bluuebunny/crossref_metadata_2025 huggingface dataset:
The laser-induced fluorescence spectrum, Renner–Teller effect, and molecular quantum beats in the Ã 2Πi-X̃ 2Πi transition of the jet-cooled HCCSe free radical
Authors: Hostutler David A. , He Sheng-Gui , Clouthier Dennis J.
Published: September 2004

The selenoketyl (HCCSe) radical has been positively identified for the first time as a product of an electric discharge through selenophene vapor. Laser-induced fluorescence, wavelength resolved emission, and fluorescence decay studies of jet-cooled HCCSe and DCCSe have given a detailed picture of the ground and excited state. The 418–400 nm band system of the HCCSe radical is assigned as Ã 2Πi-X̃ 2Πi and the available evidence suggests that the radical is linear in the ground state and quasilinear in the excited state. The fluorescence decays of some upper state rotational levels show field-free molecular quantum beats, ascribed to an internal conversion interaction with high vibrational levels of the ground state. A comparison of the molecular structures and bonding in the HCCX (X=O,S,Se) free radicals shows that nonlinear ground state HCCO is best described as the ketenyl radical (H–C=C=O) with the unpaired electron on the terminal carbon atom, whereas HCCS and HCCSe have linear ground state acetylenic (H–C≡C–X) structures with the unpaired electron on the heteroatom. On electronic excitation, B̃ 2Π HCCO reverts to the linear acetylenic structure, and Ã 2Π HCCS and HCCSe become quasilinear with the allenic structure.
Vibrational energy relaxation of naphthalene in the S1 state in various gases
Authors: Kimura Y. , Abe D. , Terazima M.
Published: September 2004

Time-resolved fluorescence spectra of naphthalene in the S1 state have been measured in various gases below 102 kPa. The band shape of the fluorescence changed in an earlier time region after the photoexcitation when an excess energy (3300 cm−1) above the 0-0 transition energy was given. The excitation energy dependence of the fluorescence band shape of an isolated naphthalene molecule was measured separately, and the time dependence of the fluorescence band shape in gases was found to be due to the vibrational energy relaxation in the S1 state. We have succeeded in determining the transient excess vibrational energy by comparing the time-resolved fluorescence band shape with the excitation energy dependence of the fluorescence band shape. The excess vibrational energy decayed almost exponentially. From the slope of the decay rate against the buffer gas pressure, we have determined the collisional decay rate of the excess vibrational energy in various gases. The dependence of the vibrational energy relaxation rate on the buffer gas species was similar to the case of azulene. The comparisons with the results in the low temperature argon and the energy relaxation rate in the S0 state in nitrogen were also discussed.
Photodissociation studies of CBr4+ and CBr3+ at 267 nm using ion velocity imaging
Authors: Greene Jamila R. , Francisco Joseph S. , Huang Jianhua , Xu Dadong , Jackson William M.
Published: September 2004

Time-of-flight (TOF) mass spectroscopy and ion velocity imaging were employed to study the formation and photodissociation of CBr4+ and CBr3+ ions that were observed in the TOF spectrum when a CBr4 beam was irradiated with 118 nm and 355 nm lasers. Energy dependence measurements show that both CBr4+ and CBr3+ ions depend on the fourth power of the 355 nm laser energy, which indicates that direct ionization and dissociative ionization of CBr4 have low probabilities from the state initially excited at 118 nm. This is likely due to the large geometry change in the CBr4+ ion. Two ionic fragments Br+ and CBr2+ were observed from the dissociation of CBr4+ and CBr3+ ions when another laser at 267 nm was introduced to the interaction region at a delayed time. The possible dissociation pathways and the angular and translational distributions are discussed in the paper.
Starting vortex dipoles in a viscous fluid: Asymptotic theory, numerical simulations, and laboratory experiments
Authors: Afanasyev Y. D. , Korabel V. N.
Published: September 2004

Translational velocity of the starting vortex dipoles generated by the continuous or impulsive action of a localized force is obtained theoretically on simple physical grounds. Solutions of the diffusion equation for vorticity which take into account the translational motion of fluid particles are then obtained and compared with the results of direct numerical simulations of vortex dipoles as well as with the laboratory experiments. The comparison shows good quantitative agreement in both cases. Theoretical results for the translational velocity of the three-dimensional (axisymmetric) flows such as starting jets or vortex rings are discussed as well.
On the role of van der Waals interaction in chemical reactions at low temperatures
Authors: Balakrishnan N.
Published: September 2004

It is shown that van der Waals interaction potential plays a crucial role in chemical reactions at low temperatures. By taking the Cl+HD reaction as an illustrative example, we demonstrate that quasibound states of the van der Waals potential preferentially undergo chemical reaction rather than vibrational predissociation. Prereaction occurs even when the wave functions of the quasibound states peak far out into the entrance channel, outside the region of the van der Waals well. It is found that chemical reaction dominates over nonreactive vibrational quenching in collisions of vibrationally excited HD molecules with ground state chlorine atoms at ultracold temperatures.
Comparative homology agreement search: An effective combination of homology-search methods
Authors: Alam Intikhab , Dress Andreas , Rehmsmeier Marc , Fuellen Georg
Published: September 2004

