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Submerged macrophytes can overgrow and negatively affect freshwater ecosystems. This study aimed to investigate the use of chlormequat (CQ) to regulate submerged Vallisneria natans growth as well as its impact on the microbial community of epiphytic biofilms. V. natans height under CQ dosages of 20, 100, and 200 mg/L decreased within 21 days by 12.57%, 30.07%, and 44.62%, respectively, while chlorophyll content increased by 1.94%, 20.39%, and 38.83%. At 100 mg/L, CQ reduced the diversity of bacteria in the biofilm attached to V. natans leaves but increased the diversity of the eukaryotic microbial community. CQ strongly inhibited Cyanobacteria; compared with the control group, the treatment group experienced a significant reduction from 36.54% to 2.61%. Treatment significantly inhibited Gastrotricha and Rotifera, two dominant phyla of eukaryotes in the leaf biofilm, reducing their relative abundances by 17.41% and 6.48%, respectively. CQ significantly changed the leaf biofilm microbial community correlation network. The treatment group exhibited lower modularity (2.012) compared with the control group (2.249); however, the central network of the treated group contained a higher number of microbial genera (13) than the control group (4), highlighting the significance of eukaryotic genera in the network. The results obtained from this study provide invaluable scientific context and technical understanding pertinent to the restoration of submerged macrophytes within aquatic ecosystems. Practitioner Points: Chlormequat reduced the plant height but increased leaf chlorophyll content.Chlormequat reduced biofilm bacterial diversity but increased eukaryotic diversity.Chlormequat affected the bacterial‐fungal association networks in biofilms. [ABSTRACT FROM AUTHOR]

The capacity to regenerate lost organs is widespread among animals, and yet the number of species in which regeneration has been experimentally probed using molecular and functional assays is very small. This is also the case for insects, for which we still lack a complete picture of their regeneration mechanisms and the extent of their conservation. Here, we contribute to filling this gap by investigating regeneration in the mayfly Cloeon dipterum. We focus on the abdominal gills of Cloeon nymphs, which are critical for osmoregulation and gas exchange. After amputation, gills re-grow faster than they do during normal development. Direct cell count and EdU assays indicate that growth acceleration involves an uniform increase in cell proliferation throughout the gill, rather than a localized growth zone. Accordingly, transcriptomic analysis reveals an early enrichment in cell cycle-related genes. Other gene classes are also enriched in regenerating gills, including protein neddylation and other proteostatic processes. We then showed the conservation of these mechanisms by functionally testing protein neddylation, the activin signalling pathway or the mRNA-binding protein Lin28, among other genes, in Drosophila larval/pupal wing regeneration. Globally, our results contribute to elucidating regeneration mechanisms in mayflies and the conservation of mechanisms involved in regeneration across insects.

Advancing the synthesis of HfO2 nanocrystals, a refined anhydrous protocol that enables kinetic trapping of the metastable tetragonal phase and modulates twinning defects in anisotropically grown monoclinic nanoprisms is presented. This evolved sol–gel approach examines the role of the capping agent tri‐n‐octylphosphine oxide (TOPO) and introduces a novel heating strategy with sequential growth stages. Replacement of TOPO with triphenylphosphine oxide (TPPO) leads to the formation of prismatic hafnia nanocrystals exhibiting pristine {011}‐facets of the monoclinic phase. Furthermore, a hot‐injection inspired heating approach yields sub‐4 nm isotropic HfO2 nanocrystals in the tetragonal phase, bypassing the need for aliovalent cation species. In contrast, a heat‐up approach culminates in the generation of well‐characterized HfO2 nanorods. With sophisticated transmission electron microscopy analysis and the Wulff construction method, insights into the structural nucleation of nanoparticle growth are provided. This synthesis offers exceptional control and facilitates the formation of self‐assemblies akin to liquid crystals, opening the door for new applications with nanocolloidal HfO2. [ABSTRACT FROM AUTHOR]

Suppressor of cytokine signaling 1 (SOCS1) is a potent regulator immune cell responses and a proven tumor suppressor. Inhibition of SOCS1 in T cells can boost antitumor immunity, whereas its loss in tumor cells increases tumor aggressivity. Investigations into the tumor suppression mechanisms so far focused on tumor cell-intrinsic functions of SOCS1. However, it is possible that SOCS1 expression in tumor cells also regulate antitumor immune responses in a cell-extrinsic manner via direct and indirect mechanisms. Here, we discuss the evidence supporting the latter, and its implications for antitumor immunity. [ABSTRACT FROM AUTHOR]

The atypical cadherins Fat and Dachsous (Ds) signal through the Hippo pathway to regulate growth of numerous organs, including the Drosophila wing. Here, we find that Ds-Fat signaling tunes a unique feature of cell proliferation found to control the rate of wing growth during the third instar larval phase. The duration of the cell cycle increases in direct proportion to the size of the wing, leading to linear-like growth during the third instar. Ds-Fat signaling enhances the rate at which the cell cycle lengthens with wing size, thus diminishing the rate of wing growth. We show that this results in a complex but stereotyped relative scaling of wing growth with body growth in Drosophila. Finally, we examine the dynamics of Fat and Ds protein distribution in the wing, observing graded distributions that change during growth. However, the significance of these dynamics is unclear since perturbations in expression have negligible impact on wing growth.

