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.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

Python interfaces for the Smoldyn simulator.

MOTIVATION: Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ application programming interface (API), which were convenient, but limited extensibility. RESULTS: We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators. It includes low-level functions that closely mimic the existing C/C++ API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions. AVAILABILITY AND IMPLEMENTATION: Smoldyn is open source and free, available at http://www.smoldyn.org and can be installed with the Python package manager pip. It runs on Mac, Windows and Linux.Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.

Effects of surfaces and macromolecular crowding on bimolecular reaction rates.

Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using analytical theory and particle-based simulations. A reaction rate equation based on only these two processes turned out to be inconsistent with simulation results. However, accounting for diffusion inhibition by the surfaces of nearby obstacles, which affects access to reactants, it led to perfect agreement for reactions near impermeable planar membranes and improved agreement for reactions in crowded spaces. A separate model that quantified reactant occlusion by crowders, and extensions to a thermodynamic 'cavity' model proposed by Berezhkovskii and Szabo [25], were comparably successful. These results help elucidate reaction dynamics in confined spaces and improve prediction of in vivo reaction rates from in vitro ones.

Using Blockchain Technology to Mitigate Challenges in Service Access for the Homeless and Data Exchange Between Providers: Qualitative Study.

BACKGROUND: In the homeless population, barriers to housing and supportive services include a lack of control or access to data. Disparate data formats and storage across multiple organizations hinder up-to-date intersystem access to records and a unified view of an individual's health and documentation history. The utility of blockchain to solve interoperability in health care is supported in recent literature, but the technology has yet to be tested in real-life conditions encompassing the complex regulatory standards in the health sector. OBJECTIVE: This study aimed to test the feasibility and performance of a blockchain system in a homeless community to securely store and share data across a system of providers in the health care ecosystem. METHODS: We performed a series of platform demonstrations and open-ended qualitative feedback interviews to determine the key needs and barriers to user and stakeholder adoption. Account creation and data transactions promoting organizational efficiency and improved health outcomes in this population were tested with homeless users and service providers. RESULTS: Persons experiencing homelessness and care organizations could successfully create accounts, grant and revoke data sharing permissions, and transmit documents across a distributed network of providers. However, there were issues regarding the security of shared data, user experience and adoption, and organizational preparedness for service providers as end users. We tested a set of assumptions related to these problems within the project time frame and contractual obligations with an existing blockchain-based platform. CONCLUSIONS: Blockchain technology provides decentralized data sharing, validation, immutability, traceability, and integration. These core features enable a secure system for the management and distribution of sensitive information. This study presents a concrete evaluation of the effectiveness of blockchain through an existing platform while revealing limitations from the perspectives of user adoption, cost-effectiveness, scalability, and regulatory frameworks.

Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli.

The outer membrane of gram-negative bacteria is composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. LPS is an endotoxin that elicits a strong immune response from humans, and its biosynthesis is in part regulated via degradation of LpxC (EC 3.5.1.108) and WaaA (EC 2.4.99.12/13) enzymes by the protease FtsH (EC 3.4.24.-). Because the synthetic pathways for both molecules are complex, in addition to being produced in strict ratios, we developed a computational model to interrogate the regulatory mechanisms involved. Our model findings indicate that the catalytic activity of LpxK (EC 2.7.1.130) appears to be dependent on the concentration of unsaturated fatty acids. This is biologically important because it assists in maintaining LPS/phospholipids homeostasis. Further crosstalk between the phospholipid and LPS biosynthetic pathways was revealed by experimental observations that LpxC is additionally regulated by an unidentified protease whose activity is independent of lipid A disaccharide concentration (the feedback source for FtsH-mediated LpxC regulation) but could be induced in vitro by palmitic acid. Further experimental analysis provided evidence on the rationale for WaaA regulation. Overexpression of waaA resulted in increased levels of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) sugar in membrane extracts, whereas Kdo and heptose levels were not elevated in LPS. This implies that uncontrolled production of WaaA does not increase the LPS production rate but rather reglycosylates lipid A precursors. Overall, the findings of this work provide previously unidentified insights into the complex biogenesis of the Escherichia coli outer membrane.

Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.

Motivation: Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Results: Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface. Availability and Implementation: Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org . Contact: steven.s.andrews@gmail.com.

Multiscale reaction-diffusion simulations with Smoldyn.

UNLABELLED: Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have. AVAILABILITY AND IMPLEMENTATION: Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.

Development of an Experimental Animal Model for Lower Back Pain by Percutaneous Injury-Induced Lumbar Facet Joint Osteoarthritis.

