Academic literature on the topic 'Nucleic Acid Databases'

The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.

Abstract The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 papers reporting on new databases and 82 updates from resources previously published in the Issue. Six more papers are updates from databases most recently published elsewhere. Major nucleic acid databases reporting updates include Genbank, ENA, ChIPBase, JASPAR, mirDIP and the Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates from BMRB and RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING and REBASE are stand-out updates in the signalling and enzymes section. Immunology-related databases include CEDAR, the second Breakthrough Article, for cancer epitopes and receptors alongside returning IPD-IMGT/HLA and the new PGG.MHC. Genomics-related resources include Ensembl, GWAS Central and UCSC Genome Browser. Major returning databases for drugs and their targets include Open Targets, DrugCentral, CTD and Pubchem. The EMPIAR image archive appears in the Issue for the first time. The entire database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, revisiting 463 entries, adding 92 new resources and eliminating 96 discontinued URLs so bringing the current total to 1764 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

Abstract The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

Abstract The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid–liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

Nucleic acid and protein databases such as GenBank are growing at a rate that perhaps eclipses even Moore’s Law of increase in computational power. This poses a problem for the biological sciences, which have become increasingly dependant on searching and manipulating these databases. It was once reasonably practical to perform exhaustive searches of these databases, for example using the algorithm described by Smith and Waterman, however it has been many years since this was the case. This has led to the development of a series of search algorithms, such as FASTA, BLAST and BLAT, that are each successively faster, but at similarly successive costs in terms of thoroughness. Attempts have been made to remedy this problem by devising search algorithms that are both fast and thorough. An example is CAFE, which seeks to construct a search system with a sub-linear relationship between search time and database size, and argues that this property must be present for any search system to be successful in the long term. This dissertation explores this notion by seeking to construct a search system that takes advantage of the growing redundancy in databases such as GenBank in order to reduce both the search time and the space required to store the databases and their indices, while preserving or increasing the thoroughness of the search. The result is the creation and implementation of new genomic sequence search and alignment, database compression, and index compression algorithms and systems that make progress toward resolving the problem of reducing search speed and space requirements while improving sensitivity. However, success is tempered by the need for databases with adequate local redundancy, and the computational cost of these algorithms when servicing un-batched queries.

Thesis (Ph. D.)--School of Dentistry and School of Pharmacy. University of Missouri--Kansas City, 2004.
"A dissertation in oral biology and pharmacology." Advisor: J. David Eick. Typescript. Vita. Title from "catalog record" of the print edition Description based on contents viewed Feb. 22, 2006. Includes bibliographical references (leaves 176-189). Online version of the print edition.

My PhD project consists of two clearly distinguishable parts. The first part includes modifications and extension of the aspherical pseudoatom databank, the UBDB (University at Buffalo Databank), and the related LSDB program. It also contains extensive tests of the databank applicability to the estimation of electrostatic properties of molecules. The second part of my Thesis is based on the use of the extended UBDB for the following scientific purposes: (1) reconstruction of the charge density distribution of macromolecules, which may constitute foundation for further estimation of electrostatic properties; (2) as a source of aspherical atomic scattering factors, which could be used in the structure refinement (so-called Transferable Aspherical Atom Model (TAAM) refinement);(3) as a starting model in the experimental charge density studies. The study is not just limited to databank-related scientific issues, but it also addresses subjects regarding the interrelations between geometry, energy, charge density and crystal morphology. Consequently, my study resulted in a new modified version of the UBDB databank extended with atoms required for modelling RNA and DNA molecules. The enhanced bank, the UBDB2011, now contains over 200 atom types present in the most relevant biochemical systems. Multipolar parameters stored in the databank were evaluated on the basis of over 600 organic molecules. During my work on the databank, I also modified the UBDB-related LSDB program, so as to include adequate atom type definitions, local coordinate systems, and updated X–H bond distances according to Allen et al. The LSDB now also writes automatically input files suitable for the MOPRO suite of programs, which is an alternative for the well-known