Many cellular activities in bacteria are organized according to their growth rate. The notion that ppGpp measures the cell’s growth rate is well accepted in the field of bacterial physiology. However, despite decades of interrogation and the identification of multiple molecular interactions that connects ppGpp to some aspects of cell growth, we lack a system-level, quantitative picture of how this alleged “measurement” is performed. Through quantitative experiments, we show that the ppGpp pool responds inversely to the rate of translational elongation in Escherichia coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole.

Suppressor of cytokine signaling 1 (SOCS1) is a potent regulator immune cell responses and a proven tumor suppressor. Inhibition of SOCS1 in T cells can boost antitumor immunity, whereas its loss in tumor cells increases tumor aggressivity. Investigations into the tumor suppression mechanisms so far focused on tumor cell-intrinsic functions of SOCS1. However, it is possible that SOCS1 expression in tumor cells also regulate antitumor immune responses in a cell-extrinsic manner via direct and indirect mechanisms. Here, we discuss the evidence supporting the latter, and its implications for antitumor immunity.

Food resources are essential for the survival and growth of the population. Soil phytopathogenic nematodes cause great damage to agricultural crops, endangering food supplies and resources in general. Different methods have been used to control them. However, this issue still requires a more effective solution. Caenorhabditis elegans (CGC strain wild-type N2) was applied as a model with an Escherichia coli OP50 feeding substrate for nematodes. Our approach was based on the thermodynamically substantiated creation of growth conditions that are unfavorable for nematodes to suppress them irreversibly. The thermodynamic calculations showed that obligate anaerobic conditions, namely the absence of oxygen and a low redox potential (−100 mV and below), were potentially unacceptable for nematodes. Anaerobic conditions were created using both abiogenic (physicochemical) and biological methods. Abiogenic anaerobic conditions were achieved by preventing oxygen access and adding low-potential sodium sulfide (Eh = −250...−200 mV) to the cultivation medium. By applying biological methods, Pleurotus ostreatus Po4 and E. coli O2 was completely removed and the redox potential was decreased from +100...+200 mV to −100...−200 mV (in particular, due to the synthesis of H2S). Even the short-term exposure (1–2 days) of nematodes under anaerobic conditions led to their suppression and death. Thus, the short-term creation of anaerobic conditions in the soil may be an effective method to control, e.g., phytopathogenic aerobic nematodes. This research contributes to the development of foundations to preserve agricultural plants and increase crop yield as well as the development of an approach for the environmentally friendly control of phytopathogens. [ABSTRACT FROM AUTHOR]

Gradients of decapentaplegic (Dpp) pattern Drosophila wing imaginal discs, establishing gene expression boundaries at specific locations. As discs grow, Dpp gradients expand, keeping relative boundary positions approximately stationary. Such scaling fails in mutants for Pentagone (pent), a gene repressed by Dpp that encodes a diffusible protein that expands Dpp gradients. Although these properties fit a recent mathematical model of automatic gradient scaling, that model requires an expander that spreads with minimal loss throughout a morphogen field. Here, we show that Pent's actions are confined to within just a few cell diameters of its site of synthesis and can be phenocopied by manipulating non-diffusible Pent targets strictly within the Pent expression domain. Using genetics and mathematical modeling, we develop an alternative model of scaling driven by feedback downregulation of Dpp receptors and co-receptors. Among the model's predictions is a size beyond which scaling fails-something we observe directly in wing discs.

Rapid growth and survival are two key traits that enable bacterial cells to thrive in their natural habitat. The guanosine tetraphosphate and pentaphosphate [(p)ppGpp], also known as “magic spot”, is a key second messenger inside bacterial cells as well as chloroplasts of plants and green algae. (p)ppGpp not only controls various stages of central dogma processes (replication, transcription, ribosome maturation and translation) and central metabolism but also regulates various physiological processes such as pathogenesis, persistence, motility and competence. Under extreme conditions such as nutrient starvation, (p)ppGpp-mediated stringent response is crucial for the survival of bacterial cells. This mini-review highlights some of the very recent progress on the key role of (p)ppGpp in bacterial growth control in light of cellular resource allocation and cell size regulation. We also briefly discuss some recent functional insights into the role of (p)ppGpp in plants and green algae from the angle of growth and development and further discuss several important open directions for future studies.

