Biology subjects

Pitchford, J. W.

Publications and source records attributed to Pitchford, J. W..

8 recordsLinked to original sources

bioRxiv2024

Cell size and selection for stress-induced binary cell fusion

In unicellular organisms, sexual reproduction typically begins with the fusion of two cells (plasmogamy) followed by the fusion of their two haploid nuclei (karyogamy) and finally meiosis. Most work on the evolution of sexual reproduction focuses on the benefits of the genetic recombination that takes place during meiosis. However, the selection pressures that may have driven the early evolution of binary cell fusion, which sets the stage for the evolution of karyogamy by bringing nuclei together in the same cell, have seen less attention. In this paper we develop a model for the coevolution of cell size and binary cell fusion rate. The model assumes that larger cells experience a survival advantage from their larger cytoplasmic volume. We find that under favourable environmental conditions, populations can evolve to produce larger cells that undergo obligate binary cell fission. However, under challenging environmental conditions, populations can evolve to subsequently produce smaller cells under binary cell fission that nevertheless retain a survival advantage by fusing with other cells. The model thus parsimoniously recaptures the empirical observation that sexual reproduction is typically triggered by adverse environmental conditions in many unicellular eukaryotes and draws conceptual links to the literature on the evolution of multicellularity. Author summarySexual reproduction is commonly observed, both in eukaryotic microorganisms and in higher multicellular organisms. Sex has evolved despite numerous apparent costs, including investment in finding a partner and the energetic requirements of sexual reproduction. Binary cell fusion is a process that sets the stage for sexual reproduction by bringing nuclei from different cells into contact. Here, we provide a mathematical explanation of the advantage conferred by binary cell fusion due to increased cell mass. We show that when unicellular organisms have the option to invest in either cell fusion or cell mass, they can evolve to fuse together as rapidly as possible in the face of adverse environments, instead of increasing their mass. These results are consistent with the empirical observation that sexual reproduction is often triggered by environmental stress in unicellular eukaryotes. Our results imply an advantage to cell fusion, which helps to shed light on the early evolution of sexual reproduction itself.

evolutionary biology↗

bioRxiv2023

Complex epistatic interactions between ELF3, PRR9, and PRR7 regulates the circadian clock and plant physiology

Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we firstly employed mathematical modelling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modelling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship amongst plant circadian genes.

plant biology↗

bioRxiv2023

Increased dispersal explains increasing local diversity with global biodiversity declines

The narrative of biodiversity decline in response to human impacts is overly simplistic because different biodiversity metrics show different trajectories at different spatial scales. It is also debated whether human-caused biodiversity changes lead to subsequent, accelerating change (cascades) in ecological communities, or alternatively build increasingly robust community networks with decreasing extinction rates and reduced invasibility. Mechanistic approaches are needed that simultaneously reconcile different metrics of biodiversity change, and explore the robustness of communities to further change. We develop a trophically-structured, mainland-archipelago metacommunity model of community assembly. Varying the parameters across model simulations shows that local alpha diversity (the number of species per island) and regional gamma diversity (the total number of species in the archipelago) depend on both the rate of extirpation per island and on the rate of dispersal between islands within the archipelago. In particular, local diversity increases with increased dispersal and heterogeneity between islands, but regional diversity declines because the islands become biotically similar and local one-island and few-island species are excluded (homogenisation, or reduced beta diversity). This mirrors changes observed empirically: real islands have gained species (increased local and island-scale community diversity) with increased human-assisted transfers of species, but global diversity has declined with the loss of endemic species. However, biological invasions may be self-limiting. High-dispersal, high local-diversity model communities become resistant to subsequent invasions, generating robust species-community networks unless dispersal is extremely high. A mixed-up world is likely to lose many species, but the resulting ecological communities may nonetheless be relatively robust. Significance StatementBiodiversity is commonly regarded as threatened due to human impacts, but biodiversity metrics at different scales produce contradictory results. A framework is needed that can reproduce and connect these results across scales and address whether biodiversity change will inexorably accelerate following perturbation or become self-limiting as new ecological communities form. We address this challenge by constructing size-structured model communities using a mainland/island paradigm and tracking diversity at different scales. Our simulations reproduce the literatures discrepancy across scales and provide new insight. Ecological communities (islands) gain species with increasing (human-assisted) dispersal, but global diversity declines with the consequent loss of endemic species. Communities also become less invasible as dispersal increases, suggesting that human-mediated dispersal favours robust communities that resist subsequent change.

ecology↗

bioRxiv2023

Parthenogenesis, sexual conflict and the evolution of oogamy

In the face of varying environments, organisms exhibit a variety of reproductive modes, from asexuality to obligate sexuality. Should reproduction be sexual, the morphology of the sex cells (gametes) produced by these organisms has important evolutionary implications; these cells can be the same size (isogamy), one larger and one smaller (anisogamy), and finally the larger cell can lose its capacity for motility (oogamy, the familiar sperm-egg system). Understanding the origin of the sexes, which lies in the types of gametes they produce, thus amounts to explaining these evolutionary transitions. Here we extend classic results in this area by exploring these transitions in a model in which organisms can reproduce both sexually and asexually (a reproductive mode present in many algae). In particular, we investigate the co-evolution of gamete cell size with fertilization rate, which is a proxy for motility and pheromone production but usually held constant in such models. Using adaptive dynamics generalized to the case of switching environments, we find that isogamy can evolve to anisogamy through evolutionary branching, and that anisogamy can evolve to oogamy or suppressed pheromone production through a further branching driven by sexual conflict. We also derive analytic conditions on the model parameters required to arrest evolution on this isogamy-oogamy trajectory, with low fertilization rates and stochastically switching environments stabilizing isogamy under a bet-hedging strategy, and low fertilization costs stabilizing anisogamy and pheromone production.

