Biology subjects

Lane, M.

Publications and source records attributed to Lane, M..

11 recordsLinked to original sources

bioRxiv2025

Investigating diurnal effects and joint nest defense behavior in Herring Gulls

Nest defense in birds is vital for the protection of their young, but can prove energetically costly. Birds often show plasticity in nest defense depending on factors such as threat level, mate presence, nest stage, and body condition. Such factors can vary over temporal extents ranging from a diel cycle to a breeding season or an individuals lifetime. Understanding diurnal variation in nest defense intensity can be particularly useful when studying a breeding population to help investigators minimize nest disturbance, yet few studies have explored diurnal variation in nest defense intensity. Here we investigated how nest defense by Herring Gulls (Larus smithsonianus) varies with time of day. We simulated predatory threat at 26 Herring Gull nests during four different times of day: "Early Morning" (0530-0600), "Late Morning" (1000-1030), "Afternoon" (1400-1430), and "Evening" (1900-1930). Based on previous findings of diurnal activity patterns in a Herring Gull, we predicted that nest defense intensity--measured as aggressiveness of response and latency to calm--would be greater during the early morning and late evening than at other times. Contrary to our prediction, we found that the time of day did not affect nest defense intensity in Herring Gulls. However, independent of time of day, we found that when both mates were present at the nest, aggression scores were elevated. Our results suggest that joint nest defense in Herring Gulls permits greater aggressiveness towards predators, perhaps due to division of labor or lowered risk of complete nest failure if one parent is injured or killed. Further, our results indicate that researchers can minimize nest disturbance and accompanying stress by limiting research activities at Herring Gull nests when both parents are present.

animal behavior and cognition↗

bioRxiv2025

Population and adaptation history of 739 Thlaspi arvense natural accessions

Pennycress (Thlaspi arvense) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels--including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architecture of traits is crucial for informing future breeding efforts. Here, we conducted the largest genomic and phenotypic survey of pennycress to date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing and field-collected phenotypes, we characterized the standing genetic variation underlying key agronomic traits and climate resilience. Our findings revealed multiple independent migration events to North America, with substantial genetic admixture. We identified homologs of Arabidopsis thaliana flowering-time genes that contribute to adaptation and demonstrated the agronomic benefits of winter-type pennycress. Furthermore, through multi-season field trials, we identified a genomic region containing a cluster of mTERF genes strongly associated with green canopy coverage, a critical trait for biomass retention and yield stability. These insights provide a genomic roadmap for accelerating pennycress domestication and improving its resilience to climate variability.

genomics↗

bioRxiv2024

A novel HLA Class II presentation prediction algorithm deciphers immunogenic CD4 epitopes specific to KRAS G12C

Accurate prediction of peptide presentation by HLA molecules is important for generation of effective individualized cancer vaccines and immunotherapies. While presentation prediction algorithms for HLA class I have been successfully applied in the context of such therapies, improved prediction algorithms for class II are needed. EDGE-II is a novel algorithm based on a protein large language model that has a learned allele deconvolution network trained on existing and new immunopeptidomics data. It delivers state-of-the-art performance on prediction of peptide presentation by HLA class II and immunogenicity elicited by CD4+ T-cell epitopes. In a patient with a KRAS G12C positive tumor treated with a KRAS G12C targeting immunotherapy, EDGE-II identified KRAS G12C class II neoantigens that elicited clonally expanded CD4+ T cells with cytotoxic transcriptional profiles post-vaccination. EDGE-II could play an important role in the development of effective cancer immunotherapies by elucidating an enriched understanding of the immunopeptidome.

bioinformatics↗

bioRxiv2024

MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research

While the proliferation of data-driven omics technologies has continued to accelerate, methods of identifying relationships among large-scale changes from omics experiments have stagnated. It is therefore imperative to develop methods that can identify key mechanisms among one or more omics experiments in order to advance biological discovery. To solve this problem, here we describe the network-based algorithm MENTOR - Multiplex Embedding of Networks for Team-Based Omics Research. We demonstrate MENTORs utility as a supervised learning approach to successfully partition a gene set containing multiple ontological functions into their respective functions. Subsequently, we used MENTOR as an unsupervised learning approach to identify important biological functions pertaining to the host genetic architectures in Populus trichocarpa associated with microbial abundance of multiple taxa. Moreover, as open source software designed with scientific teams in mind, we demonstrate the ability to use the output of MENTOR to facilitate distributed interpretation of omics experiments.

bioinformatics↗

bioRxiv2024

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

Leveraging the use of multiplex multi-omic networks, key insights into genetic and epigenetic mechanisms supporting biofuel production have been uncovered. Here, we introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelisation on high performance cluster systems, which enables high throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.