The evolutionarily conserved Target of Rapamycin (TOR) complex-2 (TORC2) is an essential regulator of plasma membrane homeostasis in budding yeast (Saccharomyces cerevisiae). In this yeast, TORC2 phosphorylates and activates the effector protein kinase Ypk1 and its paralog Ypk2. These protein kinases, in turn, carry out all the crucial functions of TORC2 by phosphorylating and thereby controlling the activity of at least a dozen downstream substrates. A previously uncharacterized interplay between the Rab5 GTPases and TORC2 signaling was uncovered through analysis of a newly suspected Ypk1 target. Muk1, one of two guanine nucleotide exchange factors for the Rab5 GTPases, was found to be a physiologically relevant Ypk1 substrate; and, genetic analysis indicates that Ypk1-mediated phosphorylation activates the guanine nucleotide exchange activity of Muk1. Second, it was demonstrated both in vivo and in vitro that the GTP-bound state of the Rab5 GTPase Vps21/Ypt51 physically associates with TORC2 and acts as a direct positive effector required for full TORC2 activity. These interrelationships provide a self-reinforcing control circuit for sustained up-regulation of TORC2-Ypk1 signaling. In this overview, we summarize the experimental basis of these findings, their implications, and speculate as to the molecular basis for Rab5-mediated TORC2 activation.

Molybdenum trioxide (MoO3) with layered structures adopts exotic physical features, which has evoked an extensive interest in electronic and photoelectronic devices. Here, we report a low-cost, simplehandle, atmospheric-pressure, and rapid-synthesis technique for growing large-scale MoO3 crystals, i.e., a modified hot plate method. The growth rate and morphology of the MoO3 crystals were well controlled by changing source temperatures and substrates. Complementary measurements, including optical microscope, atomic force microscope, X-ray diffraction, Raman spectroscope, and scanning near-field optical microscope, were used to investigate the structural and physical properties. The results reveal that large-scale MoO3 crystals with well-defined crystallinity have been obtained. Meanwhile, surface hyperbolic phonon polaritons on as-prepared MoO3 crystal planes have also been observed, which may provide an attractive insight into nanoelectronic and nanophotonic devices. [ABSTRACT FROM AUTHOR]

Extracellular signal‐regulated kinase 7 (ERK7), also known as ERK8 and MAPK15, is an atypical member of the MAP kinase family. Compared with other MAP kinases, the biological roles of ERK7 remain poorly understood. Recent work, however, has revealed several novel functions for ERK7. These include a highly conserved essential role in ciliogenesis, the ability to control cell growth, metabolism and autophagy, as well as the maintenance of genomic integrity. ERK7 functions through phosphorylation‐dependent and ‐independent mechanisms and it is activated by cellular stressors, including DNA‐damaging agents, and nutrient deprivation. Here, we summarize recent developments in understanding ERK7 function, emphasizing its conserved roles in cellular and physiological regulation. [ABSTRACT FROM AUTHOR]

Food resources are essential for the survival and growth of the population. Soil phytopathogenic nematodes cause great damage to agricultural crops, endangering food supplies and resources in general. Different methods have been used to control them. However, this issue still requires a more effective solution. Caenorhabditis elegans (CGC strain wild-type N2) was applied as a model with an Escherichia coli OP50 feeding substrate for nematodes. Our approach was based on the thermodynamically substantiated creation of growth conditions that are unfavorable for nematodes to suppress them irreversibly. The thermodynamic calculations showed that obligate anaerobic conditions, namely the absence of oxygen and a low redox potential (−100 mV and below), were potentially unacceptable for nematodes. Anaerobic conditions were created using both abiogenic (physicochemical) and biological methods. Abiogenic anaerobic conditions were achieved by preventing oxygen access and adding low-potential sodium sulfide (Eh = −250...−200 mV) to the cultivation medium. By applying biological methods, Pleurotus ostreatus Po4 and E. coli O2 was completely removed and the redox potential was decreased from +100…+200 mV to −100...−200 mV (in particular, due to the synthesis of H2S). Even the short-term exposure (1–2 days) of nematodes under anaerobic conditions led to their suppression and death. Thus, the short-term creation of anaerobic conditions in the soil may be an effective method to control, e.g., phytopathogenic aerobic nematodes. This research contributes to the development of foundations to preserve agricultural plants and increase crop yield as well as the development of an approach for the environmentally friendly control of phytopathogens.

