A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence DOI Creative Commons
Mario Ivanković, Jeremias N. Brand, Luca Pandolfini

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 23, 2023

Abstract The planarian Schmidtea mediterranea can regenerate its entire body from small tissue fragments and is studied as regeneration model species. assembly functional analysis of genomes has proven challenging due high A/T content (70% A/T), repetitive nature, limited transferability routine laboratory protocols to their divergent biochemistry. Only few often fragmented genome assemblies are currently available, open challenges include the provision well-annotated chromosome-scale reference species other planarians for a comparative evolution perspective. Here we report haplotype-phased, high-quality gene annotations sexual S2 strain S. provide putative regulatory region via optimized ATAC-seq ChIP-seq protocols. To additionally leverage sequence conservation element annotations, generated chromatin accessibility data three closest relatives : polychroa , nova lugubris . We find substantial divergence in protein-coding sequences regions, yet reveal remarkable ChIP-mark bearing regions identified promoters enhancers resulting high-confidence set evolutionary conserved provides valuable resource circuits within taxon. In addition, our four first perspective on evolution. Our analyses frequent retrotransposon-associated chromosomal inversions inter-chromosomal translocations that lead degradation synteny across genus. Interestingly, further independent near-complete losses ancestral metazoan two flatworm groups, indicating platyhelminth largely evolve without syntenic constraints. work resources research community sets foundation genomics planarians. contrast between fast structural elements, suggesting unique flatworms where positioning may not be essential.

Язык: Английский

Gene regulatory programmes of tissue regeneration DOI
Joseph Goldman, Kenneth D. Poss

Nature Reviews Genetics, Год журнала: 2020, Номер 21(9), С. 511 - 525

Опубликована: Июнь 5, 2020

Язык: Английский

Процитировано

134

Planarian stem cells specify fate yet retain potency during the cell cycle DOI Creative Commons
Amelie A. Raz, Omri Wurtzel,

Peter W. Reddien

и другие.

Cell stem cell, Год журнала: 2021, Номер 28(7), С. 1307 - 1322.e5

Опубликована: Апрель 21, 2021

Язык: Английский

Процитировано

75

Evolutionary dynamics of whole-body regeneration across planarian flatworms DOI Creative Commons
Miquel Vila‐Farré, Andrei Rozanski, Mario Ivanković

и другие.

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(12), С. 2108 - 2124

Опубликована: Окт. 19, 2023

Regenerative abilities vary dramatically across animals. Even amongst planarian flatworms, well-known for complete regeneration from tiny body fragments, some species have restricted while others are almost entirely incompetent. Here, we assemble a diverse live collection of 40 to probe the evolution head in group. Combining quantification species-specific head-regeneration with comprehensive transcriptome-based phylogeny reconstruction, show multiple independent transitions between robust whole-body and freshwater species. RNA-mediated genetic interference inhibition canonical Wnt signalling interference-sensitive bypassed all defects, suggesting that pathway is linked emergence defects. Our finding has roles reproductive system model Schmidtea mediterranea raises possibility trade-off egg-laying, asexual reproduction by fission/regeneration drives regenerative trait evolution. Although quantitative comparisons levels, yolk content strategy our remained inconclusive, they revealed divergent planarians. Altogether, study establishes planarians as taxon comparative research presents framework mechanistic abilities.

Язык: Английский

Процитировано

29

Positional information and tissue scaling during development and regeneration DOI Open Access
Daniel Čapek, Patrick Müller

Development, Год журнала: 2019, Номер 146(24)

Опубликована: Дек. 15, 2019

ABSTRACT In order to contribute the appropriate tissues during development, cells need know their position within embryo. This positional information is conveyed by gradients of signaling molecules, termed morphogens, that are produced in specific regions embryo and induce concentration-dependent responses target tissues. Positional remarkably robust, embryos often develop with correct proportions even if large parts removed. this Review, we discuss classical embryological experiments modern quantitative analyses have led mechanistic insights into how morphogen adapt, scale properly pattern differently sized domains. We analyze these experimental findings context mathematical models synthesize general principles apply multiple systems across species developmental stages.

Язык: Английский

Процитировано

59

Gamma-Secretase Inhibitor (DAPT), a potential therapeutic target drug, caused neurotoxicity in planarian regeneration by inhibiting Notch signaling pathway DOI
Zimei Dong,

Jinrui Huo,

Ang Liang

и другие.

The Science of The Total Environment, Год журнала: 2021, Номер 781, С. 146735 - 146735

Опубликована: Март 26, 2021

Язык: Английский

Процитировано

50

Whole-Body Regeneration in Sponges: Diversity, Fine Mechanisms, and Future Prospects DOI Open Access
Alexander Ereskovsky, Ilya Borisenko, Fyodor V. Bolshakov

и другие.

