Heb. (Hebrew) University Library

Digital image

Jerusalem - Nurses' School - Library

Digital image

Stretching single DNA-molecules with temperature-stabilized optical tweezers

This thesis consists of two parts; in the first part we performed a single-molecule force extension measurement with 10kb long DNA-molecules from phage-λ to validate the calibration and single-molecule capability of our optical tweezers instrument. Fitting the worm-like chain interpolation formula to the data revealed that ca. 71% of the DNA tethers featured a contour length within ±15% of the expected value (3.38 µm). Only 25% of the found DNA had a persistence length between 30 and 60 nm. The correct value should be within 40 to 60 nm. In the second part we designed and built a precise temperature controller to remove thermal fluctuations that cause drifting of the optical trap. The controller uses feed-forward and PID (proportional-integral-derivative) feedback to achieve 1.58 mK precision and 0.3 K absolute accuracy. During a 5 min test run it reduced drifting of the trap from 1.4 nm/min in open-loop to 0.6 nm/min in closed-loop.

Synthesis, Reactivity and Biological Activity of 17β-HSD1 Inhibitors Based on a Thieno[2,3-d]pryrimidin-4(3H)-one Core

Breast cancer is the most common cancer in women in Western countries. In the early stages of development most breast cancers are hormone-dependent, and estrogens, especially estradiol, have a pivotal role in their development and progression. One approach to the treatment of hormone-dependent breast cancers is to block the formation of the active estrogens by inhibiting the action of the steroid metabolising enzymes. 17beta-Hydroxysteroid dehydrogenase type 1 (17beta-HSD1) is a key enzyme in the biosynthesis of estradiol, the most potent female sex hormone. The 17beta-HSD1 enzyme catalyses the final step and converts estrone into the biologically active estradiol. Blocking 17beta-HSD1 activity with a specific enzyme inhibitor could provide a means to reduce circulating and tumour estradiol levels and thus promote tumour regression. In recent years 17beta-HSD1 has been recognised as an important drug target. Some inhibitors of 17beta-HSD1 have been reported, however, there are no inhibitors on the market nor have clinical trials been announced. The majority of known 17beta-HSD1 inhibitors are based on steroidal structures, while relatively little has been reported on non-steroidal inhibitors. As compared with 17beta-HSD1 inhibitors based on steroidal structures, non-steroidal compounds could have advantages of synthetic accessibility, drug-likeness, selectivity and non-estrogenicity. This study describes the synthesis of large group of novel 17beta-HSD1 inhibitors based on a non-steroidal thieno[2,3-d]pyrimidin-4(3H)-one core. An efficient synthesis route was developed for the lead compound and subsequently employed in the synthesis of thieno[2,3-d]pyrimidin-4(3H)-one based molecule library. The biological activities and binding of these inhibitors to 17beta-HSD1 and, finally, the quantitative structure activity relationship (QSAR) model are also reported. In this study, several potent and selective 17beta-HSD1 inhibitors without estrogenic activity were identified. This establishment of a novel class of inhibitors is a progressive achievement in 17beta-HSD1 inhibitor development. Furthermore, the 3D-QSAR model, constructed on the basis of this study, offers a powerful tool for future 17beta-HSD1 inhibitor development. As part of the fundamental science underpinning this research, the chemical reactivity of fused (di)cycloalkeno thieno[2,3-d]pyrimidin-4(3H)-ones with electrophilic reagents, i.e. Vilsmeier reagent and dimethylformamide dimethylacetal, was investigated. These findings resulted in a revision of the reaction mechanism of Vilsmeier haloformylation and further contributed to understanding the chemical reactivity of this compound class. This study revealed that the reactivity is dependent upon a stereoelectronic effect arising from different ring conformations.

