Biology subjects

Seddon, A.

Publications and source records attributed to Seddon, A..

5 recordsLinked to original sources

bioRxiv2021

Vegetation memory effects and their association with vegetation resilience in global drylands

AO_SCPLOWBSTRACTC_SCPLOWO_LIVegetation memory describes the effect of antecedent environmental and ecological conditions on the present ecosystem state and has been proposed as an important proxy for vegetation resilience. In particular, strong vegetation-memory effects have been identified in dryland regions, but the factors underlying the spatial patterns of vegetation memory remain unknown. C_LIO_LIWe aim to map the components and drivers of vegetation memory in dryland regions using state-of-the-art climate reanalysis data and refined approaches to identify vegetation-memory characteristics across dryland regions worldwide. C_LIO_LIUsing a framework which distinguishes between intrinsic and extrinsic ecological memory, we show that: (i) intrinsic memory is a much stronger component than extrinsic memory in the majority of dryland regions; and (ii) climate reanalysis data sets change the detection of extrinsic vegetation memory effects in some global dryland regions. C_LIO_LISynthesis. Our study offers a global picture of the vegetation response to two climate forcing variables using satellite data, information which is potentially relevant for mapping components and properties of vegetation responses worldwide. However, the large differences in the spatial patterns in intrinsic vegetation memory in our study compared to previous analyses show the overall sensitivity of this component in particular to the initial choice of extrinsic forcing variables. As a result, we caution against using the oversimplified link between intrinsic vegetation-memory and vegetation recovery rates at large spatial scales. C_LI

ecology↗

bioRxiv2021

The SEEL Motif and Members of the MYB-related REVEILLE Transcription Factor Family are Important for the Expression of LORELEI in the Synergid Cells of the Arabidopsis Female Gametophyte

Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs ( TAATATCT) in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of a cis-regulatory element and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells and investigate the potential connection between circadian rhythm and fertilization. One sentence summaryA newly identified SEEL motif in the promoter of LORELEI and at least three members of the REVEILLE transcription factor family are important for LORELEI expression in synergid cells of the Arabidopsis female gametophyte.

plant biology↗

bioRxiv2021

Lipid type doping of the sponge (L3) mesophase

The polymorphism of lipid aggregates has long attracted detailed study due to the myriad factors that determine the final mesophase observed. This study is driven by the need to understand mesophase behaviour for a number of applications, such as drug delivery and membrane protein crystallography. In the case of the latter, the role of the so-called sponge (L3) mesophase has been often noted, but not extensively studied by itself. The L3 mesophase can be formed in monoolein/water systems on the addition of butanediol to water, which partitions the headgroup region of the membrane, and decreases its elastic moduli. Like cubic mesophases, it is bicontinuous, but unlike them, has no long-range translational symmetry. In our present study, we show that the formation of the L3 phase can delicately depend on the addition of dopant lipids to the mesophase. While electrostatically neutral molecules similar in shape to monoolein (DOPE, cholesterol) have little effect on the general mesophase behaviour, others (DOPC, DDM) significantly reduce the region in which it can form. Additionally, we show that by combining cholesterol with the anionic lipid DOPG, it is possible to form the largest stable L3 mesophases observed to date, with correlation lengths over 220 [A].

biophysics↗

bioRxiv2020

Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

Due to the high computational cost of full-cell coarse-grained molecular dynamics modelling, being able to simulate "miniature" cells that effectively represent their full-sized counterparts would be highly advantageous. To accurately represent the morphological and elastic properties of a human red blood cell in silico, such a model is employed utilising the molecular dynamics package LAMMPS. The scale invariance of the model is first tested qualitatively by following the shape evolution of red blood cells of various diameters, then quantitatively by evaluating the membrane shear modulus from simulations of optical tweezer-style stretching. Cells of physical diameter of at least 0.5{micro}m were able to form the characteristic biconcave shape of human red blood cells, though smaller cells instead equilibrated to bowl-shaped stomatocytes. A positive correlation was found between the cell size and both magnitude of deformation from optical tweezer stretching and scaled shear modulus, indicating a lack of scale invariance in the models elastic response. However, the stable morphology and measured shear modulus of the 0.5 - 1.0{micro}m diameter cells are deemed close enough to past in vitro studies on human red blood cells for them to still offer valuable use in making simplified predictions of whole-cell mechanics. SIGNIFICANCEThe study tests the invariance of a coarse-grained molecular dynamics red blood cell (RBC) model to system scale, asking whether it is qualitatively and quantitatively viable to perform whole-cell simulations in "miniature". Simulating cells at a reduced scale greatly improves computational speed, making possible computational experiments that would otherwise be too computationally demanding. This facilitates the simulation of larger systems, both in number of whole-cells, and cells of greater structural complexity than the RBC. More generally, the accurate and efficient modelling of biological cells allows computational experimentation of real-world systems that would be very challenging or impossible to perform in vitro. Therefore, miniature-cell modelling could help both direct development in whole-cell modelling, and also developments in more widespread bio-physical studies.

biophysics↗

bioRxiv2018

A de novo peroxidase is also a promiscuous yet stereoselective carbene transferase

By constructing an in vivo assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here we show that C45s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes and amines. Not only is this the first report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.

synthetic biology↗