Evaluating the Arrhenius equation for developmental processes

Assessment of hybrid fixed and moving bed biofilm applications for wastewater treatment capacity increase - In situ tests in El-Gouna WWTP, Egypt

This paper provides a procedure for comparing the performance of different biofilm carrier medias and their surrounding suspended biomass through oxygen uptake rate (OUR) tests. For in situ (oxygen uptake rate (OUR) measurements, three identical lab scale biofilm reactors were set up at the El Gouna wastewater treatment plant (WWTP). In this setup, two options of media for moving-bed biofilm reactors (MBBR) and one media for fixed-bed biofilm reactors (FBBR) were compared. The WWTP also used the same carrier in a real scale hybrid application to analyze how the interactions between the carrier type and the suspended biomass influences the overall performance. The in situ OUR approach is recommended to measure the contribution of the biofilm fixed biomass under site specific conditions. Specifically, settleability and diffusion limitations are the two opposite poles that cannot be predicted adequately for mild climate conditions based on the literature. A biofilm carrier application can add but actually can also reduce the capacity in a hybrid activated sludge system: The added MBBR-media was able to grind down the sludge flocs forming a poorly settleable suspended biomass. The added FBBR-media can lead to extracellular polymeric substances (EPS) rich biofilms that contribute very little as substrate and oxygen are unavailable for the microorganisms present in the biofilm. In this application of the comparison procedure, Kaldnes K1 like MBBR media was compared with a recycling MBBR carrier option (poly propylene bottle caps) and Jäger Envirotech "BioCurlz™" FBBR media. The study showed higher average rates for the MBBR but decreased settleability. The FBBR showed higher peak rates when flushed to break up the biofilm and well settleable sludge. The determination of OUR per g of volatile solids (SOUR) showed comparable results for all the carriers and in warm conditions, only the capacity to accommodate biomass determines the contribution of the carrier.

Degrees of freedom: temperature's influence on developmental rate

Temperature exerts a fundamental influence across scales of biology, from the biophysical nature of molecules, to the sensitivity of cells, and the coordinated progression of development in embryos. Species-specific developmental rates and temperature-induced acceleration of development indicate that these sensing mechanisms are harnessed to influence developmental dynamics. Tracing how temperature sensitivity propagates through biological scales to influence the pace of development can therefore reveal how embryogenesis remains robust to environmental influences. Cellular protein homeostasis (proteostasis), and cellular metabolic rate are linked to both temperature-induced and species-specific developmental tempos in specific cell types, hinting toward generalized mechanisms of timing control. New methods to extract timing information from single-cell profiling experiments are driving further progress in understanding how mechanisms of temperature sensitivity can direct cell-autonomous responses, coordination across cell types, and evolutionary modifications of developmental timing.

Iron-Single-Atom Nanozyme with NIR Enhanced Catalytic Activities for Facilitating MRSA-Infected Wound Therapy

Patients with methicillin-resistant Staphylococcus aureus (MRSA) infections may have higher death rates than those with non-drug-resistant infections. Nanozymes offer a promising approach to eliminating bacteria by producing reactive oxygen species. However, most of the conventional nanozyme technologies encounter significant challenges with respect to size, composition, and a naturally low number of active sites. The present study synthesizes a iron-single-atom structure (Fe-SAC) via nitrogen doped-carbon, a Fe-N5 catalyst (Fe-SAC) with a high metal loading (4.3 wt.%). This catalyst permits the development of nanozymes consisting of single-atom structures with active sites resembling enzymes, embedded within nanomaterials. Fe-SAC displays peroxidase-like activities upon exposure to H2O2. This structure facilitates the production of hydroxyl radicals, well-known for their strong bactericidal effects. Furthermore, the photothermal properties augment the bactericidal efficacy of Fe-SAC. The findings reveal that Fe-SAC disrupts the bacterial cell membranes and the biofilms, contributing to their antibacterial effects. The bactericidal properties of Fe-SAC are harnessed, which eradicates the MRSA infections in wounds and improves wound healing. Taken together, these findings suggest that single Fe atom nanozymes offer a novel perspective on the catalytic mechanism and design, holding immense potential as next-generation nanozymes.

Immobilization of l-asparaginase on chitosan nanoparticles for the purpose of long-term application

Asparaginase holds significant commercial value as an enzyme in the food and pharmaceutical industries. This study examined the optimum and practical use of the l-asparaginase derived from Pseudomonas aeruginosa HR03. Specifically, the study focused on the effectiveness of the stabilized enzyme when applied to chitosan nanoparticles. The structure, size, and morphology of chitosan nanoparticles were evaluated in relation to the immobilization procedure. This assessment involved the use of several analytical techniques, including FT-IR, DLS, SEM, TEM, and EDS analysis. Subsequently, the durability of the enzyme that has been stabilized was assessed by evaluating its effectiveness under extreme temperatures of 60 and 70 °C, as well as at pH values of 3 and 12. The findings indicate that incorporating chitosan nanoparticles led to enhanced immobilization of the l-asparaginase enzyme. This improvement was observed in terms of long-term stability, stability under crucial temperature and pH conditions, as well as thermal stability. In addition, the optimum temperature increased from 40 to 50 °C, and the optimum pH increased from 8 to 9. Enzyme immobilization led to an increase in Km and a decrease in kcat compared to its free counterpart. Because of its enhanced long-term stability, l-asparaginase immobilization on chitosan nanoparticles may be a potential choice for use in industries that rely on l-asparaginase enzymes, particularly the pharmaceutical and food industries.

