Biomedical subjects

Jarema Malicki

Publications and source records attributed to Jarema Malicki.

13 recordsLinked to original sources

PubMed2006

oko meduzy and related crumbs genes are determinants of apical cell features in the vertebrate embryo.

BACKGROUND: Polarity is an essential attribute of most eukaryotic cells. One of the most prominent features of cell polarity in many tissues is the subdivision of cell membrane into apical and basolateral compartments by a belt of cell junctions. The proper formation of this subdivision is of key importance. In sensory cells, for example, the apical membrane compartment differentiates specialized structures responsible for the detection of visual, auditory, and olfactory stimuli. In other tissues, apical specializations are responsible for the propagation of fluid flow. Despite its importance, the role of genetic determinants of apico-basal polarity in vertebrate embryogenesis remains poorly investigated. RESULTS: We show that zebrafish oko meduzy (ome) locus encodes a crumbs gene homolog, essential for the proper apico-basal polarity of neural tube epithelia. Two ome paralogs, crb2b and crb3a, promote the formation of apical cell features: photoreceptor inner segments and cilia in renal and auditory systems. The motility of cilia is defective following the impairment of crb2b function. Apical surface defects in ome- and crb2b-deficient animals are associated with profound disorganization of neuronal architecture and with the formation of pronephric cysts, respectively. Unexpectedly, despite differences in their structure and expression patterns, crumbs genes are, at least partially, functionally interchangeable. CONCLUSIONS: ome and related crumbs genes are necessary for the formation of gross morphological features in several organs, including the CNS and the renal system. On the cellular level, crumbs genes regulate the formation of both ciliary and nonciliary apical membrane compartment.

Animals↗

PubMed2006

Reverse genetic analysis of neurogenesis in the zebrafish retina.

To gain an understanding of molecular events that underlie pattern formation in the retina, we evaluated the expression profiles of over 8000 transcripts randomly selected from an embryonic zebrafish library. Detailed analysis of cDNAs that display restricted expression patterns revealed factors that are specifically expressed in single cell classes and are potential regulators of neurogenesis. These cDNAs belong to numerous molecular categories and include cell surface receptors, cytoplasmic enzymes, and transcription factors. To test whether expression patterns that we have uncovered using this approach are indicative of function in neurogenesis, we used morpholino-mediated knockdown approach. The knockdown of soxp, a transcript expressed in the vicinity of the inner plexiform layer, revealed its role in cell type composition of amacrine and ganglion cell layers. Blocking the function of cxcr4b, a chemokine receptor specifically expressed in ganglion cells, suggests a role in ganglion cell survival. These experiments demonstrate that in situ hybridization-based reverse genetic screens can be applied to isolate genetic regulators of neurogenesis. This approach very well complements forward genetic mutagenesis studies previously used to study retinal neurogenesis in zebrafish.

Animals↗

PubMed2006

The zebrafish cornea: structure and development.

PURPOSE: To evaluate the zebrafish as a model for the studies of corneal development and disease. METHODS: Zebrafish embryos and larvae at various stages of development were used for documenting corneal morphogenesis and differentiation. Corneal samples were collected from embryos, larvae, and adult zebrafish for histologic and electron microscopy analysis. Expression patterns of corneal polypeptides were investigated by immunostaining of sections. RESULTS: The zebrafish cornea develops rapidly during embryogenesis, so that its three major layers, the epithelium, the stroma, and the endothelium, are well formed by day 3 postfertilization. The subsequent steps of corneal differentiation, such as the thickening of the corneal stroma, proceed relatively slowly. Several polypeptides are highly enriched in the epithelium or the stroma of the larval and adult zebrafish cornea and are excellent markers of corneal differentiation. CONCLUSIONS: Development and differentiation of the zebrafish cornea are easily accessible to analysis. Anatomic and ultrastructural characterization of the zebrafish cornea demonstrates many similarities to the human cornea and provides the basis for the use of the zebrafish model both to analyze the basic genetic mechanisms of corneal development and to study the causes of corneal disease.

Animals↗

PubMed2005

Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko.

