Signal integration and integral feedback control with biochemical reaction networks.

Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it enables a system's output to respond to changing inputs, but to then return exactly back to some pre-determined setpoint value afterward. To gain a deeper understanding of how biochemical networks are able to both integrate signals and perform integral feedback control, we investigated these abilities for several simple reaction networks. We found imperfect overlap between these categories, with some networks able to perform both tasks, some able to perform integration but not integral feedback control, and some the other way around. Nevertheless, networks that could either integrate or perform integral feedback control shared key elements. In particular, they included a chemical species that was neutrally stable in the open loop system (no feedback), meaning that this species does not have a unique stable steady-state concentration. Neutral stability could arise from zeroth order decay reactions, binding to a partner that was produced at a constant rate (which occurs in antithetic control), or through a long chain of covalent cycles. Mathematically, it arose from rate equations for the reaction network that were underdetermined when evaluated at steady-state.

Sensitivity and activation of endoplasmic reticulum stress response and apoptosis in the perinatal sheep heart.

While the unfolded protein response (UPR) contributes to survival by removing misfolded proteins, ER stress also activates pro-apoptotic pathways. Changed sensitivity to normal developmental stimuli may underlie observed cardiomyocyte apoptosis in the healthy perinatal heart. METHODS: We determined in vitro sensitivity to thapsigargin in sheep cardiomyocytes from four perinatal ages. In utero cardiac activation of endoplasmic reticulum (ER) stress and apoptotic pathways was determined at these same ages. RESULTS: Thapsigargin-induced phosphorylation of EIF2A decreased 72% between 135 and 143 dGA (P=0.0096) and remained low at 1 dPN (P=0.0080). Conversely, thapsigargin-induced caspase cleavage was highest around the time of birth: cleaved caspase 3 was highest at 1 dPN (3.8-fold vs. 135 dGA, P=0.0380; 7.8-fold vs. 5 dPN, P=0.0118), cleaved caspase 7 and cleaved caspase 12 both increased between 135 and 143 dGA (25-fold and 6.9-fold respectively, both P<0.0001), and remained elevated at 1 dPN. Induced apoptosis, measured by TUNEL assay, was highest around the time of birth (P<0.0001). There were changes in myocardial ER stress pathway components in utero. GRP78 protein levels were high in the fetus and declined after birth (P<0.0001). EIF2A phosphorylation was profoundly depressed at 1 dPN (vs. 143 dGA, P=0.0113). CONCLUSION: There is dynamic regulation of ER proteostasis, ER stress, and the apoptosis cascade in the perinatal heart. Apoptotic signaling is more readily activated in fetal cardiomyocytes near birth, leading to widespread caspase cleavage in the newborn heart. These pathways are important for regulation of normal maturation in the healthy perinatal heart.

KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons.

Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.

Nanoindentation into a bcc high-entropy HfNbTaTiZr alloy-an atomistic study of the effect of short-range order.

The plastic response of the Senkov HfNbTaTiZr high-entropy alloy is explored by means of simulated nanoindentation tests. Both a random alloy and an alloy with chemical short-range order are investigated and compared to the well understood case of an elementary Ta crystal. Strong differences in the dislocation plasticity between the alloys and the elementary Ta crystal are found. The high-entropy alloys show only little relaxation of the indentation dislocation network after indenter retraction and only negligible dislocation emission into the sample interior. Short-range order-besides making the alloy both stiffer and harder-further increases the size of the plastic zone and the dislocation density there. These features are explained by the slow dislocation migration in these alloys. Also, the short-range-ordered alloy features no twinning plasticity in contrast to the random alloy, while elemental Ta exhibits twinning under high stress but detwins considerably under stress relief. The results are in good qualitative agreement with our current knowledge of plasticity in high-entropy alloys.

An atomistic study of sticking, bouncing, and aggregate destruction in collisions of grains with small aggregates.

