bluuebunny/crossref_metadata_2025_split huggingface dataset:
Folding thermodynamics of the hybrid‐1 type intramolecular human telomeric G‐quadruplex
Authors: Shek Yuen Lai , Noudeh Golamreza Dehghan , Nazari Mozhgan , Heerklotz Heiko , Abu‐Ghazalah Rashid M. , Dubins David N. , Chalikian Tigran V. 
Published: June 2013

ABSTRACTGuanine‐rich DNA sequences that may form G‐quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G‐quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in emerging anticancer strategies. Thermodynamic characterization of G‐quadruplexes is an important and necessary step in developing predictive algorithms for evaluating the conformational preferences of G‐rich sequences in the presence or the absence of their complementary C‐rich strands. We use a combination of spectroscopic, calorimetric, and volumetric techniques to characterize the folding/unfolding transitions of the 26‐meric human telomeric sequence d[A3G3(T2AG3)3A2]. In the presence of K+ ions, the latter adopts the hybrid‐1 G‐quadruplex conformation, a tightly packed structure with an unusually small number of solvent‐exposed atomic groups. The K+‐induced folding of the G‐quadruplex at room temperature is a slow process that involves significant accumulation of an intermediate at the early stages of the transition. The G‐quadruplex state of the oligomeric sequence is characterized by a larger volume and compressibility and a smaller expansibility than the coil state. These results are in qualitative agreement with each other all suggesting significant dehydration to accompany the G‐quadruplex formation. Based on our volume data, 432 ± 19 water molecules become released to the bulk upon the G‐quadruplex formation. This large number is consistent with a picture in which DNA dehydration is not limited to water molecules in direct contact with the regions that become buried but involves a general decrease in solute–solvent interactions all over the surface of the folded structure. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 216–227, 2014.
Using probabilistic roadmaps in changing environments
Authors: Rantanen Mika T. , Juhola Martti 
Published: June 2013

ABSTRACTIn this paper, we examine how a path planning problem can be solved in changing environments using probabilistic roadmap planners. A probabilistic roadmap is built in static environment where all obstacles are known in advance, but we show that a roadmap can be built in such a way that it works well even when new obstacles are added to the workspace. However, our experiments show that the roadmap graph must be built carefully. We compare three different methods that are used to decide which edges are added to the roadmap graph to connect the nodes. One of these is a distance‐based method, which we present in this paper. In the tests, we built a roadmap by using only the static obstacles. Then, we added additional obstacles to the environment and tested how well the roadmap still worked. The tests showed that our distance‐based method worked quickly and that it produced roadmaps, which could be used to find a path amid additional obstacles with a high success rate.Copyright © 2013 John Wiley & Sons, Ltd.
Essential‐Oil Composition of the Tunisian Endemic Cypress (Cupressus sempervirens L. var. numidicaTrab.)
Authors: El Hamrouni‐Aschi Kaouther , Larbi Khouja Mohamed , Boussaid Mohamed , Akrimi Noureddine , Toumi Lamjed 
Published: June 2013

AbstractThe essential oils isolated from leaves, wood, and cones of the Tunisian endemic cypress Cupressus sempervirens L. var. numidica Trab. collected from three natural populations were characterized by GC‐FID and GC/MS analyses. In the wood, leaf, and cone oils, 38, 35, and 26 constituents, representing 94.4, 97.8, and 98.5% of the total oil composition, respectively, were identified. Monoterpenes constituted the major fraction of the oils from all organs and for all populations. The oils were found to be of an α‐pinene (64.2%)/δ‐car‐3‐ene (11.1%) chemotype with considerable contents of α‐humulene (3.4%) in the leaf oil, cedrol (2.8%) in the wood oil, and sabinene (3.2%) in the cone oil, respectively. α‐Pinene, δ‐car‐3‐ene, limonene, carvacrol methyl ether, α‐humulene, and α‐amorphene were the main components that differentiated the oils of the three organs in the cypress of Makthar.
Alkaloids from Zephyranthes robustaBaker and Their Acetylcholinesterase‐ and Butyrylcholinesterase‐Inhibitory Activity
Authors: Kulhánková Andrea , Cahlíková Lucie , Novák Zdeněk , Macáková Kateřina , Kuneš Jiří , Opletal Lubomír 
Published: June 2013

