of 15 ± 5, 3 ± 1, 24 ± 3, 25 ± 3, and 3 ± 1 ng mL-1, for CRP, CysC, H-FABP, cTnI, and NT-proBNP, respectively. After solving the matrix effect, and demonstrating the accuracy for each biomarker, the chip was able to determine 24 samples per microarray chip. Then, the microarray has been used on a small pilot clinical study with 29 plasma samples from clinical patients which suffered different CVD and other related disorders. Results show the superior capability of the chip to provide clinical information related to the disease in terms of turnaround time (1 h 30 min total assay and measurement) and amount of information delivered in respect to reference technologies used in hospital laboratories (clinical analyzers). Despite the failure to detect c-TnI at the reported threshold, the microarray technology could be a powerful approach to diagnose the cardiovascular disease at early stage, monitor its progress, and eventually providing information about an eminent potential risk of suffering a myocardial infarction. The microarray chip here reported could be the starting point for achieving powerful multiplexed diagnostic technologies for the diagnosis of CVDs or any other pathology for which biomarkers have been identified at different stages of the disease.
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Affiliation(s)
- Gloria Colom
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alejandro Hernandez-Albors
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Jaume Barallat
- Biochemistry Department, Metropolitan North Clinical Laboratory (LCMN), Germans Trias i Pujol Universitary Hospital, Ctra. de Canyet, s/n, Badalona, Barcelona, Spain
| | - Amparo Galan
- Institut del Cor Germans Trias I Pujol, Ctra. de Canyet, 1-3, 08916, Badalona, Spain
| | - Antoni Bayes-Genis
- Institut del Cor Germans Trias I Pujol, Ctra. de Canyet, 1-3, 08916, Badalona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Juan-Pablo Salvador
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Maria-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain
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Aggarwal RT, Lai L, Li H. Microarray fabrication techniques for multiplexed bioassay applications. Anal Biochem 2023; 683:115369. [PMID: 37914004 DOI: 10.1016/j.ab.2023.115369] [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: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.
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Affiliation(s)
| | - Leyun Lai
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada.
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Salazar-Ardiles C, Asserella-Rebollo L, Cornejo C, Arias D, Vasquez-Muñoz M, Toledo C, Andrade DC. Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences. Mol Biol Rep 2023; 50:10367-10382. [PMID: 37817022 DOI: 10.1007/s11033-023-08844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.
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Affiliation(s)
- Camila Salazar-Ardiles
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | | | - Carlos Cornejo
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Dayana Arias
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Manuel Vasquez-Muñoz
- Dirección de Docencia de Especialidades Médicas, Dirección de Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Camilo Toledo
- Laboratory of Cardiorespiratory and Sleep Physiology, Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile.
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Kekić T, Lietard J. A Canvas of Spatially Arranged DNA Strands that Can Produce 24-bit Color Depth. J Am Chem Soc 2023; 145:22293-22297. [PMID: 37787949 PMCID: PMC10591465 DOI: 10.1021/jacs.3c06500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/04/2023]
Abstract
Nucleic acid microarray photolithography combines density, throughput, and positional control in DNA synthesis. These surface-bound sequence libraries are conventionally used in large-scale hybridization assays against fluorescently labeled, perfect-match DNA strands. Here, we introduce another layer of control for in situ microarray synthesis─hybridization affinity─to precisely modulate fluorescence intensity upon duplex formation. Using a combination of Cy3-, Cy5-, and fluorescein-labeled targets and an ensemble of truncated DNA probes, we organize 256 shades of red, green, and blue intensities that can be superimposed and merged. In so doing, hybridization alone is able to produce a large palette of 16 million colors or 24-bit color depth. Digital images can be reproduced with high fidelity at the micrometer scale by using a simple process that assigns sequence to any RGB value. Largely automated, this approach can be seen as miniaturized DNA-based painting.
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Affiliation(s)
- Tadija Kekić
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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10
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Tripathi P. Medical viruses: diagnostic techniques. Virol J 2023; 20:143. [PMID: 37434239 DOI: 10.1186/s12985-023-02108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
The recent epidemics and pandemics caused by different viruses such as SARS-CoV-2, monkey pox, H1N1, ebola virus etc. have been a cause of mass destruction in the human race, the biggest decline slope in the global economy and mental trauma. A number of viruses have been discovered that may cause serious problems and to overcome this problem, early diagnosis of the viruses and understanding their infection pattern is a must. Early detection of viruses inside the host provides timely management in a strategic manner. Scientists have developed some effective and efficient methods to detect the viruses. In this review, we have explained a few types of diagnostic techniques: Biosensor based, immunological-based, and molecular-based diagnostic techniques that are prominent methodologies to identify and detect the course of infection related to the medical viruses. In biosensor-based diagnostic technique, an analytical device consisting of biological elements and physicochemical component gives a signal upon detection of viral antigen. In immunological-based diagnostic techniques, enzyme-linked antibodies are utilized to find the particular antiviral antibody or viral antigen in human specimens, and nucleic acid-based diagnostic techniques are based on the principle of amplification of the viral genome.
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Affiliation(s)
- Pratima Tripathi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP, 226002, India.
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11
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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:biom13040602. [PMID: 37189350 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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Barpanda A, Tuckley C, Ray A, Banerjee A, Duttagupta SP, Kantharia C, Srivastava S. A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer. Proteomics Clin Appl 2023; 17:e2200062. [PMID: 36408811 DOI: 10.1002/prca.202200062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer. EXPERIMENTAL DESIGN The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease. RESULTS The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.
