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103. Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV

Author

Česlovas Venclovas, Virginijus Siksnys, and Albertas Timinskas

Subjects
Models, Molecular, Stereochemistry, Molecular Sequence Data, EcoRI, HindIII, Biochemistry, Protein Structure, Secondary, Restriction fragment, Deoxyribonuclease EcoRI, chemistry.chemical_compound, Structural Biology, Escherichia coli, Amino Acid Sequence, Deoxyribonucleases, Type II Site-Specific, Molecular Biology, Peptide sequence, Binding Sites, biology, EcoRV, Restriction enzyme, Restriction site, chemistry, biology.protein, Mutagenesis, Site-Directed, DNA
Abstract

Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded beta-sheet and two alpha-helices packed against it and could be described as alpha-beta sandwich in which helices and beta-strands lie in two stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both enzymes, there are not detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used.

Published
1994

105. Kompozitais armuotos betoninės konstrukcijos

Author

Kaklauskas, Gintaris, primary, Bačinskas, Darius, additional, Gribniak, Viktor, additional, Jakubovskis, Ronaldas, additional, Ulbinas, Darius, additional, Gudonis, Eugenijus, additional, Meškėnas, Adas, additional, Timinskas, Edgaras, additional, and Sokolov, Aleksandr, additional

Published
2010
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108. ASSOCIATION STUDIES WITH PREDISPOSITION TO OXIDATIVE STRESS AND ATHEROSCLEROSIS IN LITHUANIA

Author

Zita Aušrelė Kučinskienė, Aleksandras Laucevičius, Kristina Grigalionienė, Ramūnas Janavičius, Vaidutis Kučinskas, and A. Timinskas

Subjects
business.industry, Immunology, Internal Medicine, medicine, General Medicine, Cardiology and Cardiovascular Medicine, medicine.disease_cause, business, Oxidative stress, Genetic association
Published
2008

112. The PPI3D web server for searching, analyzing and modeling protein--protein interactions in the context of 3D structures.

Author

Dapkũnas, Justas, Timinskas, Albertas, Olechnovič, Kliment, Margelevičius, Mindaugas, Dičiũnas, Rytis, and Venclovas, Česlovas

Subjects
*INTERNET servers, *DATABASE searching, *PROTEIN-protein interactions, *CLUSTERING of particles, *CENTROIDAL Voronoi tessellations
Abstract

The PPI3D web server is focused on searching and analyzing the structural data on protein--protein interactions. Reducing the data redundancy by clustering and analyzing the properties of interaction interfaces using Voronoi tessellation makes this software a highly effective tool for addressing different questions related to protein interactions. [ABSTRACT FROM AUTHOR]

Published
2017
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113. FRP reinforcement for concrete structures: state-of-the-art review of application and design.

Author

Gudonis, Eugenijus, Timinskas, Edgaras, Gribniak, Viktor, Kaklauskas, Gintaris, Arnautov, Aleksandr K., and Tamulėnas, Vytautas

Subjects
*FIBROUS composites, *ELECTROMAGNETIC fields, *REINFORCED concrete, *MANUFACTURING processes, *STRUCTURAL engineering
Abstract

Fiber reinforced polymers (FRPs) are considered to be a promising alternative to steel reinforcement, especially in concrete structures subjected to an aggressive environment or to the effects of electromagnetic fields. Although attempts to develop effective reinforcement have been followed, the application of FRPs remains limited by the solution to simple structural problems that mainly appear due to the absence of design codes, significant variation in the material properties of FRP composites and limited knowledge gained by engineers as regards the application aspects of FRP composites and structural mechanics of concrete elements reinforced with FRPs. To fill the latter gap, the current state-of-the-art report is dedicated to present recent achievements in FRPs applying practice to a broad engineers’ community. The report also revises the manufacturing process, material properties, the application area and design peculiarities of concrete elements reinforced with FRP composites. Along the focus on internal reinforcement, the paper overviews recent practices of applying FRP reinforced concrete (RC) elements in structural engineering. The review highlights the main problems restricting the application of FRPs in building industry and reveals the problematic issues (related to the material properties of the FRP) important for designing RC following the formulation of targets for further research. [ABSTRACT FROM AUTHOR]

Published
2013
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120. Accuracy analysis of design methods for concrete beams reinforced with fiber reinforced polymer bars.

