bluuebunny/crossref_metadata_2025 huggingface dataset:
Ciprofloxacin enhances the stimulation of matrix metalloproteinase 3 expression by interleukin‐1β in human tendon‐derived cells
Authors: Corps Anthony N. , Harrall Rebecca L. , Curry Valerie A. , Fenwick Steven A. , Hazleman Brian L. , Riley Graham P.
Published: November 2002

Objective

To determine whether the fluoroquinolone antibiotic ciprofloxacin, which can cause tendon pain and rupture in a proportion of treated patients, affects the expression of matrix metalloproteinases (MMPs) in human tendon‐derived cells in culture.

Methods

Cell cultures were derived from 6 separate tendon explants, and were incubated in 6‐well culture plates for 2 periods of 48 hours each, with ciprofloxacin (or DMSO in controls) and interleukin‐1β (IL‐1β), alone and in combination. Samples of supernatant medium from the second 48‐hour incubation were assayed for MMPs 1, 2, and 3 by Western blotting. RNA was extracted from the cells and assayed for MMP messenger RNA (mRNA) by semiquantitative reverse transcription–polymerase chain reaction, with normalization for GAPDH mRNA.

Results

Unstimulated tendon cells expressed low or undetectable levels of MMP‐1 and MMP‐3, and substantial levels of MMP‐2. IL‐1β induced a substantial output of both MMP‐1 and MMP‐3 into cell supernatants, reflecting increases (typically 100‐fold) in MMP mRNA, but had only minor effects on MMP‐2 expression. Ciprofloxacin had no detectable effect on MMP output in unstimulated cells. Preincubation with ciprofloxacin potentiated IL‐1β–stimulated MMP‐3 output, reflecting a similar effect on MMP‐3 mRNA expression. Ciprofloxacin also potentiated IL‐1β–stimulated MMP‐1 mRNA expression, but did not potentiate the output of MMP‐1, and had no significant effects on MMP‐2 mRNA expression or output.

Conclusion

Ciprofloxacin can selectively enhance MMP expression in tendon‐derived cells. Such effects might compromise tendon microstructure and integrity.
Replicative aging of human articular chondrocytes during ex vivo expansion
Authors: Parsch Dominik , Brümmendorf Tim H. , Richter Wiltrud , Fellenberg Jörg
Published: November 2002

Objective

To investigate the contribution of clinical ex vivo expansion protocols to replicative aging of human chondrocytes.

Methods

Primary human chondrocytes were cultured as monolayers after isolation from 7 articular cartilage specimens. Cells were passaged corresponding to 12–19 cell population doublings (cpd). Aliquots of the cells were collected from each passage and analyzed for telomere length and telomerase activity.

Results

The rate of telomere shortening was heterogeneous, ranging from 147 to 431 bp/cpd (mean ± SD 305 ± 122). Telomerase activity was detected at various time points during passaging in 5 of 7 primary chondrocytes analyzed, but not in native human articular cartilage specimens. According to our data, an 8–10‐fold (∼3 cpd) ex vivo expansion of articular chondrocytes, as typically performed for transplantation procedures, leads to telomere erosion in the range of 900 bp. This is comparable with 30 years of aging based on the in vivo rate of telomere shortening of 30 bp/year recently found in chondrocytes.

Conclusion

If telomere shortening is an important determinant of aging in human articular cartilage, an additional telomere loss due to ex vivo expansion might affect the incidence or time of onset of age‐related cartilage disorders. However, given the limited extent of expansion performed in the clinical setting to date, a significant telomere‐mediated increase in the risk of malignant transformation or replicative exhaustion of the transplanted cells seems unlikely.
Access to health care in a system transition: the case of Bulgaria
Authors: Balabanova Dina , McKee Martin
Published: November 2002

Objective

Throughout the 1990s, the Soviet‐style model in central and eastern Europe that provided free health services has been subject to radical reforms. Socio‐economic inequalities have also increased but there is little information on inequalities in health care utilization. This paper examines the pattern of illness behaviour in Bulgaria, seeking evidence of inequalities in access to services and eliciting users' pathways to care.

Design

Analysis drew on a representative population survey in Bulgaria (1997). The financial determinants of service use were tested in a multivariate model adjusted first for age, and then for age, marital status and self‐reported health. In‐depth interviews with users and providers addressed pathways to care, use of connections and other informal strategies to obtain care.

Results

As expected, rates of illness vary with income, with highest rates among the poor. After adjustment for illness, consultation rates are relatively equal across income levels, with the exception of worse‐off women who tend to consult more. For first contact, there are few differences according to income, with the better off preferring secondary level. Pathways slightly differ, with women more often treated in primary care. Private sector utilization is low. Qualitative research reveals well‐established strategies to obtain more advanced care, including use of connections, informal payments and use of emergency services.

