The J. Craig Venter Institute is developing methods to synthesize whole genomes from scratch, using machines that can string together the chemical bases that make up the genetic code: A,T,C, and G. But genomes don't do anything without a cell, and cells aren't anything without a genetic code, leaving us with the original chicken/egg problem.
Once a genome is synthesized, it needs to be transplanted into a living bacterial cell whose genome has been removed. The ability to transplant the natural genome from one species of bacteria into the cell body of another was demonstrated in 2007, with the host cell literally turning into the donor cell as it replicated the donor genome and divided.
dimanche 18 avril 2010
The Epigenome - Molecular Hide and Seek
Author:
Beck, Stephan
Olek, Alexander
Subject:Biology, Life Sciences
Published by:Wiley-VCH
Published:11/03/2003
Price:$115.00
This is the first book that describes the role of the Epigenome (cytosine methylation) in the interplay between nature and nurture. It focuses and stimulates interest in what will be one of the most exciting areas of post-sequencing genome science: the relationship between genetics and the environment.
Written by the most reputable authors in the field, this book is essential reading for researchers interested in the science arising from the human genome sequence and its implications on health care, industry and society.
Beck, Stephan
Olek, Alexander
Subject:Biology, Life Sciences
Published by:Wiley-VCH
Published:11/03/2003
Price:$115.00
This is the first book that describes the role of the Epigenome (cytosine methylation) in the interplay between nature and nurture. It focuses and stimulates interest in what will be one of the most exciting areas of post-sequencing genome science: the relationship between genetics and the environment.
Written by the most reputable authors in the field, this book is essential reading for researchers interested in the science arising from the human genome sequence and its implications on health care, industry and society.
Who is Craig Venter ?
Venter developed a method of deciphering genomes known as whole-genome shotgun sequencing. The genome to be analyzed is broken into random, overlapping fragments of DNA that are a few thousand letters in length. Each fragment is sequenced, or read. Then the fragments are reassembled by a computer into their correct order. Although there were initially many skeptics, Venter’s conviction that shotgunning would be faster and just as accurate for much genome deciphering proved to be true, and the technique is now widely used.
In 1995 Venter and his team used the technique to obtain the first complete genome (DNA sequence) of an organism other than a virus, that of the bacterium Haemophilus influenzae. In 2000, in collaboration with researchers at the University of California at Berkeley, he published almost the entire genome of the fruit fly Drosophila melanogaster. In 2001 his team and a competing group published rough drafts of the human genome.
He was the former president and founder of Celera Genomics, which became famous for running a parallel version of the Human Genome Project of its own for commercial purposes, using shotgun sequencing technology in 1999. The aim of the Celera project was to create a database of genomic data that users could subscribe to for a fee. This proved very unpopular in the genetics community and spurred several groups to redouble their efforts to produce the full sequence and release it as open access. DNA from 5 individuals was used by Celera to generate the sequence of the human genome; one of the 5 individuals used in this project was Venter. The Human Genome Project, which was composed of many groups from around the world, rendered the attempt to privatise the process unfeasible. Venter was fired by Celera in early 2002 after it became clear that selling genome data would not become profitable and Venter resisted efforts by the company board to change the strategic direction of the company.
Despite their differing motivations, Venter and rival scientist Francis Collins of the National Institute of Health jointly made the announcement of the mapping of the human genome in 2000, along with US President Bill Clinton.
In 1995 Venter and his team used the technique to obtain the first complete genome (DNA sequence) of an organism other than a virus, that of the bacterium Haemophilus influenzae. In 2000, in collaboration with researchers at the University of California at Berkeley, he published almost the entire genome of the fruit fly Drosophila melanogaster. In 2001 his team and a competing group published rough drafts of the human genome.
He was the former president and founder of Celera Genomics, which became famous for running a parallel version of the Human Genome Project of its own for commercial purposes, using shotgun sequencing technology in 1999. The aim of the Celera project was to create a database of genomic data that users could subscribe to for a fee. This proved very unpopular in the genetics community and spurred several groups to redouble their efforts to produce the full sequence and release it as open access. DNA from 5 individuals was used by Celera to generate the sequence of the human genome; one of the 5 individuals used in this project was Venter. The Human Genome Project, which was composed of many groups from around the world, rendered the attempt to privatise the process unfeasible. Venter was fired by Celera in early 2002 after it became clear that selling genome data would not become profitable and Venter resisted efforts by the company board to change the strategic direction of the company.