Many methods have been developed to search for homologous members of a protein family in databases, and the reliability of results and conclusions may be compromised if only one method is used, neglecting the others. Here we introduce a general scheme for combining such methods. Based on this scheme, we implemented a tool called comparative homology agreement search (chase) that integrates different search strategies to obtain a combined “Evalue.” Our results show that a consensus method integrating distinct strategies easily outperforms any of its component algorithms. More specifically, an evaluation based on the Structural Classification of Proteins database reveals that, on average, a coverage of 47% can be obtained in searches for distantly related homologues (i.e., members of the same superfamily but not the same family, which is a very difficult task), accepting only 10 false positives, whereas the individual methods obtain a coverage of 28–38%.
CO Sniffing through Heme‐based Sensor Proteins
Authors: Ascenzi Paolo , Bocedi Alessio , Leoni Livia , Visca Paolo , Zennaro Elisabetta , Milani Mario , Bolognesi Martino
Published: September 2004

O2, NO, and CO are substrates, products, and/or modulators in many enzymatic reactions including O2 respiration, denitrification, N2 fixation, and methanogenesis. Over the last decade, O2, NO, and CO have been reported to act as signaling molecules in the control of several distinct biological functions. Here, the heme‐based mechanisms of CO sensing by the bacterial homodimeric CooA and the mammalian heterodimeric NPAS2‐BMAL1 transcriptional factors are reviewed, and the signal transduction pathways are discussed.
IUBMB Life, 56: 309‐315, 2004
Induction of Drug‐metabolizing Enzymes and Transporters in Human Bronchial Epithelial Cells by Beclomethasone Dipropionate
Authors: Kuzuya Y. , Adachi T. , Hara H. , Anan A. , Izuhara K. , Nagai H.
Published: September 2004

Inhaled steroids are the most potent anti‐inflammatory therapy commonly used in bronchial asthma. There are, however, a small number of asthmatic patients who do not respond to inhaled steroid‐treatment. The stimulation of metabolism and excretion of inhaled drugs at bronchial tissues might lead to a decrease in the effect of the drugs, although the molecular mechanism of this resistance is unclear. In this study, we found that beclomethasone dipropionate (BDP) stimulated the expression of mRNAs for uridine 5'‐diphosphate glucuronosyl transferase 2B4 and 2B11, and transporters such as multidrug resistance P‐glycoprotein, multidrug resistance‐associated protein 1 and 2 in cultured bronchial epithelial cells. It is possible that the individual differences of expression of drug metabolizing enzymes and transporters and their enhancement with BDP are implicated in the individual differences of reactivity over steroid medical treatment.
IUBMB Life, 56: 355‐359, 2004
Development of Anti‐Retroviral Resistance of HIV‐1 Infected Individuals on Therapy: Is it inevitable?
Authors: Kolber Michael A. , Campo Rafael E. , Dickinson Gordon M.
Published: September 2004

Highly active antiretroviral therapy directed against HIV‐1 has dramatically modified morbidity and mortality in infected individuals. Enthusiasm for the success of these medications have been tempered by an inability to clear virus from the infected host leaving a virus poised to leverage any advantage into one of productive survival. One mechanism used to accomplish escape from suppression secondary to antiretroviral therapy is by developing mutations. The goal of therapy has been to diminish viral replication, thereby effectively abrogating the development of these resistance‐bearing mutations. This strategy has met with significant success but numerous host‐viral factors impact on the ability of the clinician to persistently suppress viral load, thereby providing a window of opportunity for the virus to mutate. In particular we review evidence for ongoing viral replication in the face of suppressive antiretroviral therapy and viral replication in tissue compartments. We discuss whether viral resistance can develop during transient elevations in viral load (viral blips) or as a function of the rate of viral load decay while on therapy. Finally, we touch on the therapeutic strategy that diminished viral replication capacity of mutational species can maintain host immunity.
IUBMB Life, 56: 301‐307, 2004
Anti‐Oxidative Response of Carbonic Anhydrase III in Skeletal Muscle
Authors: Zimmerman Un‐Jin P. , Wang Ping , Zhang Xiangming , Bogdanovich Sasha , Forster Robert E.
Published: September 2004

We propose that carbonic anhydrase III (CAIII) functions as an anti‐oxidant agent in skeletal muscle. To explore this hypothesis, we analyzed the gene expression profile of skeletal muscle in mice deficient in CAIII gene utilizing the murine genome U74Av2 set microarray. Pairwise comparison between CAIII knockout mice and their wild‐type littermates revealed that more than 500 of 12,000 genes in the array showed an altered level of transcription. Of particular note were transcriptional alterations among genes associated with the glutathione redox cycle, suggesting a possible involvement of CAIII in the glutathione‐mediated anti‐oxidant activity. We therefore investigated S‐glutathiolation and irreversible oxidation of the 2 reactive sulfhyryls of CAIII in skeletal muscle under oxidative stresses of ischemia, or exhaustive exercise. Analysis by isoelectric focusing followed by Western blot revealed that the two sulfhydryls were differentially and progressively oxidized. Brief ischemia of 10 ‐ 20 min provoked partial (one of the suflhydryls) modification of CAIII via reversible S‐glutathiolation. Protracted 60 min ischemia yielded equal amounts of both partially and completely (both sulfhydryls) modified CAIII due to irreversible oxidization. Twenty minutes of repetitive electrical stimulation, simulating exhaustive exercise, produced a mixed yield: partial modification by reversible S‐glutathiolation and complete modification by irreversible oxidation. Thus CAIII responds to oxidative stress with a distinctive sulfhydryl oxidation patterns reflecting duration and severity that may prove sensitive indices of extent and type of damage in muscle injury.
IUBMB Life, 56: 343‐347, 2004
Branched Mitochondrial Electron Transport in the Animalia: Presence of Alternative Oxidase in Several Animal Phyla
Authors: McDonald Allison E. , Vanlerberghe Greg C.
Published: September 2004