Conclusions

An apparent lack of inequalities in access to care conceals a more complex picture in which income and gender influence the pathways taken through the system. Copyright © 2000 John Wiley & Sons, Ltd.
Structural determination and complete NMR spectral assignments of a new bufadienolide glycoside
Authors: Ye Min , Han Jian , Guo Hongzhu , Guo Dean
Published: November 2002

The structure of a new bufadienolide glycoside, cinobufagin 3‐O‐β‐D‐glucoside, was determined by extensive 1D and 2D NMR techniques (1H, 13C, DEPT, COSY, HSQC, g‐HMBC and NOESY). The complete assignments of the 13C and 1H spectral data were also carried out. Copyright © 2002 John Wiley & Sons, Ltd.
Locally anisotropic motion in a macroscopically isotropic system: displacement correlations measured using double pulsed gradient spin‐echo NMR
Authors: Callaghan P. T. , Komlosh M. E.
Published: November 2002

We propose a novel application of double pulsed gradient spin‐echo NMR in which two pairs of gradient pulses are used successively to encode the spin magnetization. These pairs were applied with gradient directions collinear and orthogonal, and the results were compared. The method can be used to detect local diffusion anisotropy even when the distribution of domain directors in the sample is isotropic. The degree of the difference between collinear and orthogonal echo attenuation responses indicates the nature of that local anisotropy. We applied this method to a polydomain lyotropic liquid crystal system, Aerosol OT–water, and detected the local diffusion anisotropy directly. Copyright © 2002 John Wiley & Sons, Ltd.
Probing interactions within complex colloidal systems using PGSE‐NMR
Authors: Griffiths P. C. , Cheung A. Y. F. , Davies J. A. , Paul A. , Tipples C. N. , Winnington A. L.
Published: November 2002

Pulsed‐gradient spin‐echo NMR (PGSE‐NMR) has evolved into a powerful technique for probing colloidal structure, particularly that of complex mixtures. Indeed, with the exception perhaps of neutron scattering, no single technique has such universal applicability. The parameter of interest, the (self‐) diffusion coefficient, is of fundamental importance as it is determined by both the chemistry of the system—the size and shape of the individual molecular species—and its physical environment/state—dissolved, dispersed, aggregated, constrained within boundaries, etc. Understanding such behaviour is of central importance in the biological and colloidal fields. The basis of using diffusion as a probe of such systems relies on the fact that each species in a mixture can be separated by differences in their diffusion coefficient and/or by the chemical specificity of NMR. Binding, aggregation and structure elucidation studies have undergone a renaissance in the last decade owing to the increased commercial availability of hardware and improved data processing. This paper highlights just a few of the many and diverse applications to which PGSE‐NMR can be put. Copyright © 2002 John Wiley & Sons, Ltd.
HR‐DOSY experiments with radiofrequency field gradients (RFG) and their processing according to the HD method
Authors: Mouro C. , Mutzenhardt P. , Diter B. , Canet D.
Published: November 2002

The usual method for probing translational motions is the pulsed gradient spin‐echo (PGSE) experiment introduced by Stejskal and Tanner. It employs gradients of the static magnetic field. Most of the drawbacks from which this basic experiment suffers have been successfully circumvented by several modifications and compensations. Thus, it is now possible to obtain very clean experimental results amenable to optimal data processing so that they can be presented as 2D (or 3D) diffusion ordered spectra (DOSY). In first part of this paper, it is shown that radiofrequency field gradients (RFG) are immune to the drawbacks inherent to the basic PGSE sequence, and can give clean, high‐resolution diffusion data in a straightforward manner. In the second part, an alternative data processing method for reconstructing DOSY spectra based on the Hankel diagonalization (HD) is introduced. Copyright © 2002 John Wiley & Sons, Ltd.
Core–annular flow in a periodically constricted
circular tube. Part 2. Nonlinear dynamics
Authors: KOURIS CHARALAMPOS , TSAMOPOULOS JOHN
Published: November 2002

Nonlinear dynamics of the concentric, two-phase flow of two immiscible fluids in
a circular tube of variable cross-section is studied for parameter values where the
steady core–annular flow (CAF) is linearly unstable. The simulations are based on
a pseudo-spectral numerical method. They are carried out assuming axial symmetry,
that the total flow rate remains constant and that all dependent variables are periodic
in the axial direction, which includes the minimum necessary number of repeated units
so that the obtained solution is independent of this number. The time integration
originates with the numerically computed steady CAF or the steady CAF seeded
with either the most unstable mode or random small disturbances. Only a limited
number of the most interesting cases are presented. For the most part, the values
of the majority of the dimensionless parameters are such that oil flows in the centre
of the tube driven by an applied pressure gradient against gravity, whereas water
is flowing in the annulus. It is shown that, whereas the steady (unstable) solution
may indicate that the heavier water flows countercurrently with respect to the oil,
the time periodic (observable) solution may indicate the same, albeit at a much
smaller core flow rate or that concurrent flow occurs. This is due to the water being
trapped between the large-amplitude interfacial waves that are generated and being
convected by the oil. It is also shown that increasing the inverse Weber number
increases the wave amplitude to the point that the flow of the core fluid may become
discontinuous with a mechanism that depends on the viscosity ratio between the
two fluids. Increasing the amplitude of the sinusoidal variation of the tube leads to
a combination of travelling and standing waves, which interact to produce a time
periodic solution with a long period associated with the time it takes the travelling
wave to travel through the computational domain and a second much shorter period
that is related to their interaction time. Qualitative agreement has been obtained upon
comparing our numerical simulations with limited experimental reports, even though
the experimental conditions were not identical to those in our model.
Zonal flow driven by strongly supercritical
convection in rotating spherical shells
Authors: CHRISTENSEN U. R.
Published: November 2002

