Karri Haen

Publications

• 2.72

  Impact points

  RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria.

  Ajna S Rivera, Jörg U Hammel, Karri M Haen, Elizabeth S Danka, Brandon Cieniewicz, Ian P Winters, Dora Posfai, Gert Wörheide, Dennis V Lavrov, Scott W Knight, Malcolm S Hill, April L Hill, Michael Nickel

  BMC biotechnology. 06/2011; 11:67.

  The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not be... [more] The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from 'knocking down' expression of the actin gene. This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals.

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• 1.75

  Impact points

  Molecular phylogeny of glass sponges (Porifera, Hexactinellida): increased taxon sampling and inclusion of the mitochondrial protein-coding gene, cytochrome oxidase subunit I

  Martin Dohrmann, Karri M. Haen, Dennis V. Lavrov, Gert Wörheide

  Hydrobiologia. 01/2011;

  Marine sponges of the class Hexactinellida (glass sponges) are among the most understudied groups of Porifera, and molecular approaches to investigating their evolution have only recently emerged. Although these first results appeared reliable as they largely corroborated morphology-based hypotheses... [more] Marine sponges of the class Hexactinellida (glass sponges) are among the most understudied groups of Porifera, and molecular approaches to investigating their evolution have only recently emerged. Although these first results appeared reliable as they largely corroborated morphology-based hypotheses, they were almost exclusively based on ribosomal RNA genes (rDNA) and should, therefore, be further tested with independent types of genetic data, such as protein-coding genes. To this end, we established the mitochondrial-encoded cytochrome oxidase subunit I gene (COI) as an additional marker, and conducted phylogenetic analyses on DNA- and amino-acid level, as well as a supermatrix analysis based on combined COI DNA and rDNA alignments. Furthermore, we increased taxon sampling compared to previous studies by adding seven additional species. The COI-based phylogenies were largely congruent with the rDNA-based phylogeny but suffered from poor bootstrap support for many nodes. However, addition of the COI sequences to the rDNA data set increased resolution of the overall molecular phylogeny. Thus, although obtaining COI sequences from glass sponges turned out to be quite challenging, this gene appears to be a valuable supplement to rDNA data for molecular evolutionary studies of this group. Some implications of our extended phylogeny for the evolution and systematics of Hexactinellida are discussed.
• 2.72

  Impact points

  RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria

  A. Rivera, J. Hammel, K. Haen, E. Danka, B. Cieniewicz, I. Winters, D. Posfai, G. Wörheide, D. Lavrov, S. Knight, M. Hill, A. Hill, M. Nickel

  BMC Biotechnology. 01/2011; 11:67.

  Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms... [more] Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from ‘knocking down’ expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals.
• 9.87

  Impact points

  Parallel loss of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases and mtDNA-encoded tRNAs in Cnidaria.

  Karri M Haen, Walker Pett, Dennis V Lavrov

  Molecular biology and evolution. 05/2010; 27(10):2216-9.

  Unlike most animal mitochondrial (mt) genomes, which encode a set of 22 transfer RNAs (tRNAs) sufficient for mt protein synthesis, those of cnidarians have only retained one or two tRNA genes. Whether the missing cnidarian mt-tRNA genes relocated outside the main mt chromosome or were lost remains u... [more] Unlike most animal mitochondrial (mt) genomes, which encode a set of 22 transfer RNAs (tRNAs) sufficient for mt protein synthesis, those of cnidarians have only retained one or two tRNA genes. Whether the missing cnidarian mt-tRNA genes relocated outside the main mt chromosome or were lost remains unclear. It is also unknown what impact the loss of tRNA genes had on other components of the mt translational machinery. Here, we explored the nuclear genome of the cnidarian Nematostella vectensis for the presence of mt-tRNA genes and their corresponding mt aminoacyl-tRNA synthetases (mt-aaRS). We detected no candidates for mt-tRNA genes and only two mt-aaRS orthologs. At the same time, we found that all but one cytosolic aaRS appear to be targeted to mitochondria. These results indicate that the loss of mt-tRNAs in Cnidaria is genuine and occurred in parallel with the loss of nuclear-encoded mt-aaRS. Our phylogenetic analyses of individual aaRS revealed that although the nearly total loss of mt-aaRS is rare, aaRS gene deletion and replacement have occurred throughout the evolution of Metazoa.

