9 Works

Supplementary material from \"Changes in invertebrate food Web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts\"

Ana Miller-ter Kuile, Austen Apigo, An Bui, Kirsten Butner, Jasmine N. Childress, Stephanie Copeland, Bartholomew P. DiFiore, Elizabeth S. Forbes, Maggie Klope, Carina I. Motta, Devyn Orr, Katherine A. Plummer, Daniel L. Preston & Hillary S. Young
Predator–prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food Web structure. One way to capture mechanisms shaping trophic response is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods:...

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Abstract The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with...

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Abstract The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with...

Supplementary material from \"Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts\"

Ana Miller-ter Kuile, Austen Apigo, An Bui, Kirsten Butner, Jasmine N. Childress, Stephanie Copeland, Bartholomew P. DiFiore, Elizabeth S. Forbes, Maggie Klope, Carina I. Motta, Devyn Orr, Katherine A. Plummer, Daniel L. Preston & Hillary S. Young
Predator–prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods:...

Modeling the metabolic evolution of mixotrophic phytoplankton in response to rising ocean surface temperatures

Logan M. Gonzalez, Stephen R. Proulx & Holly V. Moeller
Abstract Background Climate change is expected to lead to warming in ocean surface temperatures which will have unequal effects on the rates of photosynthesis and heterotrophy. As a result of this changing metabolic landscape, directional phenotypic evolution will occur, with implications that cascade up to the ecosystem level. While mixotrophic phytoplankton, organisms that combine photosynthesis and heterotrophy to meet their energetic and nutritional needs, are expected to become more heterotrophic with warmer temperatures due to...

Modeling the metabolic evolution of mixotrophic phytoplankton in response to rising ocean surface temperatures

Logan M. Gonzalez, Stephen R. Proulx & Holly V. Moeller
Abstract Background Climate change is expected to lead to warming in ocean surface temperatures which will have unequal effects on the rates of photosynthesis and heterotrophy. As a result of this changing metabolic landscape, directional phenotypic evolution will occur, with implications that cascade up to the ecosystem level. While mixotrophic phytoplankton, organisms that combine photosynthesis and heterotrophy to meet their energetic and nutritional needs, are expected to become more heterotrophic with warmer temperatures due to...

Supplementary material from \"Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts\"

Ana Miller-ter Kuile, Austen Apigo, An Bui, Kirsten Butner, Jasmine N. Childress, Stephanie Copeland, Bartholomew P. DiFiore, Elizabeth S. Forbes, Maggie Klope, Carina I. Motta, Devyn Orr, Katherine A. Plummer, Daniel L. Preston & Hillary S. Young
Predator–prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods:...

Registration Year

  • 2022
    9

Resource Types

  • Collection
    9

Affiliations

  • University of California, Santa Barbara
    9
  • Cleveland State University
    2
  • Howard Hughes Medical Institute
    2
  • National Human Genome Research Institute
    2
  • Senckenberg Society for Nature Research
    2
  • Chongqing Medical University
    2
  • University of Wisconsin–Madison
    2
  • Georgia Institute of Technology
    2
  • Purdue University West Lafayette
    2
  • Chinese Academy of Sciences
    2