Bjarne Bartlett: Research

Drugs from Slugs: Advancing Therapeutic Applications of Conotoxins

Integrating data from multiple "omics" platforms, such as transcriptomics, proteomics, and metabolomics, provides a more comprehensive and systems-level understanding of conotoxin biology.

Many diseases lack effective treatments, and conotoxins offer a promising avenue for developing novel therapies for conditions such as chronic pain, epilepsy, and cancer. Conotoxins often exhibit exquisite selectivity for specific ion channels and receptors, minimizing side effects and maximizing therapeutic efficacy. The unique mechanisms of action of conotoxins can help overcome drug resistance that has become a significant challenge in treating many diseases. Genomic tools enable the rapid and efficient discovery of new conotoxin sequences, expanding the pool of potential therapeutic candidates and by analyzing the genomes of cone snails, we can gain a deeper understanding of the evolutionary processes that have shaped conotoxin diversity and identify key structural features that contribute to their pharmacological properties.

Bioinformatics Education

A Data Science Primer to Engage Undergraduate Students in Research

An explosion of data available in the life sciences has shifted the discipline towards genomics and quantitative data science research. Institutions of higher learning have been addressing this shift by modifying undergraduate curriculums resulting in an increasing number of bioinformatics courses and research opportunities for undergraduates. This study aimed to explore how a newly designed introductory bioinformatics seminar could leverage the combination of in-class instruction and independent research to build the practical research skillsets of undergraduate students beginning their research careers in the life sciences.

Plant Genomics

Revealing the interspecific breeding history of Hawaiian macadamia through transcriptome sequencing and analysis

Macadamia is an important agricultural crop in Hawaii, utilizing significant land and resources. Aging orchards, changing climate and increased pest pressure threaten the Macadamia industry in Hawaii. As orchards are replanted, genomic knowledge of crop wild relatives will be central to determining the possible role of breeding to mitigate these challenges. Macadamia tetraphyllais a crop wild relative of the economically valuable crop Macadamia integrifolia. We aimed to create a new genomic resource for macadamia agriculture in Hawai’i through new transcriptomic data for M. tetraphylla. A transcriptome assembly of M. tetraphylla was constructed from existing NCBI data along with new RNA-sequencing data collected from wild collected feral macadamia tetraphylla and putative hybrid breeding lines in Hawai’i.

Exploration of Taro breeding populations that show improved performance against diseases in Hawaiʻi

Yield is one of the important criteria used for selection in a taro breeding program. Each cross-pollination of the flowering structure could produce thousands of taro seedlings and initial evaluation of the offspring is done in unreplicated trials where only a few check cultivars are replicated. This leads to a poor estimation of the residual variances. This study explored a hierarchical Bayesian G ×E model, designed to deal with the unbalanced data from many trials. Further, a DNA fingerprint was established to distinguish breeding groups and help facilitate cultivar identification.

The Biohemistry of Wildfire Smoke in Wine

Using thiophenols, a chemical marker for smoke taint, to eliminate smoke taint during the winemaking process.

Extended exposure to wildfire smoke compromises the quality and value of wine grapes and adversely impacts aroma and flavor of wines. Wildfire impact is particularly accute on the United States West Coast which is comprised of three of the top four wine-producing states in the country. The changes in flavor and aroma have traditionally been attributed to a class of compounds known as volatile phenols, however recent research has attributed the undesirable smoky or burnt aroma and flavor notes found in smoke-tainted wines to thiophenols. These compounds are characterized by the presence of a sulfur atom in their molecular structure, specifically in a phenolic ring, giving them their name. At Oregon State University, I am researching ways to mitigate the impact of thiophenols and other smoke-related compounds on wine quality.

Bibliometrics Research

Digital technology helps remove gender bias in academia: Because citation metrics represent the attention of a narrow audience, they have a high potential for bias. Altmetrics could confer less bias for female scientists.

Journal influence on the short and long term impact of science: Both funders and practitioners desire to maximize the utilization of resources by creating metrics of quality and impact. This involves giving scores to journals (e.g., impact factor) as well as individual authors (e.g., h-index). In this study, we use citations as a proxy to quantify the relevance of different types of journal articles over time.
- Cancer Research
  
  The influence of mismatch repair deficiency on anti–PD-1 immunotherapy response: Tumors with mismatch repair deficiency (MMR-d) are characterized by sequence alterations in microsatellites and can accumulate thousands of mutations. This high mutational burden renders tumors immunogenic and sensitive to programmed cell death–1 (PD-1) immune checkpoint inhibitors.
  
  The miRNA Profile of Inflammatory Colorectal Tumors Identify TGF-β as a Companion Target for Checkpoint Blockade Immunotherapy: Recently, two intrinsic factors related to tumor genetics, microsatellite instability (MSI), and tumor mutation burden (TMB), have been linked to high response rates to checkpoint blockade drugs. These response rates led to the first tissue-agnostic approval of any cancer therapy by the FDA for the treatment of metastatic, MSI-H tumors with anti-PD-1 immunotherapy. But there are still very few studies focusing on the association of miRNAs with immune therapy through checkpoint inhibitors.
  
  Development of a RNA-Seq based prognostic signature for colon cancer: RNA-Seq data has recently been used to successfully develop prognostic signatures to predict cancer patients who will have a worse prognosis. We designed a study to ascertain whether a prognostic model, based on RNA-Seq data, would have clinical utility for predicting survival in patients with colon adenocarcinomas (COAD). Of particular interest are early stage COAD patients, for whom the benefits of adjuvant therapy are unclear.

Bjarne Bartlett PhD

Drugs from Slugs: Advancing Therapeutic Applications of Conotoxins

Integrating data from multiple "omics" platforms, such as transcriptomics, proteomics, and metabolomics, provides a more comprehensive and systems-level understanding of conotoxin biology.

Bioinformatics Education

A Data Science Primer to Engage Undergraduate Students in Research

Plant Genomics

Revealing the interspecific breeding history of Hawaiian macadamia through transcriptome sequencing and analysis

Exploration of Taro breeding populations that show improved performance against diseases in Hawaiʻi

The Biohemistry of Wildfire Smoke in Wine

Using thiophenols, a chemical marker for smoke taint, to eliminate smoke taint during the winemaking process.

Bibliometrics Research

Cancer Research

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