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Affiliation(s)
- Abhilash Barpanda
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arka Ray
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Siddhartha P Duttagupta
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Chetan Kantharia
- Department of surgical gastroenterology at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Salam MA, Al-Amin MY, Pawar JS, Akhter N, Lucy IB. Conventional methods and future trends in antimicrobial susceptibility testing. Saudi J Biol Sci 2023; 30:103582. [PMID: 36852413 PMCID: PMC9958398 DOI: 10.1016/j.sjbs.2023.103582] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/07/2023] [Accepted: 01/29/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial susceptibility testing is an essential task for selecting appropriate antimicrobial agents to treat infectious diseases. Constant evolution has been observed in methods used in the diagnostic microbiology laboratories. Disc diffusion or broth microdilution are classical and conventional phenotypic methods with long turnaround time and labour-intensive but still widely practiced as gold-standard. Scientists are striving to develop innovative, novel and faster methods of antimicrobial susceptibility testing to be applicable for routine microbiological laboratory practice and research. To meet the requirements, there is an increasing trend towards automation, genotypic and micro/nano technology-based innovations. Automation in detection systems and integration of computers for online data analysis and data sharing are giant leaps towards versatile nature of automated methods currently in use. Genotypic methods detect a specific genetic marker associated with resistant phenotypes using molecular amplification techniques and genome sequencing. Microfluidics and microdroplets are recent addition in the continuous advancement of methods that show great promises with regards to safety and speed and have the prospect to identify and monitor resistance mechanisms. Although genotypic and microfluidics methods have many exciting features, however, their applications into routine clinical laboratory practice warrant extensive validation. The main impetus behind the evolution of methods in antimicrobial susceptibility testing is to shorten the overall turnaround time in obtaining the results and to enhance the ease of sample processing. This comprehensive narrative review summarises major conventional phenotypic methods and automated systems currently in use, and highlights principles of some of the emerging genotypic and micro/nanotechnology-based methods in antimicrobial susceptibility testing.
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Key Words
- ADR, Adverse drug reaction
- AMR, Antimicrobial resistance
- AST, Antimicrobial susceptibility testing
- ATCC, American Type Culture Collection
- Advantages and disadvantages
- Antimicrobial susceptibility testing
- Automations
- CFU, Colony forming units
- CLSI, Clinical & Laboratory Standards Institute
- Conventional methods
- DOT-MGA, Direct-On-Target Microdroplet Growth Assay
- EUCAST, European Committee on Antimicrobial Susceptibility Testing
- Etest, Epsilometer testing
- Genotypic methods
- ID, Identification
- MALDI-TOF MS, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
- MBC, Minimum bactericidal concentration
- MDR, Multi drug resistant
- MHA, Muller Hinton Agar
- MIC, Minimum inhibitory concentration
- Micro/nanotechnology-based techniques
- NAAT, Nucleic Acid Amplification Test
- PCR, Polymerase chain reaction
- PMF, Peptide mass fingerprint
- POC, Point of care
- WGS, Whole Genome Sequencing
- ZOI, Zone of inhibition
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Affiliation(s)
- Md. Abdus Salam
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University, Malaysia
| | - Md. Yusuf Al-Amin
- Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN, USA,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jogendra Singh Pawar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Naseem Akhter
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Irine Banu Lucy
- Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh,Corresponding author at: Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh.
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [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] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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15
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Reddy Banda S, Klapproth H, Smit N, Bednar S, Brandstetter T, Rühe J. An advanced and efficient asymmetric PCR method for microarray applications. Front Bioeng Biotechnol 2022; 10:1045154. [PMID: 36532575 PMCID: PMC9748121 DOI: 10.3389/fbioe.2022.1045154] [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: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2024] Open
Abstract
The sensitivity of a PCR based biochip assay relies on the efficiency of PCR amplicons in binding to the microarray spots. The essential factor determining the sensitivity is the amount of single stranded (ss) amplicons available for biochip hybridization. Asymmetric PCR can generate ss-amplicons depending on the ratio of primers used in the amplification process, but this process is often inefficient. We report a novel variant of PCR called the Asymmetric Exponential and Linear Amplification (AELA) which can overcome these issues and generate large amounts of single stranded amplicons. AELA-PCR introduces an amplification strategy that makes use of both exponential and linear amplification of the target nucleic acid. This is done by specifically designed primers and choice of adequate thermal profiles. In conventional PCR with a classical thermal profile, these specifically designed primers will work normally and contribute to an exponential increase of amplicons. A designed sequence extension of one of the primers and a very specific thermal profile, will result in a situation that the extended primer will be the only functional one for amplification, resulting in a linear phase of the amplification process. That is why during this step only one of the two strands of the target is amplified linearly and no longer exponentially. The result of the whole process is an amplification product enriched very strongly in one of the two single strands of the target. These adaptions in PCR are particularly favorable where the generation of ss-DNA/RNA is required. We demonstrate the higher biochip sensitivity of AELA-PCR compared to conventional amplification methods with an example of the Staphylococcus aureus detection on a DNA oligonucleotide microarray.
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Affiliation(s)
- Suresh Reddy Banda
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Holger Klapproth
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Nicolaas Smit
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Sonja Bednar
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Thomas Brandstetter
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Jürgen Rühe
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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17
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Preparation of multiple-spectra encoded polyphosphazene microspheres and application for antibody detection. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-021-03811-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:bios12070489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Correspondence:
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19
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Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays 2022; 44:e2100252. [PMID: 35253252 PMCID: PMC10506734 DOI: 10.1002/bies.202100252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.
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Affiliation(s)
| | - Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lucie Laplane
- Institut d’histoire et de philosophie des sciences et des techniques (UMR8590), CNRS & Panthéon-Sorbonne University, 75006 Paris, France
- Hematopoietic stem cells and the development of myeloid malignancies (UMR1287), Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Thomas Pradeu
- ImmunoConcept (UMR5164), CNRS & University of Bordeaux, 33076 Bordeaux Cedex, France
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
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20
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RNA Microarray-Based Comparison of Innate Immune Phenotypes between Human THP-1 Macrophages Stimulated with Two BCG Strains. Int J Mol Sci 2022; 23:ijms23094525. [PMID: 35562916 PMCID: PMC9103163 DOI: 10.3390/ijms23094525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 12/10/2022] Open
Abstract
Currently, the only available vaccine against tuberculosis is Mycobacterium bovis Bacille Calmette-Guérin (BCG). Pulmonary tuberculosis protection provided by the vaccine varies depending on the strain, the patient’s age and the evaluated population. Although the adaptive immune responses induced by different BCG strains have been widely studied, little conclusive data is available regarding innate immune responses, especially in macrophages. Here, we aimed to characterize the innate immune responses of human THP-1-derived macrophages at the transcriptional level following a challenge with either the BCG Mexico (M.BCG) or Phipps (P.BCG) strains. After a brief in vitro characterization of the bacterial strains and the innate immune responses, including nitric oxide production and cytokine profiles, we analyzed the mRNA expression patterns and performed pathway enrichment analysis using RNA microarrays. Our results showed that multiple biological processes were enriched, especially those associated with innate inflammatory and antimicrobial responses, including tumor necrosis factor (TNF)-α, type I interferon (IFN-I) and IFN-γ. However, four DEGs were identified in macrophages infected with M.BCG compared to P. BCG. These findings indicated the proinflammatory stimulation of macrophages induced by both BCG strains, at the cytokine level and in terms of gene expression, suggesting a differential expression pattern of innate immune transcripts depending on the mycobacterial strain.
