bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of Oligonucleotide Derivatives Using ChemMatrix Supports
Authors: Mazzini Stefania , García‐Martin Fayna , Alvira Margarita , Aviñó Anna , Manning Brendan , Albericio Fernando , Eritja Ramon 
Published: January 2008

AbstractThe synthesis of oligonucleotides on poly(ethylene glycol)‐based (ChemMatrix) supports was studied. Results show that oligonucleotides can be indeed prepared in good yields using slightly modified synthesis cycles and automated DNA synthesizers. The use of these supports for the synthesis of oligonucleotide–peptide conjugates and for the ligation of oligonucleotides using Cu+‐catalyzed cycloadition reactions is reported. Moreover, these supports can be used for the preparation of oligonucleotides in anhydrous solvents, followed by hybridization of the complementary sequences in aqueous buffers.
Enzymatically Catalyzed DNA Synthesis Using L‐Asp‐dGMP, L‐Asp‐dCMP, and L‐Asp‐dTMP
Authors: Terrazas Montserrat , Marlière Philippe , Herdewijn Piet 
Published: January 2008

AbstractThe replacement of the pyrophosphate moiety of deoxynucleoside triphosphates by L‐aspartic acid allows incorporation of natural deoxynucleosides into DNA using HIV reverse transcriptase (RT) as enzyme, while retaining the canonical base‐pair selectivity. N‐Methylation of the L‐aspartic acid leaving group results in a reduced fidelity of incorporation.
Sugar–Oligoamides: Bound‐State Conformation and DNA Minor‐Groove‐Binding Description by TR‐NOESY and Differential‐Frequency Saturation‐Transfer‐Difference Experiments
Authors: Souard Florence , Muñoz Eva , Peñalver Pablo , Badía Concepción , del Villar‐Guerra Rafael , Asensio Juan Luis , Jiménez‐Barbero Jesús , Vicent Cristina 
Published: January 2008

AbstractSelective‐frequency saturation‐transfer‐difference (STD) spectra allow the description of complexes established between minor‐groove binders and long tracts of calf thymus DNA (ct‐DNA). Two sets of experiments with selective saturation of either the H1′ or H4′/H5′/H5′′ proton NMR regions of deoxyribose allow the description of the ligand residues close to the inner (H1′) and outer regions (H4′/H5′/H5′′) of the minor groove of double‐helical DNA. A series of complexes of sugar–oligoamides (2–6) with ct‐DNA have been studied by both TR‐NOESY and STD experiments. The binding mode of the complexes is similar to that of netropsin (1) and allows us to define a general binding mode for this family of ligands, in which an NH rim points towards the internal area (inner region) and a CH3 rim points towards the external part (outer region) of the minor groove of DNA. Also by means of both TR‐NOESY and STD experiments, a description of the asymmetric centers of the sugar residue close to the inner and outer regions of the groove has been achieved. These results confirm that the sugar is responsible for the differences previously found in binding energetics.
The Search for a Potentially Prebiotic Synthesis of Nucleotides via Arabinose‐3‐phosphate and Its Cyanamide Derivative
Authors: Anastasi Carole , Buchet Fabien F. , Crowe Michael A. , Helliwell Madeleine , Raftery Jim , Sutherland John D. 
Published: January 2008

AbstractFor the RNA world hypothesis to be accepted, the constitutional self‐assembly of RNA will have to be demonstrated. Conceptually, the simplest route to RNA involves nucleotide polymerisation. Activated pyrimidine nucleotides can be derived from arabinose‐3‐phosphate under potentially prebiotic conditions, but the prebiotic synthesis of this sugar phosphate has not hitherto been investigated. The results of synthetic approaches involving phosphorylation, phosphate migration and 2,3‐CC bond construction are described herein.
Structural Changes and Coordinatively Unsaturated Metal Atoms on Dehydration of Honeycomb Analogous Microporous Metal–Organic Frameworks
Authors: Dietzel Pascal D. C. , Johnsen Rune E. , Blom Richard , Fjellvåg Helmer 
Published: January 2008