Despite their differing motivations, Venter and rival scientist Francis Collins of the National Institute of Health jointly made the announcement of the mapping of the human genome in 2000, along with US President Bill Clinton.
lundi 5 avril 2010
Journalistes médicaux
USA
- Nicholas Wade, New York Times (Index) (Biologie, Génétique, Médecine)
- John Schwartz, New York Times (Justice et médecine)
- Andrew Pollack, New York Times (Business et nédecine)
- Nicholas Wade, New York Times (Index) (Biologie, Génétique, Médecine)
- John Schwartz, New York Times (Justice et médecine)
- Andrew Pollack, New York Times (Business et nédecine)
Non, les gènes ne sont pas brevetables: l'arrêt Myriad
Un juge américain, (’honorable Robert W. Sweet, invalide les brevets de Myriad sur les gènes BRCA1 et BRCA2, deux gènes de prédisposition majeurs pour le cancer du sein et de l’ovaire.
Cette décision fait suite à la plainte de patientes et de groupes de pression américain. Myriad par ses brevets empêchait la recherche de mutations par d’autres. Il était impossible de vérifier ses résultats sous peine de poursuite. Cette société était dans une position de monopole sur ce marché.
Elle le vend très cher ce droit indu: 3000$ le test BRCA1.
Références
- Robert W. Sweet, sur Wikipedia
- Le site Web de Myriad
- Myriad Genetics sur Wikipedia
- Le jugement de 150 pages
- Judge Invalidates Human Gene Patent, New York Times, March 29, 2010
Cette décision fait suite à la plainte de patientes et de groupes de pression américain. Myriad par ses brevets empêchait la recherche de mutations par d’autres. Il était impossible de vérifier ses résultats sous peine de poursuite. Cette société était dans une position de monopole sur ce marché.
Elle le vend très cher ce droit indu: 3000$ le test BRCA1.
Références
- Robert W. Sweet, sur Wikipedia
- Le site Web de Myriad
- Myriad Genetics sur Wikipedia
- Le jugement de 150 pages
- Judge Invalidates Human Gene Patent, New York Times, March 29, 2010
La variabilité phénotypique des chiens
Pourquoi les chiens ont-ils une telle variété de tailles, de couleurs de pelage, de morphologies ?
Ces importantes variations de taille sont contrôlées par un nombre limité de gènes.
Les petits chiens sont petits car ils portent le même haplotype de IGF-1.
L’aspect du pelage est dépendant de trois gènes: RSPO2 (poil dur ou souple) , FGF5 (longueur du poil) et KRT71 (bouclé ou non).
Ces caractéristiques physiques sont contrôlées par un nombre très restreint de gènes, responsables de la variabilité phénotypique des chiens.
Le chien de race n'est en réalité qu'un mutant sélectionné. Malgré leur diversité tous ces animaux peuvent se reproduire entre eux et appartiennent à l’espèce Canis familiaris.
Références
- Pourquoi le chien des Pyrénnées est hexadactyle? , Blog " Kystes et autres choses " , 31 mars 2010
- Abigail L. Shearin et Elaine A. Ostrander, “Canine Morphology: Hunting for Genes and Tracking Mutations,” PLoS Biol 8, no. 3 (Mars 2, 2010): e1000310.
Ces importantes variations de taille sont contrôlées par un nombre limité de gènes.
Les petits chiens sont petits car ils portent le même haplotype de IGF-1.
L’aspect du pelage est dépendant de trois gènes: RSPO2 (poil dur ou souple) , FGF5 (longueur du poil) et KRT71 (bouclé ou non).
Ces caractéristiques physiques sont contrôlées par un nombre très restreint de gènes, responsables de la variabilité phénotypique des chiens.
Le chien de race n'est en réalité qu'un mutant sélectionné. Malgré leur diversité tous ces animaux peuvent se reproduire entre eux et appartiennent à l’espèce Canis familiaris.
