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Cheong IH, Zhao Y, Jiang M, Lei S, Wang H, Kozlakidis Z, Wei Q. Technical Guideline for Low-Temperature Preservation of Pathogenic Microorganisms in China and Its Relevance to Developing Countries. Biopreserv Biobank 2024. [PMID: 38963755 DOI: 10.1089/bio.2024.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024] Open
Affiliation(s)
- Io Hong Cheong
- School of Public Health, Shanghai Jiao Tong University of Medicine, Shanghai, China
| | - Yuanyuan Zhao
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Suwen Lei
- Office of Health Standards, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University of Medicine, Shanghai, China
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing, China
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Enya K, Yamagishi A, Kobayashi K, Yoshimura Y, Tasker EJ. A Comparative Study of Methods for Detecting Extraterrestrial Life in Exploration Missions to Mars and the Solar System II: Targeted Characteristics, Detection Techniques, and Their Combination for Survey, Detection, and Analysis. ASTROBIOLOGY 2023; 23:1099-1117. [PMID: 37768711 PMCID: PMC10616949 DOI: 10.1089/ast.2022.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
Abstract
We present a comparative study of the methods used in the search for extraterrestrial microorganism life, including a summary table where different life-detection techniques can be easily compared as an aid to mission and instrument design aimed at life detection. This is an extension of previous study, where detection techniques for a series of target characteristics and molecules that could constitute a positive life detection were evaluated. This comparison has been extended with a particular consideration to sources of false positives, the causes of negative detection, the results of detection techniques when presented regarding terrestrial life, and additional science objectives that could be achieved outside the primary aim of detecting life. These additions address both the scientific and programmatic side of exploration mission design, where a successful proposal must demonstrate probable outcomes and be able to return valuable results even if no life is found. The applicability of the life detection techniques is considered for Earth life, Earth-independent life (life emerging independently from that on Earth,) and Earth-kin life (sharing a common ancestor with life on Earth), and techniques effective in detecting Earth life should also be useful in the detection of Earth-kin life. However, their applicability is not guaranteed for Earth-independent life. As found in our previous study, there exists no realistic single detection method that can conclusively determine the discovery of extraterrestrial life, and no method is superior to all others. In this study, we further consider combinations of detection techniques and identify imaging as a valuable addition to molecule detection methods, even in cases where there is insufficient resolution to observe the detailed morphology of a microbial cell. The search for extraterrestrial life is further divided into a survey-and-detection and analysis-and-conclusion step. These steps benefit from different detection techniques, but imaging is necessary for both parts.
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Affiliation(s)
- Keigo Enya
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kensei Kobayashi
- Department of Chemistry, Yokohama National University, Yokohama, Japan
- Department of Earth and Planetary Science, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Elizabeth J. Tasker
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
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Li G, Zhu S, Long J, Mao H, Dong Y, Hou Y. Differences in microbial community structure and metabolic activity among tea plantation soils under different management strategies. Front Microbiol 2023; 14:1219491. [PMID: 37601365 PMCID: PMC10433390 DOI: 10.3389/fmicb.2023.1219491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Microorganisms play an important role in the multifunctionality of soil ecosystems. Soil microbial diversity and functions have a great impact on plant growth and development. The interactions between tea trees and soil microbiota can be linked with planting patterns and management strategies, whose effects on soil microbial community structure and metabolites are still unclear. Methods Here we used amplicon sequencing and metabolomic analysis to investigate the differences in soil microbial composition and metabolites among three tea production systems: organic, non-organic, and intercropping. Results We detected significant differences among the three systems and found that Firmicutes, Proteobacteria, Acidobacteriota, Actinobacteriota and Chloroflexi were the main bacteria in the three soil groups, although they varied in relative abundance. Acidobacteria bacterium increased significantly in the organic and intercropping groups. For fungi, Ascomycota and Basidiomycota were the main differential fungal phyla. Fungi alpha-diversity in the non-organic group was significantly higher than that in the other two groups, and was correlated with multiple soil physical and chemical factors. Moreover, network analysis showed that bacteria and fungi were strongly correlated. The changes in soil microorganisms caused by management and planting patterns may affect soil quality through corresponding changes in metabolites. Metabolomic analysis showed differences in metabolite composition among different groups. It was also found that the arachidonic acid metabolic pathway was affected by changes in soil microorganisms, and may further affect soil quality in an essential manner. Discussion Planting patterns and management strategies may significantly affect soil microorganisms and therefore metabolites. Changes in soil microorganisms, especially in fungi, may alter soil quality by affecting soil physicochemical properties and metabolites. This study will provide new insights into soil quality monitoring from a microbiological perspective.