Uncovering developmental time and tempo using deep learning

During animal development, embryos undergo complex morphological changes over time. Differences in developmental tempo between species are emerging as principal drivers of evolutionary novelty, but accurate description of these processes is very challenging. To address this challenge, we present here an automated and unbiased deep learning approach to analyze the similarity between embryos of different timepoints. Calculation of similarities across stages resulted in complex phenotypic fingerprints, which carry characteristic information about developmental time and tempo. Using this approach, we were able to accurately stage embryos, quantitatively determine temperature-dependent developmental tempo, detect naturally occurring and induced changes in the developmental progression of individual embryos, and derive staging atlases for several species de novo in an unsupervised manner. Our approach allows us to quantify developmental time and tempo objectively and provides a standardized way to analyze early embryogenesis.

The Clockwork Embryo: Mechanisms Regulating Developmental Rate

Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.

Model-driven insights into the effects of temperature on metabolism

Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future climate scenarios. A systems view of the effects of temperature on cellular physiology can be obtained by focusing on metabolism since: (i) its functions depend on transcription and translation and (ii) its outcomes support organisms' development, growth, and reproduction. Here we provide a systematic review of modelling efforts directed at investigating temperature effects on properties of single biochemical reactions, system-level traits, metabolic subsystems, and whole-cell metabolism across different prokaryotes and eukaryotes. We compare and contrast computational approaches and theories that facilitate modelling of temperature effects on key properties of enzymes and their consideration in constraint-based as well as kinetic models of metabolism. In addition, we provide a summary of insights from computational approaches, facilitating integration of omics data from temperature-modulated experiments with models of metabolic networks, and review the resulting biotechnological applications. Lastly, we provide a perspective on how different types of metabolic modelling can profit from developments in machine learning and models of different cellular layers to improve model-driven insights into the effects of temperature relevant for biotechnological applications.

Efficient Removal of Nitrate in Neutral Solution Using Zero-Valent Al Activated by Soaking

Nitrate is a contaminant widely found in surface water, and a high concentration of nitrate can pose a serious threat to human health. Zero-valent iron is widely used to reduce nitrate in aqueous solution, but an acidic condition is required. Zero-valent aluminum has a much lower redox potential (E₀(Al³⁺/Al⁰) = -1.662 V) than zero-valent iron (E₀(Fe²⁺/Fe⁰) = -0.44 V), making it a better choice for reduction of nitrate. However, a passive oxide film covering on Al surfaces inhibits its electron transfer. In this work, metal Al powder was activated by a soaking procedure in deionized water. It was found that nitrate in neutral solution can be efficiently and completely reduced by soaked Al, even if the concentration of nitrate-N was up to 100 mg L^-1. Using an optimal soaking time, the soaked Al can remove >90% of nitrate in aqueous solution within ∼2 h at 50 °C. Furthermore, the nitrate reduction efficiency increased with increasing reaction temperature and dosage of Al powder. After reaction, only ∼50% of pristine N content was left in the form of ammonia ions (NH₄⁺) in aqueous solution. Mechanism analyses showed that after soaking, Al particle surfaces were covered by a layer of loose and fine Al(OH)₃ grains, which can shorten the induction time for the beginning of the reaction between inner Al and outside ions or molecules. This is the reason why soaked Al has a high efficiency for nitrate removal. The present results indicate that soaking is an effective way to activate Al to remove nitrate in water.

A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function

Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.

Co-hydrothermal carbonization of oil shale and rice husk: Combustion, pyrolysis characteristics, and synergistic effect

Countries all over the world are looking for fuel to replace fossil energy due to environmental concerns and a scarcity of fossil fuels. Oil shale (OS) and rice husk (RH) are both viable fuels, although they both have issues like high ash content and poor calorific value. OS and RH were used as feedstock for high-quality fuel in this study, which uses a hydrothermal technique to provide a novel way to utilize OS and rice. At different hydrothermal temperatures (150, 200 and 250 °C), including combustion and pyrolysis processes, the thermogravimetric analyzer (TGA) was used to analyse thermal transformation characteristics of co-hydrothermal carbonization (co-HTC) of OS and RH, as well as the synergistic effects. Results showed that the co-HTC pretreatment had a significant effect on the thermal transformation behaviour of OS and RH. On the one hand, the co-HTC has higher volatile content than its calculated value. On the other hand, a synergistic effect was found in combustion processes, and this effect was the most obvious when the hydrothermal temperature was around 200 °C, and the characteristic peak of functional groups vibration was strong. Therefore, the co-HTC was considered suitable for combustion. The combination of co-HTC modification with subsequent thermochemical processes has positive implications for the energy production and utilization of organic waste.

