Kyungreem Han

Optimization of fed-batch fermentation for xylitol production by Candida tropicalis

Xylitol, a functional sweetener, was produced from xylose by biological conversion using Candida tropicalis ATCC 13803. Based on a two-substrate fermentation using glucose for cell growth and xylose for xylitol production, fed-batch fermentations were undertaken to increase the final xylitol concentration. The effects of xylose and xylitol on xylitol production rate were studied to determine the optimum concentrations for fed-batch fermentation. Xylose concentration in the medium (100 g l−1) and less than 200 g l−1 total xylose plus xylitol concentration were determined as optimum for maximum xylitol production rate and xylitol yield. Increasing the concentrations of xylose and xylitol decreased the rate and yield of xylitol production and the specific cell growth rate, probably because of an increase in osmotic stress that would interfere with xylose transport, xylitol flux to secretion to cell metabolism. The feeding rate of xylose solution during the fed-batch mode of operation was determined by using the mass balance equations and kinetic parameters involved in the equations in order to increase final xylitol concentration without affecting xylitol and productivity. The optimized fed-batch fermentation resulted in 187 g l−1 xylitol concentration, 0.75 g xylitol g xylose−1 xylitol yield and 3.9 g xylitol l−1 h−1 volumetric productivity. Journal of Industrial Microbiology & Biotechnology (2002) 29, 16–19 doi:10.1038/sj.jim.7000257

Synaptotagmin-1 binds to PIP 2 -containing membrane but not to SNAREs at physiological ionic strength

The Ca2+ sensor synaptotagmin-1 is thought to trigger membrane fusion by binding to acidic membrane lipids and SNARE proteins. Previous work has shown that binding is mediated by electrostatic interactions that are sensitive to the ionic environment. However, the influence of divalent or polyvalent ions, at physiological concentrations, on synaptotagmins binding to membranes or SNAREs has not been explored. Here we show that binding of rat synaptotagmin-1 to membranes containing phosphatidylinositol 4,5-bisphosphate (PIP2) is regulated by charge shielding caused by the presence of divalent cations. Surprisingly, polyvalent ions such as ATP and Mg2+ completely abrogate synaptotagmin-1 binding to SNAREs regardless of the presence of Ca2+. Altogether, our data indicate that at physiological ion concentrations Ca2+-dependent synaptotagmin-1 binding is confined to PIP2-containing membrane patches in the plasma membrane, suggesting that membrane interaction of synaptotagmin-1 rather than SNARE binding triggers exocytosis of vesicles.

Characterization of Phase Transition in the Thalamocortical System during Anesthesia-Induced Loss of Consciousness

The thalamocortical system plays a key role in the breakdown or emergence of consciousness, providing bottom-up information delivery from sensory afferents and integrating top-down intracortical and thalamocortical reciprocal signaling. A fundamental and so far unanswered question for cognitive neuroscience remains whether the thalamocortical switch for consciousness works in a discontinuous manner or not. To unveil the nature of thalamocortical system phase transition in conjunction with consciousness transition, ketamine/xylazine was administered unobtrusively to ten mice under a forced working test with motion tracker, and field potentials in the sensory and motor-related cortex and thalamic nuclei were concomitantly collected. Sensory and motor-related thalamocortical networks were found to behave continuously at anesthesia induction and emergence, as evidenced by a sigmoidal response function with respect to anesthetic concentration. Hyperpolarizing and depolarizing susceptibility diverged, and a non-discrete change of transitional probability occurred at transitional regimes, which are hallmarks of continuous phase transition. The hyperpolarization curve as a function of anesthetic concentration demonstrated a hysteresis loop, with a significantly higher anesthetic level for transition to the down state compared to transition to the up state. Together, our findings concerning the nature of phase transition in the thalamocortical system during consciousness transition further elucidate the underlying basis for the ambiguous borderlines between conscious and unconscious brains. Moreover, our novel analysis method can be applied to systematic and quantitative handling of subjective concepts in cognitive neuroscience.

Assessment of β-cell function in human patients

This review focuses on the methods accessing β-cell function. β-cell failure is the critical step in the development of type 2 diabetes. Therefore, assessment of β-cell function is an important part of the evaluation and treatment of diabetic patients. However, it is not easy because of complex interaction between multiple tissues. Several parameters should be considered, such as glucose level and insulin sensitivity of diverse insulin target tissues to assess β-cell function. To overcome these difficulties, several invasive or non-invasive methods have been developed to assess β-cell function for clinical or research purposes.

Mathematical models for insulin secretion in pancreatic β-cells

Insulin secretion is one of the most characteristic features of β-cell physiology. As it plays a central role in glucose regulation, a number of experimental and theoretical studies have been performed since the discovery of the pancreatic β-cell. This review article aims to give an overview of the mathematical approaches to insulin secretion. Beginning with the bursting electrical activity in pancreatic β-cells, we describe effects of the gap-junction coupling between β-cells on the dynamics of insulin secretion. Then, implications of paracrine interactions among such islet cells as α-, β-, and δ-cells are discussed. Finally, we present mathematical models which incorporate effects of glycolysis and mitochondrial glucose metabolism on the control of insulin secretion.

