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Mendes F, Miranda E, Amaral L, Carvalho C, Castro BB, Sousa MJ, Chaves SR. Novel yeast-based biosensor for environmental monitoring of tebuconazole. Appl Microbiol Biotechnol 2024; 108:10. [PMID: 38170307 PMCID: PMC10764535 DOI: 10.1007/s00253-023-12944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 01/05/2024]
Abstract
Due to increasing demand for high and stable crop production, human populations are highly dependent on pesticide use for growing and storing food. Environmental monitoring of these agrochemicals is therefore of utmost importance, because of their collateral effects on ecosystem and human health. Even though most current-use analytical methods achieve low detection limits, they require procedures that are too complex and costly for routine monitoring. As such, there has been an increased interest in biosensors as alternative or complementary tools to streamline detection and quantification of environmental contaminants. In this work, we developed a biosensor for environmental monitoring of tebuconazole (TEB), a common agrochemical fungicide. For that purpose, we engineered S. cerevisiae cells with a reporter gene downstream of specific promoters that are expressed after exposure to TEB and characterized the sensitivity and specificity of this model system. After optimization, we found that this easy-to-use biosensor consistently detects TEB at concentrations above 5 μg L-1 and does not respond to realistic environmental concentrations of other tested azoles, suggesting it is specific. We propose the use of this system as a complementary tool in environmental monitoring programs, namely, in high throughput scenarios requiring screening of numerous samples. KEY POINTS: • A yeast-based biosensor was developed for environmental monitoring of tebuconazole. •The biosensor offers a rapid and easy method for tebuconazole detection ≥ 5 μg L-1. •The biosensor is specific to tebuconazole at environmentally relevant concentrations.
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Affiliation(s)
- Filipa Mendes
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Eduarda Miranda
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Leslie Amaral
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Carla Carvalho
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Bruno B Castro
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Maria João Sousa
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Susana R Chaves
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal.
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Panchbudhe SA, Shivkar RR, Banerjee A, Deshmukh P, Maji BK, Kadam CY. Improving newborn screening in India: Disease gaps and quality control. Clin Chim Acta 2024; 557:117881. [PMID: 38521163 DOI: 10.1016/j.cca.2024.117881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
In India, newborn screening (NBS) is essential for detecting health problems in infants. Despite significant progress, significant gaps and challenges persist. India has made great strides in genomics dueto the existence of the National Institute of Biomedical Genomics in West Bengal. The work emphasizes the challenges NBS programs confront with technology, budgetary constraints, insufficient counseling, inequality in illness panels, and a lack of awareness. Advancements in technology, such as genetic testing and next-generation sequencing, are expected to significantly transform the process. The integration of analytical tools, artificial intelligence, and machine learning algorithms could improve the efficiency of newborn screening programs, offering a personalized healthcare approach. It is critical to address gaps in information, inequities in illness incidence, budgetary restrictions, and inadequate counseling. Strengthening national NBS programs requires increased public awareness and coordinated efforts between state and central agencies. Quality control procedures must be used at every level for implementation to be successful. Additional studies endeavor to enhance NBS in India through public education, illness screening expansion, enhanced quality control, government incentive implementation, partnership promotion, and expert training. Improved neonatal health outcomes and the viability of the program across the country will depend heavily on new technology and counseling techniques.
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Affiliation(s)
- Sanjyoti A Panchbudhe
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Rajni R Shivkar
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Arnab Banerjee
- Department of Physiology (UG & PG), Serampore College, 9 William Carey Road, Serampore, Hooghly 712201, West Bengal, India
| | - Paulami Deshmukh
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Bithin Kumar Maji
- Department of Physiology (UG & PG), Serampore College, 9 William Carey Road, Serampore, Hooghly 712201, West Bengal, India
| | - Charushila Y Kadam
- Department of Biochemistry, Sukh Sagar Medical College and Hospital, Jabalpur 482003, Madhya Pradesh, India.
