Quantification of social motility indicates different colony growth phases.

colonies of the flagellated parasite exhibit characteristic fingering instability patterns. To enable data-driven and data-validated mechanistic modelling of these complex growth processes, it is crucial to first establish appropriate quantitative metrics beyond qualitative image comparisons. We present a quantification approach based on two scale-free metrics designed to characterize the shape of two-dimensional colonies.

Aggregation of adult parasitic nematodes in sex-mixed groups analysed by transient anomalous diffusion formalism.

Intestinal parasitic worms are widespread throughout the world, causing chronic infections in humans and animals. However, very little is known about the locomotion of the worms in the host gut. We studied the movement of naturally infecting mice, and used as an animal model for roundworm infections.

Inference of alveolar capillary network connectivity from blood flow dynamics.

The intricate lung structure is crucial for gas exchange within the alveolar region. Despite extensive research, questions remain about the connection between capillaries and the vascular tree. We propose a computational approach combining three-dimensional (3-D) morphological modeling with computational fluid dynamics simulations to explore alveolar capillary network connectivity based on blood flow dynamics.

Cardiac function in a large animal model of myocardial infarction at 7 T: deep learning based automatic segmentation increases reproducibility.

Cardiac magnetic resonance (CMR) imaging allows precise non-invasive quantification of cardiac function. It requires reliable image segmentation for myocardial tissue. Clinically used software usually offers automatic approaches for this step.

Self-organization as a mechanism of resilience in dryland ecosystems.

Self-organized spatial patterns are a common feature of complex systems, ranging from microbial communities to mussel beds and drylands. While the theoretical implications of these patterns for ecosystem-level processes, such as functioning and resilience, have been extensively studied, empirical evidence remains scarce. To address this gap, we analyzed global drylands along an aridity gradient using remote sensing, field data, and modeling.

Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding.

One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors.

Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection.

Introduction: Pro-thrombotic events are one of the prevalent causes of intensive care unit (ICU) admissions among COVID-19 patients, although the signaling events in the stimulated platelets are still unclear.

Methods: We conducted a comparative analysis of platelet transcriptome data from healthy donors, ICU, and non-ICU COVID-19 patients to elucidate these mechanisms. To surpass previous analyses, we constructed models of involved networks and control cascades by integrating a global human signaling network with transcriptome data.

Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization.

Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA.

The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors.

Embryos develop in a concerted sequence of spatiotemporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analyzed so far.

Recognition and reconstruction of cell differentiation patterns with deep learning.

Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell communication to replicate common spatial arrangements like checkerboard and engulfing patterns.

Assessing the agreement between the pneumatic and the flow-centrifuge method for estimating xylem safety in temperate diffuse-porous tree species.

The increasing frequency of global change-type droughts has created a need for fast, accurate and widely applicable techniques for estimating xylem embolism resistance to improve forecasts of future forest changes. We used data from 12 diffuse-porous temperate tree species covering a wide range of xylem safety to compare the pneumatic and flow-centrifuge method, two rapid methods used for constructing xylem vulnerability curves. We evaluated the agreement between parameters estimated with both methods and the sensitivity of pneumatic measurements to the duration of air discharge (AD) measurements.

Predicting Gene Regulatory Interactions Using Natural Genetic Variation.

Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds.

Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing.

During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular signaling. We present an analytically tractable mathematical model based on signaling that reliably generates different cell type patterns with specified proportions.

Theoretical assessment of persistence and adaptation in weeds with complex life cycles.

Herbicide-resistant weeds pose a substantial threat to global food security. Perennial weed species are particularly troublesome. Such perennials as Sorghum halepense spread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes.

Tissues as networks of cells: towards generative rules of complex organ development.

Network analysis is a well-known and powerful tool in molecular biology. More recently, it has been introduced in developmental biology. Tissues can be readily translated into spatial networks such that cells are represented by nodes and intercellular connections by edges.

Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance.

High-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose.

DeepCLEM: automated registration for correlative light and electron microscopy using deep learning.

In correlative light and electron microscopy (CLEM), the fluorescent images must be registered to the EM images with high precision. Due to the different contrast of EM and fluorescence images, automated correlation-based alignment is not directly possible, and registration is often done by hand using a fluorescent stain, or semi-automatically with fiducial markers. We introduce "DeepCLEM", a fully automated CLEM registration workflow.

Optimizing crop rotations via Parrondo's paradox for sustainable agriculture.

Crop rotation, a sustainable agricultural technique, has been at humanity's disposal since time immemorial and is practised globally. Switching between cover crops and cash crops helps avoid the adverse effects of intensive farming. Determining the optimum cash-cover rotation schedule for maximizing yield has been tackled on multiple fronts by agricultural scientists, economists, biologists and computer scientists, to name a few.

Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities.

Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves of Ranunculus acris and Trifolium pratense.

Corrigendum: Honeybees are buffered against undernourishment during larval stages.

[This corrects the article DOI: 10.3389/finsc.2022.

DYSCALCULIA, a Venus flytrap mutant without the ability to count action potentials.

The Venus flytrap Dionaea muscipula estimates prey nutrient content by counting trigger hair contacts initiating action potentials (APs) and calcium waves traveling all over the trap. A first AP is associated with a subcritical rise in cytosolic calcium concentration, but when the second AP arrives in time, calcium levels pass the threshold required for fast trap closure. Consequently, memory function and decision-making are timed via a calcium clock.

Predicting Microenvironment in CXCR4- and FAP-Positive Solid Tumors-A Pan-Cancer Machine Learning Workflow for Theranostic Target Structures.

(1) C-X-C Motif Chemokine Receptor 4 (CXCR4) and Fibroblast Activation Protein Alpha (FAP) are promising theranostic targets. However, it is unclear whether CXCR4 and FAP positivity mark distinct microenvironments, especially in solid tumors. (2) Using Random Forest (RF) analysis, we searched for entity-independent mRNA and microRNA signatures related to CXCR4 and FAP overexpression in our pan-cancer cohort from The Cancer Genome Atlas (TCGA) database-representing = 9242 specimens from 29 tumor entities.

Addressing controversies in the xylem embolism resistance-vessel diameter relationship.

Although xylem embolism is a key process during drought-induced tree mortality, its relationship to wood anatomy remains debated. While the functional link between bordered pits and embolism resistance is known, there is no direct, mechanistic explanation for the traditional assumption that wider vessels are more vulnerable than narrow ones. We used data from 20 temperate broad-leaved tree species to study the inter- and intraspecific relationship of water potential at 50% loss of conductivity (P ) with hydraulically weighted vessel diameter (D ) and tested its link to pit membrane thickness (T ) and specific conductivity (K ) on species level.

Seasonal flooding decreases fruit-feeding butterfly species dominance and increases spatial turnover in floodplain forests of central Amazonia.

The seasonal flood pulse in Amazonia can be considered a primary driver of community structure in floodplain environments. Although this natural periodic disturbance is part of the landscape dynamics, the seasonal inundation presents a considerable challenge to organisms that inhabit floodplain forests. The present study investigated the effect of seasonal flooding on fruit-feeding butterfly assemblages in different forest types and strata in central Amazonia.