Molecular dynamics simulations are used to study central collisions between spherical grains and between grains and small grain aggregates (up to 5 grains). For a model material (Lennard-Jones), grain-grain collisions are sticking when the relative velocity v is smaller than the so-called bouncing velocity and bouncing for higher velocities. We find a similar behavior for grain-aggregate collisions. The value of the bouncing velocity depends only negligibly on the aggregate size. However, it is by 35% larger than the separation velocity needed to break a contact; this is explained by energy dissipation processes during the collision. The separation velocity follows the predictions of the macroscopic Johnson-Kendall-Roberts theory of contacts. At even higher collision velocities, the aggregate is destroyed, first by the loss of a monomer grain and then by total disruption. In contrast to theoretical considerations, we do not find a proportionality of the collision energy needed for destruction and the number of bonds to be broken. Our study thus sheds novel light on the foundations of granular mechanics, namely the energy needed to separate two grains, the difference between grain-grain and grain-aggregate collisions, and the energy needed for aggregate destruction.

Use of interactive mathematical simulations in fundamentals of biochemistry, a LibreText online educational resource, to promote understanding of dynamic reactions.

Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as memory, consciousness, and recognition of self and non-self. To understand how these interconnected reactions lead to cellular life characterized by activation, inhibition, regulation, homeostasis, and adaptation, computational analyses and simulations are essential, a fact recognized by the biological communities. At the same time, students struggle to understand and apply binding and kinetic analyses for the simplest reactions such as the irreversible first-order conversion of a single reactant to a product. This likely results from cognitive difficulties in combining structural, chemical, mathematical, and textual descriptions of binding and catalytic reactions. To help students better understand dynamic reactions and their analyses, we have introduced two kinds of interactive graphs and simulations into the online educational resource, Fundamentals of Biochemistry, a LibreText biochemistry book. One is available for simple binding and kinetic reactions. The other displays progress curves (concentrations vs. time) for simple reactions and complex metabolic and signal transduction pathways. Users can move sliders to change dissociation and kinetic constants as well as initial concentrations and see instantaneous changes in the graphs. They can also export data into a spreadsheet for further processing, such as producing derivative Lineweaver-Burk and traditional Michaelis-Menten graphs of initial velocity (v0) versus substrate concentration.

First-order ultrasensitivity in phosphorylation cycles.

Cellular signal transduction takes place through a network of phosphorylation cycles. These pathways take the form of a multi-layered cascade of cycles. This work focuses on the sensitivity of single, double and n length cycles. Cycles that operate in the zero-order regime can become sensitive to changes in signal, resulting in zero-order ultrasensitivity (ZOU). Using frequency analysis, we confirm previous efforts that cascades can act as noise filters by computing the bandwidth. We show that n length cycles display what we term first-order ultrasensitivity which occurs even when the cycles are not operating in the zero-order regime. The magnitude of the sensitivity, however, has an upper bound equal to the number of cycles. It is known that ZOU can be significantly reduced in the presence of retroactivity. We show that the first-order ultrasensitivity is immune to retroactivity and that the ZOU and first-order ultrasensitivity can be blended to create systems with constant sensitivity over a wider range of signal. We show that the ZOU in a double cycle is only modestly higher compared with a single cycle. We therefore speculate that the double cycle has evolved to enable amplification even in the face of retroactivity.

Prospective evaluation and follow-up of nutritional status of children hospitalized in secondary-care level hospitals: a multicentre study.

