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the axolotl model for cancer research: a mini-review.gastric cancer is the sixth most common cancer worldwide with increased associated morbidity and mortality. although a multimodality treatment approach is necessary, surgery is still considered as the standard of care. there is a longstanding intercontinental debate between eastern and western upper gi surgeons in regards to the proper type of lymphadenectomy that should accompany the resection of the primary tumor. while d2 gastrectomy was performed as the standard procedure in eastern countrie ...202031983087
multiplex crispr/cas screen in regenerating haploid limbs of chimeric axolotls.axolotls and other salamanders can regenerate entire limbs after amputation as adults, and much recent effort has sought to identify the molecular programs controlling this process. while targeted mutagenesis approaches like crispr/cas9 now permit gene-level investigation of these mechanisms, genetic screening in the axolotl requires an extensive commitment of time and space. previously, we quantified crispr/cas9-generated mutations in the limbs of mosaic mutant axolotls before and after regener ...202031989926
transcriptome analysis of axolotl oropharyngeal explants during taste bud differentiation stages.the mexican salamander, ambystoma mexicanum (axolotl), is an excellent vertebrate model system to understand development and regeneration. studies in axolotl embryos have provided important insights into taste bud development. taste bud specification and determination occur in the oropharyngeal endoderm of axolotl embryos during gastrulation and neurulation, respectively, whereas taste bud innervation and taste cell differentiation occur later in development. axolotl embryos are amenable to micr ...202032044293
proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages.the presented data article reports protein expression profiles during a time course of limb regeneration in the highly regenerative neotenic and regeneration-deficient metamorphic axolotl (ambystoma mexicanum). a protein database was first generated from transcriptome data, which was used concomitantly with nanolc-ms/ms to identify and assess significant changes of protein levels among 0, 1, 4, and 7 days post-amputation (dpa) in both animal stages, yielding a total of 714 significant differenti ...202032055664
generation of chimeric axolotls with mutant haploid limbs through embryonic grafting.a growing set of genetic techniques and resources enable researchers to probe the molecular origins of the ability of some species of salamanders, such as axolotls, to regenerate entire limbs as adults. here, we outline techniques used to generate chimeric axolotls with cas9-mutagenized haploid forelimbs that can be used for exploring gene function and the fidelity of limb regeneration. we combine several embryological and genetic techniques, including haploid generation via in vitro activation, ...202032065121
biology's beloved amphibian - the axolotl - is racing towards extinction. 201732080554
multi-glomerular projection of single olfactory receptor neurons is conserved among amphibians.individual receptor neurons in the peripheral olfactory organ extend long axons into the olfactory bulb forming synapses with projection neurons in spherical neuropil regions, called glomeruli. generally, odor map formation and odor processing in all vertebrates is based on the assumption that receptor neuron axons exclusively connect to a single glomerulus without any axonal branching. we comparatively tested this hypothesis in multiple fish and amphibian species (both sexes) by applying sparse ...202032080843
a tale of two axolotls.the mexican axolotl (ambystoma mexicanum) is an icon of culture, a revered aquarium pet, and a highly valued animal model in biomedical research. unfortunately, mexican axolotls are critically endangered in their natural xochimilco habitat in mexico city. if axolotls go extinct, current efforts to conserve the xochimilico ecosystem will be undermined, as will efforts to genetically manage the laboratory populations that are needed to sustain research efforts around the world. a concerted global ...201532123398
timemeter assesses temporal gene expression similarity and identifies differentially progressing genes.comparative time series transcriptome analysis is a powerful tool to study development, evolution, aging, disease progression and cancer prognosis. we develop timemeter, a statistical method and tool to assess temporal gene expression similarity, and identify differentially progressing genes where one pattern is more temporally advanced than the other. we apply timemeter to several datasets, and show that timemeter is capable of characterizing complicated temporal gene expression associations. i ...202032123905
eya2 promotes cell cycle progression by regulating dna damage response during vertebrate limb regeneration.how salamanders accomplish progenitor cell proliferation while faithfully maintaining genomic integrity and regenerative potential remains elusive. here we found an innate dna damage response mechanism that is evident during blastema proliferation (early- to late-bud) and studied its role during tissue regeneration by ablating the function of one of its components, eyes absent 2. in eya2 mutant axolotls, we found that dna damage signaling through the h2ax histone variant was deregulated, especia ...202032142407
