Optimal Control with RdCVFL for Degenerating Photoreceptors.

Both the rod and cone photoreceptors, along with the retinal pigment epithelium have been experimentally and mathematically shown to work interdependently to maintain vision. Further, the theoredoxin-like rod-derived cone viability factor (RdCVF) and its long form (RdCVFL) have proven to increase photoreceptor survival in experimental results. Aerobic glycolysis is the primary source of energy production for photoreceptors and RdCVF accelerates the intake of glucose into the cones. RdCVFL helps mitigate the negative effects of reactive oxidative species and has shown promise in slowing the death of cones in mouse studies. However, this potential treatment and its effects have never been studied in mathematical models. In this work, we examine an optimal control with the treatment of RdCVFL. We mathematically illustrate the potential this treatment might have for treating degenerative retinal diseases such as retinitis pigmentosa, as well as compare this to the results of an updated control model with RdCVF.

A mathematical model of GLUT1 modulation in rods and RPE and its differential impact in cell metabolism.

We present a mathematical model of key glucose metabolic pathways in two cells of the human retina: the rods and the retinal pigmented epithelium (RPE). Computational simulations of glucose transporter 1 (GLUT1) inhibition in the model accurately reproduce experimental data from conditional knockout mice and reveal that modification of GLUT1 expression levels of both cells differentially impacts their metabolism. We hypothesize that, under glucose scarcity, the RPE's energy producing pathways are altered in order to preserve its functionality, impacting the photoreceptors' outer segment renewal. On the other hand, when glucose is limited in the rods, aerobic glycolysis is preserved, which maintains the lactate contribution to the RPE.

The role of RdCVFL in a mathematical model of photoreceptor interactions.

Recent experimental and mathematical work has shown the interdependence of the rod and cone photoreceptors with the retinal pigment epithelium in maintaining sight. Accelerated intake of glucose into the cones via the theoredoxin-like rod-derived cone viability factor (RdCVF) is needed as aerobic glycolysis is the primary source of energy production. Reactive oxidative species (ROS) result from the rod and cone metabolism and recent experimental work has shown that the long form of RdCVF (RdCVFL) helps mitigate the negative effects of ROS. In this work we investigate the role of RdCVFL in maintaining the health of the photoreceptors. The results of our mathematical model show the necessity of RdCVFL and also demonstrate additional stable modes that are present in this system. The sensitivity analysis shows the importance of glucose uptake, nutrient levels, and ROS mitigation in maintaining rod and cone health in light-damaged mouse models. Together, these suggests areas on which to focus treatment in order to prolong the photoreceptors, especially in situations where ROS is a contributing factor to their death such as retinitis pigmentosa.

Optimal control with MANF treatment of photoreceptor degeneration.

People afflicted with diseases such as retinitis pigmentosa and age-related macular degeneration experience a decline in vision due to photoreceptor degeneration, which is currently unstoppable and irreversible. Currently there is no cure for diseases linked to photoreceptor degeneration. Recent experimental work showed that mesencephalic astrocyte-derived neurotrophic factor (MANF) can reduce neuron death and, in particular, photoreceptor death by reducing the number of cells that undergo apoptosis. In this work, we build on an existing system of ordinary differential equations that represent photoreceptor interactions and incorporate MANF treatment for three experimental mouse models having undergone varying degrees of photoreceptor degeneration. Using MANF treatment levels as controls, we investigate optimal control results in the three mouse models. In addition, our numerical solutions match the experimentally observed surviving percentage of photoreceptors and our uncertainty and sensitivity analysis identifies significant parameters in the math model both with and without MANF treatment.

The Vicodin abuse problem: A mathematical approach.

The prescription drug epidemic in the United States has gained attention in recent years. Vicodin, along with its generic version, is the country's mostly widely prescribed pain reliever, and it contains a narcotic component that can lead to physical and chemical dependency. The majority of Vicodin abusers were first introduced via prescription, unlike other drugs which are often experienced for the first time due to experimentation. Most abusers report obtaining their supply from a prescription, either their own or someone else's. Although the problem with prescription drug abuse is well known, there is no standard method of addressing the problem. To better understand how to do this, we develop and analyze a mathematical model of Vicodin use and abuse, considering only those patients who were initially prescribed the drug. Through global sensitivity analysis, we show that focusing efforts on abuse prevention rather than treatment has greater success at reducing the population of Vicodin abusers. Our results demonstrate that relying solely on rehabilitation and other treatment programs is not enough to combat the prescription drug problem in the United States. We anticipate that implementing preventative measures in both prescribers and patients will reduce the number of Vicodin abusers.

A Mathematical Analysis of Aerobic Glycolysis Triggered by Glucose Uptake in Cones.