• Mitochondrial genome evolution in the Metazoa: Insights from Class Hexactinellida (Phylum Porifera) and Cnidaria

  Karri M. Haen

  01/2010

  Degree: Ph.D.

  Supervisor: Dennis Lavrov
• 9.87

  Impact points

  Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?

  Karri M Haen, B Franz Lang, Shirley A Pomponi, Dennis V Lavrov

  Molecular biology and evolution. 07/2007; 24(7):1518-27.

  Glass sponges (Hexactinellida) are a group of deep-water benthic animals that have a unique syncytial organization and possess a characteristic siliceous skeleton. Although hexactinellids are traditionally grouped with calcareous and demosponges in the phylum Porifera, the monophyly of sponges and t... [more] Glass sponges (Hexactinellida) are a group of deep-water benthic animals that have a unique syncytial organization and possess a characteristic siliceous skeleton. Although hexactinellids are traditionally grouped with calcareous and demosponges in the phylum Porifera, the monophyly of sponges and the phylogenetic position of the Hexactinellida remain contentious. We determined and analyzed the nearly complete mitochondrial genome sequences of the hexactinellid sponges Iphiteon panicea and Sympagella nux. Unexpectedly, our analysis revealed several mitochondrial genomic features shared between glass sponges and bilaterian animals, including an Arg --> Ser change in the genetic code, a characteristic secondary structure of one of the serine tRNAs, highly derived tRNA and rRNA genes, and the presence of a single large noncoding region. At the same time, glass sponge mtDNA contains atp9, a gene previously found only in the mtDNA of demosponges (among animals), and encodes a tRNA(Pro);(UGG) with an atypical A11-U24 pair that is also found in demosponges and placozoans. Most of our sequence-based phylogenetic analyses place Hexactinellida as the sister group to the Bilateria; however, these results are suspect given accelerated rates of mitochondrial sequence evolution in these groups. Thus, it remains an open question whether shared mitochondrial genomic features in glass sponges and bilaterian animals reflect their close phylogenetic affinity or provide a remarkable example of parallel evolution.
• 3.89

  Impact points

  Saturation mapping of a gene-rich recombination hot spot region in wheat.

  J D Faris, K.M. Haen, B S Gill

  Genetics. 03/2000; 154(2):823-35.

  Physical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant regio... [more] Physical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.

• Genomic targeting and high-resolution mapping of the Tsn1 gene in wheat.

  K.M. Haen, H. Lu, T.L. Friesen, J D Faris

  Tan spot, caused by the fungal pathogen Pyrenophora tritici-repentis (Died.) Drechs. causes severe yield losses in wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) and durum (T. turgidum L., 2n = 4x = 28, AABB). The Tsn1 gene acts dominantly to confer sensitivity to a host-selective proteinaceous ... [more] Tan spot, caused by the fungal pathogen Pyrenophora tritici-repentis (Died.) Drechs. causes severe yield losses in wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) and durum (T. turgidum L., 2n = 4x = 28, AABB). The Tsn1 gene acts dominantly to confer sensitivity to a host-selective proteinaceous toxin (Ptr ToxA) produced by the fungus. Our objectives were to: (i) target markers to the Tsn1 genomic region and (ii) develop a high-resolution map of the Tsn1 locus. The techniques of methylation-sensitive AFLP, traditional AFLP, and cDNA-AFLP were combined with bulked segregant analysis (BSA) using various wheat and durum cytogenetic stocks to target markers to the Tsn1 genomic region. Over 500 primer combinations were screened resulting in the identification of 18 low-copy markers closely linked to Tsn1. High-resolution mapping of the markers delineated the Tsn1 gene to a 0.2 cM interval in a hexaploid wheat population consisting of 1266 gametes, and to 0.8 cM in a durum wheat population consisting of 1860 gametes. Comparisons with rice BAC/PAC sequences indicated the lack of colinearity within the Tsn1 genomic region. Tsn1 was located within a gene-rich recombination hot spot region, and the physical distance separating the flanking markers may be as little as 200 kb. Therefore, these markers will serve as a basis for the map-based cloning of Tsn1. The isolation of Tsn1 will further our knowledge of wheat-tan spot interactions as well as host-pathogen interactions in general.