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Article ; Online: Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory.

Michel, Christian J / Sereni, Jean-Sébastien

2023 Volume 85, Issue 4, Page(s) 24

Abstract: Based on the circular code theory, we define a new function f that quantifies the property of reading frame retrieval (RFR) of genes from their codon usage. This RFR function f is computed on a massive scale in genes of genomes of bacteria, eukaryotes ... ...

Abstract	Based on the circular code theory, we define a new function f that quantifies the property of reading frame retrieval (RFR) of genes from their codon usage. This RFR function f is computed on a massive scale in genes of genomes of bacteria, eukaryotes and archaea. By expressing f as a function of the mean number [Formula: see text] of codons per gene, a "universal" property is identified, whatever the kingdom: the reading frame retrieval is enhanced in large genes. By investigating this property according to the theory developed, a Spearman's rank correlation with a strong negative coefficient is observed between the codon usage dispersion d (from the uniform codon distribution [Formula: see text]) and the RFR function f, whatever the kingdom (p-values [Formula: see text] in bacteria, [Formula: see text] in eukaryotes and [Formula: see text] in archaea). Thus, the reading frame retrieval is enhanced with the codon usage dispersion. Furthermore, this approach identifies a "genome centre" from which emerge two distinct "genome arms": an upper arm and a lower arm, respectively, above and below the linear regression. The RFR function by itself or combined with classical methods (alignment, phylogeny) could also be a new approach to classify the genomes in the future.
MeSH term(s)	Genetic Code ; Codon Usage ; Models, Biological ; Models, Genetic ; Mathematical Concepts ; Codon ; Reading Frames ; Bacteria/genetics ; Eukaryota
Chemical Substances	Codon
Language	English
Publishing date	2023-02-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-023-01129-4
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Article ; Online: Trinucleotide k-circular codes II: Biology.

Michel, Christian J / Sereni, Jean-Sébastien

Bio Systems

2022 Volume 217, Page(s) 104668

Abstract: ... in a companion article (Michel et al., 2022). Trinucleotide circular codes always retrieve the reading frame ...

Abstract	A code X is (⩾k)-circular if every concatenation of words from X that admits, when read on a circle, more than one partition into words from X, must contain at least k+1 words. In other words, the reading frame retrieval is guaranteed for any concatenation of up to k words from X. A code that is (⩾k)-circular for all integers k is said to be circular. Any code is (⩾0)-circular and it turns out that a code of trinucleotides is circular as soon as it is (⩾4)-circular. A code is k-circular if it is (⩾k)-circular and not (⩾k+1)-circular. The theoretical aspects of trinucleotide k-circular codes have been developed in a companion article (Michel et al., 2022). Trinucleotide circular codes always retrieve the reading frame, leaving no ambiguous sequences. On the contrary, trinucleotide k-circular codes, for k∈{0,1,2,3} all have ambiguous sequences, for which the reading frame cannot always be retrieved. However, such a trinucleotide k-circular code is still able to retrieve the reading frame for a number of sequences, thereby exhibiting a partial circularity property. We describe this combinatorial property for each class of trinucleotide k-circular codes with k∈{0,1,2,3}. The circularity, i.e. the reading frame retrieval, is an ordinary property in genes. In order to consider the different cases of ambiguous sequences, we derive a new and general formula to measure the reading frame loss, whatever the trinucleotide k-circular code. This formula allows us to study the evolution of any trinucleotide k-circular code of (maximal) cardinality 20 to the genetic code, based on the reading frame retrieval property. We apply this approach to analyse the evolution of the trinucleotide circular code X observed in genes to the genetic code. The (⩾1)-circular codes of maximal size 20 necessarily have the same number of each nucleotide, specifically 15=3⋅20/4. This balanceness property can also be achieved by trinucleotide codes of cardinality 4,8,12 and 16. We call such trinucleotide codes balanced. We develop a general mathematical method to compute the number of balanced trinucleotide codes of each size, which also applies to self-complementary trinucleotide codes. We establish and quantify a relation between this balanceness property and the self-complementarity property. The combinatorial hierarchy of trinucleotide k-circular codes is updated with the growth function results. The numbers of amino acids coded by the trinucleotide k-circular codes are given for the cases maximal, minimal, self-complementary k-, (k,k,k)- and self-complementary (k,k,k)-circular.
MeSH term(s)	Biology ; Genetic Code/genetics ; Models, Genetic ; Nucleotides/genetics ; Reading Frames
Chemical Substances	Nucleotides
Language	English
Publishing date	2022-03-28
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2022.104668
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Article ; Online: Editorial on 60

Christian, Gary / Kauffmann, Jean-Michel

Talanta

2019 Volume 204, Page(s) 883

Language	English
Publishing date	2019-04-25
Publishing country	Netherlands
Document type	Editorial
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2019.04.058
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Article ; Online: Trinucleotide k-circular codes I: Theory.

Michel, Christian J / Mouillon, Baptiste / Sereni, Jean-Sébastien

Bio Systems

2022 Volume 217, Page(s) 104667

Abstract: A code X is (⩾k)-circular if every concatenation of words from X that admits, when read on a circle, more than one partition into words from X, must contain at least k+1 words. In other words, the reading frame retrieval is guaranteed for any ... ...