XD package. Once the UBDB2011 version of the databank was ready, I extensively tested its applicability to estimating the electrostatic properties of chemical systems. The verification was based on the electrostatic interaction energy evaluation for a set of nucleic acid base and amino acid complexes, for which it was possible to run the reference ab initio calculations. I showed that the UBDB2011+EPMM (Exact Potential Multipole Method (EPMM)) method satisfactorily reproduces electrostatic interaction energies for a set of nucleic acid base complexes with respect to ab initio and/or DFT results (R2 > 0.9, RMSD = 3.7 kcal•mol–1). Correlations were found to be high, while energy trends were preserved. What is important, the UBDB databank enables taking the asphericity of atoms into consideration, therefore, unlike point-charge models, it addresses the directionality of atom–atom interactions. However, the UBDB+EPMM approach has a number of limitations. The databank parameters do not reproduce conformational variety, and do not include the crystal field influence, and some other subtle effects. The UBDB data is also constrained by the accuracy of atom type definitions and the charge density parameter computation method (basis set used, DFT method, Fourier truncation error, Hansen-Coppens model limitations, atom type definition adequacy, etc.). Consequently, when applied for electrostatic interaction energy evaluation, the UBDB2011+EPMM accuracy is of the order of 5 kcal•mol–1. Furthermore, the databank is not appropriate for describing charge density distribution of non-standard molecules, or systems containing alternated double bond fragments, which I showed using the example of Amphotericin B, and its iodoacetyl derivative. The prepared and tested UDBD2011 new databank opened up the possibilities for further studies. Thus, as mentioned in the preface, the second part of my Thesis can be divided into three separate sections. The first one is devoted to the electrostatic interaction investigations of influenza neuraminidase complexes with a series of inhibitors, with particular attention paid to the role of water molecules in the active site. The bank was used for charge density distribution reconstruction. In the second section, I focused on a set of 10 uracil derivatives. Here, the databank was applied as a source of atomic scattering factors in the TAAM refinement. Finally, I dedicated my attention to charge density studies, where I managed to obtain high resolution data, i.e. of 6-methyl-2-thiouracil (6m2tU), and a co-crystal of a complementary nucleic acid base pair, 1-methylthymine and 9-methyladenine (9mA:1mT). The studies of the neuraminidase-inhibitor complex revealed the databank potential in the analysis of biochemical systems and drug activities. Thanks to the UBDB+EPMM method, it was possible to estimate the partial contributions to the total electrostatic interaction energy coming from single fragments of ligand molecules, or from any selected aminoacid residue of the protein part. This way it is easy to identify the active site region (strongest interacting residues), or crucial atomic groups, limiting or stimulating the protein-inhibitor binding. My contribution was, though, directly related to the water molecule role in the neuraminidase active site. I succeeded to estimate the solvent influence on the complex stability. The results helped to explain some differences in the inhibition activity of selected ligands, which in certain cases were not correlated directly with the strength of electrostatic binding energy of ligand- protein complex. On the whole, such electrostatic interaction energy studies are most justified in the case of systems, where electrostatic interactions outweigh other interaction types. Influenza neuraminidase was a perfect case for such considerations. Subsequent the analysis of 10 uracil derivatives (i.e., uracil, 1-methyluracil, 1,5-dimethyluracil, 2-thiouracil, 4-thiouracil, 2,4-dithiouracil, 1-methyl-4-thiouracil, 2-thio-5-methylouracil, 2-thio-6-methyluracil, and 5-fluorouracil) revealed that the UBDB2011 databank works also very well as a source of atomic aspherical scattering factors. It occurred that TAAM refinement provides significantly more accurate molecular geometries than the standard IAM (Independent Atom Model) refinement. The energy and geometry studies showed that TAAM-derived molecular geometries are closer to those obtained from the experimental charge density studies and neutron measurement, but also to the periodically optimised structures within the CRYSTAL package. The TAAM cohesive energy and motif interaction energy trends are also in perfect agreement with the ones observed for optimised structures, whereas the IAM results differ significantly. My studies provided seven high quality structures, among which the 4-thio-uracil structure had not been earlier deposited in the CSD. All the investigated systems, apart from 2,4-dithiouracil, form layered architectures. The molecules within the layers are held by hydrogen bonds, whereas the molecular layers interact with one another via more dispersive in nature, however, significant contacts. The cohesive energy difference between the most thermodynamically stable 5-fluorouracil, and the least advantageous crystal lattice of 1-methyl-4-thiouracil, amounts to 40 kJ•mol-1. The analysis of structural motifs revealed the methyl group stimulation of stronger interlayer