The mitochondrion of most eukaryotes has multiple electron transport components that increase the points of entry and/or exit of electrons, thus giving a branched nature to the respiratory chain. In plants and many other organisms, a prominent example is alternative oxidase, a non‐energy conserving branch in the respiratory chain and an additional terminal oxidase for the exit of electrons. Our genome database searches have now revealed the presence of alternative oxidase in four animal species from three different phyla (Mollusca, Nematoda and Chordata), consistent with frequent reports of cyanide‐resistant respiration in the Animalia. In Ciona intestinalis and Crassostrea gigas, alternative oxidase is expressed in several different tissues. Phylogenetic analysis is consistent with the animal proteins having originated by vertical inheritance. We hypothesize that alternative oxidase is likely widespread in the Animalia and discuss some of the potential role(s) for such a branched respiratory chain.
IUBMB Life, 56: 333‐341, 2004
Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection
Authors: Pandit SB , Balaji S. , Srinivasan N.
Published: September 2004

Availability of the human genome data has enabled the exploration of a huge amount of biological information encoded in it. There are extensive ongoing experimental efforts to understand the biological functions of the gene products encoded in the human genome. However, computational analysis can aid immensely in the interpretation of biological function by associating known functional/structural domains to the human proteins. In this article we have discussed the implications of such associations. The association of structural domains to human proteins could help in prioritizing the targets for structure determination in the structural genomics initiatives. The protein kinase family is one of the most frequently occurring protein domain families in the human proteome while P‐loop hydrolase, which comprises many GTPases and ATPases, is a highly represented superfamily. Using the superfamily relationships between families of unknown and known structures we could increase structural information content of the human genome by about 5%. We could also make new associations of domain families to 33 human proteins that are potentially linked to genetically inherited diseases.
IUBMB Life, 56: 317‐331, 2004
Essential and separable roles for Syndecan-3 and Syndecan-4 in skeletal muscle development and regeneration
Authors: Cornelison D.D.W. , Wilcox-Adelman Sarah A. , Goetinck Paul F. , Rauvala Heikki , Rapraeger Alan C. , Olwin Bradley B.
Published: September 2004

Syndecan-3 and syndecan-4 function as coreceptors for tyrosine kinases and in cell adhesion. Syndecan-3-/- mice exhibit a novel form of muscular dystrophy characterized by impaired locomotion, fibrosis, and hyperplasia of myonuclei and satellite cells. Explanted syndecan-3-/- satellite cells mislocalize MyoD, differentiate aberrantly, and exhibit a general increase in overall tyrosine phosphorylation. Following induced regeneration, the hyperplastic phenotype is recapitulated. While there are fewer apparent defects in syndecan-4-/- muscle, explanted satellite cells are deficient in activation, proliferation, MyoD expression, myotube fusion, and differentiation. Further, syndecan-4-/- satellite cells fail to reconstitute damaged muscle, suggesting a unique requirement for syndecan-4 in satellite cell function.
Identification of a novel telomerase repressor that interacts with the human papillomavirus type-16 E6/E6-AP complex
Authors: Gewin Lindy , Myers Hadley , Kiyono Tohru , Galloway Denise A.
Published: September 2004

The critical immortalizing activity of the human papillomavirus (HPV) type-16 E6 oncoprotein is to induce expression of hTERT, the catalytic and rate-limiting subunit of telomerase. Additionally, E6 binds to a cellular protein called E6-associated protein (E6-AP) to form an E3 ubiquitin ligase that targets p53 for proteasome-dependent degradation. Although telomerase induction and p53 degradation are separable and distinct functions of E6, binding of E6 to E6-AP strongly correlated with the induction of hTERT. Here, we demonstrate using shRNAs to reduce E6-AP expression that E6-AP is required for E6-mediated telomerase induction. A yeast two-hybrid screen to find new targets of the E6/E6-AP E3 ubiquitin ligase complex identified NFX1. Two isoforms of NFX1 were found: NFX1-123, which coactivated with c-Myc at the hTERT promoter, and NFX1-91, which repressed the hTERT promoter. NFX1-91 was highly ubiquitinated and destabilized in epithelial cells expressing E6. Furthermore, knockdown of NFX1-91 by shRNA resulted in derepression of the endogenous hTERT promoter and elevated levels of telomerase activity. We propose that the induction of telomerase by the HPV-16 E6/E6-AP complex involves targeting of NFX1-91, a newly identified repressor of telomerase, for ubiquitination and degradation.
Signaling to NF-κB
Authors: Hayden Matthew S. , Ghosh Sankar
Published: September 2004

