Biology subjects

Wagner, H.

Publications and source records attributed to Wagner, H..

9 recordsLinked to original sources

bioRxiv2024

Differential expression ofCCD4(4B) drives natural variation in fruit carotenoidcontent in strawberry ( Fragaria spp.)

Pigments, mainly anthocyanins and carotenoids, are important contributors to fruits visual appearance and nutritional properties. In strawberry (Fragaria spp.), the genetic and molecular mechanisms regulating fruit carotenoid biosynthesis and its natural variation remain largely unexplored. In this study, we sought to identify genomic loci contributing to variation in yellow flesh pigmentation. A major QTL, qYellow Flesh-4B, accounting for 82% of the total phenotypic variation was identified on F. x ananassa chromosome 4B. Following a candidate gene approach, we determined that CCD4(4B), a carotenoid cleavage dioxygenase (CCD), was the underlying gene. Specific polymorphisms on CCD4(4B) promoter region were associated with the yellow flesh phenotype and with differential regulation of CCD4(4B) expression during fruit ripening. Furthermore, CCD4(4B) expression levels were negatively correlated with violaxanthin, lutein, zeaxanthin, {beta}-carotene and total carotenoid content. The role of CCD4(4B) in carotenoid turnover was confirmed by transient overexpression in F. x ananassa fruits, which led to a decrease in carotenoid accumulation. Notably, a -35 C>T SNP identified in CCD4(4B) promoter was found to be predictive for CCD4(4B) expression, and carotenoid content in fruits of a diverse germplasm collection, which included different octoploid Fragaria species. Taken together, these results provide important genetic insights into the natural variation of carotenoid content in strawberry. The High-Resolution Melting (HRM) DNA test here developed offers a fast and reliable method to predict high fruit carotenoid content, representing a useful tool for breeding projects aiming to enhance the nutritional value of this crop.

plant biology↗

bioRxiv2023

Design of a Biohybrid Materials Circuit with Binary Decoder Functionality

Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, we engineer a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited. Guided by a quantitative mathematical model and following a design-build-test-learn cycle, we wire the modules according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. We design a 2-input/4-output binary decoder for the detection of two small molecules in a material framework that could perform regulated outputs in form of distinct protease activities. The here demonstrated smart material system is strongly modular and could be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.

synthetic biology↗

bioRxiv2023

PenTag, a Versatile Platform for Covalent Bioconjugation, Purification, and Tagging of Proteins Towards the Development of Novel Biohybrid Material Systems

The site-specific and covalent conjugation of proteins on solid supports and in hydrogels is the basis for the synthesis of biohybrid materials offering broad applications. Current methods for conjugating proteins to desired targets are often challenging due to unspecific binding, unstable (non-covalent) coupling, or expensive and difficult-to-synthesize ligand molecules. Here, we present PenTag, an approach for the biorthogonal, highly-specific and covalent conjugation of a protein to its ligand for various applications in materials sciences. We engineered penicillin- binding protein 3 (PBP3) and showed that this protein can be used for the stable and spontaneous conjugation of proteins to dyes, polymers, or solid supports. We applied PenTag as a crosslinking tool for synthesizing stimuli-responsive hydrogels or for the development of a biohybrid material system performing computational operations emulating a 4:2 encoder. Based on this broad applicability and the use of a small, cheap and easy-to-functionalize ligand and a stable, soluble recombinant protein, we see PenTag as a versatile approach towards biohybrid material synthesis.

synthetic biology↗

bioRxiv2023

Urbanization and a green corridor do not impact genetic divergence in common milkweed (Asclepias syriaca)

Urbanization is altering landscapes globally at an unprecedented rate. While ecological differences between urban and rural environments often promote phenotypic divergence among populations, it is unclear to what degree these trait differences arise from genetic divergence as opposed to phenotypic plasticity. Furthermore, little is known about how specific landscape elements, such as green corridors, impact genetic divergence in urban environments. We tested the hypotheses that: 1) urbanization, and 2) proximity to an urban green corridor influence genetic divergence in Asclepias syriaca (common milkweed) populations for phenotypic traits. Using seeds from 52 populations along three urban-to-rural subtransects in the Greater Toronto Area, one of which followed a green corridor, we grew [~]1000 plants in a common garden and observed >20 ecologically-important traits associated with plant defense/damage, reproduction, and growth over four years. We found significant heritable variation for eight traits within A. syriaca populations and weak phenotypic divergence among populations. However, neither urbanization nor an urban green corridor influenced genetic divergence in individual traits or multivariate phenotype. These findings contrast with the expanding literature demonstrating that urbanization promotes rapid evolutionary change and offer preliminary insights into the eco- evolutionary role of green corridors in urban environments.

evolutionary biology↗

bioRxiv2022

Motor pattern generation is robust to neural network anatomical imbalance favoring inhibition but not excitation

During walking and running, animals display rich and coordinated motor patterns that are generated and controlled within the central nervous system. Previous computational and experimental results suggest that the balance between excitation and inhibition in neural circuits may be critical for generating such structured motor patterns. In this paper, we explore the influence of this balance on the ability of a reservoir computing artificial neural network to learn human locomotor patterns, using mean-field theory and simulations. We created networks with varying neuron numbers, connection percentages and connection strengths for the excitatory and inhibitory neuron populations, and introduced the anatomical imbalance that quantifies the overall effect of the two populations. We trained the networks to reproduce muscle activation patterns derived from human recordings and evaluated their performance. Our results indicate that network dynamics and performance depend critically on the anatomical imbalance in the network. Excitation-dominated networks lead to saturated firing rates, thereby reducing the firing rate heterogeneity and leading to muscle coactivation and inflexible motor patterns. Inhibition-dominated networks, on the other hand, perform well, displaying balanced input to the neurons and sufficient heterogeneity in the neuron firing rate patterns. This suggests that motor pattern generation may be robust to increased inhibition but not increased excitation in neural networks.