Patients affected by retinitis pigmentosa, an inherited retinal disease, experience a decline in vision due to photoreceptor degeneration leading to irreversible blindness. Rod-derived cone viability factor (RdCVF) is the most promising mutation-independent treatment today. To identify pathologic processes leading to secondary cone photoreceptor dysfunction triggering central vision loss of these patients, we model the stimulation by RdCVF of glucose uptake in cones and glucose metabolism by aerobic glycolysis. We develop a nonlinear system of enzymatic functions and differential equations to mathematically model molecular and cellular interactions in a cone. We use uncertainty and sensitivity analysis to identify processes that have the largest effect on the system and their timeframes. We consider the case of a healthy cone, a cone with low levels of glucose, and a cone with low and no RdCVF. The three key processes identified are metabolism of fructose-1,6-bisphosphate, production of glycerol-3-phosphate and competition that rods exert on cone resources. The first two processes are proportional to the partition of the carbon flux between glycolysis and the pentose phosphate pathway or the Kennedy pathway, respectively. The last process is the rods' competition for glucose, which may explain why rods also provide the RdCVF signal to compensate.

Quantifying the metabolic contribution to photoreceptor death in retinitis pigmentosa via a mathematical model.

Retinitis pigmentosa (RP) is a family of inherited retinal degenerative diseases that leads to blindness. In many cases the disease-causing allele encodes for a gene exclusively expressed in the night active rod photoreceptors. However, because rod death always leads to cone death affected individuals eventually lose their sight. Many theories have been proposed to explain the secondary loss of cones in RP; however, most fail to fully explain the different pathological transition stages seen in humans. Incorporating experimental data of rod and cone death kinetics from two mouse models of RP, we use a mathematical model to investigate the interplay and role of energy consumption and uptake of the photoreceptors as well as nutrient availability supplied through the retinal pigment epithelium (RPE) throughout the progression of RP. Our data driven mathematical model predicts that the system requires a total reduction of approximately 27-31% in nutrients available to result in the complete demise of all cones. Simulations utilizing retinal degeneration 1 (rd1) mouse cell count data in which cone death was delayed by altering cell metabolism in cones show that preventing a 1-2% decrease in nutrients available can permanently halt cone death even when 90% have already died. Our results also indicate that the ratio of energy consumption to uptake of cones, Dc, is mainly disrupted during the death wave of the rods with negligible changes thereafter and that the subsequent nutrient decrease is mainly responsible for the demise of the cones. The change in this ratio Dc highlights the compensation that the cones must undergo during rod death to meet the high metabolic demands of the entire photoreceptor population. Global sensitivity analysis confirms the results and suggests areas of focus for halting RP, even at later stages of the disease, through feasible therapeutic interventions.

Mathematical Model of the Role of RdCVF in the Coexistence of Rods and Cones in a Healthy Eye.

Understanding the essential components and processes for coexistence of rods and cones is at the forefront of retinal research. The recent discovery on RdCVF's mechanism and mode of action for enhancing cone survival brings us a step closer to unraveling key questions of coexistence and codependence of these neurons. In this work, we build from ecological and enzyme kinetic work on functional response kinetics and present a mathematical model that allows us to investigate the role of RdCVF and its contribution to glucose intake. Our model results and analysis predict a dual role of RdCVF for enhancing and repressing the healthy coexistence of the rods and cones. Our results show that maintaining RdCVF above a threshold value allows for coexistence. However, a significant increase above this value threatens the existence of rods as the cones become extremely efficient at uptaking glucose and begin to take most of it for themselves. We investigate the role of natural glucose intake and that due to RdCVF in both high and low nutrient levels. Our analysis reveals that under low nutrient levels coexistence is not possible regardless of the amount of RdCVF present. With high nutrient levels coexistence can be achieved with a relative small increase in glucose uptake. By understanding the contributions of rods to cones survival via RdCVF in a non-diseased retina, we hope to shed light on degenerative diseases such as retinitis pigmentosa.

Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae.

We investigated the dynamics of a gene regulatory network controlling the cold shock response in budding yeast, Saccharomyces cerevisiae. The medium-scale network, derived from published genome-wide location data, consists of 21 transcription factors that regulate one another through 31 directed edges. The expression levels of the individual transcription factors were modeled using mass balance ordinary differential equations with a sigmoidal production function. Each equation includes a production rate, a degradation rate, weights that denote the magnitude and type of influence of the connected transcription factors (activation or repression), and a threshold of expression. The inverse problem of determining model parameters from observed data is our primary interest. We fit the differential equation model to published microarray data using a penalized nonlinear least squares approach. Model predictions fit the experimental data well, within the 95% confidence interval. Tests of the model using randomized initial guesses and model-generated data also lend confidence to the fit. The results have revealed activation and repression relationships between the transcription factors. Sensitivity analysis indicates that the model is most sensitive to changes in the production rate parameters, weights, and thresholds of Yap1, Rox1, and Yap6, which form a densely connected core in the network. The modeling results newly suggest that Rap1, Fhl1, Msn4, Rph1, and Hsf1 play an important role in regulating the early response to cold shock in yeast. Our results demonstrate that estimation for a large number of parameters can be successfully performed for nonlinear dynamic gene regulatory networks using sparse, noisy microarray data.

Mathematical modeling of fungal infection in immune compromised individuals: The effect of back mutation on drug treatment.

