The Allende Lab

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Divulgación (en Español)

Research on zebrafish

Development of the lateral line

The lateral line is a mechanosensory organ that allows fish and aquatic amphibians to sense movements in the surrounding environment. Mechanosensation is perceived throughout the body by a series of small sensory patches called neuromasts (see image, below) made of clusters of hair cells (similar to those of the inner ear of mammals) surrounded by accesory cells. Importantly, hair cells are constantly renewed in fish, and they can be entirely replaced if hair cells are destroyed mechanically or by toxicity. Our interest lies in identifying genes that participate in the differentiation of the different cell types in this sensory system as well as understanding how hair cells regenerate after damage.

Regeneration of the components of the lateralis system

The remarkable regenerative capacity of the zebrafish mechanosensory system extends beyond hair cells. Sectioning the lateral line nerve or of individual axons is followed by quick degeneration of distal axon fragments and then regeneration of new fibers. We are trying to understand how the newly growing projections correctly navigate back to their original targets (Villegas et al., 2012 and Ceci et al., 2014). In addition, caudal tail sectioning is followed by regeneration of the fin and subsequent regeneration of the entire lateral line in the regrown tail. Ablation of single neuromasts is also followed by regeneration of the organs (Sánchez et al., 2016). How cells in the remaining sensory system acquire plasticity to repopulate the new territory and how they reorganize into a functional system is being analyzed.

Role of the innate immune system

Zebrafish embryos develop functional innate immunity one day after fertilization. Molecules involved in inflammation and innate immune cell migration are expressed during embryogenesis in specific tissues, which are poised to respond to potential infections and tissue damage. We have established a protocol for the study of the rapid innate immune response to sterile injury (see movie and our papers: d’Alençon et al., 2010 and Moya-Díaz et al., 2014). We are analyzing which signaling molecules are implicated in this response, as well as in resolution of inflammation. We are also examining the role of immunity in regeneration (Carrillo et al., 2016; Morales and Allende, 2019) and the genetic components implicated in macrophage and neutrophil function.

The Hox13 genes and tail formation in zebrafish

The development of the axial skeleton is one of the critical aspects of the evolution of vertebrates and its development depends, among many genes and pathways, on genes of the Hox complex.  We are interested in the formation of the caudal-most elements of the vertebral column and the tail. We have found the members of the Hox13 paralog group are responsible for definig the caudal vertebrae and the tail elements.

Host-Pathogen interactions

We have collaborated with the groups of Francisco Chávez, Rosalba Lagos and Andrés Marcoleta to define both host and pathogen factors that influence virulence in bacterial infection models. the role of immunity and natural defense barriers in fish are explored in order to define which components protect them against infection.


The zebrafish is an ideal system for analyzing cell migration, metastasis and immune-tumor interactions, due to the possibility of xenotransplantation and cell tracking in vivo. WIn this context, w are analyzing the relationship between neutrophils and breast cancer cells as well as the role of Hox1D in glioblastoma.

Research on killifish (work at the CGR)

Orestias ascotanensis

The cyprinidontiforms are among the most widely adapted and dispersed group of teleosts (bony fish) and those of the genus Orestias that live in the salt lakes of the Altiplano display a remarkable evolutionary history. They have speciated in single salt lakes along the Andes in allopatric fashion and have adapted to different environmental conditions, most notably, salinity of the water they inhabit. As a prime example, we have chosen Orestias ascotanensis as an organism that can provide answers as to how adaptation to this environment came about during evolution. We have also selected three more Orestias species to the list of target organisms as we intend to compare the genomes of these recently speciated groups. To date, we have a complete genomic sequence of O. ascotanensis, O. gloriae , O. laucaensis and O. chungaraensis. The quality of the data we have obtained from the genomic DNA prepared from single individuals is outstanding and shows that this species, unlike other teleosts sequenced thus far, has a genome that has less repetitive elements than other cyprinidontiforms, which normally make assembly exceedingly difficult (i.e., Atlantic salmon or A. charrua , see below). The genome of Orestias fish is less than 1Gb.

In parallel work, we are examiing the effects of UV irradiation on gene expression in these fish and comparing  this transcriptomic data with that of zebrafish. We are also studying the microbiome associated with the skin of Orestias fish.

Austrolebias charrua

Annual fish are freshwater teleosts found in South America and Africa that inhabit an extremely variable environment. They develop and reproduce in seasonal ponds that dry out during the summer. The survival of the species becomes entirely dependent upon buried and dried embryos, that hatch during the next rainy season and present a peculiar development, both features unique in vertebrates. Annual fish exhibit a unique developmental strategy in which embryogenesis occurs within a reaggregated mass of previously dispersed cells. On the other hand, they can enter a state of reversible developmental arrest (diapause) at three distinct embryonic stages. Austrolebias charrua is an annual killifish inhabiting the grasslands of the Rio de la Plata delta whose development has these features. Our aim of is to analyze the genomic structure and control of gene expression during diapause in A. charrua assuming that its adaptation to a changing environment has evolved by the acquisition of genetic traits that sustain developmental and physiological plasticity. We have sequenced the genome of A. charrua and determined a genome size of 3.2Gb, one of the largest for a diploid animal. Further, its genome is composed of 70% repetitive sequence, an unusually high percentage for animals.


Iniciativa Científica Milenio ICN2021_044. Millennium Institute Center for Genome Regulation. 2022-2032.

FONDECYT 1221360. “Deciphering the molecular crosstalk between the host and the skin microbiota controls tissue homeostasis and pathogen inhibition in zebrafish”. 2022-2026.