AbstractThe bulbs of Zephyranthes robusta (Amaryllidaceae) have been extensively analyzed for their chemical constituents, resulting in the isolation of 13 alkaloids. The chemical structures of the isolated compounds were elucidated by mass‐spectrometric, and 1D‐ and 2D‐NMR spectroscopic experiments. The complete NMR assignments were achieved for hippeastidine. All isolated alkaloids were evaluated for their erythrocytic acetylcholinesterase and serum butyrylcholinesterase inhibitory activities using the Ellman's method. Significant acetylcholinesterase inhibition activity was exhibited by 8‐O‐demethylmaritidine (IC50(HuAChE) 28.0±0.9 μM).
Bioactive Brominated Metabolites from the Natural Habitat and Tank‐Maintained Cuttings of the Jamaican Sponge Aplysina fistularis
Authors: Gallimore Winklet A. 
Published: June 2013

AbstractCut specimens of the common reef sponge of the Verongid family, Aplysina fistularis, were retained in flow‐through seawater tanks over a six‐week period to assess the metabolite profile of the sponge when subjected to stress, compare the profile with the source material, and assess the preliminary feasibility of the protocol for sponge culture. The living specimens were harvested, extracted with MeOH/CH2Cl2 1 : 1, and subjected to column chromatography to identify metabolites. The brominated isoxazoline compounds, aerothionin (1) and 11‐oxoaerothionin (2), along with aeroplysinin 2 (3) and 2‐(3,5‐dibromo‐4‐hydroxyphenol)acetamide (4), were detected in the cuttings from the tank‐maintained sponge. An examination of the metabolite profile of the sponge from the natural habitat showed that the compounds 1 and 2 were present. The identities of all the compounds were ascertained by analysis of the mass‐spectral data and NMR spectra (1H, 13C, HMBC, and HSQC) of the compounds, which were compared with reported data. The survival rate was 44% with limited necrosis or exposed skeletal tissue being observed in eight of the 18 cuttings, suggesting that protocol modifications would be required for culturing the sponge.
Molluscicidal and Leishmanicidal Activity of the Leaf Essential Oil of Syzygium cumini (L.) Skeels from Brazil
Authors: Dias Clarice N. , Rodrigues Klinger A. F. , Carvalho Fernando A. A. , Carneiro Sabrina M. P. , Maia Jose G. S. , Andrade Eloisa H. A. , Moraes Denise F. C. 
Published: June 2013

AbstractThe chemical composition and biological potential of the essential oil extracted from Syzygium cumini leaves collected in Brazil were examined. GC/MS Analyses revealed a high abundance of monoterpenes (87.12%) in the oil. Eleven compounds were identified, with the major components being α‐pinene (31.85%), (Z)‐β‐ocimene (28.98%), and (E)‐β‐ocimene (11.71%). To evaluate the molluscicidal effect of the oil, it was tested against Biomphalaria glabrata and the LC50 obtained was 90 mg/l. The essential oil also showed significant activity against Leishmania amazonensis, with an IC50 value equal to 60 mg/l. In addition, to evaluate its toxicity towards a non‐target organism, the essential oil was tested against Artemia salina and showed a LC50 of 175 mg/l. Thus, the essential oil of S. cumini showed promising activity as a molluscicidal and leishmanicidal agent and might be valuable in combating neglected tropical diseases such as schistosomiasis and leishmaniasis. Further research is being conducted with regard to the purification and isolation of the most active essential‐oil compounds.
Chemodiversity of Ursane‐ and Oleanane‐Type Triterpenes in Amazonian Burseraceae Oleoresins
Authors: Rüdiger André L. , Veiga‐Junior Valdir F. 
Published: June 2013

AbstractThe oleoresins exuded from species of the Burseraceae family present high potential due to their biological and pharmacological properties. The evaluation of the chemodiversity of the oleoresins of 23 Amazonian species of Burseraceae provided a profile of the principal constituents, viz., the ursane‐type triterpenes α‐amyrin (1), α‐amyrenone (3), and brein (5) and the oleanane‐type triterpenes β‐amyrin (2), β‐amyrenone (4), and maniladiol (6), and allowed to determine which of these species have the highest biotechnological potential and which ones are rich in other, potentially new, triterpenes or volatile compounds of interest for the cosmetics industry. The oleoresin compositions obtained by GC‐FID and GC/MS analyses were submitted to principal component analysis (PCA) and hierarchical clustering on principal components (HCPC), which divided the 23 samples in five clusters. Protium giganteum and Trattinnickia peruviana, constituting the first cluster, presented high oleoresin contents of 3 and 4 (28.8 and 16.3% on average, resp.). The seven species of Burseraceae composing the second cluster were potential producers of new triterpenes and volatile compounds. Dacryodes hopkinsii and five Protium species (third cluster) presented average contents for all the triterpenes analyzed. The highest contents of 5 and 6 (averages of 3.9 and 5.4%, resp.) were observed in P. heptaphyllum ssp. ullei and T. glaziovii (fourth cluster). Finally, the six Protium species forming the fifth cluster showed high contents of 1 and 2 (48.0 and 19.9% on average, resp.). Moreover, this study allowed the description of the triterpene composition of 13 not previously investigated species.
Spectroscopic and Biological Studies of Phenanthroline Compounds: Selective Recognition of Gene‐Promoter G‐Quadruplex DNAs Preferred over Duplex DNA
Authors: Wang Lihua , Wei Chunying 
Published: June 2013