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Affiliation(s)
- Guoyou Li
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Shaoxian Zhu
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Jiang Long
- Xishuangbanna Luoboshanren Tea Co., Ltd., Menghai, China
| | - Honglin Mao
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Yonghong Dong
- Yunnan Pulis Biotechnology Co., Ltd., Kunming, China
| | - Yan Hou
- College of Tea Science, Yunnan Agriculture University, Kunming, China
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Killer J, Bunešová VN, Modráčková N, Vlková E, Pechar R, Šplíchal I. Lactulose in combination with soybean lecithin has a cryoprotective effect on probiotic taxa of bifidobacteria and Lactobacillaceae. Lett Appl Microbiol 2023; 76:6993074. [PMID: 36657381 DOI: 10.1093/lambio/ovad008] [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: 08/26/2022] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Lactulose is commonly used in pharmacy for constipation and hepatic encephalopathy treatment. The prebiotic effect of lactulose is also often mentioned. However, its cryoprotective effect in combination with lecithin on the main representatives of probiotics has not been tested yet. The 12 taxa of bifidobacteria and Lactobacillaceae members were used for the purpose. These were mixed in a ratio of 1:1 with lactulose + lecithin (finally 5.0% and 1.25%, respectively; LL). The 25% glycerol (G+) solution and cultures themselves were applied as positive and negative controls, respectively. Bacterial suspensions were stored at a mild freezing temperature (-20°C) until the end of the experiment (210th day). The LL solution had a comparable (insignificant difference at the P-value = 0.05) cryoprotective effect as the positive control in five of six bifidobacteria and in three of six representatives of Lactobacillaceae. The better cryoprotective effect was revealed in other Lactobacillaceae. At the end of the experiment, the generally accepted therapeutic minimum (>107 Colony Forming Units/mL) was determined in LL solution in five bifidobacteria and four Lactobacillaceae strains. The presented results improve knowledge about long-term mild cryopreservation of the most commonly used probiotics and could contribute to developing new forms of (nutri)synbiotics.
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Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, v. v. i.; Vídeňská 1083, 142 20 Prague 4-Krč, Czech Republic.,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic
| | - Věra Neužil Bunešová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic
| | - Nikol Modráčková
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic.,Food Research Institute Prague, Radiová 1285/7, 102 00 Prague 10-Hostivař, Czech Republic
| | - Igor Šplíchal
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 549 22 Nový Hrádek, Czech Republic
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Helmy M, Elhalis H, Liu Y, Chow Y, Selvarajoo K. Perspective: Multiomics and Machine Learning Help Unleash the Alternative Food Potential of Microalgae. Adv Nutr 2023; 14:1-11. [PMID: 36811582 PMCID: PMC9780023 DOI: 10.1016/j.advnut.2022.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Food security has become a pressing issue in the modern world. The ever-increasing world population, ongoing COVID-19 pandemic, and political conflicts together with climate change issues make the problem very challenging. Therefore, fundamental changes to the current food system and new sources of alternative food are required. Recently, the exploration of alternative food sources has been supported by numerous governmental and research organizations, as well as by small and large commercial ventures. Microalgae are gaining momentum as an effective source of alternative laboratory-based nutritional proteins as they are easy to grow under variable environmental conditions, with the added advantage of absorbing carbon dioxide. Despite their attractiveness, the utilization of microalgae faces several practical limitations. Here, we discuss both the potential and challenges of microalgae in food sustainability and their possible long-term contribution to the circular economy of converting food waste into feed via modern methods. We also argue that systems biology and artificial intelligence can play a role in overcoming some of the challenges and limitations; through data-guided metabolic flux optimization, and by systematically increasing the growth of the microalgae strains without negative outcomes, such as toxicity. This requires microalgae databases rich in omics data and further developments on its mining and analytics methods.
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Affiliation(s)
- Mohamed Helmy
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore; Department of Computer Science, Lakehead University, Ontario, Canada
| | - Hosam Elhalis
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Yan Liu
- Institute of Sustainability for Chemistry, Energy and Environment (ISCE(2)), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Yvonne Chow
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Kumar Selvarajoo
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore; Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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Prediction of frozen virus stability based on degradation mechanisms, real-time data and modeling. Bioanalysis 2022; 14:1177-1190. [DOI: 10.4155/bio-2022-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Critical virus reagents in regulated bioanalytical assays require stability monitoring. Although stability at ultralow frozen temperatures is generally assumed, published data are limited and real-time studies are time consuming. Materials & methods: The authors reviewed literature data, typical mechanisms of molecular degradation, glass transition temperatures of commonly used buffers and available real-time storage data to model frozen virus reagent stability. Results: Storage at ultralow temperatures below the glass transition temperature was critical for virus stability. Modeling of real-time data suggested that virus potency remained within 0.5 log10 of its starting potency at a probability of >99, 90 and 73% after 10, 20 and 30 years, respectively. Conclusion: The study supports the practice of virus storage at -70°C or below for 20–30 years.
