CiteULike: Author Forterre

The virophage as a unique parasite of the giant mimivirus

Bernard La Scola — 2008-08-06T19:54:18-00:00

Nature (06 August 2008)

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

Celine Brochier — 2008-07-01T03:47:41-00:00

BMC Evolutionary Biology, Vol. 5, No. 1. (2005)

BACKGROUND:The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets.RESULTS:We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives.CONCLUSION:To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life.

Influence of Intervertebral Disc Fenestration at the Herniation Site in Association with Hemilaminectomy on Recurrence in Chondrodystrophic Dogs with Thoracolumbar Disc Disease: A Prospective MRI Study

Franck Forterre — 2008-06-11T17:11:05-00:00

Veterinary Surgery, Vol. 37, No. 4. (2008), pp. 399-405.

Objective- To describe the influence of fenestration at the disc herniation site on recurrence in thoracolumbar disc disease of chondrodystrophoid dogs. Study Design- Prospective clinical study. Animals- Chondrodystrophic dogs (n=19). Methods- Dogs were divided into 2 groups: group 1 (9 dogs) had thoracolumbar disc extrusion (Hansen type I) treated by hemilaminectomy and concomitant fenestration of the affected intervertebral disc and group 2 (10 dogs) had hemilaminectomy without fenestration. All dogs had 3 magnetic resonance imaging (MRI) examinations: preoperatively, immediately postoperatively to assess removal of herniated disc material, and again 6 weeks after surgery. Results- There were 13 male and 6 female dogs; mean age, 7.1 years. Thoracolumbar disc herniation was confirmed with MRI. Immediate post surgical MRI revealed that the herniated disc removal was complete in all but 1 dog and that fenestration did not lead to complete removal of nucleus pulposus within the intervertebral disc space. On the 3rd MRI examination, none of the group 1 dogs had further disc material herniation at the fenestrated site. Six of the 10 group 2 dogs had a recurrence of herniation leading to clinical signs in 3 dogs (pain in 2 dogs, paresis in 1 dog). Conclusion- In thoracolumbar disc herniation, fenestration of the affected intervertebral disc space prevents further extrusion of disc material. Clinical Relevance- Fenestration reduces the risk of early recurrence of disc herniation and associated postoperative complications.

Flows of Dense Granular Media

Yoel Forterre — 2008-03-06T05:28:36-00:00

Annual Review of Fluid Mechanics, Vol. 40, No. 1. (2008), pp. 1-24.

We review flows of dense cohesionless granular materials, with a special focus on the question of constitutive equations. We first discuss the existence of a dense flow regime characterized by enduring contacts. We then emphasize that dimensional analysis strongly constrains the relation between stresses and shear rates, and show that results from experiments and simulations in different configurations support a description in terms of a frictional visco-plastic constitutive law. We then discuss the successes and limitations of this empirical rheology in light of recent alternative theoretical approaches. Finally, we briefly present depth-averaged methods developed for free surface granular flows.

Flow of dense granular material: towards simple constitutive laws

O Pouliquen — 2006-08-01T00:34:07-00:00

J. Stat. Mech., Vol. 2006, No. 07. (July 2006), P07020.

A constitutive law for dense granular flows

Pierre Jop — 2006-06-07T20:26:31-00:00

Nature, Vol. 441, No. 7094. (June 2006), pp. 727-730.

Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation

Jonathan Berthon — 2008-04-09T11:01:59-00:00

Genome Biology, Vol. 9, No. 4. (2008)

