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Search Results: 1 - 10 of 1336 matches for " Sascha Strauss "
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HaMStR: Profile hidden markov model based search for orthologs in ESTs
Ingo Ebersberger, Sascha Strauss, Arndt von Haeseler
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-157
Abstract: We present a novel approach (HaMStR) to mine EST data for the presence of orthologs to a curated set of genes. HaMStR combines a profile Hidden Markov Model search and a subsequent BLAST search to extend existing ortholog cluster with sequences from further taxa. We show that the HaMStR results are consistent with those obtained with existing orthology prediction methods that require completely sequenced genomes. A case study on the phylogeny of 35 fungal taxa illustrates that HaMStR is well suited to compile informative data sets for phylogenomic studies from ESTs and protein sequence data.HaMStR extends in a standardized manner a pre-defined set of orthologs with ESTs from further taxa. In the same fashion HaMStR can be applied to protein sequence data, and thus provides a comprehensive approach to compile ortholog cluster from any protein coding data. The resulting orthology predictions serve as the data basis for a variety of evolutionary studies. Here, we have demonstrated the application of HaMStR in a molecular systematics study. However, we envision that studies tracing the evolutionary fate of individual genes or functional complexes of genes will greatly benefit from HaMStR orthology predictions as well.The amount of protein-coding DNA sequences in the public data bases is steadily increasing. This data is mainly generated by the sequencing and annotation of entire genomes and by numerous EST sequencing projects. Approaches to resolve the evolutionary relationships of eukaryotes on a molecular basis -frequently referred to as molecular systematics- particularly benefit from this data. Recent studies on the evolution of metazoans and fungi present trees with 40 to 77 taxa, reconstructed from more than 140 genes [1-6]. Still, these studies consider only a small fraction of the data available. For example, as of May 2008 dbEST contains 714 eukaryotic taxa with more than 2.000 ESTs each, and 394 taxa have more than 10,000 ESTs http://www.ncbi.nlm.nih.gov/dbEST
TonB-dependent transporters and their occurrence in cyanobacteria
Oliver Mirus, Sascha Strauss, Kerstin Nicolaisen, Arndt von Haeseler, Enrico Schleiff
BMC Biology , 2009, DOI: 10.1186/1741-7007-7-68
Abstract: We have screened all publicly available eubacterial genomes for sequences representing (putative) TBDTs. Based on sequence similarity, we identified 195 clusters, where elements of one cluster may possibly recognize similar substrates. For Anabaena sp. PCC 7120 we identified 22 genes as putative TBDTs covering almost all known TBDT subclasses. This is a high number of TBDTs compared to other cyanobacteria. The expression of the 22 putative TBDTs individually depends on the presence of iron, copper or nitrogen.We exemplified on TBDTs the power of CLANS-based classification, which demonstrates its importance for future application in systems biology. In addition, the tentative substrate assignment based on characterized proteins will stimulate the research of TBDTs in different species. For cyanobacteria, the atypical dependence of TBDT gene expression on different nutrition points to a yet unknown regulatory mechanism. In addition, we were able to clarify a hypothesis of the absence of TonB in cyanobacteria by the identification of according sequences.Filamentous cyanobacteria contain molecular machines for oxygenic photosynthesis under all growth conditions [1]. These machines, as well as those involved in respiration and nitrogen metabolism, depend on non-proteinaceous cofactors such as iron [2,3]. The level of iron found in cyanobacteria is generally one order of magnitude higher than in non-photosynthetic bacteria [4] and represents about 0.1% of their biomass [5]. Even though iron and copper are required for the function of respiratory and photosynthetic complexes, their intracellular level has to be tightly controlled as these ions pose a risk of oxidation [3]. Therefore, the uptake of iron is highly regulated in order to avoid intoxication. On the other hand, it is hypothesized that iron limitation might have been one of the selective forces in the evolution of cyanobacteria [6], and one might speculate that those cyanobacteria with the most efficient iron upt
Biogenic Isoprene and Its Impact on Human Health in Dependence on Meteorological Conditions  [PDF]
Sascha Henninger
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.329138
Abstract: Urban green areas have an important implication on the local climate. A cross-linkage of many small green spaces could result in decreasing the effect of the urban heat island, but also increase people’s thermal comfort. By the way, urban green areas could also induce a positive effect on the local urban air quality. But attention has to be paid to the assortment of the tree species. More or less all tree species are emitting biogenic volatile organic compounds in different concentration. These serve as precursors for the formation of ozone near the ground. So near surface ozone has the ability to react with different particulate matters and could become toxic, due to oxidation or nitrification. This causes inflammations and inspired allergens may increase the risk of a respiratory disease. Therefore, an analysis and assessment of the urban green area air quality could help to make a statement about the recreational effect of these areas in dependence of the leading vegetation and for that matter for the exposure to ozone. By the help of these the results can be used as a guidance of urban planning taking into account the influence of biogenic emission as a function of actual weather conditions.
A phase II study evaluating neo-/adjuvant EIA chemotherapy, surgical resection and radiotherapy in high-risk soft tissue sarcoma
Thomas Schmitt, Burkhard Lehner, Bernd Kasper, Marc Bischof, Falk Roeder, Sascha Dietrich, Antonia Dimitrakopoulou-Strauss, Ludwig G Strauss, Gunhild Mechtersheimer, Patrick Wuchter, Anthony D Ho, Gerlinde Egerer
BMC Cancer , 2011, DOI: 10.1186/1471-2407-11-510
Abstract: Patients with potentially curative high-risk STS (size ≥ 5 cm, deep/extracompartimental localization, tumor grades II-III [FNCLCC]) were included. The protocol comprised 4 cycles of neo-adjuvant chemotherapy (EIA, etoposide 125 mg/m2 iv days 1 and 4, ifosfamide 1500 mg/m2 iv days 1 - 4, doxorubicin 50 mg/m2 day 1, pegfilgrastim 6 mg sc day 5), definitive surgery with intra-operative radiotherapy, adjuvant radiotherapy and 4 adjuvant cycles of EIA.Between 06/2005 and 03/2010 a total of 50 subjects (male = 33, female = 17, median age 50.1 years) were enrolled. Median follow-up was 30.5 months. The majority of primary tumors were located in the extremities or trunk (92%), 6% originated in the abdomen/retroperitoneum. Response by RECIST criteria to neo-adjuvant CTX was 6% CR (n = 3), 24% PR (n = 12), 62% SD (n = 31) and 8% PD (n = 4). Local recurrence occurred in 3 subjects (6%). Distant metastasis was observed in 12 patients (24%). Overall survival (OS) and disease-free survival (DFS) at 2 years was 83% and 68%, respectively. Multivariate analysis failed to prove influence of resection status or grade of histological necrosis on OS or DFS. Severe toxicities included neutropenic fever (4/50), cardiac toxicity (2/50), and CNS toxicity (4/50) leading to CTX dose reductions in 4 subjects. No cases of secondary leukemias were observed so far.The current protocol is feasible for achieving local control rates, as well as OS and DFS comparable to previously published data on neo-/adjuvant chemotherapy in this setting. However, the definitive role of chemotherapy remains unclear in the absence of large, randomized trials. Therefore, the current regimen can only be recommended within a clinical study, and a possibly increased risk of secondary leukemias has to be taken into account.ClinicalTrials.gov NCT01382030, EudraCT 2004-002501-72Soft tissue sarcomas (STS) comprise a large variety of histologically distinct, rare malignant tumors. Overall, they account for less than 1% of a
Does the global warming modify the local Rwandan climate?  [PDF]
Sascha M. Henninger
Natural Science (NS) , 2013, DOI: 10.4236/ns.2013.51A019
Abstract:

