Thomas Heams | AgroParisTech - Academia.edu (original) (raw)

Papers by Thomas Heams

The necessary animal need: eating and become human - As part of an issue dedicated to vegetariani... more The necessary animal need: eating and become human - As part of an issue dedicated to vegetarianism, this paper analyzes the reasons of different kinds, for which man (generally) eats animal products. The nature of the links that were forged between humans and domestic animals is emphasized.

Animal Breeding requires a diverse spectrum of competences, from biology to social sciences and t... more Animal Breeding requires a diverse spectrum of competences, from biology to social sciences and technology, and so does its teaching and training. It results in a collective activity which benefits from moving towards three complementary directions: interdisciplinarity, internationalization, and interculturality. These dimensions open new ways to create and to adapt innovative curricula to the fast evolving needs of the professional sector, but they are also challenging. Recent joint initiatives between European institutions in the field with their successes and pitfalls could be a useful source of experience.

... Either peptides (obtained from Dr. Daria Mochly-Rosen, Stanford University, Standford, CA, US... more ... Either peptides (obtained from Dr. Daria Mochly-Rosen, Stanford University, Standford, CA, USA) were renewed after 2h or embryos were ... A. ReisA, KA PowellA, GJ McCallumA, JA RookeA, and TG McEvoyA AScottish Agricultural College, Sustainable Livestock Systems Group ...

Nucleic Acids Research, 2005

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precur... more The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 6 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 6 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Journal of Biological …, Jan 1, 2005

In somatic tissues, the CpG island of the imprinted Peg1/Mest gene is methylated on the maternal ... more In somatic tissues, the CpG island of the imprinted Peg1/Mest gene is methylated on the maternal allele. We have examined the methylation of CpG and non-CpG sites of this differentially methylated CpG island in freshly ovulated oocytes, in vitro aged oocytes, and preimplantation embryos. The CpG methylation pattern was heterogeneous in freshly ovulated oocytes, despite the fact that they all were arrested in metaphase II. After short in vitro culture, Peg1/Mest became hypermethylated, whereas prolonged in vitro culture resulted in demethylation in a fraction of oocytes. Non-CpG methylation also occurred in a stage-specific manner. On alleles that were fully methylated at CpG sites, this modification was found, and it became reduced in twocell stage embryos and blastocysts. These observations suggest that the process of establishment of the methylation imprint at this locus is more dynamic than previously thought.

European Journal of …, Jan 1, 2003

In vitro folliculogenesis of cryopreserved ovarian tissue could be an effective method for insuri... more In vitro folliculogenesis of cryopreserved ovarian tissue could be an effective method for insuring fertility for patients who receive gonadotoxic treatment. Although several culture systems have been described for growing female gametes in vitro, the production of competent oocytes for further development remains a considerable challenge. The purpose of our study was to determine whether maternal primary imprinting progresses normally during mouse oocyte growth in vitro. We analysed the DNA methylation status of differentially methylated regions of the imprinted genes H19, Mest/Peg1 and Igf2R using fully grown germinal vesicle-stage oocytes (fg oocytes) produced by in vitro folliculogenesis from early preantral follicles. When compared to fg oocytes removal from control females, we observed after in vitro development, a loss of methylation at the Igf2R locus in six out of seven independent experiments and Mest/Peg1 locus (one out of seven), and a gain of methylation at the H19 locus (one out of seven). These results provide insight into the dysregulation of the process of primary imprinting during oocyte growth in vitro and highlight the need for effective new biomarkers to identify complete nuclear reprogramming competence after in vitro folliculogenesis.

Nucleic acids …, Jan 1, 2005

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precur... more The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 ± 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 ± 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Biotechniques, Jan 1, 2003

RefDoc, THE reference in scientific document supply / Refdoc, la référence en fourniture de docum... more RefDoc, THE reference in scientific document supply / Refdoc, la référence en fourniture de documents scientifiques ...

