Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light.

Phytochrome A (phyA) is the only photoreceptor in plants, initiating responses in far-red light and, as such, essential for survival in canopy shade. Although the absorption and the ratio of active versus total phyA are maximal in red light, far-red light is the most efficient trigger of phyA-dependent responses. Using a joint experimental-theoretical approach, we unravel the mechanism underlying this shift of the phyA action peak from red to far-red light and show that it relies on specific molecular interactions rather than on intrinsic changes to phyA's spectral properties. According to our model, the dissociation rate of the phyA-FHY1/FHL nuclear import complex is a principle determinant of the phyA action peak. The findings suggest how higher plants acquired the ability to sense far-red light from an ancestral photoreceptor tuned to respond to red light.

Single cell variability of CRISPR-Cas interference and adaptation.

While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell-to-cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

Genetic and molecular analysis of trichome development in Arabis alpina.

The genetic and molecular analysis of trichome development in Arabidopsis thaliana has generated a detailed knowledge about the underlying regulatory genes and networks. However, how rapidly these mechanisms diverge during evolution is unknown. To address this problem, we used an unbiased forward genetic approach to identify most genes involved in trichome development in the related crucifer species Arabisalpina In general, we found most trichome mutant classes known in A. thaliana We identified orthologous genes of the relevant A. thaliana genes by sequence similarity and synteny and sequenced candidate genes in the A. alpina mutants. While in most cases we found a highly similar gene-phenotype relationship as known from Arabidopsis, there were also striking differences in the regulation of trichome patterning, differentiation, and morphogenesis. Our analysis of trichome patterning suggests that the formation of two classes of trichomes is regulated differentially by the homeodomain transcription factor AaGL2 Moreover, we show that overexpression of the GL3 basic helix-loop-helix transcription factor in A. alpina leads to the opposite phenotype as described in A. thaliana Mathematical modeling helps to explain how this nonintuitive behavior can be explained by different ratios of GL3 and GL1 in the two species.

Phytochrome B dynamics departs from photoequilibrium in the field.

Vegetation shade is characterized by marked decreases in the red/far-red ratio and photosynthetic irradiance. The activity of phytochrome in the field has typically been described by its photoequilibrium, defined by the photochemical properties of the pigment in combination with the spectral distribution of the light. This approach represents an oversimplification because phytochrome B (phyB) activity depends not only on its photochemical reactions but also on its rates of synthesis, degradation, translocation to the nucleus, and thermal reversion. To account for these complex cellular reactions, we used a model to simulate phyB activity under a range of field conditions. The model provided values of phyB activity that in turn predicted hypocotyl growth in the field with reasonable accuracy. On the basis of these observations, we define two scenarios, one is under shade, in cloudy weather, at the extremes of the photoperiod or in the presence of rapid fluctuations of the light environment caused by wind-induced movements of the foliage, where phyB activity departs from photoequilibrium and becomes affected by irradiance and temperature in addition to the spectral distribution. The other scenario is under full sunlight, where phyB activity responds mainly to the spectral distribution of the light.

Insight into nuclear body formation of phytochromes through stochastic modelling and experiment.

Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies (NBs). The underlying physical process of nuclear body formation remains unclear, but phytochrome B is thought to coagulate via a simple protein-protein binding process. We measure, for the first time, the distribution of the number of phytochrome B-containing NBs as well as their volume distribution. We show that the experimental data cannot be explained by a stochastic model of nuclear body formation via simple protein-protein binding processes using physically meaningful parameter values. Rather modelling suggests that the data is consistent with a two step process: a fast nucleation step leading to macroparticles followed by a subsequent slow step in which the macroparticles bind to form the nuclear body. An alternative explanation for the observed nuclear body distribution is that the phytochromes bind to a so far unknown molecular structure. We believe it is likely this result holds more generally for other nuclear body-forming plant photoreceptors and proteins.

A lipid zipper triggers bacterial invasion.