Zn-based batteries have attracted extensive attention due to their high theoretical energy density, safety, abundant resources, environmental friendliness, and low cost. They are a new energy storage and conversion technology with significant development potential and have been widely used in renewable energy and portable electronic devices. Considerable attempts have been devoted to improving the performance of Zn-based batteries. Specifically, battery cycle life and energy efficiency can be improved by electrolyte modification and the construction of highly efficient rechargeable Zn anodes. This review compiles the progress of the research related to Zn anodes and electrolytes, especially in the last five years. This review will introduce fundamental concepts, summarize recent development, and inspire further systematic research for high-performance Zn-based batteries in the future.

Metabolic engineering of microorganisms aims to design strains capable of producing valuable compounds under relevant industrial conditions and in an economically competitive manner. From this perspective, and beyond the need for a catalyst, biomass is essentially a cost-intensive, abundant by-product of a microbial conversion. Yet, few broadly applicable strategies focus on the optimal balance between product and biomass formation. Here, we present a genetic control module that can be used to precisely modulate growth of the industrial bacterial chassis Pseudomonas putida KT2440. The strategy is based on the controllable expression of the key metabolic enzyme complex pyruvate dehydrogenase (PDH) which functions as a metabolic valve. By tuning the PDH activity, we accurately controlled biomass formation, resulting in six distinct growth rates with parallel overproduction of excess pyruvate. We deployed this strategy to identify optimal growth patterns that improved the production yield of 2-ketoisovalerate and lycopene by 2.5- and 1.38-fold, respectively. This ability to dynamically steer fluxes to balance growth and production substantially enhances the potential of this remarkable microbial chassis for a wide range of industrial applications. • A genetic module was developed to precisely control growth and product formation in Pseudomonas putida KT2440. • Controllable expression of pyruvate dehydrogenase (PDH) resulted in six distinct growth rates and excess pyruvate. • Increased product formation at the expense of biomass. • Optimal growth patterns were identified that improved production yield of 2-ketoisovalerate and lycopene. [ABSTRACT FROM AUTHOR]

The evolutionarily conserved Hippo pathway coordinates cell proliferation, differentiation and apoptosis to regulate organ growth and tumorigenesis. Hippo signaling activity is tightly controlled by various upstream signals including growth factors and cell polarity, but the full extent to which the pathway is regulated during development remains to be resolved. Here, we report the identification of Shaggy, the homolog of mammalian Gsk3β, as a novel regulator of the Hippo pathway in Drosophila. Our results show that Shaggy promotes the expression of Hippo target genes in a manner that is dependent on its kinase activity. Loss of Shaggy leads to Yorkie inhibition and downregulation of Hippo pathway target genes. Mechanistically, Shaggy acts upstream of the Hippo pathway and negatively regulates the abundance of the FERM domain containing adaptor protein Expanded. Our results reveal that Shaggy is functionally required for Crumbs/Slmb-mediated downregulation of Expanded in vivo, providing a potential molecular link between cellular architecture and the Hippo signaling pathway. [ABSTRACT FROM AUTHOR]

Abstract Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems.

Plant glutamate receptor homologs (GLRs), which function as key calcium channels, play pivotal roles in various developmental processes as well as stress responses. The moss Physcomitrium patens, a representative of the earliest land plant lineage, possess multiple pathways of hormone signaling for coordinating growth and adaptation responses. However, it is not clear whether GLRs are connected to hormone-mediated growth control in the moss. In this study, we report that one of the two GLRs in P. patens, PpGLR1, involves in abscisic acid (ABA)-mediated growth regulation. ABA represses the growth of wild-type moss, and intriguingly, the PpGLR1 transcript levels are significantly increased in response to ABA treatment, based on both gene expression and the PpGLR1pro::GUS reporter results. Furthermore, the growth of Ppglr1 knockout moss mutants is hypersensitive to ABA treatment. These results suggest that PpGLR1 plays a critical role in ABA-mediated growth regulation, which provide useful information for our further investigation of the regulatory mechanism between Ca2+ signal and ABA in moss growth control.

Organ growth driven by cell proliferation is an exponential process. As a result, even small variations in proliferation rates, when integrated over a relatively long developmental time, will lead to large differences in size. How organs robustly control their final size despite perturbations in cell proliferation rates throughout development is a long-standing question in biology. Using a mathematical model, we show that in the developing wing of the fruit fly, Drosophila melanogaster, variations in proliferation rates of wing-committed cells are inversely proportional to the duration of cell recruitment, a differentiation process in which a population of undifferentiated cells adopt the wing fate by expressing the selector gene, vestigial. A time-course experiment shows that vestigial-expressing cells increase exponentially while recruitment takes place, but slows down when recruitable cells start to vanish, suggesting that undifferentiated cells may be driving proliferation of wing-committed cells. When this observation is incorporated in our model, we show that the duration of cell recruitment robustly determines a final wing size even when cell proliferation rates of wing-committed cells are perturbed. Finally, we show that this control mechanism fails when perturbations in proliferation rates affect both wing-committed and recruitable cells, providing an experimentally testable hypothesis of our model. [ABSTRACT FROM AUTHOR]

