Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm
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{"title"=>"Modeling planarian regeneration: A primer for reverse-engineering the worm", "type"=>"generic", "authors"=>[{"first_name"=>"Daniel", "last_name"=>"Lobo", "scopus_author_id"=>"23985068300"}, {"first_name"=>"Wendy S.", "last_name"=>"Beane", "scopus_author_id"=>"13406162300"}, {"first_name"=>"Michael", "last_name"=>"Levin", "scopus_author_id"=>"8880226800"}], "year"=>2012, "source"=>"PLoS Computational Biology", "identifiers"=>{"pmid"=>"22570595", "doi"=>"10.1371/journal.pcbi.1002481", "sgr"=>"84861141149", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "scopus"=>"2-s2.0-84861141149", "issn"=>"1553734X", "pui"=>"364830885"}, "id"=>"ff0e63bf-6e2d-3116-8400-2491dfe6660c", "abstract"=>"A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental biology as well as for transformative applications in regenerative biomedicine and the engineering of highly fault-tolerant cybernetic systems. Molecular biologists are working to identify the pathways underlying the remarkable regenerative abilities of model species that perfectly regenerate limbs, brains, and other complex body parts. However, a profound disconnect remains between the deluge of high-resolution genetic and protein data on pathways required for regeneration, and the desired spatial, algorithmic models that show how self-monitoring and growth control arise from the synthesis of cellular activities. This barrier to progress in the understanding of morphogenetic controls may be breached by powerful techniques from the computational sciences-using non-traditional modeling approaches to reverse-engineer systems such as planaria: flatworms with a complex bodyplan and nervous system that are able to regenerate any body part after traumatic injury. Currently, the involvement of experts from outside of molecular genetics is hampered by the specialist literature of molecular developmental biology: impactful collaborations across such different fields require that review literature be available that presents the key functional capabilities of important biological model systems while abstracting away from the often irrelevant and confusing details of specific genes and proteins. To facilitate modeling efforts by computer scientists, physicists, engineers, and mathematicians, we present a different kind of review of planarian regeneration. Focusing on the main patterning properties of this system, we review what is known about the signal exchanges that occur during regenerative repair in planaria and the cellular mechanisms that are thought to underlie them. By establishing an engineering-like style for reviews of the molecular developmental biology of biomedically important model systems, significant fresh insights and quantitative computational models will be developed by new collaborations between biology and the information sciences.", "link"=>"http://www.mendeley.com/research/modeling-planarian-regeneration-primer-reverseengineering-worm", "reader_count"=>142, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>9, "Researcher"=>29, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>16, "Student > Bachelor"=>31, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>9, "Researcher"=>29, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>16, "Student > Bachelor"=>31, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Agricultural and Biological Sciences"=>79, "Arts and Humanities"=>1, "Business, Management and Accounting"=>2, "Chemistry"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1, "Engineering"=>6, "Biochemistry, Genetics and Molecular Biology"=>24, "Mathematics"=>1, "Medicine and Dentistry"=>8, "Neuroscience"=>2, "Physics and Astronomy"=>6, "Psychology"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>6}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>6}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>79}, "Computer Science"=>{"Computer Science"=>4}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>24}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>4, "Japan"=>1, "China"=>1, "United Kingdom"=>1, "Malaysia"=>1, "France"=>1, "Portugal"=>1, "Germany"=>2, "India"=>1, "Spain"=>3}, "group_count"=>10}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/646944"], "description"=>"<p>(<b>A</b>) A bar magnet restores the original polarity after being cut transversally. (<b>B</b>) Similarly, after bisecting a worm, polarity is restored correctly in each fragment. Note that even though cells on either side of the amputation plane were direct neighbors before the cut, the ones facing posterior make a completely different structure (a tail) than the ones facing anterior (a head). The drastically different fates of cells with essentially the same positional information suggest models based on non-local control of orientation <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002481#pcbi.1002481-Oviedo1\" target=\"_blank\">[8]</a>.</p>", "links"=>[], "tags"=>["ap", "polarity"], "article_id"=>317436, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Developmental Biology"], "users"=>["Daniel Lobo", "Wendy S. Beane", "Michael Levin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002481.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Planaria_restore_their_AP_polarity_similarly_to_bar_magnets_/317436", "title"=>"Planaria restore their AP polarity similarly to bar magnets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-26 02:03:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/646778"], "description"=>"<p>(<b>A</b>) Dorsal side of the planarian <i>Schmidtea mediterranea</i>. (<b>B</b>) Planarian diagram showing the brain lobes, nerve cords, and secondary nerves (green); the two eyes (black and white); the gastrovascular tract (gray); and the pharynx (light brown). (<b>C</b>) The three main axes of the planarian anatomy: anterior-posterior (AP), dorsal-ventral (DV), and medial-lateral (ML).</p>", "links"=>[], "tags"=>["anatomy"], "article_id"=>317274, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Developmental Biology"], "users"=>["Daniel Lobo", "Wendy S. Beane", "Michael Levin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002481.