Glycosphingolipids are important structural constituents of cellular membranes. They are involved in the formation of nanodomains ("lipid rafts"), which serve as important signaling platforms. Invasive bacterial pathogens exploit these signaling domains to trigger actin polymerization for the bending of the plasma membrane and the engulfment of the bacterium--a key process in bacterial uptake. However, it is unknown whether glycosphingolipids directly take part in the membrane invagination process. Here, we demonstrate that a "lipid zipper," which is formed by the interaction between the bacterial surface lectin LecA and its cellular receptor, the glycosphingolipid Gb3, triggers plasma membrane bending during host cell invasion of the bacterium Pseudomonas aeruginosa. In vitro experiments with Gb3-containing giant unilamellar vesicles revealed that LecA/Gb3-mediated lipid zippering was sufficient to achieve complete membrane engulfment of the bacterium. In addition, theoretical modeling elucidated that the adhesion energy of the LecA-Gb3 interaction is adequate to drive the engulfment process. In cellulo experiments demonstrated that inhibition of the LecA/Gb3 lipid zipper by either lecA knockout, Gb3 depletion, or application of soluble sugars that interfere with LecA binding to Gb3 significantly lowered P. aeruginosa uptake by host cells. Of note, membrane engulfment of P. aeruginosa occurred independently of actin polymerization, thus corroborating that lipid zippering alone is sufficient for this crucial first step of bacterial host-cell entry. Our study sheds new light on the impact of glycosphingolipids in the cellular invasion of bacterial pathogens and provides a mechanistic explication of the initial uptake processes.

A continuum approximation to an off-lattice individual-cell based model of cell migration and adhesion.

Cell-cell adhesion plays a key role in the collective migration of cells and in determining correlations in the relative cell positions and velocities. Recently, it was demonstrated that off-lattice individual cell based models (IBMs) can accurately capture the correlations observed experimentally in a migrating cell population. However, IBMs are often computationally expensive and difficult to analyse mathematically. Traditional continuum-based models, in contrast, are amenable to mathematical analysis and are computationally less demanding, but typically correspond to a mean-field approximation of cell migration and so ignore cell-cell correlations. In this work, we address this problem by using an off-lattice IBM to derive a continuum approximation which does take into account correlations. We furthermore show that a mean-field approximation of the off-lattice IBM leads to a single partial integro-differential equation of the same form as proposed by Sherratt and co-workers to model cell adhesion. The latter is found to be only effective at approximating the ensemble averaged cell number density when mechanical interactions between cells are weak. In contrast, the predictions of our novel continuum model for the time-evolution of the ensemble cell number density distribution and of the density-density correlation function are in close agreement with those obtained from the IBM for a wide range of mechanical interaction strengths. In particular, we observe 'front-like' propagation of cells in simulations using both our IBM and our continuum model, but not in the continuum model simulations obtained using the mean-field approximation.

The ratio of the lateral correlation length and particle radius determines the density profile of spherical molecules near a fluctuating membrane.

Interactions between membranes and molecules are important for many biological processes, e.g., transport of molecules across cell membranes. However, the detailed physical description of the membrane-biomolecule system remains a challenge and simplified schemes allow capturing its main intrinsic features. In this work, by means of Monte Carlo computer simulations, we systematically study the distribution of uncharged spherical molecules in contact with a flexible surface. Our results show that the distribution for finite size particles has the same simple functional form as the one obtained for point-like particles and depends only on the ratio of the lateral correlation length of the membrane and the radius of the molecules.

Quantitative analysis of MBW complex formation in the context of trichome patterning.

Trichome patterning in Arabidopsis is regulated by R2R3MYB, bHLH and WDR (MBW) genes. These are considered to form a trimeric MBW protein complex that promotes trichome formation. The MBW proteins are engaged in a regulatory network to select trichome cells among epidermal cells through R3MYB proteins that can move between cells and repress the MBW complex by competitive binding with the R2R3MYB to the bHLHL protein. We use quantitative pull-down assays to determine the relative dissociation constants for the protein-protein interactions of the involved genes. We find similar binding strength between the trichome promoting genes and weaker binding of the R3MYB inhibitors. We used the dissociation constants to calculate the relative percentage of all possible complex combinations and found surprisingly low fractions of those complexes that are typically considered to be relevant for the regulation events. Finally, we predict an increased robustness in patterning as a consequence of higher ordered complexes mediated by GL3 dimerization.

Microparticles and multi-unit systems for advanced drug delivery.

