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Swer PB, Kharbuli B, Syiem D, Sharma R. Age-related decline in the expression of BRG1, ATM and ATR are partially reversed by dietary restriction in the livers of female mice. Biogerontology 2024:10.1007/s10522-024-10117-7. [PMID: 38970714 DOI: 10.1007/s10522-024-10117-7] [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: 05/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024]
Abstract
BRG1 (Brahma-related gene 1) is a member of the SWI/SNF (switch/sucrose nonfermentable) chromatin remodeling complex which utilizes the energy from ATP hydrolysis for its activity. In addition to its role of regulating the expression of a vast array of genes, BRG1 mediates DNA repair upon genotoxic stress and regulates senescence. During organismal ageing, there is accumulation of unrepaired/unrepairable DNA damage due to progressive breakdown of the DNA repair machinery. The present study investigates the expression level of BRG1 as a function of age in the liver of 5- and 21-month-old female mice. It also explores the impact of dietary restriction on BRG1 expression in the old (21-month) mice. Salient findings of the study are: Real-time PCR and Western blot analyses reveal that BRG1 levels are higher in 5-month-old mice but decrease significantly with age. Dietary restriction increases BRG1 expression in the 21-month-old mice, nearly restoring it to the level observed in the younger group. Similar expression patterns are observed for DNA damage response genes ATM (Ataxia Telangiectasia Mutated) and ATR (Ataxia Telangiectasia and Rad3-related) with the advancement in age and which appears to be modulated by dietary restriction. BRG1 transcriptionally regulates ATM as a function of age and dietary restriction. These results suggest that BRG1, ATM and ATR are downregulated as mice age, and dietary restriction can restore their expression. This implies that dietary restriction may play a crucial role in regulating BRG1 and related gene expression, potentially maintaining liver repair and metabolic processes as mice age.
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Affiliation(s)
- Pynskhem Bok Swer
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | | | - Donkupar Syiem
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Ramesh Sharma
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Cunningham-Eurich I, Kontou D, Yordanova M, Maeda-Obregon A, Favreau E, Wang J, Hart AG, Sumner S. Using citizen science data to assess the population genetic structure of the common yellowjacket wasp, Vespula vulgaris. INSECT MOLECULAR BIOLOGY 2023; 32:634-647. [PMID: 37599385 DOI: 10.1111/imb.12862] [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: 02/23/2023] [Accepted: 05/22/2023] [Indexed: 08/22/2023]
Abstract
Monitoring insect genetic diversity and population structure has never been more important to manage the biodiversity crisis. Citizen science has become an increasingly popular tool to gather ecological data affordably across a wide range of spatial and temporal scales. To date, most insect-related citizen science initiatives have focused on occurrence and abundance data. Here, we show that poorly preserved insect samples collected by citizen scientists can yield population genetic information, providing new insights into population connectivity, genetic diversity and dispersal behaviour of little-studied insects. We analysed social wasps collected by participants of the Big Wasp Survey, a citizen science project that aims to map the diversity and distributions of vespine wasps in the UK. Although Vespula vulgaris is a notorious invasive species around the world, it remains poorly studied in its native range. We used these data to assess the population genetic structure of the common yellowjacket V. vulgaris at different spatial scales. We found a single, panmictic population across the UK with little evidence of population genetic structuring; the only possible limit to gene flow is the Irish sea, resulting in significant differentiation between the Northern Ireland and mainland UK populations. Our results suggest that queens disperse considerable distances from their natal nests to found new nests, resulting in high rates of gene flow and thus little differentiation across the landscape. Citizen science data has made it feasible to perform this study, and we hope that it will encourage future projects to adopt similar practices in insect population monitoring.
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Affiliation(s)
- Iona Cunningham-Eurich
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Danai Kontou
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Monika Yordanova
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Emeline Favreau
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, UK
| | - Adam G Hart
- Department of Natural and Social Science, University of Gloucestershire, UK
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, University College London, London, UK
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3
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Assessing Molecular Diversity in Native and Introduced Populations of Red Wood Ant Formica paralugubris. Animals (Basel) 2022; 12:ani12223165. [PMID: 36428391 PMCID: PMC9687034 DOI: 10.3390/ani12223165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The Formica rufa group comprises several ant species which are collectively referred to as "red wood ants" and play key roles in boreal forest ecosystems, where they are ecologically dominant and greatly influence habitat dynamics. Owing to their intense predatory activity, some of these species are used as biocontrol agents against several forest insect pests and for this aim in Italy, nearly 6000 ant nests were introduced from their native areas in the Alps to several Appeninic sites during the last century. In this work, we assessed and compared the genetic variability and structure of native and introduced populations of F. paralugubris, thus evaluating the extent of genetic drift that may have occurred since the time of introduction, using amplified fragment length polymorphism (AFLP) markers. PCR amplification with a fam_EcoRI-TAC/MseI-ATG primers combination produced a total of 147 scorable bands, with 17 identified as outlier loci. The genetic variation was higher in the introduced population compared to the native ones that, on the other hand, showed a higher diversity between nests. AMOVA results clearly pointed out that the overall genetic structure was dominated by among-worker variation, considering all populations, the Alpine vs. Apennine groups and the comparison among native and related introduced populations (all ranging between 77.84% and 79.84%). Genetic analyses unveiled the existence of six main different groups that do not entirely mirror their geographic subdivision, pointing towards a wide admixture between populations, but, at the same time, rapid diversification of some Apennine populations. Future studies based on high-throughput genomic methods are needed to obtain a thorough understanding of the effects of environmental pressure on the genetic structure and mating system of these populations.
