Biological regulatory systems, such as cell signaling networks, nervous systems and ecological webs, consist of complex dynamical interactions among many components. Network motif models focus on ...small sub-networks to provide quantitative insight into overall behavior. However, such models often overlook time delays either inherent to biological processes or associated with multi-step interactions. Here we systematically examine explicit-delay versions of the most common network motifs via delay differential equation (DDE) models, both analytically and numerically. We find many broadly applicable results, including parameter reduction versus canonical ordinary differential equation (ODE) models, analytical relations for converting between ODE and DDE models, criteria for when delays may be ignored, a complete phase space for autoregulation, universal behaviors of feedforward loops, a unified Hill-function logic framework, and conditions for oscillations and chaos. We conclude that explicit-delay modeling simplifies the phenomenology of many biological networks and may aid in discovering new functional motifs.
Biological microswimmers exhibit versatile strategies for sensing and navigating their environment, such as run-and-tumble and curvature modulation. Here, we report a striking phototactic behaviour ...of the microswimmer Euglena gracilis, where these eukaryotic cells swim in polygonal trajectories due to a sudden increase in light intensity. While smoothly curved trajectories are common for microswimmers, such quantized ones have not been reported previously. We find that this polygonal behaviour emerges from periodic switching between the flagellar beating patterns of helical swimming and spinning behaviours. We develop and experimentally validate a biophysical model that describes the phase relationship between the eyespot, cell orientation, light detection and cellular reorientation, accounting for all three behavioural states. Coordinated switching between these behaviours selects for ballistic, superdiffusive, diffusive or subdiffusive motion (including tuning the effective diffusion constant over several orders of magnitude), thereby enabling navigation in spatially structured light fields, such as edge avoidance and gradient descent. This feedback control links multiple system scales (flagellar beats, cellular behaviours and phototaxis strategies), with implications for other natural and synthetic microswimmers.
Recent advances in sequencing and informatic technologies have led to a deluge of publicly available genomic data. While it is now relatively easy to sequence, assemble, and identify genic regions in ...diploid plant genomes, functional annotation of these genes is still a challenge. Over the past decade, there has been a steady increase in studies utilizing machine learning algorithms for various aspects of functional prediction, because these algorithms are able to integrate large amounts of heterogeneous data and detect patterns inconspicuous through rule‐based approaches. The goal of this review is to introduce experimental plant biologists to machine learning, by describing how it is currently being used in gene function prediction to gain novel biological insights. In this review, we discuss specific applications of machine learning in identifying structural features in sequenced genomes, predicting interactions between different cellular components, and predicting gene function and organismal phenotypes. Finally, we also propose strategies for stimulating functional discovery using machine learning–based approaches in plants.
Abstract In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria ...are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance.
Plants produce a diverse array of compounds through an extensive, evolutionarily malleable network of metabolic pathways. These metabolites are typically classified into two types--primary and ...specialized--with most of the diversity occurring among specialized metabolite. Metabolite presence-absence and types vary dynamically in an individual plant (within/between tissues/organs, developmental stages, across the circadian cycle), between populations, and also between species. Conservatively, it was estimated that each species harbors ~4.7 unique metabolites, and over a million metabolites were predicted to exist across the plant kingdom. Here, Moghe and Kruse discuss how the scale of metabolite diversity raises multiple challenges for the study of plant specialized metabolism.
For centuries, observational microscopy has greatly facilitated biology education, but we still cannot easily and playfully interact with the microscopic world we see. We therefore developed the ...LudusScope, an accessible, interactive do-it-yourself smartphone microscopy platform that promotes exploratory stimulation and observation of microscopic organisms, in a design that combines the educational modalities of build, play, and inquire. The LudusScope's touchscreen and joystick allow the selection and stimulation of phototactic microorganisms such as Euglena gracilis with light. Organismal behavior is tracked and displayed in real time, enabling open and structured game play as well as scientific inquiry via quantitative experimentation. Furthermore, we used the Scratch programming language to incorporate biophysical modeling. This platform is designed as an accessible, low-cost educational kit for easy construction and expansion. User testing with both teachers and students demonstrates the educational potential of the LudusScope, and we anticipate additional synergy with the maker movement. Transforming observational microscopy into an interactive experience will make microbiology more tangible to society, and effectively support the interdisciplinary learning required by the Next Generation Science Standards.