Microparticles have unique benefits in the formulation of multiparticulate and multi-unit type pharmaceutical dosage forms allowing improved drug safety and efficacy with favorable pharmacokinetics and patient centricity. On the other hand, the above advantages are served by high and well reproducible quality attributes of the medicinal product where even flexible design and controlled processability offer success as well as possible longer product life-cycle for the manufacturers. Moreover, the specific demands of patients can be taken into account, including simplified dosing regimens, flexible dosage, drug combinations, palatability, and ease of swallowing. In the more than 70 years since the first modified-release formulation appeared on the market, many new formulations have been marketed and many publications have appeared in the literature. More unique and newer pharmaceutical technologies and excipients have become available for producing tailor-made particles with micrometer dimensions and beyond. All these have contributed to the fact that the sub-units (e.g. minitablets, pellets, microspheres) that make up a multiparticulate system can vary widely in composition and properties. Some units have mucoadhesive properties and others can float to contribute to a suitable release profile that can be designed for the multiparticulate formula as a whole. Nowadays, there are some available formulations on the market, which are able to release the active substance even for several months (3 or 6 months depending on the type of treatment). In this review, the latest developments in technologies that have been used for a long time are presented, as well as innovative solutions such as the applicability of 3D printing to produce subunits of multiparticulate systems. Furthermore, the diversity of multiparticulate systems, different routes of administration are also presented, touching the ones which are capable of carrying the active substance as well as the relevant, commercially available multiparticle-based medical devices. The versatility in size from 1 µm and multiplicity of formulation technologies promise a solid foundation for the future applications of dosage form design and development.

A coherent feed-forward loop in the Arabidopsis root stem cell organizer regulates auxin biosynthesis and columella stem cell maintenance.

Stem cells in plant meristems are kept undifferentiated by signals from surrounding cells and provide the basis for continuous organ formation. In the stem cell organizer of the Arabidopsis thaliana root, the quiescent centre (QC), the WOX5 transcription factor, functions as a central hub in regulating columella stem cell (CSC) homoeostasis. However, the processes mediating WOX5 function are only poorly understood. Here we identify the transcription factor HAN as a central mediator of WOX5-regulated stem cell maintenance. HAN is required for mitotic quiescence of QC and CSC maintenance and is sufficient to induce ectopic stem cells. WOX5 and HAN repress transcription of the differentiation factor gene CDF4 in a coherent feed-forward loop (cFFL), one output of which is the expression of the auxin biosynthesis gene TAA1 and maintenance of auxin response maxima in the organizer. These findings and mathematical modelling provide a mechanistic framework for WOX5 function in the root stem cell niche.

Signatures of nonlinearity in single cell noise-induced oscillations.

A class of theoretical models seeks to explain rhythmic single cell data by postulating that they are generated by intrinsic noise in biochemical systems whose deterministic models exhibit only damped oscillations. The main features of such noise-induced oscillations are quantified by the power spectrum which measures the dependence of the oscillatory signal's power with frequency. In this paper we derive an approximate closed-form expression for the power spectrum of any monostable biochemical system close to a Hopf bifurcation, where noise-induced oscillations are most pronounced. Unlike the commonly used linear noise approximation which is valid in the macroscopic limit of large volumes, our theory is valid over a wide range of volumes and hence affords a more suitable description of single cell noise-induced oscillations. Our theory predicts that the spectra have three universal features: (i) a dominant peak at some frequency, (ii) a smaller peak at twice the frequency of the dominant peak and (iii) a peak at zero frequency. Of these, the linear noise approximation predicts only the first feature while the remaining two stem from the combination of intrinsic noise and nonlinearity in the law of mass action. The theoretical expressions are shown to accurately match the power spectra determined from stochastic simulations of mitotic and circadian oscillators. Furthermore it is shown how recently acquired single cell rhythmic fibroblast data displays all the features predicted by our theory and that the experimental spectrum is well described by our theory but not by the conventional linear noise approximation.

Hyaluronic Acid in Rheumatology.