During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster. Mutant pups were severely stunted during the suckling period, but many recovered after weaning. After comparing seven distinct HoxD alleles, including CRISPR/Cas9 deletions involving Haglr, we identified Hoxd3 as the critical component for the gut to maintain milk-digestive competence. This essential function could be abrogated by the dominant-negative effect of HOXD10 as shown by a genetic rescue approach, thus further illustrating the importance of posterior prevalence in Hox gene function. A role for the lncRNA Haglr in the control of postnatal growth could not be corroborated.

The phytohormone abscisic acid (ABA) promotes plant tolerance to major stresses such as drought, partly by modulating growth through poorly understood mechanisms. Here, we show that ABA-triggered repression of cell proliferation in the Arabidopsis thaliana root meristem relies on the swift subcellular relocalization of SNF1-RELATED KINASE 1 (SnRK1). Under favorable conditions, the SnRK1 catalytic subunit, SnRK1α1, is enriched in the nuclei of root cells, and this is accompanied by normal cell proliferation and meristem size. Depletion of two key drivers of ABA signaling, SnRK2.2 and SnRK2.3, causes constitutive cytoplasmic localization of SnRK1α1 and reduced meristem size, suggesting that, under nonstress conditions, SnRK2s promote growth by retaining SnRK1α1 in the nucleus. In response to ABA, SnRK1α1 translocates to the cytoplasm, and this is accompanied by inhibition of target of rapamycin (TOR), decreased cell proliferation, and reduced meristem size. Blocking nuclear export with leptomycin B abrogates ABA-driven SnRK1α1 relocalization to the cytoplasm and ABA-elicited inhibition of TOR. Furthermore, fusing SnRK1α1 to an SV40 nuclear localization signal leads to defective ABA-dependent TOR repression. Altogether, we demonstrate that SnRK2-dependent changes in SnRK1α1 subcellular localization are crucial for inhibiting TOR and root growth in response to ABA. Rapid relocalization of central regulators such as SnRK1 may represent a general strategy of eukaryotic organisms to respond to environmental changes [ABSTRACT FROM AUTHOR]

Many cellular activities in bacteria are organized according to their growth rate. The notion that ppGpp measures the cell's growth rate is well accepted in the field of bacterial physiology. However, despite decades of interrogation and the identification of multiple molecular interactions that connects ppGpp to some aspects of cell growth, we lack a system-level, quantitative picture of how this alleged "measurement" is performed. Through quantitative experiments, we show that the ppGpp pool responds inversely to the rate of translational elongation in Escherichia coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole. [ABSTRACT FROM AUTHOR]

A fundamental biological question is how diverse and complex signaling and patterning is controlled correctly to generate distinct tissues, organs, and body plans, but incorrectly in diseased cells and tissues. Signaling pathways important for growth control have been identified, but to identify the mechanisms their transient and context-dependent interactions encode is more difficult. Currently computational systems biology aims to infer the control mechanisms by investigating quantitative changes of gene expression and protein concentrations, but this inference is difficult in nature. We propose it is desirable to explicitly simulate events and orders of gene regulation and protein interactions, which better elucidate control mechanisms, and report a method and tool with three examples. The Drosophila wing model includes Wnt, PCP, and Hippo pathways and mechanical force, incorporates well-confirmed experimental findings, and generates novel results. The other two examples illustrate the building of three-dimensional and large-scale models. These examples support that reconstructed spatiotemporal distributions of key signaling events help elucidate growth control mechanisms. As biologists pay increasing attention to disordered signaling in diseased cells, to develop new modeling methods and tools for conducting new computational studies is important.

Organ and tissue growth result from an integration of biophysical communication across biological scales, both in time and space. In this review, we highlight new insight into the dynamic connections between control mechanisms operating at different length scales. First, we consider how the dynamics of chemical and electrical signaling in the shape of gradients or waves affect spatiotemporal signal interpretation. Then, we discuss the mechanics underlying dynamic cell behavior during oriented tissue growth, followed by the connections between signaling at the tissue and organismal levels. [Display omitted] [ABSTRACT FROM AUTHOR]

Background: Microbial co-cultures and consortia are of interest in cell-based molecular production and even as "smart" therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results: We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture's phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions: Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems. [ABSTRACT FROM AUTHOR]

