COMPUTING THE FREQUENCY RESPONSE OF BIOCHEMICAL NETWORKS: A PYTHON MODULE.

In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models can be provided in standard SBML or Antimony format. The code takes into account any conserved moieties so that this software can be used to also study signaling networks where moiety cycles are common. A utility method is also provided to make it easy to plot standard Bode plots from the generated results. The code also takes into account the possibility that the phase shift could exceed 180 degrees which can result in ugly discontinues in the Bode plot. In the paper, some of the theory behind the method is provided as well as some commentary on the code and several illustrative examples to show the code in operation. Illustrative examples include linear reaction chains of varying lengths and the effect of negative feedback on the frequency response. Software License: MIT Open Source. Availability: The code is available from https://github.com/sys-bio/frequencyResponse.

Efficacy and outcomes of per oral plication of the (neo)esophagus (POPE) for impaired emptying in achalasia and post-esophagectomy patients.

BACKGROUND: Per-oral plication of the (neo)esophagus (POPE) is an endoscopic procedure used to improve emptying of the defunctionalized esophagus or gastric conduit, with the hope of improving symptoms and quality of life. As this procedure has only been performed in the United States for the past 4 years, safety and efficacy have not been well established. METHODS: This is a retrospective case series for patients who underwent POPE from a single institution between 2019 and 2023. Data collected included demographics, preoperative diagnoses and treatments, imaging, endoscopic data, operative intervention, 90-day complications, and response to treatment. Quality of life and patient satisfaction data were collected by phone survey. RESULTS: Seventeen cases were identified, encompassing 13 primary procedures and 4 repeat POPEs (re-POPE). Eight patients had end-stage achalasia and 5 had impaired gastric emptying after esophagectomy with gastric conduits. Median age was 65 years and median ASA was 3, with 38.5% female patients. POPE was performed with 2-6 plication sutures in an average of 75 min. The majority of patients discharged home the same day. For the 17 procedures, there were 4 complications. Two patients required antibiotics for pneumonia, while 4 required procedural intervention. There were no deaths. Preoperative symptoms improved or resolved at initial follow up in 82.3% of patients. Four patients experienced symptom recurrence and required re-POPE, 1 with achalasia and 3 with gastric conduits. Although all achalasia patients had an "end-stage esophagus," none have required esophagectomy since the introduction of POPE. CONCLUSIONS: POPE is an endoscopic procedure that is efficacious in relieving emptying difficulties for the end-stage esophagus and gastric conduit. It may obviate the need for esophagectomy or conduit replacement. Also, it can be repeated in select patients. While the risk profile of complications is favorable compared to alternative operations, patients with gastric conduits are at higher risk.

Generating synthetic signaling networks for in silico modeling studies.

Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological signaling networks. Thus, there is a need to develop new approaches to create predictive mechanistic models of complex systems. To meet this need, we developed a method for generating artificial signaling networks that were reasonably realistic and thus could be treated as ground truth models. These synthetic models could then be used to generate synthetic data for developing and testing algorithms designed to recover the underlying network topology and associated parameters. We defined the reaction degree and reaction distance to measure the topology of reaction networks, especially to consider enzymes. To determine whether our generated signaling networks displayed meaningful behavior, we compared them with signaling networks from the BioModels Database. This comparison indicated that our generated signaling networks had high topological similarities with BioModels signaling networks with respect to the reaction degree and distance distributions. In addition, our synthetic signaling networks had similar behavioral dynamics with respect to both steady states and oscillations, suggesting that our method generated synthetic signaling networks comparable with BioModels and thus could be useful for building network evaluation tools.

Correction: A novel cytoskeletal action of xylosides.

[This corrects the article DOI: 10.1371/journal.pone.0269972.].

Biosensors for the detection of chorismate and cis, cis-muconic acid in Corynebacterium glutamicum.

