In this work, we have investigated the relationships between synonymous and nonsynonymous rates a... more In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the GC 2 level, the higher the amino acid replacement rate). The correlation is especially strong with T 2 , the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate and base composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have shown that the synonymous rate is strongly correlated with the GC 3 level. This correlation is observed both across genes and at the intragenic level. Similarly, the nonsynonymous rate is also affected at the intragenic level by GC 3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC 3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar way by the intragenic variation of GC 3. This result, taken together with the fact that the number of genes displaying intragenic correlation coefficients between synonymous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed), strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common evolutionary forces in genes from Gramineae.
ABSTRACT Factors, such as overpopulation, resource reduction and loss of biodiversity are conside... more ABSTRACT Factors, such as overpopulation, resource reduction and loss of biodiversity are considered most threatening for humanity and their interaction in the history of mankind are shortly revisited. These are the driving forces that led governments worldwide to the implementation of renewable energies. Among, the renewable energies that started to contribute to the energy grid, biofuels are considered as an obligate step. Here, an attempt has been made to overview the particular case of Jatropha curcas L. and show how the international scientific community has concertedly contributed to draw it from anonymity in just few years and worked to implement it as an alternative biodiesel option to feed the energy grid.
Les relations génomiques dégagées dans ce travail font apparaître que l'ancêtre commun des gramin... more Les relations génomiques dégagées dans ce travail font apparaître que l'ancêtre commun des graminées a subi une transition de la composition en bases qui se traduit par l'augmentation en GC dans tous les consitutants géniques et génomiques. Par opposition, cette transition n'a pas eu lieu dans la plupart des autres Monocots et Dicots. La transition compositionnelle renforce l'évidence de l'existence de deux classes de gènes chez les Angiospermes : les gènes pauvres et riches en GC. Les premiers sont caractérisés par la présence d'introns en plus grand nombre et de plus grande longueur que les derniers. Par ailleurs, les deux classes de gènes chez les graminées ont, sur base de l'étude des substitutions synonymes, des taux d'évolution différentes et sont associées à des plans de fonction différents. La composition en bases est un facteur déterminant de la localisation des gènes dans le génome. Chez les graminées, la plupart des gènes sont concentrés dans un intervalle de composition en bases inférieur à 2%. Chez Arabidopsis, la composition en GC est plus élevée aux parties distales des chromosomes que dans leurs parties centrales. La composition en GC des gènes et des séquences codantes suit la même tendance. Le génome d'Arabidopsis peut être décomposé en 2 composantes principales, l'une pauvre en GC correspondant à la partie centrale des chromosomes, l'autre riche en GC, et quantitativement plus importante, correspondant aux parties distales des chromosomes. S u m m ary : The work presented here shows, by a detailed analysis of the genomic features of Gramineae, that their common ancestor did the experience of a compositional transition leading to the increase in GC level of all parts of the genome and of the genes. By contrast, this transition did not occur in a number of Dicots and Monocots. With regard to GC level of t h e genes, the compositional transition stresses the existence of two classes of genes in Angiosperms. The GC-poor genes are characterised by introns higher in average number and size compared to GC-rich genes. By analysing synonymous and non-synonymous substitutions, we showed that t h e evolution rates in the two classes of genes are different and correspond to different functional patterns. The base composition is a determinant of gene location within the Angiosperm genomes. In Gramineae, most genes occur in genomic regions that have a narrow range of GC levels (≤ 2%). In Arabidopsis, the GC level of contigs is higher, on average, in the distal regions of chromosomes compared to their central regions. The GC levels of genes and coding sequences follow the same trend. The Arabidopsis genome is made up of two major components. One is GC-poor and corresponds to the central part of the chromosomes, the other, quantitatively higher, is in comparison GC-rich and corresponds to the distal regions of chromosomes.
The reactions of Beta procumbens C. Sm. and Beta webbiana ivfoq. were compared to those of Betavu... more The reactions of Beta procumbens C. Sm. and Beta webbiana ivfoq. were compared to those of Betavulgaris L. wirh regard to an infection by Cercospora beticola Sacc. The {leck reaction observed in B. zuebbiana may be interpreted as hvpersensitivity based on sympromarological, light microscopical, fluorescent microscopical and electron microscopical data. The B. procumbens clone was found to show resistance characteristics similar to those of B. t;tebbiana and B. vulgaris, as it reacted both by flecks (8. webbiana) and leaf spots (-8. tulgaris) to a C. beticola infection. Zusammenfassung Eine symptomatologische und morphologische Untersuchung der Resistenz von Sflildriibenarten der Patellares-Sektion gegen Cercospora beticola Sacc. Verglichen wurden die Reaktionen von Beta procumbens C. Sm. und B. uebbiana lvloq. mit denen von B. vulgaris L. nach einer Infektion mit Cercospora beticoh Sacc. Die bei .8. webbiana beobachtete Klecksreaktion kann als Hypersensitivitât anhand von symptometologischen, licht-, fluoreszenzsowie elektronenmikroskopischen Daten angesehen werden. Beim B. procurnbens-Klon wurden Resistenzmerkmale festgestellt, die denen von B. pebbinna und B. oulgaris âhnelten: der Klon reagierte mit Klecksen (8. zoebbiana) sowie mit Blattflecken (8. oulgaris) nach einer C. beticola-Infektion.