Thermal convection in a rotating spherical shell with free-slip boundaries can excite a
dominant mean zonal flow in the form of differentially rotating cylinders concentric to
the principal rotation axis. This process is studied numerically for Prandtl numbers of
order 1, Ekman numbers in the range E = 3 × 10−4−10−5, and Rayleigh numbers up
to 100×
critical. Small-scale convection transfers kinetic energy into the mean zonal
flow via Reynolds stresses. For low Ekman number and high Rayleigh number, the
force balance is predominantly among the Coriolis, inertial and buoyancy forces, and
viscosity plays a minor role. A modified Rayleigh number Ra* is introduced, which
does not depend on viscosity or thermal diffusivity, and asymptotic scaling laws
for the dependence of various properties on Ra* in the limit of negligible viscosity
(E → 0) are estimated from the numerical results. The ratio of kinetic energy in
the zonal flow to that in the non-zonal (convective) flow increases strongly with
Ra* at low supercritical Rayleigh number, but drops at high values of Ra*. This is
probably caused by the gradual loss of geostrophy of the convective columns and
a corresponding decorrelation of Reynolds stresses. Applying the scaling laws to
convection in the molecular hydrogen envelopes of the large gas planets predicts the
observed magnitude of the zonal winds at their surfaces.
Expression of Fas, p53 and AFP in development of human fetal germ cells in vitro
Authors: Wu Ji , Chen Yi , Li Tan
Published: November 2002

In the present study we employed a two-step culture system to study the expression of Fas, p53 and alpha-fetoprotein (AFP) in the development in vitro of human fetal germ cells. p53 mRNA was determined by Northern blotting, and Fas content was assessed by western blotting. RT-nested polymerase chain reaction (RT-nPCR) analysis was performed to determine the expression of AFP mRNA in different stages of fetal follicular development. Follicular cell apoptosis was evaluated by DNA fragmentation analyses (DNA ladder). The results showed that by day 7 of culture approximately one-sixth of fetal germ cells grew to class C oocytes (primary oocytes) from class B oocytes (primordial oocytes) or class A oocytes. On day 45 of culture, one-third of these primary follicles doubled in size. In the meantime, there was a high proportion apoptosis of follicular cells on days 35 or 45 of culture, as evident by a clear ladder pattern of DNA fragmentation upon electrophoretic analysis. Expression of Fas antigen and p53 mRNA increased in a time-dependent manner, while AFP mRNA was expressed on days 10 to 35, and disappeared on day 45. These results indicate that human fetal germ cells can develop in a two-step culture system and AFP may play an active role in the proliferation of these germ cells. At the late stage of follicular development in vitro, a number of follicular cells became apoptotic. Moreover, apoptosis may be the mechanism responsible for fetal germ cell regression and the Fas antigen and/or p53-mediated death pathway may be central in the induction of germ cell regression.
The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection
Authors: Feng Yanan , Vickers Timothy A. , Cohen Stanley N.
Published: November 2002

RNase E, a multifunctional endoribonuclease of
Escherichia coli
, attacks substrates at highly specific sites. By using synthetic oligoribonucleotides containing repeats of identical target sequences protected from cleavage by 2′-
O
-methylated nucleotide substitutions at specific positions, we investigated how RNase E identifies its cleavage sites. We found that the RNase E catalytic domain (i.e., N-Rne) binds selectively to 5′-monophosphate RNA termini but has an inherent mode of cleavage in the 3′ to 5′ direction. Target sequences made uncleavable by the introduction of 2′-
O
-methyl-modified nucleotides bind to RNase E and impede cleavages at normally susceptible sites located 5′ to, but not 3′ to, the protected target. Our results indicate that RNase E can identify cleavage sites by a 3′ to 5′ “scanning” mechanism and imply that anchoring of the enzyme to the 5′-monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive or quasiprocessive mode. In contrast, we find that RNase G, which has extensive structural homology with and size similarity to N-Rne, and can functionally complement RNase E gene deletions when overexpressed, has a nondirectional and distributive mode of action.
Dobzhansky–Muller incompatibilities in protein evolution
Authors: Kondrashov Alexey S. , Sunyaev Shamil , Kondrashov Fyodor A.
Published: November 2002

We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, ≈10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky–Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only ≈10 steps between successive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that substitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a particular CPD.
The Usher syndrome proteins cadherin 23 and harmonin form a complex by means of PDZ-domain interactions
Authors: Siemens Jan , Kazmierczak Piotr , Reynolds Anna , Sticker Melanie , Littlewood-Evans Amanda , Müller Ulrich
Published: November 2002

Usher syndrome type 1 (USH1) patients suffer from sensorineuronal deafness, vestibular dysfunction, and visual impairment. Several genetic loci have been linked to USH1, and four of the relevant genes have been identified. They encode the unconventional myosin VIIa, the PDZ-domain protein harmonin, and the putative adhesion receptors cadherin 23 (CDH23) and protocadherin 15 (PCDH15). We show here that CDH23 and harmonin form a protein complex. Two PDZ domains in harmonin interact with two complementary binding surfaces in the CDH23 cytoplasmic domain. One of the binding surfaces is disrupted by sequences encoded by an alternatively spliced CDH23 exon that is expressed in the ear, but not the retina. In the ear, CDH23 and harmonin are expressed in the stereocilia of hair cells, and in the retina within the photoreceptor cell layer. Because CDH23-deficient mice have splayed stereocilia, our data suggest that CDH23 and harmonin are part of a transmembrane complex that connects stereocilia into a bundle. Defects in the formation of this complex are predicted to disrupt stereocilia bundles and cause deafness in USH1 patients.
The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus
Authors: Nandhagopal Narayanasamy , Simpson Alan A. , Gurnon James R. , Yan Xiadong , Baker Timothy S. , Graves Michael V. , Van Etten James L. , Rossmann Michael G.
Published: November 2002

