IST Austria: PubRep (Institute of Science and Technology)
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Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize
No full textNitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops
DNA methylation dynamics in male germline development in Brassica Rapa
No full textDynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants
Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers
No full textCatalytic microswimmers convert the chemical energy from fuel into motion. They sustain chemical gradients and fluid flows that propel them by phoresis. This leads to unconventional behavior and collective dynamics, such as self-organization into complex structures. Characterizing the nonequilibrium interactions of microswimmers is crucial for advancing our understanding of active systems. However, this remains a challenge owing to the importance of fluctuations at the microscale and the difficulty in disentangling the different contributions to the interactions. Here, we show a massive dependence of the nonequilibrium interactions on the shape of catalytic microswimmers. We perform tracking experiments at high throughput to map interactions between nanocolloidal tracers and dimeric microswimmers of various aspect ratios. Our method leverages dual tracers with differing phoretic mobilities to quantitatively disentangle phoretic motion from hydrodynamic advection. This approach is validated through experiments on single chemically active sites and on immobilized catalytic microswimmers. We further investigate the activity-driven interactions of free microswimmers and directly measure their phoretic interactions. When compared to standard models, our findings highlight the important role of osmotic flows for microswimmers near surfaces and reveal an enhanced contribution of hydrodynamic advection relative to phoretic motion as the size of the microswimmer increases. Our study provides robust measurements of the nonequilibrium interactions from catalytic microswimmers and lays the groundwork for a realistic description of active systems
Chromatic alpha complexes
No full textMotivated by applications in medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided
ISTA Thesis
No full textEpithelial spreading plays a pivotal role in the development of organisms especially those
such as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the
substantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium
with cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the
cells show tissue-scale mechanosensation with mechanisms such as direct mechanical control
over the axis of cell division.
Cytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating
mechanical stability but also helping facilitate the mechanosensitive response of the cell.
Mechanosenstivity displayed by intermediate filaments is due not just to their interesting
physical properties but also to their interactions with other cytoskeletal elements such as actin
and microtubules. Keratin is the predominant intermediate filament expressed in the EVL.
It expresses concomitantly with the gastrulation movements of the developing embryo. Our
work focuses on understanding the role and dynamics of the keratin cytoskeletal network in
modulating the physical aspects of EVL spreading. We demonstrated with the combination of
physical characterisation and manipulations of the EVL, utilising a variety of biophysical tools
and microscopy, the mechanistic role of keratin in tissue spreading.
Generating novel genetic morphants and mutants, we probe the effect that the loss of the
keratin network has on the physiology of the epithelium and the developing embryo. We
show that the changing organisation of the keratin network is important for changing EVL
physical properties as the stress imposed on the EVL increases during epiboly. By modelling
the epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into
a mechanical loop to the maturation of the keratin network and hence affect the mechanics
of the epithelium. However, unlike what would be predicted by the effect of intermediate
filaments in acting as a security belt and increasing the resistance of the epithelium, we observe
that loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the
YSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation
in a keratin-dependent manner.
Furthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into
the mechanisms underlying the organisation and distribution of keratin. Interestingly, the
phenotype observed upon this loss of microtubules shows that keratins interact with the nucleus
through microtubular interactions. Together with these diverse observations, we describe
the mechanosensory feedback between resilience and that is critical for uniform and robust
spreading of the epithelium
Implicit representations of codimension-2 submanifolds and their prequantum structure
No full textThis paper explores the geometry of the space of codimension-2 submanifolds. We implicitly represent these submanifolds by a class of complex-valued functions. This reveals a prequantum bundle structure over the space of submanifolds, equipped with the well-known Marsden-Weinstein symplectic structure. This bundle allows a new physical interpretation of the Marsden-Weinstein structure as the curvature of a connection form, which measures the average of volumes swept by the deformation of the S^1-family of hypersurfaces, defined as the phases of a complex function implicitly representing a submanifold
Lumen charge governs gated ion transport in β-barrel nanopores
No full textβ-Barrel nanopores are involved in crucial biological processes, from ATP export in mitochondria to bacterial resistance, and represent a promising platform for emerging sequencing technologies. However, in contrast to ion channels, the understanding of the fundamental principles governing ion transport through these nanopores remains largely unexplored. Here we integrate experimental, numerical and theoretical approaches to elucidate ion transport mechanisms in β-barrel nanopores. We identify and characterize two distinct nonlinear phenomena: open-pore rectification and gating. Through extensive mutation analysis of aerolysin nanopores, we demonstrate that open-pore rectification is caused by ionic accumulation driven by the distribution of lumen charges. In addition, we provide converging evidence suggesting that gating is controlled by electric fields dissociating counterions from lumen charges, promoting local structural deformations. Our findings establish a rigorous framework for characterizing and understanding ion transport processes in protein-based nanopores, enabling the design of adaptable nanofluidic biotechnologies. We illustrate this by optimizing an aerolysin mutant for computing applications
Entropic costs of extracting classical ticks from a quantum clock
No full textWe experimentally realize a quantum clock by using a charge sensor to count charges tunneling through a double quantum dot (DQD). Individual tunneling events are used as the clock’s ticks. We quantify the clock’s precision while measuring the power dissipated by the DQD and, separately, the charge sensor in both direct-current and radio-frequency readout modes. This allows us to probe the thermodynamic cost of creating ticks microscopically and recording them macroscopically. Our experiment is the first to explore the interplay between the entropy produced by a microscopic clockwork and its macroscopic measurement apparatus. We show that the latter contribution not only dwarfs the former but also unlocks greatly increased precision, because the measurement record can be exploited to optimally estimate time even when the DQD is at equilibrium. Our results suggest that the entropy produced by the amplification and measurement of a clock’s ticks, which has often been ignored in the literature, is the most important and fundamental thermodynamic cost of timekeeping at the quantum scale
Less water from glaciers during future megadroughts in the Southern Andes
No full textGlacier melt sustains water discharge from mountain basins during droughts, but ongoing glacier retreat threatens this fundamental capacity. Here, we assess the response of glaciers in the Southern Andes to one of the most severe, persistent, and extensive droughts on record in South America (2010-present), and to projected end-of-century megadroughts. Using glacio-hydrological numerical simulations, we show that despite a mean annual precipitation deficit of 36%, glacier runoff in 2010-2019 remained almost unaltered compared to the preceding decade (2000-2009), sustained by a 10% loss of total ice volume. However, simulations of future glacier evolution indicate that annual and summer glacier runoff could decline by up to 20 ± 11% and 48 ± 6%, respectively, during end-of-century megadroughts compared to pre-2010 levels. Our results project a weakening of the glacier’s buffering role against precipitation deficits during extreme droughts, increasing water scarcity for ecosystems and livelihoods in the mountain regions of South America