The base composition patterns of genes, coding sequences and gene expression levels were analyzed... more The base composition patterns of genes, coding sequences and gene expression levels were analyzed in the available long sequences (contigs) of Arabidopsis. Chromosome 5 was analyzed in detail and all chromosomes for which sequence data are now available show essentially the same large-scale compositional properties. Guanine+cytosine levels of genes and of their coding regions, as well as gene densities and expression levels, all show a marked tendency to be higher in the distal regions of Arabidopsis chromosomes.
The genus Fusarium contains some of the most studied and important species of plant pathogens tha... more The genus Fusarium contains some of the most studied and important species of plant pathogens that economically affect world agriculture and horticulture. Fusarium spp. are ubiquitous fungi widely distributed in soil, plants as well as in different organic substrates and are also considered as opportunistic human pathogens. The identification of specific enzymes essential to the metabolism of these fungus is expected to provide molecular targets to control the diseases they induce to their hosts. Through applications of traditional techniques of sequence homology comparison by similarity search and Markov modeling, this report describes the characterization of enzymatic functionalities associated to protein targets that could be considered for the control of root rots induced by Fusarium oxysporum. From the analysis of 318 F. graminearum enzymes, we retrieved 30 enzymes that are specific of F. oxysporum compared to 15 species of host plants. By comparing these 30 specific enzymes of F. oxysporum with the genome of Arabidopsis thaliana, Brassica rapa, Glycine max, Jatropha curcas and Ricinus communis, we found 7 key specific enzymes whose inhibition is expected to affect significantly the development of the fungus and 5 specific enzymes that were considered here to be secondary because they are inserted in pathways with alternative routes.
Proceedings of the National Academy of Sciences of the United States of America, Nov 21, 1995
Previous investigations from our laboratory showed that the genomes of plants, like those of vert... more Previous investigations from our laboratory showed that the genomes of plants, like those of vertebrates, are mosaics of isochores, i.e., of very long DNA segments that are compositionally homogeneous and that can be subdivided into a small number of families characterized by different GC levels (GC is the mole fraction of guanine + cytosine). Compositional DNA fractions corresponding to different isochore families were used to investigate, by hybridization with appropriate probes, the gene distribution in vertebrate genomes. Here we report such a study on the genome of a plant, maize. The gene distribution that we found is most striking, in that almost all genes are present in isochores covering an extremely narrow (1-2%) GC range and only representing 10-20% of the genome. This gene distribution, which seems to characterize other Gramineae as well, is remarkably different from the gene distribution previously found in vertebrate genomes. The genomes of vertebrates are made up of isochores (1, 2), long (>300 kb) DNA segments that are homogeneous in base composition and that can be subdivided into a small number of families covering a compositional range, which is broad in warm-blooded vertebrates and narrow in cold-blooded vertebrates. The compositional distribution of isochores is reflected in the DNA fragments ('100 kb long) that derive from them as a result of the enzymatic and physical degradation accompanying DNA preparation and that can be fractionated by centrifugation in Cs2SO4 density gradients in the presence of sequence-specific ligands. The major interest of this approach is that it has allowed the definition of genome properties such as the compositional patterns (e.g., the compositional distributions of DNA fragments; see Results), the compositional
Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Ara... more Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Arabidopsis, soybean, pea, tobacco, tomato, potato). One class, the GC-rich class, contained genes with no, or few, short introns. In contrast, the GC-poor class contained genes with numerous, long introns. The similarity of the properties of each class, as present in the genomes of maize and Arabidopsis, is particularly remarkable in view of the fact that these plants exhibit large differences in genome size, average intron size, and DNA base composition. The functional relevance of the two classes of genes is stressed by (1) the conservation in homologous genes from maize and Arabidopsis not only of the number of introns and of their positions, but also of the relative size of concatenated introns; and (2) the existence of two similar classes of genes in vertebrates; interestingly, the differences in intron sizes and numbers in genes from the GC-poor and GC-rich classes are much more striking in plants than in vertebrates.