contacts, whereas the S4 substituent usually affects the stability and quality of the formed crystal. These two factors most substantially influence the aromaticity index values, HOMA and NICS. HOMA and NICS do not agree, though. The calculated deformation molecule energy between the isolated molecule and the molecule in a crystal lattice, depends on the strength and number of intermolecular interactions, in which this particular molecule participates, and can reach about 10 kJ•mol–1. I have additionally analyzed the interesting motif created by the fluorine atoms in the 5-fluorouracil (5fU) crystal lattice. Four 5fU molecules create a tetrameric motif with all the four fluorine atoms pointing into each other. On the basis of the databank, I have reconstructed the electron density of molecular fragments contributing to such a pattern. The derived deformation electron density indicated the potential stabilizing character of the F…F contact, of the ‘lump to hole’ type. The analysis of charge density distribution of nucleic acid base crystals constituted the last subject undertaken in my PhD Thesis. The project resulted in two high-resolution datasets, i.e., for 6-methyl-2-thiouracil and for the co-crystal structure of 1-methylthymine and 9-methyladenine. The 6m2tU studies showed that the databank can not only be applied as a starting charge density model, but can also be helpful in handling disorder in a crystal lattice. In my case, the UBDB2011 was used to model the problematic sulphur atom, and indicated the hypothesis of some content of the oxo-thiol 6m2tU tautomer exiting in the crystal lattice. This could explain systematic errors, which I observed during the charge density data analysis, and peculiar residual peaks visible in the vicinity of the sulphur atom. The study showed also that one has to be very careful with the modelling and data interpretation. On the other hand, regular and well-diffracting 6m2tU crystals allowed me to find the interrelations between charge density, energy and crystal morphology. It occurred that there is a connection between the crystal architecture features, and the macroscopic shape of the crystal. I have also found relations between crystal thermodynamic characteristics and crystal face stability, and crystal formation. Finally, good agreement was observed between the calculated hydrogen bond energy with that derived from the charge density in the Espinosa’s approach. The 9mA:1mT co-crystal constituted the last subject of my studies. Interestingly, the 9mA:1mT base pair does not form the standard Watson-Crick configuration in the crystal lattice, but the Hoogsteen-Watson-Crick base pair motif. It was also found out, that generally adenine derivatives when forming crystals with uracil species, tend to bind in this particular manner. At the same time, this kind of purine-pyrimidine orientation is rarely encountered even in the relatively labile RNA structures. Nonetheless, computational analysis results support slightly better stabilisation of the cHW-type dimers, than the standard cWW ones. The topological investigations gave very similar results to those obtained for the analogous molecules. What is more, the databank parameters reconstructed reasonably well the experimental charge density evaluated for 9mA:1mT, while the model satisfactorily reproduced the intermolecular interaction region. The 9mA:1mT is yet another crystal structure of layered architecture characterised by quite strong hydrogen bonds and effective π-stacking interactions. An interesting feature of the crystal network is the presence of close H…H contacts, which is not the case in the mono-component 1mT and 9mA crystals. To recapitulate, my PhD thesis provides extended and improved tools for charge density modelling, which can be successfully applied to electrostatic property study of macromolecules, for deriving more accurate structure geometries, or used in charge density analysis. Furthermore, my studies indicate the interrelations between geometry, structure motifs, lattice energy and crystal morphology. Most of the presented results have already been subjects of scientific articles (to date, I am a co-author of 11 publications). Last manuscripts, regarding these topics, are currently under preparation. The further development in the directions indicated by the presented studies concern the databank application to macromolecular systems, which are of biological importance. The UBDB databank and the idea of TAAM refinement should be popularised, as only the IAM refinement is widely applied, at present. Currently, the databank is being combined with the PHENIX package to enable the application of the TAAM procedure also to proteins. Investigations show that there should be some complementary methods provided to supplement the electrostatics derived on the basis of the databank, among which, also, solvent effects should be taken into account. On the other hand, one could consider alternative ways of accurate charge density modelling, free from the limitations of the UBDB databank, and also, the multipolar model. A comprehensive geometry, energy, and environment analysis of the non-standard nucleic acid base interactions, and also of other important factors, such as interactions with sugar moieties, phosphate groups, water or ion species seems interesting, too. This could give a better insight into the RNA binding properties, and may also lead to some pharmaceutical outcome.