Analyses of climate measurement series from Rwandan weather stations revealed that the division into the four formerly described Rwandan climate zones is not correct any more. This could be shown in a more detailed analysis based on currently available data. In the course of discussions held with the Service Meteo Rwanda it emerged that the climate charts used in Rwandan atlases and school books are based on data covering the period from 1931 to 1960. Fortunately, since then a mass of new data have been collected, which, however, until now have only been evaluated in isolated instances for a specific local as needed. This led to the initiation of the ReCCiR project. The project’s aim was to conduct a regional climatic analysis covering all of Rwanda and visualizing it on new maps.

When Air Quality Becomes Deleterious—A Case Study for Kigali, Rwanda  [PDF]
Sascha M. Henninger
Journal of Environmental Protection (JEP) , 2013, DOI: 10.4236/jep.2013.48A1001
Abstract:

Rwanda is a landlocked republic in Equatorial Africa. The capital Kigali (1°57'S, 30°04'E) can be mentioned as a typical African city due to its rising population and the rising rate of motorization. Different pollutants produced e.g. by a highusage rate of mopeds or open fireplaces burning wood for cooking and household chores could be detected. Climatological parameters as well as air pollutants were measured within the urban area. Additionally, highly frequented spatial and temporal mobile measurements of particulate matter were taken during different dry seasons regarding different conditions. These values indicated an urban heat island, which tended to rise for the last four decades. A temporary phenomenon for the air pollution indicators is visible during clear and calm weather situations, e.g. the distinctive relief caused an accumulation within small valleys called “Marais” in the night time. Unfortunately, these are the favourite places for living and agriculture. So there is no infrequence in values of PM10 > 1.000 μg·m-3. The origin of the different airborne particles was verified by using a scanning electron microscope and it could be mentioned that most particles were from the combustion of biomass and traffic.