BACKGROUND:Comparative analysis of genomes is valuable to explore evolution of genomes, deduce genes functions, or predict functional linking between proteins. Here, we have systematically analyzed the genomic environment of all known DNA replication genes in 27 archaeal genomes to infer new connections for DNA replication proteins from conserved genomic associations.RESULTS:Two distinct sets of DNA replication genes frequently co-localize in archaeal genomes: the first one includes the genes for PCNA, the small subunit of the DNA primase (PriS), and Gins15; the second one comprises the genes for MCM and Gins23. Other genomic associations of genes encoding proteins involved in informational processes that may be functionally relevant at the cellular level have also been noticed; in particular, the association between the genes for PCNA, TFS, and NudF. Surprisingly, a conserved cluster of genes coding for proteins involved in translation or ribosome biogenesis (S27E, L44E, aIF-2 alpha, Nop10) is almost systematically contiguous to the group of genes coding for PCNA, PriS, and Gins15. The functional relevance of this cluster that encodes proteins conserved in Archaea and Eukarya is strongly supported by statistical analysis. Interestingly, the gene encoding the S27E protein, also known as metallopanstimulin 1 (MPS-1) in human, is overexpressed in multiple cancer cell lines.CONCLUSIONS:Our genome context analysis suggests specific functional interactions for proteins involved in DNA replication between each others or with proteins involved in DNA repair or transcription. Furthermore, it suggests a previously unrecognized regulatory network coupling DNA replication and translation in Archaea that may also exist in Eukarya.

Looking for the most "primitive" organism(s) on Earth today: the state of the art

Patrick Forterre — 2008-03-06T09:58:53-00:00

Planetary and Space Science, Vol. 43, No. 1-2. ( 1995), pp. 167-177.

Molecular phylogenetic studies have revealed a tripartite division of the living world into two procaryotic groups, Bacteria and Archaea, and one eucaryotic group, Eucarya. Which group is the most "primitive"? Which groups are sister? The answer to these questions would help to delineate the characters of the last common ancestor to all living beings, as a first step to reconstruct the earliest periods of biological evolution on Earth. The current "Procaryotic dogma" claims that procaryotes are primitive. Since the ancestor of Archaea was most probably a hyperthermophile, and since bacteria too might have originated from hyperthermophiles, the procaryotic dogma has been recently connected to the hot origin of life hypothesis. However, the notion that present-day hyperthermophiles are primitive has been challenged by recent findings, in these unique microorganisms, of very elaborate adaptative devices for life at high temperature. Accordingly, I discuss here alternative hypotheses that challenge the procaryotic dogma, such as the idea of a universal ancestor with molecular features in between those of eucaryotes and procaryotes, or the origin of procaryotes via thermophilic adaptation. Clearly, major evolutionary questions about early cellular evolution on Earth remain to be settled before we can speculate with confidence about which kinds of life might have appeared on other planets.

Accuracy of the withdrawal reflex for localization of the site of cervical disk herniation in dogs: 35 cases (2004-2007).

F Forterre — 2008-03-01T19:41:05-00:00

J Am Vet Med Assoc, Vol. 232, No. 4. (15 February 2008), pp. 559-563.

Objective-To evaluate the accuracy of neurologic examination versus magnetic resonance imaging (MRI) in localization of cervical disk herniation and evaluate the usefulness of withdrawal reflex testing in dogs. Design-Retrospective case series. Animals-35 client-owned dogs with a single-level cervical disk herniation as determined via MRI. Procedures-1 of 2 board-certified neurologists performed a complete neurologic examination in each dog. Clinical signs of a cervical lesion included evidence of neck pain and tetraparesis. The withdrawal reflex was used for neuroanatomic localization (C1-C5 or C6-T2). Agreement between results of neurologic and MRI examinations was determined. Results-Agreement between neurologic and MRI diagnoses was 65.8%. In 11 dogs in which the lesion was clinically localized to the C6-T2 segment on the basis of a decreased withdrawal reflex in the forelimbs, MRI revealed an isolated C1-C5 disk lesion. In 1 dog, in which the lesion was suspected to be at the C1-C5 level, MRI revealed a C6-T2 lesion. Cranial cervical lesions were significantly associated with an incorrect neurologic diagnosis regarding site of the lesion. Conclusions and Clinical Relevance-Results suggested that the withdrawal reflex in dogs with cervical disk herniation is not reliable for determining the affected site and that a decreased withdrawal reflex does not always indicate a lesion from C6 to T2.