PURPOSE: To determine the genomic organization of the zebrafish crx gene and to evaluate if mutations in crx are responsible for the retinal degeneration phenotype in the zebrafish (Danio rerio) mutants niezerka (nie(m743)) and mikre oko (mok(m632)). METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). Amplicons were sequenced and sequence data assembled into contigs. Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. Linkage analysis used DNA from mapping panels of single homozygous mutant animals with mixed genetic backgrounds. RESULTS: The analysis indicated that the zebrafish crx gene consisted of three exons and 2 introns, and spans 3.8 kb of genomic DNA. The splice junctions were all located within the coding region. Highly repetitive sequences present in non-coding regions of crx and extended tetra-nucleotide repeats in intronic regions were associated with sequence variation between different strains. Homozygous mok(m632) or nie(m743) mutants and their respective wild-type sibs, showed identical patterns of heterozygosity and sequence variations within each line. No mutation in crx were identified in homozygous mok(m632) or nie(m743). Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. CONCLUSIONS: Despite the presence of sequence variations in their respective genetic backgrounds, within each line the sequence of crx was identical. Consistent with the absence of mutations, further analysis excluded linkage of the mutant phenotypes to crx. Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines.

Animals↗

PubMed2004

Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons.

Cilia play diverse roles in vertebrate and invertebrate sensory neurons. We show that a mutation of the zebrafish oval (ovl) locus affects a component of the ciliary transport (IFT) mechanism, the IFT88 polypeptide. In mutant retina, cilia are generated but not maintained, producing the absence of photoreceptor outer segments. A loss of cilia also occurs in auditory hair cells and olfactory sensory neurons. In all three sense organs, cilia defects are followed by degeneration of sensory cells. Similar phenotypes are induced by the absence of the IFT complex B polypeptides, ift52 and ift57, but not by the loss of complex A protein, ift140. The degeneration of mutant photoreceptor cells is caused, at least partially, by the ectopic accumulation of opsins. These studies reveal an essential role for IFT genes in vertebrate sensory neurons and implicate the molecular components of intraflagellar transport in degenerative disorders of these cells.

Algal Proteins↗

PubMed2004

Cell fate decisions and patterning in the vertebrate retina: the importance of timing, asymmetry, polarity and waves.

The differentiation of distinct cell populations in the retina is a multi-step process that involves cell cycle exit, migration, and dramatic changes of cell morphology. All these steps are tightly controlled by multiple regulatory pathways, which involve both cell-autonomous networks of transcription factors and cell-cell signaling events. Additional regulatory inputs into cell fate decisions have been recently suggested: accumulating evidence shows that the timing of cell cycle exit, the orientation of the mitotic spindle during the last cell division, and the polarity of neuronal progenitor cells could play important roles in cell fate determination.

Animals↗

PubMed2004

Retinal pattern and the genetic basis of its formation in zebrafish.

The vertebrate nervous system contains an immense diversity of distinct cellular components that are organized into precise spatial patterns. The importance of accurate neuronal architecture is particularly obvious in the retina, where it is necessary for the formation of visual images. The retina is structured in a distinct layered pattern that is remarkably conserved in evolution, including phyla as diverse as primates and teleost fish. Genetic analysis in zebrafish reveals mechanisms that are essential for the formation of this architecture.

Animals↗

PubMed2004

Approaches to study neurogenesis in the zebrafish retina.

Similar to other vertebrate species, the zebrafish retina is simpler than other regions of the central nervous system (CNS). Relative simplicity, rapid development, and accessibility to genetic analysis make the zebrafish retina an excellent model system for the studies of neurogenesis in the vertebrate CNS. Numerous genetic screens have led to isolation of an impressive collection of mutations affecting the retina and the retinotectal projection in zebrafish. Mutant phenotypes are being studied using a rich variety of markers: antibodies, RNA probes, retrograde and anterograde tracers, as well as transgenic lines. Particularly impressive progress has been made in the characterization of the zebrafish genome. Consequently, positional and candidate cloning of mutant genes are now fairly easy to accomplish in zebrafish. Many mutant genes have, in fact, already been cloned and their analysis has provided important insights into the gene circuitry that regulates retinal neurogenesis. Genetic screens for visual system defects will continue in the future and progressively more sophisticated screening approaches will make it possible to detect a variety of subtle mutant phenotypes in retinal development. The remarkable evolutionary conservation of the vertebrate eye provides the basis for the use of the zebrafish retina as a model of human disorders. Some of the genetic defects of the zebrafish retina indeed resemble human retinopathies. As new techniques are being introduced and improved at a rapid pace, the zebrafish will continue to be an important organism for the studies of the vertebrate visual system.