Genes, Год журнала: 2021, Номер 12(4), С. 506 - 506

Опубликована: Март 29, 2021

While virtually all animals show certain abilities for regeneration after an injury, these vary greatly among metazoans. Porifera (Sponges) is basal metazoans characterized by a wide variety of different regenerative processes, including whole-body (WBR). Considering phylogenetic position and unique body organization, sponges are highly promising models, as they can shed light on the origin early evolution in general WBR particular. The present review summarizes available data morphogenetic cellular mechanisms accompanying types sponges. Sponges high diversity WBR, which principally could be divided into (1) from fragment (2) aggregation dissociated cells. belonging to clades even species and/or differing anatomical structure undergo morphogeneses similar operations. A common characteristic feature instability main axis: change organism polarity described during WBR. across sponge classes, while cell dedifferentiations transdifferentiations involved processes Data considering molecular regulation extremely scarce. However, possibility achieve various ensured basis single makes accessible future comprehensive physiological, biochemical, studies processes.

Язык: Английский

Процитировано

49

Animal regeneration in the era of transcriptomics DOI
Loïc Bideau, Pierre Kerner, Jerome H. L. Hui

и другие.

Cellular and Molecular Life Sciences, Год журнала: 2021, Номер 78(8), С. 3941 - 3956

Опубликована: Янв. 30, 2021

Язык: Английский

Процитировано

46

A Comprehensive conceptual and computational dynamics framework for autonomous regeneration of form and function in biological organisms DOI Creative Commons
Sandhya Samarasinghe, Tran Nguyen Minh-Thai

PNAS Nexus, Год журнала: 2023, Номер 2(2)

Опубликована: Янв. 9, 2023

In biology, regeneration is a mysterious phenomenon that has inspired self-repairing systems, robots, and biobots. It collective computational process whereby cells communicate to achieve an anatomical set point restore original function in regenerated tissue or the whole organism. Despite decades of research, mechanisms involved this are still poorly understood. Likewise, current algorithms insufficient overcome knowledge barrier enable advances regenerative medicine, synthetic living machines/biobots. We propose comprehensive conceptual framework for engine with hypotheses stem cell-mediated enables system like planarian flatworm fully (form) bioelectric (function) homeostasis from any small- large-scale damage. The extends available novel intelligent self-repair machines multi-level feedback neural control systems driven by somatic cells. computationally implemented demonstrate robust recovery both form (anatomical homeostasis) silico worm that, simple way, resembles planarian. absence complete knowledge, contributes understanding generating cell mediated regeneration, which may help advance medicine biology. Further, as our bio-inspired bio-computing machine, it be useful building robots/biobots artificial systems.

Язык: Английский

Процитировано

21

A broad‐taxa approach as an important concept in ecotoxicological studies and pollution monitoring DOI
Amalia Rosner, Loriano Ballarin, Stéphanie Barnay‐Verdier

и другие.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Год журнала: 2023, Номер 99(1), С. 131 - 176

Опубликована: Сен. 12, 2023

ABSTRACT Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost‐effective and repeatable testing options. Additionally, their significance the food chain ability to represent diverse aquatic ecosystems make them valuable subjects for studies. To ensure consistency comparability across studies, international (eco)toxicology guidelines have been used establish standardised methods protocols data collection, analysis interpretation. However, current primarily focus on limited number of invertebrate species, mainly from Arthropoda, Mollusca Annelida. These are suitable basic toxicity screening, effectively assessing immediate severe effects toxic substances organisms. For more comprehensive ecologically relevant assessments, particularly those addressing long‐term ecosystem‐wide impacts, we recommended use broader diversity since present choice taxa exacerbates scope ecotoxicological This review provides overview focusing major how assess impact chemicals environments. The work supports broad‐taxa approach environmental as it better represents natural populations inhabiting various ecosystems. Advances omics other biochemical computational techniques feasible, enabling mechanistic studies non‐model By combining these approaches with vitro together approach, researchers can gain insights into less‐explored impacts pollution, such changes population diversity, development tolerance transgenerational inheritance pollution responses, organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome regeneration phenomena, disease susceptibility tissue pathologies. also emphasises need harmonised data‐reporting standards minimum annotation checklists that research results findable, accessible, interoperable reusable (FAIR), maximising reusability data. ultimate goal is encourage integrated holistic problem‐focused collaboration between scientific disciplines, standardisation organisations decision‐making bodies, transdisciplinary knowledge co‐production One‐Health approach.

Язык: Английский

Процитировано

19

Self‐Growing Organic Materials DOI

Xinhong Xiong,

Hong Wang, Lulu Xue

и другие.

Angewandte Chemie International Edition, Год журнала: 2023, Номер 62(47)

Опубликована: Июль 11, 2023

Abstract The growth of living systems is ubiquitous. Living organisms can continually update their sizes, shapes, and properties to meet various environmental challenges. Such a capability also demonstrated by emerging self‐growing materials that incorporate externally provided compounds grow as organisms. In this Minireview, we summarize these in terms six aspects. First, discuss essential characteristics, then describe the strategies for enabling crosslinked organic self‐grow from nutrient solutions containing polymerizable compounds. developed examples are grouped into five categories based on molecular mechanisms. We explain mechanism mass transport within polymer networks during growth, which critical controlling shape morphology grown products. Afterwards, simulation models built interesting phenomena observed discussed. development accompanied applications, including tuning bulk properties, creating textured surfaces, growth‐induced self‐healing, 4D printing, implants, actuation, structural coloration, others. These summed up. Finally, opportunities brought facing

Язык: Английский

Процитировано

17