ORCID Profile
0000-0003-0587-0251
Current Organisation
University of Melbourne
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Biological Mathematics | Microbial Ecology | Microbiology | Soil Chemistry (excl. Carbon Sequestration Science)
Management of Water Consumption by Plant Production | Climate Change Mitigation Strategies | Physical and Chemical Conditions of Water in Marine Environments | Expanding Knowledge in the Biological Sciences | Carbon and Emissions Trading | Expanding Knowledge in the Mathematical Sciences |
Publisher: Proceedings of the National Academy of Sciences
Date: 05-08-2016
Abstract: The ability to navigate is a hallmark of living systems, from single cells to higher animals. Searching for targets, such as food or mates in particular, is one of the fundamental navigational tasks many organisms must execute to survive and reproduce. Here, we argue that a recent surge of studies of the proximate mechanisms that underlie search behavior offers a new opportunity to integrate the biophysics and neuroscience of sensory systems with ecological and evolutionary processes, closing a feedback loop that promises exciting new avenues of scientific exploration at the frontier of systems biology.
Publisher: CSIRO Publishing
Date: 14-04-2022
DOI: 10.1071/MA22008
Abstract: Corals and their photosynthetic endosymbiotic algae (Symbiodiniaceae) produce a strong autofluorescent signal that spans the visible to near-infrared (NIR) spectrum. However, this broad-spectrum emission hinders the use of fluorescence in situ hybridisation (FISH) for the study of bacterial heterogeneity within the different niches of corals and Symbiodiniaceae, because FISH fluorophores also fluoresce within the visible to NIR spectrum. A solution to this impediment is to use fluorescence lifetime imaging microscopy (FLIM). The ‘lifetime’ property of fluorophores is a feature that enables s le (e.g. coral/Symbiodiniaceae) autofluorescence to be distinguished from FISH-labelled bacteria. In this manner, the location of bacteria around and within Symbiodiniaceae can be quantified along with their identity and spatial distribution. Furthermore, the ‘lifetime’ of the host and associated microbe cellular autofluorescence can be analysed in terms of endogenous fluorophore composition (e.g. metabolic co-factors, aromatic amino acids) and serves as information for symbiotic versus parasitic host-microbe association.
Publisher: American Physical Society (APS)
Date: 27-12-2012
Publisher: Springer Science and Business Media LLC
Date: 16-11-2015
DOI: 10.1038/NRMICRO3567
Abstract: Motility is one of the most dynamic features of the microbial world. The ability to swim or crawl frequently governs how microorganisms interact with their physical and chemical environments, and underpins a myriad of microbial processes. The ability to resolve temporal dynamics through time-lapse video microscopy and the precise control of the physicochemical microenvironment afforded by microfluidics offer powerful new opportunities to study the many motility adaptations of microorganisms and thereby further our understanding of their ecology. In this Review, we outline recent insights into the motility strategies of microorganisms brought about by these techniques, including the hydrodynamic signature of microorganisms, their locomotion mechanics, chemotaxis, their motility near and on surfaces, swimming in moving fluids and motility in dense microbial suspensions.
Publisher: The Royal Society
Date: 07-2015
Abstract: Groups of eukaryotic cilia and flagella are capable of coordinating their beating over large scales, routinely exhibiting collective dynamics in the form of metachronal waves. The origin of this behaviour—possibly influenced by both mechanical interactions and direct biological regulation—is poorly understood, in large part due to a lack of quantitative experimental studies. Here we characterize in detail flagellar coordination on the surface of the multicellular alga Volvox carteri , an emerging model organism for flagellar dynamics. Our studies reveal for the first time that the average metachronal coordination observed is punctuated by periodic phase defects during which synchrony is partial and limited to specific groups of cells. A minimal model of hydrodynamically coupled oscillators can reproduce semi-quantitatively the characteristics of the average metachronal dynamics, and the emergence of defects. We systematically study the model's behaviour by assessing the effect of changing intrinsic rotor characteristics, including oscillator stiffness and the nature of their internal driving force, as well as their geometric properties and spatial arrangement. Our results suggest that metachronal coordination follows from deformations in the oscillators' limit cycles induced by hydrodynamic stresses, and that defects result from sufficiently steep local biases in the oscillators' intrinsic frequencies. Additionally, we find that random variations in the intrinsic rotor frequencies increase the robustness of the average properties of the emergent metachronal waves.