von willebrand factor d and egf domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration.regenerative ability varies tremendously across species. a common feature of regeneration of appendages such as limbs, fins, antlers, and tails is the formation of a blastema-a transient structure that houses a pool of progenitor cells that can regenerate the missing tissue. we have identified the expression of von willebrand factor d and egf domains (vwde) as a common feature of blastemas capable of regenerating limbs and fins in a variety of highly regenerative species, including axolotl (amby ...202032163674
small circrnas with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes.ribozymes are catalytic rnas present in modern genomes but regarded as remnants of a prebiotic rna world. the paradigmatic hammerhead ribozyme (hhr) is a small self-cleaving motif widespread from bacterial to human genomes. here, we report that most of the classical type i hhrs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-ltr retrotransposons of the retrozyme class. these retroelements are expressed as abundant linear and circular rnas of ∼ ...202032198887
dissecting the molecular signature of spinal cord regeneration in the axolotl model.thousands of people are affected by central nervous system (cns) dysfunctions each year, with stroke and spinal cord injury (sci) being the most frequent causes. although there is some evidence of partial cns self-repair (via migration of neural stem cells to the injury zone and adult neurogenesis), due to restricted regeneration capacity in mammals, acute or chronic spinal cord injuries cannot be repaired completely. therefore, to expand the availability of treatment options for sci, research o ...202032211250
purification of soluble membrane-bound ambystoma mexicanum epidermal lipoxygenase from e. coli and its growth effect on human fetal foreskin fibroblast.lipoxygenases are non-heme iron-containing lipid dioxygenases enzymes that catalyze the hydroperoxidation of lipids. the mexican axolotl (ambystoma mexicanum) is a prominent source of the enzyme with a regeneration capacity in limbs. it has been shown that transfected human osteosarcoma and keratinocyte cells with epidermal lipoxygenase (loxe) have an increased rate of cell migration. in the present study, loxe, a peripheral membrane protein, was produced in escherichia coli. the enzyme was puri ...202032285244
ra signaling in limb development and regeneration in different species.this chapter brings together data on the role of retinoic acid (ra) in the embryonic development of fins in zebrafish , limbs in amphibians , chicks , and mice, and regeneration of the amphibian limb . the intention is to determine whether there is a common set of principles by which we can understand the mode of action of ra in both embryos and adults. what emerges from this synthesis is that there are indeed commonalities in the involvement of ra in processes that ventralize, posteriorize, and ...202032297297
what the salamander eye has been telling the vision scientist's brain.salamanders have been habitual residents of research laboratories for more than a century, and their history in science is tightly interwoven with vision research. nevertheless, many vision scientists - even those working with salamanders - may be unaware of how much our knowledge about vision, and particularly the retina, has been shaped by studying salamanders. in this review, we take a tour through the salamander history in vision science, highlighting the main contributions of salamanders to ...202032359891
a histological study of normal and pathological limb regeneration in the mexican axolotl ambystoma mexicanum.salamanders show unparalleled capacities of tissue regeneration amongst tetrapods (four-legged vertebrates), being able to repair and renew lost or damage body parts, such as tails, jaws, and limbs in a seemingly perfect fashion. despite countless studies on axolotl (ambystoma mexicanum) regeneration, only a few studies have thus far compared gross morphological and histological features of the original and regenerated limb skeleton. therein, most studies have focused on nerves or muscles, while ...202032394624
elastic recoil action amplifies jaw closing speed in an aquatic feeding salamander.tendon springs often influence locomotion by amplifying the speed and power of limb joint rotation. however, less is known about elastic recoil action in feeding systems, particularly for small aquatic animals. here, we ask if elastic recoil amplifies the speed of gape closing during aquatic food processing in the axolotl (ambystoma mexicanum). we measure activation of the adductor mandibulae externus via electromyography and strain of the jaw adductor muscle-tendon unit (mtu), and gape kinemati ...202032429804
