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Cephalopod DNA/Molecular/Genetic Studies/Health

DWhatley

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Make like a squid and transform

Tel Aviv University researcher discovers that squid recode their genetic make-up on-the-fly to adjust to their surroundings
American Friends of Tel Aviv University 2015 news article

The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions.

Now a new study published in eLife by Dr. Eli Eisenberg of Tel Aviv University's Department of Physics and Sagol School of Neuroscience, in collaboration with Dr. Joshua J. Rosenthal of the University of Puerto Rico, showcases the first example of an animal editing its own genetic makeup on-the-fly to modify most of its proteins, enabling adjustments to its immediate surroundings. The research, conducted in part by TAU graduate student Shahar Alon, explored RNA editing in the Doryteuthis pealieii squid.

"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force." This demonstration, he said, may have implications for human diseases as well.

Using the genetic red pencil

RNA is a copy of the genetic code that is translated into protein. But the RNA "transcript" can be edited before being translated into protein, paving the way for different versions of proteins. Abnormal RNA editing in humans has been observed in patients with neurological diseases. The changing physiological appearance of squid and octopuses over their lifetime and across different habitats has suggested extensive recoding might occur in these species. However, this could never be confirmed, as their genomes (and those of most species) have never been sequenced.

For the purpose of the new study, the researchers extracted both DNA and RNA from squid. Harnessing DNA sequencing and computational analyses at TAU, the team compared the RNA and DNA sequences to observe differences. The sequences in which the RNA and DNA did not match up were identified as "edited."

"It was astonishing to find that 60 percent of the squid RNA transcripts were edited. The fruit fly, for the sake of comparison, is thought to edit only 3% of its makeup," said Dr. Eisenberg. "Why do squid edit to such an extent? One theory is that they have an extremely complex nervous system, exhibiting behavioral sophistication unusual for invertebrates. They may also utilize this mechanism to respond to changing temperatures and other environmental parameters."

"Misfolding" the proteins

The researchers hope to use this approach to identify recoding sites in other organisms whose genomes have not been sequenced.

"We would like to understand better how prevalent this phenomenon is in the animal world. How is it regulated? How is it exploited to confer adaptability?" said Dr. Eisenberg. "There may be implications for us as well. Human diseases are often the result of 'misfolded' proteins, which often become toxic. Therefore the question of treating the misfolded proteins, likely to be generated by such an extensive recoding as exhibited in the squid cells, is very important for future therapeutic approaches. Does the squid have some mechanism we can learn from?"

###

The researchers recently received an Israel-U.S. Binational Science Foundation grant to explore the subject of genetic editing in octopuses.

American Friends of Tel Aviv University supports Israel's most influential, most comprehensive and most sought-after center of higher learning, Tel Aviv University (TAU). US News & World Report's Best Global Universities Rankings rate TAU as #148 in the world, and the Times Higher Education World University Rankings rank TAU Israel's top university. It is one of a handful of elite international universities rated as the best producers of successful startups, and TAU alumni rank #9 in the world for the amount of American venture capital they attract.

A leader in the pan-disciplinary approach to education, TAU is internationally recognized for the scope and groundbreaking nature of its research and scholarship -- attracting world-class faculty and consistently producing cutting-edge work with profound implications for the future
 

DWhatley

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The octopus genome and the evolution of cephalopod neural and morphological novelties
Caroline B. Albertin,Oleg Simakov,Therese Mitros,Z. Yan Wang,Judit R. Pungor,Eric Edsinger-Gonzales,Sydney Brenner,Clifton W. Ragsdale, Daniel S. Rokhsar 2015 (open access)

Bimaculoides genome sequenced! (DWhatley)

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire1. They have the largest nervous systems among the invertebrates2 and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system1, 3. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole-genome duplications in the octopus lineage4, 5, 6. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described7, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems. ...
 

mucktopus

Haliphron Atlanticus
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Here's an old one but I'll add it to the list:

Huffard, C. L., Saarman, N., Hamilton, H., & Simison, W. B. (2010). The evolution of conspicuous facultative mimicry in octopuses: an example of secondary adaptation?. Biological Journal of the Linnean Society, 101(1), 68-77.

The ‘Mimic Octopus’Thaumoctopus mimicus Norman & Hochberg, 2005 exhibits a conspicuous primary defence mechanism (high-contrast colour pattern during ‘flatfish swimming’) that may involve facultative imperfect mimicry of conspicuous and/or inconspicuous models, both toxic and non-toxic (Soleidae and Bothidae). Here, we examine relationships between behavioural and morphological elements of conspicuous flatfish swimming in extant octopodids (Cephalopoda: Octopodidae), and reconstructed ancestral states, to examine potential influences on the evolution of this rare defence mechanism. We address the order of trait distribution to explore whether conspicuous flatfish swimming may be an exaptation that usurps a previously evolved form of locomotion for a new purpose. Contrary to our predictions, based on the relationships we examined, flatfish swimming appears to have evolved concurrently with extremely long arms, in a clade of sand-dwelling species. The conspicuous body colour pattern displayed by swimming T. mimicus may represent a secondary adaptation potentially allowing for mimicry of a toxic sole, improved disruptive coloration, and/or aposematic coloration.