evolutionary biology↗

bioRxiv2023

The evolution of parthenogen fertilization rates in switching environments: from facultative cell-fusion to oogamy

Organisms with external fertilisation exhibit a broad range of reproductive modes, from simple parthenogenesis to sexual reproduction encompassing isogamy, anisogamy, and oogamy, and including environmentally-mediated facultative sex. Here we develop a unifying mathematical model which explains the emergence of these modes via the coevolution of fertilization rate and cell size. Using a minimal assumption that survival is dependent on cell mass, and by carefully accounting for biological and evolutionary time scales, we find two distinct evolutionary outcomes: high fertilization rate (obligate sexuality) is selected when costs to cell fusion are low, while zero fertilization rate (obligate asexuality) is selected for when these costs are high. Surprisingy, in high fertilization rate scenarios evolving populations can transition from isogamy to anisogamy and oogamy via evolutionary branching. Furthermore, in variable environments we show that, without phenotypic plasticity, intermediate fertilization rates and isogamy can be maintained through bet-hedging. Allowing phenotypic plasticity can give rise to facultative sex; sexual reproduction in harsh environmental conditions, and asexuality in more benign conditions. These results parsimoniously explain a large range of empirically observed parthenogen reproduction strategies, and offer an hypothesis for the origin of binary cell fusion, a key step in the evolution of syngamy and sexual reproduction itself.

evolutionary biology↗

bioRxiv2021

Mathematical modelling of activation-induced heterogeneity reveals cell state transitions underpinning macrophage responses to LPS

Despite extensive work on macrophage heterogeneity, the mechanisms driving activation induced heterogeneity (AIH) in macrophages remain poorly understood. Here, we use two in vitro cellular models of LPS-induced tolerance (bone marrow-derived macrophages or BMDMs and RAW 264.7 cells), single-cell protein measurements, and mathematical modelling to explore how AIH underpins primary and secondary responses to LPS. We measure expression of TNF, IL-6, pro-IL-1{beta}, and NOS2 and demonstrate that macrophage community AIH is dependent on LPS dose. We show that altered AIH kinetics in macrophages responding to a second LPS challenge underpin hypo-responsiveness to LPS. These empirical data can be explained by a mathematical 3-state model including negative, positive, and non-responsive states (NRS), but they are also compatible with a 4-state model that includes distinct reversibly NRS and non-responsive permanently states (NRPS). Our mathematical model, termed NoRM (Non-Responsive Macrophage) model identifies similarities and differences between BMDM and RAW 264.7 cell responses. In both cell types, transition rates between states in the NoRM model are distinct for each of the tested proteins and, crucially, macrophage hypo-responsiveness is underpinned by changes in transition rates to and from NRS. Overall, our findings provide support for a critical role for phenotypically negative macrophage populations as an active component of AIH and primary and secondary responses to LPS. This reveals unappreciated aspects of cellular ecology and community dynamics associated with LPS-driven training of macrophages.

immunology↗

bioRxiv2021

Spatial point pattern analysis identifies mechanisms shaping the skin parasite landscape in Leishmania donovani infection

Increasing evidence suggests that infectiousness of hosts carrying parasites of the Leishmania donovani complex, the causative agents of visceral leishmaniasis, is linked to parasite repositories in the host skin. However, a detailed understanding of the dispersal and dispersion of these obligatory-intracellular parasites and their host phagocytes in the skin is lacking. Using endogenously fluorescent parasites as a proxy, we apply image analysis combined with spatial point pattern models borrowed from ecology to characterize dispersion of parasitized myeloid cells (including ManR+ and CD11c+ cells) and predict dispersal mechanisms in a previously described immunodeficient model of L. donovani infection. Our results suggest that after initial seeding of infection in the skin, heavily parasite-infected myeloid cells are found in patches that resemble innate granulomas. Spread of parasites from these initial patches subsequently occurs through infection of recruited myeloid cells, ultimately leading to self-propagating networks of patch clusters. This combination of imaging and ecological pattern analysis to identify mechanisms driving the skin parasite landscape offers new perspectives on myeloid cell behavior following parasitism by L. donovani and may also be applicable to elucidating the behavior of other intracellular tissue-resident pathogens and their host cells.

microbiology↗

bioRxiv2020

Systematic functional analysis of Leishmania protein kinases identifies regulators of differentiation and survival

Differentiation between distinct stages is fundamental for the life cycle of intracellular protozoan parasites and for transmission between hosts, requiring stringent spatial and temporal regulation. Here we applied kinome-wide gene deletion and gene tagging in Leishmania mexicana promastigotes to define protein kinases with life cycle transition roles. Whilst 162 were dispensable, 44 protein kinase genes were refractory to deletion in promastigotes and are likely core genes required for parasite replication. Phenotyping of pooled gene deletion mutants using bar-seq and projection pursuit clustering revealed functional phenotypic groups of protein kinases involved in differentiation from metacyclic promastigote to amastigote, growth and survival in macrophages and mice, colonisation of the sand fly and motility. This unbiased interrogation of protein kinase function in Leishmania allows targeted investigation of organelle-associated signalling pathways required for successful intracellular parasitism.

microbiology↗