The transcription factor NF-κB has been the focus of intense investigation for nearly two decades. Over this period, considerable progress has been made in determining the function and regulation of NF-κB, although there are nuances in this important signaling pathway that still remain to be understood. The challenge now is to reconcile the regulatory complexity in this pathway with the complexity of responses in which NF-κB family members play important roles. In this review, we provide an overview of established NF-κB signaling pathways with focus on the current state of research into the mechanisms that regulate IKK activation and NF-κB transcriptional activity.
Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor
Authors: Kato Akinori , Groisman Eduardo A.
Published: September 2004

A fundamental question in signal transduction is how an organism integrates multiple signals into a cellular response. Here we report the mechanism by which the Salmonella PmrA/PmrB two-component system responds to the signal controlling the PhoP/PhoQ two-component system. We establish that the PhoP-activated PmrD protein binds to the phosphorylated form of the response regulator PmrA, preventing both its intrinsic dephosphorylation and that promoted by its cognate sensor kinase PmrB. This results in PmrA-mediated transcription because phosphorylated PmrA exhibits higher affinity for its target promoters than unphosphorylated PmrA. A PmrD-independent form of the PmrA protein was resistant to PmrB-catalyzed dephosphorylation and promoted transcription of PmrA-activated genes in the absence of inducing signals. This is the first example of a protein that enables a two-component system to respond to the signal governing a different two-component system by protecting the phosphorylated form of a response regulator.
Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation
Authors: Flynn Julia M. , Levchenko Igor , Sauer Robert T. , Baker Tania A.
Published: September 2004

Adaptor proteins help proteases modulate substrate choice, ensuring that appropriate proteins are degraded at the proper time and place. SspB is an adaptor that delivers ssrA-tagged proteins to the AAA+ protease ClpXP for degradation. To identify new SspB-regulated substrates, we examined proteins captured by ClpXPtrap in sspB+ but not sspB- strains. RseA1-108, a fragment of a transmembrane protein that regulates the extracytoplasmic-stress response, fits this criterion. In response to stress, RseA is cleaved on each side of the membrane and is released as a cytoplasmic fragment that remains bound in an inhibitory complex with the σE transcription factor. Trapping experiments together with biochemical studies show that ClpXP functions in concert with SspB to efficiently recognize and degrade RseA1-108, and thereby releases σE. Genetic studies confirm that ClpX and SspB participate in induction of the σE regulon in vivo, acting at the final step of an activating proteolytic cascade. Surprisingly, the SspB-recognition sequence in RseA1-108 is unrelated to its binding sequence in the ssrA tag. Thus, these experiments elucidate the final steps in induction of the extracytoplasmic stress response and reveal that SspB delivers a broader spectrum of substrates to ClpXP than has been recognized.
Slik Sterile-20 kinase regulates Moesin activity to promote epithelial integrity during tissue growth
Authors: Hipfner David R. , Keller Nadine , Cohen Stephen M.
Published: September 2004

The Drosophila Sterile-20 kinase Slik promotes tissue growth during development by stimulating cell proliferation and by preventing apoptosis. Proliferation within an epithelial sheet requires dynamic control of cellular architecture. Epithelial integrity fails in slik mutant imaginal discs. Cells leave the epithelium and undergo apoptosis. The abnormal behavior of slik mutant cells is due to failure to phosphorylate and activate Moesin, which leads to excess Rho1 activity. This is distinct from Slik's effects on cell proliferation, which are mediated by Raf. Thus Slik acts via distinct pathways to coordinate cell proliferation with epithelial cell behavior during tissue growth.
Two modes of DNA double-strand break repair are reciprocally regulated through the fission yeast cell cycle
Authors: Ferreira Miguel Godinho , Cooper Julia Promisel
Published: September 2004

Several considerations suggest that levels of the two major modes of double-strand break (DSB) repair, homologous recombination (HR), and nonhomologous end joining (NHEJ), are regulated through the cell cycle. However, this idea has not been explicitly tested. In the absence of the telomere-binding protein Taz1, fission yeast undergo lethal telomere fusions via NHEJ. These fusions occur only during periods of nitrogen starvation and fail to accumulate during logarithmic growth, when the majority of cells are in G2. We show that G1 arrest is the specific nitrogen starvation-induced event that promotes NHEJ between taz1- telomeres. Furthermore, the general levels of NHEJ and HR are reciprocally regulated through the cell cycle, so that NHEJ is 10-fold higher in early G1 than in other cell cycle stages; the reverse is true for HR. Whereas NHEJ is known to be dispensable for survival of DSBs in cycling cells, we find that it is critical for repair and survival of DSBs arising during G1.
Reinvestigation of the structure of BaCuSi2O6 – evidence for a phase transition at high temperature
Authors: Sparta Karine M. , Roth Georg
Published: September 2004

Superstructure reflections have been observed in the room-temperature X-ray diffraction pattern of BaCuSi2O6, barium copper disilicate. The tetragonal structure has a fourfold unit-cell volume compared with the original structure determined by Finger et al. [(1989), Am. Mineral.
74, 952–955]. At T

s
= 610 K BaCuSi2O6 undergoes a structural phase transition upon which the superstructure reflections disappear. The description of the structure in the larger cell removes the crystal-chemical inconsistencies observed for the original structure.
X-ray diffraction and packing analysis on vintage crystals: Wilhelm Koerner's nitrobenzene derivatives from the School of Agricultural Sciences in Milano
Authors: Demartin Francesco , Filippini Giuseppe , Gavezzotti Angelo , Rizzato Silvia
Published: September 2004