Molecular Modelling of Estrogen-Producing Enzymes CYP450 Aromatase and 17beta-Hydroxysteroid Dehydrogenase Type 1

Breast cancer is the most common cancer in women in the western countries. Approximately two-thirds of breast cancer tumours are hormone dependent, requiring estrogens to grow. Estrogens are formed in the human body via a multistep route starting from cholesterol. The final steps in the biosynthesis include the CYP450 aromatase enzyme, converting the male hormones androgens (preferred substrate androstenedione ASD) into estrogens(estrone E1), and the 17beta-HSD1 enzyme, converting the biologically less active E1 into the active hormone 17beta-hydroxyestradiol E2. E2 is bound to the nuclear estrogen receptors causing a cascade of biochemical reactions leading to cell proliferation in normal tissue, and to tumour growth in cancer tissue. Aromatase and 17beta-HSD1 are expressed in or near the breast tumour, locally providing the tissue with estrogens. One approach in treating hormone dependent breast tumours is to block the local estrogen production by inhibiting these two enzymes. Aromatase inhibitors are already on the market in treating breast cancer, despite the lack of an experimentally solved structure. The structure of 17beta-HSD1, on the other hand, has been solved, but no commercial drugs have emerged from the drug discovery projects reported in the literature. Computer-assisted molecular modelling is an invaluable tool in modern drug design projects. Modelling techniques can be used to generate a model of the target protein and to design novel inhibitors for them even if the target protein structure is unknown. Molecular modelling has applications in predicting the activities of theoretical inhibitors and in finding possible active inhibitors from a compound database. Inhibitor binding at atomic level can also be studied with molecular modelling. To clarify the interactions between the aromatase enzyme and its substrate and inhibitors, we generated a homology model based on a mammalian CYP450 enzyme, rabbit progesterone 21-hydroxylase CYP2C5. The model was carefully validated using molecular dynamics simulations (MDS) with and without the natural substrate ASD. Binding orientation of the inhibitors was based on the hypothesis that the inhibitors coordinate to the heme iron, and were studied using MDS. The inhibitors were dietary phytoestrogens, which have been shown to reduce the risk for breast cancer. To further validate the model, the interactions of a commercial breast cancer drug were studied with MDS and ligand–protein docking. In the case of 17beta-HSD1, a 3D QSAR model was generated on the basis of MDS of an enzyme complex with active inhibitor and ligand–protein docking, employing a compound library synthesised in our laboratory. Furthermore, four pharmacophore hypotheses with and without a bound substrate or an inhibitor were developed and used in screening a commercial database of drug-like compounds. The homology model of aromatase showed stable behaviour in MDS and was capable of explaining most of the results from mutagenesis studies. We were able to identify the active site residues contributing to the inhibitor binding, and explain differences in coordination geometry corresponding to the inhibitory activity. Interactions between the inhibitors and aromatase were in agreement with the mutagenesis studies reported for aromatase. Simulations of 17beta-HSD1 with inhibitors revealed an inhibitor binding mode with hydrogen bond interactions previously not reported, and a hydrophobic pocket capable of accommodating a bulky side chain. Pharmacophore hypothesis generation, followed by virtual screening, was able to identify several compounds that can be used in lead compound generation. The visualisation of the interaction fields from the QSAR model and the pharmacophores provided us with novel ideas for inhibitor development in our drug discovery project.

Phage therapy in livestock methane amelioration

Viruses of prokaryotes (phages) are obligate microbial pathogens that can, in the lytic phase of development, infect and lyse their respective bacterial or archaeal hosts. As such, these viruses can reduce the population density of their hosts rapidly, and have been viewed as possible agents of biological control (phage therapy). Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations as the use of antibiotics and chemical treatments becomes both less effective and less publicly acceptable. Phage therapy has therefore been raised as a potential strategy to reduce methane (CH 4) emissions from ruminants, providing an innovative biological approach, harnessing the potent, yet targeted, biocidal attributes of these naturally occurring microbial predators.

Phage therapy in livestock methane amelioration.