AbstractPorous metal–organic framework compounds with coordinatively unsaturated metal sites on the inner surface of the pores promise to be valuable adsorbents and catalyst systems, either in industrial applications or as model systems to study interactions with guest molecules. The dehydration process of two isostructural microporous coordination polymers, [M2(dhtp)(H2O)2]⋅8 H2O, termed CPO‐27‐M (M=Co, Zn; H4dhtp=2,5‐dihydroxyterephthalic acid) was investigated by in situ variable temperature X‐ray diffraction. Both compounds contain accessible coordination sites at the metal after complete removal of the solvent. However, despite the analogy of their crystal structures, they behave differently during dehydration. For CPO‐27‐Co, water desorption is a smooth topotactic process of second order with no concomitant space group change and no increase in microstrain, which is beneficial for the applicability of the material. Removal of the water propagates from the center of the channels outwards. The coordinating water molecule at the metal desorbs only when almost all the bulk water in the pores has disappeared. In contrast, discontinuities in the powder pattern of CPO‐27‐Zn indicate the occurrence of first‐order transitions. The crystal structures of four of the five individual phases could be determined. The structure of the intermediate phase occurring just before the framework is completely evacuated was elusive in respect to full structure solution and refinement, but it is most probably related to the removal of the axis of threefold symmetry. The zinc‐based material experiences a significant amount of strain.
Enantioselective oxidation of sulfides catalyzed by titanium complexes of 1,2‐diarylethane‐1,2‐diols: Effect of the aryl substitution
Authors: Superchi Stefano , Scafato Patrizia , Restaino Lina , Rosini Carlo 
Published: January 2008

AbstractThe effects of the substitution on the aryl moiety on the asymmetric oxidation of sulfides mediated by Ti‐complexes of chiral 1,2‐diarylethane‐1,2‐diols were investigated. The substitution of the aryl ring of the diol with both EWG and EDG substituents generally decreased the enantioselectivity with respect to the use of unsubstituted 1,2‐diphenylethane‐1,2‐diol (1a). Only in the presence of 1,2‐di(4‐t‐butyl)phenyl‐1,2‐diol (1g) were higher ee's obtained with aryl methyl and aryl benzyl sulfides affording ee's up to 90 and 99%, respectively. Lower ee's were achieved with larger naphthyl and aryl alkyl sulfides. Contrary to the other Ti‐alcoholates used in the oxidation of sulfides, the Ti‐complex of diol 1g was soluble in hexane, allowing us to perform the process with high enantioselectivity in this solvent, with great environmental advantages over the commonly used chlorinated solvents. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Fluorous “racemic” mixture synthesis: Polysaccharide‐based chiral columns for simultaneous demix and enantioseparation of racemic fluorous tagged compounds
Authors: Tonoi Takayuki , Zhang Wei , Curran Dennis P. , Mikami Koichi 
Published: January 2008

AbstractThe proof of concept experiments of fluorous “racemic” mixture synthesis (FRMS) is shown using polysaccharide‐based chiral stationary phases. The mixture of racemic O‐benzoylmandelate derivatives bearing different lengths of fluorous cleavable tags undergoes sequential reactions to provide individual derivatives as well as their enantiomers resolved on polysaccharide‐based chiral HPLC columns (DAICEL CHIRALCEL® and CHIRALPAK® series). Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Generation of Carrier Peptides for the Delivery of Nucleic Acid Drugs in Primary Cells
Authors: Rennert Robert , Neundorf Ines , Jahnke Heinz‐Georg , Suchowerskyj Philipp , Dournaud Pascal , Robitzki Andrea , Beck‐Sickinger Annette G. 
Published: January 2008

AbstractNow that the human genome has been decoded, the demand for novel therapeutic concepts, such as gene and stem cell therapy, is higher than ever before. Although new and better pharmaceutical agents are available, their efficient delivery to the intracellular site of action is still a serious challenge. A possible solution to this problem is the use of cell‐penetrating peptides as delivery vectors, including derivatives of human calcitonin (hCT). The aim of this study was to synthesise novel branched hCT‐derived peptides for the noncovalent delivery of nucleic acids. The uptake of the resulting oligocationic peptides into various cell lines as well as primary cells was monitored by fluorescence microscopy. To determine the appropriate peptide–plasmid charge ratios for efficient cell transfection, electromobility shift assays were carried out. Finally, flow cytometric and fluorescence microscopic studies of gene expression highlighted two novel hCT‐derived peptides as highly effective in the delivery of noncovalently complexed plasmid DNA. Thus, the absence of cytotoxicity paired with highly efficient cell internalisation and transfection rates, in primary cells as well, make both peptides powerful candidates as drug delivery vectors, especially for plasmid DNA, for both in vivo and ex vivo therapeutic applications.
Singlet states open the way to longer time‐scales in the measurement of diffusion by NMR spectroscopy
Authors: Cavadini Simone , Vasos Paul R. 
Published: January 2008