Biochimica et Biophysica …, Jan 1, 2006

The recent discovery of numerous catalytically active RNAs in various living species as well as t... more The recent discovery of numerous catalytically active RNAs in various living species as well as the in vitro selection of a large series of RNA aptamers able to bind specifically various molecules such as metabolites and co-factors, emphasize the adaptability of RNAs through the plasticity of their secondary structure . Furthermore, all these observations give support to the « RNA world » hypothesis as a step in the primitive development of life on Earth. On this background, we used high pressure to study the mechanism of action of a model hairpin ribozyme which exhibits self-cleavage and ligation. The activation volume (ΔV ≠ ) of the cleavage reaction (34 ±4 ml/mole) indicates that an important compaction of the RNA molecule occurs during the reaction and must be accompanied by a significant movement of water molecules . Indeed, such a release of 78 ± 4 water molecules per RNA molecule could be measured by complementary osmotic shock experiments. These results are consistent with the information provided by the structural studies which indicate that two loops of the RNA molecule should come into contact for the reaction to occur .The high pressure study of a modified form of the ribozyme whose activity is strictly dependent on the presence of adenine as a co-factor should bring some information about the structural significance of this important ∆V ≠ of activation.

Journal of Biological …, Jan 1, 2005

Page 1. CpG and non-CpG methylation of Peg1/Mest 1 DYNAMIC CPG AND NON-CPG METHYLATION OF THE PEG... more Page 1. CpG and non-CpG methylation of Peg1/Mest 1 DYNAMIC CPG AND NON-CPG METHYLATION OF THE PEG1/MEST GENE IN THE MOUSE OOCYTE AND PREIMPLANTATION EMBRYO Takuya Imamura1, 4, Antoine ...

BMC …, Jan 1, 2011

Coccidiosis is a parasitic disease with major economic impact, one of whose main causative agents... more Coccidiosis is a parasitic disease with major economic impact, one of whose main causative agents is Eimeria tenella. Chicken breeds display variable natural resistance to this disease. Unravelling the genetic bases of such variations could provide new clues for protection strategies. Transcriptomic experiments were conducted comparing resistant (Fayoumi) and susceptible (Leghorn) lines. Caecum and caecal tonsils were analysed. A global increase in differential gene expression following infection was observed for caecum comparisons, whereas a global decrease following infection was observed for caecal tonsils. Gene lists for infected tissues display 40 genes in common across breeds, 20 of which were specific to infected tissues. Among these specific genes, 9 belong to the 100 more differentially expressed genes of the infected caecum comparison. Gene expression networks were constructed in parallel, identifying highly connected genes. Comparing information from differential gene lists and gene network analysis allows one to highlight potential pivotal genes in the infection process, one of which was located in a putative significant QTL region for infection associated lesions.

Biology has long been dominated by a deterministic approach. The existence of a genetic code, eve... more Biology has long been dominated by a deterministic approach. The existence of a genetic code, even a "genetic programme", has often led to descriptions of biological processes resembling finely-regulated, precise events written in advance in our DNA. This approach has been very helpful in understanding the broad outlines of the processes at work within each cell. However, a large number of experimental arguments are challenging the deterministic approach in biology. One of the surprises of recent years has been the discovery that gene expression is fundamentally random: the problem now is to describe and understand that. Here I present the molecular and topological causes that at least partly explain it. I shall show that it is a wide-spread, controllable phenomenon that can be transmitted from one gene to another and even from one cell generation to the next. It remains to be determined whether this random gene expression is a "background noise" or a biological parameter. I shall argue for the second hypothesis by seeking to explain how this elementary disorder can give rise to order. In doing so, I hope to play a part in bringing probability theory to the heart of the study of life. Lastly, I shall discuss the possibility of moving beyond the apparent antagonism between determinism and probabilism in biology.

Св а ЙЌаа жги и в жйбИ и з о з ж и гв г д жи а з г ей а вз ин й а з ж в д ии жв г и а ж д жи а зИ... more Св а ЙЌаа жги и в жйбИ и з о з ж и гв г д жи а з г ей а вз ин й а з ж в д ии жв г и а ж д жи а зИ л гз ж йз гви вйгйзан к ж з жгб и д ж д жн иг и ви ж д в в гв и з о ж и г ил в д жи а з Ь гб зИ Ш нзК Ъ кК ОИ Н ДОМММЕ НЙ ℄К Ь м зи в г и з ж а з л и в ви жб и ж йз з глз и и и з ж и гв ...

En 2009, à l'occasion du 150e anniversaire de la publication du livre majeur de Charles Darw... more En 2009, à l'occasion du 150e anniversaire de la publication du livre majeur de Charles Darwin, L'Origine des espèces (1859), et du 200e anniversaire de la naissance de ce savant (1809), notre projet est de réaliser un livre sur les multiples ramifications actuelles de la ...