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3
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Łukaszewicz P, Siudak P, Kropidłowska K, Caban M, Haliński ŁP. Unicellular cyanobacteria degrade sulfoxaflor to its amide metabolite of potentially higher aquatic toxicity. Chemosphere 2023; 337:139440. [PMID: 37422216 DOI: 10.1016/j.chemosphere.2023.139440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Sulfoxaflor (SFX) is a fourth-generation neonicotinoid used widely in modern agriculture. Due to its high water solubility and mobility in environment, it is expected to occur in water environment. Degradation of SFX leads to formation of corresponding amide (M474), which in the light of recent studies may be much more toxic to aquatic organisms than the parent molecule. Therefore, the aim of the study was to assess the potential of two common species of unicellular bloom-forming cyanobacteria (Synechocystis salina and Microcystis aeruginosa) to metabolize SFX in a 14-day-long experiment, using elevated (10 mg L-1) and predicted highest environmental (10 μg L-1) concentrations. The results obtained support the occurrence of SFX metabolism in cyanobacterial monocultures, leading to release of M474 into the water. Differential SFX decline in culture media, followed by the presence of M474, was observed for both species at different concentration levels. For S. salina, SFX concentration decreased by 7.6% at lower concentration and by 21.3% at higher concentration; the M474 concentrations were 436 ng L-1 and 514 μg L-1, respectively. Corresponding values for M. aeruginosa were 14.3% and 3.0% for SFX decline; 282 ng L-1 and 317 μg L-1 for M474 concentration. In the same time, abiotic degradation was almost non-existent. Metabolic fate of SFX was then studied for its elevated starting concentration. Uptake of SFX to cells and amounts of M474 released to water fully addressed the decrease in SFX concentration in M. aeruginosa culture, while in S. salina 15.5% of initial SFX was transformed to yet unknown metabolites. The degradation rate of SFX observed in the present study is sufficient to produce a concentration of M474 that is potentially toxic for aquatic invertebrates during cyanobacterial blooms. Therefore, there is a need for more reliable risk assessment for the presence of SFX in natural waters.
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Affiliation(s)
- Paulina Łukaszewicz
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Przemysław Siudak
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Klaudia Kropidłowska
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Magda Caban
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Łukasz P Haliński
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland.
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Kropp M, Golubnitschaja O, Mazurakova A, Koklesova L, Sargheini N, Vo TTKS, de Clerck E, Polivka J, Potuznik P, Polivka J, Stetkarova I, Kubatka P, Thumann G. Diabetic retinopathy as the leading cause of blindness and early predictor of cascading complications-risks and mitigation. EPMA J 2023; 14:21-42. [PMID: 36866156 PMCID: PMC9971534 DOI: 10.1007/s13167-023-00314-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 02/17/2023]
Abstract
Proliferative diabetic retinopathy (PDR) the sequel of diabetic retinopathy (DR), a frequent complication of diabetes mellitus (DM), is the leading cause of blindness in the working-age population. The current screening process for the DR risk is not sufficiently effective such that often the disease is undetected until irreversible damage occurs. Diabetes-associated small vessel disease and neuroretinal changes create a vicious cycle resulting in the conversion of DR into PDR with characteristic ocular attributes including excessive mitochondrial and retinal cell damage, chronic inflammation, neovascularisation, and reduced visual field. PDR is considered an independent predictor of other severe diabetic complications such as ischemic stroke. A "domino effect" is highly characteristic for the cascading DM complications in which DR is an early indicator of impaired molecular and visual signaling. Mitochondrial health control is clinically relevant in DR management, and multi-omic tear fluid analysis can be instrumental for DR prognosis and PDR prediction. Altered metabolic pathways and bioenergetics, microvascular deficits and small vessel disease, chronic inflammation, and excessive tissue remodelling are in focus of this article as evidence-based targets for a predictive approach to develop diagnosis and treatment algorithms tailored to the individual for a cost-effective early prevention by implementing the paradigm shift from reactive medicine to predictive, preventive, and personalized medicine (PPPM) in primary and secondary DR care management.