BackgroundHow tissue and organ sizes are specified is one of the great unsolved mysteries in biology. Experiments and mathematical modeling implicate feedback control of cell lineage progression, but a broad understanding of what lineage feedback accomplishes is lacking.ResultsBy exploring the possible effects of various biologically relevant disturbances on the dynamic and steady state behaviors of stem cell lineages, we find that the simplest and most frequently studied form of lineage feedback - which we term renewal control - suffers from several serious drawbacks. These reflect fundamental performance limits dictated by universal conservation-type laws, and are independent of parameter choice. Here we show that introducing lineage branches can circumvent all such limitations, permitting effective attenuation of a wide range of perturbations. The type of feedback that achieves such performance - which we term fate control - involves promotion of lineage branching at the expense of both renewal and (primary) differentiation. We discuss the evidence that feedback of just this type occurs in vivo, and plays a role in tissue growth control.ConclusionsRegulated lineage branching is an effective strategy for dealing with disturbances in stem cell systems. The existence of this strategy provides a dynamics-based justification for feedback control of cell fate in vivo.

Summary: Growth is a widely used term in plant science and ecology, but it can have different meanings depending on the context and the spatiotemporal scale of analysis. At the meristem level, growth is associated with the production of cells and initiation of new organs. At the organ or plant scale and over short time periods, growth is often used synonymously with tissue expansion, while over longer time periods the increase in biomass is a common metric. At even larger temporal and spatial scales, growth is mostly described as net primary production. Here, we first address the question 'what is growth?'. We propose a general framework to distinguish between the different facets of growth, and the corresponding physiological processes, environmental drivers and mathematical formalisms. Based on these different definitions, we then review how plant growth can be measured and analysed at different organisational, spatial and temporal scales. We conclude by discussing why gaining a better understanding of the different facets of plant growth is essential to disentangle genetic and environmental effects on the phenotype, and to uncover the causalities around source or sink limitations of plant growth. [ABSTRACT FROM AUTHOR]

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This paper provides a meta-synthesis review of land conflict management measures in peri-urban areas and categorizes them into: (a) containment measures; (b) controller measures; (c) moderator measures and (d) intensifier measures. This paper argues that, despite these measures, the peri-urban areas are still plagued by complex land conflicts from different aspects. Such a process requires effective management measures to deal with these conflicts which are at the heart of strategic measures. These measures emphasize the productive potential of development, institutional governance, cooperative approaches, and the self-sufficiency of peri-urban areas, and outline the future outlook for peri-urban areas in the form of productive, democratic, self-sufficient and accountable areas. Certainly, such a view can improve the performance and ability of peri-urban areas and create desirable socio-economic development and environmental quality, by modifying land conflict-generating forces. [ABSTRACT FROM AUTHOR]

Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite large-scale changes in protein expression associated with sensing, adaptation, and processing different environmental nutrients, simple growth laws connect the ribosome abundance and the growth rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal regulation that coordinate proteome-wide expression changes with cell growth in a variety of nutrient conditions in the model organism Escherichia coli. We identify supply-driven feedforward activation of ribosomal protein synthesis as the key regulatory motif maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth rate control, irrespective of the details of the molecular implementation. The study highlights the interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental operating constraints, with implications for endogenous and synthetic design of microorganisms.

Background: It is commonly believed that cancer development is irreversible, organ-specific as well as systemic malignant disorder, often associated with harmful oxidative stress and inflammation. However, there are also well-documented cases of spontaneous cancer regression, the causative mechanisms of which are not understood. It is known that inflammation is a negative pathophysiological process that may support the development of cancer, but it is also believed that the immune system as well as oxidative stress play important roles in prevention of cancer development and defense against tumor progression. Hence, in animal models spontaneous regression of cancer could be mediated by rapid inflammatory response of granulocytes, acting against cancer mostly as innate immune response. In addition, the administration of granulocytes at the site of solid tumors can lead to tumor regression or can slow down tumor growth and extend the overall survival of animals. In both cases, similar to the radiotherapy, surgery and various chemotherapies, oxidative stress occurs generating lipid peroxidation product 4-hydroxynonenal (4-HNE). This “second messenger of free radicals” acts as growth regulating signaling molecule that exerts relatively selective cytotoxicity against cancer cells. Conclusions: We hypothesize that abundant inflammation and metabolic changes caused by cancer and oxidative stress producing of 4-HNE may be crucial mechanisms for spontaneous cancer regression.

