Biology subjects

Greer, J.

Publications and source records attributed to Greer, J..

5 recordsLinked to original sources

bioRxiv2026

The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms

The ability of cryo-electron microscopy (cryo-EM) to interrogate the atomic structure and motion of biomolecules has motivated the development of a wide range of algorithms for heterogeneity analysis. However, evaluating and comparing these methods remains challenging because ground-truth structures are generally unknown for experimental samples. Here, we introduce the 2026 Community-Wide Assessment of Heterogeneous Reconstruction Algorithms (CAHRA), a community-wide challenge centered on three benchmark datasets that probe distinct tasks in heterogeneity analysis. These include (1) compositional heterogeneity arising from mixtures of distinct protein complexes, (2) continuous conformational variability and atomic modeling, and (3) entanglement between molecular conformation and particle pose. We describe the design, construction, and validation of these datasets, as well as their use in the recently completed CAHRA Challenge.

biophysics↗

bioRxiv2025

Novel Adomaviruses Associated with Blotchy Bass Syndrome in Black Basses (Micropterus spp.)

Black bass (Micropterus spp.) are the most important warmwater game fishes in the United States. They have high socioeconomic and recreational value and support an important aquaculture industry. Since 2008, fisheries managers have been reporting the observation of hyperpigmented melanistic lesions (HPMLs) on smallmouth bass (M. dolomieu) in different ecoregions of the United States. Similar HPMLs have been observed in largemouth bass (M. nigricans) since the 1980s. Here, we report a close association between novel adomaviruses and the hallmark blotchy clinical presentation of hyperpigmented lesions on the skin smallmouth and largemouth black bass and provide evidence that satisfies Rivers postulates. The two adomaviruses are structurally and phylogenetically similar but share only 68.0% identity at aligned nucleotide sites and each has been found in only one host species to date. The manifestation of this skin disease appears to be seasonal in both species, primarily affects adults and is of unknown health consequence. Although the significance of infection to fish health remains unclear, understanding the disease ecology of these can inform biosecurity and the interjurisdictional movement of individuals. Moreover, as hyperpigmentation in other fish species is often idiopathic, our findings reframe perspectives for future investigations into this clinical presentation in other species.

microbiology↗

bioRxiv2024

Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions

Conformational heterogeneity of biological macromolecules is a challenge in single particle averaging (SPA). Current standard practice is to employ classification and filtering methods which may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and therefore explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine learning methods employing low-dimensional latent space representations. The non-linear nature of many of these methods pose challenges to their validation and interpretation, and to identifying functionally relevant conformational trajectories. We believe these methods would benefit from in-depth benchmarking using high quality synthetic data and concomitant ground truth information. Here we present a framework for the simulation and subsequent analysis with respect to ground-truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. This synthetic data can then be processed as if it were experimental data allowing aspects of standard SPA workflows, as well as heterogeneous reconstruction methods, to be compared with known ground-truth using available utilities. We will demonstrate the simulation and analysis of several such datasets and present an initial investigation into HRAs.

biophysics↗

bioRxiv2021

A meta-analysis of single visit pollination effectiveness

Many animals provide essential ecosystem services in the form of plant pollination. A rich literature documents considerable variation in the single visit pollination effectiveness of different plant visitors, but this literature has yet to be comprehensively synthesized. We conducted a hierarchical meta-analysis of 193 studies and extracted 1716 single visit effectiveness (SVE) comparisons for 252 plant species. We paired SVE data with visitation frequency data for 75 of these studies. Given the global dominance of honeybees in pollinator communities, we used these data to ask: 1) Do honeybees (Apis mellifera) and other floral visitors vary in their SVE?; 2) To what extent do plant and pollinator attributes predict the difference in SVE between honeybees and other visitors?; and 3) Is there a correlation between floral visitation frequency and SVE? We found that honeybees were significantly less effective than the most effective non-honeybee pollinator. Although not significantly different, honeybees also tended to be less effective than the mean community effectiveness. Honeybees were less effective as pollinators of crop plants and when compared to birds and other bees. Visitation frequency and pollination effectiveness were positively correlated, but this trend was largely driven by data from communities where honeybees were absent, suggesting that honeybees generally combine high visitation frequency and lower SVE. Our study demonstrates that non-honeybee floral visitors are highly effective pollinators of many crop and non-crop plants. While the high visitation frequency typically displayed by honeybees undoubtably makes them important pollinators, we show that honeybees are slightly less effective than the average pollinator and rarely the most effective pollinator of the plants they visit. As such, honeybees may be imperfect substitutes for the loss of wild pollinators and safeguarding global crop production will benefit from conservation of non-honeybee taxa. Open Research StatementAlthough we are fully committed to data transparency, we are also aware of different research teams working on related meta-analyses. As such, we prefer to wait until our paper is accepted to make data publicly available but are happy to share data upon request. Data will be permanently archived on Figshare following acceptance.

ecology↗

bioRxiv2018

Validation of an automated segmentation algorithm for lower leg MR images, applied to sodium quantification

ObjectiveTo develop and validate an automated segmentation algorithm for the lower leg using a multi-parametric magnetic resonance imaging protocol.\n\nMethodsAn automated algorithm combining active contour and intensity-based thresholding methods was developed to identify skin and muscle regions from proton Dixon MR images of the lower leg. Tissue sodium concentration was then computed using contemporaneously acquired sodium images with calibrated phantoms in the field of view. Resulting sodium concentration measurements were compared to a gold standard manual segmentation in 126 scans.\n\nResultsMost cases had no observable errors in segmentation of muscle and skin. Six cases had minor errors that were not expected to affect quantification; in the worst, 126 mm2 (2%) of a muscle area of 8,042 mm2 was misclassified. In one case the algorithm failed to separate the tibia from the muscle compartment. Correlation between automated and manual measurements of sodium concentration was R2 = 0.84 for skin, R2 = 0.99 for muscle. Additionally, the RMSE was 2.4mM for skin and 0.5mM for muscle; the observed physiological range was 8.5 to 37.4mM.\n\nConclusionFor the purpose of estimating sodium concentrations in muscle and skin compartments, the automated segmentations provided equally accurate results compared to the more time-intensive manual segmentations. Sodium quantification serves as a biomarker for disease progression, which would assist with early diagnostic treatments. The proposed algorithm will improve workflow, reproducibility, and consistency in such studies.

physiology↗