Local climate changes and the spread of malaria in Rwanda  [PDF]
Sascha M. Henninger
Health (Health) , 2013, DOI: 10.4236/health.2013.54096
Abstract:

A population’s health makes it possible to draw conclusions about a country’s general development level. In connection with local climatic changes, for example, we can assess how well a society adjusts to the new conditions. To that effect, it has been observed during the last few years that global climate change can also affect human health in various ways. We can differentiate direct health impacts (e.g. extreme weather events, natural catastrophes caused by the weather) from indirect ones. However, the indirect consequences cause by far the greater damages to health. They are being spread increasingly by vectors (mosquitoes, ticks, etc.). Especially when a vector-carried infectious disease (e.g. malaria) migrates into areas where it is not endemic, considerable societal problems can result. The people living there would be immunologically unprepared.

Urban-Ecological Survey for Small Settlements  [PDF]
Martin Fabisch, Sascha Henninger
Open Journal of Ecology (OJE) , 2014, DOI: 10.4236/oje.2014.410049
Abstract:

Climate change is not just a global problem. When ecological conditions are altered by people, local climate will also be transformed. This local climate change is particularly pronounced within urban areas. This can, for example, lead to urban heat islands, which can amount to up to 10 K in large cities. In addition to this, there is also an extensive effect on local wind fields, air pollution control as well as on an urban water balance. An area-wide confirmation of this urban climate effect is only possible through extensive and usually expensive empirical surveys or complex modelling. For this reason, studies of the urban climate are mainly carried out in large cities. However, even in small settlements local climate can have a negative impact on humans. In order to plan settlement developments which are suitable for urban climate, local conditions must first be analysed. Currently used methods cannot provide low-cost solutions which deliver sufficient findings with regards to how detailed and current the data are. The approach of gathering urban-climate-relevant indicators locally, even in small settlements, in order to identify possible problem areas, is already providing a starting point for ecological urban development. Many of these indicators only start showing an effect when used in combination with other indicators. In order to record these interdependencies and to obtain detailed and robust primary data for suggested courses of action, two different indicators must be evaluated and then illustrated e.g. in a matrix. This allows for individual sub-areas, which hold potential for a particular climatic phenomenon in settlements, to be easily and effectively visualized, and thus identified.

Use of Augmented Reality Methods to Support Legal Conflicts in the Planning Process for Wind Turbines Using the Example of the Landscape Conservation Area “Eulenkopf and Surroundings”  [PDF]
Timo Wundsam, Sascha M. Henninger
Energy and Power Engineering (EPE) , 2014, DOI: 10.4236/epe.2014.611030
Abstract: The world’s growing energy demand poses a serious problem. At the same time fossil fuels are finite, which we must work against. Therefore, the Federal Government of Germany has set itself the goal to push forward the use of renewable energy in order to completely do without the generation of nuclear energy by 2023. There are, however, no specific guidelines from the European Directive on the promotion of electricity from renewable energy sources for the internal electricity market regarding how high each share of the different production method should be and, above all, which specific aim should be achieved by the share of wind energy. Nevertheless, it presents a crucial step toward a nuclear phaseout and a concomitant change of course of the Federal Government of Germany in the spring of 2011 regarding the expansion of renewable energy, taking the nuclear catastrophe in Fukushima into account. Using new legal planning approaches, also including the area of Rhineland-Palatinate, opportunities should be provided to make previously protected land available for setting up facilities for the generation of renewable energy. However, it is important to examine the legal situation regarding the installation of these kinds of constructions more detailed, as no general statements can be made. This will be illustrated using the example of the landscape conservation area “Eulenkopf and surrounding area” in the district of Kaiserslautern. The stated goal of the Social Democrat/Green coalition of the federal state government of Rhineland-Palatinate is to considerably expand the generation of electricity from renewable energy sources so that by 2030 at least the entire electricity demand can be covered by those. Due to the enormous potential of wind power, it is therefore necessary to quintuple its share of electricity generation by 2020, compared to 2011 numbers. In order to achieve the desired political objectives, by 2030 the number of turbines has to be increased to around 2650, representing a capacity of 7500 MW. This increase gives reason for boundary conditions to manage the generation of wind energy to be adjusted. This is intended to facilitate management and simultaneously minimise negative effects, such as the “sprawling” of wind turbines.
Models of Function Type for Commutative Symmetric Operator Families in Krein Spaces
Vladimir Strauss
Abstract and Applied Analysis , 2008, DOI: 10.1155/2008/439781
Abstract: Commutative symmetric operator families of the so-called
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