Visualizing regulatory interactions in metabolic networks

Background  

Direct visualization of data sets in the context of biochemical network drawings is one of the most appealing approaches in the field of data evaluation within systems biology. One important type of information that is very helpful in interpreting and understanding metabolic networks has been overlooked so far. Here we focus on the representation of this type of information given by the strength of regulatory interactions between metabolite pools and reaction steps.     

Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions

(13)C metabolic flux analysis (MFA) has become an important and powerful tool for the quantitative analysis of metabolic networks in the framework of metabolic engineering. Isotopically instationary (13)C MFA under metabolic stationary conditions is a promising refinement of classical stationary MFA. It accounts for the experimental requirements of non-steady-state cultures as well as for the shortening of the experimental duration. This contribution extends all computational methods developed for classical stationary (13)C MFA to the instationary situation by using high-performance computing methods. The developed tools allow for the simulation of instationary carbon labeling experiments (CLEs), sensitivity calculation with respect to unknown parameters, fitting of the model to the measured data, statistical identifiability analysis and an optimal experimental design facility. To explore the potential of the new approach all these tools are applied to the central metabolism of Escherichia coli. The achieved results are compared to the outcome of the stationary counterpart, especially focusing on statistical properties. This demonstrates the specific strengths of the instationary method. A new ranking method is proposed making both an a priori and an a posteriori design of the sampling times available. It will be shown that although still not all fluxes are identifiable, the quality of flux estimates can be strongly improved in the instationary case. Moreover, statements about the size of some immeasurable pool sizes can be made.     

Investigating Neural Efficiency in the Visuo-Spatial Domain: An fmri Study

The neural efficiency hypothesis postulates an inverse relationship between intelligence and brain activation. Previous research suggests that gender and task modality represent two important moderators of the neural efficiency phenomenon. Since most of the existing studies on neural efficiency have used ERD in the EEG as a measure of brain activation, the central aim of this study was a more detailed analysis of this phenomenon by means of functional MRI. A sample of 20 males and 20 females, who had been screened for their visuo-spatial intelligence, was confronted with a mental rotation task employing an event-related approach. Results suggest that less intelligent individuals show a stronger deactivation of parts of the default mode network, as compared to more intelligent people. Furthermore, we found evidence of an interaction between task difficulty, intelligence and gender, indicating that more intelligent females show an increase in brain activation with an increase in task difficulty. These findings may contribute to a better understanding of the neural efficiency hypothesis, and possibly also of gender differences in the visuo-spatial domain.     

Metabolic flux model for an anchorage-dependent MDCK cell line: characteristic growth phases and minimum substrate consumption flux distribution

Up to now cell-culture based vaccine production processes only reach low productivities. The reasons are: (i) slow cell growth and (ii) low cell concentrations. To address these shortcomings, a quantitative analysis of the process conditions, especially the cell growth and the metabolic capabilities of the host cell line is required. For this purpose a MDCK cell based influenza vaccine production process was investigated. With a segregated growth model four distinct cell growth phases are distinguished in the batch process. In the first phase the cells attach to the surface of the microcarriers and show low metabolic activity. The second phase is characterized by exponential cell growth. In the third phase, preceded by a change in oxygen consumption, contact inhibition leads to a decrease in cell growth. Finally, the last phase before infection shows no further increase in cell numbers. To gain insight into the metabolic activity during these phases, a detailed metabolic model of MDCK cell was developed based on genome information and experimental analysis. The MDCK model was also used to calculate a theoretical flux distribution representing an optimized cell that only consumes a minimum of carbon sources. Comparing this minimum substrate consumption flux distribution to the fluxes estimated from experiments unveiled high overflow metabolism under the applied process conditions.     

<Superscript>13</Superscript>C labeling experiments at metabolic nonstationary conditions: An exploratory study

Background  

Stimulus Response Experiments to unravel the regulatory properties of metabolic networks are becoming more and more popular. However, their ability to determine enzyme kinetic parameters has proven to be limited with the presently available data. In metabolic flux analysis, the use of ¹³C labeled substrates together with isotopomer modeling solved the problem of underdetermined networks and increased the accuracy of flux estimations significantly.     

Local N-cadherin interactions mediate distinct steps in the targeting of lamina neurons

The organization of neuronal processes into a series of layers is a hallmark of many brain regions. Homophilic cell adhesion molecules of the cadherin family have been implicated in layer choice. How they contribute to the targeting of neurons to distinct layers remains unclear. Here we systematically explore the role of a classical cadherin, Drosophila N-cadherin (CadN), in the targeting of five classes of related neurons to a series of consecutive layers in the fly visual system. We show that CadN is required in lamina neurons at discrete developmental steps but not used in a layer-specific fashion. Local CadN expression patterns correlate with specific growth cone movements, and CadN expression on one growth cone in a specific layer is essential for the targeting of processes of another neuron to this layer. We propose that dynamic regulation of CadN enables this widely expressed protein to mediate specific local interactions during neural circuit assembly.     

Comparative Evaluation of Combined Navigated Laser Photocoagulation and Intravitreal Ranibizumab in the Treatment of Diabetic Macular Edema

Objective

To evaluate if a standardized combination therapy regimen, utilizing 3 monthly ranibizumab injections followed by navigated laser photocoagulation, reduces the number of total ranibizumab injections required for treatment of diabetic macular edema (DME).

Research Design and Methods

A 12-month, prospective comparison of 66 patients with center-involving DME: 34 patients with combination therapy were compared to 32 patients treated with ranibizumab monotherapy. All patients initially received 3 monthly ranibizumab injections (loading phase) and additional injections pro re nata (PRN). Combination therapy patients additionally received navigated laser photocoagulation after the loading phase. Main outcome measures were mean number of injections after the loading phase and change in BCVA from baseline to month 12.

Results

Navigated laser combination therapy and ranibizumab monotherapy similarly improved mean BCVA letter score (+8.41 vs. +6.31 letters, p = 0.258). In the combination group significantly less injections were required after the 3 injection loading phase (0.88±1.23 vs. 3.88±2.32, p< = 0.001). By month 12, 84% of patients in the monotherapy group had required additional ranibizumab injections as compared to 35% in the combination group (p< = 0.001).

Conclusions

Navigated laser combination therapy demonstrated significant visual gains in most patients. Retreatment rate and number of injections were significantly lower compared to ranibizumab monotherapy and compared to the results of conventional laser combination therapy previously reported in pivotal anti-VEGF studies.