Paramecium bursaria Chlorella
virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-Å resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel β-barrel, “jelly-roll” domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-Å diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.
The A14–A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4–Rpb7 pol II subunits
Authors: Peyroche Gérald , Levillain Erwann , Siaut Magali , Callebaut Isabelle , Schultz Patrick , Sentenac André , Riva Michel , Carles Christophe
Published: November 2002

A43, an essential subunit of yeast RNA polymerase I (pol I), interacts with Rrn3, a class I general transcription factor required for rDNA transcription. The pol I–Rrn3 complex is the only form of enzyme competent for promoter-dependent transcription initiation. In this paper, using biochemical and genetic approaches, we demonstrate that the A43 polypeptide forms a stable heterodimer with the A14 pol I subunit and interacts with the common ABC23 subunit, the yeast counterpart of the ω subunit of bacterial RNA polymerase. We show by immunoelectronic microscopy that A43, ABC23, and A14 colocalize in the three-dimensional structure of the pol I, and we demonstrate that the presence of A43 is required for the stabilization of both A14 and ABC23 within the pol I. Because the N-terminal half of A43 is clearly related to the pol II Rpb7 subunit, we propose that the A43–A14 pair is likely the pol I counterpart of the Rpb7–Rpb4 heterodimer, although A14 distinguishes from Rpb4 by specific sequence and structure features. This hypothesis, combined with our structural data, suggests a new localization of Rpb7–Rpb4 subunits in the three-dimensional structure of yeast pol II.
pp60Src Mediates Insulin-stimulated Sequestration of the β2-Adrenergic Receptor: Insulin Stimulates pp60Src Phosphorylation and Activation
Authors: Shumay Elena , Song Xiaosong , Wang Hsien-yu , Malbon Craig C.
Published: November 2002

Insulin stimulates a rapid phosphorylation and sequestration of the β2-adrenergic receptor. Analysis of the signaling downstream of the insulin receptor with enzyme inhibitors revealed roles for both phosphatidylinositol 3-kinase and pp60Src. Inhibition of Src with PP2, like the inhibition of phosphatidylinositol 3-kinase with LY294002 [2-(4-morpholynyl)-8-phenyl-4H-1-benzopyran-4-one], blocked the activation of Src as well as insulin-stimulated sequestration of the β2-adrenergic receptor. Depletion of Src with antisense morpholinos also suppressed insulin-stimulated receptor sequestration. Src is shown to be phosphorylated/activated in response to insulin in human epidermoid carcinoma A431 cells as well as in mouse 3T3-L1 adipocytes and their derivative 3T3-F422A cells, well-known models of insulin signaling. Inhibition of Src with PP2 blocks the ability of insulin to sequester β2-adrenergic receptors and the translocation of the GLUT4 glucose transporters. Insulin stimulates Src to associate with the β2-adrenergic receptor/AKAP250/protein kinase A/protein kinase C signaling complex. We report a novel positioning of Src, mediating signals from insulin to phosphatidylinositol 3-kinase and to β2-adrenergic receptor trafficking.
Identification and Characterization of Two Unusual cGMP-stimulated Phoshodiesterases inDictyostelium
Authors: Bosgraaf Leonard , Russcher Henk , Snippe Helena , Bader Sonya , Wind Joyce , Van Haastert Peter J.M.
Published: November 2002

Recently, we recognized two genes, gbpA andgbpB, encoding putative cGMP-binding proteins with a Zn2+-hydrolase domain and two cyclic nucleotide binding domains. The Zn2+-hydrolase domains belong to the superfamily of β-lactamases, also harboring a small family of class II phosphodiesterases from bacteria and lower eukaryotes. Gene inactivation and overexpression studies demonstrate thatgbpA encodes the cGMP-stimulated cGMP-phosphodiesterase that was characterized biochemically previously and was shown to be involved in chemotaxis. cAMP neither activates nor is a substrate of GbpA. The gbpB gene is expressed mainly in the multicellular stage and seems to encode a dual specificity phosphodiesterase with preference for cAMP. The enzyme hydrolyses cAMP ∼9-fold faster than cGMP and is activated by cAMP and cGMP with aKAvalue of ∼0.7 and 2.3 μM, respectively. Cells with a deletion of the gbpB gene have increased basal and receptor stimulated cAMP levels and are sporogeneous. We propose that GbpA and GbpB hydrolyze the substrate in the Zn2+-hydrolase domain, whereas the cyclic nucleotide binding domains mediate activation. The human cGMP-stimulated cAMP/cGMP phosphodiesterase has similar biochemical properties, but a completely different topology: hydrolysis takes place by a class I catalytic domain and GAF domains mediate cGMP activation.
CURRENT STATUS OF MODERN DARK MATTER PROBLEM
Authors: GNEDIN YU. N.
Published: November 2002