AbstractG‐Quadruplex DNA formed in the promoter regions of proto‐oncogenes would block the transcription process and eventually suppress the development of tumors, so compounds that stabilize G‐quadruplex DNA are potential antitumor drugs. This article describes the interactions of three phenanthroline compounds, a–c, with proto‐oncogene c‐kit2 and c‐myc G‐quadruplex DNAs by means of polymerase chain reaction (PCR) stop assay, fluorescence resonance energy transfer melting (FRET melting) assay, fluorescence indicator displacement (FID) assay, UV/VIS absorption, fluorescence, and circular dichroism (CD) spectroscopies. All three compounds displayed selectivity for the G‐quadruplex over duplex, with binding constants (Ka) for the both quadruplexes varying from 0.49×106 to 3.32×106 M−1 (4.1‐ to 33.2‐fold specificity). Compounds a, b, and c were potential stabilizers for the c‐kit2 G‐quadruplex with the melting‐temperature increase (ΔTm) values of 12–15°. CD Spectra indicated that a–c disrupted the structure of c‐kit2 G‐quadruplex, whereas no significant change was observed for c‐myc G‐quadruplex.
Dodecyl α‐L‐Rhamnopyranosyl‐(1→2)‐β‐D‐fucopyranoside Derivatives from the Glandular Trichome Exudate of Erodium pelargoniflorum
Authors: Sakai Takaomi , Tanemura Yuhei , Itoh Satsuki , Fujimoto Yoshinori 
Published: June 2013

AbstractChemical investigation of the glandular trichome exudate of Erodium pelargoniflorum (Geraniaceae) led to the isolation of two dodecyl disaccharide derivatives, named pelargoside A1 and pelargoside B1 (1 and 2, resp.). The structures of 1 and 2 were determined as dodecyl 4‐O‐acetyl‐α‐L‐rhamnopyranosyl‐(1→2)‐4‐O‐acetyl‐β‐D‐fucopyranoside and dodecyl 3,4‐di‐O‐acetyl‐α‐L‐rhamnopyranosyl‐(1→2)‐4‐O‐acetyl‐β‐D‐fucopyranoside, respectively, by spectroscopic studies, including 2D‐NMR, and chemical transformations. In addition, undecyl, tridecyl, and tetradecyl homologs of 1 and 2, named pelargosides A2–A4 and pelargosides B2–B4, were also characterized as minor constituents of the exudate.
From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics
Authors: Pietra Francesco 
Published: June 2013

AbstractThis work deals with two neuroglobins from phylogenetically distant organisms. Deriving from the acoelomorph Symsagittifera roscoffensis, SrNgb is functionally pentacoordinated, and is assumed to function as a reserve of dioxygen (O2). Obtained from mice, mNgb is functionally hexacoordinated, and presumably triggers signals from sensing O2. Here, it is investigated how these two globins are permeated by diatomic gases, SrNgb by O2 and mNgb by CO. With protein atomic coordinates available from high‐resolution X‐ray diffraction analysis, O2 and CO pathways were traced from molecular‐dynamics simulations in H2O solution, which makes no difference between the two gases, accelerated by applying an external randomly‐oriented minimal force to the center of mass of the diatomic gas molecule. This allowed us to explore a statistically significant large number of trajectories. It emerged that CO leaves mNgb from preferentially peripheral gates located on the side of the heme propionate chains, whereas O2 leaves SrNgb from the opposite side. This shows no analogy with either the functionally pentacoordinated, O2‐transporting, myoglobin (Mgb), or the hexacoordinated, O2‐sensing, cytoglobin, despite the same three‐over‐three typical α‐helical globin folding. The sole analogy that could be observed was a preference for the shortest diatomic gas pathways with both SrNgb and Mgb. It is tempting to speculate that this fulfills the need of being quick in delivering O2 to depleted organs.
Chemical Tools for Studying the Biological Function of Glycolipids
Authors: Stocker Bridget L. , Timmer Mattie S. M. 
Published: June 2013

