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Article ; Online: Allelic Entropy and Times until Loss or Fixation of Neutral Polymorphisms.

Ferretti, Luca / Ribeca, Paolo

2023 Volume 14, Issue 9

Abstract: In the diffusion approximation of the neutral Wright-Fisher model, the expected time until fixation or loss of a neutral allele is proportional to the initial entropy of the distribution of the allele in the population. No explanation is known for this ... ...

Abstract	In the diffusion approximation of the neutral Wright-Fisher model, the expected time until fixation or loss of a neutral allele is proportional to the initial entropy of the distribution of the allele in the population. No explanation is known for this coincidence. In this paper, we show that the rate of entropy dissipation is proportional to the number of segregating alleles. Since the final fixed state has zero entropy, the expected lifetime of segregating alleles is proportional to the initial entropy in the system. We show that classical formulae on the average time to loss of segregating alleles and the expected time to fixation of the last segregating allele stem from these properties of the diffusion process. We also extend our results to the case of population size changing in time. The dissipation of heterozygosity and entropy shows that superlinear population growth leads to infinite expected fixation times, i.e., neutral alleles in fast-growing populations could segregate forever without ever becoming fixed or disappearing by genetic drift.
MeSH term(s)	Alleles ; Entropy ; Models, Genetic ; Polymorphism, Genetic ; Genetic Drift
Language	English
Publishing date	2023-09-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14091751
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Code & data for "The timing of COVID-19 transmission"

Luca Ferretti

2020

Abstract: ... by Ferretti et al. Maximum Likelihood inference of timing of transmission relative to date of symptom onset ...

Abstract	Data and code implementing the analyses for the project "The timing of COVID-19 transmission" by Ferretti et al. Maximum Likelihood inference of timing of transmission relative to date of symptom onset and date of infection. See description in manuscript: https://www.medrxiv.org/content/10.1101/2020.09.04.20188516v1
Keywords	covid19
Publishing date	2020-09-16
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic

Villegas, Laura I / Ferretti, Luca / Wiehe, Thomas / Waldvogel, Ann-Marie / Schiffer, Philipp H

Ecology and evolution

2024 Volume 14, Issue 1, Page(s) e10831

Abstract: Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with ... ...

Abstract	Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus
Language	English
Publishing date	2024-01-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10831
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Article: Disentangling demographic effects of red deer on chamois population dynamics.

Donini, Valerio / Pedrotti, Luca / Ferretti, Francesco / Corlatti, Luca

Ecology and evolution

2021 Volume 11, Issue 12, Page(s) 8264–8280

Abstract: Investigating the impact of ecological factors on sex- and age-specific vital rates is essential to understand animal population dynamics and detect the potential for interactions between sympatric species. We used block count data and autoregressive ... ...

Abstract	Investigating the impact of ecological factors on sex- and age-specific vital rates is essential to understand animal population dynamics and detect the potential for interactions between sympatric species. We used block count data and autoregressive linear models to investigate variation in birth rate, kid survival, female survival, and male survival in a population of Alpine chamois
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.7657
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Article ; Online: A novel factor modulating X chromosome dosage compensation in Anopheles.

Krzywinska, Elzbieta / Ribeca, Paolo / Ferretti, Luca / Hammond, Andrew / Krzywinski, Jaroslaw

Current biology : CB

2023 Volume 33, Issue 21, Page(s) 4697–4703.e4

Abstract: Dosage compensation (DC), a process countering chromosomal imbalance in individuals with heteromorphic sex chromosomes, has been molecularly characterized only in mammals, Caenorhabditis elegans, and fruit flies. ...

Abstract	Dosage compensation (DC), a process countering chromosomal imbalance in individuals with heteromorphic sex chromosomes, has been molecularly characterized only in mammals, Caenorhabditis elegans, and fruit flies.
MeSH term(s)	Animals ; Male ; Female ; Drosophila melanogaster/genetics ; Anopheles/genetics ; Factor X/genetics ; Malaria/genetics ; Mosquito Vectors ; X Chromosome/genetics ; Drosophila/genetics ; Drosophila Proteins/genetics ; Mammals/genetics
Chemical Substances	Factor X (9001-29-0) ; Drosophila Proteins
Language	English
Publishing date	2023-09-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2023.09.001
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Article ; Online: A General Framework for Neutrality Tests Based on the Site Frequency Spectrum.

