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Open Access Publications from the University of California

Scholarly Works (12 results)

  • Article
  • Peer Reviewed
New Chaucer Studies: Pedagogy and Profession, Volume 4, Issue 2 (2023)

In this article, we share our perspectives (as teacher and student) on the role of modern adaptations of Chaucer in teaching and assessment, with a particular focus on the role such adaptations play in supporting the use of creative writing-based assignments in a medieval literature course. We describe our experience of an assessment composed of a creative exercise combined with a critical commentary, and discuss how the incorporation of modern adaptations of medieval texts into the medieval literature curriculum underpins and supports this assessment type. Our account demonstrates that the process by which the meaning of literary texts is generated is iterative and collaborative, a point we hope to underscore through our collaboration on this piece. We hope the experience we describe will foreground the value of dialogue in the processes of teaching, assessment, and feedback, and also highlight the role of modern adaptations in supporting students to recognise and articulate the value of their own creative and critical work within a longer tradition of literary and scholarly responses to medieval literature.

    Cover page: Collaborative Teaching and Creative Assignments Using Contemporary AdaptationCreative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2016)
    The complete 16,515bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (D-loop), the gene order of which is identical to that observed in most vertebrates. The protein-coding gene sequences of E. jacksoni mitochondrial DNA were compared with two other embiotocid surfperches with available complete mitochondrial genomes, Cymatogaster aggregata and Ditrema temminckii. Across all mitochondrial protein-coding genes in surfperches the weighted average substitution rate was 2.079% per My and average dN/dS ratios for each protein-coding gene ranged from 0.016 in CytB to 0.608 in ND3. Substitution rates and dN/dS ratios were relatively high for ATP8 compared to other protein-coding genes. Although most protein-coding genes showed signals of purifying selection, we found evidence for positive selection in ND3 in E. jacksoni.
      Cover page: The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)
      • Thesis
      • Peer Reviewed
      UC Santa Cruz Electronic Theses and Dissertations (2017)

      Proximity ligation methods are a means of capturing long-range spatial information about DNA sequences with short-read sequencing compacted and concatenated DNA molecules. HiC, a method of gathering genome spatial information by the process of chromatin proximity ligation and capture, represents a powerful and versatile tool for modern genomics. Over the course of this dissertation, I demonstrate improvements to the HiC method and novel uses for the HiC data. An early novel use of chromatin proximity data was in the form of Chicago, an in vitro assembled chromatin version of HiC primarily used for de novo genome assembly scaffolding. This method was used to scaffold nearly one hundred new, high contiguity genome assemblies over the last two years. I next describe my own improvements to the HiC method, resulting in a faster, more economical version of HiC, and apply the improvements to explore the rapid-aging ICE mouse model and to scaffold a high-contiguity assembly of the Atlantic herring genome. I also show that the haplotype informative nature of HiC, when combined with recombined germline samples, allows for individual, personalized recombination maps, using both the Atlantic herring and human samples.

        Cover page: Developing and Applying Chromatin Proximity Ligation Methods
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2021)
        The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
          Cover page: An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2016)
          Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach ("Chicago") based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline ("HiRise") that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
            • Article
            • Peer Reviewed
            UC Irvine Previously Published Works (2022)
            Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.
              Cover page: Deeply conserved synteny and the evolution of metazoan chromosomesCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC Santa Cruz Previously Published Works (2019)
              Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
                • Article
                • Peer Reviewed
                UC Santa Cruz Previously Published Works (2017)
                The American alligator, Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the sex of an embryo is determined by the incubation temperature of the egg during a critical period of development. The lack of genetic differences between male and female alligators leaves open the question of how the genes responsible for sex determination and differentiation are regulated. Insight into this question comes from the fact that exposing an embryo incubated at male-producing temperature to estrogen causes it to develop ovaries. Because estrogen response elements are known to regulate genes over long distances, a contiguous genome assembly is crucial for predicting and understanding their impact. We present an improved assembly of the American alligator genome, scaffolded with in vitro proximity ligation (Chicago) data. We use this assembly to scaffold two other crocodilian genomes based on synteny. We perform RNA sequencing of tissues from American alligator embryos to find genes that are differentially expressed between embryos incubated at male- versus female-producing temperature. Finally, we use the improved contiguity of our assembly along with the current model of CTCF-mediated chromatin looping to predict regions of the genome likely to contain estrogen-responsive genes. We find that these regions are significantly enriched for genes with female-biased expression in developing gonads after the critical period during which sex is determined by incubation temperature. We thus conclude that estrogen signaling is a major driver of female-biased gene expression in the post-temperature sensitive period gonads.
                  Cover page: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
                  • Article
                  • Peer Reviewed
                  UC Santa Cruz Previously Published Works (2018)
                  We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.
                    Cover page: Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards.
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2021)
                    We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.
                      Cover page: Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizardsCreative Commons 'BY' version 4.0 license
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