A study led by Denis Duboule and published in the June 6th 2013 edition of Science shows that the genes that preside over limb formation successively come into contact with different regulatory domains. This sequential swing enables modular limb construction, with articulations as an added bonus.
The presence of donor specific HLA antibodies is a contra-indication for renal transplantation. Highly sensitized patients accumulate and often die on the transplant waiting lists as it is almost impossible to find donors towards which they don't have antibodies.
The acceptable mismatch program of Eurotransplant has shown to be an effective tool to enhance successful transplantation of highly sensitized patients. However, 35% of the patients have rare HLA phenotypes and no suitable donor can be found.
HLA phenotype frequencies vary significantly amongst European populations, as recently investigated within the frame of a European COST Action (BM0803) chaired by Prof. Alicia Sanchez-Mazas. Rare HLA phenotypes in one population are more frequent in other populations.
This is where the public health program EUROSTAM funded by a € 2.6 million grant from the European Community (FP7-HEALTH Collaborative project) enters the stage.
The major objective of the 11 partners of this project, which includes Professor Sanchez Mazas, is to analyze the feasibility and requirements for a Europe-wide acceptable mismatch program to enhance transplantation of patients with rare HLA phenotypes in their own population.
Long waiting patients will be matched with virtual donors based on known HLA frequencies of different European populations and with actual donors from the different transplant organizations. If successful, the logistics will be tested by transplanting some of these patients with donors from elsewhere in Europe.
Second objective is to simplify the definition of acceptable HLA mismatches. Although almost 4000 HLA class I antigens are known, only 150 polymorphic residues differentially spread over the different HLA antigens are responsible for the induction of antibodies. An innovative typing and matching strategy based on the definition of acceptable HLA epitopes will facilitate the identification of suitable donors.
Third objective is to define whether antibodies against non-HLA targets on the donor endothelium affect the results of transplants in highly sensitized patients.
The abyssal plains constitute the largest archives of marine biodiversity, that beyond microfossils could also be accessed with ancient DNA. This is the conclusion of the study conducted by Franck Lejzerowicz from Prof Jan Pawlowski group and published May 8, 2013 in the journal Biology Letters, reporting the presence of short DNA fragments buried 5000 meters below the waves of the South Altantic Ocean and preserved throughout the late Pleistocene and Holocene.
Although targeting gold standard microfossil groups such as Foraminifera, most of the DNA diversity that could be exhumed using next-generation sequencing corresponded to species that do not fossilize.
This unexpected source of information may be used to fill the gap in the fossil record and provide paleoenvironmental reconstruction efforts with accurate, complementary data on the historical changes of marine biodiversity.
What can we learn from the excavations of Ounjougou in Mali? A very different story than the one we know, or at least we assumed to know.
Man of action in archeology and theorist Eric Huysecom, from the Unit of Anthropology, worked for 25 years to understand the history of human settlement in Africa.
He has just discovered that long before Europe, populations of West Africa, invented the Neolithic and, with it, a great amount of innovations..
Prof Huysecom was invited on May 8th by France Culture to talk about his research in the broadcast «Le Salon noir».
You can listen to the Podcast (in french) below.
Global specialist in developmental genetics, the Prof. Denis Duboule has been elevated on April 31st, 2013, to the rank of Knight of the Legion of Honor.
MetaPIGA, a versatile and easy-to-use software developped by the laboratory of Prof. Milinkovitch, has just reached version 3.1.
The program implements robust stochastic heuristics (including the Metapopulation Genetic Algorithm, metaGA) for large phylogeny inference under Maximum Likelihood.
It allows analyses of binary (for example morphological) and molecular (nucleotides, amino-acids, and codons) data sets under multiple substitution models, Gamma rate heterogeneity, and data partitioning.
The software is for all types of users as it can be run through an extensive and ergonomic graphical interface, or by using batch files and console interface on your local machine or on distant servers.
MetaPIGA is platform independent, runs on 32- and 64-bits systems, and easily takes advantage of multiprocessor and/or multicore computers.
Version 3.1 of MetaPIGA includes new functionalities such as ancestral-state reconstruction (using empirical Bayesian inference) and Likelihood computation on CUDA-compatible Nvidia graphic cards (reducing run time by a factor of 10 to 20 for Protein/Codon data).
You can find more informations concerning MetaPIGA either on the LANE website or on the MetaPIGA website.
The vomeronasal organ (VNO) is an olfactory structure that detects pheromones and environmental cues. This organ consists of sensory neurons that express evolutionary unrelated groups of transmembrane chemoreceptors. Two of these groups (or repertoires) – the predominant V1R and V2R – are believed to detect airborne and water-soluble molecules, respectively.
It has been suggested that the shift in habitat of early tetrapods from water to land is reflected by an increase in the ratio of V1R/V2R genes. Unfortunately, snakes are missing from this analysis.
