This also includes:

• A2Amapper: ATAC, Assembly to Assembly Comparision tool:
  • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

• Sim4db:
  • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

• LEAFF:
  • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

• Meryl:
  • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

Bdelloid rotifers are small animals well known for their ability to survive in harsh conditions. They can endure extreme dehydration by entering a state of dormancy and then revive when water becomes available again. Scientists have always been interested in the degree to which these animals resist radiation, since radiation can severely damage DNA by causing both of its strands to break. Interestingly, Adineta vaga's ability to survive radiation may be connected to the way in which it tolerates drying out, as dehydration can also damage DNA. The rotifer probably evolved strong DNA protection and repair mechanisms primarily as a response to its severe environment. Its resistance to radiation is merely a byproduct of adapting to the cycles of drying and rehydration.

In order to find out more about this ability, the researchers subjected A. vaga to proton radiation and then examined what effect it had on its chromosomes. The radiation caused serious damage, resulting in hundreds of breaks in the DNA. For the vast majority of organisms, such extensive chromosome damage would be disastrous; it's similar to going through an instruction manual in a shredder and ending up with a large number of separate fragments. The scientists believed that the rotifers would repair their chromosomes before producing offspring. However, what they discovered was unexpected: some of the broken pieces of chromosome did survive and were passed on to the next generations, where the repair process continued.

The discovery took on even greater interest when the scientists examined the offspring of the irradiated rotifers. Rather than observing the same DNA damage in all the generations, they found different sized sections missing and evidence that some of the genetic regions which had been lost were being slowly restored. The researchers proposed that the rotifers use a repair mechanism known as Break-Induced Homologous Extension Repair, or BIHER. In simple terms, a broken piece of DNA can locate a matching sequence on the other chromosome and use it as a guide to rebuild itself. If the damage is beyond what can be repaired in one generation, the repair process can continue in the next.

What makes the rotifer's method of repairing DNA so unusual is that, normally, we consider DNA repair to take place immediately after damage has occurred, with the cell rapidly repairing the damaged DNA. In A. vaga, however, the repair process can be a lot longer. Certain pieces of chromosome survive the initial damage, are inherited, and then serve as the basis for further repairs in later generations. It's as if one generation begins mending a broken book, the next one continues the work, and another eventually completes the job until all the missing parts have been restored.

One reason why this might work is that bdelloid rotifers have holocentric chromosomes. Rather than having a single point, as most chromosomes do, which controls movement during cell division, the ability to move is distributed along the entire length of their chromosomes. As a result, fragments of chromosomes are sometimes able to retain the parts that are necessary for them to move and divide, and this may account for how broken pieces of chromosome can last long enough to be passed on and then repaired.

This finding could have implications that go beyond those concerning rotifers. Scientists are interested in understanding how genomes cope with severe chromosome damage, for example in the case of chromothripsis, where chromosomes break and are then reassembled in new configurations. Investigating A. vaga could help us to learn how cells manage large genetic issues. Moreover, its high resistance to radiation might also prove useful in research into extreme environments, such as the radiation hazards encountered on long space missions. However, these are ideas for future investigation; at present the rotifer's DNA repair mechanism cannot be used to protect people from radiation.

What is perhaps the most interesting aspect of this discovery is that the rotifer's remarkable ability could have developed for a very simple reason. Since an animal living in moss constantly undergoes periods of drying out and then getting wet again, the same mechanisms that protect its DNA when it is dehydrated might also enable it to survive radiation which would damage most other animals. Therefore, the rotifer probably did not evolve solely in order to resist radiation; instead, it became extremely good at coping with the difficult conditions it encounters, and radiation resistance was just a byproduct.

