Spike train auto-structure impacts post-synaptic firing and timing-based plasticity
- Cortical neurons are typically driven by several thousand synapses. The precise spatiotemporal pattern formed by these inputs can modulate the response of a post-synaptic cell. In this work, we explore how the temporal structure of pre-synaptic inhibitory and excitatory inputs impact the post-synaptic firing of a conductance-based integrate and fire neuron. Both the excitatory and inhibitory input was modeled by renewal gamma processes with varying shape factors for modeling regular and temporally random Poisson activity. We demonstrate that the temporal structure of mutually independent inputs affects the post-synaptic firing, while the strength of the effect depends on the firing rates of both the excitatory and inhibitory inputs. In a second step, we explore the effect of temporal structure of mutually independent inputs on a simple version of Hebbian learning, i.e., hard bound spike-timing-dependent plasticity. We explore both the equilibrium weight distribution and the speed of the transient weight dynamics for different mutually independent gamma processes. We find that both the equilibrium distribution of the synaptic weights and the speed of synaptic changes are modulated by the temporal structure of the input. Finally, we highlight that the sensitivity of both the post-synaptic firing as well as the spike-timing-dependent plasticity on the auto-structure of the input of a neuron could be used to modulate the learning rate of synaptic modification.
TRENTOOL : a Matlab open source toolbox to analyse information flow in time series data with transfer entropy
- Background: Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present.
Results: In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected.
Conclusions: TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.
Short-lived brominated species : observations in the source regions and the tropical tropopause layer
Elliot L. Atlas
- We conducted measurements of up to the five important short-lived brominated species in the marine boundary layer (MBL) of the mid-latitudes (List/Sylt, North Sea) in June 2009 and of the tropical Western Pacific during the TransBrom ship campaign in October 2009. For the one-week time series in List mean mixing ratios of 2.0, 1.1, 0.2, 0.1 ppt were analysed for CHBr3, CH2Br2, CHBr2Cl and CH2BrCl, with maxima of 5.8 and 1.6 ppt for the two main components CHBr3 and CH2Br2. Along the cruise track in the Western Pacific (between 41° N and 13° S) mean mixing ratios of 1.0, 0.9, 0.2, 0.1 and 0.1 ppt for CHBr3, CH2Br2, CHBrCl2, CHBr2Cl and CH2BrCl were determined. Air samples with coastal influence showed considerably higher mixing ratios than the samples with open ocean origin. Correlation analyses of the two datasets yielded strong linear relationships between the mixing ratios of four of the five species (except for CH2BrCl). Using a combined dataset from the two campaigns, rough estimates of the molar emission ratios between the correlated substances were derived as follows: 9/1/0.3/0.3 for CHBr3/CH2Br2/CHBrCl2/CHBr2Cl. Additional measurements were made in the tropical tropopause layer (TTL) above Teresina (Brazil, 5.07° S, 42.87° W) in June 2008, using balloon-borne cryogenic whole air sampling technique. Near the level of zero clear-sky net radiative heating (LZRH) at 14.8 km about 2.25 ppt organic bromine was bound to the five short-lived species, making up 13 % of total organic bromine (17.82 ppt). CH2Br2 (1.45 ppt) and CHBr3 (0.56 ppt) accounted for 90 % of the budget of short-lived compounds in that region. Near the tropopause (at 17.5 km) organic bromine from short-lived substances was reduced to 1.35 ppt, with 1.07 ppt and 0.12 ppt attributed to CH2Br2 and CHBr3 respectively.
The isotopic composition of methane in the stratosphere : high-altitude balloon sample measurements
- The isotopic composition of stratospheric methane has been determined on a large suite of air samples from stratospheric balloon flights covering subtropical to polar latitudes and a time period of 16 yr. 154 samples were analyzed for δ13C and 119 samples for δD, increasing the previously published dataset for balloon borne samples by an order of magnitude, and more than doubling the total available stratospheric data (including aircraft samples) published to date. The samples also cover a large range in mixing ratio from tropospheric values near 1800 ppb down to only 250 ppb, and the strong isotope fractionation processes accordingly increase the isotopic composition up to δ13C = −14‰ and δD = +190‰, the largest enrichments observed for atmospheric CH4 so far. When analyzing and comparing kinetic isotope effects (KIEs) derived from single balloon profiles, it is necessary to take into account the residence time in the stratosphere in combination with the observed mixing ratio and isotope trends in the troposphere, and the range of isotope values covered by the individual profile. The isotopic composition of CH4 in the stratosphere is affected by both chemical and dynamical processes. This severely hampers interpretation of the data in terms of the relative fractions of the three important sink mechanisms (reaction with OH, O(1D) and Cl). It is shown that a formal sink partitioning using the measured data severely underestimates the fraction removed by OH, which is likely due to the insensitivity of the measurements to the kinetic fractionation in the lower stratosphere. Full quantitative interpretation of the CH4 isotope data in terms of the three sink reactions requires a global model.
