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Article ; Online: CRISPR-Cas and restriction-modification team up to achieve long-term immunity.

Cury, Jean / Bernheim, Aude

2022 Volume 30, Issue 6, Page(s) 513–514

Abstract: Bacteria have been shown to harbor a growing arsenal of various defense systems against phages. Maguin et al. have uncovered how two of the most frequent defense systems interact: the clustered regularly interspaced short palindromic repeats-Cas (CRISPR- ... ...

Abstract	Bacteria have been shown to harbor a growing arsenal of various defense systems against phages. Maguin et al. have uncovered how two of the most frequent defense systems interact: the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) system recycles by-products of the restriction-modification (RM) system to increase bacterial defense in the long run.
MeSH term(s)	Bacteria/genetics ; Bacteriophages/genetics ; CRISPR-Cas Systems
Language	English
Publishing date	2022-04-22
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2022.04.001
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Article: CRISPR-Cas and restriction–modification team up to achieve long-term immunity

Cury, Jean / Bernheim, Aude

Trends in microbiology. 2022 June, v. 30, no. 6

2022

Abstract	Bacteria have been shown to harbor a growing arsenal of various defense systems against phages. Maguin et al. have uncovered how two of the most frequent defense systems interact: the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) system recycles by-products of the restriction–modification (RM) system to increase bacterial defense in the long run.
Keywords	CRISPR-Cas systems ; bacteria ; bacteriophages ; byproducts ; immunity ; recycling ; teams
Language	English
Dates of publication	2022-06
Size	p. 513-514.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2022.04.001
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Article ; Online: Influence of keratinized mucosa on peri-implant diseases: a retrospective cohort study in humans.

Oliveira, Caroline Argolo Brito / Pereira, Vonei Luiz / Dos Santos, Jean Nunes / Araujo, Nara Santos / Cury, Patricia Ramos

Oral and maxillofacial surgery

2023 Volume 28, Issue 1, Page(s) 331–336

Abstract: Objective: The present study aimed to assess the relationship between keratinized mucosa width and peri-implant diseases, namely peri-implant mucositis and peri-implantitis.: Materials and methods: Ninety-one dental implants in function for ≥ 6 ... ...

Abstract	Objective: The present study aimed to assess the relationship between keratinized mucosa width and peri-implant diseases, namely peri-implant mucositis and peri-implantitis. Materials and methods: Ninety-one dental implants in function for ≥ 6 months from 40 partially or completely edentulous non-smoker subjects (24 females and 16 males) were evaluated clinically and radiographically. The width of keratinized mucosa, probing depth, plaque index, bleeding on probing, and marginal bone levels were assessed. Keratinized mucosa width was categorized as ≥ 2 mm or < 2 mm. Results: There was no statistically significant association between keratinized buccal mucosa width and peri-implant mucositis or peri-implantitis (p ≥ 0.37). In the regression analysis, peri-implantitis was associated with longer implant function time (RR: 2.55, 95% CI: 1.25-11.81, p = 0.02) and implants in the maxilla (RR: 3.15, 95% CI: 1.61-14.93, p = 0.003). Mucositis was not associated with any of the factors analyzed. Conclusion: In conclusion, in the present sample, keratinized buccal mucosa width was not associated with peri-implant diseases, suggesting that a band of keratinized mucosa may not be necessary to maintain peri-implant health. Prospective studies are required to better understand its role in the maintenance of peri-implant health.
MeSH term(s)	Male ; Female ; Humans ; Peri-Implantitis/etiology ; Dental Implants ; Mucositis ; Retrospective Studies ; Mouth Mucosa
Chemical Substances	Dental Implants
Language	English
Publishing date	2023-02-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2406731-3
ISSN	1865-1569 ; 1865-1550
ISSN (online)	1865-1569
ISSN	1865-1550
DOI	10.1007/s10006-023-01144-8
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Zs.A 4767: Show issues

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Article ; Online: Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation.

Sanchez, Théophile / Cury, Jean / Charpiat, Guillaume / Jay, Flora

Molecular ecology resources

2020 Volume 21, Issue 8, Page(s) 2645–2660

Abstract: For the past decades, simulation-based likelihood-free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong ... ...

