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Article: A Tool Derived from the Vicia faba Micronucleus Assay, to Assess Genotoxicity, Cytotoxicity or Biostimulation of Novel Compounds Used in Agriculture

Klein, Perrine / Chauvey, Lorelei / Kallerhoff, Jean / Pinelli, Eric / Morard, Marie / Silvestre, Jérome

Agronomy. 2021 Feb. 11, v. 11, no. 2

2021

Abstract: The increased use of biostimulants in conventional agriculture and organic farming requires the implementation of rapid tests to determine their effectiveness in enhancing plant growth and protection against abiotic stresses. However, their innocuity to ... ...

Abstract	The increased use of biostimulants in conventional agriculture and organic farming requires the implementation of rapid tests to determine their effectiveness in enhancing plant growth and protection against abiotic stresses. However, their innocuity to plant health has rarely been demonstrated. We used the Vicia faba Micronucleus Assay, as described by the standard AFNOR EN ISO 29200(2020-05) to reveal biostimulant, genotoxic and cytotoxic effects of four commercialized wood-based products by comparing mitotic indices and micronucleus frequencies with respect to the controls. Neither genotoxicity, as measured by micronucleus frequency (MN), nor cytotoxicity, assessed by Mitotic index counts, was observed. Additionally, one of these stimulants (BHS®) conferred protective effects against contaminants (maleic hydrazide or lead nitrate). We describe that plotting micronuclei frequency against mitotic indices allows discrimination between cytotoxic/genotoxic effects from growth levels. Vicia faba experiments were successfully transposed to other agronomical important crops such as corn and sunflower. This technique can be valuable to industrials, to assess growth, potential cytoxicity and genotoxicity effects of any new biostimulant or organic.
Keywords	Helianthus annuus ; Vicia faba ; agronomy ; corn ; cytotoxicity ; genotoxicity ; lead nitrate ; maleic hydrazide ; micronucleus tests ; mitosis ; mutagens ; plant growth ; plant health
Language	English
Dates of publication	2021-0211
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2607043-1
ISSN	2073-4395
ISSN	2073-4395
DOI	10.3390/agronomy11020321
Database	NAL-Catalogue (AGRICOLA)

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Article: Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA

Suchan, Tomasz / Chauvey, Lorelei / Poullet, Marine / Tonasso‐Calvière, Laure / Schiavinato, Stéphanie / Clavel, Pierre / Clavel, Benoit / Lepetz, Sébastien / Seguin‐Orlando, Andaine / Orlando, Ludovic

Molecular ecology resources. 2022 Aug., v. 22, no. 6

2022

Abstract: Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are ... ...

Abstract	Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post‐mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER‐treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st–17th century CE), including horses, donkeys and their first‐generation mule hybrids. We found that USER‐treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on‐target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey‐specific and horse‐specific alleles in mule capture sequence data, due to the combined effects of USER‐treatment, probe sets and reference bias. Our work demonstrates that while USER‐treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.
Keywords	DNA ; DNA damage ; DNA methylation ; cytosine ; deamination ; ecology ; horses ; mules ; nucleotide sequences ; France
Language	English
Dates of publication	2022-08
Size	p. 2262-2274.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13619
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Isotopic biographies reveal horse rearing and trading networks in medieval London.

Pryor, Alexander J E / Ameen, Carly / Liddiard, Robert / Baker, Gary / Kanne, Katherine S / Milton, J Andy / Standish, Christopher D / Hambach, Bastian / Orlando, Ludovic / Chauvey, Lorelei / Schiavinato, Stephanie / Calvière-Tonasso, Laure / Tressières, Gaetan / Wagner, Stefanie / Southon, John / Shapiro, Beth / Pipe, Alan / Creighton, Oliver H / Outram, Alan K

Science advances

2024 Volume 10, Issue 12, Page(s) eadj5782

Abstract: This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of ... ...

Abstract	This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites.
MeSH term(s)	Humans ; Middle Aged ; Male ; Female ; Horses ; Animals ; London ; Commerce ; Bone and Bones/chemistry ; Oxygen Isotopes/analysis ; Strontium Isotopes/analysis ; Internationality
Chemical Substances	Oxygen Isotopes ; Strontium Isotopes
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adj5782
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.