Viruses of prokaryotes (phages) are obligate microbial pathogens that can, in the lytic phase of development, infect and lyse their respective bacterial or archaeal hosts. As such, these viruses can reduce the population density of their hosts rapidly, and have been viewed as possible agents of biological control (phage therapy). Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations as the use of antibiotics and chemical treatments becomes both less effective and less publicly acceptable. Phage therapy has therefore been raised as a potential strategy to reduce methane (CH4) emissions from ruminants, providing an innovative biological approach, harnessing the potent, yet targeted, biocidal attributes of these naturally occurring microbial predators.

Specifying Reuse Interfaces for Task-Oriented Framework Specialization

Reuse of existing carefully designed and tested software improves the quality of new software systems and reduces their development costs. Object-oriented frameworks provide an established means for software reuse on the levels of both architectural design and concrete implementation. Unfortunately, due to frame-works complexity that typically results from their flexibility and overall abstract nature, there are severe problems in using frameworks. Patterns are generally accepted as a convenient way of documenting frameworks and their reuse interfaces. In this thesis it is argued, however, that mere static documentation is not enough to solve the problems related to framework usage. Instead, proper interactive assistance tools are needed in order to enable system-atic framework-based software production. This thesis shows how patterns that document a framework s reuse interface can be represented as dependency graphs, and how dynamic lists of programming tasks can be generated from those graphs to assist the process of using a framework to build an application. This approach to framework specialization combines the ideas of framework cookbooks and task-oriented user interfaces. Tasks provide assistance in (1) cre-ating new code that complies with the framework reuse interface specification, (2) assuring the consistency between existing code and the specification, and (3) adjusting existing code to meet the terms of the specification. Besides illustrating how task-orientation can be applied in the context of using frameworks, this thesis describes a systematic methodology for modeling any framework reuse interface in terms of software patterns based on dependency graphs. The methodology shows how framework-specific reuse interface specifi-cations can be derived from a library of existing reusable pattern hierarchies. Since the methodology focuses on reusing patterns, it also alleviates the recog-nized problem of framework reuse interface specification becoming complicated and unmanageable for frameworks of realistic size. The ideas and methods proposed in this thesis have been tested through imple-menting a framework specialization tool called JavaFrames. JavaFrames uses role-based patterns that specify a reuse interface of a framework to guide frame-work specialization in a task-oriented manner. This thesis reports the results of cases studies in which JavaFrames and the hierarchical framework reuse inter-face modeling methodology were applied to the Struts web application frame-work and the JHotDraw drawing editor framework.

Ammatti, ihminen ja maailmankuva murroksessa : Tutkimus yliopistokirjastoista ja kirjastonhoitajista tietoyhteiskuntakaudella 1970-2005