bioinformatics↗

bioRxiv2024

Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits

Identifying the genetic basis of traits underlying climate adaptation remains a key goal for predicting species responses to climate change, enabling the elucidation of gene targets for future climate-resilient crops. Here, we measured 14 leaf and stomatal traits under control (well-watered) and drought conditions, subsampling a diversity collection of over 1,300 Populus trichocarpa genotypes, a potential biofuel feedstock crop. Stomatal traits were correlated with the climate of origin for genotypes, such that those originating from environments subject to water deficit tended to have smaller stomata, but with higher density. Stomatal traits were also correlated with leaf morphology, with larger leaves having larger stomata and lower stomatal density mirrored in correlations to climate of origin. The direction of plastic responses - reduced stomatal size under drought - mirrors the correlations seen among genotypes with respect to the aridity of environmental origin. Genome-Wide Association Studies (GWAS) identified loci underlying trait diversity, including candidates contributing to stomatal size. We used climate of origin to predict stomatal size in genotypes with unknown trait values and found that these predicted phenotypes confirmed empirically measured allele effects. Finally, we found evidence that future climates may select for alleles contributing to decreased stomatal size, with the strength of selection depending on the availability of moisture. These findings reveal adaptive variation in stomatal and physiological traits along with underlying genetic loci, with implications for future selection and breeding - providing insights into the responses to future climate change. HighlightResearch on Populus trichocarpa reveals adaptation of physiological and stomatal traits linked to drought tolerance, with genotypes from arid regions exhibiting smaller stomata, offering insights for climate change adaptation and sustainable biofuel production.

plant biology↗

bioRxiv2022

Letrozole delays acquisition of water maze task in female BALB/c mice: possible involvement of anxiety

Letrozole, an aromatase inhibitor (AI), is used as an adjuvant therapy in estrogen receptor-positive (ER+) breast cancer patients. Similar to other AIs, it induces many side effects, including impaired cognition. Despite its negative effect in humans, results from animal models are inconsistent and suggest that letrozole can either impair or improve cognition. Here we studied effects of letrozole on cognitive behavior of adult female BALB/c mice, a relevant animal model for breast cancer studies. Mice were continuously treated with once-a-day subcutaneous (s.c.) injections of letrozole (0.1 or 0.3 mg/kg/day) or vehicle and subjected to behavioral testing starting on day 21 after treatment initiation. During the treatments, vaginal smears were taken from the mice to evaluate estrous cyclicity. Both doses of letrozole suspended cyclicity and the smears showed that the mice were in constant metestrus. Exposure to letrozole did not significantly affect response to novelty measured as a locomotor activity in open field. However, repeated testing in open field (4 days x 15 min) revealed that letrozole 0.3 mg/kg facilitated locomotor habituation (a form of non-associative learning), significantly reducing locomotor activity on 3rd and 4th day of testing. These findings suggest that certain doses of letrozole may have positive effects on cognitive behavior. Training to find a hidden platform in the Morris water maze (15 days x 4 trials), however, indicated that letrozole 0.1 mg/kg-treated mice had significant learning impairment, as, throughout the training, they swam longer times than vehicle-treated mice to reach the hidden platform. Similarly, in a probe test performed 72 h after the last day of the training, letrozole 0.1 mg/kg-treated mice did not show preference for the training platform zones. These results indicate that cognitive impairments reported by women treated with letrozole can be captured in BALB/c mice treated with clinically relevant doses of the drug. Interestingly, most of the letrozole 0.1 mg/kg-treated mice were able to learn the new platform position in reversal training and performed similar to control mice in a reversal probe test. Results of the reversal test suggest that letrozole did not completely disrupt spatial navigation but rather delayed acquisition of spatial information. The current study shows that letrozole dose dependently modulates behavioral response and that its effects are task dependent.

neuroscience↗

bioRxiv2021

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (HiC) data for all species. Abundant satellite repeats occupy the unusually long ([~]20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl configuration similar to the "bouquet" structure of meiotic cells. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

genomics↗

bioRxiv2020

Oral Pretreatment with Galantamine Effectively Mitigates the Acute Toxicity of a Supra-Lethal Dose of Soman in Cynomolgus Monkeys Post-treated with Conventional Antidotes