The crystal structures of six nitrotoluene derivatives, synthesized by Wilhelm Koerner about a century ago and retrieved from a depository at the University of Milano, were determined. The correct assignment of molecular structures is verified. The geometry of the nitro groups and factors affecting the orientation of nitro groups with respect to the benzene ring are discussed, also using an auxiliary set of crystal structures retrieved from the Cambridge Structural Database. The crystal packings have been analyzed, and lattice energies have been calculated by atom–atom potential methods and by the newly proposed Pixel method. This method allows a more complete description of intermolecular potentials in terms of the interaction between molecular electron densities and separate Coulombic, polarization, dispersion and overlap repulsion energies. Lattice vibrations and external entropies were calculated by lattice-dynamical procedures. The results of the Pixel energy calculations allow a reliable, quantitative assessment of the relative importance of stacking interactions and hydrogen bonding in the rationalization of the recognition modes of nitrobenzene derivatives, which is impossible to attain using only qualitative atom– atom geometry concepts.
Strategies for the structure determination of endohedral fullerenes applied to the example of Ba@C74·Co(octaethylporphyrin)·2C6H6
Authors: Friese Karen , Panthöfer Martin , Wu Guang , Jansen Martin
Published: September 2004

The structure determination of endohedral fullerenes is complicated because of the high degree of disorder which may affect the different structural components, e.g. the endohedral atom/molecule, the fullerene cage and solvent molecules. Even worse, the data-to-parameter ratio and, in particular, the scattering power is low. Different strategies are employed to deal with these problems. The observed fraction of the reciprocal lattice may be increased by means of synchrotron diffraction studies. The number of parameters may be reduced by applying rigid-body refinement strategies and by restricting the displacement parameters in the framework of the TLS approach. In the first section, we will give a short overview of the structure determinations of endohedral fullerenes from single-crystal data and discuss the severe problems one may encounter. Then we will give an example of a successful structure analysis of a metal-containing endohedral fullerene, i.e. Ba@C74·Co(OEP)·2C6H6 (OEP = octaethylporphyrin). Several strategies of refinement, beyond the black box level, have been checked and compared, e.g. TLS, split-atom models, twin and single crystal models, anharmonic displacement parameters, and rigid-body models.
A crystallographic titration of the dipeptide L-isoleucyl-L-isoleucine
Authors: Görbitz Carl Henrik
Published: September 2004

The dipeptide L-Ile-L-Ile has been crystallized in four different protonation states, including as a cation, a zwitterion and an anion, as well as a dimeric cation in which two peptide molecules, linked by a strong –COO...H...OOC– hydrogen bond, share an overall positive charge of +1. This unprecedented series of crystal structures exhibits differences in hydrogen-bonding capabilities, conformational properties and molecular packing arrangements. The crystallization of L-Ile-L-Ile as an anion was achieved by slow evaporation from an NH3(l) solution to give the first ever ammonium salt of a peptide (or amino acid).
Isostructurality in one and two dimensions: isostructurality of polymorphs
Authors: Fábián László , Kálmán Alajos
Published: September 2004

A set of polymorphic crystal structures was retrieved from the Cambridge Structural Database in order to estimate the frequency of isostructurality among polymorphs. Altogether, 50 structures, the polymorphs of 22 compounds, were investigated. It was found that one-, two- or three-dimensional isostructurality is exhibited by approximately half of the compounds analyzed. Among the isostructural polymorphs, the frequency of one-, two- and three-dimensional isostructurality is similar. From the examples, it appears that three-dimensional isostructurality is connected to the gradual ordering of crystal structures, while one- and two-dimensional isostructurality can often be related to specific packing interactions. The possibility of many similar interactions seems to decrease the probability of the occurrence of isostructural polymorphs. Conformational polymorphs do not exhibit isostructurality.
Structures of FeII spin-crossover complexes from synchrotron powder-diffraction data
Authors: Dova Eva , Peschar René , Sakata Makoto , Kato Kenichi , Stassen Arno F. , Schenk Henk , Haasnoot Jaap G.
Published: September 2004

Crystal structure determination and analysis have been carried out for the two spin-crossover compounds [Fe(teeX)6](BF4)2 (teeX is haloethyltetrazole; X = I: teei; X = Br: teeb), in both their high-spin (near 300 K) and their low-spin states (T = 90 K), using high-resolution powder-diffraction data collected at the ESRF (Grenoble, France) and SPring8 (Japan) synchrotron radiation facilities. The structures of teei have been solved using various direct-space structure determination techniques (grid search, genetic algorithm and parallel tempering) and refined with the Rietveld method using geometrical restraints. In the case of teeb, a structural model was found but a full refinement was not successful because of the presence of a significant amount of an amorphous component. Analysis of the structures (space group P21/c, Z = 2) and diffraction data, and the absence of phase transitions, show the overall structural similarity of these compounds and lead to the conclusion that the gradual spin-crossovers are likely to be accompanied by small structural changes only.
Torsional vibration and central bond length of N-benzylideneanilines
Authors: Harada Jun , Harakawa Mayuko , Ogawa Keiichiro
Published: September 2004