AbstractNuclear magnetic resonance is a powerful nonintrusive technique for measuring diffusion coefficients through the use of pulsed field gradients. The main limitation to the application range of this method is imposed by the relaxation time constants of the magnetization. The recently introduced singlet‐state spectroscopy affords obtaining relaxation time constants for pairs of coupled spins which can be longer by more than an order of magnitude than the spin‐lattice relaxation time constants. We review in this paper the advantages that are offered by these long relaxation time constants for diffusion measurements. Using experiments that combine singlet‐state and diffusion spectroscopy, slower diffusion constants can be determined. The coupling of the two methods constitutes an alternative to the use of special probes equipped with strong gradients for the study of large molecules that diffuse slowly in solution. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part A 32A: 68–78, 2008.
Metabolic labeling: Taking advantage of bacterial pathways to prepare spectroscopically useful isotope patterns in proteins and nucleic acids
Authors: Hoogstraten Charles G. , Johnson James E. 
Published: January 2008

AbstractUniform labeling with the stable isotopes 15N, 13C, and/or 2H is a central enabling technology for NMR studies of proteins and nucleic acids. As the field advances into structural studies of larger systems and a more detailed characterization of molecular dynamics; however, there is an increasing need for schemes that specifically introduce labels at selected molecular sites only. For many purposes, knowledge of bacterial biosynthetic pathways allows procedures to be developed that produce desired labeling patterns directly in the expression culture, rather than via laborious chemical synthesis. In this work, we review the principles and applications of such “metabolic labeling” schemes. After an overview of key metabolic and biosynthetic processes in E. coli, we discuss pioneering applications of metabolic labeling and conclude with a detailed description of the two most prominent current uses of such techniques: The introduction of hydrogen or carbon isotopes specifically at side‐chain methyl groups of proteins and the removal of one‐bond 13C‐13C dipolar couplings for spin relaxation or solid‐state structural studies via alternate‐site labeling schemes. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part A 32A: 34–55, 2008.
Effective inhibition of aromatase inhibitor‐associated bone loss by zoledronic acid in postmenopausal women with early breast cancer receiving adjuvant letrozole
Authors: Bundred Nigel J. , Campbell Ian D. , Davidson Neville , DeBoer Richard H. , Eidtmann Holger , Monnier Alain , Neven Patrick , von Minckwitz Gunter , Miller Joel C. , Schenk Nora L. , Coleman Robert E. 
Published: January 2008

AbstractBACKGROUND.Letrozole is safe and effective in postmenopausal women with estrogen receptor‐positive early breast cancer, but long‐term aromatase inhibitor use may cause bone loss and increase fracture risk. This study evaluated an immediate or delayed strategy of bone protection therapy with zoledronic acid.METHODS.A total of 1065 patients who were receiving adjuvant letrozole were randomized to immediate‐start or delayed‐start zoledronic acid (4 mg intravenously biannually for 5 years). The delayed group received zoledronic acid if lumbar spine or total hip T‐score decreased below −2.0 or when a nontraumatic fracture occurred. The primary endpoint was change in lumbar spine bone mineral density (BMD) at Month 12. Secondary endpoints included changes in total hip BMD, serum bone turnover markers, and safety at Month 12.RESULTS.Lumbar spine BMD increased from baseline in the immediate arm, while it decreased from baseline in delayed‐arm patients. At Month 12, the differences between the groups in lumbar spine and total hip BMD were 5.7% (P < .0001; 95% confidence intervals [CI], 5.2% to 6.1%), and 3.6% (P < .0001; 95% CI, 3.3 to 4.0%), respectively. Both regimens were well tolerated with few serious adverse events. Bone pain was higher in the immediate group, as expected, because some patients experienced acute‐phase reactions after zoledronic acid infusion.CONCLUSIONS.At 12 months, immediate zoledronic acid therapy prevented bone loss in postmenopausal women who were receiving adjuvant letrozole. Cancer 2008. © 2008 American Cancer Society.
Myeloperoxidase and superoxide dismutase polymorphisms are associated with an increased risk of developing pancreatic adenocarcinoma
Authors: Wheatley‐Price Paul , Asomaning Kofi , Reid Amy , Zhai Rihong , Su Li , Zhou Wei , Zhu Andrew , Ryan David P. , Christiani David C. , Liu Geoffrey 
Published: January 2008