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Affiliation(s)
- Martina Kropp
- Division of Experimental Ophthalmology, Department of Clinical Neurosciences, University of Geneva University Hospitals, 1205 Geneva, Switzerland ,Ophthalmology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Alena Mazurakova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Nafiseh Sargheini
- Max Planck Institute for Plant Breeding Research, Carl-Von-Linne-Weg 10, 50829 Cologne, Germany
| | - Trong-Tin Kevin Steve Vo
- Division of Experimental Ophthalmology, Department of Clinical Neurosciences, University of Geneva University Hospitals, 1205 Geneva, Switzerland ,Ophthalmology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Eline de Clerck
- Division of Experimental Ophthalmology, Department of Clinical Neurosciences, University of Geneva University Hospitals, 1205 Geneva, Switzerland ,Ophthalmology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Jiri Polivka
- Department of Histology and Embryology, and Biomedical Centre, Faculty of Medicine in Plzen, Charles University, Prague, Czech Republic
| | - Pavel Potuznik
- Department of Neurology, University Hospital Plzen, and Faculty of Medicine in Plzen, Charles University, 100 34 Prague, Czech Republic
| | - Jiri Polivka
- Department of Neurology, University Hospital Plzen, and Faculty of Medicine in Plzen, Charles University, 100 34 Prague, Czech Republic
| | - Ivana Stetkarova
- Department of Neurology, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Gabriele Thumann
- Division of Experimental Ophthalmology, Department of Clinical Neurosciences, University of Geneva University Hospitals, 1205 Geneva, Switzerland ,Ophthalmology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland
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Zuliani A, Khiar N, Carrillo-Carrión C. Recent progress of metal-organic frameworks as sensors in (bio)analytical fields: towards real-world applications. Anal Bioanal Chem 2023;:1-19. [PMID: 36598537 DOI: 10.1007/s00216-022-04493-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
Abstract
The deployment of metal-organic frameworks (MOFs) in a plethora of analytical and bioanalytical applications is a growing research area. Their unique properties such as high but tunable porosity, well-defined channels or pores, and ease of post-synthetic modification to incorporate additional functional units make them ideal candidates for sensing applications. This is possible because the interaction of analytes with a MOF often results in a change in its structure, eventually leading to a modification of the intrinsic physicochemical properties of the MOF which is then transduced into a measurable signal. The high porosity allows for the adsorption of analytes very efficiently, while the tunable pore sizes/nature and/or installation of specific recognition groups allow modulating the affinity towards different classes of compounds, which in turn lead to good sensor sensitivity and selectivity, respectively. Some figures are given to illustrate the potential of MOF-based sensors in the most relevant application fields, and future challenges and opportunities to their possible translation from academia (i.e., laboratory testing of MOF sensing properties) to industry (i.e., real-world analytical sensor devices) are critically discussed.
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6
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Sheehan HC, Tilly JL, Woods DC. Assaying Mitochondrial Function by Multiparametric Flow Cytometry. Methods Mol Biol 2023; 2644:65-80. [PMID: 37142916 DOI: 10.1007/978-1-0716-3052-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Flow cytometry has been a vital tool in cell biology for decades based on its versatile ability to detect and quantifiably measure both physical and chemical attributes of individual cells within a larger population. More recently, advances in flow cytometry have enabled nanoparticle detection. This is particularly applicable to mitochondria, which, as intracellular organelles have distinct subpopulations that can be evaluated based on differences in functional, physical, and chemical attributes, in a manner analogous to cells. This includes distinctions based on size, mitochondrial membrane potential (ΔΨm), chemical properties, and protein expression on the outer mitochondrial membrane in intact, functional organelles and internally in fixed samples. This method allows for multiparametric analysis of subpopulations of mitochondria, as well as collection for downstream analysis down to the level of a single organelle. The present protocol describes a framework for analysis and sorting mitochondria by flow cytometry, termed fluorescence activated mitochondrial sorting (FAMS), based on the separation of individual mitochondria belonging to subpopulations of interest using fluorescent dyes and antibody labeling.
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Affiliation(s)
- Hannah C Sheehan
- Department of Biology, Laboratory for Aging and Infertility Research, Northeastern University, Boston, MA, USA
| | - Jonathan L Tilly
- Department of Biology, Laboratory for Aging and Infertility Research, Northeastern University, Boston, MA, USA
| | - Dori C Woods
- Department of Biology, Laboratory for Aging and Infertility Research, Northeastern University, Boston, MA, USA.
