Biology subjects

Parham, J.

Publications and source records attributed to Parham, J..

6 recordsLinked to original sources

bioRxiv2026

The life cycle of an archaeon with multiple membranes

Many prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, only one archaeon, Ignicoccus hospitalis, is known to have an outer and inner membrane. Here, in exploring Ignicoccus cell division, we show by expansion microscopy that I. hospitalis uses a contractile CdvA-ESCRT-III ring to repeatedly constrict and cut its inner membrane in a way that yields clusters containing multiple cytoplasms within a shared periplasm. The outer bounding membrane then bursts to release the progeny cells, which regain their parental cell architecture via a membrane duplication process. Furthermore, this life cycle appears conserved across Ignicoccus strains, even though the precise timing of events changes. Taken together, these data show that Ignicoccus cells propagate by undergoing dynamic changes in their architecture as they transit between single and multi-cellular states.

cell biology↗

bioRxiv2026

Bridging the lipid divide: archaeal ESCRT-III binds phosphoinositol and polarises the cytokinetic membrane

All cells remodel their membranes to divide. The highly conserved ESCRT-III system forms contractile polymers which, through direct interactions with membrane lipids, remodel membranes across the tree of life. In exploring how ESCRT-III divides the chemically and structurally unique archaeal membrane, we reveal that the homologue CdvB1 is required for the establishment of a distinct membrane domain within the division bridge of Sulfolobus acidocaldarius, associated with an accumulation of membrane-spanning inositol phosphate lipids. We show that CdvB1 associates with phosphoinositides in vitro and that this interaction aids cytokinesis in vivo. Together, we suggest that although eukaryotes inherited their membrane lipids from bacteria during eukaryogenesis, key features of the ESCRT-III:membrane interface that allow these polymers to bind, organise, and remodel eukaryotic membranes, may originate in archaea.

cell biology↗

bioRxiv2025

An Asgard archaeon with internal membrane compartments

The emergence of eukaryotes from a merger between an archaeon and a bacterial cell [~]two billion years ago involved a profound change in cellular organisation. While the order in which different features of the eukaryotic cell arose remains a matter of controversy1-3, close archaeal relatives of eukaryotes have recently been identified that possess homologues of eukaryotic trafficking machinery4,5 and a complex cell architecture6,7. The members of this phylum, the Asgard archaea (syn. Prometheoarchaeota) described so far, however, lack internal membrane-bound compartments, and therefore have shed little light on origins of the hallmark eukaryotic endomembrane system. Here we report the cell biological analysis of a member of the Heimdallarchaeia, Candidatus Y. umbracryptum in enriched mixed microbial communities. Possessing a small genome encoding few homologues of eukaryotic membrane remodelling machinery8, Ca. Y. umbracryptum cells in late-stage cultures resemble previously described Asgard archaea with extensive cellular protrusions. Surprisingly, during early stages of culture growth Ca. Y. umbracryptum cells have fewer protrusions but possess numerous intracellular vesicles, most of which have a luminal surface that morphologically resembles the outer coat of the plasma membrane. These data alter our view of eukaryogenesis by identifying a close archaeal relative of eukaryotes with an endomembrane system, whose appearance changes with cell state.

cell biology↗

bioRxiv2025

Temporal and spatial coordination of DNA segregation and cell division in an archaeon.

Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segregation and division are mechanistically coupled in archaeal relatives of eukaryotes, which lack CDK/Cyclins. Using live cell imaging we first describe the series of sequential changes in DNA organisation that accompany cell division in Sulfolobus, which computational modelling shows likely aid genome segregation. Through a perturbation analysis we identify a regulatory checkpoint which ensures that the compaction of the genome into two spatially segregated nucleoids only occurs once cells have assembly a division ring - which also defines the axis of DNA segregation. Finally, we show that DNA compaction and segregation depends, in part, on a ParA homologue, SegA, and its partner SegB, whose absence leads to bridging DNA. Taken together, these data show how regulatory checkpoints like those operating in eukaryotes aid high-fidelity division in an archaeon.

cell biology↗

bioRxiv2022

Comparison of Two Individual Identification Algorithms for Snow Leopards (Panthera uncia) after Automated Detection

1. Photo-identification of individual snow leopards (Panthera uncia) is the primary technique for density estimation for the species. A high volume of images from multiple projects, combined with pre-existing historical catalogs, has made identifying snow leopard individuals within the images cost- and time-intensive. 2. To speed the classification among a high volume of photographs, we trained and evaluated image classification methods for PIE v2 (a triplet loss network), and we compared PIEs accuracy to the HotSpotter algorithm (a SIFT based algorithm). Analyzed data were collected from a curated catalog of free-ranging snow leopards photographed across years (2012-2019) in Afghanistan and from samples in captivity provided by zoos from Finland, Sweden, Germany, and the United States. 3. Results show that PIE outperforms HotSpotter. We also found weaknesses in the initial PIE model, like a minor amount of background matching, which was addressed, although likely not fully resolved, by applying background subtraction (BGS) and left-right mirroring (LR) methods. The PIE BGS LR model combined with Hotspotter showed a Rank-1: 85%, Rank-5: 95%, Rank-20: 99%. 4. Overall, our results recommend implementing PIE v2 simultaneously with HotSpotter on Whiskerbook.org.

bioinformatics↗

bioRxiv2021

Comparison of Three Individual Identification Algorithms for Sperm Whales (Physeter macrocephalus) after Automated Detection

Photo-identification of individual sperm whales (Physeter macrocephalus) is the primary technique for mark-recapture-based population analyses for the species The visual appearance of the fluke -- with its distinct nicks and notches -- often serves as the primary visual differentiator, allowing humans to make recorded sightings of specific individuals. However, the advent of digital photography and the significant increase in volume of images from multiple projects in combination with pre-existing historical catalogs has made applying the method more challenging.with the required human labor for de-duplication (reduction of Type II errors) and reconciliation of sightings between large datasets too cost- and time-prohibitive. To address this, we trained and evaluated the accuracy of PIE v2 (a triplet loss network) along with two existing fluke trailing edge-matching algorithms, CurvRank v2 and Dynamic Time Warping (DTW), as a mean to speed comparison among a high volume of photographs. Analyzed data were collected from a curated catalog of well-known sperm whales sighted across years (2005-2018) off the island of Dominica. The newly-trained PIE model outperformed the older CurvRank and DTW algorithms, and PIE provided the following top-k individual ID matching accuracy on a standard min-3/max-10 sighting training data set: Rank-1: 87.0%, Rank-5: 90.5%, and Rank-12: 92.5%. An essential aspect of PIE is that it can learn new individuals without network retraining, which can be immediately applied in the presence of (and for the resolution of) duplicate individuals in overlapping catalogs. Overall, our results recommend the use of PIE v2 and CurvRank v2 for ID reconciliation in combination due to their complementary performance.

ecology↗