Abstract	A code X is (⩾k)-circular if every concatenation of words from X that admits, when read on a circle, more than one partition into words from X, must contain at least k+1 words. In other words, the reading frame retrieval is guaranteed for any concatenation of up to k words from X. A code that is (⩾k)-circular for all integers k is said to be circular. Any code is (⩾0)-circular and it turns out that a code of trinucleotides is circular as soon as it is (⩾4)-circular. A code is k-circular if it is (⩾k)-circular and not (⩾k+1)-circular. Due to the explosive combinatorics of trinucleotide k-circular codes, we developed three classes of algorithms based on: (i) the smallest directed cycles (directed girth) in graphs; (ii) the eigenvalues of matrices; and (iii) the files that incrementally save partial results. These different approaches also allow us to verify the computational results obtained. We determine here the growth functions of trinucleotide k-circular codes, k varying between 0 and 4, in the general case and in various particular cases: minimum, minimal, maximum, self-complementary k-, (k,k,k)- and self-complementary (k,k,k)-circular.
MeSH term(s)	Genetic Code/genetics ; Models, Genetic ; Reading Frames
Language	English
Publishing date	2022-03-26
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2022.104667
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Article ; Online: Corrigendum: Sudocetaxel Zendusortide (TH1902) triggers the cGAS/STING pathway and potentiates anti-PD-L1 immune-mediated tumor cell killing.

Demeule, Michel / Currie, Jean-Christophe / Charfi, Cyndia / Zgheib, Alain / Cousineau, Isabelle / Lullier, Véronique / Béliveau, Richard / Marsolais, Christian / Annabi, Borhane

Frontiers in immunology

2024 Volume 15, Page(s) 1389603

Abstract: This corrects the article DOI: 10.3389/fimmu.2024.1355945.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2024.1355945.].
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1389603
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Article ; Online: Do We Really Have to Scale Up Local Approaches? A Reflection on Scalability, Based upon a Territorial Prospective at the Burkina Faso–Togo Border

Véronique Ancey / Jean-Michel Sourisseau / Christian Corniaux

Sustainability, Vol 14, Iss 10977, p

2022 Volume 10977

Abstract: Scaling up has become an objective and an indicator of success across many fields. We challenge this norm in the field of agricultural development, where it has recently become widespread, offering a critique and alternative approaches by presenting work ...

Abstract	Scaling up has become an objective and an indicator of success across many fields. We challenge this norm in the field of agricultural development, where it has recently become widespread, offering a critique and alternative approaches by presenting work conducted on the border between Burkina Faso and Togo. Our territorial and prospective approach to cross-border transhumance draws on 30 years of statistical data, 61 interviews, a survey of 568 people and a demographic projection. A collective ambition grew out of the three workshops. Local cross-border debates and the subsequent dialogue between actors across territorial scales demonstrate that contextualized results can be valid without being “scaled up”. A real change in scale means going beyond individual perceptions by identifying and debating the connections between actors and with resources. Resource sustainability is considered through a collective process-based approach rather than through norms. To support practical work on sustainability, rather than fantasizing about perfectly generalizable objects of study or, on the contrary, getting wrapped up in a “small is beautiful” ideal, collective reflection should be encouraged on prospects for local actions. Where tensions run high—as in the territory that we study—these are all emerging resources in the negotiations of public action.
Keywords	territorial approach ; prospective ; pastoralism ; transboundary ; Burkina Faso ; Togo ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Detection of SARS-CoV-2 RNA in a Zoo-Kept Red Fox (

Chan, Tatjana / Ginders, Julia / Kuhlmeier, Evelyn / Meli, Marina L / Bönzli, Eva / Meili, Theres / Hüttl, Julia / Hatt, Jean-Michel / Hindenlang Clerc, Karin / Kipar, Anja / Wyss, Fabia / Wenker, Christian / Ryser-Degiorgis, Marie-Pierre / Valenzuela Agüí, Cecilia / Urban, Christian / Beisel, Christian / Stadler, Tanja / Hofmann-Lehmann, Regina

Viruses

2024 Volume 16, Issue 4

Abstract: Many different animal species are susceptible to SARS-CoV-2, including a few Canidae (domestic dog and raccoon dog). So far, only experimental evidence is available concerning SARS-CoV-2 infections in red foxes ( ...

Abstract	Many different animal species are susceptible to SARS-CoV-2, including a few Canidae (domestic dog and raccoon dog). So far, only experimental evidence is available concerning SARS-CoV-2 infections in red foxes (
MeSH term(s)	Animals ; Foxes/virology ; COVID-19/diagnosis ; COVID-19/virology ; COVID-19/veterinary ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Animals, Zoo/virology ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Switzerland
Chemical Substances	RNA, Viral
Language	English
Publishing date	2024-03-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16040521
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Article ; Online: Combining independent component analysis and source localization for improving spatial sampling of stereoelectroencephalography in epilepsy.