Although disease-associated undernutrition is still an important problem in hospitalized children that is often underrecognized, follow-up studies evaluating post-discharge nutritional status of children with undernutrition are lacking. The aim of this multicentre prospective observational cohort study was to assess the rate of acute undernutrition (AU) and/or having a high nutritional risk (HR) in children on admission to seven secondary-care level Dutch hospitals and to evaluate the nutritional course of AU/HR group during admission and post-discharge. STRONGkids was used to indicate HR, and AU was based on anthropometric data (z-score < -2 for weight-for-age (WFA; <1 year) or weight-for-height (WFH; ≥1 year)). In total, 1985 patients were screened for AU/HR over a 12-month period. On admission, AU was present in 9.9% of screened children and 6.2% were classified as HR; 266 (13.4%) children comprised the AU/HR group (median age 2.4 years, median length of stay 3 days). In this group, further nutritional assessment by a dietitian during hospitalization occurred in 44% of children, whereas 38% received nutritional support. At follow-up 4-8 weeks post-discharge, 101 out of orginal 266 children in the AU/HR group (38%) had available paired anthropometric measurements to re-assess nutrition status. Significant improvement of WFA/WFH compared to admission (-2.48 vs. -1.51 SD; p < 0.001) and significant decline in AU rate from admission to outpatient follow-up (69.3% vs. 35.6%; p < 0.001) were shown. In conclusion, post-discharge nutritional status of children with undernutrition and/or high nutritional risk on admission to secondary-care level pediatric wards showed significant improvement, but about one-third remained undernourished. Findings warrant the need for a tailored post-discharge nutritional follow-up.

Design patterns of biological cells.

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

Outcomes after per-oral endoscopic myotomy for Zenker's diverticula (Z-POEM) and correlation with impedance planimetry (FLIP).

INTRODUCTION: Zenker's diverticulum (ZD) is a false pulsion diverticulum of the cervical esophagus. It is typically found in older adults and manifests with dysphagia. The purpose of this study is to describe our experience with Per-oral endoscopic myotomy for Zenker's (Z-POEM) and intraoperative impedance planimetry (FLIP). METHODS: We performed a single institution retrospective review of patients undergoing Z-POEM in a prospective database between 2014 and 2022. Upper esophageal sphincter (UES) distensibility index (DI, mm2/mmHg) was measured by FLIP before and after myotomy. The primary outcome was clinical success. Secondary outcomes included technical failure, adverse events, and quality of life as assessed by the gastroesophageal health-related quality of life (GERD-HRQL), reflux severity index (RSI), and dysphagia score. A statistical analysis of DI was done with the paired t-test (p < 0.05). RESULTS: Fifty-four patients underwent Z-POEM, with FLIP measurements available in 30 cases. We achieved technical success and clinical success in 54/54 (100%) patients and 46/54 patients (85%), respectively. Three patients (6%) experienced contained leaks. Three patients were readmitted: one for aforementioned contained leak, one for dysphagia, and one post-operative pneumonia. Three patients with residual dysphagia underwent additional endoscopic procedures, all of whom had diverticula > 4 cm. Following myotomy, mean DI increased by 2.0 ± 1.7 mm2/mmHg (p < 0.001). In those with good clinical success, change in DI averaged + 1.6 ± 1.1 mm2/mmHg. Significant improvement was found in RSI and GERD-HRQL scores, but not dysphagia score. CONCLUSION: Z-POEM is a safe and feasible for treatment of ZD. We saw zero cases of intraoperative abandonment. We propose that large diverticula (> 4 cm) are a risk factor for poor outcomes and may require additional endoscopic procedures. An improvement in DI is expected after myotomy, however, the ideal range is still not known.

Adsorption of Diclofenac and PFBS on a Hair Keratin Dimer.

Environmental pollution by man-made toxic and persistent organic compounds, found throughout the world in surface and groundwater, has various negative effects on aquatic life systems and even humans. Therefore, it is important to develop and improve water treatment technologies capable of removing such substances from wastewater and purifying drinking water. The two substances investigated are the widely used painkiller diclofenac and a member of the class of "forever chemicals", perfluorobutanesulfonate. Both are known to have serious negative effects on living organisms, especially under long-term exposure, and are detectable in human hair, suggesting adsorption to a part of the hair fiber complex. In this study, a human hair keratin dimer is investigated for its ability to absorb diclofenac and perfluorobutanesulfonate. Initial predictions for binding sites are obtained via molecular docking and subjected to molecular dynamics simulations for more than 1 µs. The binding affinities obtained by the linear interaction energy method are high enough to motivate further research on human hair keratins as a sustainable, low-cost, and easily allocatable filtration material.