Mój projekt doktorski składa się z dwóch wyraźnie zarysowanych części. Pierwsza z nich obejmuje modyfikację i rozszerzenie banku asferycznych pseudoatomów UBDB (University at Buffalo Databank) wraz ze sprzężonym programem LSDB, a także testy stosowalności opracowywanej metody do szacowania właściwości elektrostatycznych molekuł. Druga część mojej pracy opiera się na użyciu nowej wersji banku w trzech różnych celach: (1) w celu rekonstrukcji rozkładu gęstości elektronowej makromolekuł, (2) jako źródła asferycznych atomowych czynników rozpraszania, a w końcu, (3) w celu przygotowania wstępnego modelu multipolowego w eksperymentalnych badaniach gęstości elektronowej. Zastosowanie banku UBDB jest tu punktem wyjścia do dalszych, szeroko zakrojonych rozważań z obszarów biochemii i inżynierii krystalicznej. W wyniku realizacji projektu przygotowałam nową wersję banku UBDB, rozszerzoną o atomy występujące w kwasach nukleinowych, DNA i RNA, a także innych ważnych biologicznie molekułach. Zmodyfikowałam również istniejące definicje atomowe. Nowy bank UBDB2011 zawiera obecnie ponad 200 różnych typów atomowych wymodelowanych na podstawie ponad 600 cząsteczek organicznych. Dodatkowo, równolegle do pracy nad bankiem, aktualizowałam i poprawiałam program LSDB odpowiedzialny za przypisywanie atomom lokalnych układów współrzędnych i nakładanie parametrów multipolowych przechowywanych w banku na wybraną molekułę o zadanej geometrii. Do bieżącej wersji kodu włączone są również zaktualizowane ‘średnie neutronowe’ długości wiązań z wodorem, X–H (X − atom niewodorowy), zgodnie z najnowszą publikacją Allen et al. 2010. Oczywiście program jest w pełni kompatybilny z istniejącą wersją banku. Nowa wersja LSDB, oprócz plików wejściowych do pakietu XD, automatycznie produkuje także pliki w formacie coraz powszechniej używanego pakietu MOPRO. Mając rozszerzoną wersję banku, UBDB2011, przeprowadziłam testy jego stosowalności do szacowania właściwości elektrostatycznych cząsteczek. Weryfikację przeprowadziłam na podstawie analizy elektrostatycznej energii oddziaływania zestawu kompleksów zawierających zasady azotowe lub reszty aminokwasowe. Okazało się, że metoda UBDB+EPMM (EPMM, ang. Exact Potential Multipole Method) w sposób satysfakcjonujący odzwierciedla wartości energii badanych układów w odniesieniu do obliczeń teoretycznych (ab initio i DFT). Korelacja między metodami była wysoka (R2 > 0.9, RMSD = 3.7 kcal•mol–1), natomiast zmienność energii zachowana. Ważną cechą metody bazującej na banku jest również uwzględnianie kierunkowości oddziaływań, co jest niezwykle ważne, a zaniedbywane przez metody oparte na ładunkach punktowych. Podejście UBDB+EPMM ma jednak kilka ograniczeń. Parametry przechowywane w banku nie odwzorowują efektów pola krystalicznego czy zmienności konformacyjnej molekuł. Dodatkowym ograniczeniem banku jest adekwatność definicji typów atomowych oraz metodologia zastosowana do obliczania parametrów gęstościowych (użyta baza funkcyjna, metoda DFT, obcięcie transformaty Fouriera, ograniczenia formalizmu Hansena-Coppensa itd.). W konsekwencji dokładność metody UBDB+EPMM wynosi około 5 kcal•mol–1. Ponadto bank UBDB2011 nie nadaje się do opisu niestandardowych molekuł, czy układów zawierających szereg sprzężonych wiązań podwójnych, co pokazałam na przykładzie cząsteczki amfoterycyny B. Przygotowany i przetestowany bank pseudoatomów otworzył mi drogę do drugiej części doktoratu. Jak już wspomniałam we wstępie, w tej części mojej pracy można wyodrębnić trzy oddzielne analizy. Pierwsza z nich jest poświęcona badaniu elektrostatyki oddziaływań w kompleksach neuraminidazy wirusa grypy z inhibitorami z wykorzystaniem UBDB2011, ze szczególnym uwzględnieniem udziału cząsteczek wody. W