1,200 research outputs found
Modelling Interregional Trade of Energy Crops in Eastern Germany
Get PDFRenewable resources gain in importance in our modern society. The line of reasoning is based on their positive effects on agriculture, the environment and the economy. To support renewable energy from biomass the EU promotes the cultivation of energy crops. A spatial equilibrium model is applied based on the concept of maximizing net welfare, to provide information whether energy crop production competes with food production for land area. The Model of Interregional Trade of Energy Crops (ITEC) refers to Eastern Germany and adjacent areas of Poland. First results show that the regions have enough feedstocks to meet the required demand for food and biofuel production. In many cases both food crops and biofuels are either traded on interregional basis or exported to "Rest of Europe" indicating that there is no competition between food and energy crops. Only green maize for biogas production strongly competes in areas where the crop is required as feed for cattle.Energy crops, spatial equilibrium analysis, interregional trade, International Relations/Trade,
In-situ study of emerging metallicity and memory effect on ion-beam bombarded strontium titanate surface:
No full textIn this work we present an investigation of the occurrence of conductivity on the surface of SrTiO3 due to argon ion bombardment. We created a model to describe this process and found that the temperature during the ion milling is a crucial factor for the conductivity. Depending on the temperatures we found surface carrier densities ranging from 1.5*10^18 to 2.6*10^20cm^-3 by just analyzing the conductivity behavior.
Clustering of vacancies goes along with temperature and affects the conductivity significantly. Furthermore we found that ion milling is a gentle way create vacancies because the clustering rate is small compared to annealing samples in high vacuum. The amount of clusters at room temperature was measured to be around 3-4 times higher than at -140C.
We found that samples with a conducting surface change their resistance over time at room temperature due to the ongoing process of oxygen vacancy clustering. This effect may be suppressed by decreasing the temperature.
The bistable switching behavior in oxygen deficient SrTiO3 is shown without any additional doping. The vacancy migration is the major mechanism behind this memory effect. Comparing this behavior with annealed samples in high vacuum shows that the therein present amount of vacancy clusters must be much larger and has a negative effect on the bistable switching behavior.M.S.Includes bibliographical references (p. 83-87)by Heiko Gros
Handle with Care : Implementation of the List Experiment and Crosswise Model in a Large-Scale Survey on Academic Misconduct
Get PDFAcknowledgments We thank the anonymous reviewers as well as Alexander Ehlert, Isabel Raabe, and Justus Rathmann for their concise comments and constructive feedback on our work. Co-authors in alphabetical order. Study Design: Julia Jerke, David Johann, Heiko Rauhut, Kathrin Thomas, Antonia Velicu. Coding and Analysis: Julia Jerke, David Johann, Kathrin Thomas, Antonia Velicu. First draft: Julia Jerke, Heiko Rauhut, Kathrin Thomas, Antonia Velicu. Revisions: David Johann, Kathrin Thomas, Antonia Velicu. Final approval of the paper: Julia Jerke, David Johann, Heiko Rauhut, Kathrin Thomas, Antonia Velicu. Funding Information: The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research is supported by the Swiss National Science Foundation (SNSF), Starting Grant “CONCISE” BSSGIO 155981 of Heiko Rauhut.Peer reviewe
Detergent-protein and detergent-lipid interactions : implications for two-dimensional crystallization of membrane proteins and development of tools for high throughput crystallography
Get PDF2.1 Scope of this Thesis
This thesis represents an attempt to enlighten the role of the detergent in reconstitution and more specifically
in two-dimensional (2D) crystallogenesis of membrane proteins. The construction of a tool for precise
and routine measurements of detergent concentrations provided a valuable tool for better understanding
and controlling the detergent issue. Additionally, a novel approach for detergent removal in 2D crystallization,
i.e. the use of cyclodextrins was explored and a nanoliter dispensing high throughput tool was
developed allowing for profound and sophisticated screening of optimal conditions for protein reconstitution
and crystallization.