AbstractGlycolipids play an important role in many biological processes and to this end, synthetic chemists have developed a variety of new techniques and “chemical tools” that allow for the study of glycolipids in vitro and in vivo. The types of probes prepared include fluorescent, radio‐labelled, biotinylated and photoreactive ones, as well as others based on liposomes, microarrays and other supramolecular constructs—each of which offers its own advantages, as is discussed. A number of more specialised probes, such as metabolically engineered glycolipids and photopolymerisable glycolipids, have also been prepared in order to investigate various processes including substrate specificities and binding interactions.The purpose of this review is to present the key approaches that can be used for the development of glycolipid probes, organised according to application, and also to discuss the limitations of such strategies, which include the nontrivial task of ensuring that the probe does not adversely influence the biological activity of the parent compound. On the whole, it is exciting to see what can be achieved through the development of chemical probes as tools to study biological processes, and it is envisioned that the reader will be inspired by the large number of superb studies highlighted here and will be encouraged to undertake further work in this research area.
The TEAD4–YAP/TAZ Protein–Protein Interaction: Expected Similarities and Unexpected Differences
Authors: Hau Jean Christophe , Erdmann Dirk , Mesrouze Yannick , Furet Pascal , Fontana Patrizia , Zimmermann Catherine , Schmelzle Tobias , Hofmann Francesco , Chène Patrick 
Published: June 2013

AbstractThe Hippo pathway controls cell homeostasis, and its deregulation can lead to human diseases. In this pathway, the YAP and TAZ transcriptional cofactors play a key role in stimulating gene transcription through their interaction with the TEAD transcriptional factors. Our study of YAP and TAZ peptides in biochemical and biophysical assays shows that both proteins have essentially the same affinity for TEAD. Molecular modeling and structural biology data suggest that they also bind to the same site on TEAD. However, this apparent similarity hides differences in the ways in which the two proteins interact with TEAD. The secondary structure elements of their TEAD binding site do not contribute equally to the overall affinity, and critical interactions with TEAD are made through different residues. This convergent optimization of the YAP/TAZ TEAD binding site suggests that the similarity in the affinities of binding of YAP to TEAD and of TAZ to TEAD is important for Hippo pathway functionality.
Pseudo‐Fivefold Diffraction Symmetries in Tetrahedral Packing
Authors: Lee Stephen , Henderson Ryan , Kaminsky Corey , Nelson Zachary , Nguyen Jeffers , Settje Nick F. , Schmidt Joshua Teal , Feng Ji 
Published: June 2013

AbstractWe review the way in which atomic tetrahedra composed of metallic elements pack naturally into fused icosahedra. Orthorhombic, hexagonal, and cubic intermetallic crystals based on this packing are all shown to be united in having pseudo‐fivefold rotational diffraction symmetry. A unified geometric model involving the 600‐cell is presented: the model accounts for the observed pseudo‐fivefold symmetries among the different Bravais lattice types. The model accounts for vertex‐, edge‐, polygon‐, and cell‐centered fused‐icosahedral clusters. Vertex‐centered and edge‐centered types correspond to the well‐known pseudo‐fivefold symmetries in Ih and D5h quasicrystalline approximants. The concept of a tetrahedrally‐packed reciprocal space cluster is introduced, the vectors between sites in this cluster corresponding to the principal diffraction peaks of fused‐icosahedrally‐packed crystals. This reciprocal‐space cluster is a direct result of the pseudosymmetry and, just as the real‐space clusters, can be rationalized by the 600‐cell. The reciprocal space cluster provides insights for the Jones model of metal stability. For tetrahedrally‐packed crystals, Jones zone faces prove to be pseudosymmetric with one another. Lower and upper electron per atom bounds calculated for this pseudosymmetry‐based Jones model are shown to accord with the observed electron counts for a variety of Group 10–12 tetrahedrally‐packed structures, among which are the four known Cu/Cd intermetallic compounds: CdCu2, Cd3Cu4, Cu5Cd8, and Cu3Cd10. The rationale behind the Jones lower and upper bounds is reviewed. The crystal structure of Zn11Au15Cd23, an example of a 1:1 MacKay cubic quasicrystalline approximant based solely on Groups 10–12 elements is presented. This compound crystallizes in Im$\bar 3$ (space group no. 204) with a=13.842(2) Å. The structure was solved with R1=3.53 %, I>2σ;=5.33 %, all data with 1282/0/38 data/restraints/parameters.
On the Entangled Growth of NaTaO3 Cubes and Na2Ti3O7 Wires in Sodium Hydroxide Solution
Authors: Baumann Stefan O. , Liu Chang , Elser Michael J. , Sternig Andreas , Siedl Nicolas , Berger Thomas , Diwald Oliver 
Published: June 2013