We report generation and characterization of pain-related behavior in a minimally invasive facet joint degeneration (FJD) animal model in rats. FJD was produced by a non-open percutaneous puncture-induced injury on the right lumbar FJs at three consecutive levels. Pressure hyperalgesia in the lower back was assessed by measuring the vocalization response to pressure from a force transducer. After hyperalgesia was established, pathological changes in lumbar FJs and alterations of intervertebral foramen size were assessed by histological and imaging analyses. To investigate treatment options for lumber FJ osteoarthritis-induced pain, animals with established hyperalgesia were administered with analgesic drugs, such as morphine, a selective COX-2 inhibitor, a non-steroidal anti-inflammatory drug (NSAID) (ketorolac), or pregabalin. Effects were assessed by behavioral pain responses. One week after percutaneous puncture-induced injury of the lumbar FJs, ipsilateral primary pressure hyperalgesia developed and was maintained for at least 12 weeks without foraminal stenosis. Animals showed decreased spontaneous activity, but no secondary hyperalgesia in the hind paws. Histopathological and microfocus X-ray computed tomography analyses demonstrated that the percutaneous puncture injury resulted in osteoarthritis-like structural changes in the FJs cartilage and subchondral bone. Pressure hyperalgesia was completely reversed by morphine. The administration of celecoxib produced moderate pain reduction with no statistical significance while the administration of ketorolac and pregabalin produced no analgesic effect on FJ osteoarthritis-induced back pain. Our animal model of non-open percutanous puncture-induced injury of the lumbar FJs in rats shows similar characteristics of low back pain produced by human facet arthropathy.

Terahertz waveguiding between parallel dielectric films.

We report a study of terahertz waveguiding between parallel dielectric films, a system that can be viewed as a planar analogue of hollow core fibres that exploit anti-resonant reflection optical waveguiding (ARROW). With the aid of time domain waveguide mode imaging, the frequency dependent transition from ARROW to total internal reflection guiding in the individual films as the film separation is reduced and the effect on the transmission of adding variably spaced cladding layers are clearly revealed. Good agreement for the transmission, dispersion and loss is obtained with simple analytical models for film separations greater than about five wavelengths suggesting that the same models could be usefully used to predict the behavior in the case of the technologically more important cylindrical geometry.

Methods for modeling cytoskeletal and DNA filaments.

This review summarizes the models that researchers use to represent the conformations and dynamics of cytoskeletal and DNA filaments. It focuses on models that address individual filaments in continuous space. Conformation models include the freely jointed, Gaussian, angle-biased chain (ABC), and wormlike chain (WLC) models, of which the first three bend at discrete joints and the last bends continuously. Predictions from the WLC model generally agree well with experiment. Dynamics models include the Rouse, Zimm, stiff rod, dynamic WLC, and reptation models, of which the first four apply to isolated filaments and the last to entangled filaments. Experiments show that the dynamic WLC and reptation models are most accurate. They also show that biological filaments typically experience strong hydrodynamic coupling and/or constrained motion. Computer simulation methods that address filament dynamics typically compute filament segment velocities from local forces using the Langevin equation and then integrate these velocities with explicit or implicit methods; the former are more versatile and the latter are more efficient. Much remains to be discovered in biological filament modeling. In particular, filament dynamics in living cells are not well understood, and current computational methods are too slow and not sufficiently versatile. Although primarily a review, this paper also presents new statistical calculations for the ABC and WLC models. Additionally, it corrects several discrepancies in the literature about bending and torsional persistence length definitions, and their relations to flexural and torsional rigidities.

Launching a virtual decision lab: development and field-testing of a web-based patient decision support research platform.

BACKGROUND: Over 100 trials show that patient decision aids effectively improve patients' information comprehension and values-based decision making. However, gaps remain in our understanding of several fundamental and applied questions, particularly related to the design of interactive, personalized decision aids. This paper describes an interdisciplinary development process for, and early field testing of, a web-based patient decision support research platform, or virtual decision lab, to address these questions. METHODS: An interdisciplinary stakeholder panel designed the web-based research platform with three components: a) an introduction to shared decision making, b) a web-based patient decision aid, and c) interactive data collection items. Iterative focus groups provided feedback on paper drafts and online prototypes. A field test assessed a) feasibility for using the research platform, in terms of recruitment, usage, and acceptability; and b) feasibility of using the web-based decision aid component, compared to performance of a videobooklet decision aid in clinical care. RESULTS: This interdisciplinary, theory-based, patient-centered design approach produced a prototype for field-testing in six months. Participants (n = 126) reported that: the decision aid component was easy to use (98%), information was clear (90%), the length was appropriate (100%), it was appropriately detailed (90%), and it held their interest (97%). They spent a mean of 36 minutes using the decision aid and 100% preferred using their home/library computer. Participants scored a mean of 75% correct on the Decision Quality, Knowledge Subscale, and 74 out of 100 on the Preparation for Decision Making Scale. Completing the web-based decision aid reduced mean Decisional Conflict scores from 31.1 to 19.5 (p < 0.01). CONCLUSIONS: Combining decision science and health informatics approaches facilitated rapid development of a web-based patient decision support research platform that was feasible for use in research studies in terms of recruitment, acceptability, and usage. Within this platform, the web-based decision aid component performed comparably with the videobooklet decision aid used in clinical practice. Future studies may use this interactive research platform to study patients' decision making processes in real-time, explore interdisciplinary approaches to designing web-based decision aids, and test strategies for tailoring decision support to meet patients' needs and preferences.

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.

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.

Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer.

Somatic mutations are a major source of cancer development, and many driver mutations have been identified in protein coding regions. However, the function of mutations located in miRNA and their target binding sites throughout the human genome remains largely unknown. Here, we built detailed cancer-specific miRNA regulatory networks across 30 cancer types to systematically analyze the effect of mutations in miRNAs and their target sites in 3' untranslated region (3' UTR), coding sequence (CDS), and 5' UTR regions. A total of 3,518,261 mutations from 9,819 samples were mapped to miRNA-gene interactions (mGI). Mutations in miRNAs showed a mutually exclusive pattern with mutations in their target genes in almost all cancer types. A linear regression method identified 148 candidate driver mutations that can significantly perturb miRNA regulatory networks. Driver mutations in 3'UTRs played their roles by altering RNA binding energy and the expression of target genes. Finally, mutated driver gene targets in 3' UTRs were significantly downregulated in cancer and functioned as tumor suppressors during cancer progression, suggesting potential miRNA candidates with significant clinical implications. A user-friendly, open-access web portal (mGI-map) was developed to facilitate further use of this data resource. Together, these results will facilitate novel noncoding biomarker identification and therapeutic drug design targeting the miRNA regulatory networks. SIGNIFICANCE: A detailed miRNA-gene interaction map reveals extensive miRNA-mediated gene regulatory networks with mutation-induced perturbations across multiple cancers, serving as a resource for noncoding biomarker discovery and drug development.

Dynamics and Sensitivity of Signaling Pathways.

Purpose of Review: Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets. In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer. An achievement that would facilitate the use of such models is their ability to identify controlling biochemical parameters in signaling pathways, such as molecular abundances and chemical reaction rates, because this would help determine effective points of attack by therapeutics. Recent Findings: We summarize the current state of understanding the sensitivity of phosphorylation cycles with and without sequestration. We also describe some basic properties of regulatory motifs including feedback and feedforward regulation. Summary: Although much recent work has focused on understanding the dynamics and particularly the sensitivity of signaling networks in eukaryotic systems, there is still an urgent need to build more scalable models of signaling networks that can appropriately represent their complexity across different cell types and tumors.

Nutri: A Behavioral Science-Based Clinical Decision Support for Chronic Disease Management.

Clinical decision support systems (CDSS) for the ongoing decision making required to support health behavior change for chronic disease management should incorporate behavioral science (e.g., a collaborative goal setting workflow) with more common CDSS components (i.e., an evidence-based knowledge base that processes patient data). Given known challenges with CDSS usability and adoption, engaging clinician end-users in designing new CDSS is vital. Therefore, we tested Nutri, a CDSS for collaborative diet goal setting, with 10 clinicians in a simulated primary care appointment with a patient actor. Simulation recordings, usability surveys, and debriefing interviews provided a multi-method view of clinicians' perceptions of Nutri's value and usability. 100% of participating clinicians achieved Nutri's main objective: selecting a high impact diet goal during a collaborative goal setting discussion with the patient; participants found Nutri usable, potentially timesaving, and increased their diet counseling self-efficacy. Insights will improve Nutri's usability and clinical workflow integration.

Detailed simulations of cell biology with Smoldyn 2.1.

Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells.

Systems biology: a switch for sex.

The yeast pheromone response pathway works in a graded fashion, such that more pheromone leads to more response, but a recent study has shown that small modifications convert it into a bistable switch, with implications for the evolution and engineering of reaction networks.

Developing web-based online support tools: the Dartmouth decision support software.

TOPIC: This article discusses the development of Web-based online decision support tools intended for researchers examining the issue of shared decision making for the population of individuals with serious mental illnesses. PURPOSE: The authors describe the background and use of decision support tools to facilitate shared decision-making between individuals diagnosed with a psychiatric condition and clinicians and describes a novel software platform that allows researchers and other system designers to build decision support systems. CONCLUSIONS: In supporting ongoing research efforts, an online decision support tool appears to be useful for individuals facing preference-sensitive decisions and an online designer tool allows for rapid deployment of these research sites to support ongoing research efforts in shared decision making.