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Villalba R, Mirabet V. Risk assessment of hepatitis E transmission through tissue allografts. World J Gastrointest Pathophysiol 2022; 13:50-58. [PMID: 35433096 PMCID: PMC8976234 DOI: 10.4291/wjgp.v13.i2.50] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/06/2021] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis E virus (HEV) is a small non-enveloped single stranded RNA virus whose genotypes 3 and 4 have been associated with zoonotic transmission in industrialized countries. HEV infection is considered the main cause of acute hepatitis worldwide. In some cases, transfusion of blood components or organ transplantation have been reported as the source of infection. We have conducted a literature review on the risk of transmission through cell and tissue allografts. Although no case was found, measures to control this risk should be taken when donor profile (based upon geographical and behavioural data) recommended it. Issues to be considered in donor screening and tissue processing to assess and to reduce the risk of HEV transmission are approached.
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Affiliation(s)
- Rafael Villalba
- Center for Blood Transfusion, Tissues and Cells, Córdoba 14004, Spain
| | - Vicente Mirabet
- Cell and Tissue Bank, Centro de Transfusión de Valencia, Valencia 46014, Spain
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SARS-CoV-2 RNA Recovery from Air Sampled on Quartz Fiber Filters: A Matter of Sample Preservation? ATMOSPHERE 2022. [DOI: 10.3390/atmos13020340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The airborne route of transmission of SARS-CoV-2 was confirmed by the World Health Organization in April 2021. There is an urge to establish standardized protocols for assessing the concentration of SARS-CoV-2 RNA in air samples to support risk assessment, especially in indoor environments. Debates on the airborne transmission route of SARS-CoV-2 have been complicated because, among the studies testing the presence of the virus in the air, the percentage of positive samples has often been very low. In the present study, we report preliminary results on a study for the evaluation of parameters that can influence SARS-CoV-2 RNA recovery from quartz fiber filters spotted either by standard single-stranded SARS-CoV-2 RNA or by inactivated SARS-CoV-2 virions. The analytes were spiked on filters and underwent an active or passive sampling; then, they were preserved at −80 °C for different numbers of days (0 to 54) before extraction and analysis. We found a mean recovery of 2.43%, except for the sample not preserved (0 days) that showed a recovery of 13.51%. We found a relationship between the number of days and the recovery percentage. The results presented show a possible issue that relates to the quartz matrix and SARS-CoV-2 RNA recovery. The results are in accordance with the already published studies that described similar methods for SARS-CoV-2 RNA field sampling and that reported non-detectable concentrations of RNA. These outcomes could be false negatives due to sample preservation conditions. Thus, until further investigation, we suggest, as possible alternatives, to keep the filters: (i) in a sealed container for preservation at 4 °C; and (ii) in a viral transport medium for preservation at a temperature below 0 °C.
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Formulation and functionalization of linalool nanoemulsion to boost its antibacterial properties against major foodborne pathogens. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Comparison of Preservation Methods of Staphylococcus aureus and Escherichia coli Bacteria. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.3.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most important problems faced by microbiologists is to preserve bacterial isolates in the best state to study and further diagnosis. The current study aims to provide a summary of experimental results to maintain two species of bacteria alive after being stored by using some additives. This study found that the best temperature to preserve Staphylococcus aureus was -20°C for a year, while for Escherichia coli it was the same temperature except in using Glycerol (G) 100% and Food oil (FO) methods. The optimum method to preserve S. aureus was by using Normal Saline (NS), while Distilled Water (DW) was the optimum method to preserve E. coli at temperatures (4, 25 and -20)°C for a year, the phenotypic patterns for examining bacteria were maintained except in NS at 4°C for S. aureus after a year ago. Glycerol was used alone at concentrations (100, 50, 30 and 15)%, and another group used G+NS in the same volumes, good results were achieved when it used alone or with NS to preserve bacteria for six months at 4°C except for methods of G100% and (G100% + NS) for examining bacteria. FO has never been used as preservation liquid, it is successful to survive S. aureus at -20°C for a year, and when it was added to NS, E. coli survived for a year at three temperatures (4, 25 and -20)°C, while S. aureus didn’t survive for a year when FO+NS method used at room temperature. The precipitation method was used for bacterial suspension, then added the preserving liquid, but the results were not effective compared to the First method.
