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Towards a Sustainable and Open Science : Recommendations for Enhancing Responsible Research and Innovation in the Biosciences at the University of Bremen
Full text linkStarbios2 is a four-year project (2016-2020) within the European Commission s Science with and for Society Programme, focusing on Responsible Research and Innovation (RRI). The project is generously funded by the European Union under the HORIZON 2020 Programme. Nine research institutions from European countries and three international partners are involved in the project coordinated by the Universita degli studi di Roma Tor Vergata in Italy. The goal of the project is to support research institutions in the implementation of RRI. The booklet Towards a Sustainable and Open Science - Enhancing Responsible Research and Innovation in the Biosciences at the University of Bremen summarizes 35 recommendations developed for the implementation of the RRI issues societal engagement, gender, ethics, open access and education. It is primarily directed at researchers and students of the Biosciences at the University of Bremen. It is also intended to encourage other research institutions to engage with RRI in practice
microRNAs as novel biomarkers for patients with testicular germ cell tumours
No full textTesticular cancer is the most common malignancy in men aged 14 - 44 years. In clinical management of testicular germ cell tumours (TGCTs), measurement of biomarkers is essential. However, only <60 % of cases show increased levels of the classical markers (AFP, b-HCG, and LDH) and novel tumour markers are urgently needed. microRNAs (miRNAs) are small non-coding RNA molecules and play an important role in biological processes. They are dysregulated in cancer and expression profiles might be useful biomarkers. The aim of this thesis was to validate the application of miRNAs of two clusters (miR-371-3 and miR-302/367) as novel serum markers for TGCTs. In each of the three studies, expression analyses demonstrated that serum levels of miR-371 fulfil all prerequisites for a valuable biomarker and the large-scale multicentre study showed 88.7 % sensitivity and 93.4 % specificity. Further studies are necessary to determine the miR-371 expression in metastasised patients especially during follow-up
Hydrocarbon Seepage at Campeche-Sigsbee Salt Province, Southern Gulf of Mexico (Detection, Mapping, and Seafloor Manifestation)
Full text linkHydrocarbon seepage is a process during which hydrocarbon fluids are emitted from the seafloor into the water column. This phenomenon has been observed globally from continental margins to the deep abyssal. Hydrocarbon seepage has significant impacts on the marine environment such as (a) influence on sediment composition and dynamics at the seafloor, (b) increasing the habitat heterogeneity on seep biodiversity and (c) contributes to the global carbon cycle. However, the occurrence, distribution, and dynamics of hydrocarbon seepage in the marine environment, especially in the deep ocean remains unclear due to limited investigation. The northern Gulf of Mexico is a well-known prolific petroleum-producing region where numerous gas and oil emissions, associated with salt tectonism, have been observed. The Campeche-Sigsbee salt province in the southern GoM is considered to be an analog to the salt province in the northern GoM, but there has been very little research conducted in this region. Based on the occurrence of natural oil slicks on the sea surface resolved by satellite images, previous studies suggested that there is a widespread distribution of oil seeps in the Campeche-Sigsbee salt province. However, there is still a lack of direct evidence for the presence and the distribution of gas emissions. In addition to gas and oil seepage, Chapopote asphalt volcanism, a novel type of hydrocarbon seepage was first introduced in 2003. Since then, submarine asphalt deposits have attracted considerable research interest. This study aims to have a comprehensive understanding of the hydrocarbon seepage system and dynamics in the southern GoM. The objectives are to investigate the distribution of gas emissions and to understand the controlling factors on the distribution. Furthermore, detailed investigations were carried out at Challenger Knoll and Mictlan Knoll to gain a better understanding of the diverse hydrocarbon seepage system including gas and oil emissions, as well as asphalt deposits. Consequently, the research questions about the fate of the methane bubbles and the quantity of gas bubble released from gas emission site are finally addressed in this study. During research cruise M114 of R/V METEOR, a multidisciplinary approach was conducted, including hydroacoustic surveys, visual seafloor observations, and sampling of gas bubbles. Ship-based multibeam echosounder was used for seafloor bathymetry, backscatter and water column flare mapping in the Campeche-Sigsbee salt province. In addition, multibeam echosounder mounted on Autonomous Underwater Vehicle (AUV) was utilized to obtain high-resolution seafloor bathymetry, backscatter, and water column data at Mictlan Knoll. Remotely Operated Vehicle (ROV) and TV-sled were applied for investigating and documenting seafloor manifestations of hydrocarbon seepage at the seafloor. Gas bubbles were collected by pressure-tight