Hyaluronic acid (HA), also known as hyaluronan, is an anionic glycosaminoglycan widely distributed throughout various tissues of the human body. It stands out from other glycosaminoglycans as it lacks sulfation and can attain considerable size: the average human synovial HA molecule weighs about 7 million Dalton (Da), equivalent to roughly 20,000 disaccharide monomers; although some sources report a lower range of 3-4 million Da. In recent years, HA has garnered significant attention in the field of rheumatology due to its involvement in joint lubrication, cartilage maintenance, and modulation of inflammatory and/or immune responses. This review aims to provide a comprehensive overview of HA's involvement in rheumatology, covering its physiology, pharmacology, therapeutic applications, and potential future directions for enhancing patient outcomes. Nevertheless, the use of HA therapy in rheumatology remains controversial with conflicting evidence regarding its efficacy and safety. In conclusion, HA represents a promising therapeutic option to improve joint function and alleviate inflammation and pain.

9-Methyl-ß-carboline-induced cognitive enhancement is associated with elevated hippocampal dopamine levels and dendritic and synaptic proliferation.

ß-Carbolines (BCs) belong to the heterogenous family of carbolines, which have been found exogenously, that is, in various fruits, meats, tobacco smoke, alcohol and coffee, but also endogenously, that is, blood, brain and CSF. These exogenous and endogenous BCs and some of their metabolites can exert neurotoxic effects, however, an unexpected stimulatory effect of 9-methyl-ß-carboline (9-me-BC) on dopaminergic neurons in primary mesencephalic cultures was recently discovered. The aim of the present study was to extend our knowledge on the stimulatory effects of 9-me-BC and to test the hypothesis that 9-me-BC may act as a cognitive enhancer. We found that 10 days (but not 5 days) of pharmacological treatment with 9-me-BC (i) improves spatial learning in the radial maze, (ii) elevates dopamine levels in the hippocampal formation, and (iii) results after 10 days of treatment in elongated, more complex dendritic trees and higher spine numbers on granule neurons in the dentate gyrus of 9-me-BC-treated rats. Our results demonstrate that beyond its neuroprotective/neurorestorative and anti-inflammatory effects, 9-me-BC acts as a cognitive enhancer in a hippocampus-dependent task, and that the behavioral effects may be associated with a stimulatory impact on hippocampal dopamine levels and dendritic and synaptic proliferation.

Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling.

Plant organs grow to characteristic sizes that are genetically controlled. In animals, signaling by mobile growth factors is thought to be an effective mechanism for measuring primordium size, yet how plants gauge organ size is unclear. Here, we identify the Arabidopsis cytochrome P450 KLUH (KLU)/CYP78A5 as a stimulator of plant organ growth. While klu loss-of-function mutants form smaller organs because of a premature arrest of cell proliferation, KLU overexpression leads to larger organs with more cells. KLU promotes organ growth in a non-cell-autonomous manner, yet it does not appear to modulate the levels of known phytohormones. We therefore propose that KLU is involved in generating a mobile growth signal distinct from the classical phytohormones. The expression dynamics of KLU suggest a model of how the arrest of cell proliferation is coupled to the attainment of a certain primordium size, implying a common principle of size measurement in plants and animals.

Mathematical Modelling in Plant Synthetic Biology.

Mathematical modelling techniques are integral to current research in plant synthetic biology. Modelling approaches can provide mechanistic understanding of a system, allowing predictions of behaviour and thus providing a tool to help design and analyse biological circuits. In this chapter, we provide an overview of mathematical modelling methods and their significance for plant synthetic biology. Starting with the basics of dynamics, we describe the process of constructing a model over both temporal and spatial scales and highlight crucial approaches, such as stochastic modelling and model-based design. Next, we focus on the model parameters and the techniques required in parameter analysis. We then describe the process of selecting a model based on tests and criteria and proceed to methods that allow closer analysis of the system's behaviour. Finally, we highlight the importance of uncertainty in modelling approaches and how to deal with a lack of knowledge, noisy data, and biological variability; all aspects that play a crucial role in the cooperation between the experimental and modelling components. Overall, this chapter aims to illustrate the importance of mathematical modelling in plant synthetic biology, providing an introduction for those researchers who are working with or working on modelling techniques.

Comparative expression analysis in three Brassicaceae species revealed compensatory changes of the underlying gene regulatory network.