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Santos MC, Antonin VS, Souza FM, Aveiro LR, Pinheiro VS, Gentil TC, Lima TS, Moura JPC, Silva CR, Lucchetti LEB, Codognoto L, Robles I, Lanza MRV. Decontamination of wastewater containing contaminants of emerging concern by electrooxidation and Fenton-based processes - A review on the relevance of materials and methods. Chemosphere 2022; 307:135763. [PMID: 35952792 DOI: 10.1016/j.chemosphere.2022.135763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
In recent years, there has been an increasingly growing interest regarding the use of electrochemical advanced oxidation processes (EAOPs) which are considered highly promising alternative treatment techniques for addressing environmental issues related to pollutants of emerging concern. In EAOPs, electrogenerated oxidizing agents, such as hydroxyl radical (HO•), can react non-selectively with a wide range of organic compounds, degrading and mineralizing their structures to unharmful molecules like CO2, H2O, and inorganic ions. To this date, a broad spectrum of advanced electrocatalysts have been developed and applied for the treatment of compounds of interest in different matrices, specifically aiming at enhancing the degradation performance. New combined methods have also been employed as alternative treatment techniques targeted at circumventing the major obstacles encountered in Fenton-based processes, such as high costs and energy consumption, which still contribute significantly toward inhibiting the large-scale application of these processes. First, some fundamental aspects of EAOPs will be presented. Further, we will provide an overview of electrode materials which have been recently developed and reported in the literature, highlighting different anode and cathode structures employed in EAOPs, their main advantages and disadvantages, as well as their contribution to the performance of the treatment processes. The influence of operating parameters, such as initial concentrations, pH effect, temperature, supporting electrolyte, and radiation source, on the treatment processes were also studied. Finally, hybrid techniques which have been reported in the literature and critically assess the most recent techniques used for evaluating the degradation efficiency of the treatment processes.
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Affiliation(s)
- Mauro C Santos
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil.
| | - Vanessa S Antonin
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Felipe M Souza
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil; Departamento de Química, Instituto Federal de Educação, Ciência e Tecnologia Goiano, BR-153, Km 633, Zona Rural, CEP: 75650-000, Morrinhos, GO, Brazil
| | - Luci R Aveiro
- São Paulo Federal Institute of Education, Science and Technology, Rua Pedro Vicente, 625, Canindé São Paulo, CEP: 01109-010, SP, Brazil
| | - Victor S Pinheiro
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Tuani C Gentil
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Thays S Lima
- Department of Chemistry, Institute of Chemical and Pharmaceutical Environmental Sciences, Federal University of São Paulo (UNIFESP), Rua Prof. Artur Riedel, n 275 - Jd. Eldorado, CEP: 09972-270, Diadema, SP, Brazil
| | - João P C Moura
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Carolina R Silva
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Lanna E B Lucchetti
- Laboratory of Eletrochemistry and Nanostructured Materials (LEMN) Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), CEP: 09210-170, Rua Santa Adélia 166, Bairro Bangu, Santo André, SP, Brazil
| | - Lucia Codognoto
- Department of Chemistry, Institute of Chemical and Pharmaceutical Environmental Sciences, Federal University of São Paulo (UNIFESP), Rua Prof. Artur Riedel, n 275 - Jd. Eldorado, CEP: 09972-270, Diadema, SP, Brazil
| | - Irma Robles
- Center for Research and Technological Development in Electrochemistry, S.C., Parque Tecnológico Querétaro, 76703, Sanfandila, Pedro Escobedo, Querétaro, Mexico
| | - Marcos R V Lanza
- São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Avenida Trabalhador São-carlense 400, São Carlos, SP, 13566-590, Brazil
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Wang N, Jin S. Meta-Analysis for Epigenome-Wide Association Studies. Methods Mol Biol 2022; 2432:101-111. [PMID: 35505210 DOI: 10.1007/978-1-0716-1994-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the rapid development of methylation profiling technology, many datasets are generated to quantify genome-wide methylation patterns. Given the heavy burden of multiple testing of hundreds of thousands of DNA methylation markers, individual studies often have limited sample sizes and power. The EWAS meta-analysis is an approach that combines results from multiple studies on the same scientific question. It helps to improve statistical power by combining information from individual studies and reduce the chances of false positives. This chapter introduces commonly used meta-analysis methods and analytical tools with application to EWAS data.