Introduction: T-cell acute lymphoblastic leukemia (T-ALL) accounts for 12% to 15% of all cases of... more Introduction: T-cell acute lymphoblastic leukemia (T-ALL) accounts for 12% to 15% of all cases of ALL diagnosed in children and 25% in adults. It is a genetically heterogeneous disease caused by the malignant transformation of T-cell precursors. Twenty percent of all TALL patients relapse within two years after diagnosis. Recurrent disease is challenging to cure, and relatively few new drugs have been developed for children with resistant disease. Intensive care is essential to improve the chances of survival in patients. However, the treatment is very long and not rarely, with life-threatening side effects. Identifying new molecular targets in TALL is essential to minimize and overcome the harmful impacts of current therapeutic regimens. Objectives: Our goal is to identify these targets by evaluating differentially expressed genes in TALL along with the application of systems biology in order to identify highly connected proteins. Methodology: We used RNA-seq data (freely available in databases) of peripheral T cells and thymocytes at different stages of maturation from healthy individuals for comparison with the RNA-seq of Jurkat and MOLT-4 TALL cell lines. Normalized controls' RNA-seq data were subtracted from cell lines' RNA-seq data to calculate the differential expression. Proteins classified as overexpressed were extracted from the reference list of interactome genes (IntAct, 2017 version, EBI) to calculate the number of connections of each gene. Results: Five of the ten main targets for each cell lineage were common to both, including oncogenes, chaperones, regulatory proteins, and histone modifiers. However, unique genes were also identified for each cell lineage. More importantly, the identified targets showed few differences depending on the control used for comparison, suggesting that our method is consistent. Conclusion: Therefore, we successfully identified new therapeutic targets not previously described in the literature and initiated knockdown experiments to express specific shRNA molecules for the target genes to reduce the amount of corresponding proteins in the cell lines and evaluate the cell phenotypes in the future.
... Double-layer culture technique as a tool for the selection of calluses resistant to toxic mat... more ... Double-layer culture technique as a tool for the selection of calluses resistant to toxic material from plant pathogenic fungi. Auteur(s) / Author(s). LEPOIVRE P. ; VISEUR J. ; DUHEM K. ; CARELSN. ; Affiliation(s) du ou des auteurs / Author(s) Affiliation(s). Fac. sci. ...
Since the ratification of the Kyoto protocol, a significant effort has been made worldwide to boo... more Since the ratification of the Kyoto protocol, a significant effort has been made worldwide to boost biofuels with the expectation of a positive contribution to renewable fuel and greenhouse gas reduction. The initial recommendations were generally not acted upon except in some particular cases, such as Brazil and Vietnam. The positive contribution of first generation biofuels has been challenged because
Proceedings of the National Academy of Sciences of the United States of America, Jun 24, 1997
Recent investigations showed that most maize genes are present in compositional fractions of nucl... more Recent investigations showed that most maize genes are present in compositional fractions of nuclear DNA that cover only a 1-2% GC (molar fraction of guanosine plus cytosine in DNA) range and represent only 10-20% of the genome. These fractions, which correspond to compositional genome compartments that are distributed on all chromosomes, were collectively called the ''gene space.'' Outside the gene space, the maize genome appears to contain no genes, except for some zein genes and for ribosomal genes. Here, we investigated the distribution of genes in the genomes of two other Gramineae, rice and barley, and used a new set of probes to study further the gene distribution of maize. We found that the distribution of genes in these three genomes is basically similar in that all genes, except for ribosomal genes and some storage protein genes, were located in gene spaces that (i) cover GC ranges of 0.8%, 1.0%, and 1.6% and represent 12%, 17%, and 24% of the genomes of barley, maize, and rice, respectively; (ii) are due to a remarkably uniform base composition in the sequences surrounding the genes, which are now known to consist mainly of transposons; (iii) have sizes approximately proportional to genome sizes, suggesting that expansion-contraction phenomena proceed in parallel in the gene space and in the gene-empty regions of the genome; and (iv) only hybridize on the gene spaces (and not on the other DNA fractions) of other Gramineae.
Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivit... more Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about diatom cell biology or about their genome structure. For diatom researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species. Phaeodactylum tricornutum is an obvious candidate because of its ease of culture and because it can be genetically transformed. Therefore, we have examined its genome composition by the generation of approximately 1,000 expressed sequence tags. Although more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had high similarity with a range of genes defined functionally at the protein level. It is interesting that many of these sequences are more similar to animal rather than plant counterparts. Base composition at each codon position and GC content of the genome were compared with Arabidopsis, maize (Zea mays), and Chlamydomonas reinhardtii. It was found that distribution of GC within the coding sequences is as homogeneous in P. tricornutum as in Arabidopsis, but with a slightly higher GC content. Furthermore, we present evidence that the P. tricornutum genome is likely to be small (less than 20 Mb). Therefore, this combined information supports the development of this species as a model system for molecular-based studies of diatom biology. The nucleotide sequence data reported has been deposited in GenBank Nucleotide Sequence Database (dbEST section) under accession nos. BI306757 through BI307753.
bioRxiv (Cold Spring Harbor Laboratory), May 13, 2023
Since cancer is a genetic disease, studying gene regulatory networks related to this pathology of... more Since cancer is a genetic disease, studying gene regulatory networks related to this pathology offers the possibility of obtaining helpful information for therapeutic purposes. However, the complexity expressed by the interconnections between network components grows exponentially with the number of genes in the system. In this report, the Boolean logic's use for regulating the existing relationships between network components has allowed us to simplify the modeling capable of producing attractors representing the cell phenotypes from breast cancer RNA-seq data. From this point of view, a therapeutic objective is to induce the cell, through appropriate interventions, to leave the current cancer attractor to migrate toward another attractor physiologically different from cancer. In this report, we developed a computational method that identifies network nodes whose inhibition achieves the therapeutic objective of transitioning from one tumor attractor to another associated with apoptosis based on transcriptomic data from cell lines. We used previously published in vitro experiments, in which the knockdown of a few proteins led a breast cancer cell line to death, to validate the model taking into account genes related to apoptosis in cancer cells. The method proposed in this manuscript uses heterogeneous data integration, structural network analysis, and biological knowledge to identify potential targets of interest for breast cancer on a personalized medicine approach.
bioRxiv (Cold Spring Harbor Laboratory), Apr 28, 2023
Glioblastoma Multiforme (GBM) is the most common and aggressive type of brain tumor. With a media... more Glioblastoma Multiforme (GBM) is the most common and aggressive type of brain tumor. With a median survival of around 15 months, it has only approximately a 10% chance of 5-year overall survival. Fortunately, the availability and variety of large sets of omics data is a positive factor for modeling its biology. But once a malignant state can take a long time to develop, the data usually ends up as a static description of the system's states in a short time interval. By incorporating ergodicity concepts associated with GBM aggressiveness, we might connect available single-cell RNA sequencing data with system dynamics theoretical background. Egodicity incorporation enabled using clustering techniques as a basis for parameter estimation, studying the deterministic and stochastic dynamics through stochastic simulations and computing the (epi)genetic landscape of GBM subtypes. Ultimately, this report contributed to imporve the power of the model predictivity and provided valuable insights into the statistical dynamics of the disease, opening possibilities for a more comprehensive understanding of the malignant state progression.
In this work, we have investigated the relationships between synonymous and nonsynonymous rates a... more In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the GC 2 level, the higher the amino acid replacement rate). The correlation is especially strong with T 2 , the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate and base composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have shown that the synonymous rate is strongly correlated with the GC 3 level. This correlation is observed both across genes and at the intragenic level. Similarly, the nonsynonymous rate is also affected at the intragenic level by GC 3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC 3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar way by the intragenic variation of GC 3. This result, taken together with the fact that the number of genes displaying intragenic correlation coefficients between synonymous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed), strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common evolutionary forces in genes from Gramineae.
ABSTRACT Factors, such as overpopulation, resource reduction and loss of biodiversity are conside... more ABSTRACT Factors, such as overpopulation, resource reduction and loss of biodiversity are considered most threatening for humanity and their interaction in the history of mankind are shortly revisited. These are the driving forces that led governments worldwide to the implementation of renewable energies. Among, the renewable energies that started to contribute to the energy grid, biofuels are considered as an obligate step. Here, an attempt has been made to overview the particular case of Jatropha curcas L. and show how the international scientific community has concertedly contributed to draw it from anonymity in just few years and worked to implement it as an alternative biodiesel option to feed the energy grid.
