Biology subjects

Nock, C.

Publications and source records attributed to Nock, C..

4 recordsLinked to original sources

bioRxiv2024

Partitioning changes in ecosystem productivity by effects of species interactions in biodiversity experiments

Species interactions affect ecosystem productivity. Positive interactions (resource partitioning and facilitation) increase productivity while negative interactions (species interference) decrease productivity relative to the null expectations defined by monoculture yields. Effects of competitive interactions (resource competition) can be either positive or negative. Distinguishing effects of species interactions is therefore difficult, if not impossible, with current biodiversity experiments involving mixtures and full density monocultures. To partition changes in ecosystem productivity by effects of species interactions, we modify null expectations with competitive growth responses, i.e., proportional changes in individual size (biomass or volume) expected in mixture based on species differences in growth and competitive ability. We use partial density (species density in mixture) monocultures and the competitive exclusion principle to determine maximum competitive growth responses and full density monoculture yields to measure species ability to achieve maximum competitive growth responses in mixture. Deviations of observed yields from competitive expectations represent the effects of positive/negative species interactions, while the differences between competitive and null expectations reflect the effects of competitive interactions. We demonstrate the effectiveness of our competitive partitioning model in distinguishing effects of species interactions using both simulated and experimental species mixtures. Our competitive partitioning model enables meaningful assessments of species interactions at both species and community levels and helps disentangle underlying mechanisms of species interactions responsible for changes in ecosystem productivity and identify species mixtures that maximize positive effects.

ecology↗

bioRxiv2024

Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy

Fluorescence lifetime imaging (FLIM) is widely used for functional and multiplexed bioimaging. The lifetime of autofluorescence or fluorescent sensors encodes physiologically relevant parameters. Thus, FLIM is especially relevant for the investigation of living systems. However, application of FLIM to live specimen is hampered by its slow speed and high phototoxicity. To enable faster and gentler FLIM, we integrated single-objective light-sheet microscopy with pulsed excitation and time-resolved detection on a novel SPAD array detector. We achieved 10-100-fold acceleration compared to confocal FLIM, down to 100 ms acquisition time per image, with excellent quantitative agreement. The massively enhanced speed enables volumetric FLIM acquisitions on live multicellular specimens, which we demonstrate with lifetime-based multiplexing in 3D and time-lapse FLIM of tension probes on living embryonic organoids. We benchmark both scanned and static light-sheet modalities to facilitate adding FLIM capability to a large variety of light-sheet microscopes.

biophysics↗

bioRxiv2021

The genome of the endangered Macadamia jansenii displays little diversity but represents an 1 important genetic resource for plant breeding

Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

genomics↗

bioRxiv2020

Mutually inclusive mechanisms of drought-induced tree mortality

An extreme summer drought caused unprecedented tree dieback across Central Europe in 2018, highlighting the need for a better mechanistic understanding of drought-induced tree mortality. While numerous physiological risk factors have been identified, the principal mechanisms, hydraulic failure and carbon starvation, are still debated. We studied 9,435 trees from 12 temperate species planted in a diversity experiment in 2013 to assess how hydraulic traits, carbon dynamics, pest infestation, tree height and neighbourhood competition influence individual mortality risk. We observed a reduced mortality risk for trees with wider hydraulic safety margins, while a rising sugar fraction of the non-structural carbohydrate pool and bark beetle infestation were associated with higher risk. Taller trees had a lower mortality risk. The sign and magnitude of neighbourhood effects on mortality risk depended on the species-identity of the involved trees, with most species having beneficial and some having deleterious effects on their neighbours. While severe tissue dehydration causing hydraulic failure precedes drought-induced tree mortality, we show that the probability of this event depends on a series of mutually inclusive processes including pest infestation and starch depletion for osmotic adjustment, and is modulated by the size and species identity of a tree and its neighbours.

ecology↗