Alleles↗

PubMed2004

Genetics of photoreceptor development and function in zebrafish.

The vertebrate photoreceptor is a cell of unique morphology and function. It is an exquisite light detector, both sensitive and adaptable. Several unusual morphological features facilitate photoreceptor function. Signal detection is accomplished by a specialized apical structure, the outer segment. There, the capture of light produces fluctuations in cell membrane potential, which are then transmitted to the downstream circuitry of the retina via a rare type of synaptic junction, the ribbon synapse. The development, maintenance and function of the vertebrate photoreceptor cell have been studied mainly in four model organisms, ranging from an amphibian to man. A teleost fish, the zebrafish, is an important recent addition to this group. Genetic screens in zebrafish have identified an impressive collection of photoreceptor cell mutants, including the absence or malformation of specific morphological features as well as functional abnormalities. These mutant strains are currently studied using both molecular and embryological tools and provide important insights into photoreceptor biology.

Animals↗

PubMed2003

Zebrafish N-cadherin, encoded by the glass onion locus, plays an essential role in retinal patterning.

Genetic screens in zebrafish identified several loci that play essential roles in the patterning of retinal architecture. Here, we show that one of them, glass onion, encodes the N-cadherin gene. The glo(m117) mutant allele contains a substitution of the Trp2 residue known for its essential role in the adhesive properties of classic cadherins. Both the glo(m117) and pac(tm101b) mutant N-cadherin alleles affect the polarity of the retinal neuroepithelial sheet and, unexpectedly, both result in cell-nonautonomous phenotypes in retinal patterning. The late onset of mutant N-cadherin phenotypes may be due to the ability of classic cadherins to substitute each other's function.

Amino Acid Sequence↗

PubMed2002

nagie oko, encoding a MAGUK-family protein, is essential for cellular patterning of the retina.

A layered organization of cells is a common architectural feature of many neuronal formations. Mutations of the zebrafish gene nagie oko (nok) produce a severe disruption of retinal architecture, indicating a key role for this locus in neuronal patterning. We show that nok encodes a membrane-associated guanylate kinase-family scaffolding protein. Nok localizes to the vicinity of junctional complexes in retinal neuroepithelium and in the photoreceptor cell layer. Mosaic analysis indicates that the nok retinal patterning phenotype is not cell-autonomous. We propose that nok function in patterning of postmitotic neurons is mediated through neuroepithelial cells and is necessary for guiding neurons to their proper destinations in retinal laminae.

Amino Acid Sequence↗

PubMed2002

Genetic analysis of photoreceptor cell development in the zebrafish retina.

To gain insight into the genetic mechanisms of photoreceptor development, we analyzed a collection of zebrafish mutations characterized by early photoreceptor cell loss. The mutant defects impair outer segment formation and are accompanied by an abnormal distribution of visual pigments. Rods and different cone types display defects of similar severity suggesting that genetic pathways common to all photoreceptors are affected. To investigate whether these phenotypes involve cell-cell interaction defects, we analyzed genetically mosaic animals. Interaction of niezerka photoreceptors with wild-type tissues improves the survival of mutant cells and restores their elongated morphology. In contrast, cells carrying mutations in the loci brudas, elipsa, fleer, and oval retain their defective phenotypes in a wild-type environment indicating cell-autonomy. These experiments identify distinct phenotypic categories of photoreceptor mutants and indicate that zebrafish photoreceptor defects involve both cell-autonomous and cell-nonautonomous mechanisms.

Animals↗

PubMed2002

Analysis of gene function in the zebrafish retina.

Mutagenesis screens in zebrafish have uncovered several hundred mutant alleles affecting the development of the retina and established the zebrafish as one of the leading models of vertebrate eye development. In addition to forward genetic mutagenesis approaches, gene function in the zebrafish embryo is being studied using several reverse genetic techniques. Some of these rely on the overexpression of a gene product, others take advantage of antisense oligonucleotides to block function of selected loci. Here we describe these methods in the context of the developing eye.

Animals↗