Snakes exhibit spectacular and exceptional adaptations that are readily recognizable. Deeply embedded in the popular psyche, snake tongue flicking (whose function is to deliver odorant molecules to the VNO) is for sure one of the characters most readily recognized by the public as "reptilian".
It is likely that the evolutionary success of snakes is largely due to the exceptional development of their VNO. Indeed, the spectacular chemo-sensorial abilities of snakes are due to the exceptional development of their VNO associated with a sophisticated tongue delivery system. Blind snakes can survive in the wild because they rely much more on their VNO than on their visual system!
The laboratory of Pr Michel Milinkovitch, in collaboration with Prof Ivan Rodriguez, both from our department, has used various molecular techniques to analyse the diversity, evolution, and expression pattern of the corn snake vomeronasal receptor repertoires. Their results have been recently published in the «Genome Biology & Evolution» journal.
They indicate that snakes and lizards retain an extremely limited number of V1R genes but exhibit a large number of V2R genes, including multiple lineages of reptile-specific and snake-specific expansions.
Hence, this analyses do not support the hypothesis that the shift to a vomeronasal receptor repertoire dominated by V1Rs in mammals reflects the evolutionary transition of early tetrapods from water to land.
This study sheds light on the evolutionary dynamics of the vomeronasal receptor families in vertebrates and reveals how mammals and squamate reptiles differentially adapted the same ancestral vomeronasal toolbox to succeed in a terrestrial environment.
Finally, the authors show that the peculiar bigenic pattern of V2R vomeronasal receptor gene transcription observed in mammals is conserved in squamate reptiles, hinting at an important but unknown functional role played by this expression strategy.
The island of Española in the Galápagos archipelago previously hosted a distinct and endemic species of giant tortoise (Chelonoidis hoodensis).
Originally numbering in the thousands, the number of individuals for this species was reduced to just 12 females and 3 males by the late 1960's because of initial decimation by whalers and destruction of habitats by human-introduced goats.
Since 1971, the 15 survivors are bred in captivity at the Galápagos National Park Service headquarters.
Eradication of goats on Española Island was completed in 1978, and nearly two thousands captive-born offspring descended from the 15 survivors have been repatriated in the last 40 years to Española Island. They occupy about one-third of the suitable habitats available to them on the island.
The laboratory of Pr. Milinkovitch has shown through molecular genetic analyses that the individuals repatriated to the island demonstrate substantial and increasing in situ reproduction once again.
Indeed, none of the tortoises sampled on Española in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007.
This recovery occurred despite the parental captive population having a very low genetic diversity due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity.
These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population.
This new study also indicates that the strongly heterogeneous distribution of tortoise sizes on the island is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40 years.
This study published in the 'Evolutionary Applications' journal reveals that some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts.
The Laboratory of Artificial & Natural Evolution (LANE; Pr. Michel C.
Milinkovitch) is looking for two new PhD students and a new Technical Assistant & Lab manager:
Update (7.1.2013)
The crocodile makes the cover of 'Science'!
The feathers, fur and scales of vertebrates develop according to genetically controlled processes. An exception to this rule, previously thought to be universal, has just been discovered by the team of Professor Michel Milinkovitch from our department, in collaboration with Matthias Zwicker at the University of Bern.
The work of these researchers, published on November 29th, 2012 in the journal Science, reveals that the scales on the face and jaws of crocodiles are not developmental units but emerge from a stochastic process entirely analogous to cracking of the skin during embryonic development.
It is the tension exerted on the thick and rigid skin by the rapid growth of the underlying skeleton that generates random polygonal domain of skin (erroneously called 'scales').
These results are clearing a new path, leading to the exploration of the subtle interactions between genetic and physical parameters during animal development.
The January 2013 issue of Molecular Biology and Evolution will publish a cover story by Prof. Pawlowski's laboratory on Elphidium.
Elphidium is a foraminiferal genus, which members feed on diatom algae and selectively retain their chloroplasts, while digesting the rest of the algal cell.
During that process, known as kleptoplastidy, the acquired plastids remain active inside the foraminifera for several months.
As most of the genes required to sustain the activity of the chloroplasts are encoded in the diatom nucleus, it is unknown how the host cell can maintain the photosynthetic activity without this information.
It has been proposed that Horizontal Gene Transfer (HGT) from the prey to the host nuclei could explain the maintenance of kleptoplastids.
To test this hypothesis Loïc Pillet of the Pawlowski lab obtained 17,125 EST sequences of Elphidium margaritaceum and screened this data set for diatom nuclear-encoded proteins having a function in photosynthetic activity or plastid maintenance.
These analyses show no evidence for the presence of such transcriptionally active genes and suggest that HGT hypothesis alone cannot explain the chloroplast's longevity in Elphidium.
The french journal «La Recherche» (No. 469, October 24, 2012) devoted last month's Portrait to Professor Alicia Sanchez-Mazas.