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Higdon SM, Pozzo T, Tibbett EJ, Chiu C, Jeannotte R, Weimer BC, Bennett AB. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts. PLoS One 2020; 15:e0239081. [PMID: 32925972 PMCID: PMC7489573 DOI: 10.1371/journal.pone.0239081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N2-fixing) bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and composed three major diazotrophic groups based on nitrogen fixation gene content. In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization as alternative mechanisms of direct plant growth promotion (PGP). Genome mining showed that isolates of all diazotrophic groups possessed marker genes for multiple mechanisms of direct plant growth promotion (PGP). Implementing in vitro assays corroborated isolate genotypes by measuring each isolate's potential to confer the targeted PGP traits and revealed phenotypic variation among isolates based on diazotrophic group assignment. Investigating the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta led to the identification of 16 bio-stimulant candidates. Conducting nitrogen-stress greenhouse experiments demonstrated that potato inoculation with a synthetic community of bio-stimulant candidates, as well as with its individual components, resulted in PGP phenotypes. We further demonstrated that one diazotrophic isolate conferred PGP to a conventional maize variety under nitrogen-stress in the greenhouse. These results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize, potentially through the use of multiple promotion mechanisms.
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Affiliation(s)
- Shawn M. Higdon
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Tania Pozzo
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Emily J. Tibbett
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Colleen Chiu
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Bart C. Weimer
- Department of Population Health and Reproduction, University of California, Davis, California, United States of America
| | - Alan B. Bennett
- Department of Plant Sciences, University of California, Davis, California, United States of America
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Zak JD, Wallace J, Murthy VN. How neuroscience labs can limit their environmental impact. Nat Rev Neurosci 2020; 21:347-348. [PMID: 32385420 DOI: 10.1038/s41583-020-0311-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joseph D Zak
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jenelle Wallace
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Molecules, Cells, and Organisms Training Program, Harvard University, Cambridge, MA, USA
| | - Venkatesh N Murthy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Center for Brain Science, Harvard University, Cambridge, MA, USA.
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Cushnie TPT, Cushnie B, Echeverría J, Fowsantear W, Thammawat S, Dodgson JLA, Law S, Clow SM. Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls. Pharm Res 2020; 37:125. [PMID: 32529587 DOI: 10.1007/s11095-020-02849-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022]
Abstract
Bioprospecting is the exploration, extraction and screening of biological material and sometimes indigenous knowledge to discover and develop new drugs and other products. Most antibiotics in current clinical use (eg. β-lactams, aminoglycosides, tetracyclines, macrolides) were discovered using this approach, and there are strong arguments to reprioritize bioprospecting over other strategies in the search for new antibacterial drugs. Academic institutions should be well positioned to lead the early stages of these efforts given their many thousands of locations globally and because they are not constrained by the same commercial considerations as industry. University groups can lack the full complement of knowledge and skills needed though (eg. how to tailor screening strategy to biological source material). In this article, we review three key aspects of the bioprospecting literature (source material and in vitro antibacterial and toxicity testing) and present an integrated multidisciplinary perspective on (a) source material selection, (b) legal, taxonomic and other issues related to source material, (c) cultivation methods, (d) bioassay selection, (e) technical standards available, (f) extract/compound dissolution, (g) use of minimum inhibitory concentration and selectivity index values to identify progressible extracts and compounds, and (h) avoidable pitfalls. The review closes with recommendations for future study design and information on subsequent steps in the bioprospecting process.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand.