kolejnej zajęłam się tematyką serii pochodnych uracylu. Tu bank służył, jako źródło asferycznych czynników rozpraszania atomowego i został użyty w stosunkowo nowym typie udokładnienia struktury tzw. udokładnieniu TAAM (ang. Transferable Aspherical Atom Model). Ostatnie badanie polegało zaś na zastosowaniu banku do przygotowania startowego modelu gęstości elektronowej. Tu zajęłam się dwoma układami, dla których uzyskałam dane wysokorozdzielcze, tj. 6-metylo-2-tiouracylem i ko-kryształem komplementarnej pary zasad DNA 1-metylotyminy z 9-metyloadeniną. Badania układu neuraminidaza-inhibitor pokazały potencjał banku w analizie kompleksów biochemicznych oraz aktywności leków. Dzięki użyciu metody UBDB+EPMM możliwe było oszacowanie wkładów do całkowitej elektrostatycznej energii oddziaływania pochodzących od pojedynczych grup funkcyjnych ligandu, czy też poszczególnych aminokwasów części białkowej. W ten sposób łatwo jest zidentyfikować miejsce aktywne, czy kluczowe grupy funkcyjne limitujące, bądź wspomagające wiązanie inhibitora. Moim zadaniem było zbadanie wpływu cząsteczek wody na trwałość układu neuraminidaza-inhibitor. Udało mi się ustalić poglądowy udział rozpuszczalnika w stabilizacji kompleksu. To przyczyniło się po części do wytłumaczenia różnic w aktywności inhibicyjnej wybranych ligandów, która w niektórych przypadkach nie korelowała bezpośrednio z elektrostatyczną energią wiązania samego ligandu z białkiem. Takie badania mają większe znaczenie dla układów naładowanych, gdzie elektrostatyka przeważa w zdecydowany sposób nad innymi rodzajami oddziaływań. Takim właśnie układem był badany kompleks. Analiza serii 10 pochodnych uracylowych (uracylu, 1-metylouracylu, 1,5-dimetylouracylu, 2-tiouracylu, 4-tiouracylu, 2,4-ditiouracylu, 1-metylo-4-tiouracylu, 2-tio-5-metylouracylu, 2-tio-6-metylouracylu, 5-fluorouracylu) pokazała zaś wyższość udokładnienia typu TAAM nad standardowym udokładnieniem struktury w sferycznym modelu niezależnych atomów IAM (ang. Independent Atom Model). Badania energetyczne i geometryczne wykazały, że uzyskane przeze mnie geometrie cząsteczek z wykorzystaniem banku są bardzo zbliżone zarówno do tych uzyskanych z badań gęstościowych czy neutronowych, jak również do struktur periodycznie zoptymalizowanych w pakiecie CRYSTAL. Również w przypadku energii kohezji, czy oddziaływania motywów strukturalnych, trendy są zgodne z danymi teoretycznymi, podczas gdy wyniki dla struktur uzyskanych w metodzie IAM silnie od nich odbiegają. Moja analiza zaowocowała siedmioma dobrej jakości strukturami badanych układów, w tym jednej zupełnie nowej dla 4-tiouracylu. Wszystkie związki, poza 2,4-ditiouracylem, tworzą warstwy molekularne utrzymywane przez wiązania wodorowe i wzajemnie oddziaływujące za pomocą kontaktów π-elektronowych i z przewagą oddziaływań dyspersyjnych. Różnica energii kohezji między najstabilniejszym termodynamicznie 5-fluorouracylem a najmniej korzystną siecią krystaliczną 1-metylo-4-tiouracylu wynosi około 40 kJ•mol-1. Analiza energii motywów strukturalnych badanych związków pokazała wpływ grupy metylowej na stabilizację oddziaływań międzypłaszczyznowych oraz podstawnika siarkowego w pozycji 4 na jakość struktury. Również te dwa czynniki istotnie wpływają na wartości indeksów aromatyczności, NICS i HOMA, które jednak nie są wzajemnie zgodne. Wielkość energii deformacji molekuły przy przeniesieniu jej z próżni do sieci krystalicznej zależy natomiast od siły i liczby oddziaływań, w które zaangażowana jest dana cząsteczka. Dodatkowo analizowanym problemem okazał się szczególny motyw tworzony przez cząsteczki w strukturze 5-fluorouracylu. Tu atomy fluoru grupują się po cztery w tetramerycznym motywie. Na podstawie banku została odtworzona