Author

Timinskas, Edgaras, Jakštaitė, Rūta, Gribniak, Viktor, Tamulėnas, Vytautas, and Kaklauskas, Gintaris

Subjects
*REINFORCED concrete corrosion, *CONCRETE beams, *BUILDING reinforcement, *FIBROUS composites, *STEEL research
Abstract

Traditional steel reinforcement does not resist corrosion and its resources are limited; therefore, carbon, glass, aramid and basalt fibre reinforced polymer bars were developed. The composite reinforcement has a high tensile strength and resistance to electromagnetic fields. Different kinds of materials and application of various surface coatings are used in the production of the composite bars. This results in different adhesion to concrete and mechanical properties of composite bars. In comparison with steel reinforcement, glass, aramid and basalt fibre reinforced polymer bars have a lower modulus of elasticity. Thus, structural rigidity provided by these bars is smaller in respect to reinforced concrete elements. Current reinforced concrete design codes and recommendations are based on empirical and simplified methods of strain evaluation, which may be inadequate for design of structures with composite bars. In this paper, an adequacy of the empirical models was checked against the experimental data of concrete beams reinforced with composite bars. The moment-curvature data of 52 beams reported in the literature and conducted by the authors were used for assessment of accuracy of design methods. In order to perform the analysis, different methods from design codes (European (LST 2007), American (ACI Committee 318 2011) and Russian (NIIZhB 2006)) and recommendations (Italian (CNR 2007) and American (ACI Committee 440 2006)) have been selected. The results of the investigation will provide engineers with more information on design of concrete beams with fibre reinforced polymer bars. This will encourage an extensive use of these innovative materials in different types of structures. [ABSTRACT FROM PUBLISHER]

Published
2013
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121. A Novel PCR-RFLP Detection Method Using an Optimized Set of Restriction Enzymes.

Author

Boulton, Alan A., Baker, Glen B., Bateson, Alan N., Petronis, A., Timinskas, A., Basile, V., Vicente, A., Janulaitis, A., and Kennedy, J. L.

Abstract

A number of new and useful mutation detection methods have evolved in recent years enabled by the advent of polymerase chain reaction (PCR) (Grompe, 1993). These methods can be divided into two groups: (1) the PCR-based techniques aimed at scanning DNA sequences for unknown mutations and (2) the techniques for identification of known polymorphisms. The essence of the first group is sensitivity, and this group is represented by single-strand conformation polymorphism (SSCP) analysis, denaturing gradient gel electrophoresis (DGGE), heteroduplex analysis (HA), RNase A cleavage, chemical mismatch cleavage, Escherichia coli mismatch repair enzyme-based analysis (Grompe, 1993), and restriction endonuclease fingerprinting (Liu and Sommer, 1995). Once a polymorphism is detected by the techniques described above, there is a clear necessity to switch to a simpler technique. The methods designed for simplicity and speed of genotyping large numbers of individuals are represented by oligodeoxynucleotide hybridization assay, the oligonucleotide ligation assay, allele-specific PCR amplification or, if the DNA variation is detected by a restriction enzyme (RE), PCR-restriction fragment length polymorphism (RFLP) (Grompe, 1993). [ABSTRACT FROM AUTHOR]

Published
1999
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123. KOMPOZITINIAIS STRYPAIS ARMUOTŲ SIJŲ PLEIŠĖJIMO IR DEFORMACIJŲ ANALIZĖ.

Author

Timinskas, Edgaras, Jakubovskis, Ronaldas, Mcškėnas, Adas, and Gudonis, Eugenijus

Subjects
*GIRDERS, *REINFORCED concrete, *STEEL, *NUMERICAL analysis, *MATERIAL fatigue
Abstract

The paper discusses the results of experimental and numerical modelling using two beams reinforced with GFRP bars. One beam was made of plain concrete while the other contained short steel fibres. The influence of steel fibres on deflection and cracking behaviour was studied. A comparative analysis of experimental results has shown that steel fibres significantly reduce deflections and average crack width of the beam. Moreover, an addition of steel fibres to the concrete mix led to a more ductile failure mode of the beam. Numerical analysis employing nonlinear finite element software ATENA has revealed that a good agreement between calculated and experimental results regarding an ordinary concrete GFRP reinforced beam can be obtained. [ABSTRACT FROM AUTHOR]

Published
2012
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127. Tempiamųjų GelžBetoninių Elementų Diskrečiųjų Plyšių Modelio Analizė