| | - Benjamart Cushnie
- Faculty of Pharmacy, Mahasarakham University, Kantarawichai, Thailand
| | - Javier Echeverría
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Winita Fowsantear
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | - Sutthiwan Thammawat
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | | | - Samantha Law
- National Collection of Industrial, Food and Marine Bacteria (NCIMB) Ltd, Aberdeen, UK
| | - Simon M Clow
- PMI BioPharma Solutions LLC, Nashville, Tennessee, USA
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Nguyen TH, Kim Y, Kim JS, Jeong Y, Park HM, Kim JW, Kim JE, Kim H, Paek NS, Kang CH. Evaluating the Cryoprotective Encapsulation of the Lactic Acid Bacteria in Simulated Gastrointestinal Conditions. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0406-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Experimental Evidence Reveals Both Cross-Infection and Cross-Contamination Risk of Embryo Storage in Liquid Nitrogen Biobanks. Animals (Basel) 2020; 10:ani10040598. [PMID: 32244732 PMCID: PMC7222773 DOI: 10.3390/ani10040598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary This study was conducted to demonstrate the potential hazards of cross-infection and cross-contamination of embryos during storage in liquid nitrogen biobanks. For the harmless and successful cryopreservation of embryos, the vitrification method must be chosen meticulously to guarantee not only a high post-thaw survival of embryos, but also to reduce the risk of disease transmission when those embryos are in storage for long periods. Abstract In recent decades, gamete and embryo cryopreservation have become routine procedures in livestock and human assisted reproduction. However, the safe storage of germplasm and the prevention of disease transmission continue to be potential hazards of disease transmission through embryo transfer. This study aimed to demonstrate the potential risk of cross-infection of embryos from contaminated liquid nitrogen, and cross-contamination of sterile liquid nitrogen from infected embryos in naked and closed devices. Additionally, we examined the effects of antibiotic-free media on culture development of infected embryos. The study was a laboratory-based analysis using rabbit as a model. Two experiments were performed to evaluate both cross-infection (liquid nitrogen to embryos) and cross-contamination (embryos to liquid nitrogen) of artificially inoculated Salmonella Typhimurium, Staphylococcus aureus, Enterobacter aerogenes, and Aspergillus brasiliensis. Rapid cooling through vitrification was conducted on rabbit embryos, stored for a year, thawed, and cultured. In vivo produced late morulae–early blastocyst stages (72 h) embryos were used (n = 480). Embryos were cultured for 1 h in solutions with and without pathogens. Then, the embryos were vitrified and stored in naked and closed devices for one year in two liquid nitrogen biobanks (one pathogen-free and the other artificially contaminated). Embryos were warmed and cultured for a further 48 h, assessing the development and the presence of microorganism (chromogenic media, scanning electron microscopy). Embryos stored in naked devices in artificially contaminated liquid nitrogen became infected (12.5%), while none of the embryos stored in closed devices were infected. Meanwhile, storage of artificially infected embryos incurred liquid nitrogen biobank contamination (100%). Observations by scanning electron microscopy revealed that all the microorganisms were caught in the surface of embryos after the vitrification-thawed procedure. Nevertheless, embryos cultured in antibiotics and antimycotic medium developed to the hatched blastocyst stage, while artificially infected embryos cultured in antibiotic-free medium failed to develop. In conclusion, our findings support that both cross-contamination and cross-infection during embryo storage in liquid nitrogen biobanks are plausible. So, to ensure biosafety for the cryogenic storage, closed systems that avoid direct contact with liquid nitrogen must be used. Moreover, it seems essential to provide best practice guidelines for the cryogenic preservation and storage of gametes and embryos, to define appropriate quality and risk management procedures.
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Nascimento CRSD, Souto ADSS, Galvão RM, Lazéra MDS, Trilles L. Genotypic and Phenotypic Stability of Mixed Primary Isolates of Cryptococcus gattii and Cryptococcus neoformans: A Comparative Analysis of Four Preservation Methods. Biopreserv Biobank 2020; 18:196-203. [PMID: 32213084 DOI: 10.1089/bio.2019.0096] [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: 11/12/2022] Open
Abstract
The choice of a suitable preservation method is critical for long-term microorganisms' viability. The strains should be preserved for long periods using reliable and reproducible methods that minimize genotypic and phenotypic variations and viability losses. The methodologies are usually designed for a better performance in isolated microorganisms. However, atypical primary isolates of Cryptococcus neoformans or Cryptococcus gattii, such as mixed species or even different species of a species complex, are a challenge for long-term preservation and taxonomic review studies. The aim of this study was to evaluate which of the four preservation methods tested presented better performance in the preservation of simulated coexistence strains of C. neoformans and C. gattii. Two environmental strains, one C. gattii and one C. neoformans, were mixed in vitro to test four different preservation methods (freezing at -20°C, -80°C, -196°C, and freeze-drying). The colony-forming units from each preservation method were evaluated, and colonies were randomly selected and cultivated in canavanine glycine bromothymol blue (CGB) agar to evaluate the amounts of CGB-positive (C. gattii) and CGB-negative (C. neoformans) colonies resulting from each preservation method after 1 week, 15 days, 1 month, 6 months, and 1 year. According to our results, cryopreservation at -20°C demonstrated was preferable for C. neoformans species, and further studies after long-term storage are necessary. Recovery of yeast cells after freeze-dried preservation in skim milk is better for both species. Ultrafreezing methods evaluated (-80°C and -196°C) also showed better results in the maintenance of C. gattii. Freeze-drying should be preferred for the maintenance of multilineage isolates from the C. neoformans and C. gattii species complexes.
