34 research outputs found
Single molecule force spectroscopy of single stranded DNA binding protein and Rep helicase
No full textSingle-stranded DNA binding (SSB) proteins are essential accessory proteins that protect single-stranded DNA (ssDNA) during genome maintenance. Escherichia coli SSB is a prototypical homo-tetrameric SSB protein that can wrap up to 65 nucleotides of ssDNA in one of its binding modes. Here we present mechanical studies of E. coli SSB bound to ssDNA using high-resolution optical tweezers. This method allows us to probe the interaction of individual SSBs to ssDNA in real time, with nanometer resolution. By detecting directly the wrapping of ssDNA by a single protein, we are able to characterize the thermodynamics and kinetics of nucleoprotein complex formation. Mechanical pulling of ssDNA in the presence of SSB reveals that the protein condenses ssDNA in the force range 0-10pN and that tension can be used to modulate the ssDNA wrapping state of SSB. Measurements of SSB kinetics indicate that SSB-ssDNA complex formation occurs in a two-step process consisting of a diffusion-limited binding step in which the protein associates weakly with its substrate, followed by a fast wrapping step in which ssDNA is condensed. We also quantify how tension modulates the ssDNA wrapping state of SSB, revealing features of the energy landscape for SSB-ssDNA interactions. Lastly, we carried out measurements of SSB interaction with long ssDNA binding substrate as a function of mechanical force. The data indicate that SSBs bound to longer stretches of ssDNA bound much tighter, probably due to nucleoprotein filament formation. And we have evidence that SSB can bind to ssDNA in intermediate wrapping states and are transiently wrapping and unwrapping from their substrates.
In addition we present for the first time study on the conformational control of Rep helicase using an optical trap. We found that crosslinking-mediated conformational arrest of a dynamic subdomain in so-called “closed” orientation converted the Superfamily I (SFI) helicase, Rep, from a very poor DNA helicase into a powerful motor protein with a highly processive DNA unwinding activity. In contrast, the wild type Rep helicase cannot efficiently unwind DNA over 18 bp in vitro. A single Rep-X (cross-linked Rep) molecule can processively unwind DNA up to 4 kbp and generate forces in excess of 40 pN, making it the most powerful helicase known. The same modification on the related PcrA helicase produced the same activity increase characteristics strengthening the possibility of widespread application of this conformational control technique. Thus our results directly answer the question of the role of different conformations observed in SF-I helicase crystal structures and offer a mechanism for how partner proteins in vivo may regulate helicase function via conformational control.Item withdrawn by Mark Zulauf ([email protected]) on 2012-05-11T20:33:15Z
Item was in collections:
University of Illinois Theses & Dissertations (ID: 1)
No. of bitstreams: 1
Khafizov_Rustem.pdf: 2247881 bytes, checksum: e9bfd5cf73be72cb17e627afab577cf7 (MD5)Made available in DSpace on 2012-09-18T21:17:18Z (GMT). No. of bitstreams: 2
Khafizov_Rustem.pdf: 2247888 bytes, checksum: ceb8f0e4d4b167108ecf2addf30b5cd1 (MD5)
license.txt: 4065 bytes, checksum: 06a3dffcd6b87651e2149a8f1c6ff6f8 (MD5)Restriction data tranferred 2014-07-01T11:11:19-05:00
Original Data
Group with Access UIUC Users [automated]
Release Date: 2014-09-18 16:21:01 UTC
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemItem marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Seth Robbins ([email protected]) on 2012-09-18T21:21:02Z
Item is restricted until 2014-09-18T21:21:01ZU of I Only Restriction Lifted for Item 34715 on 2014-09-18T10:00:58Z
In Memory of a Friend
No full textThe article is dedicated to the memory of Rustem Sultanovich Gabyashev (1941-2010), an outstanding Kazan archeologist. He was one of the renowned experts in the Mesolithic and the Neolithic of the Volga-Kama region. The author, the researcher’s colleague and friend, narrates about his scientific and, first of all, expedition activities, offers some biographical data and characterizes his personal qualitie
Co-aligning user-centered design and software engineering courses: A case study
No full textIntroducing students to different perspectives and roles in the development process allows them to engage in the work of cross-disciplinary diverse teams and even can enable them to change roles in designer-developer interactions. Industry work often places recent graduates in preexisting polarized relationship dynamics between different participants in the design and development process. This paper describes a two-stage attempt at co-alignment of software engineering and user-centered design courses: from full alignment with topic intersections and joint project to partial alignment through separate activities. We discuss challenges of both ways including time or technical constraints, increased effort from the program developers and instructors, students' and instructors' frustrations. We finalize by describing benefits of providing students with early experience identifying trade-offs between design requirements and architecture and opportunities for diverse group with different background in computer science.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Internet of Thing
Mehmed Senai: A Crimean Historian at Sarai of Khan Islam Giray »
No full textThe article is devoted to the creative work of Mehmed Senai – the Crimean chronicler at the serai of the khan Islam Geray III, as well as his chronicle “Tarih-i Islam Geray khan” (“History of the khan Islam Geray III”, 1651). The researcher gives biographical information about the author and a brief description of the source. The identity of the writer is defined and based on the text of the Preface to the Chronicle: background, education, position, religious status. The meaning of the pseudonym of Senai is under the study, the text of the chronogram in which it occurs is reproduced. Especially noted thing is the originality of the artistic structure of the Chronicle “Tarih-i Islam Geray khan”.The Chronicle “Tarih-i Islam Geray khan” is the panegyric to the Crimean khan Islam Geray whose reign represents the brilliant epoch in the history of the Crimean Khanate. The writing consists of the ceremonies of public appointments, episodes of military campaigns and making treaties, the text of khan Islam Geray’s pedigree (shejere), construction and repair of buildings.