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Planarian_anatomy_and_body_axes_/317274", "title"=>"Planarian anatomy and body axes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-26 02:01:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/646860"], "description"=>"<p>(<b>A</b>) Cutting experiments amputate part of the planarian body (shadowed); normally, a complete regenerated worm results within 1–2 weeks. (<b>B</b>) Transplantation of diverse parts also regenerates into a complete worm. (<b>C</b>) Planarians degrowth when starved; they restore their original size upon feeding. (<b>D</b>) Octanol blocks gap junction communication between the worm cells; a trunk fragment treated with octanol regenerates into a double-headed worm. (<b>E</b>) A post-pharyngeal fragment treated with octanol and with the nerve cords partially amputated regenerates into a quadruple-headed worm. (<b>F</b>) An external electric field applied to a trunk fragment disturbs AP polarity during regeneration when the anode is located in the head wound; low-intensity currents cause double-headed worms, whereas high-intensity currents cause reversed-polarity worms. (<b>G</b>) The drugs <i>ivermectin</i> (<i>IVM</i>) and <i>SCH-28080</i> (<i>SCH</i>) disturb the ion pumps in the worm cells, altering their membrane voltage. <i>IVM</i> causes cell depolarization (more positive) and trunk fragments to regenerate into double-headed worms; <i>SCH</i> causes cell hyperpolarization (more negative) and trunk fragments to regenerate into worms with no heads.</p>", "links"=>[], "tags"=>["planarian", "regeneration", "experiments"], "article_id"=>317356, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Developmental Biology"], "users"=>["Daniel Lobo", "Wendy S. Beane", "Michael Levin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002481.g002", "stats"=>{"downloads"=>3, "page_views"=>364, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagrams_of_the_main_planarian_regeneration_experiments_found_in_the_literature_/317356", "title"=>"Diagrams of the main planarian regeneration experiments found in the literature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-26 02:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/647011"], "description"=>"<p>(<b>A</b>) <i>S. mediterranea</i> (left, rounded head) and <i>P. felina</i> (right, hammerhead) are planarian species with different head morphology. (<b>B</b>) Half the neoblasts of the rounded-head worm are killed by using irradiation and a lead shield. (<b>C</b>) Half the neoblasts of the hammerhead worm are transplanted to the rounded-head worm. (<b>D</b>) After the neoblasts have diffused, the head of the rounded-head worm is amputated. Without a model of how target morphology is determined, it is impossible to predict what shape will regenerate.</p>", "links"=>[], "tags"=>["illustrating"], "article_id"=>317502, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Developmental Biology"], "users"=>["Daniel Lobo", "Wendy S. Beane", "Michael Levin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002481.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypothetical_experiment_illustrating_the_concept_of_target_morphology_/317502", "title"=>"Hypothetical experiment illustrating the concept of target morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-26 02:05:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/332876"], "description"=>"<div><p>A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental biology as well as for transformative applications in regenerative biomedicine and the engineering of highly fault-tolerant cybernetic systems. Molecular biologists are working to identify the pathways underlying the remarkable regenerative abilities of model species that perfectly regenerate limbs, brains, and other complex body parts. However, a profound disconnect remains between the deluge of high-resolution genetic and protein data on pathways required for regeneration, and the desired spatial, algorithmic models that show how self-monitoring and growth control arise from the synthesis of cellular activities. This barrier to progress in the understanding of morphogenetic controls may be breached by powerful techniques from the computational sciences—using non-traditional modeling approaches to reverse-engineer systems such as planaria: flatworms with a complex bodyplan and nervous system that are able to regenerate any body part after traumatic injury. Currently, the involvement of experts from outside of molecular genetics is hampered by the specialist literature of molecular developmental biology: impactful collaborations across such different fields require that review literature be available that presents the key functional capabilities of important biological model systems while abstracting away from the often irrelevant and confusing details of specific genes and proteins. To facilitate modeling efforts by computer scientists, physicists, engineers, and mathematicians, we present a different kind of review of planarian regeneration. Focusing on the main patterning properties of this system, we review what is known about the signal exchanges that occur during regenerative repair in planaria and the cellular mechanisms that are thought to underlie them. By establishing an engineering-like style for reviews of the molecular developmental biology of biomedically important model systems, significant fresh insights and quantitative computational models will be developed by new collaborations between biology and the information sciences.</p> </div>", "links"=>[], "tags"=>["modeling", "planarian", "primer", "reverse-engineering", "worm"], "article_id"=>125735, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics", "Developmental Biology"], "users"=>["Daniel Lobo", "Wendy S. Beane", "Michael Levin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002481", "stats"=>{"downloads"=>21, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Modeling_Planarian_Regeneration_A_Primer_for_Reverse_Engineering_the_Worm/125735", "title"=>"Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-26 01:35:35"}

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Relative Metric

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