Abstract	For the past decades, simulation-based likelihood-free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong opportunity to tackle tasks that current methods hardly solve. However, high data dimensionality forces most methods to summarize large genomic data sets into a relatively small number of handcrafted features (summary statistics). Here, we propose an alternative to summary statistics, based on the automatic extraction of relevant information using deep learning techniques. Specifically, we design artificial neural networks (ANNs) that take as input single nucleotide polymorphic sites (SNPs) found in individuals sampled from a single population and infer the past effective population size history. First, we provide guidelines to construct artificial neural networks that comply with the intrinsic properties of SNP data such as invariance to permutation of haplotypes, long scale interactions between SNPs and variable genomic length. Thanks to a Bayesian hyperparameter optimization procedure, we evaluate the performance of multiple networks and compare them to well-established methods like Approximate Bayesian Computation (ABC). Even without the expert knowledge of summary statistics, our approach compares fairly well to an ABC approach based on handcrafted features. Furthermore, we show that combining deep learning and ABC can improve performance while taking advantage of both frameworks. Finally, we apply our approach to reconstruct the effective population size history of cattle breed populations.
MeSH term(s)	Animals ; Bayes Theorem ; Cattle ; Computer Simulation ; Deep Learning ; Genetics, Population ; Models, Genetic ; Population Density
Language	English
Publishing date	2020-07-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13224
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Article: IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.

Néron, Bertrand / Littner, Eloi / Haudiquet, Matthieu / Perrin, Amandine / Cury, Jean / Rocha, Eduardo P C

Microorganisms

2022 Volume 10, Issue 4

Abstract: Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance ... ...

Abstract	Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000
Language	English
Publishing date	2022-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10040700
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Article: Genotoxicity induced by endodontic sealers: A systematic review.

Guedes Pinto, Thiago / Claudia Muniz Renno, Ana / Nunes Dos Santos, Jean / Ramos Cury, Patricia / Araki Ribeiro, Daniel

The Saudi dental journal

2023 Volume 36, Issue 2, Page(s) 249–257

Abstract: Introduction: This systematic review aimed to help further elucidate the following question: are endodontics sealers able to induce DNA damage in vitro or in vivo?: Methods: This study was conducted following the Preferred Reporting Items for ... ...

Abstract	Introduction: This systematic review aimed to help further elucidate the following question: are endodontics sealers able to induce DNA damage in vitro or in vivo? Methods: This study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement 2020 criteria. A total of 23 studies were carefully selected by the authors. Results: Regarding the general characteristics, most studies evaluated, on average, 3-5 types of sealers (resin epoxy, salicylate, salicylate + MTA, zinc oxide-eugenol, bioceramic products, calcium hydroxide), performing comparisons between them. Our results demonstrate that endodontic sealers may be a genotoxic agent since most studies demonstrated positive findings, with the resin-based ones being the most potentially genotoxic. Conclusion: The type of genotoxicity assay, material evaluated, and dilution concentration levels influenced the outcome. This study clarifies whether and to what extent endodontic sealers are capable of inducing DNA injury in oral tissues.
Language	English
Publishing date	2023-11-17
Publishing country	Saudi Arabia
Document type	Journal Article ; Review
ZDB-ID	1058421-3
ISSN	1658-3558 ; 1013-9052
ISSN (online)	1658-3558
ISSN	1013-9052
DOI	10.1016/j.sdentj.2023.11.019
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Zs.A 3103: Show issues

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Article ; Online: Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites.

Loot, Céline / Millot, Gael A / Richard, Egill / Littner, Eloi / Vit, Claire / Lemoine, Frédéric / Néron, Bertrand / Cury, Jean / Darracq, Baptiste / Niault, Théophile / Lapaillerie, Delphine / Parissi, Vincent / Rocha, Eduardo P C / Mazel, Didier

Nature microbiology

2024 Volume 9, Issue 1, Page(s) 228–240

Abstract: Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between ... ...

