Project description:Since the discovery of the presence of biogenic magnetites in living organisms, there have been speculations on the role that these biomagnetites play in cellular processes. It seems that the formation of biomagnetite crystals is a universal phenomenon and not an exception in living cells. Many experimental facts show that features of organic and inorganic processes could be indistinguishable at nanoscale levels. Living cells are quantum "devices" rather than simple electronic devices utilizing only the charge of conduction electrons. In our opinion, due to their unusual biophysical properties, special biomagnetites must have a biological function in living cells in general and in the brain in particular. In this paper, we advance a hypothesis that while biomagnetites are developed jointly with organic molecules and cellular electromagnetic fields in cells, they can record information about the Earth's magnetic vector potential of the entire flight in migratory birds.
Project description:Human skin has been classified as a non-volatile memristor and it is shown that information can be stored within for at least three minutes. Here we investigate whether it is possible to store information up to 20 minutes. Furthermore, we investigate whether the information can be based on four different states, not just two (binary). We stored the information into the skin of the forehead of the test subjects under three different electrodes, which allows in principle for 64 different combinations (3 electrodes, 4 states) and one can think of numbers on the base of four. For this experiment, we decided on the numbers 1234 and 3024 (that correspond to numbers 27 and 50 in the decimal system). Writing of the different states was done by the application of DC voltage pulses that cause electro-osmosis in the sweat ducts (nonlinear electrical measurements). Based on our results, we were not able to distinguish between four different states. However, we can show that binary information storage in human skin is possible for up to 20 minutes.
Project description:The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
Project description:BackgroundLong-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects.ResultsWe have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration.ConclusionsMolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org.
Project description:Excitatory synaptic signaling in cortical circuits is thought to be metabolically expensive. Two fundamental brain functions, learning and memory, are associated with long-term synaptic plasticity, but we know very little about energetics of these slow biophysical processes. This study investigates the energy requirement of information storing in plastic synapses for an extended version of BCM plasticity with a decay term, stochastic noise, and nonlinear dependence of neuron's firing rate on synaptic current (adaptation). It is shown that synaptic weights in this model exhibit bistability. In order to analyze the system analytically, it is reduced to a simple dynamic mean-field for a population averaged plastic synaptic current. Next, using the concepts of nonequilibrium thermodynamics, we derive the energy rate (entropy production rate) for plastic synapses and a corresponding Fisher information for coding presynaptic input. That energy, which is of chemical origin, is primarily used for battling fluctuations in the synaptic weights and presynaptic firing rates, and it increases steeply with synaptic weights, and more uniformly though nonlinearly with presynaptic firing. At the onset of synaptic bistability, Fisher information and memory lifetime both increase sharply, by a few orders of magnitude, but the plasticity energy rate changes only mildly. This implies that a huge gain in the precision of stored information does not have to cost large amounts of metabolic energy, which suggests that synaptic information is not directly limited by energy consumption. Interestingly, for very weak synaptic noise, such a limit on synaptic coding accuracy is imposed instead by a derivative of the plasticity energy rate with respect to the mean presynaptic firing, and this relationship has a general character that is independent of the plasticity type. An estimate for primate neocortex reveals that a relative metabolic cost of BCM type synaptic plasticity, as a fraction of neuronal cost related to fast synaptic transmission and spiking, can vary from negligible to substantial, depending on the synaptic noise level and presynaptic firing.
Project description:The olfactory system, like other sensory systems, can detect specific stimuli of interest amidst complex, varying backgrounds. To gain insight into the neural mechanisms underlying this ability, we imaged responses of mouse olfactory bulb glomeruli to mixtures. We used this data to build a model of mixture responses that incorporated nonlinear interactions and trial-to-trial variability and explored potential decoding mechanisms that can mimic mouse performance when given glomerular responses as input. We find that a linear decoder with sparse weights could match mouse performance using just a small subset of the glomeruli (∼15). However, when such a decoder is trained only with single odors, it generalizes poorly to mixture stimuli due to nonlinear mixture responses. We show that mice similarly fail to generalize, suggesting that they learn this segregation task discriminatively by adjusting task-specific decision boundaries without taking advantage of a demixed representation of odors.
Project description:The work described in this paper focuses on the utilisation of silicon nanowires as the information storage element in flash-type memory devices. Silicon nanostructures have attracted attention due to interesting electrical and optical properties, and their potential integration into electronic devices. A detailed investigation of the suitability of silicon nanowires as the charge storage medium in two-terminal non-volatile memory devices are presented in this report. The deposition of the silicon nanostructures was carried out at low temperatures (less than 400 °C) using a previously developed a novel method within our research group. Two-terminal non-volatile (2TNV) memory devices and metal-insulator-semiconductor (MIS) structures containing the silicon nanowires were fabricated and an in-depth study of their characteristics was carried out using current-voltage and capacitance techniques.
Project description:When sight-reading music, pianists have to decode a large number of notes and immediately transform them into finger actions. How do they achieve such fast decoding? Pianists may use geometrical features contained in the musical score, such as the distance between notes, to improve their efficiency in reading them. The aim of this study is to investigate the visual information pianists rely on when reading music. We measured the accuracy of the musical score reading of 16 skilled pianists and investigated its relationship with the geometrical features. When a single note was presented, pianists easily read it when it was located within three ledger lines. When two notes with an octave interval were presented, interestingly, their readable range was extended compared to that of the single note. The pianists were also able to recognize the octave interval correctly even if they misread the height (or pitch) of the target notes. These results suggest that the pianists decoded two notes composing an octave interval as a single "two-tone geometric pattern." Analyzing the characteristics of incorrect responses, we also found that pianists used the geometrical features of the spatial relationship between the note head and the ledger line, and that the cause of the misreading could be categorized into four types: [Type I] Confusion to a neighboring note having the same ledger line configuration; [Type II] Interference from a commonly used height note having the same note name; [Type III] Misunderstanding based on the appearance probability; [Type IV] Combination of the above three. These results all indicate that the pianists' abilities in score reading rely greatly on the correlation between the geometric features and playing action, which the pianists acquired through long-time training.