preclinical molecular signatures of spinal cord functional restoration: optimizing the metamorphic axolotl (ambystoma mexicanum) model in regenerative medicine.regenerative medicine offers hope for patients with diseases of the central and peripheral nervous system. urodele amphibians such as axolotl display an exceptional regenerative capacity and are considered as essential preclinical model organisms in neurology and regenerative medicine research. earlier studies have suggested that the limb regeneration ability of this salamander notably decreases with induction of metamorphosis by thyroid hormones. metamorphic axolotl requires further validation ...202032496969
neural regulation in tooth regeneration of ambystoma mexicanum.the presence of nerves is an important factor in successful organ regeneration in amphibians. the mexican salamander, ambystoma mexicanum, is able to regenerate limbs, tail, and gills when nerves are present. however, the nerve-dependency of tooth regeneration has not been evaluated. here, we reevaluated tooth regeneration processes in axolotls using a three-dimensional reconstitution method called combi and found that tooth regeneration is nerve-dependent although the dentary bone is independen ...202032518359
a versatile depigmentation, clearing, and labeling method for exploring nervous system diversity.tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. we have developed a fast depigmentation-plus-clearing method (deep-clear) that is easily incorporated in existing workflows and combines whole system labeling with a spe ...202032523996
introducing www.axolotl-omics.org - an integrated -omics data portal for the axolotl research community.genomic resources are indispensable for biological investigations in model organisms. in recent years, a number of genomic resources including a full genome assembly, extensive transcriptomic data, as well as genome editing has been developed for the axolotl, a classical model organism for developmental, neurobiological and regeneration studies, making the axolotl a highly versatile system. here we describe the axolotl-omics website that allows rapid ortholog searches, and access to genome and t ...202032540400
identification of immune and non-immune cells in regenerating axolotl limbs by single-cell sequencing.immune cells are known to be critical for successful limb regeneration in the axolotl (ambystoma mexicanum), but many details regarding their identity, behavior, and function are yet to be resolved. we isolated peripheral leukocytes from the blood of adult axolotls and then created two samples for single-cell sequencing: 1) peripheral leukocytes (n = 7889) and 2) peripheral leukocytes with presumptive macrophages from the intraperitoneal cavity (n = 4998). using k-means clustering, we identified ...202032562784
exploring the role of micrornas in axolotl regeneration.the axolotl, ambystoma mexicanum, is used extensively for research in developmental biology, particularly for its ability to regenerate and restore lost organs, including in the nervous system, to full functionality. regeneration in mammals typically depends on the healing process and scar formation with limited replacement of lost tissue. other organisms, such as spiny mice (acomys cahirinus), salamanders, and zebrafish, are able to regenerate some damaged body components. blastema is a tissue ...202032638401
inhibition of wound epidermis formation via full skin flap surgery during axolotl limb regeneration.classical experiments in salamander regenerative biology over the last century have long established that the wound epidermis is a crucial signaling structure that forms rapidly post-amputation and is required for limb regeneration. however, methods to study its precise function at the molecular level over the last decades have been limited due to a paucity of precise functional techniques and genomic information available in salamander model systems. excitingly, the recent plethora of sequencin ...202032658179
bmp signaling is essential for sustaining proximo-distal progression in regenerating axolotl limbs.amputation of a salamander limb triggers a regeneration process that is perfect. a limited number of genes have been studied in this context and even fewer have been analyzed functionally. in this work, we use the bmp signaling inhibitor ldn193189 on ambystoma mexicanum to explore the role of bmps in regeneration. we find that bmp signaling is required for proper expression of various patterning genes and that its inhibition causes major defects in the regenerated limbs. fgf8 is downregulated wh ...202032665245
dynamic cell transition and immune response landscapes of axolotl limb regeneration revealed by single-cell analysis. 202032748350
transcriptome dataset for rna-seq analysis of axolotl embryonic oropharyngeal endoderm explants.animal nutrition and toxin deterrence rely on the ability to taste, which occurs through columnar taste cells clustered within taste buds. taste buds in mammals are located within specialized tissues, called papillae. however, taste buds in fish and amphibians, such as axolotls (ambystoma mexicanum), are not housed in papillae, rather they are embedded within the pharyngeal epithelium. this simplified tissue level organization, along with the ability of cultured oropharyngeal explants from early ...202032802925
