OPUS 4 | Universitätspublikationen

Three-dimensional model study of the arctic ozone loss in 2002/2003 and comparison with 1999/2000 and 2003/2004 (2004)

Wuhu Feng Martyn P. Chipperfield Stewart Davies Bhaswar Sen Geoffrey C. Toon Jean-François Blavier Christopher R. Webster C.-Michael Volk Alexey Ulanovsky Fabrizio Ravegnani Peter von der Gathen Hans-Jürg Jost Erik C. Richard Hans Claude

We have used the SLIMCAT 3-D off-line chemical transport model (CTM) to quantify the Arctic chemical ozone loss in the year 2002/2003 and compare it with similar calculations for the winters 1999/2000 and 2003/2004. Recent changes to the CTM have improved the model's ability to reproduce polar chemical and dynamical processes. The updated CTM uses σ-θ as a vertical coordinate which allows it to extend down to the surface. The CTM has a detailed stratospheric chemistry scheme and now includes a simple NAT-based denitrification scheme in the stratosphere. In the model runs presented here the model was forced by ECMWF ERA40 and operational analyses. The model used 24 levels extending from the surface to ~55 km and a horizontal resolution of either 7.5°×7.5° or 2.8°×2.8°. Two different radiation schemes, MIDRAD and the CCM scheme, were used to diagnose the vertical motion in the stratosphere. Based on tracer observations from balloons and aircraft, the more sophisticated CCM scheme gives a better representation of the vertical transport in this model which includes the troposphere. The higher resolution model generally produces larger chemical O3 depletion, which agrees better with observations. The CTM results show that very early chemical ozone loss occurred in December 2002 due to extremely low temperatures and early chlorine activation in the lower stratosphere. Thus, chemical loss in this winter started earlier than in the other two winters studied here. In 2002/2003 the local polar ozone loss in the lower stratosphere was ~40% before the stratospheric final warming. Larger ozone loss occurred in the cold year 1999/2000 which had a persistently cold and stable vortex during most of the winter. For this winter the current model, at a resolution of 2.8°×2.8°, can reproduce the observed loss of over 70% locally. In the warm and more disturbed winter 2003/2004 the chemical O3 loss was generally much smaller, except above 620 K where large losses occurred due to a period of very low minimum temperatures at these altitudes.

Isolation and X-ray crystal structure of tetrahydroisoquinoline alkaloids from Calycotome villosa Subsp. intermedias (2004)

Ali El Antri Ibtissam Messouri Mohamed Bouktaib Rachid El Alami Michael Bolte Brahim El Bali Mohammed Lachkar

Two tetrahydroisoquinoline alkaloids were extracted from the alkaloid fraction of a methanol extract of the seeds of Calycotome Villosa Subsp. intermedia. Their structures were established as (R)-1-hydroxymethyl-7-8-dimethoxy-1,2,3,4-tetrahydro- isoquinoline (1) and (S)-7-hydroxymethyl-2-3-dimethoxy-7,8,9,10-tetrahydroisoquinoline chloride (2) by spectroscopic techniques and X-ray diffraction analysis.

Models of chronic obstructive pulmonary disease (2004)

Jan David Alexander Groneberg K Fan Chung

Chronic obstructive pulmonary disease (COPD) is a major global health problem and is predicted to become the third most common cause of death by 2020. Apart from the important preventive steps of smoking cessation, there are no other specific treatments for COPD that are as effective in reversing the condition, and therefore there is a need to understand the pathophysiological mechanisms that could lead to new therapeutic strategies. The development of experimental models will help to dissect these mechanisms at the cellular and molecular level. COPD is a disease characterized by progressive airflow obstruction of the peripheral airways, associated with lung inflammation, emphysema and mucus hypersecretion. Different approaches to mimic COPD have been developed but are limited in comparison to models of allergic asthma. COPD models usually do not mimic the major features of human COPD and are commonly based on the induction of COPD-like lesions in the lungs and airways using noxious inhalants such as tobacco smoke, nitrogen dioxide, or sulfur dioxide. Depending on the duration and intensity of exposure, these noxious stimuli induce signs of chronic inflammation and airway remodelling. Emphysema can be achieved by combining such exposure with instillation of tissue-degrading enzymes. Other approaches are based on genetically-targeted mice which develop COPD-like lesions with emphysema, and such mice provide deep insights into pathophysiological mechanisms. Future approaches should aim to mimic irreversible airflow obstruction, associated with cough and sputum production, with the possibility of inducing exacerbations.