Les relations génomiques dégagées dans ce travail font apparaître que l'ancêtre commun des gramin... more Les relations génomiques dégagées dans ce travail font apparaître que l'ancêtre commun des graminées a subi une transition de la composition en bases qui se traduit par l'augmentation en GC dans tous les consitutants géniques et génomiques. Par opposition, cette transition n'a pas eu lieu dans la plupart des autres Monocots et Dicots. La transition compositionnelle renforce l'évidence de l'existence de deux classes de gènes chez les Angiospermes : les gènes pauvres et riches en GC. Les premiers sont caractérisés par la présence d'introns en plus grand nombre et de plus grande longueur que les derniers. Par ailleurs, les deux classes de gènes chez les graminées ont, sur base de l'étude des substitutions synonymes, des taux d'évolution différentes et sont associées à des plans de fonction différents. La composition en bases est un facteur déterminant de la localisation des gènes dans le génome. Chez les graminées, la plupart des gènes sont concentrés dans un intervalle de composition en bases inférieur à 2%. Chez Arabidopsis, la composition en GC est plus élevée aux parties distales des chromosomes que dans leurs parties centrales. La composition en GC des gènes et des séquences codantes suit la même tendance. Le génome d'Arabidopsis peut être décomposé en 2 composantes principales, l'une pauvre en GC correspondant à la partie centrale des chromosomes, l'autre riche en GC, et quantitativement plus importante, correspondant aux parties distales des chromosomes. S u m m ary : The work presented here shows, by a detailed analysis of the genomic features of Gramineae, that their common ancestor did the experience of a compositional transition leading to the increase in GC level of all parts of the genome and of the genes. By contrast, this transition did not occur in a number of Dicots and Monocots. With regard to GC level of t h e genes, the compositional transition stresses the existence of two classes of genes in Angiosperms. The GC-poor genes are characterised by introns higher in average number and size compared to GC-rich genes. By analysing synonymous and non-synonymous substitutions, we showed that t h e evolution rates in the two classes of genes are different and correspond to different functional patterns. The base composition is a determinant of gene location within the Angiosperm genomes. In Gramineae, most genes occur in genomic regions that have a narrow range of GC levels (≤ 2%). In Arabidopsis, the GC level of contigs is higher, on average, in the distal regions of chromosomes compared to their central regions. The GC levels of genes and coding sequences follow the same trend. The Arabidopsis genome is made up of two major components. One is GC-poor and corresponds to the central part of the chromosomes, the other, quantitatively higher, is in comparison GC-rich and corresponds to the distal regions of chromosomes.
The reactions of Beta procumbens C. Sm. and Beta webbiana ivfoq. were compared to those of Betavu... more The reactions of Beta procumbens C. Sm. and Beta webbiana ivfoq. were compared to those of Betavulgaris L. wirh regard to an infection by Cercospora beticola Sacc. The {leck reaction observed in B. zuebbiana may be interpreted as hvpersensitivity based on sympromarological, light microscopical, fluorescent microscopical and electron microscopical data. The B. procumbens clone was found to show resistance characteristics similar to those of B. t;tebbiana and B. vulgaris, as it reacted both by flecks (8. webbiana) and leaf spots (-8. tulgaris) to a C. beticola infection. Zusammenfassung Eine symptomatologische und morphologische Untersuchung der Resistenz von Sflildriibenarten der Patellares-Sektion gegen Cercospora beticola Sacc. Verglichen wurden die Reaktionen von Beta procumbens C. Sm. und B. uebbiana lvloq. mit denen von B. vulgaris L. nach einer Infektion mit Cercospora beticoh Sacc. Die bei .8. webbiana beobachtete Klecksreaktion kann als Hypersensitivitât anhand von symptometologischen, licht-, fluoreszenzsowie elektronenmikroskopischen Daten angesehen werden. Beim B. procurnbens-Klon wurden Resistenzmerkmale festgestellt, die denen von B. pebbinna und B. oulgaris âhnelten: der Klon reagierte mit Klecksen (8. zoebbiana) sowie mit Blattflecken (8. oulgaris) nach einer C. beticola-Infektion.
The base composition patterns of genes, coding sequences and gene expression levels were analyzed... more The base composition patterns of genes, coding sequences and gene expression levels were analyzed in the available long sequences (contigs) of Arabidopsis. Chromosome 5 was analyzed in detail and all chromosomes for which sequence data are now available show essentially the same large-scale compositional properties. Guanine+cytosine levels of genes and of their coding regions, as well as gene densities and expression levels, all show a marked tendency to be higher in the distal regions of Arabidopsis chromosomes.
The genus Fusarium contains some of the most studied and important species of plant pathogens tha... more The genus Fusarium contains some of the most studied and important species of plant pathogens that economically affect world agriculture and horticulture. Fusarium spp. are ubiquitous fungi widely distributed in soil, plants as well as in different organic substrates and are also considered as opportunistic human pathogens. The identification of specific enzymes essential to the metabolism of these fungus is expected to provide molecular targets to control the diseases they induce to their hosts. Through applications of traditional techniques of sequence homology comparison by similarity search and Markov modeling, this report describes the characterization of enzymatic functionalities associated to protein targets that could be considered for the control of root rots induced by Fusarium oxysporum. From the analysis of 318 F. graminearum enzymes, we retrieved 30 enzymes that are specific of F. oxysporum compared to 15 species of host plants. By comparing these 30 specific enzymes of F. oxysporum with the genome of Arabidopsis thaliana, Brassica rapa, Glycine max, Jatropha curcas and Ricinus communis, we found 7 key specific enzymes whose inhibition is expected to affect significantly the development of the fungus and 5 specific enzymes that were considered here to be secondary because they are inserted in pathways with alternative routes.