Autophagy mediates phase transitions from cell death to life

Autophagy is a lysosomal degradation pathway, which is critical for maintaining normal cellular functions. Despite considerable advances in defining the specific molecular mechanism governing the autophagy pathway during the last decades, we are still far from understanding the underlying principle of the autophagy machinery and its complex role in human disease. As an alternative attempt to reinvigorate the search for the principle of the autophagy pathway, we in this study make use of the computer-aided analysis, complementing current molecular-level studies of autophagy. Specifically, we propose a hypothesis that autophagy mediates cellular phase transitions and demonstrate that the autophagic phase transitions are essential to the maintenance of normal cellular functions and critical in the fate of a cell, i.e., cell death or survival. This study should provide valuable insight into how interactions of sub-cellular components such as genes and protein modules/complexes regulate autophagy and then impact on the dynamic behaviors of living cells as a whole, bridging the microscopic molecular-level studies and the macroscopic cellular-level and physiological approaches.

Mathematical model for glucose regulation in the whole-body system.

The human body needs continuous and stable glucose supply for maintaining its biological functions. Stable glucose supply comes from the homeostatic regulation of the blood glucose level, which is controlled by various glucose consuming or producing organs. Therefore, it is important to understand the whole-body glucose regulation mechanism. In this article, we describe various mathematical models proposed for glucose regulation in the human body, and discuss the difficulty and limitation in reproducing real processes of glucose regulation.

Quantitative indices of autophagy activity from minimal models

BackgroundA number of cellular- and molecular-level studies of autophagy assessment have been carried out with the help of various biochemical and morphological indices. Still there exists ambiguity for the assessment of the autophagy status and of the causal relationship between autophagy and related cellular changes. To circumvent such difficulties, we probe new quantitative indices of autophagy which are important for defining autophagy activation and further assessing its roles associated with different physiopathological states.MethodsOur approach is based on the minimal autophagy model that allows us to understand underlying dynamics of autophagy from biological experiments. Specifically, based on the model, we reconstruct the experimental context-specific autophagy profiles from the target autophagy system, and two quantitative indices are defined from the model-driven profiles. The indices are then applied to the simulation-based analysis, for the specific and quantitative interpretation of the system.ResultsTwo quantitative indices measuring autophagy activities in the induction of sequestration fluxes and in the selective degradation are proposed, based on the model-driven autophagy profiles such as the time evolution of autophagy fluxes, levels of autophagosomes/autolysosomes, and corresponding cellular changes. Further, with the help of the indices, those biological experiments of the target autophagy system have been successfully analyzed, implying that the indices are useful not only for defining autophagy activation but also for assessing its role in a specific and quantitative manner.ConclusionsSuch quantitative autophagy indices in conjunction with the computer-aided analysis should provide new opportunities to characterize the causal relationship between autophagy activity and the corresponding cellular change, based on the system-level understanding of the autophagic process at good time resolution, complementing the current in vivo and in vitro assays.

COMPUTER SIMULATIONS UNVEIL THE DYNAMICS OF AUTOPHAGY AND ITS IMPLICATIONS FOR THE CELLULAR QUALITY CONTROL

Since the discovery of autophagy half a century ago, a number of physiological and molecular-level studies of autophagy have been carried out, revealing the basic mechanism and role of autophagy in the protein and organelle quality control. However, a reliable assessment method for the autophagy-mediated protein/organelle quality control with the help of an adequate mathematical model has not yet been reported. Based on the previous mathematical modeling of autophagy, we have carried out simulations to prove whether and how basal autophagy achieves substrate specificity and contributes to the cellular protein/organelle quality control. By means of numerical simulations, we probe the selective autophagic mode and observe that autophagic fluxes from abnormal protein/organelle are much greater than those from resident protein/organelle. Such a selective autophagic mode is found to correlate with the fractional abnormal protein/organelle concentration. Finally, it is shown that the fractional abnormal protein/organelle concentration against cellular damaging is efficiently controlled and regulated by suppression or promotion of the autophagosome formation rate. Mathematical modeling and numerical simulations allow one to analyze the autophagic protein/organelle quality control in a specific and quantitative manner and disclose that autophagy serves as a critical cellular quality control mechanism.

Failure of Arm Movement Control in Stroke Patients, Characterized by Loss of Complexity.

We study the mechanism of human arm-posture control by means of nonlinear dynamics and quantitative time series analysis methods. Utilizing linear and nonlinear measures in combination, we find that pathological tremors emerge in patient dynamics and serve as a main feature discriminating between normal and patient groups. The deterministic structure accompanied with loss of complexity inherent in the tremor dynamics is also revealed. To probe the underlying mechanism of the arm-posture dynamics, we further analyze the coupling patterns between joints and components, and discuss their roles in breaking of the organization structure. As a result, we elucidate the mechanisms in the arm-posture dynamics of normal subjects responding to the gravitational force and for the reduction of the dynamic degrees of freedom in the patient dynamics. This study provides an integrated framework for the origin of the loss of complexity in the dynamics of patients as well as the coupling structure in the arm-posture dynamics.