immunochemical detection of modified cytosine species in lampbrush chromatin.the lampbrush chromosomes found in the giant nucleus or germinal vesicle (gv) of amphibian oocytes provide unique opportunities for discrete closed and open chromatin structural domains to be directly observable by simple light microscopy. moreover, the method described here for preparing spreads of lampbrush chromatin for immunostaining enables a straightforward approach to establishing the distributions of modified nucleotides within and between structurally and functionally distinctive chroma ...202132822030
an aryl hydrocarbon receptor from the caecilian gymnopis multiplicata suggests low dioxin affinity in the ancestor of all three amphibian orders.the aryl hydrocarbon receptor (ahr) plays pleiotropic roles in the development and physiology of vertebrates in conjunction with xenobiotic and endogenous ligands. it is best known for mediating the toxic effects of dioxin-like pollutants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (tcdd). while most vertebrates possess at least one ahr that binds tcdd tightly, amphibian ahrs bind tcdd with very low affinity. previous analyses of ahrs from xenopus laevis (a frog; order anura) and ambystoma mexic ...202032858041
the rax homeobox gene is mutated in the eyeless axolotl, ambystoma mexicanum.vertebrate eye formation requires coordinated inductive interactions between different embryonic tissue layers, first described in amphibians. a network of transcription factors and signaling molecules controls these steps, with mutations causing severe ocular, neuronal, and craniofacial defects. in eyeless mutant axolotls, eye morphogenesis arrests at the optic vesicle stage, before lens induction, and development of ventral forebrain structures is disrupted.202032864847
axolotl ambystoma mexicanum extract induces cell cycle arrest and differentiation in human acute myeloid leukemia hl-60 cells.acute myeloid leukemia is the most common form of acute leukemia in adults, constituting about 80% of cases. although remarkable progress has been made in the therapeutic scenario for patients with acute myeloid leukemia, research and development of new and effective anticancer agents to improve patient outcome and minimize toxicity is needed. in this study, the antitumor activity of axolotl (axo) ambystoma mexicanum crude extract was assessed in vitro on the human acute myeloid leukemia hl-60 c ...202032873193
intrinsic heart regeneration in adult vertebrates may be strictly limited to low-metabolic ectotherms.the heart has a high-metabolic rate, and its "around-the-clock" vital role to sustain life sets it apart in a regenerative setting from other organs and appendages. the landscape of vertebrate species known to perform intrinsic heart regeneration is strongly biased toward ectotherms-for example, fish, salamanders, and embryonic/neonatal ectothermic mammals. it is hypothesized that intrinsic heart regeneration is exclusively limited to the low-metabolic hearts of ectotherms. the biomedical field ...202032914411
immunity in salamander regeneration: where are we standing and where are we headed?salamanders exhibit the most extensive regenerative repertoire among vertebrates, being able to accomplish scar-free healing and faithful regeneration of significant parts of the eye, heart, brain, spinal cord, jaws and gills, as well as entire appendages throughout life. the cellular and molecular mechanisms underlying salamander regeneration are currently under extensive examination, with the hope of identifying the key drivers in each context, understanding interspecies differences in regener ...202032924213
author correction: label-free imaging of tissue architecture during axolotl peripheral nerve regeneration in comparison to functional recovery.an amendment to this paper has been published and can be accessed via a link at the top of the paper.202032929166
limb regeneration in salamanders: the plethodontid tale.salamanders are the only vertebrates that can regenerate limbs as adults. this makes them ideal models to investigate cellular and molecular mechanisms of tissue regeneration. ambystoma mexicanum and nothopthalmus viridescens have long served as primary salamander models of limb regeneration, and the recent sequencing of the axolotl genome now provides a blueprint to mine regeneration insights from other salamander species. in particular, there is a need to study south american plethodontid sala ...202032930368
divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association.influenza viruses (family orthomyxoviridae) infect a variety of vertebrates, including birds, humans, and other mammals. recent metatranscriptomic studies have uncovered divergent influenza viruses in amphibians, fish and jawless vertebrates, suggesting that these viruses may be widely distributed. we sought to identify additional vertebrate influenza-like viruses through the analysis of publicly available rna sequencing data. accordingly, by data mining, we identified the complete coding segmen ...202032962015
large-scale variation in snp density within the laboratory axolotl (ambystoma mexicanum).recent efforts to assemble and analyze the ambystoma mexicanum genome have dramatically improved the potential to develop molecular tools and pursue genome-wide analyses of genetic variation.202033001517