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21
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Abraham GR, Morrow AJ, Oliveira J, Weir-McCall JR, Davenport EE, Berry C, Davenport AP, Hoole SP. Mechanistic study of the effect of Endothelin SNPs in microvascular angina – Protocol of the PRIZE Endothelin Sub-Study. IJC HEART & VASCULATURE 2022; 39:100980. [PMID: 35242999 PMCID: PMC8885580 DOI: 10.1016/j.ijcha.2022.100980] [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: 01/08/2022] [Revised: 02/02/2022] [Accepted: 02/20/2022] [Indexed: 11/17/2022]
Abstract
Microvascular angina is a common cause of ischemia with non-obstructive coronary arteries (INOCA). Endothelin-1 (ET-1) is a potent vasoconstrictor implicated in the pathophysiology of microvascular angina. Zibotentan, an Endothelin Receptor Antagonist is being tested as a treatment for microvascular angina in the ‘PRIZE’ trial using a genetic ‘precision medicine’ approach. The PRIZE ET Sub-study will provide a comprehensive genotype and phenotype bio-resource for microvascular angina patients.
Introduction Microvascular angina is a common cause of ischemia with non-obstructive coronary arteries (INOCA) and limited therapeutic options are available to those affected. Endothelin-1 (ET-1) is a potent vasoconstrictor implicated in the pathophysiology of microvascular angina. A large randomised, double blinded, placebo controlled crossover trial, the PRecIsion medicine with ZibotEntan in microvascular angina (PRIZE) trial is currently underway, investigating an endothelin receptor antagonist – Zibotentan, as a new drug treatment for microvascular angina. The trial uses a 'precision medicine' approach by preferential selection of those with higher ET-1 expression conferred by the PHACTR1 minor G allele single nucleotide polymorphism (SNP). The incidence of this SNP occurs in approximately one third of the population therefore a considerable number of screened patients will be ineligible for randomisation and the treatment phase of the trial. Methods In the PRIZE Endothelin (ET) Sub-Study, patients screened out of the PRIZE trial will be genotyped for other genetic variants in the ET-1 pathway. These will be correlated with phenotypic characteristics including exercise tolerance, angina severity and quantitative measures of microvascular function on cardiovascular MRI as well as mechanistic data on endothelin pathway signalling. Conclusions The study will provide a comprehensive genotype and phenotype bio-resource identifying novel ET-1 genotypes to inform the potential wider use of endothelin receptor antagonists for this indication.
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22
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Forte G, Ventimiglia G, Pesaturo M, Petralia S. A highly sensitive PNA-microarray system for miRNA122 recognition. Biotechnol J 2022; 17:e2100587. [PMID: 35225426 DOI: 10.1002/biot.202100587] [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: 11/01/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022]
Abstract
Surface chemistry is a fundamental aspect of the development of the sensitive biosensor based on microarray technology. Here we described an advanced PNA-microarray system for the detection of miRNA, composed by a multilayered Si/Al/Agarose component. A straightforward optical signal enhancement is achieved thanks to a combination of the Al film mirror effect and the positive interference for the emission wavelength of the Cy5 fluorescent label tuned by the agarose film. The PNA-microarray was investigated for the detection of miRNA_122, resulting in a sensitivity of about 1.75 μM-1 and Limit of Detection in the range of 0.043 nM as a function of the capture probe sequence. The contribution, in terms of H-bonds amounts at 298 and 333 K, of the agarose coating to the dsPNA-RNA interactions was demonstrated by Molecular Dynamic simulations. These results pave the way for advanced sensing strategies suitable for the environmental monitoring and the public safety. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Giuseppe Forte
- Department of Drug Science and Health, University of Catania, via S. Sofia 64, 95125, Catania, Italy
| | - Giorgio Ventimiglia
- EM Microelectronic, Rue de Sors 3, 2074, Marin (Suisse), Marin-Epagnier, Switzerland
| | | | - Salvatore Petralia
- Department of Drug Science and Health, University of Catania, via S. Sofia 64, 95125, Catania, Italy
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Sun KH(M, Wong YT(H, Cheung KM(C, Yuen C(M, Chan YT(T, Lai WY(J, Chao C(D, Fan WS(K, Chow YK(K, Law MF, Tam HC(T. Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12020409. [PMID: 35204500 PMCID: PMC8871212 DOI: 10.3390/diagnostics12020409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) infection has long been proposed as the major etiology of lymphomagenesis. The adoption of high-throughput sequencing has allowed us to gain more insight into the molecular mechanisms of ENKTCL, which largely involve chromosome deletion and aberrations in Janus kinase (JAK)-signal transducer and activator of transcription (STAT), programmed cell death protein-1 (PD-1)/PD-ligand 1 (PD-L1) pathways, as well as mutations in tumor suppressor genes. The molecular findings could potentially influence the traditional chemoradiotherapy approach, which is known to be associated with significant toxicity. This article will review the latest molecular findings in NKTCL and recent advances in the field of molecular diagnosis in NKTCL. Issues of quality control and technical difficulties will also be discussed, along with future prospects in the molecular diagnosis and treatment of NKTCL.