The basic methods of searching for dark matter candidates are discussed. The main topics of this talk are: (a) ground - based cavity experiments with searching for galactic axions; (b) searching for hadronic axion decay line into galactic and extragalactic light; (c) experimental search for solar and stellar axions; (d) basic methods of searching for WIMPs as candidates into dark matter; (e) limits on axion and WIMP masses and their coupling constants to photons and ordinary matter; (f) novels of searching for nonbaryonic dark matter.
WARPED GEOMETRY OF BRANE WORLDS
Authors: FELDER GARY
Published: November 2002

We study the dynamical equations for extra-dimensional dependence of a warp factor and a bulk scalar in 5D brane world scenarios with 3+1 de Sitter slices. We show that these equations are similar to the equations for 4D scalar field cosmology, but with the sign of the scalar field potential reversed. We construct three dimensional phase portraits for this system for a variety of potentials. We show that for many potentials there will be an unavoidable singularity occuring a finite distance from the brane. This singularity can be shielded by the addition of a second brane. The properties of these branes will generally fix the inter-brane separation and effective 4D cosmological constants, thus providing a possible mechanism for stabilizing the braneworld. Some of these results were previously known for some models, but we bring together a variety of results and show how they can all be easily seen using phase portraits.
ON FRIEDMANN'S EQUATION IN BRANE-WORLDS
Authors: MAIA M. D. , MONTE E. M. , MAIA J. M. F.
Published: November 2002

The modified Friedmann's equation is derived from the minimal set of postulates in the brane-world program. It is shown that the recently observed accelerated expansion of the universe can be explained in terms of the extrinsic curvature of the universe along the radial direction.
ON SCHWARZSCHILD'S TOPOLOGY IN BRANE-WORLDS
Authors: MONTE E. M. , MAIA M. D.
Published: November 2002

The topological structure of Schwazschild's space-time and its maximal analytic extension are investigated in the context of brane worlds. Using the embedding coordinates, these geometries are seen as different states of the evolution of a single brane-world. Comparing the topologies and the embeddings it is shown that this evolution must be followed by a signature change in the bulk.
Genetics of Motility and Chemotaxis of a Fascinating Group of Bacteria: The Spirochetes
Authors: Charon Nyles W. , Goldstein Stuart F.
Published: November 2002

▪ Abstract  Spirochetes are a medically important and ecologically significant group of motile bacteria with a distinct morphology. Outermost is a membrane sheath, and within this sheath is the protoplasmic cell cylinder and subterminally attached periplasmic flagella. Here we address specific and unique aspects of their motility and chemotaxis. For spirochetes, translational motility requires asymmetrical rotation of the two internally located flagellar bundles. Consequently, they have swimming modalities that are more complex than the well-studied paradigms. In addition, coordinated flagellar rotation likely involves an efficient and novel signaling mechanism. This signal would be transmitted over the length of the cell, which in some cases is over 100-fold greater than the cell diameter. Finally, many spirochetes, including Treponema, Borrelia, and Leptospira, are highly invasive pathogens. Motility is likely to play a major role in the disease process. This review summarizes the progress in the genetics of motility and chemotaxis of spirochetes, and points to new directions for future experimentation.
Origins of Spontaneous Mutations: Specificity and Directionality of Base-Substitution, Frameshift, and Sequence-Substitution Mutageneses
Authors: Maki Hisaji
Published: November 2002

▪ Abstract  Spontaneous mutations are derived from various sources, including errors made during replication of undamaged template DNA, mutagenic nucleotide substrates, and endogenous DNA lesions. These sources vary in their frequencies and resultant mutations, and are differently affected by the DNA sequence, DNA transactions, and cellular metabolism. Organisms possess a variety of cellular functions to suppress spontaneous mutagenesis, and the specificity and effectiveness of each function strongly affect the pattern of spontaneous mutations. Base substitutions and single-base frameshifts, two major classes of spontaneous mutations, occur non-randomly throughout the genome. Within target DNA sequences there are hotspots for particular types of spontaneous mutations; outside of the hotspots, spontaneous mutations occur more randomly and much less frequently. Hotspot mutations are attributable more to endogenous DNA lesions than to replication errors. Recently, a novel class of mutagenic pathway that depends on short inverted repeats was identified as another important source of hotspot mutagenesis.
Coronary Artery Pattern and Outcome of Arterial Switch Operation for Transposition of the Great Arteries
Authors: Pasquali Sara K. , Hasselblad Vic , Li Jennifer S. , Kong David F. , Sanders Stephen P.
Published: November 2002

Background—

Prior studies of coronary pattern and outcome after arterial switch operation (ASO) for transposition of the great arteries (TGA) have been hindered by limited statistical power. This meta-analysis assesses the effect of coronary anatomy on post-ASO mortality, both overall and adjusted for time.