Author

Salys, Donatas, Kaklauskas, Gintaris, Timinskas, Edgaras, Gribniak, Viktor, Ulbinas, Darius, and Gudonis, Eugenijus

Abstract

SantraukaŠiame straipsnyje aptariamas gelžbetoninių elementų pleišėjimo diskretusis modelis. Pastaraisiais metais pleišėjimo diskretieji modeliai tobulinami ypač intensyviai tikintis, kad būtent šis modeliavimo būdas ateityje galėtų tapti universalia gelžbetoninių elementų projektavimo priemone. Analizuojamas modelis pagrįstas šlyties įtempių armatūros ir betono sąlyčio zonoje bei armatūros slinkties deformacijų priklausomybėmis. Taikant šį modelį galima apskaičiuoti plyšio plotį ir nustatyti deformacijų bei įtempių pasiskirstymą supleišėjusiame betone. Straipsnyje atliktas eksperimentinių tempiamųjų gelžbetoninių elementų modeliavimas bei parodyta, kad literatūroje rekomenduojamos šlyties įtempių sąlyčio zonoje ir armatūros slinkties idealizacijos gali buti netikslios.

Published
2010
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128. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases

Author

Saulius Klimašauskas, Arvydas Janulaitis, Menkevicius Saulius, Albertas Timinskas, V. Butkus, and Danguolè Butkienè

Subjects
DNA, Bacterial, Site-Specific DNA-Methyltransferase (Adenine-Specific), Methyltransferase, DNA-Cytosine Methylases, Molecular Sequence Data, Biology, Micrococcus, chemistry.chemical_compound, Citrobacter, Sequence Homology, Nucleic Acid, Genetics, Escherichia coli, Amino Acid Sequence, DNA (Cytosine-5-)-Methyltransferases, Peptide sequence, Base Sequence, Nucleic acid sequence, Protein primary structure, biology.organism_classification, Citrobacter freundii, Biochemistry, chemistry, Genes, Bacterial, Sequence motif, Cytosine, DNA
Abstract

The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M.Pvu II, revealed extended regions of homology. The sequence comparison of the three DNA[cytosine-N4]-methylases using originally developed software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found similar also to those of adenine and DNA[cytosine-C5]-methylases. These data provided a basis for global alignment and classification of DNA-methylase sequences. Structural considerations led us to suggest that the first region could be the binding site of AdoMet, while the second is thought to be directly involved in the modification of the exocyclic amino group.

Published
1989

129. Basaltmaterjalide kasutusuuring betoonsilla paindeelementide tugevdamiseks.

Author

Gribniak, Viktor, Arnautov, Aleksandr K., Kaklauskas, Gintaris, Tamulenas, Vytautas, Timinskas, Edgaras, and Sokolov, Aleksandr

Abstract

Copyright of Baltic Journal of Road & Bridge Engineering (Baltic Journal of Road & Bridge Engineering) is the property of Baltic Journal of Road & Bridge Engineering and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2015

130. Bazalta polimēra stiegrojuma pielietojuma pētījums liektiem betona tilta elementiem.

Author

Gribniak, Viktor, Arnautov, Aleksandr K., Kaklauskas, Gintaris, Tamulenas, Vytautas, Timinskas, Edgaras, and Sokolov, Aleksandr

Abstract

Copyright of Baltic Journal of Road & Bridge Engineering (Baltic Journal of Road & Bridge Engineering) is the property of Baltic Journal of Road & Bridge Engineering and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2015

131. Bazalto medžiagos naudojimo betoniniu tiltu lenkiamiesiems elementams armuoti tyrimas.

Author

Gribniak, Viktor, Arnautov, Aleksandr K., Kaklauskas, Gintaris, Tamulenas, Vytautas, Timinskas, Edgaras, and Sokolov, Aleksandr

Abstract

Copyright of Baltic Journal of Road & Bridge Engineering (Baltic Journal of Road & Bridge Engineering) is the property of Baltic Journal of Road & Bridge Engineering and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2015

132. Naudotojo lygmens IT trikčių sprendimas, paremtas dirbtiniu intelektu

Author

Zdanevičiūtė, Aušra, Sokas, Algirdas, Makutėnienė , Daiva, Čiupaila , Lionginas, Šostak , Olga Regina, Timinskas, Edgaras, Sakalauskienė, Lina, Dereškevičius, Saulius, and Vilnius Gediminas Technical University