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Affiliation(s)
- Carlos Roberto Sobrinho do Nascimento
- Microbiology Department, National Institute for Quality Control in Health, Fiocruz, Rio de Janeiro, Brazil.,Mycology Laboratory, National Institute of Infectious Diseases Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | | | - Raíssa Maria Galvão
- Microbiology Department, National Institute for Quality Control in Health, Fiocruz, Rio de Janeiro, Brazil
| | - Marcia Dos Santos Lazéra
- Mycology Laboratory, National Institute of Infectious Diseases Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Luciana Trilles
- Mycology Laboratory, National Institute of Infectious Diseases Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
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17
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Azarsa M, Ohadian Moghadam S, Rahbar M, Baseri Z, Pourmand MR. Molecular serotyping and genotyping of penicillin non-susceptible pneumococci: the introduction of new sequence types, Tehran, Iran. New Microbes New Infect 2019; 32:100597. [PMID: 31641513 PMCID: PMC6796605 DOI: 10.1016/j.nmni.2019.100597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/25/2019] [Accepted: 08/30/2019] [Indexed: 12/04/2022] Open
Abstract
The emergence of penicillin non-susceptible Streptococcus pneumoniae (PNSP) isolates can pose significant challenges to today's health-care system. Resistant clonal isolates are disseminated in different regions and countries, and this study was focused on the description of the epidemiological spread of these strains. Clinical samples were collected from individuals admitted to hospitals affiliated to the Tehran University of Medical Sciences, Iran. To investigate the molecular characteristics of PNSP isolates, they were subjected to molecular typing using multi-locus sequence typing (MLST). Serotype distributions of S. pneumoniae isolates were also evaluated by multiplex PCR assay. The most prevalent serotypes in the PNSP isolates were 23F, 19F, 14, 3 and 9V. Two isolates were considered as a non-vaccine serotype. The MLST analysis showed that PNSP isolates belonged to five different clonal complexes (CC180, CC217, CC81, CC63 and CC320) and 42% (5/12) of the sequence types were novel (12936, 12937, 12938, 12939 and 12940). This study indicates the high level of heterogeneity that is present among PNSP isolates. Unexpected high genetic diversity in small populations indicates consecutive diversification of resistant strains.
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Affiliation(s)
- M Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
| | - S Ohadian Moghadam
- Uro-Oncology Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - M Rahbar
- Department of Microbiology, Reference Health Laboratories Research Centre, Ministry of Health and Medical Education, Tehran, Iran
| | - Z Baseri
- Central Laboratory of Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - M R Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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18
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Zhao L, Wang M, Li J, Cui Z, Volk GM, Wang Q. Cryobiotechnology: A Double-Edged Sword for Obligate Plant Pathogens. PLANT DISEASE 2019; 103:1058-1067. [PMID: 30958107 DOI: 10.1094/pdis-11-18-1989-fe] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pathogen-free stock plants are required as propagation materials in nurseries and healthy materials are needed in germplasm exchange between countries or regions through quarantine programs. In addition, plant gene banks also prefer to maintain pathogen-free germplasm collections. Shoot tip cryotherapy is a novel biotechnology method whereby cryopreservation methods are used to eradicate obligate pathogens from vegetatively propagated plants. Long-term preservation of pathogens is necessary in all types of virus-related basic research and applications such as antigen preparation for virus detection by immunology-based methods, production of plant-based vaccines, genetic transformation to produce virus-derived resistant transgenic plants, and bionanotechnology to produce nano drugs. Obligate plant pathogens such as viruses and viroids are intracellular parasites that colonize only living cells of the hosts. Therefore, their long-term preservation is difficult. Cryotreatments cannot completely eradicate the obligate pathogens that do not infect meristematic cells and certain proportions of plants recovered from cryotreatments are still pathogen-infected. Furthermore, cryotreatments often fail to eradicate the obligate pathogens that infect meristematic cells. Cryopreservation can be used for the long-term cryopreservation of the obligate plant pathogens. Thus, cryobiotechnology functions as a double-edged sword for plant pathogen eradication and cryopreservation. This review provides updated a synthesis of advances in cryopreservation techniques for eradication and cryopreservation of obligate plant pathogens.