Références
- Pourquoi le chien des Pyrénnées est hexadactyle? , Blog " Kystes et autres choses " , 31 mars 2010
- Abigail L. Shearin et Elaine A. Ostrander, “Canine Morphology: Hunting for Genes and Tracking Mutations,” PLoS Biol 8, no. 3 (Mars 2, 2010): e1000310.
Le chien des Pyrénées a six doigts
Le chien des Pyrénées a six doigts au niveau des pattes arrières.
Il a une délétion de 51 pb dans le gène Alx-4 responsable d’une perte de fonction de ce gène. Pour maintenir cette anomalie caractéristique, il faut croiser ces animaux entre eux pour maintenir l’homozygotie sur ce locus, ce qui favorise l’émergence de maladies génétiques récessives.
Références
- Pourquoi le chien des Pyrénnées est hexadactyle? , Blog "Kystes et autres choses", 31 mars 2010
Il a une délétion de 51 pb dans le gène Alx-4 responsable d’une perte de fonction de ce gène. Pour maintenir cette anomalie caractéristique, il faut croiser ces animaux entre eux pour maintenir l’homozygotie sur ce locus, ce qui favorise l’émergence de maladies génétiques récessives.
Références
- Pourquoi le chien des Pyrénnées est hexadactyle? , Blog "Kystes et autres choses", 31 mars 2010
samedi 27 mars 2010
Un nouveau type d'hominidé découvert en Sibérie par l'équipe de Svante Pääbo
L’analyse d’un fragment d’os provenant d’une phalange humaine trouvée dans une grotte de Denisova en Sibérie révèlerait l’existence d’un troisième type d’hominidé.
Celui-ci aurait vécu il y a 40.000 ans en Sibérie, à la même période que l’homme de Néanderthal et que l’homme moderne Homo sapiens sapiens, nous apprend un article du magazine Nature publié le 25 mars 2010.
En été 2008, des chercheurs russes déterraient un fragment d'os provenant de la phalange d’un auriculaire humain dans une caverne située à Denisova, dans les monts Altaï en Sibérie.
L’équipe n’y avait pas prêté d’attention particulière et l’avait laissé de côté pour effectuer de futures recherches. Les chercheurs pensaient que ce fragment provenait d’un homme de Néanderthal et ne s’attendaient pas à cette découverte.
Seulement, lors des analyses, l’ADN provenant des mitochondries du fragment d’os ne correspondait pas à celui de l’homme de Néanderthal ni à celui des hommes modernes qui vivaient aussi à proximité à cette époque.
Les données génétiques publiées en ligne sur le site du magazine Nature révèlent que l’os pourrait appartenir à une espèce humaine jusqu’alors inconnue. Elle aurait migré de l’Afrique bien avant les ancêtres connus et se serait ensuite éteinte.
Références
- Un nouveau genre d’hominidé découvert ?, Maxisciences, 25 mars 2010
- The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. Nature. 2010 Mar 24. PMID: 20336068
With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined, the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans.
- A complete mtDNA genome of an early modern human from Kostenki, Russia. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. Curr Biol. 2010 Feb 9;20(3):231-6. PMID: 20045327
The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia.
Celui-ci aurait vécu il y a 40.000 ans en Sibérie, à la même période que l’homme de Néanderthal et que l’homme moderne Homo sapiens sapiens, nous apprend un article du magazine Nature publié le 25 mars 2010.
En été 2008, des chercheurs russes déterraient un fragment d'os provenant de la phalange d’un auriculaire humain dans une caverne située à Denisova, dans les monts Altaï en Sibérie.
L’équipe n’y avait pas prêté d’attention particulière et l’avait laissé de côté pour effectuer de futures recherches. Les chercheurs pensaient que ce fragment provenait d’un homme de Néanderthal et ne s’attendaient pas à cette découverte.
Seulement, lors des analyses, l’ADN provenant des mitochondries du fragment d’os ne correspondait pas à celui de l’homme de Néanderthal ni à celui des hommes modernes qui vivaient aussi à proximité à cette époque.
Les données génétiques publiées en ligne sur le site du magazine Nature révèlent que l’os pourrait appartenir à une espèce humaine jusqu’alors inconnue. Elle aurait migré de l’Afrique bien avant les ancêtres connus et se serait ensuite éteinte.