Publisher: The Royal Society
Date: 14-11-2018
Abstract: In group-living species, social stability is an important trait associated with the evolution of complex behaviours such as cooperation. While the drivers of stability in small groups are relatively well studied, little is known about the potential impacts of unstable states on animal societies. Temporary changes in group composition, such as a social group splitting and recombining (i.e. a disturbance event), can result in in iduals having to re-establish their social relationships, thus taking time away from other tasks such as foraging or vigilance. Here, we experimentally split socially stable groups of captive zebra finches ( Taeniopygia guttata ), and quantified the effects of repeated disturbance events on (1) group foraging efficiency, and (2) co-feeding associations when subgroups were recombined. We found that the efficiency of groups to deplete a rich, but ephemeral, resource patch decreased after just a single short disturbance event. Automated tracking of in iduals showed that repeated disturbances reduced efficiency by causing social relationships to become more differentiated and weaker, resulting in fewer in iduals simultaneously accessing the patch. Our experiment highlights how short-term disturbances can severely disrupt social structure and group functionality, revealing potential costs associated with group instability that can have consequences for the evolution of animal societies.
Publisher: Wiley
Date: 13-03-2018
DOI: 10.1111/BRV.12408
Publisher: Wiley
Date: 16-04-2018
Publisher: The Royal Society
Date: 10-2018
Abstract: Despite evidence for a hydrodynamic origin of flagellar synchronization between different eukaryotic cells, recent experiments have shown that in single multi-flagellated organisms, coordination hinges instead on direct basal body connections. The mechanism by which these connections lead to coordination, however, is currently not understood. Here, we focus on the model biflagellate Chlamydomonas reinhardtii , and propose a minimal model for the synchronization of its two flagella as a result of both hydrodynamic and direct mechanical coupling. A spectrum of different types of coordination can be selected, depending on small changes in the stiffness of intracellular couplings. These include prolonged in-phase and anti-phase synchronization, as well as a range of multi-stable states induced by spontaneous symmetry breaking of the system. Linking synchrony to intracellular stiffness could lead to the use of flagellar dynamics as a probe for the mechanical state of the cell.
Publisher: The Royal Society
Date: 2016
Abstract: Many chemotactic bacteria inhabit environments in which chemicals appear as localized pulses and evolve by processes such as diffusion and mixing. We show that, in such environments, physical limits on the accuracy of temporal gradient sensing govern when and where bacteria can accurately measure the cues they use to navigate. Chemical pulses are surrounded by a predictable dynamic region, outside which bacterial cells cannot resolve gradients above noise. The outer boundary of this region initially expands in proportion to the square root of time before rapidly contracting. Our analysis also reveals how chemokinesis—the increase in swimming speed many bacteria exhibit when absolute chemical concentration exceeds a threshold—may serve to enhance chemotactic accuracy and sensitivity when the chemical landscape is dynamic. More generally, our framework provides a rigorous method for partitioning bacteria into populations that are ‘near’ and ‘far’ from chemical hotspots in complex, rapidly evolving environments such as those that dominate aquatic ecosystems.
Publisher: MyJove Corporation
Date: 31-01-2020
DOI: 10.3791/60589
Publisher: Cambridge University Press (CUP)
Date: 05-03-2021
DOI: 10.1017/JFM.2020.885
Publisher: American Physical Society (APS)
Date: 13-12-2016
Publisher: Springer Science and Business Media LLC
Date: 04-2017
DOI: 10.1038/NATURE22058
Abstract: Vaccine-induced high-avidity IgA can protect against bacterial enteropathogens by directly neutralizing virulence factors or by poorly defined mechanisms that physically impede bacterial interactions with the gut tissues ('immune exclusion'). IgA-mediated cross-linking clumps bacteria in the gut lumen and is critical for protection against infection by non-typhoidal Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). However, classical agglutination, which was thought to drive this process, is efficient only at high pathogen densities (≥10
Publisher: Springer Science and Business Media LLC
Date: 09-02-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 16-05-2019
Abstract: The limited precision of sensory organs places fundamental constraints on organismal performance. An open question, however, is whether organisms are routinely pushed to these limits and how limits might influence interactions between populations of organisms and their environment. By combining a method to generate dynamic, replicable resource landscapes, high-speed tracking of freely moving bacteria, a mathematical theory, and agent-based simulations, we show that sensory noise ultimately limits when and where bacteria can detect and climb chemical gradients. Our results suggest that the typical chemical landscapes bacteria inhabit are dominated by noise that masks shallow gradients and that the spatiotemporal dynamics of bacterial aggregations can be predicted by mapping the region where gradient signal rises above noise.