Corynebacterium glutamicum ATCC 13032 is a promising microbial chassis for industrial production of valuable compounds, including aromatic amino acids derived from the shikimate pathway. In this work, we developed two whole-cell, transcription factor based fluorescent biosensors to track cis, cis-muconic acid (ccMA) and chorismate in C. glutamicum. Chorismate is a key intermediate in the shikimate pathway from which value-added chemicals can be produced, and a shunt from the shikimate pathway can divert carbon to ccMA, a high value chemical. We transferred a ccMA-inducible transcription factor, CatM, from Acinetobacter baylyi ADP1 into C. glutamicum and screened a promoter library to isolate variants with high sensitivity and dynamic range to ccMA by providing benzoate, which is converted to ccMA intracellularly. The biosensor also detected exogenously supplied ccMA, suggesting the presence of a putative ccMA transporter in C. glutamicum, though the external ccMA concentration threshold to elicit a response was 100-fold higher than the concentration of benzoate required to do so through intracellular ccMA production. We then developed a chorismate biosensor, in which a chorismate inducible promoter regulated by natively expressed QsuR was optimized to exhibit a dose-dependent response to exogenously supplemented quinate (a chorismate precursor). A chorismate-pyruvate lyase encoding gene, ubiC, was introduced into C. glutamicum to lower the intracellular chorismate pool, which resulted in loss of dose-dependence to quinate. Further, a knockout strain that blocked the conversion of quinate to chorismate, also resulted in absence of dose-dependence to quinate, validating that the chorismate biosensor is specific to intracellular chorismate pool. The ccMA and chorismate biosensors were dually inserted into C. glutamicum to simultaneously detect intracellularly produced chorismate and ccMA. Biosensors, such as those developed in this study, can be applied in C. glutamicum for multiplex sensing to expedite pathway design and optimization through metabolic engineering in this promising chassis organism.

An Update to the SBML Human-Readable Antimony Language.

Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax. It allows users to easily create, modify, and distribute reproducible computational models. By allowing the concise representation of complex biological processes, Antimony enhances collaborative efforts, improves reproducibility, and accelerates the iterative development of models in systems biology. This paper provides an update to the Antimony language since it was introduced in 2009. In particular, we highlight new annotation features, support for flux balance analysis, a new rateOf method, support for probability distributions and uncertainty, named stochiometries, and algebraic rules. Antimony is also now distributed as a C/C++ library, together with python and Julia bindings, as well as a JavaScript version for use within a web browser. Availability: https://github.com/sys-bio/antimony.

MakeSBML: a tool for converting between Antimony and SBML.

We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language (SBML) and vice-versa. Since MakeSBML is a web-based application it requires no installation on the user's part. Currently, MakeSBML is hosted on a GitHub page where the client-based design makes it trivial to move to other hosts. This model for software deployment also reduces maintenance costs since an active server is not required. The SBML modeling language is often used in systems biology research to describe complex biochemical networks and makes reproducing models much easier. However, SBML is designed to be computer-readable, not human-readable. We therefore employ the human-readable Antimony language to make it easy to create and edit SBML models.

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.

Although the unfolded protein response (UPR) contributes to survival by removing misfolded proteins, endoplasmic reticulum (ER) stress also activates proapoptotic pathways. Changed sensitivity to normal developmental stimuli may underlie observed cardiomyocyte apoptosis in the healthy perinatal heart. We determined in vitro sensitivity to thapsigargin in sheep cardiomyocytes from four perinatal ages. In utero cardiac activation of ER stress and apoptotic pathways was determined at these same ages. Thapsigargin-induced phosphorylation of eukaryotic initiation factor 2 (EIF2A) was decreased by 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 TdT-mediated dUTP nick-end labeling (TUNEL) assay, was highest around the time of birth (P < 0.0001). There were changes in myocardial ER stress pathway components in utero. Glucose (78 kDa)-regulated protein (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). In conclusion, there is dynamic regulation of ER proteostasis, ER stress, and 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 the regulation of normal maturation in the healthy perinatal heart.NEW & NOTEWORTHY Cardiomyocyte apoptosis occurs even in the healthy, normally developing perinatal myocardium. As cardiomyocyte number is a critical contributor to heart health, the sensitivity of cardiomyocytes to endoplasmic reticulum stress leading to apoptosis is an important consideration. This study suggests that the heart has less robust protective mechanisms in response to endoplasmic reticulum stress immediately before and after birth, and that more cardiomyocyte death can be induced by stress in this period.

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.

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.

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.

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.

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.