Suchan, Tomasz / Chauvey, Lorelei / Poullet, Marine / Tonasso-Calvière, Laure / Schiavinato, Stéphanie / Clavel, Pierre / Clavel, Benoit / Lepetz, Sébastien / Seguin-Orlando, Andaine / Orlando, Ludovic

Molecular ecology resources

2022 Volume 22, Issue 6, Page(s) 2262–2274

Abstract	Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.
MeSH term(s)	Animals ; Cytosine ; DNA Damage ; DNA Methylation ; DNA, Ancient ; Equidae/genetics ; Horses/genetics ; Sequence Analysis, DNA/methods
Chemical Substances	DNA, Ancient ; Cytosine (8J337D1HZY)
Language	English
Publishing date	2022-04-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13619
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interdisciplinary evidence for early domestic horse exploitation in southern Patagonia.

Taylor, William Timothy Treal / Belardi, Juan Bautista / Barberena, Ramiro / Coltrain, Joan Brenner / Marina, Flavia Carballo / Borrero, Luis Alberto / Conver, Joshua L / Hodgins, Gregory / Admiraal, Marjolein / Craig, Oliver Edward / Lucquin, Alexandre / Talbot, Helen Marie / Lundy, Jasmine / Liu, Xuexue / Chauvey, Lorelei / Schiavinato, Stéphanie / Seguin-Orlando, Andaine / Le Roux, Petrus / Lucas, Mary /

Orlando, Ludovic / Roberts, Patrick / Jones, Emily Lena

Science advances

2023 Volume 9, Issue 49, Page(s) eadk5201

Abstract: The introduction of domestic horses transformed Indigenous societies across the grasslands of Argentina, leading to the emergence of specialized horse cultures across the Southern Cone. However, the dynamics of this introduction are poorly chronicled by ... ...

Abstract	The introduction of domestic horses transformed Indigenous societies across the grasslands of Argentina, leading to the emergence of specialized horse cultures across the Southern Cone. However, the dynamics of this introduction are poorly chronicled by historic records. Here, we apply archaeozoological and biomolecular techniques to horse remains from the site of Chorrillo Grande 1 in southern Argentina. Osteological and taphonomic analyses suggest that horses were pastorally managed and used for food by Aónikenk/Tehuelche hunter-gatherers before the onset of permanent European settlement, as early as the mid-17th century. DNA-based sex identifications suggest consumption of both male and female horses, while ceramic residue also shows use of guanaco products. Sequential isotope analyses on horse dentition reveal an origin in southern Patagonia and movement of these animals between the Río Coig and Río Gallegos basins. These results reinforce emerging evidence for rapid Indigenous-mediated dispersal of horses in the Americas and demonstrate that horses catalyzed rapid economic and social transformations.
MeSH term(s)	Animals ; Horses ; Male ; Female ; Argentina ; Food
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adk5201
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

iScience

2023 Volume 26, Issue 3, Page(s) 106144

Abstract: Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit ... ...

Abstract	Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
Language	English
Publishing date	2023-02-05
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106144
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Improving the extraction of ancient

iScience

2023 Volume 26, Issue 5, Page(s) 106787

Abstract: Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental ... ...

Abstract	Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient
Language	English
Publishing date	2023-05-02
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106787
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Clavel, Pierre / Dumoncel, Jean / Der Sarkissian, Clio / Seguin-Orlando, Andaine / Calvière-Tonasso, Laure / Schiavinato, Stephanie / Chauvey, Lorelei / Perdereau, Aude / Aury, Jean-Marc / Wincker, Patrick / Onar, Vedat / Clavel, Benoît / Lepetz, Sébastien / Braga, José / Orlando, Ludovic

Journal of archaeological science. 2021 July, v. 131

2021

Abstract: Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance ... ...