The present study was designed to evaluate the effectiveness of galantamine administered orally as a pre-treatment to mitigate the acute toxicity of 4.0xLD50 soman in Cynomolgus monkeys post-treated with atropine, 2-PAM, and midazolam. Pharmacokinetic experiments revealed that the oral doses of 1.5 and 3.0 mg/kg galantamine HBr were quickly absorbed and produced plasma concentrations of galantamine that generated approximately 20% to 40% reversible inhibition of blood acetylcholinesterase (AChE) activity. This degree of reversible AChE inhibition has been shown to be safe and sufficient to protect AChE from the irreversible inhibition by nerve agents, and, thereby, suppress the acute toxicity of these agents. Thus, in subsequent experiments, adult male Cynomolgus monkeys were pretreated orally with 1.5 or 3.0 mg/kg galantamine, challenged intramuscularly with 4.0xLD50, and post-treated with intramuscular injections of 0.4 mg/kg atropine, 30 mg/kg 2-PAM, and 0.32 mg/kg midazolam. All animals subjected to these treatments survived the soman. By contrast, none of the animals that were pretreated with saline and only 40% of the animals that were pretreated with pyridostigmine survived the soman challenge when post-treated with the same conventional antidotal therapy as that delivered to the galantamine-pretreated, soman-challenged monkeys. In addition, large numbers of degenerating neurons were visualized in the hippocampi of soman-challenged monkeys that had been pretreated with pyridostigmine or saline, but not in the hippocampi of animals that had been pretreated with galantamine. To our knowledge, this is the first study to demonstrate the effectiveness of clinically relevant oral doses of galantamine to prevent the acute toxicity of supra-lethal doses of soman in non-human primates.

pharmacology and toxicology↗

bioRxiv2020

Synchronized genetic activities in Alzheimer's brains revealed by heterogeneity-capturing network analysis

It is becoming increasingly evident that the efficacy of single-gene computational analyses for complex traits is nearly exhausted and future advances hinge on unraveling the intricate combinatorial interactions among multiple genes. However, the discovery of modules of genes working in concert to manifest a complex trait has been crippled by combinatorial complexity, genetic heterogeneity, and validation biases. We introduce Maestro, a novel network approach that employs a multifaceted correlation measure, which captures heterogeneity, and a rigorous validation method. Maestros utilization for Alzheimers disease (AD) reveals an expression pattern that has virtually zero probability of simultaneous expression by an individual, assuming independence. Yet this pattern is exhibited by 19.0% of AD cases and 7.3% of controls, establishing an unprecedented pattern of synchronized genetic activities in the human brain. This pattern is significantly associated with AD, with an odds ratio of 3.0. This study substantiates Maestros power for discovery of orchestrated genetic activities underlying complex traits. More generally, Maestro can be applied in diverse domains in which heterogeneity exists. HighlightsO_LISynchronized genetic activities associated with Alzheimers disease C_LIO_LINovel vector-based correlation measure that captures genetic heterogeneity C_LIO_LIEnhanced network model for revealing combinatorial genetic interactions C_LIO_LIPro-survival genetic activities associated with Alzheimers disease C_LIO_LIGeneral approach for revealing patterns in data subject to heterogeneity C_LI

bioinformatics↗

bioRxiv2019

Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities

Strongyloidiasis is caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni subsp. fuelleborni and Strongyloides fuelleborni subsp. kellyi. The zoonotic potential of S. stercoralis and the potential role of dogs in the maintenance of strongyloidiasis transmission has been a topic of interest and discussion for many years. In Australia, strongyloidiasis is prevalent in remote socioeconomically disadvantaged communities in the north of the continent. Being an isolated continent that has been separated from other regions for a long geological period, description of the diversity of Australian Strongyloides genotypes adds to our understanding of the genetic diversity within the genus. Using PCR enrichment combined with Illumina sequencing technology, we sequenced the Strongyloides SSU 18S rDNA hyper-variable I and hyper-variable IV regions using Strongyloides-specific primers, and a fragment of the mtDNA cox1 gene using primers that are broadly specific for Strongyloides sp. and hookworms. These loci were amplified from DNA extracted from Australian human and dog faeces, and one human sputum sample. Using this approach, we confirm for the first time that potentially zoonotic S. stercoralis genotypes are present in Australia, suggesting that dogs represent a potential reservoir of human strongyloidiasis in remote Australian communities. Author summaryStrongyloides stercoralis is a soil-transmitted nematode that causes the disease strongyloidiasis. Due to the autoinfective nature of this parasite, it can re-infect a host causing chronic infection. If not diagnosed and treated it can be highly detrimental to human health and has a high mortality rate. Strongyloidiasis is common in remote communities in the north of Australia and has been an issue for decades. Despite various successful intervention programs to treat human strongyloidiasis, the disease remains endemic in those communities. Here for the first time we looked at the Australian dogs potential to infect humans and found that they carry two genetically distinct strains of Strongyloides spp., one of which also infects humans. This supports the hypothesis that dogs are a potential source for human strongyloidiasis. We also found that dogs in Australia might be carrying unique haplotypes. Whether these new haplotypes are also human infective is to be confirmed by further research.

zoology↗