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Affiliation(s)
- Lei Zhao
- 1 State Key Laboratory of Crop Stress Biology in Arid Region, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
- 2 College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Minrui Wang
- 1 State Key Laboratory of Crop Stress Biology in Arid Region, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Jingwei Li
- 1 State Key Laboratory of Crop Stress Biology in Arid Region, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
| | - Zhenhua Cui
- 3 College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, P.R. China
| | - Gayle M Volk
- 4 National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, U.S.A
| | - Qiaochun Wang
- 1 State Key Laboratory of Crop Stress Biology in Arid Region, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China
- 3 College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong, P.R. China
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Hasan M, Fayter AER, Gibson MI. Ice Recrystallization Inhibiting Polymers Enable Glycerol-Free Cryopreservation of Microorganisms. Biomacromolecules 2018; 19:3371-3376. [PMID: 29932648 PMCID: PMC6588267 DOI: 10.1021/acs.biomac.8b00660] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/20/2018] [Indexed: 02/08/2023]
Abstract
All modern molecular biology and microbiology is underpinned by not only the tools to handle and manipulate microorganisms but also those to store, bank, and transport them. Glycerol is the current gold-standard cryoprotectant, but it is intrinsically toxic to most microorganisms: only a fraction of cells survive freezing and the presence of glycerol can impact downstream applications and assays. Extremophile organisms survive repeated freeze/thaw cycles by producing antifreeze proteins which are potent ice recrystallization inhibitors. Here we introduce a new concept for the storage/transport of microorganisms by using ice recrystallization inhibiting poly(vinyl alcohol) in tandem with poly(ethylene glycol). This cryopreserving formulation is shown to result in a 4-fold increase in E. coli yield post-thaw, compared to glycerol, utilizing lower concentrations, and successful cryopreservation shown as low as 1.1 wt % of additive. The mechanism of protection is demonstrated to be linked not only to inhibiting ice recrystallization (by comparison to a recombinant antifreeze protein) but also to the significantly lower toxicity of the polymers compared to glycerol. Optimized formulations are presented and shown to be broadly applicable to the cryopreservation of a panel of Gram-negative, Gram-positive, and mycobacteria strains. This represents a step-change in how microorganisms will be stored by the design of new macromolecular ice growth inhibitors; it should enable a transition from traditional solvent-based to macromolecular microbiology storage methods.
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Affiliation(s)
- Muhammad Hasan
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Alice E. R. Fayter
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Matthew I. Gibson
- Department
of Chemistry and Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
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Wang MR, Yang W, Zhao L, Li JW, Liu K, Yu JW, Wu YF, Wang QC. Cryopreservation of virus: a novel biotechnology for long-term preservation of virus in shoot tips. PLANT METHODS 2018; 14:47. [PMID: 29942344 PMCID: PMC5996562 DOI: 10.1186/s13007-018-0312-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/29/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Preservation of plant virus is a fundamental requirement in all types of virus-related research and applied applications. Development of efficient, reliable strategies for long-term preservation of plant virus would largely assist these studies. RESULTS The present study reported a novel biotechnology allowing cryopreservation of Apple stem grooving virus (ASGV) in living shoot tips. Following cryopreservation by droplet-vitrification or encapsulation-dehydration, about 62-67% of shoot regrowth and 100% of ASGV cryopreservation were obtained. Although shoot proliferation and virus concentration were reduced in cryopreserved diseased shoots after 8 weeks of shoot regeneration, continuous subculture for 4 times (16 weeks) increased shoot proliferation and virus concentration to comparative levels as those produced by shoot tip culture (as a control to shoot tip cryopreservation). Cryopreserved ASGV was efficiently transmitted to a woody plant by micrografting and to a herbaceous indicator by mechanical inoculation. Gene sequencing in three fragments of ASGV genome including coat protein and movement protein showed that cryopreserved ASGV shared 99.87% nucleotide identities with shoot tip culture-preserved virus, indicating cryopreserved virus is genetically stable. CONCLUSIONS The present study demonstrates ASGV, a representative virus that can infect meristematic cells of shoot tips, can be efficiently cryopreserved in shoot tips. To the best of our knowledge, this is the first report on plant virus cryopreservation in living tissues, and has great potential applications to long-term preservation of plant viruses.