The isotopic composition of methane in the stratosphere : high-altitude balloon sample measurements
- The isotopic composition of stratospheric methane has been determined on a large suite of air samples from stratospheric balloon flights covering subtropical to polar latitudes and a time period of 16 yr. 154 samples were analyzed for δC and 119 samples for δD, increasing the previously published dataset for balloon borne samples by an order of magnitude, and more than doubling the total available stratospheric data (including aircraft samples) published to date. The samples also cover a large range in mixing ratio from tropospheric values near 1800 ppb down to only 250 ppb, and the strong isotope fractionation processes accordingly increase the isotopic composition up to δ13C=−14‰ and δD= +190‰, the largest enrichments observed for atmospheric CH4 so far. When analyzing and comparing kinetic isotope effects (KIEs) derived from single balloon profiles, it is necessary to take into account the residence time in the stratosphere in combination with the observed mixing ratio and isotope trends in the troposphere, and the range of isotope values covered by the individual profile. Temporal isotope trends can also be determined in the stratosphere and compare reasonably well with the tropospheric trends. The effects of chemical and dynamical processes on the isotopic composition of CH4 in the stratosphere are discussed in detail. Different ways to interpret the data in terms of the relative fractions of the three important sink mechanisms (reaction with OH, O(1D)) and Cl, respectively), and their limitations, are investigated. The classical approach of using global mean KIE values can be strongly biased when profiles with different minimum mixing ratios are compared. Approaches for more local KIE investigations are suggested. It is shown that any approach for a formal sink partitioning from the measured data severely underestimates the fraction removed by OH, which is likely due to the insensitivity of the measurements to the kinetic fractionation in the lower stratosphere. Attempts can be made to correct for the lower stratospheric sink bias, but full quantitative interpretation of the CH4 isotope data in terms of the three sink reactions requires a global model.
A new estimation of the recent tropospheric molecular hydrogen budget using atmospheric observations and variational inversion
Isabelle C. Pison
Ole Amund Søvde
Rebecca E. Fisher
Euan G. Nisbet
Martin K. Vollmer
William T. Sturges
Grant L. Forster
Chris Rene Lunder
Viacheslav I. Privalov
Nina N. Paramonova
- This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks.
Numerical simulation of flow, H2SO4 cycle and new particle formation in the CERN CLOUD chamber
- To study the effect of galactic cosmic rays on aerosols and clouds, the Cosmic Leaving OUtdoor Droplets (CLOUD) project was established. Experiments are carried out at a 26 m3 tank at CERN (Switzerland). In the experiments, the effect of ionising particle radiation on H2SO4 particle formation and growth is investigated. To evaluate the experimental configuration, the experiment was simulated using a coupled multidimensional CFD – particle model (CLOUD-FPM). In the model the coupled fields of gas/vapour species, temperature, flow velocity and particle properties were computed to investigate the tank's mixing state and mixing times. Simulation results show that the mixing state of the tank's contents largely depends on the characteristics of the mixing fans and a 1-fan configuration, as used in first experiments, may not be sufficient to ensure a homogeneously mixed chamber. To mix the tank properly, 2 fans are necessary. The 1/e response times for instantaneous changes of wall temperature and saturation ratio inside the chamber were found to be in the order of few minutes. Particle nucleation and growth was also simulated and particle number size distribution properties of the freshly nucleated particles (particle number, mean size, standard deviation of the assumed log-normal distribution) were found to be mixed over the tank's volume similar to the gas species.