Methods and Results—

A literature search revealed 9 independent series that reported post-ASO mortality by coronary pattern in a total of 1942 patients. Odds ratios comparing all-cause mortality in patients with usual versus variant coronary patterns were calculated and combined by use of an empirical Bayesian model. Single coronary patterns, both of which loop around the great vessels, were associated with significant mortality (OR 2.9, 95% CI 1.3 to 6.8), whereas looping patterns that arose from 2 separate ostia were not (OR 1.2, 95% CI 0.8 to 1.9). This latter group includes patients with the most common variant, circumflex from right coronary artery. Patients with an intramural coronary artery had the greatest mortality (OR 6.5, 95% CI 2.9 to 14.2). Overall, patients with any variant coronary pattern had nearly twice the mortality seen in those with the usual pattern (OR 1.7, 95% CI 1.3 to 2.4). Single ostium patterns and intramural coronary arteries remained associated with significant added mortality after adjustment for time-trend effects.

Conclusions—

Over the past 2 decades, patients with common coronary variants have undergone ASO without added mortality compared with those with the usual coronary pattern. Those with intramural or single coronary arteries have significant added mortality that has persisted over time.
Total assignments of 1H and 13C NMR spectra of a new prenylated flavanone from Dioclea grandiflora
Authors: Lemos Virgínia S. , dos Santos Marcelo H. , Rabelo Luiza A. , Côrtes Steyner F.
Published: November 2002

A new prenylated flavanone, floranol (1) 3,5,7,2′‐ tetrahydroxy‐6‐methoxy‐8‐prenylflavanone and a known flavanone (dioclein) were isolated from the roots of Dioclea grandiflora (Fabaceae). The structure and the relative stereochemistry were established by 2D NMR spectroscopic techniques (HMQC and HMBC) Copyright © 2002 John Wiley & Sons, Ltd.
The use of PGSE NMR and DECRA for determining polymer composition
Authors: Antalek Brian , Hewitt J. Michael , Windig Willem , Yacobucci Paul D. , Mourey Thomas , Le Kim
Published: November 2002

Pulsed gradient spin‐echo (PGSE) NMR, when coupled with the appropriate data processing algorithm, is a useful method for mixture analysis. Direct exponential curve resolution algorithm (DECRA) is demonstrated as a method that may be used to obtain polymer composition information as a function of molecular weight for a poly(urea‐urethane). DECRA resolves both self‐diffusion coefficients and corresponding spectral components from a single experiment without the need for physical separation. Molecular weight estimates from the NMR data are compared with that determined by size‐exclusion chromatography (SEC). DECRA‐resolved spectral components are directly compared with NMR spectra of SEC fractions. Subtle compositional changes among three different polymer solutions are clearly detected by the NMR analysis. Copyright © 2002 John Wiley & Sons, Ltd.
Material presence and the mystery of the object
Authors: Self Pamela
Published: November 2002

La Congiunta, Peter Märkli's house
for sculptures in the Leventina
valley, is an enigmatic concrete
structure. It has the appearance of
a large rock, its density
strengthened by a complete
absence of visible openings. No hint
is given of its content or its
entrance. And so our curiosity
impels us to explore the block's
exterior. The horizontal divisions
of the shuttering create at a glance
the impression of large stone slabs.
On closer viewing, the individual
boards and the grain of the timber
are revealed as traces of
construction. Our understanding
of the volume develops gradually,
through contact with its material
qualities.
Stirling's variability
Authors: Spens Michael
Published: November 2002

Thomas Muirhead's letter (arq 6/1,
pp5–6) raises interesting points
concerning Stirling's ‘variability’ –
a quality I for one do not dispute: in
my article (arq 5/4, pp333–353) I had
chosen to focus on schemes which
for one reason or another have
been less fully revisited than more
celebrated icons.
Repair of topoisomerase I covalent complexes in the absence of the tyrosyl-DNA phosphodiesterase Tdp1
Authors: Liu Chunyan , Pouliot Jeffrey J. , Nash Howard A.
Published: November 2002

Accidental or drug-induced interruption of the breakage and reunion cycle of eukaryotic topoisomerase I (Top1) yields complexes in which the active site tyrosine of the enzyme is covalently linked to the 3′ end of broken DNA. The enzyme tyrosyl-DNA phosphodiesterase (Tdp1) hydrolyzes this protein-DNA link and thus functions in the repair of covalent complexes, but genetic studies in yeast show that alternative pathways of repair exist. Here, we have evaluated candidate genes for enzymes that might act in parallel to Tdp1 so as to generate free ends of DNA. Despite finding that the yeast Apn1 protein has a Tdp1-like biochemical activity, genetic inactivation of all known yeast apurinic endonucleases does not increase the sensitivity of a
tdp1
mutant to direct induction of Top1 damage. In contrast, assays of growth in the presence of the Top1 poison camptothecin (CPT) indicate that the structure-specific nucleases dependent on
RAD1
and
MUS81
can contribute independently of
TDP1
to repair, presumably by cutting off a segment of DNA along with the topoisomerase. However, cells in which all three enzymes are genetically inactivated are not as sensitive to the lethal effects of CPT as are cells defective in double-strand break repair. We show that the
MRE11
gene is even more critical than the
RAD52
gene for double-strand break repair of CPT lesions, and comparison of an
mre11
mutant with a
tdp1 rad1 mus81
triple mutant demonstrates that other enzymes complementary to Tdp1 remain to be discovered.
Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups
Authors: Chamberlin Stacy I. , Merino Edward J. , Weeks Kevin M.
Published: November 2002