Alawi syncretism : beliefs and traditions in the shrine of Hüseyin Gazi (2004)

Hüseyin Türk

Religious Anthropology studies the origins, evolution and functions of religions. The discipline researching religious beliefs and rituals comparatively with cross-cultural perspectives tries to enlighten the belief world of the mankind. Religion, as a term, can be defined as "believing as well as worshipping to the supernatural powers and/or beings by the individual who are emotionally or consciously devoted to them" (Örnek 1988: 127). There have been a number of theories so far which try to bring an explanation to the origins and the evolution of religion. In these theories, Fetishism, cults of nature, animism, Totemism, dynamism, Manism, magic, polytheism, monotheism as well as certain physiological phenomena have been particularized as evolutionary stages and forms of belief (Evans-Pritchard 1998: 124). All of these theories have the perspective of so called "progressive" and / or "unilinear" that maintain a religion which has reached ongoing stages and that communities which have developed from primitiveness to civilization. They argue that there has only been one single line of progress, and all of the communities are bound to go through the same evolutionary stages.

Islam and pluralism : does Quran approve religious pluralism? (2004)

Ali Ihsan Yitik

As for the relation between Islam and pluralism, it seems a little bit complicated. There are some verses in The Koran for pluralism and at the same time we have some verses against. Among the sayings of Prophet Muhammad like the some Koranic verses, we came across with something good and bad for non-Muslims in special contexts. By another saying, we find both positive and negative statements for Jews and Christians in different circumstances. Muslim scholars the complexity still exists. We find both positive and negative stances. So it is difficult to see a standard or official view on this issue. However, we should point out that Islam recognizes all the sacred (Semitic) books and their messages. It accepts all prophets of that traditions. It defines itself as the last and perfect religion of Semitic tradition and states that no other religion will be accepted from anybody else other then itself. It criticizes both the Jews and Christians especially about their failure to uphold the Oneness of God, tawhid, and to preserve the authenticity of their scripture from interventions. This exclusivist aspect of Islam as many conservative scholars formed with putting together some evidences from the Koran is generally accepted by Muslims.

Untouchability and inter-caste relations in rural India : the case of southern Tamil villages (2004)

A. Ramaiah

Justice and equality are the two subjects often talked about by most of the nationalists and leaders of various political and ideological streams across the world including India. India was at the fore-front in condemning racial discrimination particularly apartheid and also the influence of super powers) on the internal affairs of independent nations. Her commitment to secure its citizens' freedom, justice, equality and fraternity is reflected in the very preamble of the Indian Constitution. Towards achieving these challenging goals, special provisions have also been made in the Constitution to protect and promote the interests of the most oppressed section of Indian society - traditionally known as Untouchables and Constitutionally as the Scheduled Castes. These provisions are expected to alter the given unjust distribution of power (political and economic) and status (social) among different sections of people and thereby transform India into an egalitarian society. Given India's unequivocal commitment to secure its citizens these noble ideals - particularly the most exploited and pilloried section of India -, we shall attempt here to understand Indian villages, which host over 80 per cent of the Indian population, from the point of view of whether or not these villages patronise the institution of caste which is in contravention of these ideals or whether there are these little republics ideal for realising the said goals and thus to be preserved as they are as claimed by many social reformers including Mahatma Gandhi. In the process, we shall also address the question of how caste has remained unchanged, how it controls social interaction between higher and lower caste groups and accordingly perpetuates unequal control over power and status. And most importantly we shall also understand whether all the Scheduled Castes (lower castes) treat their members as equals or there is hierarchy, discrimination and practice of untouchability even among them.

Recombinant DNA-carrier proteins with improved intracellular trafficking capabilities for nonviral gene delivery (2004)