Modern analytical methods combined with the modern concepts of redox signaling revealed 4-hydroxy-2-nonenal (4-HNE) as particular growth regulating factor involved in redox signaling under physiological and pathophysiological circumstances. In this review current knowledge of the relevance of 4-HNE as "the second messenger of reactive oxygen species" (ROS) in redox signaling of representative major stress-associated diseases is briefly summarized. The findings presented allow for 4-HNE to be considered not only as second messenger of ROS, but also as one of fundamental factors of the stress- and age-associated diseases. While standard, even modern concepts of molecular medicine and respective therapies in majority of these diseases target mostly the disease-specific symptoms. 4-HNE, especially its protein adducts, might appear to be the bioactive markers that would allow better monitoring of specific pathophysiological processes reflecting their complexity. Eventually that could help development of advanced integrative medicine approach for patients and the diseases they suffer from on the personalized basis implementing biomedical remedies that would optimize beneficial effects of ROS and 4-HNE to prevent the onset and progression of the illness, perhaps even providing the real cure. Image 1 • 4-HNE plays important roles in pathophysiology of major stress-associated diseases. • 4-HNE affects signaling pathways in concentration- and cell-type dependent manner. • Pathophysiological effects of 4-HNE mostly involve relevant protein modifications. • Current pharmacological designs are unaware of pathophysiological roles of 4-HNE. • Integrative biomedicine should tackle the pathophysiology of 4-HNE signaling. [ABSTRACT FROM AUTHOR]

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Background: Oxygen availability and extracellular acidity both have a strong impact on growth and cultivation characteristics of eukaryotes, however they are often considered in isolation, whereby a single parameter is varied at a time to identify its impact, rendering the investigation of synergistic effects created by two or more factors nonachievable. This study identified the synergistic effect between environmental pH and oxygen levels on the physiological and cellular characteristics of the simplest eukaryote, Saccharomyces cerevisiae. Materials and methods: The physiological, transcriptomic, and metabolic responses of yeast were investigated during batch growth in a 2 × 2 factorial design setting; environmental pH and oxygen availability were either controlled at their optimal settings, or allowed to follow their own course during cultivation. Results: Synergistic effects had a significant impact on yeast physiology, which was provoked further by both the modulation of gene expression by transcription, and the modification of metabolite pools. Genes involved in cytoplasmic translation, the extracellular and intracellular amino acid and their precursor metabolite pools were significantly responsive to concurrent variations in these two factors. Conclusion: The synergistic effect of extracellular acidity and oxygenation on eukaryotic landscape of growth-associated events was significantly more pronounced than their individual effects. [ABSTRACT FROM AUTHOR]

The regulation of growth and the determination of organ-size in animals is an area of research that has received much attention during the past two and a half decades. Classic regeneration and cell-competition studies performed during the last century suggested that for size to be determined, organ-size is sensed and this sense of size feeds back into the growth control mechanism such that growth stops at the "correct" size. Recent work using Drosophila imaginal discs as a system has provided a particularly detailed cellular and molecular understanding of growth. Yet, a clear mechanistic basis for size-sensing has not emerged. I re-examine these studies from a different perspective and ask whether there is scope for alternate modes of size control in which size does not need to be sensed. [ABSTRACT FROM AUTHOR]

We designed a novel growth controller regulated by feeding of an unnatural amino acid, Nε-benzyloxycarbonyl-l-lysine (ZK), using a specific incorporation system at a sense codon. This system is constructed by a pair of modified pyrrolisyl-tRNA synthetase (PylRS) and its cognate tRNA (tRNApyl). Although ZK is non-toxic for normal organisms, the growth of Escherichia coli carrying the ZK incorporation system was inhibited in a ZK concentration-dependent manner without causing rapid bacterial death, presumably due to generation of non-functional or toxic proteins. The extent of growth inhibition strongly depended on the anticodon sequence of the tRNApyl gene. Taking advantage of the low selectivity of PylRS for tRNApyl anticodons, we experimentally determined the most effective anticodon sequence among all 64 nucleotide sequences in the anticodon region of tRNApyl gene. The results suggest that the ZK-regulated growth controller is a simple, target-specific, environmental noise-resistant and titratable system. This technique may be applicable to a wide variety of organisms because the growth inhibitory effects are caused by “informational disturbance”, in which the highly conserved system for transmission of information from DNA to proteins is perturbed.

