Biology subjects

Landry, S.

Publications and source records attributed to Landry, S..

5 recordsLinked to original sources

bioRxiv2025

Expanding the Global Map of Protein Post Translational Modifications with Immunoaffinity Enrichment and nDIA Analysis on the Orbitrap Astral Mass Spectrometer

Post-translational modifications (PTMs) contribute greatly to the diversity of the human proteome by affecting protein structure, function, interactions, stability, localization, and more. The study of PTMs is essential to understand various cellular functions, disease mechanisms, and aid in the development of biomarkers and design of therapeutic targets. Owing to their diversity, dynamic nature, and low stoichiometry compared to unmodified proteome counterparts, the analysis of PTMs remains challenging. In this study, immunoaffinity enrichment of PTM peptides was combined with analysis using Data Dependent Acquisition (DDA) and narrow window Data Independent Acquisition (nDIA) on the Orbitrap Astral mass spectrometer (MS) as well as comparative analysis using the Orbitrap Fusion Lumos MS for Ubiquitination, Phosphorylation, Acetylation, Succinylation, and Methylation. Human cell line and mouse tissue samples at various input peptide amounts were immuno-enriched and mass spectrometry data was acquired on both instruments to assess depth of coverage and number of novel sites identified. The study identified a total of 88,731 unique ubiquitin sites, 64,397 phosphorylation sites (43,721 phosphoserine, 8,414 phosphothreonine and 12,262 phosphotyrosine), 11,629 acetylation, 5,272 succinylation and 1,461 mono-methylation sites. In half the acquisition time, nDIA analysis of immuno-enriched samples on Orbitrap Astral MS provided much greater depth of coverage for all PTMs compared to DDA analysis on Orbitrap Fusion Lumos MS, with up to 33-fold more PTM peptides identified and quantified. Overall, the data presented in this study demonstrates the need for enrichment for PTM detection and the utility of combining antibody-based peptide capture and nDIA on the Orbitrap Astral MS as powerful tools for discovery and profiling of protein post-translational modifications in cells and tissues.

biochemistry↗

bioRxiv2024

Effects of satellite-linked telemetry tags on humpback whales in the Gulf of Maine: photographic assessment of tag sites

Hundreds of large whales have been tracked using consolidated (Type-C) satellite tags, yet there have been few studies on their impacts on whale health. In 2011, we initiated the first study designed to evaluate the effects of these tags in a baleen whale. Between 2011 and 2018, we tagged 79 North Atlantic humpback whales in the Gulf of Maine. We initially deployed commonly-used tags with an articulation between the anchor and transmitter (n=35, 2011-2012). However, evidence of breakage prompted the development and use of more robust, integrated tags (n=45). Tagged individuals were photographed immediately prior to, during and up to 11 years after tagging. They were re-encountered on an average of 41.3 days (SD=44.3), yielding 2,971 photographed sightings through 2022. An objective scoring system was developed to characterise tag site tissue responses based on photographs and to identify risk factors for prolonged healing. The initial tissue response to tagging was minimal, followed by skin loss around the tag, sometimes a degree of swelling, occasional extrusion of blubber, changes in skin colour, local depression formation, tag loss and skin healing over the tag site, sometimes with a depression remaining. At last sighting, most non-integrated and integrated tag sites exhibited small shallow skin depressions (58.8% and 66.7%, respectively). Some exhibited deeper depressions with differing adjacent skin coloration (26.5% and 15.6%, respectively) or barely detectable marks (11.8% and 15.6%, respectively). Mild swellings occasionally persisted at the tag site, but this was uncommon for both tag designs (2.9% and 2.2%, respectively). More severe tissue responses were associated with non-integrated tags and placements lower on the body. This study highlights the importance of using robust tag designs to minimise negative effects from Type-C tags. Furthermore, because tag placement was shown to affect outcome, precision equipment, experienced taggers and vessel operators are critical for optimal deployments.

ecology↗

bioRxiv2024

Before and after delisting: population dynamics of North Atlantic humpback whales over two decades in the Gulf of Maine

Whales are long-lived, slow-reproducing species that were decimated by commercial whaling. Although some populations seem close to recovery, others are challenging to assess. We studied humpback whales (Megaptera novaeangliae) in the Gulf of Maine, an area of the North Atlantic (NA) with well-documented threats. Long-term studies and mark-recapture data were used to estimate humpback whale apparent survival, abundance and population growth from 2000 through 2019. Estimates were derived from a hierarchical, Bayesian state-space model with sex, age, and random time effects on survival while accounting for individual capture probability. Abundance increased from 744 (95% CI: 726-762) in 2000 to 1,706 (95% CI: 1,639-1,771) in 2019, with 4.6% mean annual growth. However, adult males exhibited higher survival and outnumbered adult females by the end of the study. Over time, fewer calves were observed, calf survival varied and the juvenile class declined. These are rare insights into the dynamics underlying whale abundance trends and they revealed similarities to an endangered species that is declining due to environmental and human impacts. The results inform a listing change under the U.S. Endangered Species Act, a mortality event of unprecedented magnitude off the U.S and humpback whale recovery from historical whaling in the NA.

ecology↗

bioRxiv2018

Strong and lasting impacts of past global warming on baleen whale and prey abundance

AbstractThe demography of baleen whales and their prey during the past 30 thousand years was assessed to understand the effects of past rapid global warming on marine ecosystems. Mitochondrial and genome-wide DNA sequence variation in eight baleen whale and seven prey species revealed strong, ocean-wide demographic changes that were correlated with changes in global temperatures and regional oceanographic conditions. In the Southern Ocean baleen whale and prey abundance increased exponentially and in apparent synchrony, whereas changes in abundance varied among species in the more heterogeneous North Atlantic Ocean. The estimated changes in whale abundance correlated with increases in the abundance of prey likely driven by reductions in sea-ice cover and an overall increase in primary production. However, the specific regional oceanographic environment, trophic interactions and species ecology also appeared to play an important role. Somewhat surprisingly the abundance of baleen whales and prey continued to increase for several thousand years after global temperatures stabilized. These findings warn of the potential for dramatic, long-term effects of current climate changes on the marine ecosystem.\n\nOne Sentence SummaryThe effects of past global warming on marine ecosystems were drastic, system-wide and long-lasting.

evolutionary biology↗

bioRxiv2018

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

HighlightsO_LIMitochondrial monophyly is commonly employed to define evolutionary significant units.\nC_LIO_LIMonophyly may be caused by insufficient sampling or a recent common ancestor.\nC_LIO_LIMitogenomic studies are generally based on few samples and prone to sampling issues.\nC_LIO_LIExpanded mitogenome sampling negates previous monophyly in fin whales.\nC_LI\n\nAbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively \"trivial\" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC=\"FIGDIR/small/488130v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1e38e54org.highwire.dtl.DTLVardef@9533eborg.highwire.dtl.DTLVardef@183b5b5org.highwire.dtl.DTLVardef@eae09_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