Ramos-Onsins, Sebastián E / Marmorini, Giacomo / Achaz, Guillaume / Ferretti, Luca

Genes

2023 Volume 14, Issue 9

Abstract: One of the main necessities for population geneticists is the availability of sensitive statistical tools that enable to accept or reject the standard Wright-Fisher model of neutral evolution. A number of statistical tests have been developed to detect ... ...

Abstract	One of the main necessities for population geneticists is the availability of sensitive statistical tools that enable to accept or reject the standard Wright-Fisher model of neutral evolution. A number of statistical tests have been developed to detect specific deviations from the null frequency spectrum in different directions (e.g., Tajima's D, Fu and Li's F and D tests, Fay and Wu's H). A general framework exists to generate all neutrality tests that are linear functions of the frequency spectrum. In this framework, it is possible to develop a family of optimal tests with almost maximum power against a specific alternative evolutionary scenario. In this paper we provide a thorough discussion of the structure and properties of linear and nonlinear neutrality tests. First, we present the general framework for linear tests and emphasise the importance of the property of scalability with the sample size (that is, the interpretation of the tests should not depend on the sample size), which, if missing, can lead to errors in interpreting the data. After summarising the motivation and structure of linear optimal tests, we present a more general framework for the optimisation of linear tests, leading to a new family of tunable neutrality tests. In a further generalisation, we extend the framework to nonlinear neutrality tests and we derive nonlinear optimal tests for polynomials of any degree in the frequency spectrum.
MeSH term(s)	Animals ; Biological Evolution ; Genetic Drift ; Motivation ; Mustelidae ; Sample Size
Language	English
Publishing date	2023-08-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14091714
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Article ; Online: Evaluation of antibiofilm activity of cefiderocol alone and in combination with imipenem against Pseudomonas aeruginosa.

Ferretti, Caterina / Poma, Noemi Violeta / Bernardo, Mariano / Rindi, Laura / Cesta, Novella / Tavanti, Arianna / Tascini, Carlo / Di Luca, Mariagrazia

Journal of global antimicrobial resistance

2024 Volume 37, Page(s) 53–61

Abstract: Objectives: The main aim of this study was to evaluate the antibiofilm activity of cefiderocol alone and in combination with imipenem vs. sessile cells of Pseudomonas aeruginosa, assessing a potential synergistic bactericidal effect.: Methods: Ten P. ...

Abstract	Objectives: The main aim of this study was to evaluate the antibiofilm activity of cefiderocol alone and in combination with imipenem vs. sessile cells of Pseudomonas aeruginosa, assessing a potential synergistic bactericidal effect. Methods: Ten P. aeruginosa clinical isolates from infected implants and bloodstream were included in the study. Cefiderocol was tested alone and in combination with imipenem on 24-h-old P. aeruginosa biofilm formed on porous glass beads. For each antibiotic formulation, minimum bactericidal biofilm concentration (MBBC), defined as the lowest concentration that determined a reduction of at least 3 log10 CFU/mL compared with the untreated control, was evaluated. Scanning electron microscopy (SEM) was used to investigate the biofilm of P. aeruginosa treated with cefiderocol, imipenem, or their combination. Results: Cefiderocol and imipenem were tested alone on P. aeruginosa biofilm and a reasonable reduction in the number of viable cells was observed, especially at high drug concentrations tested. The synergistic effect of cefiderocol in combination with imipenem was evaluated for five selected isolates. Cotreatment with the two drugs led to a remarkable reduction of cell viability by resulting in synergistic bactericidal activity in all tested strains and in synergistic eradicating activity in only one isolate. SEM analysis revealed that, in cefiderocol-treated biofilm, bacterial cells became more elongated than in the untreated control, forming filaments in which bacterial division seems to be inhibited. Conclusions: Cefiderocol exhibited an encouraging antibiofilm activity against tested strains, representing a valid option for the treatment of P. aeruginosa biofilm-associated infections, especially when administered in combination with imipenem.
Language	English
Publishing date	2024-02-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2710046-7
ISSN	2213-7173 ; 2213-7173
ISSN (online)	2213-7173
ISSN	2213-7173
DOI	10.1016/j.jgar.2024.01.021
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Article ; Online: Establishment and a comparative transcriptomic analysis of a male-specific cell line from the African malaria mosquito Anopheles gambiae.