On the structural changes in the Brewer-Dobson circulation after 2000
David W. Tarasick
Eric A. Ray
- In this paper we present evidence that the observed increase in tropical upwelling after the year 2000 may be attributed to a change in the Brewer-Dobson circulation pattern. For this purpose, we use the concept of transit times derived from residual circulation trajectories and different in-situ measurements of ozone and nitrous dioxide. Observations from the Canadian midlatitude ozone profile record, probability density functions of in-situ N2O observations and a shift of the N2O-O3 correlation slopes, taken together, indicate that the increased upwelling in the tropics after the year 2000 appears to have triggered an intensification of tracer transport from the tropics into the extratropics in the lower stratosphere below about 500 K. This finding is corroborated by the fact that transit times along the shallow branch of the residual circulation into the LMS have decreased for the same time period (1993–2003). On a longer time scale (1979–2009), the transit time of the shallow residual circulation branch show a steady decrease of about −1 month/decade over the last 30 yr, while the transit times of the deep branch remain unchanged. This highlights that changes in the upwelling across the tropical tropopause are not sufficient as an indicator for changes in the entire Brewer-Dobson circulation.
Klonierung, Expression und Aufreinigung von Derivaten des α-Amylase-Inhibitors Parvulustat
- Parvulustat ist ein kleines Protein (8,2 kDA), das aus dem Bodenbakterium Streptomyces
parvulus sekretiert wird. Es ist ein saures Polypeptid mit einem isoelektrischen Punkt von 4,49
und inhibiert spezifisch α-Amylasen (Ki = 9 x 10-12).
In der vorliegenden Arbeit sollen neben der Isotopenmarkierung des Parvulustats PL-Mutanten
mittels PCR-Mutagenese und DNA Rekombinationstechnick hergestellt werden.
Zur Charakterisierung und Strukturbestimmung der Mutanten werden größere Mengen des
jeweiligen Proteins benötigt, wofür wiederum ein effektives Expressionssystem bereitstehen
muß. Ein Expressionssystem besteht aus einem Wirtsorganismus der seinen Protein-Biosynthese-
Apparat zur Verfügung stellt und einem Vektor (Plasmid) der das Zielgen trägt. Im Falle des
Parvulustats und seiner Mutanten bietet sich der gut charakterisierte Stamm Streptomyces
lividans TK 24 (Hopwood et al, 1985) als Wirtsorganismus an. Der Inhibitor wird in ihm als
Vorläuferprotein mit Signalpeptid als Transportsignal (Leader) gebildet. Da dieses Bakterium
keine äußere Membran besitzt, wird der Inhibitor direkt ins Kulturmedium ausgeschleust. Dabei
wird das Signalpeptid durch die Signalpeptidase abgespalten.
Das Strukturgen wird zuerst im Klonierungsplasmid pSH09 in E. coli vervielfältigt, bevor es mit
den Enzymen EcoRI und SpeI geschnitten wird, um in den Expressionsvektor pSH017 integriert
zu werden. Dieser Shuttlevektor trägt genauso die gewünschten Restriktionsschnittstellen, SpeI
und EcoRI, die die paßgenaue Ligation des rekombinanten Strukturgens mit den funktionellen
Nach erfolgtem Einbau des Zielgens in das neue Vektorkonstrukt kann dieser Expressionsvektor
leicht in den Wirtsorganismus eingebracht werden und sich dort vermehren. Nach Klonierung der
mutierten Parvulustatsgene in den Expressionsvektor werden die damit transformierten Zellen auf
R2YE-Platten aufgebracht und bei einer Temperatur zwischen 20 und 28°C je nach PL-Mutanten
inkubiert. Zur Selektion wird Thiostrepton verwendet. Nach Transformation und Vermehrung
geeigneter Wirtszellen wird das klonierte Gen transkribiert. Durch anschließende Translation der
gebildeten mRNA in der Wirtszelle entsteht das gewünschte Protein in großen Mengen. Zur
Überprüfung der Aktivität der einzelnen Mutanten steht der qualitative α-Amylase-Plattentest zur
Verfügung, wobei die aktiven Mutanten einen blauen Hemmhof bilden (siehe Abbildung 24). Der
blaue Jod-Stärke-Komplex weist, bei gleichzeitigem Vorhandensein von α-Amylase, auf nicht
abgebaute Stärke und damit indirekt auf die Produktion des α-Amylase-Inhibitors hin.