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

MOTIVATION: Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development. At present, the tools for text-based model development are limited, typically just a textual editor that provides features such as copy, paste, find, and replace. Since these tools are not "model aware," they do not provide features for: (i) model building such as autocompletion of species names; (ii) model analysis such as hover messages that provide information about chemical species; and (iii) model translation to convert between model representations. We refer to these as BAT features. RESULTS: We present VSCode-Antimony, a tool for building, analyzing, and translating models written in the Antimony modeling language, a human readable representation of Systems Biology Markup Language (SBML) models. VSCode-Antimony is a source editor, a tool with language-aware features. For example, there is autocompletion of variable names to assist with model building, hover messages that aid in model analysis, and translation between XML and Antimony representations of SBML models. These features result from making VSCode-Antimony model-aware by incorporating several sophisticated capabilities: analysis of the Antimony grammar (e.g. to identify model symbols and their types); a query system for accessing knowledge sources for chemical species and reactions; and automatic conversion between different model representations (e.g. between Antimony and SBML). AVAILABILITY AND IMPLEMENTATION: VSCode-Antimony is available as an open source extension in the VSCode Marketplace https://marketplace.visualstudio.com/items?itemName=stevem.vscode-antimony. Source code can be found at https://github.com/sys-bio/vscode-antimony.

The effect of collisions on the chemomechanics of ice-covered silica slabs: a molecular dynamics study.

Using molecular dynamics simulation and the REAX potential, we study the collision of two planar silica surfaces covered by water ice. Without the ice cover, the two surfaces stick at all velocities investigated (160-1800 m s-1), due to the formation of chemical bonds between the colliding surfaces. A narrow ice cover - here of thickness 2 nm - prevents the sticking above a characteristic velocity, the bouncing velocity νb. During the collision, reactions occur at the silica-water interface; in particular, water molecules are dissociated and silanols are formed at the surface of the silica slabs. Passivation of the silica surface by H atoms is of little consequence to the magnitude of vb but reduces the number of surface reactions occurring.

Sensitivity and Frequency Response of Biochemical Cascades.

Signal transduction from a cell's surface to cytoplasmic and nuclear targets takes place through a complex network of interconnected pathways. Phosphorylation cycles are common components of many pathways and may take the form of a multi-layered cascade of cycles or incorporate species with multiple phosphorylation sites that effectively create a sequence of cycles with increasing states of phosphorylation. This work focuses on the frequency response and sensitivity of such systems, two properties that have not been thoroughly examined. Starting with a singularly phosphorylated single-cycle system, we compare the sensitivity to perturbation at steady-state across a range of input signal strengths. This is followed by a frequency response analysis focusing on the gain and associated bandwidth. Next, we consider a two-layer cascade of single phosphorylation cycles and focus on how the two cycles interact to produce various effects on the bandwidth and damping properties. Then we consider the (ultra)sensitivity of a doubly phosphorylated system, where we describe in detail first-order ultrasensitivity, a unique property of these systems, which can be blended with zero-order ultrasensitivity to create systems with relatively constant gain over a range of signal input. Finally, we give an in-depth analysis of the sensitivity of an n-phosphorylated system.

Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids.

About 100 genes have been associated with significantly increased risks of autism spectrum disorders (ASD) with an estimate of ~1000 genes that may be involved. The new challenge now is to investigate the molecular and cellular functions of these genes during neural and brain development, and then even more challenging, to link the altered molecular and cellular phenotypes to the ASD clinical manifestations. In this study, we use single cell RNA-seq analysis to study one of the top risk gene, CHD8, in cerebral organoids, which models early neural development. We identify 21 cell clusters in the organoid samples, representing non-neuronal cells, neural progenitors, and early differentiating neurons at the start of neural cell fate commitment. Comparisons of the cells with one copy of the CHD8 knockout and their isogenic controls uncover thousands of differentially expressed genes, which are enriched with function related to neural and brain development, with genes and pathways previously implicated in ASD, but surprisingly not for Schizophrenia and intellectual disability risk genes. The comparisons also find cell composition changes, indicating potential altered neural differential trajectories upon CHD8 reduction. Moreover, we find that cell-cell communications are affected in the CHD8 knockout organoids, including the interactions between neural and glial cells. Taken together, our results provide new data for understanding CHD8 functions in the early stages of neural lineage development and interaction.