The crystal structures of N-benzylideneaniline (1), N-benzylidene-4-carboxyaniline (2), N-(4-methylbenzylidene)-4-nitroaniline (3), N-(4-nitrobenzylidene)-4-methoxyaniline (4), N-(4-nitrobenzylidene)-4-methylaniline (5), N-(4-methoxybenzylidene)aniline (6) and N-(4-methoxybenzylidene)-4-methylaniline (7) were determined by X-ray diffraction analyses at various temperatures. In the crystal structures of all the compounds, an apparent shortening of the central C=N bond was observed at room temperature. As the temperature was lowered, the observed bond lengths increased to approximately 1.28 Å at 90 K, irrespective of substituents in the molecules. The shortening and the temperature dependence of the C=N bond length are interpreted in terms of an artifact caused by the torsional vibration of the C—Ph and N—Ph bonds in the crystals. In the crystal structures of (1) and (7), a static disorder around the C=N bond was observed, which is also responsible for the apparent shortening of the C=N bond.
Distribution of molecular centres in unit cells with respect to packing patterns
Authors: Pidcock Elna , Motherwell W. D. Sam
Published: September 2004

Packing patterns, a new description of the limited number of possible arrangements of molecular building blocks in a unit cell, were assigned to many thousands of structures belonging to the space groups P21/c, P\bar 1, P212121, P21 and C2/c [Pidcock & Motherwell (2004). Cryst. Growth. Des.
4, 611–620]. The position of the molecular centre (in fractional coordinates) in the unit cell for these structures has been surveyed, with respect to the space group and the packing pattern. The results clearly show that the position at which the molecular centre is found in the unit cell is correlated with the packing pattern. The relationships between the orientation of the packing pattern in the unit cell and the symmetry operators of the space group are explored. Popular orientations of packing patterns within the unit cell are given.
Temperature dependence of the crystal structure of 3,5-di-tert-butylpyrazole from 10 K
Authors: Sobolev Alexandre N. , White Allan H.
Published: September 2004

A single crystal of 3,5-di-tert-butylpyrazole has been the subject of structure determinations at 10, 100, 120 and 299 K. Above ∼ 110 K, the structure is Pbca, a ≃ 11.3, b ≃ 20.6, c ≃ 10 Å, Z = 8. Below 110 K, the c axis is doubled and the space group becomes Pb21
a, Z = 16. Here the asymmetric unit is comprised of four molecules, arranged as a pair of overlapping hydrogen-bonded dimers, all components being ordered. In each case one methyl group of each t-butyl group lies coplanar with its parent pyrazole ring and, within each quasi-inversion-related dimer, one molecule has both of these methyl groups directed away from the N2 component `cis', while in the other, one methyl group is toward (`trans'). Above 110 K the four molecules collapse into one, with one t-butyl group (corresponding to an overlaid `cis/trans' pair of the low-temperature form) modelled as disordered. The disorder has been previously described as `temperature dependent' (Deacon et al., 2001), but the present studies suggest it to be dependent on the history of the particular specimen as well.
Structures of three salts of phthalic acid; variation in crystal packing and geometry of the hydrogen phthalate ion
Authors: Langkilde Annette , Madsen Dennis , Larsen Sine
Published: September 2004

The hydrogen-bond patterns in hydrogen phthalates (HP) have been elucidated by the determination of the crystal structures of hydrogen phthalate salts of [Mg(H2O)4-(CH3OH)2]2+, 2-(2′-pyridylamine)pyridinium and diethylammonium. The stoichiometry of the latter salt corresponds to a hydrogen phthalate salt; however, it contains the phthalic acid in its three possible acid–base forms. The hydrogen phthalate ions in the three salts display the two common hydrogen-bonding motifs. One has a very short intramolecular O—H—O hydrogen bond (Intra-H), as seen in the magnesium salt [O...O 2.397 (2) Å]. In the other two salts the hydrogen phthalate ions are connected by hydrogen bonds into infinite chains (Chain-H) with O...O distances of 2.460 (1) Å in the diethylamine salt and 2.610 (1) Å in the 2,2′-dipyridylamine salt. This difference in hydrogen-bond pattern was further elucidated by a search in the Cambridge Structural Database for other hydrogen phthalate salts. Intra-H possesses the shortest O...O distances and an almost planar hydrogen phthalate ion, whereas the hydrogen phthalate ions show significantly more variation in the Chain-H salts. The two hydrogen-bonding motifs are reflected in the molecular geometry of the hydrogen phthalate ion.
Conformational analysis: crystallographic, molecular mechanics and quantum chemical studies of C—H...O hydrogen bonding in the flexible bis(nosylate) derivative of catechol
Authors: Munro Orde Quentin , Mariah Lynette
Published: September 2004