There is the brief information about the Chronicle and about M. Senai in “Catalogue of the Turkish Manuscripts in the British Museum” (1888). The primary work on writing was conducted by Polish orientalists who prepared the edition of the original text, its translation and processing, backed with comments.
At the time of writing the Chronicle, Mehmed Senai was in his old age, he served as the kadi (religious judge). In his youth he worked as munshi (decorator of papers) in the khan’s office. He got education in the Ottoman Empire, and was engaged in the implementation of diplomatic correspondence. The prospect of identification of the author on the basis of other sources is important to clarify the hypothesis of identifying M. Senai with such Crimean Tatar author as Dzhanmuhammed.
The Chronıcle’s plot consists of the diary notes on the military expeditions, eyewitness accounts (including those of the author). The author of the work focuses the historical events of 1648–1651 covering the Crimean Tatar-Ukrainian-Polish relations. The bulk of the official documents used by Senai was narrow. Details and brevity in the coverage of events indicates that certain materials were available to the author, while others were unavailable.
The aesthetic peculiarities of the Chronicle are also notable as well as historical. The author created the vivid images of the central characters in the writing – Islam Geray, Sefer Gazi aga and Tugay bey. The work is characterized by the use of various expressive means for the purpose of idealization of the images and emotional perception of characters and events
PRE-ISLAMIC WORLD VIEWS OF THE KAZAKH PEOPLE: FROM THE END OF THE 19TH TO THE BEGINNING OF THE 21ST CENTURY
No full textThis article analyses the problems of the traditional world views and beliefs of the Kazakh people. The main purpose of the article is to show the features of such cultural phenomena as âreligious syncretismâ and âhybrid worldviewâ. The author pays attention to the cosmogonic and cosmological beliefs, the perception and feeling of place and time, religious consciousness and national identity, folk customs and traditions, cultural branding. The farming and cattle-breeding practices in the harsh climatic conditions of wide steppe spaces influenced the formation of a special type of culture and unique worldview. In the long history of the nomadic peoples who inhabited the Eurasian steppes, the history of the development of the religious worldview occupies a special place. Being in the crossroad of civilization, Central Asia has been a region of interaction between different world religious traditions, such as Zoroastrianism, Buddhism, Christianity (in their earliest forms as Nestorianism), ManiÑhaiesm, and Islam. However, the Kazakh people did not break ties with nature due to their way of life, so peopleâs beliefs and superstitions were based on the animistic, totemistic beliefs and magic. The author concludes that the cornerstone of the entire system of worldview was the faith in the opportunity to transform the world for the good of peopleâs traditions and it was reflected in the special rites, traditions, and practices
Transport Properties of Mixed-Matrix Membranes: A Kinetic Monte Carlo Study
No full textKinetic Monte Carlo (KMC) simulations are used to study transport of guest molecules in a two-phase medium in which the minority phase forms closed regions. This type of model system resembles compositions of mixed-matrix membranes (MMMs) made of a matrix and imbedded filler particles with different permeabilities. Based on an ideal filler-matrix composite morphology as defined in [H. Vinh-Thang, S. Kaliaguine, Chem. Rev. 113, 4980, 2013], the effects of the filler-particle volume fraction, particle size, shape (aspect ratio), and the spatial particle distribution on gas transport through MMMs are addressed. The results obtained for nonoverlapping and randomly placed spherical filler particles are found to be in good agreement with the analytical models available in the literature and have proven their good accuracy also for thin membranes where finite-size effects are expected to play an appreciable role. Furthermore, the prominent influence of the aspect ratio for nonspherical particles on the effective permeability is shown and scenarios are discussed where the alignment of the asymmetric filler particles give rise to anisotropic transport properties potentially favorable for the performance of MMMs. The KMC approach developed guides the optimal spatial arrangement and orientation of the filler particles for the different strategies to increase the membrane permeability and separation selectivity by transport enhancement or inhibition.ChemE/Catalysis Engineerin
Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways
No full textLiberation of classes and liberation of nations
No full textThe urgency of an issue is caused by modern scientific and public interest in a role of ethno-confessional question in the first parliament of Russia – the State Duma of 1906-1917.