gęstość deformacyjna wskazująca na potencjalny udział stabilizujących kontaktów F…F typu ‘lump to hole’. Ostatnim tematem poruszanym w mojej pracy doktorskiej jest analiza rozkładu gęstości w kryształach zasad azotowych. Badania 6-metylo-2-tiouracylu pokazały, że bank UBDB może być wykorzystany nie tylko, jako startowy model gęstości elektronowej, ale może również być pomocny w przypadku analizy nieporządku w sieci. W moim badaniu UBDB2011 posłużył do wymodelowania problematycznego atomu siarki, oraz przyczynił się do wysnucia hipotezy o obecności okso-tiolowej formy tautomerycznej w badanej strukturze, tłumaczącej systematyczny błąd rejestrowany podczas analizy danych gęstościowych i zagadkowe piki resztowe wokół siarki. Badanie pokazało również, jak ostrożnym należy być przy interpretacji danych i dobieraniu modelu. Przypadek 6-metylo-2-tiouracylu i regularne kryształy, które tworzy, umożliwił znalezienie zależności między strukturą wewnętrzną kryształu a jego cechami makroskopowymi. Badanie pokazało także zgodność energii oddziaływań wodorowych uzyskanych na podstawie analizy topologicznej danych gęstościowych z tymi uzyskanymi z obliczeń teoretycznych. Podobną analizę przeprowadziłam dla ko-kryształu 9-metyloadeniny z 1-metylotyminą. Para zasad w krysztale występuje w nietypowym dla struktur kwasów nukleinowych kontakcie typu Hoogsteen-Watson-Crick (HW). Okazuje się, że pochodne adeniny wiążąc się w krysztale z modyfikacjami uracyli wykazują tendencję do tworzenia preferencyjnie właśnie tego motywu, podczas gdy nawet w cząsteczce RNA, o wiele bardziej labilnej niż DNA, tylko niewielki procent par zasad typu A:U występuje w takiej konfiguracji. Jednakże z obliczeń energetycznych wynika, że orientacja zasad typu HW jest nieznacznie stabilniejsza niż standardowe ustawienie typu Watsona-Cricka. Ponadto charakterystyka topologiczna rozkładu gęstości elektronowej układu jest zgodna z wynikami uzyskanymi dla analogicznych związków, np. 1-metylotymina tylko nieznacznie różni się od 6-metylouracylu przy porównaniu wspólnych fragmentów molekularnych. Podobnie, jak w 6-metylo-2-tiouracylu, również i w przypadku ko-kryształu energia wiązań wodorowych jest dobrze estymowana na podstawie parametrów topologicznych. Co więcej, model uzyskany bezpośrednio z banku, mimo że w detalach różny od eksperymentalnego rozkładu gęstości uzyskanego dla ko-kryształu, odzwierciedla satysfakcjonująco wielkość tych oddziaływań. Podsumowując, moja praca doktorska dostarczyła pełniejszej wersji narzędzi do opisu gęstości elektronowej cząsteczek, które z powodzeniem mogą być wykorzystywane zarówno do badania elektrostatyki układów makromolekularnych, jak i do poprawiania geometrii udokładnianych struktur czy w analizie gęstości elektronowej. Ponadto przeprowadzone badania uwypuklają zależności między geometrią układów, motywami strukturalnymi, energetyką sieci a morfologią. Większość wyników została już opublikowana w liczących się czasopismach (w sumie do tej pory jestem współautorką 11 publikacji), a ostatnie manuskrypty są w przygotowaniu. Kierunkami rozwoju wskazanymi przez wyniki moich badań może być analiza kompleksów makromolekularnych ważnych biologicznie, rozpowszechnianie użycia banku w udokładnieniu strukturalnym i jego dalszy rozwój lub też poszukiwanie lepszych modeli gęstości elektronowej w celu wyeliminowania przytoczonych wcześniej ograniczeń metody. Dodatkowo, ciekawą byłaby szersza analiza energetyczna, geometryczna i środowiskowa różnych połączeń zasad azotowych, a także ich oddziaływań z wodą, jonami metali i resztami cukrowymi. Przyczyniłoby się to do lepszego zrozumienia mechanizmów powstawania konkretnych kontaktów międzycząsteczkowych, także tych ważnych farmaceutycznie.