The single-crystal X-ray diffraction analysis of 2-{[(4-nitrophenoxy)sulfonyl]oxy}phenyl 4-nitrophenyl sulfate (4) reveals that an interesting intermolecular or extended structure (a one-dimensional hydrogen-bonded polymer) is formed because of pairs of intermolecular (aryl)C—H...O(nitro) hydrogen bonds between the C
2 symmetry monomer units. The axis of the hydrogen-bonded polymer runs co-linear with the [101] face diagonal of the monoclinic unit cell. Molecular mechanics calculations using a modified version of the MM+ force field and a random conformational search algorithm have been used to locate the important low-energy in vacuo conformations of (4). The MM-calculated conformation of (4) that most closely matches the X-ray structure lies some 26.5 kJ mol−1 higher in energy than the global minimum-energy conformation, consistent with the notion that the crystallographically observed molecular architecture of (4) is a local energy minimum in the absence of its crystal lattice environment. Since the X-ray conformation of (4) was correctly calculated only when all of the neighbouring molecules in the crystal lattice were included in the simulation, hydrogen bonding and other non-bonded interactions in the crystal lattice clearly dictate the experimentally observed conformation of (4). Quantum chemical calculations (AM1 method) confirm the critical role played by the intermolecular (aryl)C—H...O(nitro) hydrogen bonds in controlling the crystallographically observed conformation of (4) and show that self-recognition in this system by hydrogen bonding is favoured on electrostatic grounds. Collectively, the molecular simulations suggest that because the lowest-energy molecular conformation of (4) does not permit the formation of an extended hydrogen-bonded `supramolecular' structure, it is not the preferred conformation in the crystalline solid state.
A common aberration with water‐immersion objective lenses
Authors: ARIMOTO R. , MURRAY J. M.
Published: September 2004

We describe here an aberration that is frequently encountered with water‐immersion but not oil‐immersion objectives. The aberration is shown to be induced by tilt of the coverslip out of the plane normal to the optical axis. Model calculations taking into account the path‐length distortions introduced by a tilted coverslip satisfactorily reproduce the observed effect on the images of small subresolution fluorescent beads.
Quantification of micrometre‐sized porosity in quasicrystals using coherent synchrotron radiation imaging
Authors: AGLIOZZO S. , CLOETENS P.
Published: September 2004

Phase contrast radiography has been applied to investigate porosity in the bulk of quasicrystals. The pores act on X‐rays as lenses, leading to drastic changes in the phase contrast images of pores. Depending on the recording conditions and pore features, different imaging regimes are accessed. The variation of the contrast makes the direct characterization of pores from image data, in terms of a precise determination of their size and volume, unreliable. The contrast in Fresnel diffraction images of pores was thus investigated with the support of numerical simulations. A phase retrieval procedure was carried out in order to obtain the correct information from the pore images.
Viability of endolithic micro‐organisms in rocks from the McMurdo Dry Valleys of Antarctica established by confocal and fluorescence microscopy
Authors: WIERZCHOS J. , DE LOS RÍOS A. , SANCHO L. G. , ASCASO C.
Published: September 2004

The rocks of the McMurdo Dry Valleys desert in Antarctica harbour endolithic communities of micro‐organisms such as lichens, fungi, cyanobacteria and bacteria. Establishing the physiological status and viability of these microbial colonies in their natural microhabitat has far‐reaching implications for understanding the microbial ecology of the harsh environment of this polar desert. Here we describe the use of confocal microscopy and a specific fluorescent probe (FUN‐1) to evaluate the metabolic activity of fungal cells. Application of confocal microscopy also served to identify living and dead bacteria or cyanobacteria using the fluorescent assay reagents Live/Dead SYTO 9 and propidium iodide or SYTOX Green, respectively. In addition, through the use of epifluorescence microscopy, live/dead bacteria and cyanobacteria could be detected by estimating fluorescence from their cell components provoked by simultaneously staining with nucleic acids stains such as DAPI and SYTOX Green.
Cytopathological changes induced by selected Brazilian flaviviruses in mouse macrophages
Authors: BARROS V. E. D. , THOMAZINI J. A. , FIGUEIREDO L. T. M.
Published: September 2004

Scanning and transmission electron microscopy were used to analyse the ultrastructure of peritoneal mouse macrophage cells infected with Brazilian flavivirus (yellow fever, Rocio, Bussuquara and Saint Louis encephalitis viruses). Macrophage cells collected 3 days after viral infection had a flattened shape, with an increased number of large spikes of cytoplasm prolongations, giving an appearance of hairy cells. Cytopathological changes to the macrophage cells were similar regardless of the infecting flavivirus. Rough and smooth endoplasmic reticulum of the macrophage cells infected with flavivirus were abundant, hypertrophic and enlarged. A large number of free ribosomes were seen in the cytoplasm of these infected cells. Spherical particles approximately 50–70 nm in diameter, some of which were empty, were observed in the cytoplasm, generally inside vesicles. These particles probably correspond to viral particles.
Image calibration in fluorescence microscopy
Authors: ZWIER J. M. , VAN ROOIJ G. J. , HOFSTRAAT J. W. , BRAKENHOFF G. J.
Published: September 2004

A fluorescence image calibration method is presented based on the use of standardized uniformly fluorescing reference layers. It is demonstrated to be effective for the correction of non‐uniform imaging characteristics across the image (shading correction) as well as for relating fluorescence intensities between images taken with different microscopes or imaging conditions. The variation of the illumination intensity over the image can be determined on the basis of the uniform bleaching characteristics of the layers. This permits correction for the latter and makes bleach‐rate‐related imaging practical. The significant potential of these layers for calibration in quantitative fluorescence microscopy is illustrated with a series of applications. As the illumination and imaging properties of a microscope can be evaluated separately, the methods presented are also valuable for general microscope testing and characterization.
Watching molecular processes with the atomic force microscope: dynamics of polymer adsorption and desorption at the single molecule level
Authors: GUNNING A. P. , KIRBY A. R. , MACKIE A. R. , KROON P. , WILLIAMSON G. , MORRIS V. J.
Published: September 2004