The functional groups found among the RNA bases and in the phosphoribose backbone represent a limited repertoire from which to construct a ribozyme active site. This work investigates the possibility that simple RNA phosphodiester and hydroxyl functional groups could catalyze amide bond synthesis. Reaction of amine groups with activated esters would be catalyzed by a group that stabilizes the partial positive charge on the amine nucleophile in the transition state. 2′-Amine substitutions adjacent to 3′-phosphodiester or 3′-hydroxyl groups react efficiently with activated esters to form 2′-amide and peptide products. In contrast, analogs in which the 3′-phosphodiester is replaced by an uncharged phosphotriester or is constrained in a distal conformation react at least 100-fold more slowly. Similarly, a nucleoside in which the 3′-hydroxyl group is constrained
trans
to the 2′-amine is also unreactive. Catalysis of synthetic reactions by RNA phosphodiester and ribose hydroxyl groups is likely to be even greater in the context of a preorganized and solvent-excluding catalytic center. One such group is the 2′-hydroxyl of the ribosome-bound P-site adenosine substrate, which is close to the amine nucleophile in the peptidyl synthesis reaction. Given ubiquitous 2′-OH groups in RNA, there exists a decisive advantage for RNA over DNA in catalyzing reactions of biological significance.
In vivo
stabilization of the Dnmt1 (cytosine-5)- methyltransferase protein
Authors: Ding Feng , Chaillet J. Richard
Published: November 2002

The Dnmt1o form of the Dnmt1 (cytosine-5)-methyltransferase enzyme is synthesized and stored in the cytoplasm of the oocyte and is used after fertilization to maintain methylation patterns on imprinted genes. After implantation of the blastocyst, Dnmt1o is replaced by the Dnmt1 form, which has an additional 118 aa at its amino terminus. To investigate functional differences between Dnmt1o and Dnmt1, mice were generated with a mutant allele,

Dnmt1
V

, which synthesized Dnmt1o instead of Dnmt1 in all somatic cells. Homozygous

Dnmt1
V

mice were phenotypically normal, and had normal levels of genomic methylation, indicating that Dnmt1o adopts the maintenance methyltransferase function of Dnmt1. Despite the apparent equivalence of Dnmt1o and Dnmt1 maintenance methyltransferase function in somatic cells, the Dnmt1o protein was found at high levels (with a corresponding high enzymatic activity) in

Dnmt1
V

mice. In heterozygous

Dnmt1
V

/
+
embryonic stem cells and early embryos, equal steady-state levels of Dnmt1o and Dnmt1 proteins were produced from the

Dnmt1
V

and the WT
Dnmt1
alleles, respectively. However, in older embryos and adults, the

Dnmt1
V

allele produced five times the steady-state level of protein of the WT
Dnmt1
allele. The difference in Dnmt1o and Dnmt1 levels is due to a developmentally regulated mechanism that degrades the Dnmt1 protein. The intrinsic stability of the Dnmt1o protein is the most likely reason for its use as a maternal-effect protein; stable ooplasmic stores of Dnmt1o would be available to traffick into the nuclei of the eight-cell stage embryo and maintain methylation patterns on alleles of imprinted genes during the fourth embryonic S phase.
DIRAC BOUND STATES IN A ONE-DIMENSIONAL SCALAR SCREENED COULOMB POTENTIAL
Authors: KAGALI B. A. , RAO NAGALAKSHMI A. , SIVRAMKRISHNA VIJAY
Published: November 2002

In this paper we illustrate the existence of genuine bound states for a Dirac particle interacting with a scalar screened Coulomb potential in a 1 + 1 dimension. In contrast to the bare Coulomb potential, the screened Coulomb potential can bind both spin-zero and spin-1/2 particles in the scalar prescription.
A FIVE DIMENSIONAL MODEL OF EFFECTIVE GRAVITATIONAL AND FINE-STRUCTURE CONSTANTS
Authors: MBELEK J. P. , LACHIÈZE-REY M.
Published: November 2002

It is shown that the coupling of the Kaluza-Klein (KK) internal scalar field both to an external stabilizing bulk scalar field and to the geomagnetic field may explain the observed dispersion in laboratory measurements of the (effective) gravitational constant. Except the PTB 95 value, the predictions are found in good agreement with all of the experimental data. The cosmological variation of the fine-structure constant is also addressed.
HODGE TYPE COHOMOLOGICAL GAUGE THEORIES
Authors: GEYER BODO , MÜLSCH DIETMAR
Published: November 2002

NT = 4 and NT = 8 cohomological TQFT's in D = 2 are presented whose generators of topological shift, co–shift and gauge symmetry (Qa, ⋆Qa, W) together with a discrete duality operation obey the same algebra as de Rham cohomology operators (d, δ, Δ) and the Hodge ⋆–operation.
Arterial Stiffness and Endothelial Function in Patients With β-Thalassemia Major
Authors: Cheung Y.F. , Chan Godfrey C.F. , Ha S.Y.
Published: November 2002

Background—

Increased iron store has been linked to risk of cardiovascular disease. Structural alterations of arteries in β-thalassemia major patients and in vitro functional disturbance of vascular endothelial cells by thalassemic serum have been described. We sought to determine whether arterial stiffness and endothelial function are altered in vivo.