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2021
DOI: 10.1101/2021.02.08.430277
Abstract: Culturally transmitted communication signals – such as human language or bird song – can change over time through a process of cultural drift, and may consequently enhance the separation of populations, potentially leading to reproductive isolation 1–4 . Local song dialects have been identified in bird species with relatively simple songs where in iduals show high cultural conformity 5–10 . In contrast, the emergence of cultural dialects has been regarded as unlikely 11–13 for species with more variable song, such as the zebra finch ( Taeniopygia guttata ). Instead, it has been proposed that selection for in idual recognition and distinctiveness may lead to a complete spread across the space of acoustic and syntactical possibilities 11–15 . However, another possibility is that analytical limitations have meant that subtle but possibly salient group differences have not yet been discovered in such species. Here we show that machine learning can distinguish the songs from multiple captive zebra finch populations with remarkable precision, and that these ‘cryptic song dialects’ drive strong assortative mating in this species. We studied mating patterns across three consecutive generations using captive populations that have evolved in isolation for about 100 generations. Cross-fostering eggs within and between these populations and quantifying social interactions of the resulting offspring later in life revealed that mate choice primarily targets cultural traits that are transmitted during a short developmental time window. Detailed social networks showed that females preferentially approached males whose song resembled that of their adolescent peers. Our study shows that birds can be surprisingly sensitive to cultural traits for mating that have hitherto remained cryptic, even in this well-studied species that is used as a model for song-learning 13,14,16–28 .
Publisher: Elsevier BV
Date: 05-2022
Publisher: American Physical Society (APS)
Date: 31-01-2022
Publisher: CSIRO Publishing
Date: 19-04-2022
DOI: 10.1071/MA22010
Abstract: The combination of mathematical modelling and quantitative video-microscopy provides exciting opportunities for elucidating the mechanisms behind key processes in microbial ecology, ranging from cell navigation and nutrient cycling to biofilm establishment and symbioses. Central to this approach is the iterative process, whereby experiments and modelling inform one another in a virtuous cycle: vast quantities of experimental data help to test and refine mathematical models, the predictions from which feed back to the experimental design itself. This paper discusses recent technologies, emerging applications, and ex les where calibrated mathematical models enable calculation of quantities that are otherwise extremely difficult to measure.
Publisher: Cambridge University Press (CUP)
Date: 31-05-2016
DOI: 10.1017/JFM.2016.306
Abstract: Colonies of the green alga Volvox are spheres that swim through the beating of pairs of flagella on their surface somatic cells. The somatic cells themselves are mounted rigidly in a polymeric extracellular matrix, fixing the orientation of the flagella so that they beat approximately in a meridional plane, with axis of symmetry in the swimming direction, but with a roughly $20^{\\circ }$ azimuthal offset which results in the eponymous rotation of the colonies about a body-fixed axis. Experiments on colonies of Volvox carteri held stationary on a micropipette show that the beating pattern takes the form of a symplectic metachronal wave (Brumley et al. Phys. Rev. Lett. , vol. 109, 2012, 268102). Here we extend the Lighthill/Blake axisymmetric, Stokes-flow model of a free-swimming spherical squirmer (Lighthill Commun. Pure Appl. Maths , vol. 5, 1952, pp. 109–118 Blake J. Fluid Mech. , vol. 46, 1971 b , pp. 199–208) to include azimuthal swirl. The measured kinematics of the metachronal wave for 60 different colonies are used to calculate the coefficients in the eigenfunction expansions and hence predict the mean swimming speeds and rotation rates, proportional to the square of the beating litude, as functions of colony radius. As a test of the squirmer model, the results are compared with measurements (Drescher et al. Phys. Rev. Lett. , vol. 102, 2009, 168101) of the mean swimming speeds and angular velocities of a different set of 220 colonies, also given as functions of colony radius. The predicted variation with radius is qualitatively correct, but the model underestimates both the mean swimming speed and the mean angular velocity unless the litude of the flagellar beat is taken to be larger than previously thought. The reasons for this discrepancy are discussed.
