Auto-regulation of Secretory Flux by Sensing and Responding to the Folded Cargo Protein Load in the Endoplasmic Reticulum.

Maintaining the optimal performance of cell processes and organelles is the task of auto-regulatory systems. Here we describe an auto-regulatory device that helps to maintain homeostasis of the endoplasmic reticulum (ER) by adjusting the secretory flux to the cargo load. The cargo-recruiting subunit of the coatomer protein II (COPII) coat, Sec24, doubles as a sensor of folded cargo and, upon cargo binding, acts as a guanine nucleotide exchange factor to activate the signaling protein Gα12 at the ER exit sites (ERESs). This step, in turn, activates a complex signaling network that activates and coordinates the ER export machinery and attenuates proteins synthesis, thus preventing large fluctuations of folded and potentially active cargo that could be harmful to the cell or the organism. We call this mechanism AREX (autoregulation of ER export) and expect that its identification will aid our understanding of human physiology and diseases that develop from secretory dysfunction.

An Optimal Decision Support System Based on Crop Dynamic Model for N-Fertilizer Treatment.

The efficient handling of nitrogen has become a critical issue in modern agriculture, from a financial standpoint, as well as in regard to reducing the environmental impacts of using an excessive amount of nitrogen fertilizer. Manure compost is useful for maintaining or raising soil chemical levels without excessive NO3- accumulation; however, for the best grain yield, it should be combined with N fertilizer. Via this study, we aimed to develop an optimal decision support system that indicates when to initiate fertilization based on nitrogen-limited (N-limited) crop growth dynamics. An optimal nitrogen fertilizer (N-fertilizer) management system increases crop yield while maintaining a balance between fertilizer supply and crop demand. This study used the N-limited crop growth model (LINTUL3) to develop an optimal decision support system. In this work, we formulated and resolved two optimization challenges: (i) maximization of biomass growth; and (ii) maximization of growth with the least cost paid on N-fertilizer and its application. Furthermore, two case studies were developed based on the number of fields: (i) optimization for a single field, and (ii) optimization for multiple fields. In the case of multiple fields, it is hypothesized that a fertilizer treatment for one field can leak to other fields and affect the nitrogen dynamics of different fields. Finally, numerical simulations were carried out supporting the theory developed in the paper. The simulations showed that when the proposed work was employed to achieve the goal of optimal nitrogen management for a crop, a 28% to 53% increase in biomass growth under certain scenarios was attained.

Effects of selection and mutation on epidemiology of X-linked genetic diseases.

The epidemiology of X-linked recessive diseases, a class of genetic disorders, is modeled with a discrete-time, structured, non linear mathematical system. The model accounts for both de novo mutations (i.e., affected sibling born to unaffected parents) and selection (i.e., distinct fitness rates depending on individual's health conditions). Assuming that the population is constant over generations and relying on Lyapunov theory we found the domain of attraction of model's equilibrium point and studied the convergence properties of the degenerate equilibrium where only affected individuals survive. Examples of applications of the proposed model to two among the most common X-linked recessive diseases (namely the red and green color blindness and the Hemophilia A) are described.

Selection and mutation in X-linked recessive diseases epidemiological model.

To describe the epidemiology of X-linked recessive diseases we developed a discrete time, structured, non linear mathematical model. The model allows for de novo mutations (i.e. affected sibling born to unaffected parents) and selection (i.e., distinct fitness rates depending on individual's health conditions). Applying Lyapunov direct method we found the domain of attraction of model's equilibrium point and studied the convergence properties of the degenerate equilibrium where only affected individuals survive.

Point process modeling reveals anatomical non-uniform distribution across the subthalamic nucleus in Parkinson's disease.

Deep brain stimulation (DBS) is a highly promising therapy for Parkinson's disease (PD). However, most patients do not get full therapeutic benefit from DBS, due to its critical dependence on electrode location in the Subthalamic Nucleus (STN). For this reason, we believe that the development of a novel surgical tool for DBS placement, i.e., an automated intraoperative closed-loop DBS localization system, is essential. In this paper, we analyze single unit spiking activity of 120 neurons in different STN locations collected from 4 PD patients. Specifically, for each neuron, we estimate a point process model (PPM) of the spiking activity for different depths within the STN by which we are able to detect pathological bursting and oscillations. Our results suggest that these signatures are more prominent in the dorsolateral part of the STN. Therefore, accurately placing the DBS electrode in this target may result in maximal therapeutic benefit with less power effort required by DBS. Furthermore, PPMs might be an effective tool for modeling of the STN neuronal activities as a function of location within the STN, which may pave the way towards developing a closed-loop navigation tool for optimal DBS electrode placement.

Closed-loop control of deep brain stimulation: a simulation study.

Deep brain stimulation (DBS) is an effective therapy to treat movement disorders including essential tremor, dystonia, and Parkinson's disease. Despite over a decade of clinical experience the mechanisms of DBS are still unclear, and this lack of understanding makes the selection of stimulation parameters quite challenging. The objective of this work was to develop a closed-loop control system that automatically adjusted the stimulation amplitude to reduce oscillatory neuronal activity, based on feedback of electrical signals recorded from the brain using the same electrode as implanted for stimulation. We simulated a population of 100 intrinsically active model neurons in the Vim thalamus, and the local field potentials (LFPs) generated by the population were used as the feedback (control) variable for closed loop control of DBS amplitude. Based on the correlation between the spectral content of the thalamic activity and tremor (Hua , 1998), (Lenz , 1988), we implemented an adaptive minimum variance controller to regulate the power spectrum of the simulated LFPs and restore the LFP power spectrum present under tremor conditions to a reference profile derived under tremor free conditions. The controller was based on a recursively identified autoregressive model (ARX) of the relationship between stimulation input and LFP output, and showed excellent performances in tracking the reference spectral features through selective changes in the theta (2-7 Hz), alpha (7-13 Hz), and beta (13-35 Hz) frequency ranges. Such changes reflected modifications in the firing patterns of the model neuronal population, and, differently from open-loop DBS, replaced the tremor-related pathological patterns with patterns similar to those simulated in tremor-free conditions. The closed-loop controller generated a LFP spectrum that approximated more closely the spectrum present in the tremor-free condition than did open loop fixed intensity stimulation and adapted to match the spectrum after a change in the neuronal oscillation frequency. This computational study suggests the feasibility of closed-loop control of DBS amplitude to regulate the spectrum of the local field potentials and thereby normalize the aberrant pattern of neuronal activity present in tremor.

System identification of local field potentials under deep brain stimulation in a healthy primate.

High frequency (HF) Deep Brain Stimulation (DBS) in the Sub-Thalamic Nucleus (STN) is a clinically recognized therapy for the treatment of motor disorders in Parkinson Disease (PD). The underlying mechanisms of DBS and how it impacts neighboring nuclei, however, are not yet completely understood. Electrophysiological data has been collected in PD patients and primates to better understand the impact of DBS on STN and the entire Basal Ganglia (BG) motor circuit. We use single unit recordings from Globus Pallidus, both pars interna and externa segments (GPi and GPe) in the BG, in a normal primate before and after DBS to reconstruct Local Field Potentials (LFPs) in the region. We then use system identification techniques to understand how GPe LFP activity and the DBS signal applied to STN influence GPi LFP activity. Our models suggest that when no stimulation is applied, the GPe LFPs have an inhibitory effect on GPi LFPs with a 2-3 ms delay, as is the case for single unit neuronal activity. On the other hand, when DBS is ON the models suggest that stimulation has a dominant effect on GPi LFPs which mask the inhibitory effects of GPe.