Proceedings of the National Academy of Sciences of the United States of America, Nov 21, 1995
Previous investigations from our laboratory showed that the genomes of plants, like those of vert... more Previous investigations from our laboratory showed that the genomes of plants, like those of vertebrates, are mosaics of isochores, i.e., of very long DNA segments that are compositionally homogeneous and that can be subdivided into a small number of families characterized by different GC levels (GC is the mole fraction of guanine + cytosine). Compositional DNA fractions corresponding to different isochore families were used to investigate, by hybridization with appropriate probes, the gene distribution in vertebrate genomes. Here we report such a study on the genome of a plant, maize. The gene distribution that we found is most striking, in that almost all genes are present in isochores covering an extremely narrow (1-2%) GC range and only representing 10-20% of the genome. This gene distribution, which seems to characterize other Gramineae as well, is remarkably different from the gene distribution previously found in vertebrate genomes. The genomes of vertebrates are made up of isochores (1, 2), long (>300 kb) DNA segments that are homogeneous in base composition and that can be subdivided into a small number of families covering a compositional range, which is broad in warm-blooded vertebrates and narrow in cold-blooded vertebrates. The compositional distribution of isochores is reflected in the DNA fragments ('100 kb long) that derive from them as a result of the enzymatic and physical degradation accompanying DNA preparation and that can be fractionated by centrifugation in Cs2SO4 density gradients in the presence of sequence-specific ligands. The major interest of this approach is that it has allowed the definition of genome properties such as the compositional patterns (e.g., the compositional distributions of DNA fragments; see Results), the compositional
Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Ara... more Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Arabidopsis, soybean, pea, tobacco, tomato, potato). One class, the GC-rich class, contained genes with no, or few, short introns. In contrast, the GC-poor class contained genes with numerous, long introns. The similarity of the properties of each class, as present in the genomes of maize and Arabidopsis, is particularly remarkable in view of the fact that these plants exhibit large differences in genome size, average intron size, and DNA base composition. The functional relevance of the two classes of genes is stressed by (1) the conservation in homologous genes from maize and Arabidopsis not only of the number of introns and of their positions, but also of the relative size of concatenated introns; and (2) the existence of two similar classes of genes in vertebrates; interestingly, the differences in intron sizes and numbers in genes from the GC-poor and GC-rich classes are much more striking in plants than in vertebrates.
Introduction: T-cell acute lymphoblastic leukemia (T-ALL) accounts for 12% to 15% of all cases of... more Introduction: T-cell acute lymphoblastic leukemia (T-ALL) accounts for 12% to 15% of all cases of ALL diagnosed in children and 25% in adults. It is a genetically heterogeneous disease caused by the malignant transformation of T-cell precursors. Twenty percent of all TALL patients relapse within two years after diagnosis. Recurrent disease is challenging to cure, and relatively few new drugs have been developed for children with resistant disease. Intensive care is essential to improve the chances of survival in patients. However, the treatment is very long and not rarely, with life-threatening side effects. Identifying new molecular targets in TALL is essential to minimize and overcome the harmful impacts of current therapeutic regimens. Objectives: Our goal is to identify these targets by evaluating differentially expressed genes in TALL along with the application of systems biology in order to identify highly connected proteins. Methodology: We used RNA-seq data (freely available in databases) of peripheral T cells and thymocytes at different stages of maturation from healthy individuals for comparison with the RNA-seq of Jurkat and MOLT-4 TALL cell lines. Normalized controls' RNA-seq data were subtracted from cell lines' RNA-seq data to calculate the differential expression. Proteins classified as overexpressed were extracted from the reference list of interactome genes (IntAct, 2017 version, EBI) to calculate the number of connections of each gene. Results: Five of the ten main targets for each cell lineage were common to both, including oncogenes, chaperones, regulatory proteins, and histone modifiers. However, unique genes were also identified for each cell lineage. More importantly, the identified targets showed few differences depending on the control used for comparison, suggesting that our method is consistent. Conclusion: Therefore, we successfully identified new therapeutic targets not previously described in the literature and initiated knockdown experiments to express specific shRNA molecules for the target genes to reduce the amount of corresponding proteins in the cell lines and evaluate the cell phenotypes in the future.
... Double-layer culture technique as a tool for the selection of calluses resistant to toxic mat... more ... Double-layer culture technique as a tool for the selection of calluses resistant to toxic material from plant pathogenic fungi. Auteur(s) / Author(s). LEPOIVRE P. ; VISEUR J. ; DUHEM K. ; CARELSN. ; Affiliation(s) du ou des auteurs / Author(s) Affiliation(s). Fac. sci. ...