gas bubble samplers operated by ROV at the seafloor of Mictlan Knoll for gas analyses, quantification of gas bubble emissions, and finally gas flux calculation. In summary, gas emissions are found in large numbers in the Campeche-Sigsbee salt province. Their distributions are controlled by the present geological structures. The case study in the Sigsbee Knolls suggests that the edges of flat-top knolls might provide an effective migration pathway for hydrocarbons. As there is no direct evidence for the presence of current oil seepage in the Sigsbee Knolls, we suggested that oil seepage occurs intermittently. Gas, oil seepage and asphalt volcanism are found to occur close together at the Mictlan Knoll, indicating that this diverse hydrocarbon seepage system might be a common phenomenon in the Campeche Knolls. This thesis shows the complex association between the dynamics of diverse hydrocarbon seepage and the geological controls in the southern GoM
Particulate organic matter : Vector for carbon export, indicator for aquaculture impact and microbial hotspot
Full text linkMarine particulate organic matter (POM) can serve as vector for carbon (C) export, indicator for aquaculture impact and microbial hotspot: Off NW Africa, upwelling stimulates primary production. Despite the importance of bacteria for the biological C pump (BCP), little is known about bacterial communities (BCC) off NW Africa. Hence, the first objective is the description of the free-living (FL) and particle-attached (PA) BCC off NW Africa and potential key players in C degradation. Results reveal high relative abundances of C degrading bacteria, suggesting their key role in POM turnover. Aquacultures in the tropics are often accompanied by eutrophication and high POM loads. In Bolinao, Philippines, recurring hypoxia leads to major fish kills. So far POM characteristics have not been quantified. Results indicate the aquaculture activities in POM characteristics, rendering them ideal indicators for aquaculture impact. Overall, the results advance our understanding of the BCP and biogeochemical processes on aquaculture-derived POM. Furthermore, they indicate how processes occurring on the microscale are relevant for current global challenge
Decentralized Robust Capacity Control of Job Shop Systems with Reconfigurable Machine Tools
Full text linkManufacturing companies are confronted with various challenges from the perspective of customers individual requirements concerning variations of types of products, quantities and delivery dates. This renders the manufacturing process to be more dynamic and complex, which may result in bottlenecks and unbalanced capacity distributions. To cope with these problems, capacity adjustment is an effective approach to balance capacity and load for short or medium term fluctuations on the operational layer. Particularly, new technologies and algorithms need to be developed for the implementation of capacity adjustment. Reconfigurable machine tools (RMTs) and operator-based robust right coprime factorization (RRCF) provide an opportunity for a new capacity control strategy. Therefore, the main purpose of the research is to develop an effective machinery-oriented capacity control strategy by incorporating RMTs and RRCF for a job shop system to deal with volatile customer demands
Carbon Metabolism of Methylotrophic Methanogens and Asgard Archaea in Marine Sediments
Full text linkCarbon is the central element of life, as it is involved in building up of biological constituents and energy metabolisms in the cell. Archaea, - the most recently recognized domain of life - hold a crucial phylogenetic position in the evolution of life, but for most archaeal phyla, little is known about their role and activity in carbon metabolism. Archaea inhabit a variety of environments such as soils, sediments, sea water, and the guts of animals. Specifically in marine sediments, Thaumarchaeota, Euryarchaeota, Bathyarchaeota, Woesearchaeota and Asgard archaea are commonly found in archaeal communities. Methanogens affiliated to Euryarchaeota are well-known players in carbon metabolism, i.e., acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. Based on pure culture studies and genomic evidence, significant amounts of the biomass of methylotrophic methanogens growing on methyl substrates is derived from inorganic carbon. However, the in situ activity of these methanogens in carbon assimilation is unclear as the large inorganic carbon pool in marine sediment potentially affects carbon utilization patterns. To address this hypothesis, we initially applied nucleic acid stable isotope probing (SIP) to detect methylotrophic methanogens in marine sediment incubations. SIP results showed that 13C-labeled dissolved inorganic carbon (DIC) is necessary to identify methylotrophic methanogens, as illustrated by the nucleic acid synthesis pathway in these methanogens that 70-80% of carbon stems from DIC rather than methanol. In parallel, lipid-SIP suggested that DIC contributed to more than 60% from incubations with sediment from the sulfate reduction zone (SRZ), i.e., 20% higher than expected from lipid synthesis pathway. We further unexpectedly found that up to 12% methane was formed from DIC in autoclaved slurry incubations inoculated with the marine methylotrophic methanogen Methanococcoides methylutens. Similarly, methane