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Affiliation(s)
- Ka-Hei (Murphy) Sun
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | | | - Ka-Man (Carmen) Cheung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Carmen (Michelle) Yuen
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | - Yun-Tat (Ted) Chan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Yan (Jennifer) Lai
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Chun (David) Chao
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Sum (Katie) Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Yuen-Kiu (Karen) Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Man-Fai Law
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
- Correspondence:
| | - Ho-Chi (Tommy) Tam
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
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Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Wu Q, Li J, Wang W, Zhou J, Wang D, Fan B, Zhang X, Sun D, Gong G, Suolang S, Li B. Next-Generation Sequencing Reveals Four Novel Viruses Associated with Calf Diarrhea. Viruses 2021; 13:v13101907. [PMID: 34696337 PMCID: PMC8537473 DOI: 10.3390/v13101907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/31/2022] Open
Abstract
Calf diarrhea is one of the common diseases involved in the process of calf feeding. In this study, a sample of calf diarrhea that tested positive for bovine coronavirus and bovine astrovirus was subjected to high-throughput sequencing. The reassembly revealed the complete genomes of bovine norovirus, bovine astrovirus, bovine kobuvirus, and the S gene of bovine coronavirus. Phylogenetic analysis showed that the ORF2 region of bovine astrovirus had the lowest similarity with other strains and gathered in the Mamastrovirus unclassified genogroup, suggesting a new serotype/genotype could appear. Compared with the most closely related strain, there are six amino acid mutation sites in the S gene of bovine coronavirus, most of which are located in the S1 subunit region. The bovine norovirus identified in our study was BNoV-GIII 2, based on the VP1 sequences. The bovine kobuvirus is distributed in the Aichi virus B genus; the P1 gene shows as highly variable, while the 3D gene is highly conserved. These findings enriched our knowledge of the viruses in the role of calf diarrhea, and help to develop an effective strategy for disease prevention and control.
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Affiliation(s)
- Qi Wu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi 860000, China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Infection Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Wei Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Infection Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinzhu Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Infection Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dandan Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Infection Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Xuehan Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi 860000, China
- Correspondence: (G.G.); (S.S.); (B.L.)
| | - Sizhu Suolang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi 860000, China
- Correspondence: (G.G.); (S.S.); (B.L.)
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing 210014, China; (Q.W.); (J.L.); (W.W.); (J.Z.); (D.W.); (B.F.); (X.Z.)
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Jiangsu Co-Infection Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (G.G.); (S.S.); (B.L.)
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Ali A, Zaman A, Sayed E, Evans D, Morgan S, Samwell C, Hall J, Arshad MS, Singh N, Qutachi O, Chang MW, Ahmad Z. Electrohydrodynamic atomisation driven design and engineering of opportunistic particulate systems for applications in drug delivery, therapeutics and pharmaceutics. Adv Drug Deliv Rev 2021; 176:113788. [PMID: 33957180 DOI: 10.1016/j.addr.2021.04.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022]
Abstract
Electrohydrodynamic atomisation (EHDA) technologies have evolved significantly over the past decade; branching into several established and emerging healthcare remits through timely advances in the engineering sciences and tailored conceptual process designs. More specifically for pharmaceutical and drug delivery spheres, electrospraying (ES) has presented itself as a high value technique enabling a plethora of different particulate structures. However, when coupled with novel formulations (e.g. co-flows) and innovative device aspects (e.g., materials and dimensions), core characteristics of particulates are manipulated and engineered specifically to deliver an application driven need, which is currently lacking, ranging from imaging and targeted delivery to controlled release and sensing. This demonstrates the holistic nature of these emerging technologies; which is often overlooked. Parametric driven control during particle engineering via the ES method yields opportunistic properties when compared to conventional methods, albeit at ambient conditions (e.g., temperature and pressure), making this extremely valuable for sensitive biologics and molecules of interest. Furthermore, several processing (e.g., flow rate, applied voltage and working distance) and solution (e.g., polymer concentration, electrical conductivity and surface tension) parameters impact ES modes and greatly influence the production of resulting particles. The formation of a steady cone-jet and subsequent atomisation during ES fabricates particles demonstrating monodispersity (or near monodispersed), narrow particle size distributions and smooth or textured morphologies; all of which are successfully incorporated in a one-step process. By following a controlled ES regime, tailored particles with various intricate structures (hollow microspheres, nanocups, Janus and cell-mimicking nanoparticles) can also be engineered through process head modifications central to the ES technique (single-needle spraying, coaxial, multi-needle and needleless approaches). Thus, intricate formulation design, set-up and combinatorial engineering of the EHDA process delivers particulate structures with a multitude of applications in tissue engineering, theranostics, bioresponsive systems as well as drug dosage forms for specific delivery to diseased or target tissues. This advanced technology has great potential to be implemented commercially, particularly on the industrial scale for several unmet pharmaceutical and medical challenges and needs. This review focuses on key seminal developments, ending with future perspectives addressing obstacles that need to be addressed for future advancement.
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Recent advances in microarray 3D bioprinting for high-throughput spheroid and tissue culture and analysis. Essays Biochem 2021; 65:481-489. [PMID: 34296737 DOI: 10.1042/ebc20200150] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022]
Abstract
Three-dimensional (3D) cell culture in vitro has proven to be more physiologically relevant than two-dimensional (2D) culture of cell monolayers, thus more predictive in assessing efficacy and toxicity of compounds. There have been several 3D cell culture techniques developed, which include spheroid and multicellular tissue cultures. Cell spheroids have been generated from single or multiple cell types cultured in ultralow attachment (ULA) well plates and hanging droplet plates. In general, cell spheroids are formed in a relatively short period of culture, in the absence of extracellular matrices (ECMs), via gravity-driven self-aggregation, thus having limited ability to self-organization in layered structure. On the other hand, multicellular tissue cultures including miniature tissues derived from pluripotent stem cells and adult stem cells (a.k.a. 'organoids') and 3D bioprinted tissue constructs require biomimetic hydrogels or ECMs and show highly ordered structure due to spontaneous self-organization of cells during differentiation and maturation processes. In this short review article, we summarize traditional methods of spheroid and multicellular tissue cultures as well as their technical challenges, and introduce how droplet-based, miniature 3D bioprinting ('microarray 3D bioprinting') can be used to improve assay throughput and reproducibility for high-throughput, predictive screening of compounds. Several platforms including a micropillar chip and a 384-pillar plate developed to facilitate miniature spheroid and tissue cultures via microarray 3D bioprinting are introduced. We excluded microphysiological systems (MPSs) in this article although they are important tissue models to simulate multiorgan interactions.