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Affiliation(s)
- Nan Wang
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| | - Shuilin Jin
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, China.
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Yue J, Zuo Z, Huang H, Wang Y. Application of Identification and Evaluation Techniques for Ethnobotanical Medicinal Plant of Genus Panax: A Review. Crit Rev Anal Chem 2020; 51:373-398. [PMID: 32166968 DOI: 10.1080/10408347.2020.1736506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Genus Panax, as worldwide medicinal plants, has a medical history for thousands of years. Most of the entire genus are traditional ethnobotanical medicine in China, Myanmar, Thailand, Vietnam and Laos, which have given rise to international attention and use. This paper reviewed more than 210 articles and related books on the research of Panax medicinal plants and their Chinese patent medicines published in the last 30 years. The purpose was to review and summarize the species classification, geographical distribution, and ethnic minorities medicinal records of the genus Panax, and further to review the analytical tools and data analysis methods for the authentication and quality assessment of Panax medicinal materials and Chinese patent medicines. Five main technologies applied in the identification and evaluation of Panax have been introduced and summarized. Chromatography was the most widely used one. Further research and development of molecular identification technology had the potential to become a mainstream identification technology. In addition, some novel, controversial, and worthy methods including electronic noses, electronic eyes, and DNA barcoding were also introduced. At the same time, more than 80% of the researches were carried out by a combination of chemometric pattern-recognition technologies and multi-analysis technologies. All the technologies and methods applied can provide strong support and guarantee for the identification and evaluation of genus Panax, and also conduce to excellent reference value for the development and in-depth research of new technologies in Panax.
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Affiliation(s)
- Jiaqi Yue
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.,College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhitian Zuo
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hengyu Huang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Yuanzhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Melnyk T, Đorđević S, Conejos-Sánchez I, Vicent MJ. Therapeutic potential of polypeptide-based conjugates: Rational design and analytical tools that can boost clinical translation. Adv Drug Deliv Rev 2020; 160:136-169. [PMID: 33091502 DOI: 10.1016/j.addr.2020.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
The clinical success of polypeptides as polymeric drugs, covered by the umbrella term "polymer therapeutics," combined with related scientific and technological breakthroughs, explain their exponential growth in the development of polypeptide-drug conjugates as therapeutic agents. A deeper understanding of the biology at relevant pathological sites and the critical biological barriers faced, combined with advances regarding controlled polymerization techniques, material bioresponsiveness, analytical methods, and scale up-manufacture processes, have fostered the development of these nature-mimicking entities. Now, engineered polypeptides have the potential to combat current challenges in the advanced drug delivery field. In this review, we will discuss examples of polypeptide-drug conjugates as single or combination therapies in both preclinical and clinical studies as therapeutics and molecular imaging tools. Importantly, we will critically discuss relevant examples to highlight those parameters relevant to their rational design, such as linking chemistry, the analytical strategies employed, and their physicochemical and biological characterization, that will foster their rapid clinical translation.