formation from CO2 during methylotrophic methanogenesis was also observed with SRZ sediment incubations. In the same sediment incubations a higher amount of inorganic carbon was incorporated into lipids than expected, indicating that more DIC was assimilated into biomass than expected. Thus, the CO2 conversion to methane and biomass may play an important role in marine sediments. In the most recently discovered super phylum of the Archaea, the Asgard archaea might hold the key to understand the evolutionary origin of eukaryotes. Unlike methanogens, however, the diversity, carbon metabolism and the activity of Asgard archaea in marine sediments are still unknown. In this study, five new groups of Asgard archaea namely Kariarchaeota, Balderarchaeota, Hodarchaeota, Lagarchaeota and Gerdarchaeota are reported. In experiments with 13C-DIC, potential electron donors and electron acceptors, subgroup of Asgard archaea i.e., Lokiarchaeota was detected in the heavy SIP fractions from the incubations amended with organic polymers or sulfur, suggesting their activities of carbon fixation, organic polymers (cellulose, lignin and humic acid) degradation and sulfur metabolism. Furthermore, metagenomes were sequenced from heavy fractions of DNA-SIP samples obtained in the aforementioned experiments and from DNA extracted from mangrove sediments in the southeast coast of China. These metagenomes indicate that Asgard archaea harbor pathways of inorganic carbon fixation and degradation of cellulose, protein, short-chain and medium-chain alkane as well as assimilatory sulfate reduction. Crucially, the methyl coenzyme M reductase genes found in Helarchaeota have extended the potential of short-chain hydrocarbon oxidation to the Asgard archaea in this study. Overall, these findings illustrate that Asgard archaea actively utilize organic and inorganic carbon at the same time in mixotrophic fashion, which might play critical roles in carbon cycling of marine sediments. In particular, the successful detection of methylotrophic methanogens and Asgard archaea in marine sediments by nucleic acid-SIP with 13C-DIC suggested a crucial role of inorganic carbon in carbon metabolisms of these archaea. Given that many archaea harbor the acetyl-CoA associated carbon fixation pathway, my findings indicate that inorganic carbon assimilation might be ubiquitous in archaea when supply or availability of organic carbon are not sufficient in marine sediments
Microbiome in shrimp Litopenaeus vannamei aquaculture : dynamic changes and bacterial lifestyles
Full text linkThe Pacific white leg shrimp Litopenaeus vannamei is the most frequently cultured shrimp species, comprising more than 70% of the world shrimp commodities since 2010. Shrimp indoor and outdoor aquacultures are affected by water quality deteriorations and bacterial diseases. These cultivation problems lead to a substantial annual loss of shrimp harvest. Traditionally, water quality is quantified by plankton density, total suspended solids/particulate matter, pH, salinity and inorganic nutrients, particularly ammonium, nitrite and phosphate. Especially, the quantitative assessment of the carbon cycle in shrimp aquaculture is required to determine oxygen demand and depletion. However, optimal and acceptable but potentially stressful conditions have not systematically been determined in pond aquaculture. Excess biomass formed by photosynthesis of phytoplankton and by heterotrophic bacteria in the microbial loop poses a particular problem in shrimp aquaculture. While particulate matter in pond water may serve as additional feed source for shrimps, it also provides niches for particle-associated bacteria, such as pathogenic Vibrio species. In this study, water quality parameters as well as bacterial community compositions were observed in Indonesian shrimp aquacultures over the complete rearing process. Semi-intensive and intensive aquacultures differed in suspended particulate matter content, chlorophyll a, pH, and dissolved oxygen, while inorganic nutrient concentrations and the population size of cultivable heterotrophic bacteria were comparable. Halomonas, Salegentibacter, and Sulfitobacter were the most abundant free-living bacteria, whereas particle-associated bacteria were dominated by Halomonas and Psychrobacter. Vibrio were more frequently found in the intensive aquaculture system, particularly in the particle-associated fraction and at low pH conditions. White feces disease (WFD) event, which is a disease repeatedly occurring in shrimp aquaculture, was further documented in this thesis. To better understand pond water conditions as well as bacterial community dynamics during the disease event, the quantification of physico-chemical water parameters was combined with molecular analyses of the microbiome of shrimps, feces, and aquaculture water including the particles. The WFD event coincided with a low water pH and a high proportion of Alteromonas in the feces. Virulence genes of Vibrio, i.e toxin regulator (toxR) and termolabile hemolysin (tlh) were detected in the particle fraction ( 3 AAmicrometre), in the intestine of healthy shrimps and feces of WFD-infected shrimps. An increase of pH above 8 via limestone addition enabled a recovery from WFD. In addition, the bacterial community composition also changed with the rise in pH. This observation led to a