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Affiliation(s)
- Min-Rui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wen Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jing-Wei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ke Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jing-Wei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yun-Feng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Abstract
In a view of growing interest in bacteriophages as the most abundant members of microbial communities and as antibacterial agents, reliable methods for bacteriophage long-term preservation, that warrant the access to original or mutant stocks of unchanged properties, have become of crucial importance. A storage method that retains the infectivity of any kind of bacteriophage virions, either in a cell lysate or in a purified suspension, does not exist, due to the enormous diversity of bacteriophages and hence the differentiation of their sensitivity to various storage conditions. Here, we describe a method of long-term bacteriophage preservation, which is based on freezing of freshly infected susceptible bacteria at early stages of bacteriophage development. The infected bacteria release mature bacteriophages upon melting enabling the recovery of bacteriophage virions with high efficiency. The only limitation of this method is the sensitivity of bacteriophage host to deep-freezing, and thus it can be used for the long-term preservation of the vast majority of bacteriophages.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland.
- Faculty of Agriculture and Biology, Autonomous Department of Microbial Biology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, Warsaw, 02-776, Poland.
| | - Aleksandra Głowacka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Piotr Golec
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5A, Gdańsk, 02-106, Poland
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22
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Risk of Contamination of Gametes and Embryos during Cryopreservation and Measures to Prevent Cross-Contamination. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1840417. [PMID: 28890894 PMCID: PMC5584362 DOI: 10.1155/2017/1840417] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/17/2017] [Accepted: 07/10/2017] [Indexed: 11/30/2022]
Abstract
The introduction and widespread application of vitrification are one of the most important achievements in human assisted reproduction techniques (ART) of the past decade despite controversy and unclarified issues, mostly related to concerns about disease transmission. Guidance documents published by US Food and Drug Administration, which focused on the safety of tissue/organ donations during Zika virus spread in 2016, as well as some reports of virus, bacteria, and fungi survival to cryogenic temperatures, highlighted the need for a review of the way how potentially infectious material is handled and stored in ART-related procedures. It was experimentally demonstrated that cross-contamination between liquid nitrogen (LN2) and embryos may occur when infectious agents are present in LN2 and oocytes/embryos are not protected by a hermetically sealed device. Thus, this review summarizes pertinent data and opinions regarding the potential hazard of infectious transmission through cryopreserved and banked reproductive cells and tissues in LN2. Special attention is given to the survival of pathogens in LN2, the risk of cross-contamination, vitrification methods, sterility of LN2, and the risks associated with the use of straws, cryovials, and storage dewars.
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23
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Evaluation of lytB Gene for Detection of Streptococcus pneumoniae in Isolates and Clinical Specimens by Real-Time PCR. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.14378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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24
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Sprouffske K, Aguilar-Rodríguez J, Wagner A. How Archiving by Freezing Affects the Genome-Scale Diversity of Escherichia coli Populations. Genome Biol Evol 2016; 8:1290-8. [PMID: 26988250 PMCID: PMC4898790 DOI: 10.1093/gbe/evw054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus each sample archived in this way, consists of many unique genotypes and phenotypes. The effect of archiving on such a heterogeneous population is unknown. Here, we identified optimal archiving conditions for E. coli. We also used genome sequencing of archived samples to study the effects that archiving has on genomic population diversity. We observed no allele substitutions and mostly small changes in allele frequency. Nevertheless, principal component analysis of genome-scale allelic diversity shows that archiving affects diversity across many loci. We showed that this change in diversity is due to selection rather than drift. In addition, ∼1% of rare alleles that occurred at low frequencies were lost after treatment. Our observations imply that archived populations may be used to conduct fitness or other phenotypic assays of populations, in which the loss of a rare allele may have negligible effects. However, caution is appropriate when sequencing populations restarted from glycerol stocks, as well as when using glycerol stocks to restart or replay evolution. This is because the loss of rare alleles can alter the future evolutionary trajectory of a population if the lost alleles were strongly beneficial.
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Affiliation(s)
- Kathleen Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - José Aguilar-Rodríguez
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland The Santa Fe Institute, Santa Fe, NM, USA
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25
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Alonso S. Novel Preservation Techniques for Microbial Cultures. NOVEL FOOD FERMENTATION TECHNOLOGIES 2016. [DOI: 10.1007/978-3-319-42457-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Bielanski A. Biosafety in Embryos and Semen Cryopreservation, Storage, Management and Transport. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 753:429-65. [DOI: 10.1007/978-1-4939-0820-2_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Bielanski A. A review of the risk of contamination of semen and embryos during cryopreservation and measures to limit cross-contamination during banking to prevent disease transmission in ET practices. Theriogenology 2012; 77:467-82. [DOI: 10.1016/j.theriogenology.2011.07.043] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 07/12/2011] [Accepted: 07/29/2011] [Indexed: 10/14/2022]
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