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Boissinot K, Peytavi R, Chapdelaine S, Geissler M, Boissinot M, Martel EA, Béliveau-Viel D, Gravel JF, Malic L, Veres T, Boudreau D, Bergeron MG. Real-time monitoring of bead-based DNA hybridization in a microfluidic system: study of amplicon hybridization behavior on solid supports. Analyst 2021; 146:4226-4234. [PMID: 34095908 DOI: 10.1039/d1an00394a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA hybridization phenomena occurring on solid supports are not understood as clearly as aqueous phase hybridizations and mathematical models cannot predict some empirically obtained results. Ongoing research has identified important parameters but remains incomplete to accurately account for all interactions. It has previously been shown that the length of the overhanging (dangling) end of the target DNA strand following hybridization to the capture probe is correlated to interactions with the complementary strand in solution which can result in unbinding of the target and its release from the surface. We have developed an instrument for real-time monitoring of DNA hybridization on spherical particles functionalized with oligonucleotide capture probes and arranged in the form of a tightly packed monolayer bead bed inside a microfluidic cartridge. The instrument is equipped with a pneumatic module to mediate displacement of fluid on the cartridge. We compared this system to both conventional (passive) and centrifugally-driven (active) microfluidic microarray hybridization on glass slides to establish performance levels for the detection of single nucleotide polymorphisms. The system was also used to study the effect of the dangling end's length in real-time when the immobilized target DNA is exposed to the complementary strand in solution. Our findings indicate that increasing the length of the dangling end leads to desorption of target amplicons from bead-bound capture probes at a rate approaching that of the initial hybridization process. Finally, bead bed hybridization was performed with Streptococcus agalactiae cfb gene amplicons obtained from randomized clinical samples, which allowed for identification of group B streptococci within 5-15 min. The methodology presented here is useful for investigating competitive hybridization mechanisms on solid supports and to rapidly validate the suitability of microarray capture probes.
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Affiliation(s)
- Karel Boissinot
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Régis Peytavi
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Sébastien Chapdelaine
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Matthias Geissler
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Maurice Boissinot
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada.
| | - Eric A Martel
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada.
| | - David Béliveau-Viel
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Jean-François Gravel
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Lidija Malic
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Teodor Veres
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Denis Boudreau
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada and Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
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Fruncillo S, Su X, Liu H, Wong LS. Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors. ACS Sens 2021; 6:2002-2024. [PMID: 33829765 PMCID: PMC8240091 DOI: 10.1021/acssensors.0c02704] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm2 to m2, maintaining cost effectiveness, high throughput (>100 cm2 h-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.
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Affiliation(s)
- Silvia Fruncillo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xiaodi Su
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Department of Chemistry, National University of Singapore, Block S8, Level 3, 3 Science Drive, Singapore 117543, Singapore
| | - Hong Liu
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Lu Shin Wong
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics (Basel) 2021; 10:565. [PMID: 34065815 PMCID: PMC8151116 DOI: 10.3390/antibiotics10050565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Paulo Zoio
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Luís P. Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
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Hoff K, Ding X, Carter L, Duque J, Lin JY, Dung S, Singh P, Sun J, Crnogorac F, Swaminathan R, Alden EN, Zhu X, Shimada R, Posavi M, Hull N, Dinwiddie D, Halasz AM, McGall G, Zhou W, Edwards JS. Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4763-4771. [PMID: 33848173 PMCID: PMC8056606 DOI: 10.1021/acs.langmuir.0c02927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/31/2021] [Indexed: 06/02/2023]
Abstract
SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.
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Affiliation(s)
| | - Xun Ding
- Centrillion Technologies, Palo Alto, CA 94303
| | | | - John Duque
- Centrillion Technologies, Palo Alto, CA 94303
| | - Ju-Yu Lin
- Centrillion Technologies, Palo Alto, CA 94303
| | | | | | - Jiayi Sun
- Centrillion Technologies, Palo Alto, CA 94303
| | | | - Radha Swaminathan
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Emily N Alden
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Ryota Shimada
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Marijan Posavi
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Noah Hull
- Wyoming Public Health Laboratory, Wyoming Department of Health, Cheyenne, WY 82007
| | - Darrell Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Adam M. Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV, 26506
| | | | - Wei Zhou
- Centrillion Technologies, Palo Alto, CA 94303
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
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34
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Kim DY, Kim JM. Multi-omics integration strategies for animal epigenetic studies - A review. Anim Biosci 2021; 34:1271-1282. [PMID: 33902167 PMCID: PMC8255897 DOI: 10.5713/ab.21.0042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.
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Affiliation(s)
- Do-Young Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Korea
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35
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López-Vázquez C, Bandín I, Dopazo CP. Design and Evaluation of a Macroarray for Detection, Identification, and Typing of Viral Hemorrhagic Septicemia Virus (VHSV). Animals (Basel) 2021; 11:841. [PMID: 33809757 PMCID: PMC8002285 DOI: 10.3390/ani11030841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
The viral hemorrhagic septicemia virus (VHSV) is the causative agent of an important disease in freshwater and marine fishes. Its diagnosis officially relies on the isolation of the virus in cell culture and its identification by serological or polymerase chain reaction (PCR) methodologies. Nowadays, reverse transcription real-time quantitative PCR (RT-qPCR) is the most widely employed technique for the detection of this virus and some studies have reported the validation of RT-qPCR procedures for the detection, typing, and quantification of VHSV isolates. However, although the efficacy of this technique is not in doubt, it can be cumbersome and even impractical when it comes to processing large numbers of samples, a situation in which cross-contamination problems cannot be ruled out. In the present study, we have designed and validated a macroarray for the simultaneous detection, typing, and quantification of VHSV strains. Its analytical sensitivity (5-50 TCID50/mL), analytical specificity (intra and intergroup), efficiency (E = 100.0-101.1) and reliability (repeatability and reproducibility with CV < 5%, and standard curves with R2 < 0.95) with strains from any VHSV genotype have been widely demonstrated. The procedure is based on the 'binary multiplex RT-qPCR system (bmRT-qPCR)' previously reported by the same team, applied to arrays of 96-well PCR strip tubes plates, which can be stored at -25 °C for three months and up to one year before their use, without significant loss of efficiency.
