Erika Fodor- PhD Student at Eötvös Loránd University
Erika Fodor
- PhD Student at Eötvös Loránd University
About
18
Publications
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Introduction
Skills and Expertise
Current institution
Publications
Publications (18)
Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolu...
Paradise fish (Macropodus opercularis) is an air-breathing freshwater fish species with a signature labyrinth organ capable of extracting oxygen from the air that helps these fish to survive in hypoxic environments. The appearance of this evolutionary innovation in anabantoids resulted in a rewired circulatory system, but also in the emergence of s...
Background
Over the decades, a small number of model species, each representative of a larger taxa, have dominated the field of biological research. Amongst fishes, zebrafish (Danio rerio) has gained popularity over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such...
Simple Summary
Paradise fish (Macropodus opercularis) has been a favored subject of behavioral research during the last decades of the 20th century. Lately, however, with a massively expanding genetic toolkit and a well annotated, fully sequenced genome, zebrafish (Danio rerio) became a central model of recent behavioral research. But, as the zebra...
Autophagy (cellular self-eating) is a highly regulated degradation process of the eukaryotic cell during which parts of the cytoplasm are delivered into, and broken down within, the lysosomal compartment. The process serves as a main route for the elimination of superfluous and damaged cellular constituents, thereby mediating macromolecular and org...
Abstract From a hitherto underappreciated phenomenon, autophagy has become one of the most intensively studied cellular processes in recent years. Its role in cellular homeostasis, development and disease is supported by a fast growing body of evidence. Surprisingly, only a small fraction of new observations regarding the physiological functions of...
Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be c...
In silico
binding site analysis for candidate and randomly selected genes.
(XLS)
Sequence of PCR primers used for the nested PCR reactions.
(DOC)
Majority of the candidate genes are upregulated after MBT. Using a previously published dataset ([31] in Main Text), we tested whether the expression of our candidate genes is upregulated at MBT, as expected. Our results show that indeed, this is the case for all, except two genes: map2k6 and tmem68. The former showed a weak maternal expression, wh...
Genes with stochastic early expression. Genes belonging to this class show stochastic expression at the onset of the zygotic transcription. We could detect clusters of cells both in wild type and ich embryos that upregulated these particular genes, but no clear pattern emerged. For aplnrb (A–F) and isg15 (G–N), the expression pattern later became m...
Identification of candidate genes. Genes showing a significant (more than 1.5 fold in the case of DESeq) upregulation after normalization were considered for further analysis. Two complementary approaches, DESeq ([29] in the Main Text) (A) and Cufflinks ([30] in the Main Text) (B) packages were used to identify differentially regulated genes. Posit...
Extended genomic region analysis of validated genes. (A) For multi-exon genes, statistical analysis of the first introns for enrichment in putative TcfLef, XVent1 or Pou5f1 binding sites yielded negative results. (B) In the 4 kb downstream genomic regions, we could not detect significant differences between the random and validated gene-sets in the...
Questions
Question (1)
Hi, I would like to use Scr7 to increase the efficiency of CRISPR/Cas9 mediated knock-in. It seems like various cell types and mouse zygotes can tolerate a pretty high concentration of the compound (http://www.nature.com/nbt/journal/v33/n5/full/nbt.3190.html), so instead of incubation I would like to inject the inhibitor right into the embryos. However, I don't know what is the highest amount of DMSO that fish can tolerate.
Also, I was wondering if anyone has already used Scr7 to inhibit NHEJ in zebrafish. I would be grateful for any tips regarding the concentration, incubation time.
Thanks for any input,
Erika