The case of Adineta vaga demonstrates that survival does not always mean avoiding damage; on some occasions it involves being able to recover from damage which appears to be impossible to repair. This small animal can survive having its chromosomes broken into many pieces, retain some of those pieces, pass them on to its offspring, and continue to repair them over successive generations. Although we generally regard DNA as something fragile that must always remain intact, the rotifer indicates an alternative possibility: perhaps a genome does not have to be perfect in order to survive, since sometimes the pieces last long enough for life to reassemble them, bit by bit, generation after generation.

Ream more at https://www.science.org/doi/10.1126/sciadv.aee0891

All applications sent before 2nd of February 2015.

http://www.mind-project.eu/career

ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction.

apomorphy -- specialized (=derived) characters of an organism.

basal group -- The earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals.

biological classification -- The orderly arrangement of organisms in hierarchical system that ideally reflects evolutionary history.

cDNA -- Complementary DNA; DNA that is synthesized, by reverse transcriptase, from a Messenger RNA template ( Messenger RNA contains the coded information for protein synthesis).

character -- Heritable trait possessed by an organism.

character state -- characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.

clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.

cladogenesis -- The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.

cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.

convergence -- Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology. 

crown group -- All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

derived -- Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

diversity -- Term used to describe numbers of taxa, or variation in morphology. 

evolution -- Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.

evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.

expressed sequence tag (EST) -- A partial coding sequence isolated at random from a cDNA library, used for identification and mapping of coding sequences, for discovery of new genes and (by reference to sequence data banks) for discovery of identities with other genes.

extinction -- When all the members of a clade or taxon die, the group is said to be extinct.

genetic marker -- A DNA sequence that can be recognized and thus used to characterize the larger DNA sequence and the chromosome in which it occurs. 

homolog -- A feature that appears similar in two or more taxa with a common ancestor that also possessed that feature.

homology -- Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent.

hypothesis -- A concept or idea that can be falsified by various scientific methods.

ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.

lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.

monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade.

outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.

paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.

parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

phylogenetics -- Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern.

phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

plesiomorphy -- A primitive character state for the taxa under consideration.

polarity of characters -- The states of characters used in a cladistic analysis, either original or derived. Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.

polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group.

primitive -- Describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

radiation -- Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.

rank -- In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.

relatedness -- Two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade.

repetitive DNA -- Sequences of DNA that are found to be repeated, sometimes thousands of times over.  

reticulation -- Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.

selection -- Process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproduction -- those with the favored feature produce more offspring than those with the other feature, such that they become a greater percentage of the population in the next generation.

sister group -- The two clades resulting from the splitting of a single lineage.

stem group -- All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group.

sympleisiomorphy – A ancestral character shared by the taxa under consideration

synapomorphy -- A character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry (shared derived state).

synteny -- Portions of chromosomes in which gene order is conserved. 

systematics -- Field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy.

taxon -- Any named group of organisms, not necessarily a clade

taxonomy -- The science of naming and classifying organisms. 

JOB QUALIFICATION
- PhD/Engineer/MSc in bioinformatics, biostatistics, genetics/genomics
or any related field.
- Advanced knowledge of Bash/Perl scripting and job management on a Unix
HPC and in at least one basic language for data
manipulation/statistics (such as R/Python/Matlab) are required.
- Knowledge of at least one programming language (e.g. C), experience
processing -omics data or skills in advanced graphical representation
of data would be a plus.

DURATION
1 year, not extensible

SALARY
Gross salary is commensurate with experience and grade (MSc from
1,882=80/month and PhD/equivalent from 2,099=80/month).

APPLICATIONS/OPENING
Please send a motivation letter, a CV and the names of two referees to
pierre.faux@univ-amu.fr. The expected starting date is April 1st, 2021;
the job offer will however remain opened until the position is filled.

Pierre Faux

Research Area

Investigating the role in disease of both the microbe and its host (i.e immune system failure), using genomics and systems biology-based approaches
Using genomics and network analysis to characterize disease outbreaks and their environmental/social/genetic causes, and
Identifying new anti-infective and immune modulating therapies/biomarkers.

Link @ http://www.brinkman.mbb.sfu.ca/