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Affiliation(s)
- Carmen López-Vázquez
- Unidad de Ictiopatología, Instituto de Acuicultura y Departamento de Microbiología, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Isabel Bandín
- Unidad de Ictiopatología, Instituto de Acuicultura y Departamento de Microbiología, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos P Dopazo
- Unidad de Ictiopatología, Instituto de Acuicultura y Departamento de Microbiología, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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36
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María Hernández-Domínguez E, Sofía Castillo-Ortega L, García-Esquivel Y, Mandujano-González V, Díaz-Godínez G, Álvarez-Cervantes J. Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.89594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.
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37
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Teng F, Wu X, Hong T, Munk GB, Libera M. Integrating nucleic acid sequence-based amplification and microlensing for high-sensitivity self-reporting detection. Analyst 2020; 145:7528-7533. [PMID: 32966360 DOI: 10.1039/d0an01231a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We use electron-beam patterned functional microgels to integrate self-reporting molecular beacons, dielectric microlenses, and solid-phase and/or solution-phase nucleic acid amplification in a viral-detection microarray model. The detection limits for different combinations of these elements range from 10-10 M for direct target-beacon hybridization alone to 10-18 M when all elements are integrated simultaneously.
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Affiliation(s)
- Feiyue Teng
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, New Jersey 07030, USA.
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38
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Bahrami A, Davis S, Mousavi Khaneghah A, Williams L. The efficiency of technologies used for epidemiological characterization of Listeria monocytogenes isolates : an update. Crit Rev Food Sci Nutr 2020; 62:1079-1091. [PMID: 33092402 DOI: 10.1080/10408398.2020.1835816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The characterization of pathogenic bacteria by providing information regarding the identification and source-tracking of the causes of outbreaks is vital for the epidemiological investigations of foodborne diseases. The knowledge of transmission of Listeria monocytogenes (L. monocytogenes) strains from the environment, directly or indirectly (through food processing facilities) to the final food products, due to the complexity of evaluating numerous, affecting parameters is quite limited. The food trade globalization also adds difficulties in tracking the association between the infection occurrence and causative pathogens, aiming to prevent their spread. The occurrence of listeriosis, a notifiable disease throughout the world, can either be sporadic or outbreak-related. Due to the importance of foodborne outbreaks from a public health aspect and its correspondence enormous economic losses, cross-linked surveillance studies regarding the contamination of foods by L. monocytogenes, besides identifying clusters and tracing the sources of infections on an international-scale to prevent and control L. monocytogenes outbreaks sounds very crucial. Contrary to the conventional typing methods, molecular-based techniques, such as whole-genome sequencing, owing to the capacity to discriminate L. monocytogenes strains down to single nucleotide differences, provide an accurate characterization of strains and tracking the causes of outbreaks. However, routinely using molecular-based methods depends on the required improvements in the affordability, proper timing, and preparing reliable, standardized bioinformatics facilities. This work was conducted to critically review the practical potential of diverse typing methods have been used for the characterization of L. monocytogenes and discuss how they might change the future of efforts for control of listeriosis.
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Affiliation(s)
- Akbar Bahrami
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Shurrita Davis
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Amin Mousavi Khaneghah
- Department of Food Science, Faculty of Food Engineering (FEA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Leonard Williams
- Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural, and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
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39
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Antkowiak PL, Lietard J, Darestani MZ, Somoza MM, Stark WJ, Heckel R, Grass RN. Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction. Nat Commun 2020; 11:5345. [PMID: 33093494 PMCID: PMC7582880 DOI: 10.1038/s41467-020-19148-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. The current hamstring of DNA data storage systems-both in cost and speed-is synthesis. The key idea for breaking this bottleneck pursued in this work is to move beyond the low-error and expensive synthesis employed almost exclusively in today's systems, towards cheaper, potentially faster, but high-error synthesis technologies. Here, we demonstrate a DNA storage system that relies on massively parallel light-directed synthesis, which is considerably cheaper than conventional solid-phase synthesis. However, this technology has a high sequence error rate when optimized for speed. We demonstrate that even in this high-error regime, reliable storage of information is possible, by developing a pipeline of algorithms for encoding and reconstruction of the information. In our experiments, we store a file containing sheet music of Mozart, and show perfect data recovery from low synthesis fidelity DNA.
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Affiliation(s)
- Philipp L Antkowiak
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria
| | - Mohammad Zalbagi Darestani
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354, Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354, Freising, Germany
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX, 77005, USA.
- Department of Electrical and Computer Engineering, Technical University of Munich, Theresienstr. 90, 80333, Munich, Germany.
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.