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Affiliation(s)
- Tetiana Melnyk
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Snežana Đorđević
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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11
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Cejas P, Long HW. Principles and methods of integrative chromatin analysis in primary tissues and tumors. Biochim Biophys Acta Rev Cancer 2019; 1873:188333. [PMID: 31759992 DOI: 10.1016/j.bbcan.2019.188333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Recent methodological advances have enabled the genome-wide interrogation of chromatin from primary tumor tissues. Integrative analysis of histone post-translational modifications, transcription factor (TF) binding and open chromatin sites in tumors across cancer stages can elucidate the aberrant epigenetic states accompanying tumor progression. Cancer-associated chromatin alterations can activate or inactivate enhancers at genes involved in cancer while still respecting cell-of-origin constrictions. Accordingly, enhancer analysis in cancer could have uses for biomarker discovery to further refine patient diagnosis and potentially sub-classify patients for tailored therapy. Methodologies used for chromatin analyses of primary tissues need to address issues distinct from cell line studies including the specific sources of variability coming from the heterogeneous cellular composition of tissues and from inter-individual (epi)genetic differences. This leads to requirements for careful histological analysis to select the specific samples and cells of interest. In analyzing tumors somatic changes should be taken into account to distinguish the genuine epigenetic changes across tumor specimens from any genetic alterations such as copy number variations (CNV). In this contribution we review a selection of current results from chromatin profiling, examine experimental methodologies and discuss specific analysis approaches. We also review specific considerations regarding tissue preparation for epigenetic analysis and conclude with our perspectives on emerging approaches that will impact studies of chromatin landscapes of clinical samples in the future.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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12
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Grassino AN, Barba FJ, Brnčić M, Lorenzo JM, Lucini L, Brnčić SR. Analytical tools used for the identification and quantification of pectin extracted from plant food matrices, wastes and by-products: A review. Food Chem 2018; 266:47-55. [PMID: 30381214 DOI: 10.1016/j.foodchem.2018.05.105] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 11/18/2022]
Abstract
Pectin is the methylated ester of polygalacturonic acid and has a wide range of applications. It can be used in food and animal feed as well as in pharmaceutical and cosmetic products. Pectin is traditionally used as a gelling agent in fruit-based products, as a stabilizer in some fruit juices and milk drinks and fruit filling for bakery and confectionary products, but their potential applications differ according to their chemical composition. Therefore, at this stage of development, it is of a great importance to find fast, reliable methods to not only identify and quantify pectin, but also to determine its chemical structure and composition when it is extracted from plant matrices, wastes and by-products. The present review will focus on the analytical tools used to identify and quantify the amount of pectin obtained from plant matrices, wastes and by-products as well as determining its chemical and structural composition.
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Affiliation(s)
| | - Francisco J Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Avda. Vicent Andrés Estellés, s/n, 46100 Burjassot, València, Spain.
| | - Mladen Brnčić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia.
| | - Jose M Lorenzo
- Centro Tecnológico de la Carne de Galicia, c/Galicia, 4, San Ciprián de Viñas, Ourense, Spain
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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Bayart C, Peronin S, Jean E, Paladino J, Talaga P, Borgne ML. The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1054:80-92. [PMID: 28448854 DOI: 10.1016/j.jchromb.2017.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/27/2017] [Accepted: 04/02/2017] [Indexed: 10/19/2022]
Abstract
Aldehyde detoxification is a process used to convert toxin into toxoid for vaccine applications. In the case of tetanus toxin (TT), formaldehyde is used to obtain the tetanus toxoid (TTd), which is used either for the tetanus vaccine or as carrier protein in conjugate vaccines. Several studies have already been conducted to better understand the exact mechanism of this detoxification. Those studies led to the identification of a number of formaldehyde-induced modifications on lab scale TTd samples. To obtain greater insights of the changes induced by formaldehyde, we used three industrial TTd batches to identify repeatable modifications in the detoxification process. Our strategy was to combine seven analytical tools to map these changes. Mass spectrometry (MS), colorimetric test and amino acid analysis (AAA) were used to study modifications on amino acids. SDS-PAGE, asymmetric flow field flow fractionation (AF4), fluorescence spectroscopy and circular dichroism (CD) were used to study formaldehyde modifications on the whole protein structure. We identified 41 formaldehyde-induced modifications across the 1315 amino acid primary sequence of TT. Of these, five modifications on lysine residues were repeatable across TTd batches. Changes in protein conformation were also observed using SDS-PAGE, AF4 and CD techniques. Each analytical tool brought a piece of information regarding formaldehyde induced-modifications, and all together, these methods provided a comprehensive overview of the structural changes that occurred with detoxification. These results could be the first step leading to site-directed TT mutagenesis studies that may enable the production of a non-toxic equivalent protein without using formaldehyde.