2.2 Combining Electron Microscopy
and Atomic Force
Microscopy
Although electron crystallography has proven to be
a powerful approach to structure determination of
membrane proteins (for a recent example see (Gonen
et al., 2005)) successes are somehow restricted
to certain classes of membrane proteins (e.g., outer
membrane porins, aquaporins, naturally occurring
crystalline proteins). This is mainly due to the stability
of these proteins with respect to biochemical
manipulation. One can not exclude however, that
these are simply more amenable to crystallization
due to the nature of their molecular surfaces.
2D crystallization exhibits several advantages
compared to 3D crystallization of membrane proteins:
The simple fact that the proteins are allowed
to reside in a native-like environment, i.e.,
the membrane and that their function is not impaired
by the lateral crystal contacts is of considerable
interest. If structural investigations shall not
be restricted to static snapshots of different conformations
and moreover structure-function relationships
shall be established, then electron microscopy
(EM) in combination with atomic force microscopy
(AFM) surely represent a valuable approach.
In Chapter 2 the combination of such data has
been successfully applied to the ammonium transporter
AmtB from Escherichia coli. The aim was to
determine the crystal packing of the double-layered
2D crystals of AmtB by AFM in order to process the
cryo EM data. Additionally, the AFM images, due
to their outstanding signal-to-noise ratio, enabled
the direct visualization of trimers in the reconstituted
membranes. The topographical data from
the AFM allowed the assessment of a single layer
within the double layered crystals.
2.3 Investigating the Role of the
Detergent
In Chapter 3 the development of a fast and precise
method for detergent concentration determination
is presented. The robustness and wide application
range of this method has been demonstrated
by comparing concentrations of radioactively
labeled dodecyl-[beta],D-maltoside (DDM) with
measured contact angles, by measuring the amount
of DDM bound to the proton/galactose symporter
GalP from E. coli, by measuring the effects
of 100 mM NaCl on the cmc of dodecyl-N,Ndimethylamine-
N-oxide, by characterizing the surface
energy of Parafilm, and finally by revealing
the stoichiometry of complex formation between
methyl-[beta]-cyclodextrin (MBCD) and different de-
tergents. The possibility of performing such measurements
routinely in membrane biochemistry is
unique compared to all other methods available to
date.
Chapter 4 addresses the major aspects of detergent
use in membrane protein purification and
crystallization. First, the stability of GalP in different
detergents is assessed, unveiling profound
differences in the capacity of detergents to keep
the protein in solution. Second, it is demonstrated,
that the amount of a detergent, i.e., dodecyl-�,Dmaltoside,
bound to a protein can be controlled
during purification. At last the amount of different
detergents for solubilization of E. coli lipids is
determined, showing differences in the mechanisms
by which detergents promote solubilization.
Banerjee et al. (Banerjee et al., 1995) examined
the preferential affinity of detergents for different
lipids in mixed membranes (such as biological membranes).
They showed that different detergents extract
the serotonin 5-HT1A receptor from native
membranes along with different lipids. The effect
is considerable and might explain why different detergents
exhibit such a different ability to keep a
protein in its native state, because some might simply
not be able to co-solubilize native lipids essential
for the stability (and function) of the protein.
The amount of detergent bound to a protein is
of special interest when using dialysis or dilution
for detergent removal. Furthermore, in most cases
the protein must not be exposed to excess detergent
which anyway fails to satisfactorily mimic the
native bilayer. As pointed out in the discussion of
Chapter 4, protein reconstitution is facilitated when
the detergent collar that is present around the hydrophobic
region of membrane proteins in solution
is near its solubility limit (Psol).
The same is true for the lipid: Reconstitution is
likely to happen when liposomes are forming, therefore
an excess of detergent is not desirable either.
Additionally, even detergents known to have adverse
effects on protein stability can be used for
lipid solubilization, given that they are present at a
minimal concentration. The use of detergent mixtures
in crystallization can also have the effect of
reducing the size of the detergent collar around the
protein. Moreover, the free detergent concentration
in detergent mixtures is altered by the presence of
the second species and can be crucial to the formation
of crystals in some cases (Koning, 2003).
When using minimal amounts of detergent in a
crystallization mixture, special care should be taken
with respect to the formation of ternary micelles.
Ideally, equilibration of the ternary mixtures prior
to detergent removal needs to be completed.