The origin of viruses and their possible roles in major evolutionary transitions

Patrick Forterre — 2006-06-20T22:59:33-00:00

Virus Research, Vol. 117, No. 1. (April 2006), pp. 5-16.

Viruses infecting cells from the three domains of life, Archaea, Bacteria and Eukarya, share homologous features, suggesting that viruses originated very early in the evolution of life. The three current hypotheses for virus origin, e.g. the virus first, the escape and the reduction hypotheses are revisited in this new framework. Theoretical considerations suggest that RNA viruses may have originated in the nucleoprotein world by escape or reduction from RNA-cells, whereas DNA viruses (at least some of them) might have evolved directly from RNA viruses. The antiquity of viruses can explain why most viral proteins have no cellular homologues or only distantly related ones. Viral proteins have replaced the ancestral bacterial RNA/DNA polymerases and primase during mitochondrial evolution. It has been suggested that replacement of cellular proteins by viral ones also occurred in early evolution of the DNA replication apparatus and/or that some DNA replication proteins originated directly in the virosphere and were later on transferred to cellular organisms. According to these new hypotheses, viruses played a critical role in major evolutionary transitions, such as the invention of DNA and DNA replication mechanisms, the formation of the three domains of life, or else, the origin of the eukaryotic nucleus.

Ventral Intraspinal Cysts Associated with the Intervertebral Disc: Magnetic Resonance Imaging Observations in Seven Dogs

Martin Konar — 2008-01-14T18:28:25-00:00

Veterinary Surgery, Vol. 37, No. 1. (January 2008), pp. 94-101.

Iatrogenic Sciatic Nerve Injury in Eighteen Dogs and Nine Cats (1997-2006)

Franck Forterre — 2007-07-05T08:59:47-00:00

Veterinary Surgery, Vol. 36, No. 5. (2007), pp. 464-471.

Objective- To report clinical features associated with iatrogenic peripheral nerve injury in dogs and cats admitted (1997-2006) to a referral teaching hospital. Study Design- Retrospective study. Animals- Dogs (n=18), 9 cats. Methods- Patients had acute signs of monoparesis attributable to sciatic nerve dysfunction that developed after treatment. Neurologic examination and electrodiagnostic testing were performed. Surgical therapy was used for nerve entrapment and delayed reconstructive surgery used in other cases. Results- Of 27 nerve injuries, 25 resulted from surgery (18 with treatment of pelvic injuries). Iliosacral luxation repair resulted in tibial (4 cats) and peroneal (3 dogs) nerve dysfunction. Other causes were intramedullary pinning of femoral fractures (3), other orthopedic surgery (cemented hip prosthesis [2] and tibial plateau-leveling osteotomy [1]), and perineal herniorrhaphy [1]. Nerve injury occurred after intramuscular injection (1 cat, 1 dog). Immediate surgical treatment was removal of intramedullary nails, extruded cement, or entrapping suture. Delayed nerve transplantation was performed in 2 dogs. Within 1 year, 13 patients recovered completely, clinical improvement occurred in 7, and there was no improvement in 7. Five of the 7 dogs that did not recover had acetabular or ilium fracture. Conclusion- Iatrogenic sciatic nerve injury occurred most commonly during treatment of pelvic orthopedic diseases and had a poor prognosis. Clinical variation in sciatic nerve dysfunction in dogs and cats can be explained by species anatomic differences. Clinical Relevance- Iatrogenic sciatic nerve injury leads to severely debilitating locomotor dysfunction with an uncertain prognosis for full-functional recovery.

Adenocarcinoma Metastasis of the Intertransversarius Cervicis Muscle Eliciting a Right Forelimb Lameness in a Dog

F Forterre — 2007-05-24T00:25:02-00:00

Journal of Veterinary Medicine Series A, Vol. 54, No. 5. (2007), pp. 250-253.