If you have a free account with Research gate, you can download the full pdf- it has pics of the mimic's relatives:

http://www.researchgate.net/profile...adaptation/links/00463539b96653a1d5000000.pdf
 

DWhatley

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I repeat: Octopuses are NOT aliens
Rant by PZ Meyers in his Pharyngula blog
Jebus. The stupidity of the media is maddening. Here are two articles now out there: Don’t freak out, but scientists think octopuses ‘might be aliens’ after DNA study and Octopuses ‘are aliens’, scientists decide after DNA study. These reporters are embarrassing.

Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.

The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.

Bullshit.

As I said earlier, the study is open access. Read it. If you can’t understand the big words and the details, then you shouldn’t be writing news stories on science.

The study says exactly the opposite. It shows that octopuses use genes shared with vertebrates — the common metazoan toolbox. They have amplified genes used by other earthly animal life in unique ways, but protocadherins are a known earthly family of molecules, and zinc finger genes are a known earthly family of genes. This study reinforces the concept of common ancestry.

Do I need to add that it’s even plainly said in the abstract? Just read the abstract!

The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians

I just know this nonsense is going to be propagated by creationists everywhere, and I’m going to have to slam it down repeatedly. The only good thing is that it’s an easy one to rebut, and I’ll have many excuses to wrap my virtual tentacles around their rhetorical throats and squeeze.

It begins.

Proving that octopuses are creatures that arrived from another planet, possibly from another solar system, may not be revealed any time soon. However, their alien existence upon the Earth is expected to be the focus of significant research in the coming years. It is likely that they will be found to be born of the Earth, but the mysticism that they may be aliens makes the genome discovery quite intriguing.
 

DWhatley

Kraken
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Experimental infection of Octopus vulgaris (Cuvier, 1797) with Photobacterium damsela subsp. piscicida. Immunohistochemical tracking of antigen and tissue responses.
Vasileios Bakopoulos,Daniella White, Michail-Aggelos Valsamidis, Feli Vasilaki 2017 (Science Direct Subscription)

Abstract
Adult common octopus individuals were intramuscularly infected with Photobacterium damsela subsp. piscicida in order to investigate if this species is sensitive to this common and important fish pathogen. The fate of the bacterial antigens and the tissue responses of Octopus vulgaris were studied employing immunohistochemical techniques.

Strong reaction at the site of injection was evident from day 2 post-infection that continued until day 14. Great numbers of hemocytes that were attracted at the site of infection were involved in phagocytosis of bacteria. Very early in the infection, a transition of cells to fibroblasts and an effort to isolate the infection was observed. During the course of the study, very large necrotic cells were seen at the site of infection, whereas during the later stages hemocytes with phagocytosed bacteria were observed in well-defined pockets inside the muscle tissue. None of the internal organs tested for the presence of the bacterium were positive with the exception of the digestive gland where antigen staining was observed which was not associated with hemocyte infiltration. The high doses of bacterial cells used in this experimental infection and the lack of disease signs from Octopus vulgaris suggest that, under normal conditions, octopus is resistant to Photobacterium damsela subsp. piscicida.
 

DWhatley

Kraken
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Metal bioaccumulation and detoxification processes in cephalopods: A review
Virginie Penicaud, Thomas Lacoue-Labarthe, Paco Bustamante 2017 (subscription Science Direct Environmental Research)

Abstract
In recent decades, cephalopods have been shown to have very high capacities to accumulate most trace elements, regardless of whether they are essential (e.g., Cu and Zn) or non-essential (e.g., Ag and Cd). Among the different pathways of exposure to trace elements, the trophic pathway appears to be the major route of assimilation for numerous metals, including Cd, Co, Hg and Zn. Once assimilated, trace elements are distributed in the organism, accumulating in storage organs. The digestive gland is the main organ in which many trace elements accumulate, whichever of the exposure pathway. For example, this organ can present Cd concentrations reaching hundreds to thousands of ppm for some species, even though the digestive gland represents only a small proportion of the total mass of the animal. Such a specific organotropism towards the digestive gland of both essential and non-essential elements, regardless of the exposure pathway, poses the question of the detoxification processes evolved by cephalopods in order to sustain these high concentrations. This paper reviews the current knowledge on the bioaccumulation of trace elements in cephalopods, the differences in pharmaco-dynamics between organs and tissues, and the detoxification processes they use to counteract trace element toxicity. A peculiar focus has been done on the bioaccumulation within the digestive gland by investigating the subcellular locations of trace elements and their protein ligands.
 