Abstract	Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 10
MeSH term(s)	Integrons/genetics ; Genome, Bacterial ; Bacteria/genetics ; Bacteria/metabolism ; Integrases/genetics ; Integrases/metabolism ; Genomics
Chemical Substances	Integrases (EC 2.7.7.-)
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-023-01548-y
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Article ; Online: Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences.

Guez, Jérémy / Achaz, Guillaume / Bienvenu, François / Cury, Jean / Toupance, Bruno / Heyer, Évelyne / Jay, Flora / Austerlitz, Frédéric

Genetics

2023 Volume 223, Issue 4

Abstract: Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny size of parents ... ...

Abstract	Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of children's survival through allocare from uncles and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity over time under cultural transmission of reproductive success. Cultural transmission of reproductive success has a threefold impact on population genetics: (1) the effective population size decreases when cultural transmission of reproductive success starts, mimicking a population contraction, and increases back to its original value when cultural transmission of reproductive success stops; (2) coalescent tree topologies are distorted under cultural transmission of reproductive success, with higher imbalance and a higher number of polytomies; and (3) branch lengths are reduced nonhomogenously, with a higher impact on older branches. Under long-lasting cultural transmission of reproductive success, the effective population size stabilizes but the distortion of tree topology and the nonhomogenous branch length reduction remain, yielding U-shaped site frequency spectra under a constant population size. We show that this yields a bias in site frequency spectra-based demographic inference. Considering that cultural transmission of reproductive success was detected in numerous human and animal populations worldwide, one should be cautious because inferring population past histories from genomic data can be biased by this cultural process.
MeSH term(s)	Animals ; Child ; Humans ; Trees ; Models, Genetic ; Reproduction/genetics ; Genomics ; Demography ; Phylogeny
Language	English
Publishing date	2023-02-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyad007
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Article ; Online: Are Cytomorphogenetic Events Correlated with Oral Mucosal Lesions Induced by Crack Cocaine Use? A Systematic Review.

Guedes Pinto, Thiago / Viana, Milena de Barros / Cury, Patricia Ramos / Martins, Manoela Domingues / Dos Santos, Jean Nunes / Ribeiro, Daniel Araki

Pathophysiology : the official journal of the International Society for Pathophysiology

2023 Volume 30, Issue 4, Page(s) 630–639

Abstract: The aim of this systematic review was to answer the question of whether crack cocaine can induce cellular and molecular alterations and whether such alterations are somehow related to clinical lesions in the oral mucosa. The searches were undertaken in ... ...

Abstract	The aim of this systematic review was to answer the question of whether crack cocaine can induce cellular and molecular alterations and whether such alterations are somehow related to clinical lesions in the oral mucosa. The searches were undertaken in three electronic databases and conducted based on the PRISMA 2020 statement. Eleven studies published between 1994 and 2020 were analyzed. The quality of the included studies was assessed by two independent reviewers (TGP and DAR) through a confounder's categorization methodology, in which final ratings were attributed (strong, moderate or weak) for each study. From 11 studies included, 7 evaluated the cellular/molecular impact of the addiction in a total of 492 individuals and compared to a control (non-exposure) group (n = 472). The main tests used for cellular alteration were MN and AgNORs. Cells from crack cocaine groups exhibited increased proliferation and MN counting. Only four studies evaluated the prevalence of oral lesions. All of them showed that individuals exposed to crack cocaine presented an increased number of oral lesions. Most studies showed good quality. In conclusion, our results demonstrate that crack use may induce changes at the cellular and molecular level and also exhibit an increased number of oral lesions. However, a correlation between such changes and oral mucosa lesions still needs further investigation and elucidation through other clinical studies in humans.
Language	English
Publishing date	2023-12-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1212740-1
ISSN	1873-149X ; 0928-4680
ISSN (online)	1873-149X
ISSN	0928-4680
DOI	10.3390/pathophysiology30040045
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Article ; Online: Author Correction: The chromosomal organization of horizontal gene transfer in bacteria.

Oliveira, Pedro H / Touchon, Marie / Cury, Jean / Rocha, Eduardo P C

Nature communications

2020 Volume 11, Issue 1, Page(s) 1155

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-02-26
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-15091-5
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