PROFESSION, PERSON AND WORLDVIEW AT A TURNING POINT A Study of University Libraries and Library Staff in the Information Age 1970 - 2005 The incongruity between commonly held ideas of libraries and librarians and the changes that have occurred in libraries since 2000 provided the impulse for this work. The object is to find out if the changes of the last few decades have penetrated to a deeper level, that is, if they have caused changes in the values and world views of library staff and management. The study focuses on Finnish university libraries and the people who work in them. The theoretical framework is provided by the concepts of world view (values, the concept of time, man and self, the experience of the supernatural and the holy, community and leadership). The viewpoint, framework and methods of the study place it in the area of Comparative Religion by applying the world view framework. The time frame is the information age, which has deeply affected Finnish society and scholarly communication from 1970 to 2005. The source material of the study comprises 30 life stories; somewhat more than half of the stories come from the University of Helsinki, and the rest from the other eight universities. Written sources include library journals, planning documents and historical accounts of libraries. The experiences and research diaries of the research worker are also used as source material. The world view questions are discussed on different levels: 1) recognition of the differences and similarities in the values of the library sphere and the university sphere, 2) examination of the world view elements, community and leadership based on the life stories, and 3) the three phases of the effects of information technology on the university libraries and those who work in them. In comparing the values of the library sphere and the university sphere, the appreciation of creative work and culture as well as the founding principles of science and research are jointly held values. The main difference between the values in the university and library spheres concerns competition and service. Competition is part of the university as an institution of research work. The core value of the library sphere is service, which creates the essential ethos of library work. The ethical principles of the library sphere also include the values of democracy and equality as well as the value of intellectual freedom. There is also a difference between an essential value in the university sphere, the value of autonomy and academic freedom on the one hand, and the global value of the library sphere - organizing operations in a practical and efficient way on the other hand. Implementing this value can also create tension between the research community and the library. Based on the life stories, similarities can be found in the values of the library staff members. The value of service seems to be of primary importance for all who are committed to library work and who find it interesting and rewarding. The service role of the library staff can be extended from information services provider to include the roles of teacher, listener and even therapist, all needed in a competitive research community. The values of democracy and equality also emerge fairly strongly. The information age development has progressed in three phases in the libraries from the 1960s onward. In the third phase beginning in the mid 1990s, the increased usage of electronic resources has set fundamental changes in motion. The changes have affected basic values and the concept of time as well as the hierarchies and valuations within the library community. In addition to and as a replacement for the library possessing a local identity and operational model, a networked, global library is emerging. The changes have brought tension both to the library communities and to the relationship between the university community and the library. Future orientation can be said to be the key concept for change; it affects where the ideals and models for operations are taken from. Future orientation manifests itself as changes in metaphors, changes in the model of a good librarian and as communal valuations. Tension between the libraries and research communities can arise if the research community pictures the library primarily as a traditional library building with a local identity, whereas the 21st century library staff and directors are affected by future orientation and membership in a networked library sphere, working proactively to develop their libraries.

Abstract of subject index of New York State Library, Part 1

Digital image

Lecture by Jacques Judah Lyons on the history of the Jews, given before the Hebrew Religious and Literary Library Association

Digital image

Living Poetically in the Modern Age : The Situational Aspects of Kierkegaard's Thought

How did Søren Kierkegaard (1813 1855) situate the human subject into historical and social actuality? How did he take into consideration his own situatedness? As key for understanding these questions the research takes the ideal of living poetically that Kierkegaard outlined in his dissertation. In The Concept of Irony (1841) Kierkegaard took up this ideal of the Romantic ironists and made it into an ethical-religious ideal. For him the ideal of living poetically came to mean 1) becoming brought up by God, while 2) assuming ethical-religiously one s role and place in the historical actuality. Through an exegesis of Kierkegaard s texts from 1843 to 1851 it is shown how this ideal governed Kierkegaard s thought and action throughout his work. The analysis of Kierkegaard s ideal of living poetically not only a) shows how the Kierkegaardian subject is situated in its historical context. It also b) sheds light on Kierkegaard s social and political thought, c) helps to understand Kierkegaard s character as a religious thinker, and d) pits his ethical-religious orientation in life against its scientific and commonsense alternatives. The research evaluates the rationality of the way of life championed by Kierkegaard by comparing it with ways of life dominated by reflection and reasoning. It uses Kierkegaard s ideal of living poetically in trying to understand the tensions between religious and unreligious ways of life.