Abdominal Organ Preservation Solutions in the Age of Machine Perfusion

The past decade has been the foreground for a radical revolution in the field of preservation in abdominal organ transplantation. Perfusion has increasingly replaced static cold storage as the preferred and even gold standard preservation method for marginal-quality organs. Perfusion is dynamic and offers several advantages in comparison with static cold storage. These include the ability to provide a continuous supply of new metabolic substrates, clear metabolic waste products, and perform some degree of organ viability assessment before actual transplantation in the recipient. At the same time, the ongoing importance of static cold storage cannot be overlooked, in particular when it comes to logistical and technical convenience and cost, not to mention the fact that it continues to work well for the majority of transplant allografts. The present review article provides an overview of the fundamental concepts of organ preservation, providing a brief history of static cold preservation and description of the principles behind and basic components of cold preservation solutions. An evaluation of current evidence supporting the use of different preservation solutions in abdominal organ transplantation is provided. As well, the range of solutions used for machine perfusion of abdominal organs is described, as are variations in their compositions related to changing metabolic needs paralleling the raising of the temperature of the perfusate from hypothermic to normothermic range. Finally, appraisal of new preservation solutions that are on the horizon is provided.

Manipulating the nature of embryonic mitotic waves

Early embryogenesis is characterized by rapid and synchronous cleavage divisions, which are often controlled by wave-like patterns of Cdk1 activity. Two mechanisms have been proposed for mitotic waves: sweep and trigger waves.1,2 The two mechanisms give rise to different wave speeds, dependencies on physical and molecular parameters, and spatial profiles of Cdk1 activity: upward sweeping gradients versus traveling wavefronts. Both mechanisms hinge on the transient bistability governing the cell cycle and are differentiated by the speed of the cell-cycle progression: sweep and trigger waves arise for rapid and slow drives, respectively. Here, using quantitative imaging of Cdk1 activity and theory, we illustrate that sweep waves are the dominant mechanism in Drosophila embryos and test two fundamental predictions on the transition from sweep to trigger waves. We demonstrate that sweep waves can be turned into trigger waves if the cell cycle is slowed down genetically or if significant delays in the cell-cycle progression are introduced across the embryo by altering nuclear density. Our genetic experiments demonstrate that Polo kinase is a major rate-limiting regulator of the blastoderm divisions, and genetic perturbations reducing its activity can induce the transition from sweep to trigger waves. Furthermore, we show that changes in temperature cause an essentially uniform slowdown of interphase and mitosis. That results in sweep waves being observed across a wide temperature range despite the cell-cycle durations being significantly different. Collectively, our combination of theory and experiments elucidates the nature of mitotic waves in Drosophila embryogenesis, their control mechanisms, and their mutual transitions.

Thermodynamic principles for system biology and the patterns of flower pigmentation

The thermodynamic principles for system biology are reviewed and formulated, and then basic patterns of flower pigmentation are interpreted. Main thoughts: (1) any biological trait (color or function of a cell) is logically related to a thermodynamic system (or physiological system, signaling network of the cell), (2) the striped, speckled and circle are three basic patterns of flower pigmentation, the development of flowers is an irreversible process, (3) the patterns of flower pigmentation are formed in flower development, (4) the flower cells can change its color in a period of development and this process is controlled thermodynamically, (5) there is giant space of physiology within an organism and within its numerous thermal states can appear under different conditions. In this theory, the dominant inheritance means that a gene contributes great to the thermodynamic stability of a trait related system; different genes can be interacted or integrated thermodynamically according to their contribution to the stability of its related system. By combination of Turing theory and our views, complex patterns of pigmentation could be explained theoretically.

Deviations from temporal scaling support a stage-specific regulation for C. elegans postembryonic development

Background

After embryonic development, Caenorhabditis elegans progress through for larval stages, each of them finishing with molting. The repetitive nature of C. elegans postembryonic development is considered an oscillatory process, a concept that has gained traction from regulation by a circadian clock gene homologue. Nevertheless, each larval stage has a defined duration and entails specific events. Since the overall duration of development is controlled by numerous factors, we have asked whether different rate-limiting interventions impact all stages equally.

Results

We have measured the duration of each stage of development for over 2500 larvae, under varied environmental conditions known to alter overall developmental rate. We applied changes in temperature and in the quantity and quality of nutrition and analysed the effect of genetically reduced insulin signalling. Our results show that the distinct developmental stages respond differently to these perturbations. The changes in the duration of specific larval stages seem to depend on stage-specific events. Furthermore, our high-resolution measurement of the effect of temperature on the stage-specific duration of development has unveiled novel features of temperature dependence in C. elegans postembryonic development.

Conclusions

Altogether, our results show that multiple factors fine tune developmental timing, impacting larval stages independently. Further understanding of the regulation of this process will allow modelling the mechanisms that control developmental timing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01295-2.

Temporal scaling in C. elegans larval development

An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development.

It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.