AbstractBACKGROUND.Pancreatic cancer risk has been linked to chronic pancreatitis and periodontitis, suggesting a role for inflammation in disease etiology. Myeloperoxidase (MPO) and superoxide dismutase (SOD2) are enzymes that regulate reactive oxygen species and contain recognized single nucleotide polymorphisms (SNPs) that confer altered enzyme activity.METHODS.One hundred twenty‐two patients with pancreatic cancer and 331 age‐ and sex‐matched controls were analyzed for polymorphisms of the MPO − guanine 463 adenine (−G463A) and the SOD2 alanine (Ala)‐to‐valine (Val) polymorphism at codon 16 (Ala16Val) genes. Cases and controls were analyzed for associations between these polymorphisms, adjusting for sex, age, history of alcohol use and smoking history.RESULTS.The variant A allele of MPO −G463A was associated with a lower risk of pancreatic cancer (adjusted odds ratio [OR] for pancreatic cancer, 0.57; 95% confidence interval [95% CI], 0.4–0.9; P = .02). The SOD2 homozygous variant genotype (Val/Val) was associated with a greater risk of pancreatic cancer (adjusted OR, 1.96; 95% CI, 1.0–3.8; P = .04). Compared with individuals who carried both low‐risk alleles (A/− and Ala/−), significantly more cases than controls carried both high‐risk genotypes (G/G and Val/Val; adjusted OR, 4.31; 95% CI, 1.8–10; P = .001), or 1 high‐risk genotype (adjusted OR, 1.96; 95% CI, 1.1–3.4; P = .01).CONCLUSIONS.Polymorphisms of the inflammatory pathway genes MPO −G463A and SOD2 Ala16Val are associated with elevated pancreatic cancer risk. Oxidative stress may play an important role in pancreatic cancer carcinogenesis. Cancer 2008. © 2008 American Cancer Society.
Differential projections from subfields in the lateral preoptic area to the lateral habenular complex of the rat
Authors: Kowski Alexander B. , Geisler Stefanie , Krauss Michael , Veh Ruediger W. 
Published: January 2008

AbstractThe lateral habenular complex (LHb) constitutes an important link in the dorsal diencephalic conduction system conveying information from limbic forebrain structures to regulatory midbrain nuclei. In line with the considerable number of biological functions in which the habenula is thought to be involved, a complex subnuclear organization of the LHb has been suggested. However, the precise connectivity of habenular subnuclei remains to be identified. We hypothesize that axons from the lateral preoptic area (LPOA) project to distinct subnuclei of the LHb. As a result of an unexpected heterogeneity within the LPOA, we first examined its subregional morphology. Based on the analysis of several coronal series of sections, seven subfields were identified within the LPOA. Retrograde tracing experiments revealed that neurons projecting to the LHb were concentrated in the dorsal, ventral, and ventromedial subfields of the rostral LPOA and in the caudal LPOA. Anterograde tracing experiments confirmed that all LPOA subfields containing retrogradely labelled cells project to the LHb. Neurons in rostral subfields of the LPOA target predominantly the lateral area of the LHb, whereas caudal LPOA fibers innervate the medial LHb. Afferent labelling is most prominent within the magnocellular subnucleus in the LHbM, and only few fibers can be observed in the parvocellular subnucleus of the LHbM. The superior subnucleus of the LHbM and the oval subnucleus of the LHbL do not receive any fibers from the LPOA at all. This is the first comprehensive study so far to show that projections from LPOA subfields individually target subnuclei in the lateral habenular complex. J. Comp. Neurol. 507:1465–1478, 2008. © 2008 Wiley‐Liss, Inc.
Transient expression of the conserved zinc finger gene INSM1 in progenitors and nascent neurons throughout embryonic and adult neurogenesis
Authors: Duggan Anne , Madathany Thomas , de Castro Sandra C.P. , Gerrelli Dianne , Guddati Kumar , García‐Añoveros Jaime 
Published: January 2008