Theoretical studies focusing on the nature of landscapes that correlate molecular sequences to molecular function have mainly been carried out in silico due to the vast amounts of data that are needed for analysis. In vitro selections of aptamers are a good model system to study theoretical questions at a experimental level. With the introduction of robotic platforms that conduct in vitro selections, it is now capable of producing significant amounts of data in a short time, making theoretical modeling with real experimental data attainable. I will be using a Biomek 2000 Laboratory Automation Workstation to carry out multiple in vitro nucleic acid selections in parallel. I will explore the sequence space to examine whether existing in vitro selection systems are optimal at isolating the best winning species. New methods will be introduced that will allow for the selection of identical targets with identical pools free of cross contamination on the open robotic system. This will open the doors to further conduct selections against other identical or highly similar targets, such as complex cellular targets. Finally, I will investigate the methods to improve the effectiveness at isolating aptamers against the highly complex lung cancer cell lines. These targets are highly challenging for isolating specific aptamers because of the great diversity of biomarkers found among them. Moreover, their highly morphological similarity of the cultured cells makes selections for specific aptamers very difficult. I explore the different methods that will allow for the generation of aptamers that can distinguish between non-small cell lung cancer and small cell lung cancer, and between non-small cell lung cancer and normal lung cells. Fine-tuning of this process is essential at transferring this process to automated platforms for large-scale generation of biosensors against tumor biomarkers.

In order to conform to the new regulatory standard in Japan, seawater is regarded as the alternative water source both for BWRs (Boiling water reactors) and PWRs (Pressurized water reactors). For preventing further accident evolutions occurred in Fukushima Daiichi nuclear power plants, seawater was injected into the reactors for more than one week. With long-term seawater injection, sea salt compositions are condensed and many of them will precipitate when saturated concentrations are exceeded. Unlike corrosion issues, impacts of sea salt precipitation on the heat removal has not been studied widely in the past because it has not been regarded as the alternative water source before Fukushima Daiichi nuclear power plants accident. The existent knowledge base of boric acid precipitation under LOCA conditions was studied. Based on the existent study on impacts of boric acid precipitation under LOCA conditions, the experimental project of seawater consisting of four experiments was proposed. The existent database of physical properties, such as viscosity, of seawater is rather poor under severe accident conditions. In addition, it is likely that boric acid will be injected with water or seawater to prevent re-criticality. It is known that physical properties of boric acid vary widely under high temperature conditions. Measurement of viscosity of the seawater-boric acid mixture was conducted in high temperature using a rotational viscometer. Under conditions equivalent to the estimated bulk coolant conditions under a long-term cooling phase of severe accidents. In this range, no obvious change of viscosity is expected. Then a detailed structure of seawater precipitates was observed using a mockup fuel bundle with 5×5 in the square lattice and 500 mm in the length. Images of precipitates were taken using the X-ray CT. The water level, the concentration of sea salt and the heat flux are employed as experimental parameters. The heat flux, bubble stirring in downstream of spacers and heat loss by a non-heated channel box were identified as influential factors to local and overall precipitates in fuel bundles.

Abstract Failure rate is very important for the reliability and risk assessment of in-service pressure vessels. As early as in the 1970s and 1980s, the failure rate data of in-service pressure vessels has been collected in various countries, such as Europe and the United States, and in great detail. These data were incorporated into the relevant reliability database such as OREDA and CEMHD5. However, the failure rate data of pressure vessels in China is rarely reported so far, which limits the development of reliability and risk assessment technology for the pressure vessels in non-nuclear and nuclear industries. In this paper, about fifty thousand in-service pressure vessels data in China’s non-nuclear industry were collected. The potential and catastrophic failure rate were counted based on exponential distribution model. The statistical results were compared and analyzed with those of other countries such as the United States, the United Kingdom and Germany. The analysis results showed that the thickness thinning and cracking caused by corrosive medium were two main causes for pressure vessel failures in China. The failure rate of in-service pressure vessels in China is higher than that in the Europe and the United States countries, which may be caused by the high sulfur and high acid crude oil.

The occurrence of metabolic syndrome, which includes several chronic severe diseases such as cardiovascular disease, dyslipidemia, hypertension, stroke, and type 2 diabetes mellitus, is becoming a serious public health concern on a global scale. Peroxisome proliferator-activated receptor alpha (PPARα) is a ligand-activated transcription factor that are members of the nuclear hormone receptor superfamily. PPARα plays a crucial function in regulating the expression of genes involved in fatty acid beta-oxidation and glucose homeostasis, making it a potential drug target for treating metabolic syndrome. In experimental models, several coumarins, such as graphene, ostiole, and interruption B, have been found to activate PPARα. In this study, we focus our attention on exogenous natural ligands known as coumarins. Using in silico screening, we searched for the most promising coumarin candidates from the Chemical Synthesis Database. Using a combination of ligand-based virtual screening and molecular docking, we identified (E)-3-[(2-oxo-chromen-3-yl)-methyleneamino]-acrylaldehyde as the most favorable candidate PPARα agonist and proposed it for subsequent experimental testing.