Pour la science, Jan 1, 2009

The necessary animal need: eating and become human - As part of an issue dedicated to vegetariani... more The necessary animal need: eating and become human - As part of an issue dedicated to vegetarianism, this paper analyzes the reasons of different kinds, for which man (generally) eats animal products. The nature of the links that were forged between humans and domestic animals is emphasized.

Animal Breeding requires a diverse spectrum of competences, from biology to social sciences and t... more Animal Breeding requires a diverse spectrum of competences, from biology to social sciences and technology, and so does its teaching and training. It results in a collective activity which benefits from moving towards three complementary directions: interdisciplinarity, internationalization, and interculturality. These dimensions open new ways to create and to adapt innovative curricula to the fast evolving needs of the professional sector, but they are also challenging. Recent joint initiatives between European institutions in the field with their successes and pitfalls could be a useful source of experience.

... Either peptides (obtained from Dr. Daria Mochly-Rosen, Stanford University, Standford, CA, US... more ... Either peptides (obtained from Dr. Daria Mochly-Rosen, Stanford University, Standford, CA, USA) were renewed after 2h or embryos were ... A. ReisA, KA PowellA, GJ McCallumA, JA RookeA, and TG McEvoyA AScottish Agricultural College, Sustainable Livestock Systems Group ...

Nucleic Acids Research, 2005

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precur... more The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 6 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 6 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Journal of Biological …, Jan 1, 2005

In somatic tissues, the CpG island of the imprinted Peg1/Mest gene is methylated on the maternal ... more In somatic tissues, the CpG island of the imprinted Peg1/Mest gene is methylated on the maternal allele. We have examined the methylation of CpG and non-CpG sites of this differentially methylated CpG island in freshly ovulated oocytes, in vitro aged oocytes, and preimplantation embryos. The CpG methylation pattern was heterogeneous in freshly ovulated oocytes, despite the fact that they all were arrested in metaphase II. After short in vitro culture, Peg1/Mest became hypermethylated, whereas prolonged in vitro culture resulted in demethylation in a fraction of oocytes. Non-CpG methylation also occurred in a stage-specific manner. On alleles that were fully methylated at CpG sites, this modification was found, and it became reduced in twocell stage embryos and blastocysts. These observations suggest that the process of establishment of the methylation imprint at this locus is more dynamic than previously thought.

European Journal of …, Jan 1, 2003

In vitro folliculogenesis of cryopreserved ovarian tissue could be an effective method for insuri... more In vitro folliculogenesis of cryopreserved ovarian tissue could be an effective method for insuring fertility for patients who receive gonadotoxic treatment. Although several culture systems have been described for growing female gametes in vitro, the production of competent oocytes for further development remains a considerable challenge. The purpose of our study was to determine whether maternal primary imprinting progresses normally during mouse oocyte growth in vitro. We analysed the DNA methylation status of differentially methylated regions of the imprinted genes H19, Mest/Peg1 and Igf2R using fully grown germinal vesicle-stage oocytes (fg oocytes) produced by in vitro folliculogenesis from early preantral follicles. When compared to fg oocytes removal from control females, we observed after in vitro development, a loss of methylation at the Igf2R locus in six out of seven independent experiments and Mest/Peg1 locus (one out of seven), and a gain of methylation at the H19 locus (one out of seven). These results provide insight into the dysregulation of the process of primary imprinting during oocyte growth in vitro and highlight the need for effective new biomarkers to identify complete nuclear reprogramming competence after in vitro folliculogenesis.

Nucleic acids …, Jan 1, 2005

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precur... more The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 ± 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 ± 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.

Biotechniques, Jan 1, 2003

RefDoc, THE reference in scientific document supply / Refdoc, la référence en fourniture de docum... more RefDoc, THE reference in scientific document supply / Refdoc, la référence en fourniture de documents scientifiques ...