Arjen Sloots

Safety concerns associated with the use of viral vectors in gene therapy applications have attracted considerable attention towards the development of nonviral vectors as alternatives for DNA delivery. While nonviral vectors are commonly not associated with safety problems, they are still very inefficient compared to viral vectors, and require significant improvements to approach the efficiency of their viral counterparts. Meanwhile ligands or single-chain antibody fragments that bind to cell surface receptors for increased and/or specific cellular uptake, endosome escape activities, and nuclear localization sequences (NLSs) to enhance transport of plasmid DNA into the nucleus, have become available that can be incorporated into nonviral vectors to improve their efficacy. However, as gene delivery is a multistep process, the challenge is to incorporate multiple of these functional elements into a single nonviral vector system, while retaining their specific activities. A promising method to attach such entities to plasmid DNA is the use of multifunctional fusion proteins that bind to DNA through a DNA-binding domain. In principle, two types of DNA-binding domains/proteins can be used to anchor additional functional domains or peptides to a plasmid, namely sequence-specific DNA-binding domains, described in the first part of this thesis, or those that bind DNA independent of its sequence, exemplified in the second part of this work by a derivative of the human HMGB2 protein. The first fusion protein constructed and analyzed contained the E. coli LexA repressor as a sequence-specific DNA-binding domain. In addition, this DNA-carrier protein, termed TEL, included a bacterial translocation domain as an integrated endosome escape activity, and human TGF-a for specific targeting to the EGF-receptor (EGFR). TEL was expressed in E. coli and purified under both native and denaturing conditions. Purified, denatured TEL was refolded and subsequently shown to bind specifically to EGFR-expressing cells. However, inclusion of TEL in complexes of plasmid DNA and poly-L-lysine (pL) did not lead to increased gene delivery into EGFR-expressing COS-1 cells. Most likely this was due to the absence of DNA-binding activity of the LexA moiety in TEL. In contrast, native TEL was able to interact specifically with DNA. Nevertheless, since this interaction was rather weak, and refolding of denatured TEL had not resulted in functional activity of all of its protein domains, it seemed unlikely that fusion proteins containing LexA would exhibit gene transfer capabilities superior to those of similar DNA-carrier proteins previously constructed in our group. Further work therefore focused on the use of the E2C-Sp1C protein as an alternative sequencespecific DNA-binding domain. This artificial zinc-finger protein was fused to the single-chain antibody fragment scFv(FRP5), directed against the human ErbB2 growth factor receptor. The resulting 5-E2C fusion protein was expressed in E. coli and purified under native and denaturing conditions. Refolded and native 5-E2C were found to bind specifically to ErbB2-expressing cells, indicating that scFv(FRP5) in 5-E2C was functional in both preparations. In contrast, whereas refolded 5-E2C bound DNA only weakly, significant DNA binding was observed for native 5-E2C. In addition, it could not only be shown that the interaction of native 5-E2C with DNA containing its recognition sequence was specific, but also that this protein was able to bind DNA and recombinant ErbB2 simultaneously, demonstrating the functionality of both domains in native 5-E2C. Despite these encouraging results, the inclusion of native 5-E2C in pL- or polyethyleneimine (PEI)-DNA complexes did not lead to an (5-E2C-specific) enhancement of gene transfer efficiency, irrespective of the presence of the endosome-disruptive reagent chloroquine during transfection. In the second part of this thesis an alternative approach for the development of DNA-carrier proteins for nonviral gene delivery is described, based on human HMGB2, a DNA-binding protein without sequence specificity. HMGB2 contains an acidic C-terminus that has been found to decrease the affinity of the protein for DNA. Therefore, this C-terminal tail was deleted, resulting in an HMGB2-variant consisting of amino acids 1-186. HMGB2186, purified under native conditions from E. coli lysates, was able to interact with DNA and bound to the surface of different cell lines. Importantly, after binding to plasmid DNA HMGB2186 mediated gene delivery into COS-7 cells with higher efficiency than pL. In addition, HMGB2186-mediated gene transfer was strongly enhanced in the presence of chloroquine, indicating that the endocytic pathway was involved in cellular uptake. To improve internalization and intracellular routing of HMGB2186 as a DNA-carrier, a derivative containing the TAT47-57 cell-penetrating peptide (CPP), reported to facilitate cell entry independent of endocytosis, was constructed. Since this peptide also contains an NLS, in addition an HGMB2186-variant containing the SV40-NLS was constructed to investigate the effect of a peptide that has only nuclear localizing properties. Interestingly, the resulting TAT-HMGB2186 and SV40-HMGB2186 fusion proteins displayed DNA-binding activities similar to HMGB2186, but mediated gene delivery into different cell lines clearly more efficiently than the parental molecule. Furthermore, the efficacy of both fusion proteins was enhanced markedly in the presence of chloroquine, an indication that endocytosis was involved in the transfection process mediated by these proteins. This suggests that the increased transfection efficiency observed for TAT-HMGB2186 was more likely due to the NLS function present in the TAT47-57 peptide, rather than to its ‘cell penetrating properties’. Finally, the incorporation of functional peptides derived from human proteins into HMGB2186 was investigated. An uncharged CPP originating from Kaposi-FGF, reported to facilitate efficient cellular uptake of fused protein domains in an endocytosis-independent manner, was fused to HMGB2186 together with the SV40-NLS. Interestingly, the resulting KSV40-HMGB2186 fusion protein bound DNA similarly as previously tested DNA-carrier proteins, but did not mediate enhanced transfection compared to HMGB2186. In addition, the importin-b-binding (IBB) domain derived from human importin-a2 was investigated as a component of a DNA-carrier protein. Since the IBB domain can function as an NLS, it was fused to HMGB2186 resulting in the DNA-carrier protein IBBHMGB2186. Although IBB-HMGB2186 bound DNA in a similar manner as the other HMGB2186-derivatives, gene delivery mediated by IBB-HMGB2186 was only as effective as HMGB2186 mediated transfection, suggesting no significant role of the IBB domain. However, addition of chloroquine resulted in a remarkable enhancement of IBB-HMGB2186-mediated gene transfer, which was now more efficient than with any other HMGB2186-variant tested, and not much lower than gene transfer mediated by PEI, one of the most efficient transfection reagents available to date. To enhance nonviral gene delivery even further, the HMGB2186-based DNA-carrier proteins described in this thesis might now serve as building blocks for novel fusion proteins that include additional complementing activities. In this respect it seems particularly promising that, under conditions of effective end some escape, IBB-HMGB2186, which consists entirely of protein domains of human origin, was the most efficient of all proteins tested in this work.