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Affiliation(s)
- Caroline Bayart
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453 -INSERM US7, 8 avenue Rockefeller, F-69373, Lyon Cedex 8, France; Reaction and Coupling Chemistry Laboratory, MTech, Sanofi Pasteur, 31/33 quai Armand Barbès, 69250 Neuville-sur-Saône, France
| | - Sébastien Peronin
- Structural Analysis Laboratory, MTech, Sanofi Pasteur, 31/33 quai Armand Barbès, 69250 Neuville-sur-Saône, France
| | - Elisa Jean
- Reaction and Coupling Chemistry Laboratory, MTech, Sanofi Pasteur, 31/33 quai Armand Barbès, 69250 Neuville-sur-Saône, France
| | - Joseph Paladino
- Reaction and Coupling Chemistry Laboratory, MTech, Sanofi Pasteur, 31/33 quai Armand Barbès, 69250 Neuville-sur-Saône, France
| | - Philippe Talaga
- Analytical Research and Development Department, Sanofi Pasteur, Campus Mérieux,1541 Avenue Marcel Mérieux, 69280 Marcy L'Etoile, France
| | - Marc Le Borgne
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453 -INSERM US7, 8 avenue Rockefeller, F-69373, Lyon Cedex 8, France.
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Adler C, Schönenberger M, Teleki A, Leuenberger B, Kuentz M. Flow-through cross-polarized imaging as a new tool to overcome the analytical sensitivity challenges of a low-dose crystalline compound in a lipid matrix. J Pharm Biomed Anal 2015; 115:20-30. [PMID: 26142560 DOI: 10.1016/j.jpba.2015.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/19/2015] [Accepted: 06/21/2015] [Indexed: 11/18/2022]
Abstract
Assessing the physical state of a low-dose active compound in a solid lipid or polymer matrix is analytically challenging, especially if the matrix exhibits some crystallinity. The aim of this study was first to compare the ability of current methods to detect the presence of a crystalline model compound in lipid matrices. Subsequently, a new technique was introduced and evaluated because of sensitivity issues that were encountered with current methods. The new technique is a flow-through version of cross-polarized imaging in transmission mode. The tested lipid-based solid dispersions (SDs) consisted of β-carotene (BC) as a model compound, and of Gelucire 50/13 or Geleol mono- and diglycerides as lipid matrices. The solid dispersions were analyzed by (hyper) differential scanning calorimetry (DSC), X-ray powder diffraction (XRPD), and microscopic techniques including atomic force microscopy (AFM). DSC and XRPD could analyze crystalline BC at concentrations as low as 3% (w/w) in the formulations. However, with microscopic techniques crystalline particles were detected at significantly lower concentrations of even 0.5% (w/w) BC. A flow-through cross-polarized imaging technique was introduced that combines the advantage of analyzing a larger sample size with high sensitivity of microscopy. Crystals were detected easily in samples containing even less than 0.2% (w/w) BC. Moreover, the new tool enabled approximation of the kinetic BC solubility in the crystalline lipid matrices. As a conclusion, the flow-through cross-polarized imaging technique has the potential to become an indispensable tool for characterizing low-dose crystalline compounds in a lipid or polymer matrix of solid dispersions.
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Affiliation(s)
- Camille Adler
- University of Applied Sciences and Arts Northwestern Switzerland, Institute of Pharmaceutical Technology, Gründenstrasse 40, 4132 Muttenz, Switzerland; University of Basel, Institute of Pharmaceutical Technology, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Monica Schönenberger
- Swiss Nanoscience Institute, Nanotech Service Lab, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Alexandra Teleki
- DSM Nutritional Products Ltd., Research Center Formulation & Application, P.O. Box 2676, 4002 Basel, Switzerland
| | - Bruno Leuenberger
- DSM Nutritional Products Ltd., Research Center Formulation & Application, P.O. Box 2676, 4002 Basel, Switzerland
| | - Martin Kuentz
- University of Applied Sciences and Arts Northwestern Switzerland, Institute of Pharmaceutical Technology, Gründenstrasse 40, 4132 Muttenz, Switzerland.
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Abstract
Tick-borne diseases (TBDs) are a major public health concern that has increased in the past three decades. Nevertheless, emerging or reemerging TBDs may be still misdiagnosed. Molecular biology techniques for the screening of ticks, use of “Omics” approaches and the incorporation of analytical methods such as mass spectrometry or nuclear magnetic resonance, to the study of ticks and their associated pathogens or potential pathogens are promising tools for a more accurate differential diagnosis of TBDs. However, this huge amount of data needs to be carefully interpreted before being incorporated to the routine of clinical practice. In the meantime, a clinical approach and high level of suspicion keep being essential for the diagnosis and proper handling of TBDs.
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