Publisher: Springer Science and Business Media LLC
Date: 28-03-2022
DOI: 10.1038/S41467-022-28881-W
Abstract: Culturally transmitted communication signals – such as human language or bird song – can change over time through cultural drift, and the resulting dialects may consequently enhance the separation of populations. However, the emergence of song dialects has been considered unlikely when songs are highly in idual-specific, as in the zebra finch ( Taeniopygia guttata ). Here we show that machine learning can nevertheless distinguish the songs from multiple captive zebra finch populations with remarkable precision, and that ‘cryptic song dialects’ predict strong assortative mating in this species. We examine mating patterns across three consecutive generations using captive populations that have evolved in isolation for about 100 generations. We cross-fostered eggs within and between these populations and used an automated barcode tracking system to quantify social interactions. We find that females preferentially pair with males whose song resembles that of the females’ adolescent peers. Our study shows evidence that in zebra finches, a model species for song learning, in iduals are sensitive to differences in song that have hitherto remained unnoticed by researchers.
Publisher: American Physical Society (APS)
Date: 22-05-2019
Publisher: Frontiers Media SA
Date: 24-07-2020
Publisher: eLife Sciences Publications, Ltd
Date: 29-07-2014
DOI: 10.7554/ELIFE.02750
Abstract: Flows generated by ensembles of flagella are crucial to development, motility and sensing, but the mechanisms behind this striking coordination remain unclear. We present novel experiments in which two micropipette-held somatic cells of Volvox carteri, with distinct intrinsic beating frequencies, are studied by high-speed imaging as a function of their separation and orientation. Analysis of time series shows that the interflagellar coupling, constrained by lack of connections between cells to be hydrodynamical, exhibits a spatial dependence consistent with theory. At close spacings it produces robust synchrony for thousands of beats, while at increasing separations synchrony is degraded by stochastic processes. Manipulation of the relative flagellar orientation reveals in-phase and antiphase states, consistent with dynamical theories. Flagellar tracking with exquisite precision reveals waveform changes that result from hydrodynamic coupling. This study proves unequivocally that flagella coupled solely through a fluid can achieve robust synchrony despite differences in their intrinsic properties.
Publisher: AIP Publishing
Date: 05-2010
DOI: 10.1063/1.3397926
Abstract: The ability to calculate flows generated by oscillating cylinders immersed in fluid is a cornerstone in micro- and nanodevice development. In this article, we present a detailed theoretical analysis of the hydrodynamic load experienced by an oscillating rigid cylinder, of arbitrary rectangular cross section, that is immersed in an unbounded viscous fluid. We also consider the formal limit of inviscid flow for which exact analytical and asymptotic solutions are derived. Due to its practical importance in application to the atomic force microscope and nanoelectromechanical systems, we conduct a detailed assessment of the dependence of this load on the cylinder thickness-to-width ratio. We also assess the validity and accuracy of the widely used infinitely-thin blade approximation. For thin rectangular cylinders of finite thickness, this approximation is found to be excellent for out-of-plane motion, whereas for in-plane oscillations it can exhibit significant error. A database of accurate numerical results for the hydrodynamic load as a function of the thickness-to-width ratio and normalized frequency is also presented, which is expected to be of value in practical application and numerical benchmarking.
Publisher: Elsevier BV
Date: 12-2021
Location: United Kingdom of Great Britain and Northern Ireland
Location: United States of America
Start Date: 2018
End Date: 07-2022
Amount: $365,058.00
Funder: Australian Research Council
View Funded ActivityStart Date: 12-2022
End Date: 12-2025
Amount: $389,258.00
Funder: Australian Research Council
View Funded Activity