Biology subjects

Boardman, L.

Publications and source records attributed to Boardman, L..

4 recordsLinked to original sources

bioRxiv2026

Development of molecular markers for western honey bee (Apis mellifera L.) subspecies of regulatory concern in the United States

Rapid, accurate and cost-effective identification of Apis mellifera subspecies is needed for subspecies of regulatory concern. We designed and validated subspecies markers based on single nucleotide polymorphisms (SNP) on mitochondrial cytochrome b (Cytb) and NADH dehydrogenase 4 (ND4) genes. We used a combination of established and novel real-time qPCRs in a stepwise series, with increasing discrimination power, to (1) differentiate honey bees of African (A-lineage) ancestry from those of other lineages (Cytb SNP #1), (2) identify African-derived honey bees (AHBs) (Cytb SNP #2), and (3) detect A. m. capensis exclusively in the bees indigenous region of South Africa (ND4 SNP). We also developed a restriction fragment length polymorphism assay targeting a SNP on the NADH dehydrogenase 2 (ND2 RFLP) gene to detect the specific mitochondrial A-lineage clade. These assays allow for reliable time- and cost-effective results that provide increased accuracy on subspecies assignation.

ecology↗

bioRxiv2022

Nucleosome sensitivity distinguishes colon polyps based on their transformation status

One of the keys to eliminating the personal and financial costs of cancer lies in the early detection of the disease. Consequently, effective cancer interventions increasingly rely on our understanding of the earliest cellular and nuclear events that lead to oncogenic transformation. Colorectal cancer, the third most prevalent cancer in the United States, results from the transformation of polyps. Our group demonstrated that the alteration of chromatin organization is a pivotal event in this oncogenic transformation. Here, we analyze the differences of the nucleosomal sensitivity to mocroccocal nuclease (MNase) between histopathologically matched pre-cancerous polyps taken from patients that did not develop cancer (cancer-free polyps, CFP) and those that did develop cancer (cancer-associated polyps, CAP). We produced high-resolution nucleosome distribution and nucleosome sensitivity maps from each of the five CFP patient samples and three CAP patient samples. We show that nucleosome distribution is largely invariant between CFP and CAP samples. Nucleosome sensitivity, however, is a powerful analysis that can identify genomic locations that distinguish CFP from CAP. We have identified more than 1000 genomic locations with altered nucleosomal sensitivity that discriminate between CAP and CFP. Furthermore, we show that these genomic locations with altered nucleosomal sensitivity between CFP and CAP include genes that play critical roles in oncogenic transformation. We propose that nucleosome sensitivity serves as a robust biomarker indicating the oncogenic potential of precancerous polyps and could be used for the early detection of polyps that will become cancerous.

molecular biology↗

bioRxiv2022

Novel eDNA approaches to monitor Western honey bee (Apis mellifera) microbial and arthropod communities

Pests and pathogens are a continuous threat to the health of Western honey bees Apis mellifera L. Monitoring honey bee colonies for arthropod pests, disease-causing bacteria and fungi, and early detection of new invasions is essential to maintain the pollination services provided by honey bees. Here, we investigated the feasibility of using eDNA metabarcoding to detect honey bee pests and pathogens in their hives and across their foraging environment. We sampled 13 different surfaces within and outside hives from our test apiary to determine where the most informative eDNA could be obtained. Furthermore, we compared two main eDNA collection techniques - wiping surfaces with moistened forensic swabs and using a spray/wash technique that washed surface DNA into a bucket, before collecting the DNA on a filter. We used DNA metabarcoding with universal primer sets to target arthropod, bacterial and fungal communities. Our results showed that most surfaces yielded usable DNA, and that results of the swabs and spray/wash methods were similar when they could be applied to the same surface. We were able to detect DNA from the small hive beetle (Aethina tumida), Varroa destructor mites and European foulbrood (Melissococcus plutonius), all of which matched our visual observations of clinical signs of these pests and pathogens in the hives we tested. DNA from some species was location specific, which has implications for using eDNA as a monitoring tool. Collectively, our data show that eDNA metabarcoding can accurately detect DNA from arthropods and microbes honey bees contact and has the potential to provide information on disease and pest incidence, Apis species identity, and A. mellifera subspecies identity of the colony and/or apiary. In sum, eDNA metabarcoding can be used as a comprehensive molecular predictor tool for colony health surveys.

ecology↗

bioRxiv2018

Distinct Microbes, Metabolites, and Ecologies Define the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers

Background\n\nThe link between colorectal cancer (CRC) and the gut microbiome has been established, but the specific microbial species and their role in carcinogenesis remain controversial. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.\n\nMethods\n\nWe collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject sample correlation, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.\n\nResults\n\nWe demonstrate distinct roles for microbes in dMMR and pMMR CRC. Sulfidogenic Fusobacterium nucleatum and hydrogen sulfide production were significantly enriched in dMMR CRC, but not pMMR CRC. We also surveyed the butyrate-producing microbial species, but did not find a significant difference in predicted or actual butyrate production between dMMR and pMMR microbial communities. Finally, we observed that dMMR microbial communities were predicted to be less stable than pMMR microbial communities. Community stability may play an important role in CRC development, progression, or immune activation within the respective MMR subtypes.\n\nConclusions\n\nIntegrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.

cancer biology↗