Outside the immediate visage of regional policy analysts and smart growth boosters, the local growth control & growth management (LGC&M) movement remains extremely active, especially at the ballot box and especially in California. Analyses show LGC&M activity to be strongly correlated with state and regional growth rates—rising during expansionary periods such as the late-1980s and late-1990s, and falling during slowdown periods such as the early-1990s. Although exact numbers are hard to come by, it is estimated that about three-quarters of California cities and two-thirds of California counties have adopted some form of LGC&M program since 1980.Their continuing popularity notwithstanding, many questions remain about the efficacy and effects of LGC&M programs. Four are of particular interest:(1) To what extent do different LGC&M approaches really restrict the amount, pace, or location of growth? (2) To what extent are the resulting supply restrictions reflected in local real estate prices, especially housing prices? (3) Which LGC&M programs and approaches yield their promised benefits and which do not? (4) Do LGC&M programs cause growth to be systematically displaced from more restrictive to less restrictive communities, leading to such negative outcomes as sprawl and wasteful commuting?Using California as its lens, this report focuses on these unresolved questions. In no other US state is growth as tightly managed at the local level as California. Likewise, in no other state is there such a diversity of local growth management approaches and experiences. From a research perspective, because California lacks a statewide growth management framework, the effectiveness or ineffectiveness of growth management can be traced back to its local implementation. The report is organized into six sections: (1) Recent theoretical and empirical research into the use and efficacy of LGC&M programs; (2) An updated taxonomy of growth management and growth control measures, paying special attention to the circumstances under which such measures are likely to affect housing supplies; (3) Considering the question of efficacy by comparing pre- and post-control building permit volumes between specific growth-managed communities and carefully selected sets of comparison or peer communities; (4) Using GIS and cross-sectional regression analysis to identify empirical relationships between LGC&M programs, housing production shortfalls, and local housing prices; (5) Extending the peer-based comparison analysis to consider some of the potential benefits of growth management; and (6) Looking at the spatial displacement effects of LGC&M programs.

Amino acids stimulate the eukaryotic target of rapamycin complex 1 (TORC1), and hence growth, through the Rag GTPases and their regulators. Among these, the yeast Lst4-Lst7 Rag GTPase GAP complex clusters, as we previously reported, at the vacuolar membrane upon amino acid starvation. In response to amino acid refeeding, it activates the Rag GTPase-TORC1 branch and is then dispersed from the vacuolar surface. Here, we show that the latter effect is driven by TORC1 itself, which directly phosphorylates several residues within the intra-DENN loop of Lst4 that, only in its non-phosphorylated state, tethers the Lst4-Lst7 complex to the vacuolar membrane. An Lst4 variant disrupting this feedback inhibition mechanism causes TORC1 hyperactivation and proliferation defects in cells grown on poor nitrogen sources. Thus, we identify Lst4 as a TORC1 target and key node of a homeostatic mechanism that adjusts TORC1 activity to the availability of amino acids.

Reduced copy number of ribosomal protein (Rp) genes adversely affects both flies and mammals. Xrp1 encodes a reportedly Drosophila-specific AT-hook, bZIP protein responsible for many of the effects including the elimination of Rp mutant cells by competition with wild type cells. Irbp18, an evolutionarily conserved bZIP gene, heterodimerizes with Xrp1 and with another bZip protein, dATF4. We show that Irbp18 is required for the effects of Xrp1, whereas dATF4 does not share the same phenotype, indicating that Xrp1/Irbp18 is the complex active in Rp mutant cells, independently of other complexes that share Irbp18. Xrp1 and Irbp18 transcripts and proteins are upregulated in Rp mutant cells by auto-regulatory expression that depends on the Xrp1 DNA binding domains and is necessary for cell competition. We show that Xrp1 is conserved beyond Drosophila, although under positive selection for rapid evolution, and that at least one human bZip protein can similarly affect Drosophila development.

A newly discovered mechanism that causes the 'Minute' phenotype in fruit flies can explain how organisms are able to eliminate the mutant cells that arise occasionally during development.

Objective: To evaluate the effect of concentrations of different growth regulators and explant types on the formation of calluses from M. alba variety acorazonada. Materials and Methods: The work was conducted in the Plant Biotechnology Study Center of the University of Granma, Cuba. Fifteen treatments were carried out with the combination of three culture media with the explant types and positions. The culture media were complemented with the growth regulators 2,4-dicholorophenoxyacetic acid (2,0 mg L-1), 6-benzylaminopurine (2,0 mg L-1) + naphthaleneacetic acid (0,5 mg L-1) and 6-benzylaminopurine (2,0 mg L-1) + 2,4-dicholorophenoxyacetic acid (0,5 mg L-1). The explant types were leaf blades in abaxial and adaxial position, transversally and longitudinally sectioned stems and petioles. After 15 and 30 days, the beginning of callus formation, the zone in which they were formed, callus percentage, color and consistency, as well as the root formation percentage, were evaluated. Results: After 15 days, in all the explants and culture media morphological changes occurred. These modifications proved the beginning of callus formation, which reached higher values than 86% at 30 days of cultivation. The calluses that were formed from sectioned stems in culture media complemented with 6-benzylaminopurine (2,0 mg L-1) + 2,4-dicholorophenoxyacetic acid (0,5 mg L-1) showed better morphogenic characteristics. Conclusions: Callus formation was obtained in the different culture media and explant types of M. alba variety acorazonada, with higher values than 86%. The highest explant percentage with root formation was recorded from transversally sectioned stems in the culture medium with 2,4-dicholorophenoxyacetic acid, reaching values of 75%. [ABSTRACT FROM AUTHOR]