Stefan Siebert

• PhD
• Researcher at University of California, Davis

The characterization of a novel paralogous myc gene in Hydra, termed myc3, with conserved biochemical and oncogenic functions reveals a high complexity of the Myc network in this cnidarian. Based on its specific expression pattern, myc3 appears to function in nerve and gland cell differentiation, where its protein product could act as a dominant ne...

The proto-oncogene myc has been intensively studied primarily in vertebrate cell culture systems. Myc transcription factors control fundamental cellular processes such as cell proliferation, cell cycle control and stem cell maintenance. Myc interacts with the Max protein and Myc/Max heterodimers regulate thousands of target genes. The genome of the...

The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained...

The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained...

Siphonophores are complex colonial animals, consisting of asexually-produced bodies (zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to...

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown....

In Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes we performed RNAseq and identified genes that are differentially regulated in response to 48 hours...

The Notch pathway is highly conserved and essential for animal development. We investigated the function of Notch-signalling in Hydra by using the presenilin inhibitor DAPT, which efficiently blocks propagation of Notch-signals. In Hydra, DAPT treatment prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. M...

Intratumoral heterogeneity is associated with aggressive tumor behavior, therapy resistance, and poor patient outcomes. Such heterogeneity is thought to be dynamic, shifting over periods of minutes to hours in response to signaling inputs from the tumor microenvironment. However, models of this process have been inferred from indirect or post-hoc m...

Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have t...

Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. However, these mechanisms often fail over time leading to de-repression of TEs in aging tissues. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function o...

Mapping Hydra development cell by cell Hydra continually renews all cells in its body using three stem cell populations. This feature of Hydra allowed Siebert et al. to identify the transcriptional signatures of stem cells, progenitors, and terminally differentiated cells using single-cell RNA sequencing of adult Hydra (see the Perspective by Reddi...

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the Vascular-related NAC Domain 7 (VND7), MYB46, and MYB83 transcription factors, which are proposed to act in interconnec...

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the VASCULAR-RELATED NAC DOMAIN7 (VND7), MYB46 and MYB83 transcription factors which are proposed to act in interconnected...

The EGFR/Ras/ERK signalling pathway is a driver of cancer cell proliferation and metastasis in tumours that exhibit high cell-to-cell heterogeneity. While the signalling activity of this pathway is frequently amplified in tumours, it is not understood how the kinetic aspects of its activation in tumours differ from normal cellular signalling. Using...

The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations, but the genetic pathways enabling homeostatic tissue maintenance are not well understood. We used Drop-seq to sequence transcriptomes of 24,985 single Hydra cells and identified the molecular signatures of a broad spectrum of cell states, from ste...

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provid...

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA ge...

Significance Comparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here, we show that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, a...

There is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the e...

Mechanisms of sex determination vary greatly among animals. Here we survey what is known in Cnidaria, the clade that forms the sister group to Bilateria and shows a broad array of sexual strategies and sexual plasticity. This observed diversity makes Cnidaria a well-suited taxon for the study of the evolution of sex determination, as closely relate...

Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that are the sites...

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology , lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. H...

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology , lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. H...

The siphonophore Nanomia bijuga is a pelagic hydrozoan (Cnidaria) with complex morphological organization. Each siphonophore is made up of many asexually produced, genetically identical zooids that are functionally specialized and morphologically distinct. These zooids predominantly arise by budding in two growth zones, and are arranged in precise...

The siphonophore Nanomia bijuga is a pelagic hydrozoan (Cnidaria) with complex morphological organization. Each siphonophore is made up of many asexually produced, genetically identical zooids that are functionally specialized and morphologically distinct. These zooids predominantly arise by budding in two growth zones, and are arranged in precise...

Background: Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that a...

Siphonophores are polymorphic planktonic marine Cnidarians. The family Apolemiidae is sister to all other species of physonect and calycophoran siphonophores. Although this enigmatic group arguably includes the longest animal species on the planet, their colony-level organization and growth patterns are not well understood. Here we describe two new...

Background Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective...

Correlation of gene expression quantification using SOLiD SAGE. The top row shows the three pairwise correlations of counts per reference sequence between the three nectophore samples. The middle row shows the pairwise correlations between the three gastrozooid samples. The bottom row shows the correlation between pairs of nectophore and gastrozooi...