Biochimica et Biophysica …, Jan 1, 2006

The recent discovery of numerous catalytically active RNAs in various living species as well as t... more The recent discovery of numerous catalytically active RNAs in various living species as well as the in vitro selection of a large series of RNA aptamers able to bind specifically various molecules such as metabolites and co-factors, emphasize the adaptability of RNAs through the plasticity of their secondary structure . Furthermore, all these observations give support to the « RNA world » hypothesis as a step in the primitive development of life on Earth. On this background, we used high pressure to study the mechanism of action of a model hairpin ribozyme which exhibits self-cleavage and ligation. The activation volume (ΔV ≠ ) of the cleavage reaction (34 ±4 ml/mole) indicates that an important compaction of the RNA molecule occurs during the reaction and must be accompanied by a significant movement of water molecules . Indeed, such a release of 78 ± 4 water molecules per RNA molecule could be measured by complementary osmotic shock experiments. These results are consistent with the information provided by the structural studies which indicate that two loops of the RNA molecule should come into contact for the reaction to occur .The high pressure study of a modified form of the ribozyme whose activity is strictly dependent on the presence of adenine as a co-factor should bring some information about the structural significance of this important ∆V ≠ of activation.

Journal of Biological …, Jan 1, 2005

Page 1. CpG and non-CpG methylation of Peg1/Mest 1 DYNAMIC CPG AND NON-CPG METHYLATION OF THE PEG... more Page 1. CpG and non-CpG methylation of Peg1/Mest 1 DYNAMIC CPG AND NON-CPG METHYLATION OF THE PEG1/MEST GENE IN THE MOUSE OOCYTE AND PREIMPLANTATION EMBRYO Takuya Imamura1, 4, Antoine ...

BMC …, Jan 1, 2011

Coccidiosis is a parasitic disease with major economic impact, one of whose main causative agents... more Coccidiosis is a parasitic disease with major economic impact, one of whose main causative agents is Eimeria tenella. Chicken breeds display variable natural resistance to this disease. Unravelling the genetic bases of such variations could provide new clues for protection strategies. Transcriptomic experiments were conducted comparing resistant (Fayoumi) and susceptible (Leghorn) lines. Caecum and caecal tonsils were analysed. A global increase in differential gene expression following infection was observed for caecum comparisons, whereas a global decrease following infection was observed for caecal tonsils. Gene lists for infected tissues display 40 genes in common across breeds, 20 of which were specific to infected tissues. Among these specific genes, 9 belong to the 100 more differentially expressed genes of the infected caecum comparison. Gene expression networks were constructed in parallel, identifying highly connected genes. Comparing information from differential gene lists and gene network analysis allows one to highlight potential pivotal genes in the infection process, one of which was located in a putative significant QTL region for infection associated lesions.

Biology has long been dominated by a deterministic approach. The existence of a genetic code, eve... more Biology has long been dominated by a deterministic approach. The existence of a genetic code, even a "genetic programme", has often led to descriptions of biological processes resembling finely-regulated, precise events written in advance in our DNA. This approach has been very helpful in understanding the broad outlines of the processes at work within each cell. However, a large number of experimental arguments are challenging the deterministic approach in biology. One of the surprises of recent years has been the discovery that gene expression is fundamentally random: the problem now is to describe and understand that. Here I present the molecular and topological causes that at least partly explain it. I shall show that it is a wide-spread, controllable phenomenon that can be transmitted from one gene to another and even from one cell generation to the next. It remains to be determined whether this random gene expression is a "background noise" or a biological parameter. I shall argue for the second hypothesis by seeking to explain how this elementary disorder can give rise to order. In doing so, I hope to play a part in bringing probability theory to the heart of the study of life. Lastly, I shall discuss the possibility of moving beyond the apparent antagonism between determinism and probabilism in biology.

Св а ЙЌаа жги и в жйбИ и з о з ж и гв г д жи а з г ей а вз ин й а з ж в д ии жв г и а ж д жи а зИ... more Св а ЙЌаа жги и в жйбИ и з о з ж и гв г д жи а з г ей а вз ин й а з ж в д ии жв г и а ж д жи а зИ л гз ж йз гви вйгйзан к ж з жгб и д ж д жн иг и ви ж д в в гв и з о ж и г ил в д жи а з Ь гб зИ Ш нзК Ъ кК ОИ Н ДОМММЕ НЙ ℄К Ь м зи в г и з ж а з л и в ви жб и ж йз з глз и и и з ж и гв ...

En 2009, à l'occasion du 150e anniversaire de la publication du livre majeur de Charles Darw... more En 2009, à l'occasion du 150e anniversaire de la publication du livre majeur de Charles Darwin, L'Origine des espèces (1859), et du 200e anniversaire de la naissance de ce savant (1809), notre projet est de réaliser un livre sur les multiples ramifications actuelles de la ...

Pour la science, Jan 1, 2009