DWhatley

Kraken
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Biosynthesis of Polyunsaturated Fatty Acids in Octopus vulgaris: Molecular Cloning and Functional Characterisation of a Stearoyl-CoA Desaturase and an Elongation of Very Long-Chain Fatty Acid 4 Protein
Óscar Monroig, Rosa de Llanos, Inmaculada Varó, Francisco Hontoria, Douglas R. Tocher, Sergi Puig,Juan C. Navarro 2017 (Full study Marine Drugs)

1. Introduction
Cephalopods have been regarded as promising candidates for the diversification of marine aquaculture due to their great commercial interest [1]. Despite significant progress made over the last decade, culture of cephalopod species with pelagic paralarval stages like the common octopus Octopus vulgaris is still challenging due to the massive mortalities occurring upon the settlement phase [2]. The specific factors causing such mortalities of paralarvae remain unclear, although it has become increasingly obvious that nutritional issues associated with inadequate supply of essential nutrients such as lipids are crucial to ensure normal growth and development of O. vulgaris paralarvae and ultimately improve their viability [3].
 

DWhatley

Kraken
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Nerve degeneration and regeneration in the cephalopod mollusc Octopus vulgaris: the case of the pallial nerve
Pamela Imperadore, Sameer B. Shah, Helen P. Makarenkova, Graziano Fiorito 2017 (full article Scientific Reports)
Abstract
Regeneration is a process that restores structure and function of tissues damaged by injury or disease. In mammals complete regeneration is often unsuccessful, while most of the low phyla animals can re-grow many parts of their body after amputation. Cephalopod molluscs, and in particular Octopus vulgaris, are well known for their capacity to regenerate their arms and other body parts, including central and peripheral nervous system. To better understand the mechanism of recovery following nerve injury in this species we investigated the process of axon regrowth and nerve regeneration after complete transection of the Octopus pallial nerves. This injury induces scar formation and activates the proliferation of hemocytes which invade the lesion site. Hemocytes appear involved in debris removal and seem to produce factors that foster axon re-growth. Connective tissue is involved in driving regenerating fibers in a single direction, outlining for them a well-defined pathway. Injured axons are able to quickly re-grow thus to restoring structure and function.
 

DWhatley

Kraken
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Nerve regeneration in the cephalopod mollusc Octopus vulgaris: label-free multiphoton microscopy as a tool for investigation
Pamela Imperadore, Ortrud Uckermann, Roberta Galli, Gerald Steiner, Matthias Kirsch, Graziano Fiorito 2018 (Full paper Journal of the Royal Society Interface)

Abstract
Octopus and cephalopods are able to regenerate injured tissues. Recent advancements in the study of regeneration in cephalopods appear promising encompassing different approaches helping to decipher cellular and molecular machinery involved in the process. However, lack of specific markers to investigate degenerative/regenerative phenomena and inflammatory events occurring after damage is limiting these studies. Label-free multiphoton microscopy is applied for the first time to the transected pallial nerve of Octopus vulgaris. Various optical contrast methods including coherent anti-Stokes Raman scattering (CARS), endogenous two-photon excited fluorescence (TPEF) and second harmonic generation (SHG) have been used. We detected cells and structures often not revealed with classical staining methods. CARS highlighted the involvement of haemocytes in building up scar tissue; CARS and TPEF facilitated the identification of degenerating fibres; SHG allowed visualization of fibrillary collagen, revealing the formation of a connective tissue bridge between the nerve stumps, likely involved in axon guidance. Using label-free multiphoton microscopy, we studied the regenerative events in octopus without using any other labelling techniques. These imaging methods provided extremely helpful morpho-chemical information to describe regeneration events. The techniques applied here are species-specific independent and should facilitate the comparison among various animal species.
 

DWhatley

Kraken
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Octopus vulgaris: An Alternative in Evolution
Anna Di Cosmo,, Valeria Maselli, Gianluca Polese 2018 (Subscription Marine Organisms as Model Systems in Biology and Medicine)

Abstract
Octopus vulgaris underwent a radical modification to cope with the benthic lifestyle. It diverged from other cephalopods in terms of body plan, anatomy, behavior, and intelligence. It independently evolved the largest and most complex nervous system and sophisticated behaviors among invertebrates in a separate evolutionary lineage. It is equipped with unusual traits that confer it an incredible evolutionary success: arms capable of a wide range of movements with no skeletal support; developed eyes with a complex visual behavior; vestibular system; primitive “hearing” system; chemoreceptors located in epidermis, suckers, and mouth; and a discrete olfactory organ. As if these were not enough, the occurrence of recently discovered adult neurogenesis and the high level of RNA editing give it a master key to face environmental challenges. Here we provide an overview of some of the winning evolutionary inventions that octopus puts in place such as the capacity to see color, smell by touch, edit own genes, and rejuvenate own brain.
 

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