AbstractINSM1 is a zinc‐finger protein expressed in the developing nervous system and pancreas as well as in medulloblastomas and neuroendocrine tumors. With in situ hybridization combined with immunohistochemistry, we detected INSM1 mRNA in all embryonic to adult neuroproliferative areas examined: embryonic neocortex, ganglionic eminence, midbrain, retina, hindbrain, and spinal cord; autonomic, dorsal root, trigeminal and spiral ganglia; olfactory and vomeronasal organ epithelia; postnatal cerebellum; and juvenile to adult subgranular zone of dentate gyrus, subventricular zone, and rostral migratory stream leading to olfactory bulb. In most of these neurogenic areas, subsets of neuronal progenitors and nascent, but not mature, neurons express INSM1. For example, in developing cerebellum, INSM1 is present in proliferating progenitors of the outer external granule layer (EGL) and in postmitotic cells of the inner EGL, but not in mature granule cell neurons. Also, lining the neural tube from spinal cord to neocortex in mouse as well as human embryos, cells undergoing mitosis apically do not express INSM1. By contrast, nonsurface progenitors located in the basal ventricular and/or subventricular zones express INSM1. Whereas apical progenitors are proliferative and generate one or two additional progenitors, basal progenitors are thought to divide terminally and symmetrically to produce two neurons. The nematode ortholog of INSM1, EGL‐46, is expressed during terminal symmetric neurogenic divisions and regulates the termination of proliferation. We propose that, in mice and humans, INSM1 is likewise expressed transiently during terminal neurogenic divisions, from late progenitors to nascent neurons, and particularly during symmetric neuronogenic divisions. J. Comp. Neurol. 507:1497–1520, 2008. © 2008 Wiley‐Liss, Inc.
Intrinsic neurons of Drosophila mushroom bodies express short neuropeptide F: Relations to extrinsic neurons expressing different neurotransmitters
Authors: Johard Helena A.D. , Enell Lina E. , Gustafsson Elisabeth , Trifilieff Pierre , Veenstra Jan A. , Nässel Dick R. 
Published: January 2008

AbstractMushroom bodies constitute prominent paired neuropils in the brain of insects, known to be involved in higher olfactory processing and learning and memory. In Drosophila there are about 2,500 intrinsic mushroom body neurons, Kenyon cells, and a large number of different extrinsic neurons connecting the calyx, peduncle, and lobes to other portions of the brain. The neurotransmitter of the Kenyon cells has not been identified in any insect. Here we show expression of the gene snpf and its neuropeptide products (short neuropeptide F; sNPFs) in larval and adult Drosophila Kenyon cells by means of in situ hybridization and antisera against sequences of the precursor and two of the encoded peptides. Immunocytochemistry displays peptide in intrinsic neuronal processes in most parts of the mushroom body structures, except for a small core in the center of the peduncle and lobes and in the α′‐ and β′‐lobes. Weaker immunolabeling is seen in Kenyon cell bodies and processes in the calyx and initial peduncle and is strongest in the more distal portions of the lobes. We used different antisera and Gal4‐driven green fluorescent protein to identify Kenyon cells and different populations of extrinsic neurons defined by their signal substances. Thus, we display neurotransmitter systems converging on Kenyon cells: neurons likely to utilize dopamine, tyramine/octopamine, glutamate, and acetylcholine. Attempts to identify other neurotransmitter components (including vesicular glutamate transporter) in Kenyon cells failed. However, it is likely that the Kenyon cells utilize an additional neurotransmitter, yet to be identified, and that the neuropeptides described here may represent cotransmitters. J. Comp. Neurol. 507:1479–1496, 2008. © 2008 Wiley‐Liss, Inc.
Hyperchaotic signal generation via DSP for efficient perturbations to liquid mixing
Authors: Zhang Zhong , Chen Guanrong , Yu Simin 
Published: January 2008

AbstractThis paper presents the design, simulation, hardware implementation and an application in liquid mixing of some hyperchaotic circuits, based on the digital signal processing (DSP) technology. The hyperchaotic Chen's system is used as an example to show the system discretization and variable renormalization in the design process. Numerical simulation is given to verify the hardware signal generator. The implemented hardware of Chen's system generates outputs in good agreement with the numerical simulation. The hyperchaotic signal output from the DSP is applied to generate complex perturbations in liquid mixing experiments. Dye dispersion experiments show that the induced hyperchaotic motion effectively helps enhance the mixing homogeneity in the stirred‐tank‐based mixer in our laboratory. Copyright © 2008 John Wiley & Sons, Ltd.