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40
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Stivanelli P, Tararam CA, Trabasso P, Levy LO, Melhem MSC, Schreiber AZ, Moretti ML. Visible DNA microarray and loop-mediated isothermal amplification (LAMP) for the identification of Cryptococcus species recovered from culture medium and cerebrospinal fluid of patients with meningitis. Braz J Med Biol Res 2020; 53:e9056. [PMID: 33053095 PMCID: PMC7561074 DOI: 10.1590/1414-431x20209056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 07/20/2020] [Indexed: 12/29/2022] Open
Abstract
Cryptococcal meningitis affects normal hosts and immunocompromised patients exhibiting high mortality rates. The objective of this study was to design two molecular assays, visible microarray platforms and loop-mediated isothermal amplification (LAMP), to identify Cryptococcus spp. and the species neoformans and gattii from the cerebral spinal fluid (CSF). To identify Cryptococcus and the two species, we designed two microarrays DNA platforms based on the internal transcribed spacer (ITS) region and CAP59 gene and LAMP assays specific for Cryptococcus species. The assays were tested using CSF from patients with cryptococcal meningitis. CSF from patients with cryptococcal meningitis was cultured in Sabouraud culture medium, and the Cryptococcus spp. grown in the culture medium were also tested for LAMP and microarray platforms. The results were compared to DNA sequencing of the same genetic regions. A total of 133 CSF samples were studied. Eleven CSFs were positive for Cryptococcus (9 C. neoformans and 2 C. gattii), 15 were positive for bacteria, and 107 were negative. The CAP59 platform correctly identified 73% of the CSF samples, while the ITS platform identified 45.5%. CAP59 platform correctly identified 100% of the Cryptococcus isolates, and ITS platform identified 70%. The two sets of LAMP primers correctly identified 100% of the Cryptococcus isolates. However, for CSF samples, the amplification occurred only in 55.5% of C. neoformans. The methodologies were reliable in the identification of Cryptococcus species, mainly for isolates from culture medium, and they might be applied as adjunctive tests to identify Cryptococcus species.
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Affiliation(s)
- P Stivanelli
- Departamento de Medicina Interna, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - C A Tararam
- Departamento de Medicina Interna, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - P Trabasso
- Departamento de Medicina Interna, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - L O Levy
- Departamento de Medicina Interna, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - M S C Melhem
- Instituto Adolfo Lutz, São Paulo, SP, Brasil.,Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - A Z Schreiber
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - M L Moretti
- Departamento de Medicina Interna, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Centro de Pesquisa em Obesidade e Comorbidades (CEPIDI), Universidade Estadual de Campinas, Campinas, SP, Brasil
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41
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The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020; 34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
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42
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Jones NK, Conway Morris A, Curran MD, Parmar S, Sule O, Enoch DA, Aliyu SH, Zhang H, Jalal H, Navapurkar V, Murphy ME. Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care. J Med Microbiol 2020; 69:971-978. [PMID: 32552987 DOI: 10.1099/jmm.0.001218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis.Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs.Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge's Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records.Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation.Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.
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Affiliation(s)
- Nick K Jones
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Conway Morris
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Olajumoke Sule
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sani H Aliyu
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hongyi Zhang
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hamid Jalal
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Vilas Navapurkar
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael E Murphy
- NHS GGC, Glasgow Royal Infirmary, Department of Clinical Microbiology, New Lister Building, Alexandra Parade, Glasgow, UK.,Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
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43
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Kumar A, Pandey SC, Samant M. DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment. Acta Trop 2020; 208:105512. [PMID: 32389452 DOI: 10.1016/j.actatropica.2020.105512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/04/2020] [Accepted: 04/18/2020] [Indexed: 02/05/2023]
Abstract
Visceral leishmaniasis (VL) is one of the major infectious diseases affecting the poorest regions of the world. Current therapy is not very much satisfactory. The alarming rise of drug resistance and the unavailability of an effective vaccine against VL urges research towards identifying new targets or biomarkers for its effective treatment. New technology developments offer some fresh hope in its diagnosis, treatment, and control. DNA microarray approach is now broadly used in parasitology research to facilitate the thoughtful of mechanisms of disease and identification of drug targets and biomarkers for diagnostic and therapeutic development. An electronic search on "VL" and "Microarray" was conducted in Medline and Scopus and papers published in the English mentioning use of DNA microarray on VL were selected and read to write this paper review. Functional analysis and interpretation of microarray results remain very challenging due to the inherent nature of experimental workflows, access, cost, and complexity of data obtained. We have explained and emphasized the use of curate knowledge of microarray in the case of VL for the identification of therapeutic target and biomarker and their selection/implementation in clinical use.
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Affiliation(s)
- Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur (Chhattisgarh), INDIA
| | - Satish Chandra Pandey
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA; Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Nainital (Uttarakhand), INDIA
| | - Mukesh Samant
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA.
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Zindler T, Frieling H, Neyazi A, Bleich S, Friedel E. Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies. BMC Bioinformatics 2020; 21:271. [PMID: 32605541 PMCID: PMC7328269 DOI: 10.1186/s12859-020-03559-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/26/2020] [Indexed: 12/04/2022] Open
Abstract
Background Systematic technical effects—also called batch effects—are a considerable challenge when analyzing DNA methylation (DNAm) microarray data, because they can lead to false results when confounded with the variable of interest. Methods to correct these batch effects are error-prone, as previous findings have shown. Results Here, we demonstrate how using the R function ComBat to correct simulated Infinium HumanMethylation450 BeadChip (450 K) and Infinium MethylationEPIC BeadChip Kit (EPIC) DNAm data can lead to a large number of false positive results under certain conditions. We further provide a detailed assessment of the consequences for the highly relevant problem of p-value inflation with subsequent false positive findings after application of the frequently used ComBat method. Using ComBat to correct for batch effects in randomly generated samples produced alarming numbers of false discovery rate (FDR) and Bonferroni-corrected (BF) false positive results in unbalanced as well as in balanced sample distributions in terms of the relation between the outcome of interest variable and the technical position of the sample during the probe measurement. Both sample size and number of batch factors (e.g. number of chips) were systematically simulated to assess the probability of false positive findings. The effect of sample size was simulated using n = 48 up to n = 768 randomly generated samples. Increasing the number of corrected factors led to an exponential increase in the number of false positive signals. Increasing the number of samples reduced, but did not completely prevent, this effect. Conclusions Using the approach described, we demonstrate, that using ComBat for batch correction in DNAm data can lead to false positive results under certain conditions and sample distributions. Our results are thus contrary to previous publications, considering a balanced sample distribution as unproblematic when using ComBat. We do not claim completeness in terms of reporting all technical conditions and possible solutions of the occurring problems as we approach the problem from a clinician’s perspective and not from that of a computer scientist. With our approach of simulating data, we provide readers with a simple method to assess the probability of false positive findings in DNAm microarray data analysis pipelines.