Since the ratification of the Kyoto protocol, a significant effort has been made worldwide to boo... more Since the ratification of the Kyoto protocol, a significant effort has been made worldwide to boost biofuels with the expectation of a positive contribution to renewable fuel and greenhouse gas reduction. The initial recommendations were generally not acted upon except in some particular cases, such as Brazil and Vietnam. The positive contribution of first generation biofuels has been challenged because
Proceedings of the National Academy of Sciences of the United States of America, Jun 24, 1997
Recent investigations showed that most maize genes are present in compositional fractions of nucl... more Recent investigations showed that most maize genes are present in compositional fractions of nuclear DNA that cover only a 1-2% GC (molar fraction of guanosine plus cytosine in DNA) range and represent only 10-20% of the genome. These fractions, which correspond to compositional genome compartments that are distributed on all chromosomes, were collectively called the ''gene space.'' Outside the gene space, the maize genome appears to contain no genes, except for some zein genes and for ribosomal genes. Here, we investigated the distribution of genes in the genomes of two other Gramineae, rice and barley, and used a new set of probes to study further the gene distribution of maize. We found that the distribution of genes in these three genomes is basically similar in that all genes, except for ribosomal genes and some storage protein genes, were located in gene spaces that (i) cover GC ranges of 0.8%, 1.0%, and 1.6% and represent 12%, 17%, and 24% of the genomes of barley, maize, and rice, respectively; (ii) are due to a remarkably uniform base composition in the sequences surrounding the genes, which are now known to consist mainly of transposons; (iii) have sizes approximately proportional to genome sizes, suggesting that expansion-contraction phenomena proceed in parallel in the gene space and in the gene-empty regions of the genome; and (iv) only hybridize on the gene spaces (and not on the other DNA fractions) of other Gramineae.
Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivit... more Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about diatom cell biology or about their genome structure. For diatom researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species. Phaeodactylum tricornutum is an obvious candidate because of its ease of culture and because it can be genetically transformed. Therefore, we have examined its genome composition by the generation of approximately 1,000 expressed sequence tags. Although more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had high similarity with a range of genes defined functionally at the protein level. It is interesting that many of these sequences are more similar to animal rather than plant counterparts. Base composition at each codon position and GC content of the genome were compared with Arabidopsis, maize (Zea mays), and Chlamydomonas reinhardtii. It was found that distribution of GC within the coding sequences is as homogeneous in P. tricornutum as in Arabidopsis, but with a slightly higher GC content. Furthermore, we present evidence that the P. tricornutum genome is likely to be small (less than 20 Mb). Therefore, this combined information supports the development of this species as a model system for molecular-based studies of diatom biology. The nucleotide sequence data reported has been deposited in GenBank Nucleotide Sequence Database (dbEST section) under accession nos. BI306757 through BI307753.
bioRxiv (Cold Spring Harbor Laboratory), May 13, 2023
Since cancer is a genetic disease, studying gene regulatory networks related to this pathology of... more Since cancer is a genetic disease, studying gene regulatory networks related to this pathology offers the possibility of obtaining helpful information for therapeutic purposes. However, the complexity expressed by the interconnections between network components grows exponentially with the number of genes in the system. In this report, the Boolean logic's use for regulating the existing relationships between network components has allowed us to simplify the modeling capable of producing attractors representing the cell phenotypes from breast cancer RNA-seq data. From this point of view, a therapeutic objective is to induce the cell, through appropriate interventions, to leave the current cancer attractor to migrate toward another attractor physiologically different from cancer. In this report, we developed a computational method that identifies network nodes whose inhibition achieves the therapeutic objective of transitioning from one tumor attractor to another associated with apoptosis based on transcriptomic data from cell lines. We used previously published in vitro experiments, in which the knockdown of a few proteins led a breast cancer cell line to death, to validate the model taking into account genes related to apoptosis in cancer cells. The method proposed in this manuscript uses heterogeneous data integration, structural network analysis, and biological knowledge to identify potential targets of interest for breast cancer on a personalized medicine approach.
bioRxiv (Cold Spring Harbor Laboratory), Apr 28, 2023
Glioblastoma Multiforme (GBM) is the most common and aggressive type of brain tumor. With a media... more Glioblastoma Multiforme (GBM) is the most common and aggressive type of brain tumor. With a median survival of around 15 months, it has only approximately a 10% chance of 5-year overall survival. Fortunately, the availability and variety of large sets of omics data is a positive factor for modeling its biology. But once a malignant state can take a long time to develop, the data usually ends up as a static description of the system's states in a short time interval. By incorporating ergodicity concepts associated with GBM aggressiveness, we might connect available single-cell RNA sequencing data with system dynamics theoretical background. Egodicity incorporation enabled using clustering techniques as a basis for parameter estimation, studying the deterministic and stochastic dynamics through stochastic simulations and computing the (epi)genetic landscape of GBM subtypes. Ultimately, this report contributed to imporve the power of the model predictivity and provided valuable insights into the statistical dynamics of the disease, opening possibilities for a more comprehensive understanding of the malignant state progression.