Design Patterns of Biological Cells.

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology in order to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

An automated model annotation system (AMAS) for SBML models.

MOTIVATION: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations. For example, recommender tools have been developed for annotations of genes. Although annotating genes is conceptually similar to annotating biochemical models, there are important technical differences that make it difficult to directly apply this prior work. RESULTS: We present AMAS, a system that predicts annotations for elements of models represented in the Systems Biology Markup Language (SBML) community standard. We provide a general framework for predicting model annotations for a query element based on a database of annotated reference elements and a match score function that calculates the similarity between the query element and reference elements. The framework is instantiated to specific element types (e.g. species, reactions) by specifying the reference database (e.g. ChEBI for species) and the match score function (e.g. string similarity). We analyze the computational efficiency and prediction quality of AMAS for species and reactions in BiGG and BioModels and find that it has subsecond response times and accuracy between 80% and 95% depending on specifics of what is predicted. We have incorporated AMAS into an open-source, pip-installable Python package that can run as a command-line tool that predicts and adds annotations to species and reactions to an SBML model. AVAILABILITY AND IMPLEMENTATION: Our project is hosted at https://github.com/sys-bio/AMAS, where we provide examples, documentation, and source code files. Our source code is licensed under the MIT open-source license.

Tissue Forge: Interactive biological and biophysics simulation environment.

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.

Severe neonatal enterovirus infection in twins with different outcomes: A case report.

Enteroviruses are among the most common causes of acute viral illness worldwide, and in neonates, the clinical course of these infections is heterogeneous. Severe complications, such as myocarditis, are associated with high mortality rates. In this case report, we present the clinical course of premature twins born at 35 weeks of gestational age, suffering from a severe neonatal enterovirus infection with cardiac involvement, which proved fatal in one of the twins. This course led to prompt identification in the other twin and facilitated timely transfer to a neonatal intensive care unit with neonatal hemodynamic expertise, and facilitated the timely transfer to a neonatal intensive care nit with hemodynamic expertise and immediate availability of AZCMO would it have been indicated. Early supportive therapy in the other twin contributed to a positive outcome. Therefore, we emphasize the importance of early recognition in averting adverse consequences. As a recommendation, we propose routine screening of enterovirus in viral panels for febrile newborns.

Strain-rate-dependent plasticity of Ta-Cu nanocomposites for therapeutic implants.

Recently, Ta/Cu nanocomposites have been widely used in therapeutic medical devices due to their excellent bioactivity and biocompatibility, antimicrobial property, and outstanding corrosion and wear resistance. Since mechanical yielding and any other deformation in the patient's body during treatment are unacceptable in medicine, the characterization of the mechanical behavior of these nanomaterials is of great importance. We focus on the microstructural evolution of Ta/Cu nanocomposite samples under uniaxial tensile loading conditions at different strain rates using a series of molecular dynamics simulations and compare to the reference case of pure Ta. The results show that the increase in dislocation density at lower strain rates leads to the significant weakening of the mechanical properties. The strain rate-dependent plastic deformation mechanism of the samples can be divided into three main categories: phase transitions at the extreme strain rates, dislocation slip/twinning at lower strain rates for coarse-grained samples, and grain-boundary based activities for the finer-grained samples. Finally, we demonstrate that the load transfer from the Ta matrix to the Cu nanoparticles via the interfacial region can significantly affect the plastic deformation of the matrix in all nanocomposite samples. These results will prove useful for the design of therapeutic implants based on Ta/Cu nanocomposites.