Countfile. Tab-delimited text file with read counts and other relevant data for each sequence in the reference. A complete list of file contents is provided within the file. (TXT)

De novo transcriptome assembly using 454 sequencing. Overview of the assembly process for 454 data, including the number of sequences at each step (A). The distribution of the reference sequence length (B). For isogroups with multiple isotigs, gene length was calculated as the sum of the length of all contigs. (PNG)

Correlation of gene expression quantification using Illumina mRNA-Seq. The top row shows the three pairwise correlations of counts per reference sequence between the three nectophore samples. The middle row shows the pairwise correlations between the three gastrozooid samples. The bottom row shows the correlation between pairs of nectophore and gas...

Mapped read distribution across selected transcripts. Read distribution is shown for ten different reference sequences (A–J) and all replicates (necto 1–3, gastro 1–3). Sequences are orientated in 5′ to 3′ direction. The physical distributions of mapped reads (non-normalized counts) across reference sequences were consistent for each platform acros...

Variability of gene expression across field collected specimen of Nanomia bijuga. Comparison of likelihood ratio test p-values with or without considering that the samples are paired. Consistent p-values indicate low specimen-specific effects. (PNG)

Overview of sample preparation procedures for the three short-read sequencing protocols used to quantify transcript expression. The Digital Gene Expression protocol (Helicos) and the SAGE protocol (SOLiD) generate a single sequencing read (tag) from a particular region of each sequenced RNA molecule. The mRNA-Seq protocol (Illumina) generates multi...

Congruence in detection of DE across sequencing workflows, considering all sequences in the reference. Visualized are scatterplots of pairwise comparisons (significance cuttoff Z>4.707364) (left), the frequency of DE in nectophores and gastrozooids for each category (middle) and DE in dependency of gene length. Positive Z values represent higher ex...

Sequencing statistics for the three short-read platforms used to quantify gene expression in Nanomia bijuga. Shown are mean values and standard deviations for read numbers (in million reads) collected from three different animals. Percentage of mapped reads was calculated relative to raw reads. (PNG)

Correlation of gene expression quantification using Helicos DGE. The top row shows the three pairwise correlations of counts per reference sequence between the three nectophore samples. The middle row shows the pairwise correlations between the three gastrozooid samples. The bottom row shows the correlation between pairs of nectophore and gastrozoo...

Congruences in detection of DE across sequencing workflows, considering the subset of reference sequences with the 3′-most NlaIII site. Visualized are scatterplots of pairwise comparisons (significance cutoff Z>4.382159) (left), the frequency of DE in nectophores and gastrozooids for each category (middle) and DE in dependency of gene length. Posit...

Gene reference (in FASTA format). Contigs (fasta format) of both the Newbler and the CAP3 assembly of 454 reads which were used for mapping the short reads. Unique counts of Newbler contigs belonging to the same isogroup were summed up to generate isogroup counts. (FASTA)

In situ observations of the siphonophore Nanomia bijuga, and sampling procedure using a remotely operated underwater vehicle. In Monterey Bay Nanomia bijuga can be found from surface waters down to a depth of 700 m. This video was taken at a depth of 612 m. (MOV)

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replic...

In the absence of migratory phagocytic cells the basal metazoan Hydra has developed a very effective immune system. Previous work has shown that epithelial cells, both in the ectoderm and endoderm, recognize PAMPs by TLR and produce a number of antimicrobial peptides. In this study we demonstrate that not only epithelial cells but also gland cells...

Various cnidarians have adapted their life style to interstitial habitats of marine sediments. Recently, for the first time a hydroid was reported from the interstitial brine channel system of Arctic fast ice. Due to its derived features, the new genus and species Sympagohydra tuuli was introduced. Here we describe findings of S. tuuli in sea ice a...

Understanding the mechanisms controlling the stability of the differentiated cell state is a fundamental problem in biology. To characterize the critical regulatory events that control stem cell behavior and cell plasticity in vivo in an organism at the base of animal evolution, we have generated transgenic Hydra lines [Wittlieb, J., Khalturin, K.,...

Hydra is a classical model organism to understand fundamental developmental biological processes such as regeneration and axis formation. Here, we show that two genes which share some similarity with members of the Dickkopf family of proteins, HyDkk1/2/4-A and HyDkk1/2/4-C, are co-expressed in gland cells and regulated by the positional value gradi...

Homeodomain transcription factor CnNK-2 seems to play a major role in foot formation in Hydra. Recently, we reported in vitro evidence indicating that CnNK-2 has autoregulatory features and regulates expression of the morphogenetic peptide pedibin. We proposed that CnNK-2 and pedibin synergistically orchestrate foot differentiation processes. Here,...