Trichomes are regularly distributed on the leaves of Arabidopsis thaliana. The gene regulatory network underlying trichome patterning involves more than 15 genes. However, it is possible to explain patterning with only five components. This raises the questions about the function of the additional components and the identification of the core network. In this study, we compare the relative expression of all patterning genes in A. thaliana, A. alpina and C. hirsuta by qPCR analysis and use mathematical modelling to determine the relative importance of patterning genes. As the involved proteins exhibit evolutionary conserved differential complex formation, we reasoned that the genes belonging to the core network should exhibit similar expression ratios in different species. However, we find several striking differences of the relative expression levels. Our analysis of how the network can cope with such differences revealed relevant parameters that we use to predict the relevant molecular adaptations in the three species.

Review on Starter Pellets: Inert and Functional Cores.

A significant proportion of pharmaceuticals are now considered multiparticulate systems. Modified-release drug delivery formulations can be designed with engineering precision, and patient-centric dosing can be accomplished relatively easily using multi-unit systems. In many cases, Multiple-Unit Pellet Systems (MUPS) are formulated on the basis of a neutral excipient core which may carry the layered drug surrounded also by functional coating. In the present summary, commonly used starter pellets are presented. The manuscript describes the main properties of the various nuclei related to their micro- and macrostructure. In the case of layered pellets formed based on different inert pellet cores, the drug release mechanism can be expected in detail. Finally, the authors would like to prove the industrial significance of inert cores by presenting some of the commercially available formulations.

Candida glabrata tryptophan-based pigment production via the Ehrlich pathway.

Pigments contribute to the pathogenicity of many fungi, mainly by protecting fungal cells from host defence activities. Here, we have dissected the biosynthetic pathway of a tryptophan-derived pigment of the human pathogen Candida glabrata, identified key genes involved in pigment production and have begun to elucidate the possible biological function of the pigment. Using transcriptional analyses and a transposon insertion library, we have identified genes associated with pigment production. Targeted deletion mutants revealed that the pigment is a by-product of the Ehrlich pathway of tryptophan degradation: a mutant lacking a tryptophan-upregulated aromatic aminotransferase (Aro8) displayed significantly reduced pigmentation and a recombinantly expressed version of this protein was sufficient for pigment production in vitro. Pigment production is tightly regulated as the synthesis is affected by the presence of alternative nitrogen sources, carbon sources, cyclic AMP and oxygen. Growth of C. glabrata on pigment inducing medium leads to an increased resistance to hydrogen peroxide, an effect which was not observed with a mutant defective in pigmentation. Furthermore, pigmented yeast cells had a higher survival rate when exposed to human neutrophils and caused increased damage in a monolayer model of human epithelia, indicating a possible role of pigmentation during interactions with host cells.

Gene acquisition, duplication and metabolic specification: the evolution of fungal methylisocitrate lyases.

Gene duplication represents an evolutionary mechanism for expanding metabolic potential. Here we analysed the evolutionary relatedness of isocitrate and methylisocitrate lyases, which are key enzymes of the glyoxylate and methylcitrate cycle respectively. Phylogenetic analyses imply that ancient eukaryotes acquired an isocitrate lyase gene from a prokaryotic source, but it was lost in some eukaryotic lineages. However, protists, oomycetes and most fungi maintained this gene and successfully integrated the corresponding enzyme into the glyoxylate cycle. A second gene, encoding a highly related enzyme, is present in fungi, but absent from other eukaryotes. This methylisocitrate lyase is specifically involved in propionyl-CoA degradation via the methylcitrate cycle. Although bacteria possess methylisocitrate lyases with a structural fold similar to that of isocitrate lyases, their sequence identity to fungal methylisocitrate lyases is low. Phylogenetic analyses imply that fungal methylisocitrate lyases arose from gene duplication of an ancient isocitrate lyase gene from the basidiomycete lineage. Mutagenesis of active-site residues of a bacterial and fungal isocitrate lyase, which have been predicted to direct the substrate specificity of iso- and methylisocitrate lyases, experimentally confirmed the possibility of direct evolution of methylisocitrate lyases from isocitrate lyases. Thus, gene duplication has increased the metabolic capacity of fungi.