Abstract This paper reports on a research effort involving design of a class of significantly complex products — nuclear submarines. It focuses on the use of features as a means of design abstraction, and it is found that a principal motivation for the use of features in this design environment is the convenience of the early stage submarine designer. To support this argument, a review of feature research is presented. Experiments in the development of feature catalogs are described, and implementation through two generations of feature based submarine CAD systems are discussed. The architecture of the feature based submarine CAD systems includes the use of Microsoft Foundation Classes (MFC), the ACIS geometric modeler, and user interfaces which store/recall hierarchical submarine feature information easily. Strong connections to object-oriented programming and object-oriented databases are recognized. Conclusions are drawn regarding the use of features for designer convenience and regarding support provided by hierarchical, parameterized features for other means of design automation.

The research problem: Bacterial spot and bacterial speck diseases of tomato are causedby strains of Xanthomonas campestris pv. vesicatoria (Xcv) and Pseudomonas syringae pv.tomato (Pst), respectively. These bacteria colonize aerial parts of the plant and causesignificant losses in tomato production worldwide. Protection against Xcv and Pst bycultural practices or chemical control has been unsuccessful and there are only limitedsources of genetic resistance to these pathogens. In previous research supported in part byBARD IS-3237-01, we extensively characterized changes in tomato gene expression uponthe onset of spot and speck disease resistance. A remarkable finding of these studies wasthe inducibility in tomato leaves by both Xcv and Pst strains of genes encodingtranscriptional activator of the GRAS family, which has not been previously linked todisease resistance. Goals: Central goals of this research were to investigate the role of GRAS genes in tomatoinnate immunity and to assess their potential use for disease control.Specific objectives were to: 1. Identify GRAS genes that are induced in tomato during thedefense response and analyze their role in disease resistance by loss-of-function experiments.2. Overexpress GRAS genes in tomato and characterize plants for possible broad-spectrumresistance. 3. Identify genes whose transcription is regulated by GRAS family. Our main achievements during this research program are in three major areas:1. Identification of tomato GRAS family members induced in defense responses andanalysis of their role in disease resistance. Genes encoding tomato GRAS family memberswere retrieved from databases and analyzed for their inducibility by Pst avirulent bacteria.Real-time RT-PCR analysis revealed that six SlGRAS transcripts are induced during theonset of disease resistance to Pst. Further expression analysis of two selected GRAS genesshowed that they accumulate in tomato plants in response to different avirulent bacteria orto the fungal elicitor EIX. In addition, eight SlGRAS genes, including the Pst-induciblefamily members, were induced by mechanical stress in part in a jasmonic acid-dependentmanner. Remarkably, SlGRAS6 gene was found to be required for tomato resistance to Pstin virus-induced gene silencing (VIGS) experiments.2. Molecular analysis of pathogen-induced GRAS transcriptional activators. In aheterologous yeast system, Pst-inducible GRAS genes were shown to have the ability toactivate transcription in agreement with their putative function of transcription factors. Inaddition, deletion analysis demonstrated that short sequences at the amino-terminus ofSlGRAS2, SlGRAS4 and SlGRAS6 are sufficient for transcriptional activation. Finally,defense-related SlGRAS proteins were found to localize to the cell nucleus. 3. Disease resistance and expression profiles of transgenic plants overexpressing SlGRASgenes. Transgenic plants overexpressing SlGRAS3 or SlGRAS6 were generated. Diseasesusceptibility tests revealed that these plants are not more resistant to Pst than wild-typeplants. Gene expression profiles of the overexpressing plants identified putative direct orindirect target genes regulated by SlGRAS3 and SlGRAS6. Scientific and agricultural significance: Our research activities established a novel linkbetween the GRAS family of transcription factors, plant disease resistance and mechanicalstress response. SlGRAS6 was found to be required for disease resistance to Pstsuggesting that this and possibly other GRAS family members are involved in thetranscriptional reprogramming that takes place during the onset of disease resistance.Their nuclear localization and transcriptional activation ability support their proposed roleas transcription factors or co-activators. However, the potential of utilizing GRAS familymembers for the improvement of plant disease resistance in agriculture has yet to bedemonstrated.