Pyrrolizidine alkaloids (PAs) are a typical class of plant secondary metabolites that are constitutively produced as part of the plant’s chemical defense. While roots are a well-established site of ...pyrrolizidine alkaloid biosynthesis, comfrey plants (
Symphytum officinale
; Boraginaceae) have been shown to additionally activate alkaloid production in specialized leaves and accumulate PAs in flowers during a short developmental stage in inflorescence development. To gain a better understanding of the accumulation and role of PAs in comfrey flowers and fruits, we have dissected and analyzed their tissues for PA content and patterns. PAs are almost exclusively accumulated in the ovaries, while petals, sepals, and pollen hardly contain PAs. High levels of PAs are detectable in the fruit, but the elaiosome was shown to be PA free. The absence of 7-acetyllycopsamine in floral parts while present in leaves and roots suggests that the additional site of PA biosynthesis provides the pool of PAs for translocation to floral structures. Our data suggest that PA accumulation has to be understood as a highly dynamic system resulting from a combination of efficient transport and additional sites of synthesis that are only temporarily active. Our findings are further discussed in the context of the ecological roles of PAs in comfrey flowers.
The shape of the flagellar beat determines the path along which a sperm cell swims. If the flagellum bends periodically about a curved mean shape then the sperm will follow a path with non-zero ...curvature. To test a simple hydrodynamic theory of flagellar propulsion known as resistive force theory, we conducted high-precision measurements of the head and flagellum motions during circular swimming of bull spermatozoa near a surface. We found that the fine structure of sperm swimming represented by the rapid wiggling of the sperm head around an averaged path is, to high accuracy, accounted for by resistive force theory and results from balancing forces and torques generated by the beating flagellum. We determined the anisotropy ratio between the normal and tangential hydrodynamic friction coefficients of the flagellum to be 1.81+/-0.07 (mean+/-s.d.). On time scales longer than the flagellar beat cycle, sperm cells followed circular paths of non-zero curvature. Our data show that path curvature is approximately equal to twice the average curvature of the flagellum, consistent with quantitative predictions of resistive force theory. Hence, this theory accurately predicts the complex trajectories of sperm cells from the detailed shape of their flagellar beat across different time scales.
Key message
Nicotiana benthamiana
acylsugar acyltransferase (ASAT) is required for protection against desiccation and insect herbivory. Knockout mutations provide a new resource for investigation of ...plant-aphid and plant-whitefly interactions.
Nicotiana benthamiana
is used extensively as a transient expression platform for functional analysis of genes from other species. Acylsugars, which are produced in the trichomes, are a hypothesized cause of the relatively high insect resistance that is observed in
N. benthamiana.
We characterized the
N. benthamiana
acylsugar profile, bioinformatically identified two acylsugar acyltransferase genes,
ASAT1
and
ASAT2
, and used CRISPR/Cas9 mutagenesis to produce acylsugar-deficient plants for investigation of insect resistance and foliar water loss. Whereas
asat1
mutations reduced accumulation,
asat2
mutations caused almost complete depletion of foliar acylsucroses. Three hemipteran and three lepidopteran herbivores survived, gained weight, and/or reproduced significantly better on
asat2
mutants than on wildtype
N. benthamiana
. Both
asat1
and
asat2
mutations reduced the water content and increased leaf temperature. Our results demonstrate the specific function of two ASAT proteins in
N. benthamiana
acylsugar biosynthesis, insect resistance, and desiccation tolerance. The improved growth of aphids and whiteflies on
asat2
mutants will facilitate the use of
N. benthamiana
as a transient expression platform for the functional analysis of insect effectors and resistance genes from other plant species. Similarly, the absence of acylsugars in
asat2
mutants will enable analysis of acylsugar biosynthesis genes from other Solanaceae by transient expression.
The eukaryotic flagellum beats periodically, driven by the oscillatory dynamics of molecular motors, to propel cells and pump fluids. Small but perceivable fluctuations in the beat of individual ...flagella have physiological implications for synchronization in collections of flagella as well as for hydrodynamic interactions between flagellated swimmers. Here, we characterize phase and amplitude fluctuations of flagellar bending waves using shape mode analysis and limit-cycle reconstruction. We report a quality factor of flagellar oscillations Q = 38.0 ± 16.7 (mean ± s.e.). Our analysis shows that flagellar fluctuations are dominantly of active origin. Using a minimal model of collective motor oscillations, we demonstrate how the stochastic dynamics of individual motors can give rise to active small-number fluctuations in motor-cytoskeleton systems.
PDF