Krzywinska, Elzbieta / Ferretti, Luca / Krzywinski, Jaroslaw

Scientific reports

2022 Volume 12, Issue 1, Page(s) 6885

Abstract: Cell lines allow studying various biological processes that may not be easily tractable in whole organisms. Here, we have established the first male-specific cell line from the African malaria mosquito, Anopheles gambiae. The cells, named AgMM and ... ...

Abstract	Cell lines allow studying various biological processes that may not be easily tractable in whole organisms. Here, we have established the first male-specific cell line from the African malaria mosquito, Anopheles gambiae. The cells, named AgMM and derived from the sex-sorted neonate larvae, were able to undergo spontaneous contractions for a number of passages following establishment, indicating their myoblast origin. Comparison of their transcriptome to the transcriptome of an A. gambiae-derived Sua5.1 hemocyte cells revealed distinguishing molecular signatures of each cell line, including numerous muscle-related genes that were highly and uniquely expressed in the AgMM cells. Moreover, the AgMM cells express the primary sex determiner gene Yob and support male sex determination and dosage compensation pathways. Therefore, the AgMM cell line represents a valuable tool for molecular and biochemical in vitro studies of these male-specific processes. In a broader context, a rich transcriptomic data set generated in this study contributes to a better understanding of transcribed regions of the A. gambiae genome and sheds light on the biology of both cell types, facilitating their anticipated use for various cell-based assays.
MeSH term(s)	Animals ; Anopheles/genetics ; Cell Line ; Dosage Compensation, Genetic ; Humans ; Infant, Newborn ; Malaria/genetics ; Male ; Transcriptome
Language	English
Publishing date	2022-04-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-10686-y
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Article: Spatial variation in antler investment of Apennine red deer.

Mattioli, Stefano / Ferretti, Francesco / Nicoloso, Sandro / Corlatti, Luca

Ecology and evolution

2021 Volume 11, Issue 12, Page(s) 7850–7864

Abstract: Heterogeneity in resource availability and quality can trigger spatial patterns in the expression of sexually selected traits such as body mass and weaponry. While relationships between habitat features and phenotypic quality are well established at ... ...

Abstract	Heterogeneity in resource availability and quality can trigger spatial patterns in the expression of sexually selected traits such as body mass and weaponry. While relationships between habitat features and phenotypic quality are well established at broad geographical scales, information is poor on spatial patterns at finer, intrapopulation scales. We analyzed biometric data collected on 1965 red deer
Language	English
Publishing date	2021-05-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.7617
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Article ; Online: Establishment and a comparative transcriptomic analysis of a male-specific cell line from the African malaria mosquito Anopheles gambiae

Elzbieta Krzywinska / Luca Ferretti / Jaroslaw Krzywinski

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 8

Abstract: Abstract Cell lines allow studying various biological processes that may not be easily tractable in whole organisms. Here, we have established the first male-specific cell line from the African malaria mosquito, Anopheles gambiae. The cells, named AgMM ... ...

Abstract	Abstract Cell lines allow studying various biological processes that may not be easily tractable in whole organisms. Here, we have established the first male-specific cell line from the African malaria mosquito, Anopheles gambiae. The cells, named AgMM and derived from the sex-sorted neonate larvae, were able to undergo spontaneous contractions for a number of passages following establishment, indicating their myoblast origin. Comparison of their transcriptome to the transcriptome of an A. gambiae-derived Sua5.1 hemocyte cells revealed distinguishing molecular signatures of each cell line, including numerous muscle-related genes that were highly and uniquely expressed in the AgMM cells. Moreover, the AgMM cells express the primary sex determiner gene Yob and support male sex determination and dosage compensation pathways. Therefore, the AgMM cell line represents a valuable tool for molecular and biochemical in vitro studies of these male-specific processes. In a broader context, a rich transcriptomic data set generated in this study contributes to a better understanding of transcribed regions of the A. gambiae genome and sheds light on the biology of both cell types, facilitating their anticipated use for various cell-based assays.
Keywords	Medicine ; R ; Science ; Q
Subject code	571
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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