Biology subjects
Publications and source records attributed to Parr, M..
Viruses co-evolve with their hosts and adapt various genomic level strategies to ensure their fitness. Previous studies have demonstrated that viruses share high dimensional silent patterns with their hosts. In this study, based on a novel computational measure, we demonstrated for the first time that this high dimensional information encodes regulatory codes related to viral tropism.
While there is growing interest in sustainable management practices to mitigate the biodiversity impacts of agriculture, logging, and other critical societal needs, implementation of such practices is often hindered by a lack of cost-effective, fine-scale metrics that directly link management actions to conservation outcomes. We introduce the BirdsPlus Index (BPI), a novel, scalable approach that integrates monitoring data, remote sensing, and conservation-weighted species scores to quantify deviations of observed site scores from spatiotemporally explicit expectations. Using nearly 29,000 recordings from the Macaulay Library, we generated acoustic checklists with the Merlin and BirdNET sound identification models under multiple detection thresholds. We matched these acoustic checklists with species-specific conservation values (BirdsPlus species scores), then trained random forest models to predict total, site-level biodiversity (the sum of these species scores) given environmental and effort covariates. The resulting model also enabled us to map expected BirdsPlus site scores across the landscape. These scores integrate information on species conservation status, ecological roles, and phylogenetic and functional uniqueness. BPI was calculated as the residual between observed and expected site scores, thereby providing a direct site-level measure of conservation value. Across 30 sites, we found that BPI values were consistent across acoustic models and detection thresholds, with high-scoring sites supporting regionally uncommon breeders and habitat specialists. While acoustic- and observer-based (eBird) models showed differing spatial patterns, both aligned with known ecological drivers such as urban density, elevation, and wetland cover. Our results demonstrate that acoustic checklists can be used to model expected biodiversity over time and space, and that the BPI provides a robust, interpretable metric for evaluating the ecological integrity of local sites. Beyond its immediate application to conservation planning, this framework lays the foundation for global, real-time biodiversity monitoring that leverages automated acoustic classifiers, citizen science, and remote sensing to integrate conservation value into development and management decisions.
A growing awareness, now enshrined in the Kunming-Montreal Global Biodiversity Framework, of the need to monitor biodiversity effectively at scale has led to a proliferation of novel solutions for doing so. Although global biodiversity encompasses all life, from tiny nitrogen-fixing bacteria to emergent rainforest trees, birds have several characteristics that make them a frequent focus of such monitoring efforts. In particular, birds frequently give diagnostic, species-specific vocalizations that simplify monitoring, they perform a number of critical ecosystem services, they are widely distributed in most ecosystems with strong representation on all continents, and the basic ecology, conservation status, populations, and distributions of many species is well known; birds thus provide a window into the underlying health and habitats of the systems under study. How best to summarize biodiversity monitoring results is a research question that has led to the development of approaches that incorporate species IUCN Red List threat assessments into site-level biodiversity scores. Notably, birds vocal behavior means that they can be effectively surveyed at scale with passive acoustic monitoring, and the potential to link such monitoring with automated identification and therefore quickly generate site-level biodiversity scores is an appealing approach to implement rigorous evaluations of global biodiversity. Yet, while many of the worlds birds are suffering worrisome population declines, the vast majority of species (78%) are still ranked "Least Concern" by the Red List. In an effort to develop a species scoring system that would be more conducive to such site-level valuations, we integrated key databases of species population status assessments, exposure to known vulnerability factors, and their functional and phylogenetic uniqueness to provide quantitative summaries of their conservation significance. We augmented these databases with two novel data sets available for most of the worlds birds: quantitative measurements of migration distances, and species-level phylogenetic and functional uniqueness values comparing each species to those it co-occurs with throughout its range. While the resulting BirdsPlus species scores also inherently reflect our own scientific expertise and judgement, our approach is transparent, dynamic, easily updated, and readily modified by users with different goals or values.
Polyproline sequences (XPPX) stall ribosomes, thus being deleterious for all living organisms. In bacteria, translation elongation factor P (EF-P) plays a crucial role in overcoming such arrests. 12% of eubacteria possess an EF-P paralog - YeiP (EfpL) of unknown function. Here, we functionally and structurally characterize EfpL from Escherichia coli and demonstrate its yet unrecognized role in the translational stress response. Through ribosome profiling, we analyzed the EfpL arrest motif spectrum and discovered additional stalls beyond the canonical XPPX motifs at single-proline sequences (XPX), that both EF-P and EfpL can resolve. Notably, the two factors can also induce pauses. We further report that, contrary to the housekeeping EF-P, EfpL can sense the metabolic state of the cell, via lysine acylation. Together, our work uncovers a new player in ribosome rescue at proline-containing sequences, and provides evidence that co-occurrence of EF-P and EfpL is an evolutionary driver for higher bacterial growth rates.
One third of the human proteome are membrane proteins. They are particularly vulnerable to misfolding, often requiring assistance by molecular chaperones. Calnexin (CNX), one of the most abundant ER chaperones, plays an important role in membrane protein biogenesis and engages clients via its sugar-binding lectin domain. Using mass spectrometric analyses, we show that Calnexin (CNX) interacts with a large number of non-glycosylated membrane proteins, suggesting additional binding modes. We find that misfolded membrane proteins are preferentially bound by CNX and that CNX uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by CNX and identify sequence motifs within the CNX TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of CNX. Together, this study reveals a widespread role of CNX client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.