This book presents the theoretical foundations of Systems Biology, as well as its application in ... more This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.
Jatropha curcas, or physic nut, is a small tree that, in tropical climates, produces fruits with ... more Jatropha curcas, or physic nut, is a small tree that, in tropical climates, produces fruits with seeds containing ~38% oil. The physic nut has the potential to be highly productive and is amenable to subculture in vitro and to genetic modification. It also displays remarkable diversity and is relatively easy to cross hybridize within the genus. Thanks to these promising features, J. curcas is emerging as a promising oil crop and is gaining commercial interest among the biofuel research communities. However, as a crop, physic nut has been an economic flop since 2012, because the species was not fully domesticated and the average productivity was less than 2 t/ha, which is below the threshold of profitability.^7 t/ha could be reached and it is contributing to new markets in some countries. As such, it is important fro research to focus on the physiology and selective breeding of Jatropha . This book provides a positive global update on Jatropha, a crop that has suffered despite its promising agronomic and economic potential. The editors have used their collective expertise in agronomy, botany, selective breeding, biotechnology, genomics and bioinformatics to seek out high-quality contributions that address the bottleneck features in order to improve the economic trajectory of physic nut breeding.
Jatropha curcas or Physic Nut is a small tree (bush plant) that produces fruits under tropical cl... more Jatropha curcas or Physic Nut is a small tree (bush plant) that produces fruits under tropical climate. The fruits contained seed that are ~40% oil rich. This oil is excellent for biodiesel. The bush is a now new coming crop because it may cope with harsh environmental conditions such as semi-aridity and poor land. It is considered as one alternative for climate mitigation that does not compete with arable land normally dedicated to food crop and can be used to regain degraded land or fight desertification. This bush has been considered seriously by the international community only recently (2006-2008), but worldwide scientists did an outstanding job to drawn Jatropha out of its semi-wild status and bring it on the industrial scene. Problems remains, but we have now a comprehensive picture of this crop and almost every technological challenged were addressed. From now, the job will have to concentrate on breeding in order to domesticate this species. Therefore, it is the right time to sum up worldwide contributions in a comprehensive book with a breeding looking to improve the chance of this plant to stabilize as a crop and to fulfil with the expectations that humans invested in it. A book with this perspective will help international community to give a step on. The book will be a broad and comprehensive look on Jatropha until the details since the book is being contributed by international experts worldwide that have already published works in the international press of Science. Illustrations, tables geographic maps, GPS location, etc are added by each contributors according to the feeling they have concerning what they think their contribution should be.
The book will be a broad and comprehensive look on Jatropha until the details since the book is b... more The book will be a broad and comprehensive look on Jatropha until the details since the book is being contributed by international experts worldwide that have already published works in the international press of Science. Illustrations, tables geographic maps, GPS location, etc are added by each contributors according to the feeling they have concerning what they think their contribution should be. This book will benefit the scientific community immensely. Being aware of any challenges related to Jatropha, i.e. (i) its economy in Asia (India, China) and South America (Brazil), (ii) basics of biofuel technology, (iii) physiology, (iv) farming, (v) byproducts, (vi) biotechnology, (vii) genetic resource (germplasm) and their benefit for the crop by genetic transfer, (viii) genetic map, (ix) comparative genetics, (x) genomics. Breeders and technologist will have access to a complete digested view on Jatropha to decide where and how they should move on with their investigations.
We present a compilation on the evolutive processes that led to the gene emergence that should he... more We present a compilation on the evolutive processes that led to the gene emergence that should help readers who are not familiar with the subject to understand the mechanisms that might have shaped it over time. The main challenge in these processes is that they must be coherent with the emergence of self-reproducing systems from simple in- and organic chemistry as well as being compatible with natural selection. As in other sciences like physics, the detailed understanding of the most fundamental processes led to key breakthrough technological achievements. For instance, the artificially induced evolution of catalytic systems under directed selective constraints is an important issue for the processing industry. It is amazing to realize how fast complex biological systems arose and evolved in the early time of Earth. Here, it has been our aim to try to give a constructive view of how chemical information contributed to biological self-organization.
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This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.