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Milton A, Muhanguzi D, Male A, Kajubi A, Buah S, Kubiriba J, Tumuhimbise R. Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:637-646. [PMID: 35021224 DOI: 10.1093/jee/toab213] [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: 07/30/2021] [Indexed: 06/14/2023]
Abstract
The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.
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Affiliation(s)
- Ali Milton
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dennis Muhanguzi
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Allan Male
- International Center for Tropical Agriculture, Kampala, Uganda
| | - Ali Kajubi
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Stephen Buah
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Jerome Kubiriba
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Robooni Tumuhimbise
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort-Portal, Uganda
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5
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Rattanapanadda P, Kuo HC, Chang SK, Tell LA, Shia WY, Chou CC. Effect of Carbonyl Cyanide Chlorophenylhydrazone on Intrabacterial Concentration and Antimicrobial Activity of Amphenicols against Swine Resistant Actinobacillus pleuropneumoniae and Pasteurella multocida. Vet Res Commun 2022; 46:903-916. [PMID: 35322371 DOI: 10.1007/s11259-022-09917-4] [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: 10/23/2021] [Accepted: 03/15/2022] [Indexed: 12/13/2022]
Abstract
Effects and mechanism of carbonyl cyanide chlorophenylhydrazone (CCCP) on antimicrobial activity of florfenicol (FF) and thiamphenicol (TAP) were investigated against amphenicol-resistant Actinobacillus pleuropneumoniae and Pasteurella multocida isolated from diseased swine. Broth microdilution and time-kill assays indicated that CCCP dose-dependently and substantially (4-32 fold MIC reduction) improved amphenicol antimicrobial activity. When combined with CCCP at the lowest literature reported dose (2-5 μg/mL), 85% FF resistant A. pleuropneumoniae and 92% resistant P. multocida showed significantly reduced FF MICs (≥ 4-fold). In contrast, none or few of the susceptible A. pleuropneumoniae and P. multocida had FF MICs reduction ≥ 4-fold. 90% FF resistant A. pleuropneumoniae and 96% resistant P. multocida carried the floR gene, indicating strong association with the FloR efflux pump. With CCCP, the intracellular FF concentration increased by 71% in floR+ resistant A. pleuropneumoniae and 156% in floR+ resistant P. multocida strains but not the susceptible strains. The degree of reduction in TAP MICs was found consistently in parallel to FF for both bacteria. Taken together, partially attributed to blockage of drug-efflux, the combination of FF or TAP with CCCP at sub-cytotoxic concentrations was demonstrated and showed feasibility to combat amphenicol-resistant A. pleuropneumoniae and P. multocida isolated from diseased swine.
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Affiliation(s)
- Porjai Rattanapanadda
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, 402.,Department of Livestock Development, Ministry of Agriculture and Cooperatives, Bangkok, 10400, Thailand
| | - Hung-Chih Kuo
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan, 600
| | - Shao-Kuang Chang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan, 106
| | - Lisa Ann Tell
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Wei-Yau Shia
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, 402
| | - Chi-Chung Chou
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, 402.
