Posfai A, Taillefumier T, Wingreen NS
. Metabolic trade-offs promote diversity in a model ecosystem
. Physical Review Letter [Internet]. 118 (2). Publisher's VersionAbstract
In nature a large number of species can coexist on a small number of shared resources, however resource competition models predict that the number of species in steady coexistence cannot exceed the number of resources. Motivated by recent studies of phytoplankton, we introduce trade-offs into a resource competition model, and find that an unlimited number of species can coexist. Our model spontaneously reproduces several features of natural ecosystems including keystone species and population dynamics/abundances characteristic of neutral theory, despite an underlying non- neutral competition for resources.
Blackwell JM, Taillefumier TO, Natan RG, Carruthers IM, Magnasco MO, Geffen MN
. Stable encoding of sounds over a broad range of statistical parameters in the auditory cortex
. European Journal of Neuroscience [Internet]. 43 :751–764. Publisher's VersionAbstract
Natural auditory scenes possess highly structured statistical regularities, which are dictated by the physics of sound production in nature, such as scale-invariance. We recently identified that natural water sounds exhibit a particular type of scale invariance, in which the temporal modulation within spectral bands scales with the centre frequency of the band. Here, we tested how neurons in the mammalian primary auditory cortex encode sounds that exhibit this property, but differ in their statistical parameters. The stimuli varied in spectro-temporal density and cyclo-temporal statistics over several orders of magnitude, corresponding to a range of water-like percepts, from pattering of rain to a slow stream. We recorded neuronal activity in the primary auditory cortex of awake rats presented with these stimuli. The responses of the majority of individual neurons were selective for a subset of stimuli with specific statistics. However, as a neuronal population, the responses were remarkably stable over large changes in stimulus statistics, exhibiting a similar range in firing rate, response strength, variability and information rate, and only minor variation in receptive field parameters. This pattern of neuronal responses suggests a potentially general principle for cortical encoding of complex acoustic scenes: while individual cortical neurons exhibit selectivity for specific statistical features, a neuronal population preserves a constant response structure across a broad range of statistical parameters.
Kaykov A, Taillefumier T, Bensimon A, Nurse P
. Molecular Combing of Single DNA Molecules on the 10 Megabase Scale
. Scientific Reports [Internet]. 6 :19636 - . Publisher's VersionAbstract
DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200–500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions.