Cell Systems Biology Research Articles

Fractional optimal control of compartmental SIR model of COVID-19: Showing the impact of effective vaccination.

In this work a compartmental SIR model has been proposed for describing the dynamics of COVID-19 with Caputo’s fractional derivative(FD). SIR compartmental model has been used here with fractional differential equations(FDEs). The mathematical model of the pandemic consists of three compartments namely susceptible, infected and recovered individuals. The dynamics of the pandemic COVID-19 with FDEs for showing the effect of memory as most of the cell biological systems can be described accurately by FDEs Time dependent control(Effective vaccination) has been applied model to formulated fractional optimal control problem(FOCP) to reduce the viral load. Pontryagin’s Maximum Principle(PMP) has been used to formulate FOCP. An effective vaccination is very helpful for controlling the pandemic, which is observed through the numerical simulation via Grunwald-Letnikov(G-L) approximation. All numerical simulation work has been carried in MATLAB platform.

Oncogenic Viruses as Entropic Drivers of Cancer Evolution.

Viral infection is an indisputable causal factor for nearly 17% of all human cancers. However, the diversity and complexity of oncogenic mechanisms raises new questions as to the mechanistic role of viruses in cancer. Classical viral oncogenes have been identified for all tumor-associated viruses. These oncogenes can have multiple oncogenic activities that may or may not be utilized in a particular tumor cell. In addition, stochastic events, like viral mutation and integration, as well as heritable host susceptibilities and immune deficiencies are also implicated in tumorigenesis. A more contemporary view of tumor biology highlights the importance of evolutionary forces that select for phenotypes better adapted to a complex and changing environment. Given the challenges of prioritizing singular mechanistic causes, it may be necessary to integrate concepts from evolutionary theory and systems biology to better understand viral cancer-driving forces. Here, we propose that viral infection provides a biological “entropy” that increases genetic variation and phenotypic plasticity, accelerating the main driving forces of cancer cell evolution. Viruses can also influence the evolutionary selection criteria by altering the tumor microenvironment and immune signaling. Utilizing concepts from cancer cell evolution, population genetics, thermodynamics, and systems biology may provide new perspectives on viral oncogenesis and identify novel therapeutic strategies for treating viruses and cancer.

A three-dimensional finite element model of cAMP signals

This paper presents a three-dimensional finite element model for cyclic adenosine monophosphate (cAMP) signaling. Governing equations for the synthesis, diffusion, and degradation of cAMP were numerically implemented using the finite element method. Simulated results were displayed as time course plots of cAMP concentrations at selected nodes within the discretized geometry. The validity of the finite element model was assessed by comparing simulated results against analytical or other numerical solutions of cAMP concentration distribution for a spherical cellular volume. An endothelial cell was also simulated using its discretized geometry obtained from microscopic cellular cross-sectional images. Simulated solutions using the spherical cellular volume produced near identical cAMP concentration plots to the analytical solutions and were in good agreements with numerical results obtained from VCell, an existing software package for modeling cell biological systems. The validated 3-D finite element model was then employed to simulate the cAMP signaling pathway within a pulmonary microvascular endothelial cell geometry.

Curauá-derived carbon dots: Fluorescent probes for effective Fe(III) ion detection, cellular labeling and bioimaging

This study reports the generation of curauá-derived carbon dots (C-dots) and their suitability for Fe(III) detection, bioimaging and FACS analysis. C-dots were generated from curauá (Ananas erectifolius) fibers by a facile one-step hydrothermal approach. They exhibited graphite-like structure with a mean diameter of 2.4 nm, high water solubility, high levels of carboxyl and hydroxyl functional groups, excitation-dependent multicolor fluorescence emission (in the range 450 nm - 560 nm) and superior photostability. C-dots were highly selective and effective for the detection of ferric Fe(III) ion in an aqueous medium with a detection limit of 0.77 μM in the linear range of 0–30 μM, a value much lower than the guideline limits proposed by the World Health Organization (WHO). In biological cell systems, C-dots were very well tolerated by B16F1 mouse melanoma and J774.A1 mouse macrophages cell lines, both of which effectively internalized C-dots in their cytoplasmic compartment. Finally, C-dots were effective probes for long-term live cell imaging experiments and multi-channel flow cytometry analysis. Collectively, our findings demonstrate that curauá-derived C-dots serve as versatile and effective natural products for Fe(III) ion sensing, labeling and bioimaging of various cell types. This study adds novel C-dots to the library of carbon-based probes and paves the way towards a sustainable conversion of a most abundant biomass waste into value-added products.

Dictyostelium discoideum: An Alternative Nonanimal Model for Developmental Toxicity Testing.

A critical aspect of toxicity evaluation is developmental and reproductive toxicity (DART) testing. Traditionally, DART testing has been conducted in vivo in mammalian model systems. New legislation aimed at reducing animal use and the prohibitive costs associated with DART testing, together with a need to understand the genetic pathways underlying developmental toxicity means there is a growing demand for alternative model systems for toxicity evaluation. Here we explore the potential of the eukaryotic social amoeba Dictyostelium discoideum, which is already widely used as a simple model system for cell and developmental biology, as a potential nonanimal model for DART testing. We developed assays for high-throughput screening of toxicity during D. discoideum growth and development. This allowed the toxicity of a broad range of test compounds to be characterized, which revealed that D. discoideum can broadly predict mammalian toxicity. In addition, we show that this system can be used to perform functional genomic screens to compare the molecular modes of action of different compounds. For example, genome-wide screens for mutations that affect lithium and valproic acid toxicity allowed common and unique biological targets and molecular processes mediating their toxicity to be identified. These studies illustrate that D. discoideum could represent a predictive nonanimal model for DART testing due to its amenability to high-throughput approaches and molecular genetic tractability.

Creating a Pro-Regenerative Tissue Microenvironment: Local Control is the Key.

Creating a Pro-Regenerative Tissue Microenvironment: Local Control is the Key.

Obtaining Xenopus tropicalis Eggs.

Xenopus is a powerful model system for cell and developmental biology in part because frogs produce thousands of eggs and embryos year-round. For cell biological studies, egg extracts can mimic many processes in a cell-free system. For developmental biology, Xenopus embryos are a premier system, combining cut-and-paste embryology with modern gene manipulation tools. Xenopus tropicalis are particularly suited to genetic studies because of their diploid genome, as compared to the tetraploid genome of Xenopus laevis When collecting eggs, there are differences in timing of steps, amounts of hormone administered, and handling of females between these species. In this protocol, X. tropicalis females are induced with a hormone that stimulates ovulation, and then eggs are collected. To administer the ovulation hormone and express eggs, it is necessary to be comfortable with handling frogs. Proficient handling of X. tropicalis requires practice, as they are relatively small, active, and slippery.

Obtaining Xenopus tropicalis Embryos by Natural Mating.

Xenopus is a powerful model system for cell and developmental biology in part because frogs produce thousands of eggs and embryos year-round. Natural matings are a simple and common method to obtain embryos for injection or other experimental use or to raise to adulthood. This method does not require sacrificing a male as in vitro fertilization (IVF) does. Male and female frogs are injected with an ovulation hormone, placed together in a mating bucket, and left for 4-6 h or overnight to mate. Embryos are then collected, treated with cysteine to remove the sticky jelly coat, and used for injections and/or raised to later stages or adulthood. For embryos raised past free-swimming stages, the cysteine step can optionally be skipped, and tadpoles can be allowed to hatch naturally from the jelly coat. Although there are many similarities between natural mating protocols for Xenopus laevis and Xenopus tropicalis, there are key differences such as hormone dosage, timing of ovulation, and embryo incubation temperature. Here we provide a specific protocol for inducing natural matings in X. tropicalis.

Obtaining Xenopus tropicalis Embryos by In Vitro Fertilization.

Xenopus is a powerful model system for cell and developmental biology in part because frogs produce thousands of eggs and embryos year-round. In vitro fertilization (IVF) is ideal for obtaining developmentally synchronized embryos for microinjection or when natural mating has failed to produce a fertilization. In IVF, females are induced to ovulate, and then eggs are collected by manual expression. After testes are collected from a euthanized male frog, the eggs are fertilized in vitro. The embryos are then treated with cysteine to remove the sticky protective jelly coat. Dejellied embryos are much easier to manipulate during microinjection or when sorting in a Petri dish. The jelly coat is also very difficult to penetrate with an injection needle. After microinjection, embryos are maintained in Petri dishes until desired stages are reached. Although in vitro fertilization in X. laevis and X. tropicalis is similar, critical differences in solutions, handling of testis, response of fertilized eggs directly after introduction of sperm, and developmental timing are required for successful fertilization in X. tropicalis.

Control of Chaotic Calcium Oscillations in Biological Cells

The contribution of this present paper is to propose a method that combines a chemical Brusselator reaction-diffusion system with a biological cell system via gap junction for controlling and visualizing the frequency and magnitude of chaotic intracellular calcium oscillations in two cell types, including nonexcitable cells and the glial cells. This produces a wide variety of oscillatory behaviors similar to those reported in numerous biological experiments. We particularly show that in the majority of chaos cases, the reactor to cell coupling can induce the generation of regular calcium oscillations as the coupling strength is varied. Together with the proposed method of coupled models, the regularity of these chaotic oscillations enables us to gain better understanding and extensive insights into the overall coupling dynamics.

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems.

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.

Dual‐peptide functionalized nanoparticles for therapeutic use

AbstractPeptide‐functionalized nanoparticles combine the best of both; the ability of nanoparticles to deliver a drug “cargo” throughout the body and the ability of peptides to selectively target certain cell types or biological systems. The vast majority of peptide‐functionalized nanoparticles employ only one type of peptide, however, to truly realize the potential of these systems in medicine, nanoparticles equipped with two or even more peptide functionalities are desirable. In this review, the latest developments in dual‐peptide functionalized nanoparticles are discussed. These are categorized depending on their structure; first broadly into grafted and self‐assembled dual‐peptide‐nanoparticles with the former then subdivided further into nonconjugated, linearly conjugated and branched conjugated dual‐peptide functionalized nanoparticles. These different categories of dual‐peptide nanoparticles are then discussed with regards to the type of functional peptides used and their role in selective targeting nanomedicine.

Oxidative stress on-chip: Prussian blue-based electrode array for in situ detection of H2O2 from cell populations

A Prussian blue-based electrode array (PBEA) constituted by eight stencil-printed electrodes on a flexible PET (polyethylene terephthalate) substrate is proposed for in-situ HeLa cell culturing and real-time detection of the released H2O2. The array was suitably interfaced with a poly- (methyl methacrylate) (PMMA) well-containing holders resulting in a low cost multichambered chip. PBEA fabrication was carried out employing a xurography-based cost-effective benchtop microfabrication technology using just a desktop cutting plotter and office grade thermal-laminator. The hydrophobicity of the PET isolating layer allows to constrain cell-containing drops directly on top of the electrochemical cells. HeLa cells growth in the very close vicinity of the working electrode ensures in-situ cell seeding, incubation, and further electrochemical detection of the H2O2 released, enabling high-throughput analysis. Selective and sensitive electrochemical sensing of hydrogen peroxide was carried out at −100 mV vs Ag|AgCl; the resulting LOD was 1.9 μM. Remarkably, the analytical exploitability of the approach was demonstrated by detection of the hydrogen peroxide released from HeLa cells stimulated with N-Formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLP) and after pretreatment of the cells with cocoa polyphenols, that induced a decreased oxidative stress levels. These data make our approach a promising tool for oxidative stress evaluation in cell cultures and biological systems.

Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model.

We present the software platform 2CALM that allows for a comparative analysis of 3D localisation microscopy data representing protein distributions in two biological samples. The in-depth statistical analysis reveals differences between samples at the nanoscopic level using parameters such as cluster-density and -curvature. An automatic classification system combines multiplex and multi-level statistical approaches into one comprehensive parameter for similarity testing of the compared samples. We demonstrated the biological importance of 2CALM, comparing the protein distributions of CD41 and CD62p on activated platelets in a 3D artificial clot. Additionally, using 2CALM, we quantified the impact of the inflammatory cytokine interleukin-1β on platelet activation in clots. The platform is applicable to any other cell type and biological system and can provide new insights into biological and medical applications.

Conditionally Reprogrammed Human Normal Airway Epithelial Cells at ALI: A Physiological Model for Emerging Viruses.

Cancer cell lines have been used widely in cancer biology, and as biological or functional cell systems in many biomedical research fields. These cells are usually defective for many normal activities or functions due to significant genetic and epigenetic changes. Normal primary cell yields and viability from any original tissue specimens are usually relatively low or highly variable. These normal cells cease after a few passages or population doublings due to very limited proliferative capacity. Animal models (ferret, mouse, etc.) are often used to study virus-host interaction. However, viruses usually need to be adapted to the animals by several passages due to tropism restrictions including viral receptors and intracellular restrictions. Here we summarize applications of conditionally reprogrammed cells (CRCs), long-term cultures of normal airway epithelial cells from human nose to lung generated by conditional cell reprogramming (CR) technology, as an ex vivo model in studies of emerging viruses. CR allows to robustly propagate cells from non-invasive or minimally invasive specimens, for example, nasal or endobronchial brushing. This process is rapid (2 days) and conditional. The CRCs maintain their differentiation potential and lineage functions, and have been used for studies of adenovirus, rhinovirus, respiratory syncytial virus, influenza viruses, parvovirus, and SARS-CoV. The CRCs can be easily used for air-liquid interface (ALI) polarized 3D cultures, and these coupled CRC/ALI cultures mimic physiological conditions and are suitable for studies of viral entry including receptor binding and internalization, innate immune responses, viral replications, and drug discovery as an ex vivo model for emerging viruses.

The comparative analysis of prebiological evolution models

Several models of prebiological systems are described and analyzed. The following models are characterized: a quasispecies model, a hypercycle model, a syser model (the term "syser" is an abbreviation of SYstem of SElf-Reproduction), a stochastic corrector model, a model of the origin of a primordial genome through spontaneous symmetry breaking. The quasispecies model analyzes the Darwinian evolution of information chains; this evolution is similar to the evolution of RNA molecules. Rather general estimates of the speed and efficiency of evolutionary processes can be obtained in the framework of the quasispecies model. We briefly describe the method for obtaining these estimates and the corresponding results. The hypercycle model considers the interaction of RNA chains and enzymes. The syser model characterizes a rather general scheme of the self-reproducing system, which is similar to the self-reproducing systems of biological cells. Syser includes a polynucleotide sequence, a replication enzyme, a translation enzyme, and other enzymes; these macromolecules are located inside the protocell. The stochastic corrector model describes the process of using a relatively small number of molecules of competing and cooperating replicators in protocells. The model of the origin of a primordial genome through spontaneous symmetry breaking characterizes an interesting and important process of the appearance of genotypes in protocells. This model was proposed and investigated by Takeuchi, Hogeweg, and Kaneko in 2017; we call it further “the THK model.” The current article characterizes and compares all these models.

Harnessing cells to build functional materials

Researchers have shown that they can co-opt specific cells in biological systems to orchestrate the construction of functional materials. In turn, those materials can alter cell behavior, in this c...

Abstract P4-06-03: Assessment of intratumoral heterogeneity in early stage estrogen receptor (ER) positive breast cancer

Abstract Introduction: Tumor heterogeneity is a hallmark of cancer and its underlying clinical relevance has been well established across different tumor types. In the context of ER-positive breast cancer, variation in ER expression among different tumors or distinct cell populations within a single tumor are predicted to account for differences in clinical behavior, treatment response, and disease recurrence. However, a clear understanding of the molecular and cellular mechanisms of tumor heterogeneity that are relevant to the prognosis and therapy of early stage ER-positive breast cancer has not been established. Previous results from bulk RNA-sequencing (RNA-seq) of ER-positive biopsies represent an average of gene expression patterns; this might obscure biologically relevant differences between cells. Single-cell RNA-sequencing (scRNA-seq) is an approach to overcome this problem, allowing assessment of intratumoral cell populations and biological systems at unprecedented resolution. In this study, our aim is to compare gene expression profiles of bulk RNA-seq and scRNA-seq from tumor biopsies of early stage ER-positive patients. Methods: Tumor and normal biopsies obtained from ER-positive patients were divided into 3 parts; two being dissociated by enzymatic disaggregation and one by direct total RNA isolation. Tumor tissues were subjected to both scRNA-seq and bulk RNA-seq analyses while single-cell suspension of the normal matched tissue was used for bulk RNA-seq alone. Furthermore, patient-derived organoids were generated from both normal and tumor samples. Single-cell isolation and barcoding were assessed using the 10x Genomics technology followed by RNA sequencing with the Illumina NovaSeq6000 system (50PE), whereas bulk RNA-seq was performed using an Illumina PE150 strategy. Results: Our preliminary data represents an assessment of tumor and normal adjacent tissues collected after mastectomy from an 80-year old ER-positive, PR-positive, HER2-negative patient diagnosed with early stage infiltrating ductal carcinoma in situ (stage IB). scRNA-seq of tumor tissue from this patient identified 10 distinct clusters of cells, consisting of both immune and non-immune stromal populations (epithelial, endothelial, fibroblasts, and immune cells). 95% of single cells were luminal. However, there was a minor group (2%) of cells showing a basal-like signature, which can lead to disease recurrence. Interestingly, although the patient was clinically characterized as HER2-negative by IHC and FISH, HER2 overexpression is observed in the vast majority (95%) of single cells isolated. Furthermore, organoid cultures recapitulated the features of patients' tumors and presented similar transcriptomic profiles. We have adapted similar sequencing and downstream analyses for an additional number of patient biopsies. Our ongoing study is geared towards comparing bulk and single cell transcriptome profiles from these ER-positive cases and identifying overlapping populations that can predict recurrence or novel therapeutic vulnerabilities. Conclusions: Bulk RNA-seq approaches lack the resolution to visualize the true extent of stromal heterogeneity and may mask rare populations or cellular phenotypes that could be critical for tumor survival. ScRNA-seq highlights the dynamic and adaptive nature of all cellular populations within an evolving tumor microenvironment and reveal potential crosstalk between these two compartments. Lastly, establishment of organoid cultures presents the opportunity of high-throughput drug screening studies and the identification of new, patient-tailored therapeutic strategies. Citation Format: Sofia Mastoraki, Juliana Navarro-Yepes, Tuan Tran, Aysegul Sahin, Kelly Hunt, Nicholas Navin, Khandan Keyomarsi. Assessment of intratumoral heterogeneity in early stage estrogen receptor (ER) positive breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-03.

Integration and Querying of Heterogeneous Omics Semantic Annotations for Biomedical and Biomolecular Knowledge Discovery

Background:Exploring various functional aspects of a biological cell system has been a focused research trend for last many decades. Biologists, scientists and researchers are continuously striving for unveiling the mysteries of these functional aspects to improve the health standards of life. For getting such understanding, astronomically growing, heterogeneous and geographically dispersed omics data needs to be critically analyzed. Currently, omics data is available in different types and formats through various data access interfaces. Applications which require offline and integrated data encounter a lot of data heterogeneity and global dispersion issues.Objective:For facilitating especially such applications, heterogeneous data must be collected, integrated and warehoused in such a loosely coupled way so that each molecular entity can computationally be understood independently or in association with other entities within or across the various cellular aspects.Methods:In this paper, we propose an omics data integration schema and its corresponding data warehouse system for integrating, warehousing and presenting heterogeneous and geographically dispersed omics entities according to the cellular functional aspects.Results & Conclusion:Such aspect-oriented data integration, warehousing and data access interfacing through graphical search, web services and application programing interfaces make our proposed integrated data schema and warehouse system better and useful than other contemporary ones.

I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells.

The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), that is exclusively expressed in intestinal progenitor cells. This method uses UV crosslinked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4 When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identifies 98.8% of transcripts found after progenitor cell sorting, and has low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile X mental retardation protein (FMRP), using enhanced crosslinking and immunoprecipitation (eCLIP), and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wild-type and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions crucial for stem cell function.