recommendation, that aquacultures of L. vannamei should maintain a pH above 8. Lastly, bacterial dynamic on aggregates, which form in large numbers in shrimp aquaculture, was investigated to monitor the growth of potential pathogenic Vibrio species. In the rolling tank experiments, the addition of carbon-rich molasses was shown to rapidly reduce toxic ammonium and nitrite pools. Furthermore, it enabled the fast growth of halophilic heterotrophic bacteria, such as Halomonas, Psychrobacter, and Salegentibacter. Conversely, in the presence of Chlorella vulgaris aggregates V. parahaemolyticus population remained constant without decay. The algal biomass seemed to maintain the Vibrio population and density. I conclude that water parameters such as salinity and pH shape bacterial communities in shrimp pond aquaculture, and that a deterioration of water quality may cause detrimental shifts in bacterial community composition. However, bacterial communities will recover to the initial composition if water parameters are adjusted to former condition. To improve shrimp farming practices, I propose to perform regular pond water assessment, not only for the physicochemical parameters, but also for bacterial community composition. For this purpose, I recommend to analyze the bacterial communities in the particle fraction, including virulence genes of pathogenic bacteria. In addition, sludge discharge and regular addition of lime stones are necessary to improve and maintain shrimp production. As consequence, sustainable shrimp pond farming systems should include sludge as well as clean water reservoirs
Lithium recovery from diluted brines by means of a flow-through electrodes electrochemical reactor
Full text linkLithium has become an important raw material in various sectors because of the continuously growing market of its derivative products, in particular of rechargeable batteries. Its demand is expected to grow hugely in the near future, due to the development and spread of hybrid and fully electric vehicles and of lithium-ion batteries for stationary energy storage. Currently, lithium is mainly extracted from brine by means of the lime-soda evaporation process, consisting in a solar evaporation to increase its initial concentration and other following chemical treatments to remove unwanted cations. This process has several disadvantages, such as the unreliability due to the weather conditions, the water consumption, the slowness, and the large amount of chemical wastage. Therefore, a more efficient, faster and environmental friendly lithium recovery technology is urgently needed. In the last decade, many efforts have been done in order to find better alternatives for the extraction of lithium from brine. In particular, La Mantia et al. have firstly introduced a new technique, known as electrochemical ion pumping. The electrochemical ion pumping technique consists in applying a current to extract lithium cations from brine, driving them in a lithium-selective electrode by means of the intercalation mechanism. The cations are then released in a recovery solution applying the current in the opposite direction. The lighter environmental impact and the higher speed of this technique compared to the lime-soda evaporation process make the electrochemical ion pumping a good alternative for the lithium production. The other problem related to the production of lithium regards its global sources. The brine sources with a relative high lithium concentration to be exploited through the evaporation-based process are located mostly in South America. Together with the increase in the demand, the economic monopoly of lithium production is the reason of lithium increasing price. On this grounds, the diversification of the lithium supply will play an important role in the spread and competitiveness of lithium based technologies. The possibility to exploit other more diluted lithium sources (10-50 mg/l of lithium concentration), such as geothermal waters, brines produced in salt-works, waste waters from gas and oil extraction wells, is of worldwide interest. The aim of this PhD thesis has been to design and test a suitable electrochemical reactor for the extraction of lithium through electrochemical ion pumping from diluted brines, down to a lithium concentration of 7 mg/l (1 mM). The extraction from low concentrated solution is challenging due to the mass transport limitations in the liquid phase that reduce the process efficiency. Therefore a flow-through electrodes reactor has been designed, in order to improve the mass transport by adding a convective flux of the electrolyte. Firstly, a preliminary study of the thermodynamic behavior of the materials used in the reactor was carried out. Then the capturing process has been implemented and investigated at various conditions. The capture efficiency was tested at various lithium concentrations and flow rates, finding that the amount of captured lithium increases with the flow rate up to a maximum value that decreases with the concentrations. The efficiency at low concentrations has been optimized by improving the active material distribution on the electrode. Further investigations on the capturing process have been carried out at various currents. The results show that, by decreasing the current, the amount of captured lithium increases, while the flow rate to be