2.4 The Use of Cyclodextrins for
High Thorughput 2D Crystallization
of Membrane Proteins
Chapter 5 demonstrates the feasibility of the
cyclodextrin-based detergent removal for twodimensional
crystallization. The possibility of
choosing different kinetics, simply by adding different
amounts of cyclodextrin at various time intervals
is one of the major advantages of this method.
By implementing optical spectroscopy, it would be
possible to slow down the detergent removal rate at
the onset of proteoliposome and 2D crystal formation.
As pointed out by Lichtenberg et al. (Lichtenberg
et al., 2000) the rate of detergent removal has
to be slow enough to allow for detergent-induced
vesicle size growth, a process which is usually quite
slow. This aspect is important to keep in mind as
one defines the rate of detergent neutralization (in
contrast to dialysis). At a first glance one might
think that in this respect the cyclodextrin approach
bears no advantage compared to dialysis. However,
the rate of low-cmc detergent removal using dialysis
can be too slow, thereby keeping the protein out
from its native environment for too long, ultimately
promoting its precipitation.
In Chapter 6 we present an apparatus for parallel
quantitative reconstitution and 2D crystallization
of membrane proteins. Cyclodextrin provides a
unique opportunity for high throughput implementation
compared to other methods available today.
Protein concentrating through controlled evaporation
with concomitant detergent neutralization (to
prevent detergent concentrating) is advantageous
compared to commercially available protein concentrating
devices which very often concentrate detergent
micelles too. Moreover, the possibility of using
one protein preparation for wide screening ensures
that inconsistencies in results arising from preparative
differences are excluded. Often, the detergent
and lipid concentration of the purified protein are
ill characterized, and this variability may be a cause
for much of the irreproducibility and failure in crystallization
(Wiener, 2004).
So far the use of wide screening matrices (sparse
matrix design) in 2D crystallography was restricted
by the enormous number of experiments and
amount of protein needed for a rigorous screening.
The presented machine makes it possible to partially
compensate for the first bottleneck in protein
structure elucidation, which is the over-expression
of membrane proteins.
Fig. 2.1 summarizes the screening strategy based
on the criteria discussed in Chapter 6 and above.
Screening efficiency is provided by the subdivision
of the problem into multiple subproblems and by
their sequential screening.
With the high throughput approach however, a
new bottleneck arises as one will produce a large
number of crystallization trials, which have to be
screened for their outcome. Therefore –in analogy
to the x-ray community– the development of automated
sample preparation and automated electron
microscopic analysis would provide substantial support
to the 2D crystallographer.
Combining step-by-step identification of key values
necessary for crystallization (and/or efficient reconstitution)
together with high throughput screening
matrices opens up new prospects in the en
deavor to membrane protein structure and function
determination. Now it is possible to apply a
semi-rational screening strategy and this might contribute
to transform 2D crystallization from art to
science (Jap et al., 1992)
Pitfall trap sampling bias depends on body mass, temperature, and trap number: insights from an individual-based model
Get PDFThe diversity and community composition of ground arthropods is routinely analyzed by pitfall trap sampling, which is a cost- and time-effective method to gather large numbers of replicates but also known to generate data that are biased by species-specific differences in locomotory activity. Previous studies have looked at factors that influence the sampling bias. These studies, however, were limited to one or few species and did rarely quantify how the species-specific sampling bias shapes community-level diversity metrics. In this study, we systematically quantify the species-specific and community-level sampling bias with an allometric individual-based model that simulates movement and pitfall sampling of 10 generic ground arthropod species differing in body mass. We perform multiple simulation experiments covering different scenarios of pitfall trap number, spatial trap arrangement, temperature, and population density. We show that the sampling bias decreased strongly with increasing body mass, temperature, and pitfall trap number, while population density had no effect and trap arrangement only had little effect. The average movement speed of a species in the field integrates body mass and temperature effects and could be used to derive reliable estimates of absolute species abundance. We demonstrate how unbiased relative species abundance can be derived using correction factors that need only information on species body mass. We find that community-level diversity metrics are sensitive to the particular community structure, namely the relation between body mass and relative abundance across species. Generally, pitfall trap sampling flattens the rank-abundance distribution and leads to overestimations of ground arthropod Shannon diversity. We conclude that the correction of the species-specific pitfall trap sampling bias is necessary for the reliability of conclusions drawn from ground arthropod field studies. We propose bias correction is a manageable task using either body mass to derive unbiased relative abundance or the average speed to derive reliable estimates of absolute abundance from pitfall trap sampling