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Araújo PM, Batista E, Fernandes MH, Fernandes MJ, Gama LT, Fraqueza MJ. Assessment of biofilm formation by Campylobacter spp. isolates mimicking poultry slaughterhouse conditions. Poult Sci 2022; 101:101586. [PMID: 34896965 PMCID: PMC8664863 DOI: 10.1016/j.psj.2021.101586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
This research aimed to assess the biofilm formation ability of Campylobacter strains under temperature and oxygen stress conditions, similar to those found in the industrial environment, to explain the persistence of this pathogen on the poultry slaughter line. A collection of C. jejuni and C. coli isolates (n = 143) obtained from poultry samples (cecal content and neck skin), collected at slaughterhouse level, from diverse flocks, on different working days, was genotyped by flaA-restriction fragment length polymorphism (RFLP) typing method. A clustering analysis resulted in the assignment of 10 main clusters, from which 15 strains with different flaA-RFLP genotypes were selected for the assessment of biofilm formation ability and antimicrobial susceptibility. Biofilm assays, performed by crystal violet staining method, were conducted with the goal of mimicking some conditions present at the slaughterhouse environment, based on temperature, atmosphere, and contamination levels. Results indicated that many C. jejuni strains with similar flaA-RFLP profiles were present at the slaughterhouse on different processing days. All the strains tested (n = 15) were multidrug-resistant except for one. Biofilm formation ability was strain-dependent, and it appeared to have been affected by inoculum concentration, temperature, and tolerance to oxygen levels. At 10°C, adherence levels were significantly lower than at 42°C. Under microaerobic and aerobic atmospheres, at 42°C, 3 strains (C. jejuni 46E, C. jejuni 61C, and C. coli 65B) stood out, exhibiting significant levels of biofilm formation. C. jejuni strains 46E and 61C were inserted in clusters with evidence of persistence at the slaughterhouse for a long period of time. This study demonstrated that Campylobacter strains from broilers are capable of forming biofilms under conditions resembling the slaughterhouse environment. These results should be seen as a cue to improve the programs of hygiene implemented, particularly in those zones that can promote biofilm formation.
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Affiliation(s)
- P M Araújo
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal
| | - E Batista
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal
| | - M H Fernandes
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal
| | - M J Fernandes
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal
| | - L T Gama
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal
| | - M J Fraqueza
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon 1300-477, Portugal.
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7
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Krause JL, Engelmann B, Nunes da Rocha U, Pierzchalski A, Chang HD, Zenclussen AC, von Bergen M, Rolle-Kampczyk U, Herberth G. MAIT cell activation is reduced by direct and microbiota-mediated exposure to bisphenols. ENVIRONMENT INTERNATIONAL 2022; 158:106985. [PMID: 34991247 DOI: 10.1016/j.envint.2021.106985] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/15/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Oral uptake is the primary route of human bisphenol exposure, resulting in an exposure of the intestinal microbiota and intestine-associated immune cells. Therefore, we compared the impact of bisphenol A (BPA), bisphenol F (BPF) and bisphenol S (BPS) on (i) intestinal microbiota, (ii) microbiota-mediated immunomodulatory effects and (iii) direct effects on mucosal-associated invariant T (MAIT) cells in vitro. We acutely exposed human fecal microbiota, Bacteroides thetaiotaomicron and Escherichia coli to BPA and its analogues BPF and BPS referring to the European tolerable daily intake (TDI), i.e. 2.3 µg/mL, 28.3 µg/mL and 354.0 µg/mL. Growth and viability of E. coli was most susceptible to BPF, whereas B.thetaiotaomicron and fecal microbiota were affected by BPA > BPF > BPS. At 354.0 µg/mL bisphenols altered microbial diversity in compound-specific manner and modulated microbial metabolism, with BPA already acting on metabolism at 28.3 µg/mL. Microbiota-mediated effects on MAIT cells were observed for the individual bacteria at 354.0 µg/mL only. However, BPA and BPF directly modulated MAIT cell responses at low concentrations, whereby bisphenols at concentrations equivalent for the current TDI had no modulatory effects for microbiota or for MAIT cells. Our findings indicate that acute bisphenol exposure may alter microbial metabolism and impact directly on immune cells.
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Affiliation(s)
- J L Krause
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; present address: German Rheumatism Research Center Berlin, a Leibniz Institute - DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
| | - B Engelmann
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - U Nunes da Rocha
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - A Pierzchalski
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - H D Chang
- present address: German Rheumatism Research Center Berlin, a Leibniz Institute - DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany; Chair of Cytometry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - A C Zenclussen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - M von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany
| | - U Rolle-Kampczyk
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - G Herberth
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany.
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8
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Lienhard A, Krisper G. Hidden biodiversity in microarthropods (Acari, Oribatida, Eremaeoidea, Caleremaeus). Sci Rep 2021; 11:23123. [PMID: 34848782 PMCID: PMC8632897 DOI: 10.1038/s41598-021-02602-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/17/2021] [Indexed: 11/22/2022] Open
Abstract
A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other "well-known" euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.