applied reduces, thus sparing hydraulic energy. A mathematical model has been developed to explain and support the experimental results. The model is based on a simplified description of the electrode porous distribution and it reproduces the experimental behavior at various flow rates, concentrations, porous distributions and currents. The results show that the model can be used to investigate the optimal process parameters and to size the cell components. Finally the total process (capturing and release) has been performed. More than one litre of brine at 1 mM LiCl was treated, extracting lithium with a capturing yield of 60 %. The lithium cations were released back in 5 ml of solution reaching a concentration of 100 mM (700 mg/l) and a purity of 94 %, with a release efficiency of 75 %. The high achieved concentration and purity of the final solution demonstrate that the developed reactor can extract efficiently lithium from diluted brine and it represents a valid response to the envisaged lithium market demand
Interactive Multiagent Adaptation of Individual Classification Models for Decision Support
Full text linkAn essential prerequisite for informed decision-making of intelligent agents is direct access to empirical knowledge for situation assessment. This contribution introduces an agent-oriented knowledge management framework for learning agents facing impediments in self-contained acquisition of classification models. The framework enables the emergence of dynamic knowledge networks among benevolent agents forming a community of practice in open multiagent systems. Agents in an advisee role are enabled to pinpoint learning impediments in terms of critical training cases and to engage in a goal-directed discourse with an advisor panel to overcome identified issues. The advisors provide arguments supporting and hence explaining those critical cases. Using such input as additional background knowledge, advisees can adapt their models in iterative relearning organized as a search through model space. An extensive empirical evaluation in two real-world domains validates the presented approach
Chemie, Geographie, Nachhaltigkeit : innovative und interdisziplinäre Ansätze zur Nachhaltigkeitsbildung
Full text linkThis dissertation aims at supporting a meaningful integration of geographical perspectives and contexts into chemistry teaching for strengthening Education for Sustainable Development. In order to elaborate on this framework, theoretical considerations were made, and an interview study was conducted followed by three case studies on fracking, pesticides and phosphate recovery. The inclusion of sustainability-related topics in chemistry education, which seems to be necessary in light of current trends such as the planetary boundaries, the United Nations Sustainable Development Goals, or the discourse on the Anthropocene, is still rare. For designing and conducting the case studies, socio-scientific issue-oriented approaches were used, which go beyond learning the pure chemical content. For determining the teachersa beliefs on integrating a geographic perspective into chemistry teaching, an exploratory interview study was conducted. The teachersa beliefs towards this perspective are mostly positive but are predominantly limited to a physical-geographical dimension. A common aspect is a more holistic view which could be beneficial for students. Some teachers also named time constraints as an obstacle for integration. The case studies were designed by using participatory action research with a group of experienced teachers in a multi-cyclical procedure and evaluated by questionnaires. The case study on fracking was implemented in Germany using a digital learning environment and was generally positively perceived. In addition, the learning environment was translated into English and tested in the USA in a general chemistry course. The case study on pesticides involves a comparison of glyphosate with green pesticides in order to develop spider charts. The teaching approach is supported by video vignettes of an authentic Brazilian chemist working on alternative pesticides. The feedback, especially on the spider charts, is positive and provides the chance to discuss current topics in the classroom. The case study on phosphate recovery in Germany includes lab activities for which current recovery processes were adapted and a digital learning environment was created. The feedback on the experiments, the learning environment and the links between these aspects were positive. Subsequently, the learning environment was translated into English analogous to the Fracking case study and used in the USA. Feedback from students on both case studies in the US is positive, but some students question their usefulness due to lack of connection to a test. The studies in the USA were designed through an action research-oriented approach, which is presented and explained by using a specially developed model. Finally, this work demonstrates the potential of the orientation of chemistry towards a more societal perspective in order to arouse greater interest and possibly show in which areas chemistry impacts daily life. Although the subject of geography was used here, it can generally be said that thinking out of the box for a subject can be profitable and should therefore be used more intensively in the future