Abstract	Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance and resistance. The reconstruction of the respective role that horses, donkeys and mules played in past societies requires prior identification of their osseous elements in archaeological assemblages. This, however, remains difficult on the basis of morphological data alone and in the absence of complete skeletal elements. While DNA sequencing provides almost certain identification success, this approach requires dedicated infrastructure and sufficient ancient DNA (aDNA) preservation. Here, we assessed the performance of a cost-effective alternative approach based on geometric morphometric (GMM) analysis of the bony labyrinth, a structure carried within the petrosal bone. This extremely compact osseous structure provides good aDNA preservation and is frequently found in archaeological assemblages. To assess the GMM performance, we first used High-throughput DNA sequencing to identify 41 horses, 24 donkeys, 36 mules and one hinny from 11 archaeological sites from France and Turkey spanning different time periods. This provided a panel of 102 ancient equine remains for micro-computed tomography (microCT) and GMM assessment of the variation of the bony labyrinth shape, including the cochlea and the semicircular canals. Our new method shows good-to-excellent prediction rates (85.7%–95.2%) for the identification of species and hybrids when considering the cochlea and semicircular canals together. It provides a cheap, non-destructive alternative to aDNA for the taxonomic identification of past equine assemblages.
Keywords	DNA ; archaeology ; cost effectiveness ; geometry ; hinnies ; horses ; infrastructure ; micro-computed tomography ; morphometry ; prediction ; species identification ; transportation ; France
Language	English
Dates of publication	2021-07
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1468969-8
ISSN	0305-4403
ISSN	0305-4403
DOI	10.1016/j.jas.2021.105383
Database	NAL-Catalogue (AGRICOLA)

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Article: Performance and automation of ancient DNA capture with RNA hyRAD probes

Suchan, Tomasz / Kusliy, Mariya A. / Khan, Naveed / Chauvey, Loreleï / Tonasso‐Calvière, Laure / Schiavinato, Stéphanie / Southon, John / Keller, Marcel / Kitagawa, Keiko / Krause, Johannes / Bessudnov, Alexander N. / Bessudnov, Alexander A. / Graphodatsky, Alexander S. / Valenzuela‐Lamas, Silvia / Wilczyński, Jarosław / Pospuła, Sylwia / Tunia, Krzysztof / Nowak, Marek / Moskal‐delHoyo, Magdalena /

Tishkin, Alexey A. / Pryor, Alexander J. E. / Outram, Alan K. / Orlando, Ludovic

Molecular ecology resources. 2022 Apr., v. 22, no. 3

2022

Abstract: DNA hybridization‐capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental ... ...

Abstract	DNA hybridization‐capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design‐free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5‐fold on‐target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%–30%), while the fraction of endogenous reads mapping on‐ and off‐target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on‐target coverage up to 3.6‐fold. Additionally, we used methylation‐sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post‐mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost‐effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
Keywords	DNA ; DNA damage ; RNA ; automation ; carbon radioisotopes ; cost effectiveness ; data quality ; ecology ; genome ; genomics ; horses ; robots
Language	English
Dates of publication	2022-04
Size	p. 891-907.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13518
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 2005/725: Show issues

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Article ; Online: Performance and automation of ancient DNA capture with RNA hyRAD probes.

Suchan, Tomasz / Kusliy, Mariya A / Khan, Naveed / Chauvey, Loreleï / Tonasso-Calvière, Laure / Schiavinato, Stéphanie / Southon, John / Keller, Marcel / Kitagawa, Keiko / Krause, Johannes / Bessudnov, Alexander N / Bessudnov, Alexander A / Graphodatsky, Alexander S / Valenzuela-Lamas, Silvia / Wilczyński, Jarosław / Pospuła, Sylwia / Tunia, Krzysztof / Nowak, Marek / Moskal-delHoyo, Magdalena /

Tishkin, Alexey A / Pryor, Alexander J E / Outram, Alan K / Orlando, Ludovic

Molecular ecology resources

2021 Volume 22, Issue 3, Page(s) 891–907

Abstract: DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental ... ...

Abstract	DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
MeSH term(s)	Animals ; Automation ; DNA, Ancient ; Horses/genetics ; RNA/genetics ; RNA Probes ; Sequence Analysis, DNA/methods
Chemical Substances	DNA, Ancient ; RNA Probes ; RNA (63231-63-0)
Language	English
Publishing date	2021-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13518
Database	MEDical Literature Analysis and Retrieval System OnLINE

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