Références
- Un nouveau genre d’hominidé découvert ?, Maxisciences, 25 mars 2010
- The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. Nature. 2010 Mar 24. PMID: 20336068
With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined, the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans.
- A complete mtDNA genome of an early modern human from Kostenki, Russia. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. Curr Biol. 2010 Feb 9;20(3):231-6. PMID: 20045327
The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia.
Turritopsis nutricula, une méduse immortelle
La méduse Turritopsis nutricula pourrai être le seul animal immortel. En effet, cette méduse pourrait inverser le processus de sénescence et passer d'une phase de vie avancée à une phase de vie plus jeune.
Turritopsis nutricula pourrait inverser son vieillissement et revenir à l'état de polype, sa première phase de vie.
Ce processus s'expliquerait par un phénomène appelé "trans-différentiation", qui signifie qu'un type de cellule peut se transformer en un autre type de cellule.
Seuls quelques animaux dans le monde peuvent être le siège d'une trans-différentiation, mais celle-ci est toujours limitée. Ainsi, la salamandre peut refaire repousser sa queue lorsqu'elle la perd.
La méduse Turritopsis nutricula peut régénérer l'ensemble de son corps, et cela de façon infinie.
Plusieurs chercheurs et équipes scientifiques étudient attentivement cette espèce afin de déterminer de quelle façon il est possible de reproduire ce processus de vieillissement/rajeunissement.
Évoluant souvent en eaux profondes, ces méduses se développent dans les eaux du monde entier, et non plus seulement dans les eaux des Caraïbes, leur habitat d'origine.
Le Dr Maria Miglietta, du Smithsonian Tropical Marine Institute déclare : "Nous sommes en train d'assister à une invasion mondiale silencieuse."
Références
- Turritopsis nutricula sur Wikipedia anglais et français
- Une méduse serait le seul animal immortel, yahoo.com, 19 mars 2010
- Une méduse immortelle se multiplie aux quatre coins du globe, maxisciencess, 29 janvier 2009
- Cheating Death: The Immortal Life Cycle of Turritopsis, DevBio
- Induction of reverse development in two marine Hydrozoans. Schmich J, Kraus Y, De Vito D, Graziussi D, Boero F, Piraino S. Int J Dev Biol. 2007;51(1):45-56.
PMID: 17183464
Cnidarians are unique organisms in the animal kingdom because of their unequalled potential to undergo reverse development (RD). The life cycle of some species can temporarily shift ordinary, downstream development from zygote to adult into the opposite ontogenetic direction by back-transformation of some life stages. The potential for RD in cnidarians offers the possibility to investigate how integrative signalling networks operate to control directionality of ontogeny (reverse vs. normal development). Striking examples are found in some hydrozoans, where RD of medusa bud or liberated medusa stages leads to rejuvenation of the post-larval polyp stage. Artificial stress may determine ontogeny reversal. We describe here the results of experimental assays on artificial induction of RD by different chemical and physical inducers on two marine hydrozoans, Turritopsis dohrnii and Hydractinia carnea, showing a different potential for RD. A cascade of morphogenetic events occurs during RD by molecular mechanisms and cellular patterns recalling larval metamorphosis. For the first time, we show here that exposure to cesium chloride (CsCl), an inducer of larval metamorphosis, may also induce RD, highlighting similarities and differences between these two master ontogenetic processes in cnidarians.
- Morphological and ultrastructural analysis of Turritopsis nutricula during life cycle reversal. Carla' EC, Pagliara P, Piraino S, Boero F, Dini L. Tissue Cell. 2003 Jun;35(3):213-22. PMID: 12798130
The hydrozoa life cycle is characterized, in normal conditions, by the alternation of a post-larval benthic polyp and an adult pelagic medusa; however, some species of Hydrozoa react to environmental stress by reverting their life cycle: i.e. an adult medusa goes back to the juvenile stage of polyp. This very uncommon life cycle could be considered as some sort of inverted metamorphosis. A morphological study of different stages during the reverted life cycle of Turritopsis nutricula led to the characterization of four different stages: healthy medusa, unhealthy medusa, four-leaf clover and cyst. The ultrastructural study of the cellular modifications (during the life cycle reversion of T. nutricula) showed the presence of both degenerative and apoptotic processes. Degeneration was prevalent during the unhealthy medusa and four-leaf clover stages, while the apoptotic rate was higher during the healthy medusa and cyst stages. The significant presence of degenerative and apoptotic processes could be related to the occurrence of a sort of metamorphosis when an adult medusa transforms itself into a polyp.