Da das Parvulustat von den Bakterien ins Medium abgegeben wird, besteht die Abtrennung der
Zellen durch Zentrifugation des Kulturmediums. Es folgen Ammoniumsulfatfällung des
Überstandes, Auftragung auf PAGE und präparative HPLC, nach der reines, einheitliches Protein
isoliert werden konnte.
Molecular Characterization of the HCV Polymerase Derived from Different Genotypes with the Substituted N-Phenyl-Benzenesulphonamides as Novel Classified Non-Nucleoside Inhibitor Chemotype
Marina Maja May
- The NS5B protein of the hepatitis C virus (HCV) is a RNA-dependent RNA
polymerase, which is the key enzyme for viral replication. It is recognized as
one of the promising targets for antiviral intervention within the new HCV
treatment approach of direct-acting antivirals (DAA). However, several of the
known non-nucleoside HCV polymerase inhibitors (NNIs) identified by screening
approaches show limitations in the coverage of all six major HCV genotypes
(GT). Genotypic profiling therefore has to be implemented early in the screening
cascade to discover new broadly active NNIs. This implies knowledge of the
specific individual biochemical properties of polymerases from all GTs which
is to date limited to GT 1 only.
The work submitted here gives a comprehensive overview of the biochemical
properties of HCV polymerases derived from all major GTs 1 - 6. Biochemical
analysis of polymerases from 38 individual sequences revealed that the optima
for monovalent cations, pH and temperature were similar between the GTs,
whereas significant differences concerning concentration of the preferred cofactor
Mg2+ were identified. Implementing the optimal requirements for the
polymerases from each individual GT led to significant improvements in their
enzymatic activities. However, the specific activity was distributed unequally
across the GTs and could be ranked in the following descending order: 1b, 6a
> 2a, 3a, 4a, 5a > 1a.
Furthermore, the optimized assay conditions for GT profiling were confirmed
by testing the inhibitory activity of four known prototype NNIs, each addressing
one of the four NNI binding sites. Additionally, a novel NNI chemotype
- identified by screening - is described, the substituted N-phenyl-benzenesulphonamides
(SPBS). This inhibitor class showed reversible inhibition of NS5B
from HCV 1b Con1 with IC50 values up to 39 nM. Based on the decreased
inhibitory activity against a recombinant NS5B protein carrying the mutation
L419M, it was assumed that the SPBS inhibitors bound to the thumb site II
as it has been described for the carboxy thiophene inhibitors. The postulated
binding site was consequently confirmed by analysing a provided co-crystal
structure of NS5B in complex with a SPBS analogue. Notably, the two SPBS
analogues SPBS-1 and SPBS-2 reported here revealed significant differences in
addressing the NH-group of the main chain Y477 by hydrogen-bonds, watermediated
or directly, which provoked a shift of the carboxyphenyl group of the
inhibitors towards the H475 position for the water-mediated binding mode.
Interestingly, the differences observed in the binding mode led to a different
cross resistance profile at positions M423 and I482. Using the previously optimized
biochemical primer-dependent transcription assay, inhibitory activity
of the SPBS could be demonstrated against polymerases from HCV GTs 1a
and 1b whereas the inhibitor class failed to inhibit any of the non-GT 1 polymerases.
Furthermore, initial antiviral activity for SPBS was demonstrated
against the subgenomic replicons of HCV GTs 1a and 1b, respectively, and no
considerable cytotoxic potential against a panel of ten different cell types.
Finally, concerning a possible future treatment without PEG-IFN α or ribavirin,
the SPBS analogues were found to display additive to synergistic effects
in combination with the benzothiadiazine, the benzofuran and the indole
- representative inhibitors for the binding sites palm I, palm II and thumb
I, repectively - in the biochemical assay. Within the same binding site as the
SPBS, the reference compound hydroxydihydropyranone displayed additive interactions
only with the benzothiadiazine (palm I) in the biochemical assay as
well as in cell culture. Hence it could be concluded that, having characterized
one individual NNI, no universal predication is possible concerning the combinatory
behaviour of NNIs binding to the same binding site. As synergistic,
antagonistic or additive interactions are inhibitor-dependent (not binding sitedependent)
each novel NNI has to be characterized individually in one-to-one