Subjects
Informatics Engineering, Fuzzy logic, Incident, ITIL, Neraiškioji logika, Atveju paremtas samprotavimas, IT help-desk, IT pagalbos centras, Case based reasoning, IT triktis, Trouble ticket
Abstract

Magistriniame darbe nagrinėjamas pakartotinis informacijos ir žinių panaudojimas IT pagalbos tarnybose. Trumpai apžvelgti svarbiausi tokio tipo organizacijų veiklos principai, kurie standartizuojami taikant ITIL metodologiją. Darbo tikslas – sukurti IT trikčių registravimo sistemą, kuri panaudodama sukauptą informaciją apie praeityje įvykusias IT triktis spręstų dabartines problemas. Siekiant šio tikslo pasirinkta taikyti neraiškiąją logiką ir atveju paremtą samprotavimą. Darbe pateikiama neraiškiosios logikos ir atveju paremto samprotavimo teorinė apžvalga ir praktinės pritaikymo galimybės, apžvelgiamos intelektualios IT trikčių registravimo sistemos. Atlikus tyrimą ir įvertinus anksčiau sukurtas intelektualias IT trikčių registravimo sistemas, formuojamas naujosios modelis. Nauja sistema, pritaikiusi atveju paremtą samprotavimą ir neraiškiąją logiką, pateikia galimus IT trikčių sprendimus jos naudotojui, tai yra IT pagalbos tarnybos darbuotojui. Sistema yra nepriklausoma nuo kalbos, nes atskirų atvejų paieška vykdoma taikant neraiškiąją logiką. Darbą sudaro 4 dalys: įvadas, IT organizacijos pagal ITIL samprata, teorinė neraiškiosios logikos ir atveju paremto samprotavimo apžvalga, praktinis neraiškiosios logikos pritaikymas IT trikčių registravime bei išvados ir siūlymai, literatūros sąrašas. Darbo apimtis – 75 p. teksto be priedų, 26 iliustr., 5 lent., 60 bibliografiniai šaltiniai. Atskirai pridedami darbo priedai. The final Master thesis analyses the reuse of information and knowledge in IT helpdesk organizations. Briefly are discussed most important activities of such companies, that are standardized according ITIL. The main goal of the Master thesis is development of IT help-desk ticketing tool, which would reuse past information and knowledge in order to resolve current problems. Adaptation of fuzzy logic and case based reasoning is chosen to accomplish this goal. The second part of work contains theoretical information about fuzzy logic and cased based reasoning, practical application of these sciences; also discusses intelligent IT help-desk incident ticketing systems. After the research of scientific articles about intelligent IT help-desk systems and application of fuzzy logic and case based reasoning, the new model of IT trouble tickets system is created. The new system suggests possible solutions of an IT incident. The solution is found among previous incidents using fuzzy logic. Volume of the thesis – 75 p. of text without appendices, 26 figures, 5 tables, 60 bibliographic sources.

Published
2014

133. Trumpalaike ir ilgalaike apkrovomis veikiamų gelžbetoninių elementų netiesinė skaitinė analizė

Author

Lapėnas, Vitalijus, Bačinskas, Darius, Gribniak, Viktor, Kaklauskas, Gintaris, Sokolov, Aleksandr, Čibirka, Arvydas, Jatulis, Donatas, Ulbinas, Darius, Timinskas, Edgaras, and Vilnius Gediminas Technical University

Subjects
Analizė, Reinforced concrete, Gelžbetonis, Netiesinis, Long-term, Ilgalaikė, Nonlinear, Civil Enginering, Analysis
Abstract