The article aims to show that the Duma of the first two convocations in 1906-1907 played a noticeable role not only in the class struggle, as it was widely covered in the literature, but also was clear in ethno-political process of multi-ethnic Russia. Based on the systematic, statutory and regulatory and statistical methods the author traces as special Election Rules from outlying regions (1905-1906) with the low level of representation, especially from non-Russian population group, and territorial and ethnic districts that created as a result new ethno-political geography of the Russian Empire.
The author concludes that despite these restrictions, the non-Russian peoples’ representation in the First and Second Duma was very noticeable that allowed to organize the Duma ethno-confessional factions. These factions and groups legally demonstrated ethnical, confessional and regional interests and tried to join in legislative process with requirements of ethnic and confessional groups equality, restoration of an autonomy of Poland and development of local governance, the court and the school in national languages.peer-reviewe
Globalization and Changeable Cognitive Constructions
No full textThe article presents the overview of turbulent processes, resulting in complex configurations of different ethnocultural discourses. The situation is dramatic because of absence of parity and actor's consensus, which summons painful social and psychological reaction of the participants of these contacts. It is emphasized that only a logical interpretation of a cultural phenomenon could not cover all the diversity of features and characteristics of cultural artefact as a part of sociocultural coexistence. For these reasons, researchers experience an urgent need to expand the arsenal of research approaches and practices. In particular, bring them into some kind of consolidated education with the help of new principles and methodologies of the approach. Analyzing the problem of multiculturalism from the point of view of comparative studies, the author comes to the preliminary conclusion that the intensification of protest social movements in the Middle East and “right movements”, nationalism and isolationism in Europe represent a spontaneous response to the process of globalization and an attempt to preserve ethno-cultural identity. These same reasons can explain the decline of the influence and attractiveness of liberal-democratic models of social development. In the medium term, we can expect spontaneous turbulent processes in the social and political life of developing countries, but also countries with stable sociopolitical traditions as well
Зміна міфологічних мотивів за ланцюгом "фольклор-міфологія-література" (на основі міфів "Цар Едіп", "Рустем і Шахраб" і роману Орхана Памука "Рудоволоса жінка") (Change of mythological motifs in the chain "folklore-mythology-literature" (on the example of myths “King Oedipus”, “Rustem and Suhrab” and Orhan Pamuk's novel “The Red-Haired Woman”)
No full textІснує чимало робіт присвячених вивченню еволюції літературних мотивів, які зустрічаються у фольклорі і
міфах «Цар Едіп» і «Рустем і Шахраб». Однак ґрунтовних досліджень щодо їхнього використання у літературі доби
постмодернізму досить мало. У період постмодернізму поняття «оригінал» повністю зникає, що робить посилання
автора роману на інші твори усної та писемної творчості, зокрема міфи, досить частотним явищем. У зв’язку з тим, що
запозичений автором міфологічний мотив у процесі інтерпретації зазнає змін, існує загроза набуття міфом нової форми, що може призвести до його повної віддаленості від першоджерела. Ця стаття присвячена дослідженню процесу
деформації таких мотивів за ланцюгом «фольклор-міфологія-література» і визначенню етапу міфів на якому вони перебувають. Перспективи подальших досліджень полягають в аналізі функціонування досліджених нами мотивів у межах інших романів написаних в добу постмодернізму.There are many works devoted to the study of the evolution of literary motifs common for a folklore and myths “King Oedipus”
and “Rustem and Suhrab”. However, there are quite a few thorough studies on their use in the literature of the postmodern era. In the
postmodern period, the concept of "originality" completely disappears, which makes the reference of the author of a novel to other works of
oral and written literature, in particular myths, quite frequent. Due to the fact that the mythological motif borrowed by the author undergoes
changes in the process of interpretation, there is a threat that the myth will acquire a new form, which may lead to its complete remoteness
from the original source. This article is devoted to the study of the process of deformation of such motifs in the chain "folklore-mythologyliterature" and determining the stage at which the myths are located. Prospects for further research lie in the analysis of the functioning of the
motives we have studied in other novels written in the postmodern era