The Definitive Guide to NetBeans Platform
No full textThe Definitive Guide to NetBeans(t) Platform is a thorough and definitive introduction to the NetBeans Platform, covering all its major APIs in detail, with relevant code examples used throughout. The original German book on which this title is based was well received. The NetBeans Platform Community has put together this English translation, which author Heiko Bock updated to cover the latest NetBeans Platform 6.5 APIs. With an introduction by known NetBeans Platform experts Jaroslav Tulach, Tim Boudreau, and Geertjan Wielenga, this is the most up-to-date book on this topic at the moment. Al
An adaptive system for patient-controlled analgesia vol.1
Get PDFVolume 2 is the actual data. Please contact the author for this information. Heiko Rudolph [[email protected]] http://www.set.rmit.edu.au/~e55643/Deposited with permission of the author. © 1995 Dr. Heiko E. R. Rudolph.Patient-Controlled Analgesia (PCA) has become accepted as an important means of self-regulated relief from post-surgical pain. In commonly used PCA systems, patients use a hand-held push-button to indicate the presence of pain and initiate a predetermined bolus of drug infusion. A disadvantage of this system is that no means is provided to accommodate variations in the intensity of pain or the sensitivity of the patient to the analgesic in use apart from the frequency of button pushing. A fixed rate background infusion is usually an option. A new adaptive PCA system is proposed to provide improved PCA through the use a variable background infusion, the provision for an extended high range of analgesic dosages and a novel handset which allows patients to rate their pain. The total system is under the control of an expert algorithm and is proposed to overcome some of the shortcomings of current systems. (For complete abstract open document
Bicycle Ambulances in rural Uganda - Analysis of factors influencing its usage
No full textThis article reports on a study undertaken to analyze the usage of the bicycle ambulances in Uganda. Since 1997, approximately 400 bicycle ambulances have been distributed to villages in rural Uganda to improve accessibility to health centers. Approximately 20% of the population of Uganda have to travel more than 5 km to a health center, in a country where most transportation is by foot. A bicycle ambulance is a bicycle with an attached trailer used to transport seriously sick patients up to 15 km. The author conducted guided interviews with receivers and the distributors of bicycle ambulances in selected villages. Factors have been defined that influence the usage of bicycle ambulances, including individual village characteristics, the features of the bicycle ambulance, the system of distribution, and the organization of the groups using the bicycle ambulances. The distance to the health center, nor the distance to the main road and quality of the road itself significantly influenced the usage of the bicycle ambulance. The frequency of usage of the bicycle ambulances was limited to a few cases in a month or year. The only significant influence on the frequency of usage was observed based on the different organizational structures of the bicycle ambulance groups. The author considers some of the barriers to use, including long distances to health centers and costs of repairs, but notes that these and other barriers can be overcome through the positive attitude of group members
Bicycle Ambulances in rural Uganda - Analysis of factors influencing its usage
No full textThis article reports on a study undertaken to analyze the usage of the bicycle ambulances in Uganda. Since 1997, approximately 400 bicycle ambulances have been distributed to villages in rural Uganda to improve accessibility to health centers. Approximately 20% of the population of Uganda have to travel more than 5 km to a health center, in a country where most transportation is by foot. A bicycle ambulance is a bicycle with an attached trailer used to transport seriously sick patients up to 15 km. The author conducted guided interviews with receivers and the distributors of bicycle ambulances in selected villages. Factors have been defined that influence the usage of bicycle ambulances, including individual village characteristics, the features of the bicycle ambulance, the system of distribution, and the organization of the groups using the bicycle ambulances. The distance to the health center, nor the distance to the main road and quality of the road itself significantly influenced the usage of the bicycle ambulance. The frequency of usage of the bicycle ambulances was limited to a few cases in a month or year. The only significant influence on the frequency of usage was observed based on the different organizational structures of the bicycle ambulance groups. The author considers some of the barriers to use, including long distances to health centers and costs of repairs, but notes that these and other barriers can be overcome through the positive attitude of group members
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