Gelžbetoninių elementų pleišėjimas priklauso nuo medžiagų fizikinių savybių, ilgalaikių procesų betone, armatūros ir betono sąveikos ir kt. Dėl betono ir armatūros sąveikos pasireiškia tempiamojo sustandėjimo efektas, turintis didelės įtakos elementų deformacijoms. Skirtingi mokslininkų tyrimai atskleidė, kad tempiamasis sustandėjimas yra sudėtingas netiesinis reiškinys, kuriam įvertinti būtina taikyti netiesinę skaitinę analizę. Medžiagų fizikinių modelių adekvatus pasirinkimas dažniausiai nulemia gaunamo galutinio rezultato patikimumą. Darbe atlikta skaitinė netiesinė tempiamųjų gelžbetoninių elementų analizė. Modeliavime panaudoti VGTU ilgalaike ir trumpalaike apkrova išbandytų tempiamųjų gelžbetoninių elementų eksperimentiniai duomenys. Bandymų tikslas – įvertinti tempiamojo sustandėjimo kitimą laikui bėgant, išnagrinėti atstumų tarp plyšių įtaką tempiamajam sustandėjimui, įvertinti susitraukimo ir valkšnumo efektų įtaką elementų deformacijoms. Netiesinio modeliavimo metu buvo išanalizuota įvairių parametrų įtaka gautiems skaitiniams rezultatams. Palyginus modeliavimo rezultatus su eksperimentiniais nustatyta, kad programinis paketas ATENA tiksliai apskaičiavo gelžbetoninių elementų poslinkius veikiant trumpalaikei apkrovai. Ilgalaikės apkrovos atveju gauti rezultatai su didesnėmis paklaidomis, jų analizei reikia išsamesnių tyrimų. Darbo struktūra ir apimtis – 76 p. teksto be priedų, 77 iliustracijos, 6 lentelės, 38 bibliografijos šaltinių sąrašas. Behaviour of reinforced concrete structures mostly depends on physical characteristics of materials, long-term processes in concrete, interaction between steel and concrete, etc. The result of such an interaction is the effect of tension-stiffening, which has a great influence on deformations of reinforced concrete structures. Various researchers have shown that tension-stiffening is a complex, nonlinear phenomenon that might be assessed only by means of a non-linear numerical analysis. The choice of adequate material governs confidence of the results obtained by simulation. In this paper a non-linear numerical analysis of reinforced concrete ties was carried out. In the numerical simulation data from the short-term and long-term experiment conducted in VGTU was used. The subject of the experiment was to assess the degradation of long-term tension-stiffening effect in reinforced concrete as well as to evaluate influence of crack spacing, shrinkage and creep on long-term deformations of concrete members. Study on effect of various parameters on obtained results was carried out. Data from nonlinear analyses conducted by ATENA were compared to the experimental results and gave good agreement in terms of short-term loading. The results of long-term loading showed only moderate agreement and need further investigation. Thesis consists of: 76 p. text without appendixes, 77 pictures, 6 tables, 38 bibliographical entries.

Published
2014

134. Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV.

Author

Venclovas C, Timinskas A, and Siksnys V

Subjects
Amino Acid Sequence, Binding Sites, Deoxyribonuclease EcoRI genetics, Deoxyribonucleases, Type II Site-Specific genetics, Escherichia coli enzymology, Escherichia coli genetics, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Deoxyribonuclease EcoRI chemistry, Deoxyribonucleases, Type II Site-Specific chemistry, Protein Structure, Secondary
Abstract

Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded beta-sheet and two alpha-helices packed against it and could be described as alpha-beta sandwich in which helices and beta-strands lie in two stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both enzymes, there are not detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used.

Published
1994
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135. CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.

Author

Siksnys V, Zareckaja N, Vaisvila R, Timinskas A, Stakenas P, Butkus V, and Janulaitis A

Subjects
Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial, Deoxyribonuclease EcoRI metabolism, Deoxyribonucleases, Type II Site-Specific metabolism, Escherichia coli, Gene Expression, Genes, Bacterial, Molecular Sequence Data, Mycoplasma genetics, Open Reading Frames, Sequence Homology, Amino Acid, Substrate Specificity, Deoxyribonuclease EcoRI genetics, Deoxyribonucleases, Type II Site-Specific genetics, Mycoplasma enzymology
Abstract

The genes coding for the MunI restriction-modification (R-M) system, which recognize the sequence 5'-CAATTG, have been cloned and expressed in Escherichia coli, and their nucleotide sequences have been determined. The restriction endonuclease (ENase; R.MunI) is encoded by an open reading frame (ORF) of 606 bp, and a 699-bp ORF codes for the methyltransferase (MTase). The two genes are transcribed divergently from a 355-bp region. The gene encoding the ENase is preceded by a short co-linear ORF of 222 bp. The deduced amino acid (aa) sequence of this short ORF (SORF) closely resembles the sequences of a family of regulatory proteins that are associated with other type-II R-M systems. Comparative analysis of the deduced aa sequence of R.MunI revealed several regions of similarity to the EcoRI and RsrI ENases that recognize the GAATTC sequence. The similar mode of interaction of MunI, EcoRI and RsrI with the tetranucleotide AATT, common to the recognition sequences of these ENases, was suggested.

Published
1994
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