The formation of networks is an important step in the synthesis of many biological assemblies. For example, during the synthesis of plant cell walls the factors which dictate the arrangement of the polymeric constituents that make up the cell wall are not yet understood. Factors such as site‐directed binding provide a possible theoretical background for beginning to understand the assembly of complex biological structures, but modelling of this process is difficult, time consuming and lacks experimental methods for verification. Through the use of atomic force microscopy (AFM) it has been demonstrated that changes in the binding of a single heterogeneous cell wall polysaccharide to a charged substrate can be followed in real time. Furthermore, subsequent image analysis allows the probability of binding of the molecule to be mapped to produce a real data set which is comparable with those obtained in simulation studies. In addition, these AFM studies have provided new mechanistic clues to the adsorption/desorption process of this polysaccharide.
Design‐based estimation of surface area in thick tissue sections of arbitrary orientation using virtual cycloids
Authors: GOKHALE A. M. , EVANS R. A. , MACKES J. L. , MOUTON P. R.
Published: September 2004

Surface area is a first‐order stereological parameter with important biological applications, particularly at the intersection of biological phases. To deal with the inherent anisotropy of biological surfaces, state‐of‐the‐art design‐based methods require tissue rotation around at least one axis prior to sectioning. This paper describes the use of virtual cycloids for surface area estimation of objects and regions in thick, transparent tissue sections cut at any arbitrary (convenient) orientation. Based on the vertical section approach of Baddeley et al., the present approach specifies the vertical axis as the direction of sectioning (i.e. the direction perpendicular to the tissue section), and applies computer‐generated cycloids (virtual cycloids) with their minor axis parallel to the vertical axis. The number of surface‐cycloid intersections counted on focal planes scanned through the z‐axis is proportional to the surface area of interest in the tissue, with no further assumptions about size, shape or orientation. Optimal efficiency at each x–y location can be achieved by three virtual cycloids orientated with their major axes (which are parallel to the observation planes) mutually at an angle of 120°. The major practical advantage of the present approach is that estimates of total surface area (S) and surface density (SV) can be obtained in tissue sections cut at any convenient orientation through the reference space.
Phase‐retrieved pupil functions in wide‐field fluorescence microscopy
Authors: HANSER B. M. , GUSTAFSSON M. G. L. , AGARD D. A. , SEDAT J. W.
Published: September 2004

Pupil functions are compact and modifiable descriptions of the three‐dimensional (3D) imaging properties of wide‐field optical systems. The pupil function of a microscope can be computationally estimated from the measured point spread function (PSF) using phase retrieval algorithms. The compaction of a 3D PSF into a 2D pupil function suppresses artefacts and measurement noise without resorting to rotational averaging. We show here that such ‘phase‐retrieved’ pupil functions can reproduce features in the optical path, both near the sample and in the microscope. Unlike the PSF, the pupil function can be easily modified to include known aberrations, such as those induced by index‐mismatched mounting media, simply by multiplying the pupil function by a calculated aberration function. PSFs calculated from such a modified pupil function closely match the corresponding measured PSFs collected under the aberrated imaging conditions. When used for image deconvolution of simulated objects, these phase‐retrieved, calculated PSFs perform similarly to directly measured PSFs.
Optical microscopy of isothermally decomposed β copper based SM alloys
Authors: CASTRO M. L. , ROMERO R.
Published: September 2004

The usefulness of two etching procedures for revealing the microstructural features in thermal treated beta copper‐based SM alloys is shown. Colour etching is used to improve the detection of the phases and achieve a higher accuracy in their identification.
A Late Mesolithic Hunting Station at Agernæs, Fyn, Denmark
Authors: Richter Jane , Noe-Nygaard Nanna
Published: September 2004

The Late Ertebølle hunting site from Agernæs, Fyn/Funen, Denmark, around 4200 cal yrs BC (51–5600 14C yr BP), has yielded a total of 32 animal species. They include eight species of fur animals comprising pine marten, polecat, wolf, fox, domestic dog, lynx, wild cat and otter. Neonatal red deer and roe deer were apparently only hunted for their skins. Animals hunted for consumption comprise aurochs, wild boar, adult red deer and roe deer. The season of activity is determined by the presence of newborn red deer, roe deer, piglets of wild boar and the time of skinning of the pine marten. The biometrical data from red deer, roe deer and wild boar indicate free migration between the island of Fyn and the mainland, Jylland/Jutland.

The inhabitants of the site seem to have been highly focused on the hunting of fur animals. Pine marten has been a major target with 33 individuals. Specialized hunting strategies have further been applied. Bones from 10 species indicate that the main animal food source was terrestrial, while the isotope data from man and dog indicate a dominant marine diet. It is thus likely that Agernæs was a hunting station, and represents a specialized site, indicating that economic differentiation already was in progress. The termination of the Late Atlantic climatic optimum (8000–5000 14C BP), radical changes of the forested landscape during the elm decline, and diversification of economic activities may have created the foundation for the introduction of domestic animals only a few hundred years later than the habitation of the Agernæs site. The main habitation period of the site appears to fall between the Late Atlantic and the Subboreal Littorina transgression by comparison with data from the Littorina-transgressions of Sjælland/Zealand at Vedbæk, Storebælt, Trundholm Mose, Troldestuen, and Tengslemark.