Medina Villalon, Samuel / Makhalova, Julia / López-Madrona, Victor J / Garnier, Elodie / Badier, Jean-Michel / Bartolomei, Fabrice / Bénar, Christian G

Scientific reports

2024 Volume 14, Issue 1, Page(s) 4071

Abstract: Stereoelectroencephalography is a powerful intracerebral EEG recording method for the presurgical evaluation of epilepsy. It consists in implanting depth electrodes in the patient's brain to record electrical activity and map the epileptogenic zone, ... ...

Abstract	Stereoelectroencephalography is a powerful intracerebral EEG recording method for the presurgical evaluation of epilepsy. It consists in implanting depth electrodes in the patient's brain to record electrical activity and map the epileptogenic zone, which should be resected to render the patient seizure-free. Stereoelectroencephalography has high spatial accuracy and signal-to-noise ratio but remains limited in the coverage of the explored brain regions. Thus, the implantation might provide a suboptimal sampling of epileptogenic regions. We investigate the potential of improving a suboptimal stereoelectroencephalography recording by performing source localization on stereoelectroencephalography signals. We propose combining independent component analysis, connectivity measures to identify components of interest, and distributed source modelling. This approach was tested on two patients with two implantations each, the first failing to characterize the epileptogenic zone and the second giving a better diagnosis. We demonstrate that ictal and interictal source localization performed on the first stereoelectroencephalography recordings matches the findings of the second stereo-EEG exploration. Our findings suggest that independent component analysis followed by source localization on the topographies of interest is a promising method for retrieving the epileptogenic zone in case of suboptimal implantation.
MeSH term(s)	Humans ; Epilepsy/diagnosis ; Epilepsy/surgery ; Stereotaxic Techniques ; Electroencephalography/methods ; Brain ; Electrodes, Implanted
Language	English
Publishing date	2024-02-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-54359-4
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Article ; Online: Sudocetaxel Zendusortide (TH1902) triggers the cGAS/STING pathway and potentiates anti-PD-L1 immune-mediated tumor cell killing.

Demeule, Michel / Currie, Jean-Christophe / Charfi, Cyndia / Zgheib, Alain / Cousineau, Isabelle / Lullier, Véronique / Béliveau, Richard / Marsolais, Christian / Annabi, Borhane

Frontiers in immunology

2024 Volume 15, Page(s) 1355945

Abstract: The anticancer efficacy of Sudocetaxel Zendusortide (TH1902), a peptide-drug conjugate internalized through a sortilin-mediated process, was assessed in a triple-negative breast cancer-derived MDA-MB-231 immunocompromised xenograft tumor model where ... ...

Abstract	The anticancer efficacy of Sudocetaxel Zendusortide (TH1902), a peptide-drug conjugate internalized through a sortilin-mediated process, was assessed in a triple-negative breast cancer-derived MDA-MB-231 immunocompromised xenograft tumor model where complete tumor regression was observed for more than 40 days after the last treatment. Surprisingly, immunohistochemistry analysis revealed high staining of STING, a master regulator in the cancer-immunity cycle. A weekly administration of TH1902 as a single agent in a murine B16-F10 melanoma syngeneic tumor model demonstrated superior tumor growth inhibition than did docetaxel. A net increase in CD45 leukocyte infiltration within TH1902-treated tumors, especially for tumor-infiltrating lymphocytes and tumor-associated macrophages was observed. Increased staining of perforin, granzyme B, and caspase-3 was suggestive of elevated cytotoxic T and natural killer cell activities. Combined TH1902/anti-PD-L1 treatment led to increases in tumor growth inhibition and median animal survival. TH1902 inhibited cell proliferation and triggered apoptosis and senescence in B16-F10 cells
MeSH term(s)	Humans ; Mice ; Animals ; B7-H1 Antigen ; Cell Line, Tumor ; Xenograft Model Antitumor Assays ; Nucleotidyltransferases ; Cell Death
Chemical Substances	B7-H1 Antigen ; Nucleotidyltransferases (EC 2.7.7.-)
Language	English
Publishing date	2024-02-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1355945
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Book ; Online: Hérésies

Peperstraete, Sylvie / Biget, Jean-Louis / Courtieu, Gilles / Dépret, Isabelle / De Smet, Daniel / Edwards, Mark / Gabriel, Frédéric / Le Boulluec, Alain / Martinez-Gros, Gabriel / Tardieu, Michel / Teule, Herman / Brouwer, Christian / Dye, Guillaume / Van Rompaey, Anja

2015

Abstract: What kinds of communities bring people together? How are they built? Where is unity, where is the multiplicity of humanity? Men can form separate, antagonistic, violently opposing communities. Is external division necessary to build internal cohesion? ... ...

Abstract	What kinds of communities bring people together? How are they built? Where is unity, where is the multiplicity of humanity? Men can form separate, antagonistic, violently opposing communities. Is external division necessary to build internal cohesion? Nothing is more current than these questions
Keywords	Religion (General)
Size	1 electronic resource (264 pages)
Publisher	Éditions de lUniversité de Bruxelles
Document type	Book ; Online
Note	French ; Open Access
HBZ-ID	HT020481453
ISBN	9782800415840 ; 2800415843
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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