Harvest: A biotextile future

- Description of the work Harvest: A biotextile future consists of four bags constructed from kombucha, each utilizing a different approach to this material. The kombucha material is a byproduct of the fermented green tea, kombucha, and is comprised of a symbiotic culture of bacteria and yeast (SCOBY) that forms a fast growing curd or pellicle on the surface of the tea. This pellicle is harvested, washed, and dried to make a material with characteristics that can range between leather and paper in handle. The pellicle is one hundred per cent cellulose, with the individual fibres growing together to produce a durable and strong non-woven textile. Techniques explored with the dry kombucha material include folding, stitching, and laser etching. The final bags were designed with reference to classic tropes of fashion accessories: the briefcase, the clutch, the valise and the handbag. The valise included three jars in which the kombucha was displayed as ‘growing’ within the bag. - Research Background This work sits within an emerging field of practice in which fashion design intersects with biotechnology. Designers such as Suzanne Lee have explored constructing garments from bacteria byproducts, and bio-artists Oron Catts and Ionat Zurr have created ‘victimless leather’ grown from cultured cells. Although still speculative, these collaborations between science and design point to new material applications for fashion. Our work contributes to this area through testing both the growing of the textile and its application to construct durable fashion artefacts. - Research Contribution Harvest: A biotextile future makes two contributions to new knowledge in the area of design for sustainability within fashion. The first contribution lies in extending the technical experimentation required to grow and manipulate the textile. For the briefcase, the pattern shape was ‘grown’ into the required shape, using a shaped container. Other techniques used in the bags included weaving, folding and laser etching the material to extend its functional and decorative properties. Experimentation with the growing and drying of the material led to the production of a wide range of physical properties, in which the material was more brittle or flexible as required. The second research contribution lies in the proposal of this material for use in durable fashion accessories. The material is still speculative and small-scale in production, however the four bags illustrate the potential for kombucha as a biodegradable alternative to leather or synthetic materials. - Research Significance This interplay of science and design research opens up an exploration for a speculative future of sustainable, biodegradable textiles using live bacteria to enable ‘homegrown’ vegan apparel. The collaborators on this project include scientist Peter Musk and fashion designers Alice Payne and Dean Brough. Harvest: A biotextile future was exhibited at the State Library of Queensland’s Asia Pacific Design Library, 1-5 November 2015, as part of The International Association of Societies of Design Research’s (IASDR) biannual design conference. The work was chosen for display by a panel of experts, based on the criteria of design innovation and contribution to new knowledge in design.

A Nonmoving-Part Fluidic Display Using Photoelastic Effect

Digital fluidic and pneumatic systems incorporate displays for the presentation of information to the operator. Displays reported so far for such systems use moving pistons, tapes, and other mechanisms leading to lower reliability. This paper describes a nonmoving part fluidic display employing the photoelastic effect. The display is pressure actuated and has a long life. When fabricated from compatible materials, this device can withstand hostile environments like nuclear radiation, vibrations, etc. The display is compact, economical and is virtually maintenance free. The display unit has been tested in the laboratory for reliability and speed of response.

DNA Packaging and Host Cell Lysis: Late Events in Bacteriophage PRD1 Infection

The object of this study is a tailless internal membrane-containing bacteriophage PRD1. It has a dsDNA genome with covalently bound terminal proteins required for replication. The uniqueness of the structure makes this phage a desirable object of research. PRD1 has been studied for some 30 years during which time a lot of information has accumulated on its structure and life-cycle. The two least characterised steps of the PRD1 life-cycle, the genome packaging and virus release are investigated here. PRD1 shares the main principles of virion assembly (DNA packaging in particular) and host cell lysis with other dsDNA bacteriophages. However, this phage has some fascinating individual peculiarities, such as DNA packaging into a membrane vesicle inside the capsid, absence of apparent portal protein, holin inhibitor and procapsid expansion. In the course of this study we have identified the components of the DNA packaging vertex of the capsid, and determined the function of protein P6 in packaging. We managed to purify the procapsids for an in vitro packaging system, optimise the reaction and significantly increase its efficiency. We developed a new method to determine DNA translocation and were able to quantify the efficiency and the rate of packaging. A model for PRD1 DNA packaging was also proposed. Another part of this study covers the lysis of the host cell. As other dsDNA bacteriophages PRD1 has been proposed to utilise a two-component lysis system. The existence of this lysis system in PRD1 has been proven by experiments using recombinant proteins and the multi-step nature of the lysis process has been established.