neuroscience↗

bioRxiv2022

Urbanization and green corridors influence reproductive success and pollinators of common milkweed

Urbanization exerts many pressures on species, yet little is known about how these pressures impact species interactions. Studies of urban plant-pollinator systems provide mounting evidence that urbanization impairs pollinator movement in fragmented urban landscapes, yet the consequences for pollinator-mediated plant reproduction remains unclear. In non-urban areas, habitat corridors can facilitate the movement of organisms including pollinators, but whether these corridors facilitate plant-pollinator interactions in urban areas remains understudied. To examine how urban environments and green corridors influence plant-pollinator interactions, we measured reproductive success in the native plant common milkweed (Asclepias syriaca), and the community structure of its pollinators, for two years along two urban-rural transects in the Greater Toronto Area, Canada, one of which followed a green corridor. We found that urbanization decreased male fitness (i.e., pollen removal), increased fruit set (i.e., mean no. of follicles per inflorescence), and inconsistently affected female fitness (i.e., no. of follicles) in A. syriaca. Urbanization simultaneously decreased pollinator abundance but increased pollinator richness. Proximity to a green corridor inconsistently affected male fitness but increased reproductive effort (i.e., no. of inflorescences) in A. syriaca, while pollinator diversity and richness was lower in corridors. Notably, there were no consistent relationships between pollinator community structure and reproductive success in A. syriaca in both the presence, and absence, of a green corridor. These results demonstrate the complexity with which urbanization, green corridors, and pollinator communities can shape the reproductive investment and fitness of native plant populations.

ecology↗

bioRxiv2020

The influence of body side and sex on neck muscle responses to left-frontal-oblique impacts

Low-velocity motor vehicle crashes frequently induce chronic neck disorders also referred to as whiplash-associated disorders (WAD). The etiology of WAD is still not fully understood. Women are affected more often and more severely than men. A frontal-oblique collision direction leads to WAD relatively frequently, but is poorly investigated as compared to rear-end or frontal collision directions. An oblique impact direction is assumed to strain the contralateral neck side more than the ipsilateral side, provoking an asymmetrical response pattern of the left and right cervical muscles. In this study, we examined the muscle reflex responses of the sternocleidomastoid, the paraspinal, and the trapezius muscles as well as the kinematic responses of 60 subjects during left-frontal-oblique collisions. Neither the reflex delay nor the peak head acceleration revealed significant sex differences. Thus, the elsewhere reported higher injury risk of females as compared to males cannot be explained by the electromyographic and kinematic results of this study. In females as well as in males the right muscle responses revealed shorter onset times than the left muscle responses. Thus, cervical muscles seem to be activated depending on the specific direction of the impact. Moreover, the difference between right and left muscle responses cannot be explained by a startle reflex. The movement of the head in relation to the torso (female mean {+/-} SD: 92 {+/-} 16 ms; male: 87 {+/-} 16 ms) started almost simultaneously to the onset of the first muscle activation (right paraspinal muscles: female mean: 95 ms and 95%-CI 82 - 109; male mean: 95 ms and 95%-CI 84 - 108) indicating that the initial muscle activity seems not to be triggered by a stretch reflex in the PARA muscles.

physiology↗

bioRxiv2020

A model of uniform cortical composition predicts the scaling laws of the mammalian cerebrum

The size of the mammalian cerebrum spans more than 5 orders of magnitude. The smallest cerebrums have a smooth (lissencephalic) cortical surface, which gets increasingly folded (gyrencephalic) with cerebral size. Further, the proportion of white-to-gray matter volume increases with the total volume. These scaling relations have unusually little variation. Even though a number of theories and models have been proposed, it remains an open question, why this is so. Here, we show that almost all variance is explained by assuming a homogeneous composition of the cortex across mammals. On the basis of this assumption we derive quantitative analytical computational models. The first model predicts the cortical surface area from the gray and white matter volume. A single free parameter, for the height of cortical columns is estimated as{lambda} = 2.9 mm (r2 = 0.996). The second model predicts the white matter volume as a function of the gray volume and the cerebral size (with parameters for intra- and extra-gyral connections lint, lext; [Formula]). The models are validated by predicting the effective cortical thickness and the folding parameter{kappa} . The results accurately predict the human intraspecific variation of the surface relations. As expected, we find a reduced{lambda} for cetaceans, and that preterm human infants do not follow the model. We also find deviations of gray and white matter volume for large cerebrums. Overall, the models thus show how the regular architecture of the cortex shapes the cerebrum. We conclude that the mammalian cerebrum scales in an isomorphic, rather than isometric, manner.

neuroscience↗

bioRxiv2020

Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit

Anthocyanins are the principal color-producing compounds synthesized in developing fruits of strawberry (Fragaria spp.). Substantial natural variation in color have been observed in fruits of diploid and octoploid accessions, resulting from distinct accumulation and distribution of anthocyanins in fruits. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. xananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon insertion in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, residing in the F. iinumae-derived subgenome, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression and anthocyanin accumulation. Our findings suggest that putative cis regulatory elements provided by FaEnSpm-2 are required for high and ectopic MYB10-2 expression and induction of anthocyanin biosynthesis in fruit flesh. We developed MYB10-2 (sub-genome) specific DNA markers for marker-assisted selection that accurately predicted anthocyanin phenotypes in octoploid segregating populations.

plant biology↗