Role of phosphorylated RcsB in the Rcs phosphorelay pathway (2004)

Soma Sengupta

RcsB is a central transcriptional regulator in enteric bacteria involved in exopolysaccharide (EPS) biosynthesis, in cell division, in the expression of osmoregulated genes, and regulates at least 20 other genes and operons. It is a member of a phosphorelay system and signal transfer is mediated by phosphorylation through the RcsC/YojN phosphorelay. RcsB proteins modified with the phosphorylation mimic BeF3- as shown by its conformational changes and DNA binding properties and resulted phosphorylated RcsB derivatives with sufficient stability. Both, the wild type RcsB protein and the mutant RcsBD11A could be modified with BeF3-. Non-phosphorylated RcsB has been shown to bind as a heterodimer with the coinducer RcsA at the conserved RcsAB box in Rcs regulated promoters. In this study, it has been shown that the modification of RcsB by BeF3 - (I) has a negative effect on its homodimerization, (II) abolishes the complex formation of RcsAB with the RcsAB box as shown by the EMSA and SPR technique. All the effects were found to be reversible by increasing the NaF concentration in the assays presumably leading to the formation of the inactive BeF4 2- salt. This hypothesis of RcsB being modified by BeF3- was also supported by other phosphodonors like ATP and acetyl phosphate, both of them showed the same negative effect on DNA binding by RcsAB heterodimer giving evidence that BeF3- could be used as a phosphorylation mimic. In addition, the phosphorylation mimic BeF3- was found to be a better phosphorylating agent than ATP and acetyl phosphate. This is the first evidence that phosphorylation of RcsB might have a negative effect on the activation of RcsAB regulated operons. Autophosphorylation of RcsB proves that it has the ability to take up phosphoryl groups and the mutant protein also become autophosphorylated with less efficiency or stability than the wild type protein. RcsB probably takes up phosphoryl groups through RcsC -> YojN -> RcsB phosphorelay pathway. To study the interaction among the proteins in this pathway, fluorescence spectroscopy, NMR spectroscopy, and an in vivo ß galactosidase assay were performed by using two domains of RcsC (T-RcsC and R-RcsC), HPt domain of the protein YojN, and RcsB. The interactions between R-RcsC/YojN-HPt and YojN-HPt/RcsB supports the proposed pathway of phosphorylating RcsB. RcsB might also be phosphorylated by YojN-HPt that is phosphorylated by other sensor kinase other than RcsC in a cross-talk mechanism. The phosphorylation of RcsB by YojN-HPt probably has the same negative effect on cps induction as obtained with BeF3 - effect on DNA binding by RcsAB heterodimer.