Turritopsis nutricula pourrait inverser son vieillissement et revenir à l'état de polype, sa première phase de vie.
Ce processus s'expliquerait par un phénomène appelé "trans-différentiation", qui signifie qu'un type de cellule peut se transformer en un autre type de cellule.
Seuls quelques animaux dans le monde peuvent être le siège d'une trans-différentiation, mais celle-ci est toujours limitée. Ainsi, la salamandre peut refaire repousser sa queue lorsqu'elle la perd.
La méduse Turritopsis nutricula peut régénérer l'ensemble de son corps, et cela de façon infinie.
Plusieurs chercheurs et équipes scientifiques étudient attentivement cette espèce afin de déterminer de quelle façon il est possible de reproduire ce processus de vieillissement/rajeunissement.
Évoluant souvent en eaux profondes, ces méduses se développent dans les eaux du monde entier, et non plus seulement dans les eaux des Caraïbes, leur habitat d'origine.
Le Dr Maria Miglietta, du Smithsonian Tropical Marine Institute déclare : "Nous sommes en train d'assister à une invasion mondiale silencieuse."
Références
- Turritopsis nutricula sur Wikipedia anglais et français
- Une méduse serait le seul animal immortel, yahoo.com, 19 mars 2010
- Une méduse immortelle se multiplie aux quatre coins du globe, maxisciencess, 29 janvier 2009
- Cheating Death: The Immortal Life Cycle of Turritopsis, DevBio
- Induction of reverse development in two marine Hydrozoans. Schmich J, Kraus Y, De Vito D, Graziussi D, Boero F, Piraino S. Int J Dev Biol. 2007;51(1):45-56.
PMID: 17183464
Cnidarians are unique organisms in the animal kingdom because of their unequalled potential to undergo reverse development (RD). The life cycle of some species can temporarily shift ordinary, downstream development from zygote to adult into the opposite ontogenetic direction by back-transformation of some life stages. The potential for RD in cnidarians offers the possibility to investigate how integrative signalling networks operate to control directionality of ontogeny (reverse vs. normal development). Striking examples are found in some hydrozoans, where RD of medusa bud or liberated medusa stages leads to rejuvenation of the post-larval polyp stage. Artificial stress may determine ontogeny reversal. We describe here the results of experimental assays on artificial induction of RD by different chemical and physical inducers on two marine hydrozoans, Turritopsis dohrnii and Hydractinia carnea, showing a different potential for RD. A cascade of morphogenetic events occurs during RD by molecular mechanisms and cellular patterns recalling larval metamorphosis. For the first time, we show here that exposure to cesium chloride (CsCl), an inducer of larval metamorphosis, may also induce RD, highlighting similarities and differences between these two master ontogenetic processes in cnidarians.
- Morphological and ultrastructural analysis of Turritopsis nutricula during life cycle reversal. Carla' EC, Pagliara P, Piraino S, Boero F, Dini L. Tissue Cell. 2003 Jun;35(3):213-22. PMID: 12798130
The hydrozoa life cycle is characterized, in normal conditions, by the alternation of a post-larval benthic polyp and an adult pelagic medusa; however, some species of Hydrozoa react to environmental stress by reverting their life cycle: i.e. an adult medusa goes back to the juvenile stage of polyp. This very uncommon life cycle could be considered as some sort of inverted metamorphosis. A morphological study of different stages during the reverted life cycle of Turritopsis nutricula led to the characterization of four different stages: healthy medusa, unhealthy medusa, four-leaf clover and cyst. The ultrastructural study of the cellular modifications (during the life cycle reversion of T. nutricula) showed the presence of both degenerative and apoptotic processes. Degeneration was prevalent during the unhealthy medusa and four-leaf clover stages, while the apoptotic rate was higher during the healthy medusa and cyst stages. The significant presence of degenerative and apoptotic processes could be related to the occurrence of a sort of metamorphosis when an adult medusa transforms itself into a polyp.
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