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Affiliation(s)
- Tristan Zindler
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany.
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexandra Neyazi
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Stefan Bleich
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Eva Friedel
- Department of Psychiatry and Psychotherapy, Charité Campus Mitte (CCM), Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), 10178, Berlin, Germany
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45
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Benkova M, Soukup O, Marek J. Antimicrobial susceptibility testing: currently used methods and devices and the near future in clinical practice. J Appl Microbiol 2020; 129:806-822. [DOI: 10.1111/jam.14704] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- M. Benkova
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - O. Soukup
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
- Department of Toxicology and Military Pharmacy Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
| | - J. Marek
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
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Baddal B. Next-generation technologies for studying host-pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips. Pathog Dis 2020; 77:5593955. [PMID: 31626299 DOI: 10.1093/femspd/ftz060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Pathogens constantly interact with their hosts and the environment, and therefore have evolved unique virulence mechanisms to target and breach host defense barriers and manipulate host immune response to establish an infection. Advances in technologies that allow genome mining, gene editing such as CRISPR/Cas9, genomic, epigenomic and transcriptomic studies such as dual RNA-seq, coupled with bioinformatics, have accelerated the field of host-pathogen interactions within a broad range of infection models. Underpinning of the molecular changes that accompany invasion of eukaryotic cells with pathogenic microorganisms at the intersection of host, pathogen and their local environment has provided a better understanding of infectious disease mechanisms and antimicrobial strategies. The recent evolution of physiologically relevant three-dimensional (3-D) tissue/organ models and microfluidic organ-on-chip devices also provided a window to a more predictive framework of infectious disease processes. These approaches combined hold the potential to highly impact discovery of novel drug targets and vaccine candidates of the future. Here, we review three of the available and emerging technologies-dual RNA-seq, CRISPR/Cas9 screening and organs-on-chips, applicable to the high throughput study and deciphering of interaction networks between pathogens and their hosts that are critical for the development of novel therapeutics.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Near East Boulevard, Nicosia 99010, Cyprus
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Song Y. The poly-thymine based DNA photolithography onto electrostatic coupling substrates. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 111:110795. [PMID: 32279781 DOI: 10.1016/j.msec.2020.110795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/14/2019] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
In order to develop a rapid and high fidelity process for DNA self-assembly with patterning, the pattern of thymine dimerization is presented onto electrostatically bound DNA substrate by photolithography. The ability of binding for the process, which is attenuated conditions such as contact with photomask and washing by solution buffer is evaluated by X-ray photoelectron spectroscopy (XPS). Through thymine dimerization and hybridization chain reaction (HCR), DNA patterns, including multi-patterns, are demonstrated. For expansion to protein molecular patterning, the target DNA is tethered to biotin, allowing patterning with streptavidin linked fluorophores such as Cy3-streptavidin and phyecocayine-streptavidin.
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Affiliation(s)
- Youngjun Song
- Department of Nano-Bioengineering, College of Life Science and Bioengineering, Incheon National University, Republic of Korea.
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Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens. EMERGING AND REEMERGING VIRAL PATHOGENS 2020. [PMCID: PMC7149755 DOI: 10.1016/b978-0-12-814966-9.00007-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite scientific advances, the diagnosis of infectious diseases is primarily possible through vaccination and later by antibiotics. Emerging and reemerging pathologies are still considered to be dangerous to humanity because of the unique nature of these diseases: it is the encounter between two living organisms that have coexisted for millions of years within the people on the same planet without being previously recognized. These infectious agents, such as bacteria, viruses, fungi, or parasites, pose no threat to humans. In fact, only a few hundred are able to inflict damage to the human host. In addition, the spectrum of human disease caused by a particular pathogen varies considerably depending on the factors related to the ecological agent, the host, and the infectious agents. Several emerging or reemerging infectious agents are organisms that could be used in biological control. The differentiation of a natural epidemic from a bioterrorian event is based on several epidemiological indices as well as on the molecular characterization of the pathogen(s) involved. The role of pathologists is indeed very important. It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. In a viral infection context, miRNAs have been connected with the interplay between host and pathogen and occupy a major role in the host–parasite interaction and pathogenesis. It is in this context that various molecular and nanomethods for the detection of emerging viruses and experimental validation of miRNAs during quelling viruses target transcripts will be discussed in this chapter.
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Benešová L, Golian J, Martišová P, Semjon B, Zajác P, Čapla J, Vlčko T. Authentication and preference mapping of ham. POTRAVINARSTVO 2019. [DOI: 10.5219/1263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Effective connection between the food industry and consumer demands are specific needs of consumers whitch were monitored in this study by using a preferential mapping method. Preference mapping is based on Principal Component Analysis (PCA), which is performed on preferences ratings given for each product and preferences of each consumer through an online questionnaire. Key features for the consumer choice were colour, odour, consistency, total flavour and overall appearance. We verified the composition and mapped the preferences of 10 hams purchased in Slovakia. In view of the persistence of identified cases of food counterfeiting and meat fraud, intensive monitoring and scrutiny is required through effective and accurate analytical methods, which are crucial for maintaining consumer confidence and ensuring compliance with local legislation and labeling. The reference approach for identifying animal species in food is the PCR method, which is however limited to several animal species, meat types. The use of microarray technology enables the identification of a wider range of animal species and greater user comfort, especially the speed of obtaining the results. It allows 24 animal species to be identified in one analysis in 8 samples at a time. Detection was performed using Chipron LCD Aarray Kit Meat 5.0. In all analyzed samples, components of animal origin were identified in accordance on the packaging of the products. The Meat 5.0 LCD chip, which was used for analysis, has detected the presence of other animal species.
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Clinical Studies of Ci-5, Sol-gel Encapsulated Multiplex Antibody Microarray for Quantitative Fluorometric Detection of Simultaneous Five Different Tumor Antigens. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3409-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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