Methods and Results—

Thirty thalassemia patients (16 male) aged 22.2±7.4 years were recruited. Left ventricular (LV) mass and function were assessed echocardiographically. Carotid and brachioradial artery stiffness was assessed by stiffness index and pulse-wave velocity (PWV), respectively. Brachial artery endothelial function was assessed by vascular response to reactive hyperemia (flow-mediated dilation [FMD]) and sublingual glyceryl trinitrate. These indexes were compared with those of 30 age- and sex-matched controls. None of the patients had LV systolic or diastolic dysfunction. When compared with controls, patients had greater absolute (113.8±38.0 versus 109.0± 32.6 g,
P
=0.04) and indexed (82.4±17.5 versus 66.7±12.7 g/m
2
,
P
<0.001) LV mass, carotid artery stiffness index (8.1±3.5 versus 5.5±1.6,
P
<0.001), and brachioradial PWV (8.9±2.4 versus 7.9±1.7 m/s,
P
= 0.03). Their FMD was impaired (3.5±3.3% versus 8.8±3.9%,
P
<0.001), whereas glyceryl trinitrate– mediated dilation was preserved (17.9±7.6% versus 16.3±6.1%,
P
=0.40). Both stiffness index and PWV correlated inversely with magnitude of FMD (
r
=−0.40,
P
=0.03;
r
=−0.41,
P
=0.03) and positively with indexed LV mass (
r
=0.50,
P
=0.005;
r
=0.40,
P
=0.027). Nonetheless, no significant correlation existed between ferritin level and carotid stiffness, PWV, or FMD.

Conclusions—

Increased arterial stiffness, endothelial dysfunction, and LV hypertrophy occur in patients with β-thalassemia major, which may result in reduction of mechanical efficiency of the heart.
Heterocoagulation of polychloroprene on natural rubber latex particles for use in the preparation of toughened polystyrene
Authors: Tangboriboonrat P. , Buranabunya U. , Sangribsub S.
Published: November 2002

The toughness of high‐impact polystyrene based on γ‐radiation‐vulcanized natural rubber (NR) was effectively enhanced by the addition of a block copolymer at the NR/polystyrene interface. An NR/polychloroprene (CR) composite latex particle was produced by the heterocoagulation technique for its use as a model in a compatibilization study. A nonionic surfactant (Tween 80), whose molecule bore poly(ethylene oxide) (PEO), was adsorbed onto the CR particle and allowed to form a complex between PEO and an indigenous surfactant (protein–lipid) on the NR particle surface. The presence of CR–Tween on the outer layer of the obtained composite polymer particle was characterized by the particle size, ζ potential, and glass‐transition temperature. That the film cast from the heterocoagulated latex showed better oil resistance than the NR film confirmed the NR/CR core–shell structure. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 9–13, 2003
13C cross‐polarization magic angle spinning NMR of ferrocene derivatives
Authors: Okada Yutaka , Oguri Kouji , Sakamoto Kazuhisa , Miyako Yukio , Hayashi Takatoshi
Published: November 2002

The 13C chemical shifts of the CP/MAS NMR for ferrocene derivatives have been measured. Copyright © 2002 John Wiley & Sons, Ltd.
Experimental investigation on the secondary
instability of liquid-fluidized beds and the
formation of bubbles
Authors: DURU PAUL , GUAZZELLI ÉLISABETH
Published: November 2002

The objective of the present work is to investigate experimentally the secondary
instability of the one-dimensional voidage waves occurring in two-dimensional liquid-
fluidized beds and to examine the physical origin of bubbles, i.e. regions devoid of
particles, which arise in fluidization. In the case of moderate-density glass particles,
we observe the formation of transient buoyant blobs clearly resulting from the
destabilization of the one-dimensional wavy structure. With metallic beads of the same
size but larger density, the same destabilization occurs but it leads to the formation of
real bubbles. Comparison with previous analytical and numerical studies is attempted.
Whereas the linear and weakly nonlinear analytical models are not appropriate,
the direct nonlinear simulations provide a qualitative agreement with the observed
destabilization mechanism.
A
Lotus
basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation
Authors: Nishimura Rieko , Ohmori Masayuki , Fujita Hironori , Kawaguchi Masayoshi
Published: November 2002

The developmental program of nodulation is regulated systemically in leguminous host species. A mutant
astray
(
Ljsym77
) in
Lotus japonicus
has lost some sort of its ability to regulate this symtem, and shows enhanced and early nodulation. In the absence of rhizobia, this mutant exhibits characteristics associated with defects in light and gravity responses. These nonsymbiotic phenotypes of
astray
are very similar to those observed in photomorphogenic
Arabidopsis
mutant
hy5
. Based on this evidence, we predicted that
astray
might contain a mutation in the
HY5
homologue of
L. japonicus
. The homologue, named
LjBzf
, encodes a basic leucine zipper protein in the C-terminal half that shows the highest level of identity with HY5 of all
Arabidopsis
proteins. It also encodes legume-characteristic combination of motifs, including a RING-finger motif and an acidic region in the N-terminal half. The
astray
phenotypes were cosegregated with
LjBzf
, and the failure to splice the intron was detected. Nonsymbiotic and symbiotic phenotypes of
astray
were complemented by introduction of
CaMV35S
:
LjBzf
. It is noteworthy that although
Arabidopsis hy5
showed an enhancement of lateral root initiation,
Lotus astray
showed an enhancement of nodule initiation but not of lateral root initiation. Legume-characteristic combination of motifs of ASTRAY may play specific roles in the regulation of nodule development.