a comparative perspective on lung and gill regeneration.the ability to continuously grow and regenerate the gills throughout life is a remarkable property of fish and amphibians. considering that gill regeneration was first described over one century ago, it is surprising that the underlying mechanisms of cell and tissue replacement in the gills remain poorly understood. by contrast, the mammalian lung is a largely quiescent organ in adults but is capable of facultative regeneration following injury. in the course of the past decade, it has been reco ...202033037099
mandibular musculature constrains brain-endocast disparity between sarcopterygians.the transition from water to land by the earliest tetrapods in the devonian period is seen as one of the greatest steps in evolution. however, little is understood concerning changes in brain morphology over this transition. here, we determine the brain-braincase relationship in fishes and basal lissamphibians as a proxy to elucidate the changes that occurred over the fish-tetrapod transition. we investigate six basal extant sarcopterygians spanning coelacanths to salamanders (latimeria chalumna ...202033047053
3d visualization of macromolecule synthesis.measuring nascent macromolecular synthesis in vivo is key to understanding how cells and tissues progress through development and respond to external cues. here, we perform in vivo injection of alkyne- or azide-modified analogs of thymidine, uridine, methionine, and glucosamine to label nascent synthesis of dna, rna, protein, and glycosylation. three-dimensional volumetric imaging of nascent macromolecule synthesis was performed in axolotl salamander tissue using whole mount click chemistry-base ...202033051003
axolotl liver regeneration is accomplished via compensatory congestion mechanisms regulated by erk signaling after partial hepatectomy.axolotls have remarkable organ-level regeneration capability. they can regenerate their limbs, tail, brain, gills, and heart. the liver had been considered to be a regenerative organ in these highly regeneration-competent animals. therefore, no research had been performed on liver regeneration in urodele amphibians. in the present study, we focused on axolotl liver regeneration and found a unique regeneration mechanism compared with other vertebrates.202033064366
salamander-eci: an optical clearing protocol for the three-dimensional exploration of regeneration.salamander limb regeneration is a complex biological process that entails the orchestration of multiple cellular and molecular mechanisms in a three-dimensional space. hence, a comprehensive understanding of this process requires whole-structure level explorations. recent advances in imaging and optical clearing methods have transformed the study of regenerative phenomena, allowing the three-dimensional visualization of structures and entire organisms.202033084146
single-cell rna-seq reveals novel mitochondria-related musculoskeletal cell populations during adult axolotl limb regeneration process.while the capacity to regenerate tissues or limbs is limited in mammals, including humans, axolotls are able to regrow entire limbs and major organs after incurring a wound. the wound blastema has been extensively studied in limb regeneration. however, due to the inadequate characterization of ecm and cell subpopulations involved in the regeneration process, the discovery of the key drivers for human limb regeneration remains unknown. in this study, we applied large-scale single-cell rna sequenc ...202033116295
conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in ambystoma mexicanum.ambystoma mexicanum (axolotl) has been one of the major experimental models for the study of regeneration during the past 100 years. axolotl limb regeneration takes place through a multi-stage and complex developmental process called epimorphosis that involves diverse events of cell reprogramming. such events start with dedifferentiation of somatic cells and the proliferation of quiescent stem cells to generate a population of proliferative cells called blastema. once the blastema reaches a matu ...202033127453
the first report on circulating micrornas at pre- and post-metamorphic stages of axolotls.micrornas (mirnas) are endogenously coded small rnas, implicated in post-transcriptional gene regulation by targeting messenger rnas (mrnas). circulating mirnas are cell-free molecules, found in body fluids, such as blood and saliva, and emerged recently as potential diagnostic biomarkers. functions of circulating mirnas and their roles in target tissues have been extensively investigated in mammals, and the reports on circulating mirnas in non-mammalian clades are largely missing. salamanders d ...202033131713
surface contraction waves or cell proliferation waves in the presumptive neurectoderm during amphibian gastrulation: mexican axolotl versus african clawed frog.this essay represents a critical analysis of the literary data on various types of waves occurring in the amphibian embryos during gastrulation. a surface contraction wave travels through the presumptive neurectoderm during mexican axolotl gastrulation. this wave coincides temporally and spatially with involution of the inducing chordomesoderm and with the prospective neural plate. by contrast, there is no similar surface contraction wave during african clawed frog gastrulation. however, the cla ...202033181236
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