Summary This article describes identification of a metastatic adenocarcinoma to the intertransversarius cervicis muscle using magnetic resonance imaging (MRI) in a dog that presented with chronic lameness of the right forelimb. Magnetic resonance imaging revealed a right sided, ovoid signal abnormality within the intertransversarius cervicis muscle lateral to the sixth cervical (C6) vertebra. The lesion was uniform, hyperintense on T2- and isointense on T1-weighted images to muscle and exhibited uniform contrast enhancement on T1-weighted images. The MRI findings were consistent with a neoplasia. Surgical excision was performed. Histopathological diagnosis was metastatic fibrous adenocarcinoma. The dog recovered rapidly but 6 months post-operatively he was killed because of lung metastases. Necropsy was declined and the primary tumour could not be identified.

Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi.

S Lucas — 2007-04-20T18:09:29-00:00

Appl Environ Microbiol, Vol. 68, No. 11. (November 2002), pp. 5528-5536.

Our understanding of the genetics of species of the best-studied hyperthermophilic archaea, Pyrococcus spp., is presently limited by the lack of suitable genetic tools, such as a stable cloning vector and the ability to select individual transformants on plates. Here we describe the development of a reliable host-vector system for the hyperthermophilic archaeon Pyrococcus abyssi. Shuttle vectors were constructed based on the endogenous plasmid pGT5 from P. abyssi strain GE5 and the bacterial vector pLitmus38. As no antibiotic resistance marker is currently available for Pyrococcus spp., we generated a selectable auxotrophic marker. Uracil auxotrophs resistant to 5-fluoorotic acid were isolated from P. abyssi strain GE9 (devoid of pGT5). Genetic analysis of these mutants revealed mutations in the pyrE and/or pyrF genes, encoding key enzymes of the pyrimidine biosynthetic pathway. Two pyrE mutants exhibiting low reversion rates were retained for complementation experiments. For that purpose, the pyrE gene, encoding orotate phosphoribosyltransferase (OPRTase) of the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius, was introduced into the pGT5-based vector, giving rise to pYS2. With a polyethylene glycol-spheroplast method, we could reproducibly transform P. abyssi GE9 pyrE mutants to prototrophy, though with low frequency (10(2) to 10(3) transformants per micro g of pYS2 plasmid DNA). Transformants did grow as well as the wild type on minimal medium without uracil and showed comparable OPRTase activity. Vector pYS2 proved to be very stable and was maintained at high copy number under selective conditions in both Escherichia coli and P. abyssi.

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain.

P Forterre — 2006-04-27T12:38:24-00:00

Proc Natl Acad Sci U S A, Vol. 103, No. 10. (7 March 2006), pp. 3669-3674.

The division of the living world into three cellular domains, Archaea, Bacteria, and Eukarya, is now generally accepted. However, there is no consensus about the evolutionary relationships among these domains, because all of the proposed models have a number of more or less severe pitfalls. Another drawback of current models for the universal tree of life is the exclusion of viruses, otherwise a major component of the biosphere. Recently, it was suggested that the transition from RNA to DNA genomes occurred in the viral world, and that cellular DNA and its replication machineries originated via transfers from DNA viruses to RNA cells. Here, I explore the possibility that three such independent transfers were at the origin of Archaea, Bacteria, and Eukarya, respectively. The reduction of evolutionary rates following the transition from RNA to DNA genomes would have stabilized the three canonical versions of proteins involved in translation, whereas the existence of three different founder DNA viruses explains why each domain has its specific DNA replication apparatus. In that model, plasmids can be viewed as transitional forms between DNA viruses and cellular chromosomes, and the formation of different levels of cellular organization (prokaryote or eukaryote) could be traced back to the nature of the founder DNA viruses and RNA cells.

How the Venus flytrap snaps

Yoel Forterre — 2005-01-26T20:24:28-00:00

Nature, Vol. 433, No. 7024. (27 January 2005), pp. 421-425.

Viruses of the Archaea: a unifying view

David Prangishvili — 2006-10-16T18:41:53-00:00

Nat Rev Micro, Vol. 4, No. 11. (November 2006), pp. 837-848.

The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.

P Forterre — 2006-01-25T16:32:39-00:00

Biochimie, Vol. 87, No. 9-10. (t 2005), pp. 793-803.

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).