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Affiliation(s)
- Andrea Lienhard
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Günther Krisper
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
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9
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Chapman E, Meichanetzoglou A, Boa AN, Hetjens H, Faetsch S, Teuchies J, Höss S, Moore D, Bervoets L, Kay P, Heise S, Walker P, Rotchell JM. The Uptake of Sporopollenin Exine Capsules and Associated Bioavailability of Adsorbed Oestradiol in Selected Aquatic Invertebrates. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 107:876-882. [PMID: 34459949 PMCID: PMC8556174 DOI: 10.1007/s00128-021-03364-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Lycopodium clavatum sporopollenin exine capsules (SpECs) are known to both adsorb and absorb chemicals. The aim of the present work was to determine whether oestradiol (E2) is 'bioavailable' to bioindicator species, either pre-adsorbed to, or in the presence of, SpECs. SpEC uptake was confirmed for Daphnia magna and Dreissena bugensis. E2 levels varied among treatments for Caenorhabditis elegans though there was no relationship to SpEC load. E2 was not detected in D. bugensis tissues. Expression changes of general stress and E2-specific genes were measured. For C. elegans, NHR-14 expression suggested that SpECs modulate E2 impacts, but not general health responses. For D. magna, SpECs alone and with E2 changed Vtg1 and general stress responses. For D. bugensis, SpECS were taken up but no E2 or change in gene expression was detected after exposure to E2 and/or SpECs. The present study is the first to investigate SpECs and bound chemical dynamics.
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Affiliation(s)
- Emma Chapman
- Department of Biological and Marine Sciences, University of Hull, Cottingham Rd, Hull, HU6 7RX, UK
| | | | - Andrew N Boa
- Department of Chemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - Hanne Hetjens
- Department of Biology, SPHERE, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Sonja Faetsch
- Hamburg University of Applied Sciences, Ulmenliet 20, 21033, Hamburg, Germany
| | - Johnny Teuchies
- Department of Biology, SPHERE, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | | | - Dean Moore
- Department of Chemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - Lieven Bervoets
- Department of Biology, SPHERE, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Paul Kay
- School of Geography/water@leeds, University of Leeds, Leeds, LS2 9JT, UK
| | - Susanne Heise
- Hamburg University of Applied Sciences, Ulmenliet 20, 21033, Hamburg, Germany
| | - Paul Walker
- SOCOTEC UK Ltd, Etwall House, Bretby Business Pk, Ashby Road, Burton on Trent, DE15 0YZ, UK
| | - Jeanette M Rotchell
- Department of Biological and Marine Sciences, University of Hull, Cottingham Rd, Hull, HU6 7RX, UK.
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10
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A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes. Genes (Basel) 2021; 12:genes12081138. [PMID: 34440312 PMCID: PMC8392835 DOI: 10.3390/genes12081138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.
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11
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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida). Mol Phylogenet Evol 2021; 163:107240. [PMID: 34197900 DOI: 10.1016/j.ympev.2021.107240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/28/2022]
Abstract
There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
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12
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Sloan S, Jenvey CJ, Piedrafita D, Preston S, Stear MJ. Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes. BMC Biotechnol 2021; 21:35. [PMID: 34001079 PMCID: PMC8130168 DOI: 10.1186/s12896-021-00695-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00695-6.
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Affiliation(s)
- S Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia.
| | - C J Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - D Piedrafita
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - S Preston
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - M J Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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13
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Gumińska N, Łukomska-Kowalczyk M, Chaber K, Zakryś B, Milanowski R. Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids. Environ Microbiol 2021; 23:2992-3008. [PMID: 33830624 PMCID: PMC8359987 DOI: 10.1111/1462-2920.15495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species‐level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB‐based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Maja Łukomska-Kowalczyk
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Katarzyna Chaber
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
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14
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Weigand AM, Desquiotz N, Weigand H, Szucsich N. Application of propylene glycol in DNA-based studies of invertebrates. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.57278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.
The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.
When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.
Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.
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15
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de Melo Pereira GV, de Carvalho Neto DP, Maske BL, De Dea Lindner J, Vale AS, Favero GR, Viesser J, de Carvalho JC, Góes-Neto A, Soccol CR. An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far? Crit Rev Food Sci Nutr 2020; 62:1870-1889. [PMID: 33207956 DOI: 10.1080/10408398.2020.1848787] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.
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Affiliation(s)
- Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Dão Pedro de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Bruna L Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Alexander S Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Jéssica Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio C de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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Angthong P, Uengwetwanit T, Pootakham W, Sittikankaew K, Sonthirod C, Sangsrakru D, Yoocha T, Nookaew I, Wongsurawat T, Jenjaroenpun P, Rungrassamee W, Karoonuthaisiri N. Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform. PeerJ 2020; 8:e10340. [PMID: 33240651 PMCID: PMC7668203 DOI: 10.7717/peerj.10340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kanchana Sittikankaew
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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17
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Fluorescence quenching of the SYBR Green I-dsDNA complex by in situ generated magnetic ionic liquids. Anal Bioanal Chem 2020; 412:2743-2754. [DOI: 10.1007/s00216-020-02538-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
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18
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Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
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Efficient preservation of DNA extracted from blood in FTA cards by Chelex method. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Derkarabetian S, Benavides LR, Giribet G. Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Mol Ecol Resour 2019; 19:1531-1544. [DOI: 10.1111/1755-0998.13072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Ligia R. Benavides
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
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