AbstractThe entangled growth of sodium titanate Na2Ti3O7 nanowires and sodium tantalate NaTaO3 cubes was investigated with electron microscopy, X‐ray diffraction, and UV diffuse reflectance spectroscopy. Depending on the composition of the Ta2O5‐ and TiO2‐particle‐based powder mixtures, which served as educts, we observed different types of hybridization effects. These include the titanium‐induced contraction of the NaTaO3 perovskite‐type unit cell and the generation of electronic defect states in NaTaO3 that give rise to optical subbandgap transitions and tantalum‐induced limitations of the Na2Ti3O7 nanowire growth. The transformation from Ta2O5 to NaTaO3 occurs through a dissolution–recrystallization process. A systematic analysis of the impact of different titanium sources on NaTaO3 dispersion and, thus, on the properties of the entangled nanostructures revealed that a perfect intermixture of cubes and nanowires can only be achieved when titanate nanosheets emerge during transformation as reaction intermediates and shield nucleation and growth of isolated NaTaO3 cubes. The here demonstrated approach can be highly instrumental for understanding the nucleation and growth of composite and entangled nanostructures in solution and—at the same time—provides an interesting new class of photoactive composite materials.
Energy Transfer at the Single‐Molecule Level: Synthesis of a Donor–Acceptor Dyad from Perylene and Terrylene Diimides
Authors: Kim Ha Na , Puhl Larissa , Nolde Fabian , Li Chen , Chen Long , Basché Thomas , Müllen Klaus 
Published: June 2013

AbstractIn 2004, we reported single‐pair fluorescence resonance energy transfer (spFRET), based on a perylene diimide (PDI) and terrylene diimide (TDI) dyad (1) that was bridged by a rigid substituted para‐terphenyl spacer. Since then, several further single‐molecule‐level investigations on this specific compound have been performed. Herein, we focus on the synthesis of this dyad and the different approaches that can be employed. An optimized reaction pathway was chosen, considering the solubilities, reactivities, and accessibilities of the building blocks for each individual reaction whilst still using established synthetic techniques, including imidization, Suzuki coupling, and cyclization reactions. The key differentiating consideration in this approach to the synthesis of dyad 1 is the introduction of functional groups in a nonsymmetrical manner onto either the perylene diimide or the terrylene diimide by using imidization reactions. Combined with well‐defined purification conditions, this modified approach allows dyad 1 to be obtained in reasonable quantities in good yield.
Sequence‐Selective DNA Recognition with Peptide–Bisbenzamidine Conjugates
Authors: Sánchez Mateo I. , Vázquez Olalla , Vázquez M. Eugenio , Mascareñas José L. 
Published: June 2013

AbstractTranscription factors (TFs) are specialized proteins that play a key role in the regulation of genetic expression. Their mechanism of action involves the interaction with specific DNA sequences, which usually takes place through specialized domains of the protein. However, achieving an efficient binding usually requires the presence of the full protein. This is the case for bZIP and zinc finger TF families, which cannot interact with their target sites when the DNA binding fragments are presented as isolated monomers. Herein it is demonstrated that the DNA binding of these monomeric peptides can be restored when conjugated to aza‐bisbenzamidines, which are readily accessible molecules that interact with A/T‐rich sites by insertion into their minor groove. Importantly, the fluorogenic properties of the aza‐benzamidine unit provide details of the DNA interaction that are eluded in electrophoresis mobility shift assays (EMSA). The hybrids based on the GCN4 bZIP protein preferentially bind to composite sequences containing tandem bisbenzamidine–GCN4 binding sites (TCAT⋅AAATT). Fluorescence reverse titrations show an interesting multiphasic profile consistent with the formation of competitive nonspecific complexes at low DNA/peptide ratios. On the other hand, the conjugate with the DNA binding domain of the zinc finger protein GAGA binds with high affinity (KD≈12 nM) and specificity to a composite AATTT⋅GAGA sequence containing both the bisbenzamidine and the TF consensus binding sites.
Study of hybrid drag models for predicting hydrodynamic behaviour in a spouted bed
Authors: Santos Dyrney A. , Petri Irineu J. , Duarte Claudio R. , Barrozo Marcos A. S. 
Published: June 2013

AbstractA hybridisation study of drag models was performed in a conical–cylindrical spouted bed by means of CFD simulations using an Eulerian–Eulerian multiphase model. In order to evaluate the simulation results, time‐averaged velocity distributions of the particulate phase were compared with the experimental data obtained by means of an optical fibre probe. The hybrid drag model considering both the volume fraction and the granular temperature distribution in the drag force calculation predicted the experimental data of the particle velocity distribution better than the other simulations performed in this work using other hybrid drag models.