Biomarkers in Lake Albano and Lake Constance sediment records : implications for palaeoclimate and palaeoenvironment (2004)

Sabine Hanisch

The biomarker record in two different lakes in central Europe, Lake Albano and Lake Constance, is used to reflect environmental changes and lake system response during the Late Glacial and Holocene. Extractable organic compounds in lake sediments, which can be assigned to their biological source (biomarkers) function as fingerprints of past aquatic or land plant organisms. Using gas chromatography coupled with mass spectrometry, 21 different biomarkers (predominantly steroids and triterpenoids) as well as a variety of n-alkanes, nalkanols, and n-alkanoic acids could be identified in the sediment records of Lake Albano and Lake Constance. In the Holocene sediments of Lake Albano, the distribution of biomarkers such as dinosterol (dinoflagellates), isoarborinol, and diplopterol (aquatic organisms) indicate three biomarker zones: The period between 0-3,800 years BP (zone 3) is characterized by high concentrations of these biomarkers and others such as tetrahymanol and diploptene. Conversely, zone 2 (3,800-6,500 years BP) shows very low concentrations of all autochthonous biomarkers. In zone 1 (6,500–11,480 years BP), dinosterol, isoarborinol, and diplopterol range on a relatively high level, whereas diploptene and tetrahymanol display comparatively low concentrations. The results suggest at least two distinct changes in the predominance of primary producers during the Holocene, which are related to changes in the lake system such as lake mixing and water column stratification. This interpretation is consistent with previous investigations of Lake Albano sediments including pigment and hydrogen index data (Ariztegui et al., 1996b; Guilizzoni et al., 2002). Allochthonous biomarkers such as long-chain n-alkanes, amyrenones and friedelin indicate a development from forest to a more open landscape from 6,000 and 5.000 years BP, respectively. After a period of high concentrations during the first half of the Holocene, all biomarkers derived from deciduous trees exhibit relatively low values until around 1,000 years BP. Again, this is consistent with results from previous pollen investigations (Ariztegui et al., 2000). The sediment core from Upper Lake Constance comprises the Late Glacial and Holocene. It was analysed for biomarkers and inorganic tracers in order to compare the biomarker results with other proxy data from the same core. Magnetic susceptibility (MS) was measured to get a high-resolution stratigraphic framework of the core and to obtain further information about changes of the proportions of allochthonous and autochthonous input. Enhanced concentrations and accumulation rates of dinosterol (biomarker for dinoflagellates) and biogenic calcite give evidence of increasing lake productivity at the beginning of the Holocene followed by a decrease in bioproductivity after around 7,000 years BP. Younger Dryas sediments are characterized by low amounts of both dinosterol and biogenic calcite indicating a low productivity. The comparison of the concentrations and accumulation rates of b-sitosterol and stigmastanol with parameters reflecting lake productivity suggests that both steroids in Lake Constance sediments are mainly derived from terrigenous sources. Biomarkers as well as concentrations and accumulation rates of allochthonous inorganic compounds such as titanium, magnesium and strontium indicate a slightly enhanced allochthonous input after 8,500 years BP. Significant increase of erosive matter input from enhanced soil erosion is not observed before 4,000 years BP. This can be attributed to the combined effects of precipitation increase as a result of climatic deterioration and anthropogenic deforestation which is consistent with observations from other lakes in Central Europe. The MS record of Lake Constance confirms these results by tracing the climatically induced shifts of more intense bioproduction (low MS caused by increased calcite deposition) during the ‘climatic optimum’. This is followed by increasing input of terrigenous sediment compounds during colder and wetter periods which lead to higher MS values in the lake sediments. The occurrence of tetrahymanol in Lake Constance sediments questions the unambiguous use of tetrahymanol as an indicator for water column stratification. Anaerobic organic macroaggregates within the oxygenated, photic zone of the water column have to be considered as a possible living space for anaerobic microorganisms containing tetrahymanol. The direct comparison of two very different lakes Albano and Constance with respect to biomarkers indicating climate or environmental change provides a contribution to the recent biomarker research for a better understanding of biomarkers in lacustrine sediments.

Proximities and innovation : evidence from the Indian IT industry in Bangalore (2004)

Florian Arun Täube

Much has been written on the success of the Indian software industry, enumerating systemic factors like first-class higher education and research institutions, both public and private; low labour costs, stimulating (state) policies etc. However, although most studies analyzing the 'Indian' software industry cover essentially the South (and West) Indian clusters, this issue has not been tackled explicitly. This paper supplements the economic geography explanations mentioned above with the additional factor social capital, which is not only important within the region, but also in transnational (ethnic) networks linking Indian software clusters with the Silicon Valley. In other words, spatial proximity is complemented with cultural proximity, thereby, extending the system of innovation. The main hypothesis is that some Indian regions are more apt to economic development and innovation due to their higher affinity to education and learning, as well as, their more general openness, which has been a main finding of my interviews. In addition, the transnational networks of Silicon Valley Indians seem to be dominated by South Indians, thus, corroborating the regional clustering of the Indian software industry. JEL Classifications: O30, R12, Z13, L86

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