We present a mathematical model that describes treatment of a fungal infection in an immune compromised patient in which both susceptible and resistant strains are present with a mutation allowing the susceptible strain to become resistant as well as a back mutation allowing resistant fungus to again become susceptible. The resulting nonlinear differential equations model the biological outcome, in terms of strain growth and cell number, when an individual is treated with a fungicidal or fungistatic drug. The model demonstrates that under any levels of the drug both strains will be in stable co-existence and high levels of treatment will never completely eradicate the susceptible strain. A modified model is then described in which the drug is changed to one in which both strains are susceptible, and subsequently, at the appropriate level of treatment, complete eradication of both fungal strains ensues. We discuss the model and implications for treatment options within the context of an immune compromised patient.

The mathematical and theoretical biology institute--a model of mentorship through research.

This article details the history, logistical operations, and design philosophy of the Mathematical and Theoretical Biology Institute (MTBI), a nationally recognized research program with an 18-year history of mentoring researchers at every level from high school through university faculty, increasing the number of researchers from historically underrepresented minorities, and motivating them to pursue research careers by allowing them to work on problems of interest to them and supporting them in this endeavor. This mosaic profile highlights how MTBI provides a replicable multi-level model for research mentorship.

Tracing the progression of retinitis pigmentosa via photoreceptor interactions.

Retinitis pigmentosa (RP) is a group of inherited degenerative eye diseases characterized by mutations in the genetic structure of the photoreceptors that leads to the premature death of both rod and cone photoreceptors. Defects in particular genes encoding proteins that are involved in either the photoreceptor structure, phototransduction cascades, or visual cycle are expressed in the rods but ultimately affect both types of cells. RP is "typically" manifested by a steady death of rods followed by a period of stability in which cones survive initially and then inevitably die too. In some RP cases, rods and cones die off simultaneously or even cone death precedes rod death (reverse RP). The mechanisms and factors involved in the development of the different types of RP are not well understood nor have researchers been able to provide more than a limited number of short-term therapies. In this work we trace the progression of RP to complete blindness through each subtype via bifurcation theory. We show that the evolution of RP from one stage to another often requires the failure of multiple components. Our results indicate that a delicate balance between the availability of nutrients and the rates of shedding and renewal of photoreceptors is needed at every stage of RP to halt its progression. This work provides a framework for future physiological investigations potentially leading to long-term targeted multi-facet interventions and therapies dependent on the particular stage and subtype of RP under consideration. The results of this mathematical model may also give insight into the progression of many other degenerative eye diseases involving genetic mutations or secondary photoreceptor death and potential ways to circumvent these diseases.

Mathematical modeling of fungal infection in immune compromised individuals: implications for drug treatment.

We present a mathematical model that describes treatment of a fungal infection in an immune compromised patient in which both susceptible and resistant strains are present. The resulting nonlinear differential equations model the biological outcome, in terms of strain growth and cell number, when an individual, who has both a susceptible and a resistant population of fungus, is treated with a fungicidal or fungistatic drug. The model demonstrates that when the drug is only successful at treating the susceptible strain, low levels of the drug cause both strains to be in stable co-existence and high levels eradicate the susceptible strain while allowing the resistant strain to persist or to multiply unchecked. A modified model is then described in which the drug is changed to one in which both strains are susceptible, and subsequently, at the appropriate level of treatment, complete eradication of both fungal strains ensues. We discuss the model and implications for treatment options within the context of an immune compromised patient.

A mathematical model for photoreceptor interactions.

The interactions between rods and cones in the retina have been the focus of innumerable experimental and theoretical biological studies in previous decades yet the understanding of these interactions is still incomplete primarily due to the lack of a unified concept of cone photoreceptor organization and its role in retinal diseases. The low abundance of cones in many of the non-primate mammalian models that have been studied make conclusions about the human retina difficult. A more complete knowledge of the human retina is crucial for counteracting the events that lead to certain degenerative diseases, in particular those associated with photoreceptor cell death (e.g., retinitis pigmentosa). In an attempt to gain important insight into the role and interactions of the rods and the cones we develop and analyze a set of mathematical equations that model a system of photoreceptors and incorporate a direct rod-cone interaction. Our results show that the system can exhibit stable oscillations, which correspond to the rhythmic renewal and shedding of the photoreceptors. In addition, our results show the mathematical necessity of this rod-cone direct interaction for survival of both and gives insight into this mechanism.

Static behavioral effects on gonorrhea transmission dynamics in a MSM population.

An SIS/SAS model of gonorrhea transmission in a population of highly active men-having-sex-with-men (MSM) is presented in this paper to study the impact of safe behavior on the dynamics of gonorrhea prevalence. Safe behaviors may fall into two categories-prevention and self-awareness. Prevention will be modeled via consistent condom use and self-awareness via STD testing frequency. Stability conditions for the disease free equilibrium and endemic equilibrium are determined along with a complete analysis of global dynamics. The control reproductive number is used as a means for measuring the effect of changes to model parameters on the prevalence of the disease. We also find that appropriate intervention would be in the form of a multifaceted approach at overall risk reduction rather than tackling one specific control individually.