bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of a strong mutator phenotype in yeast by imbalanced base excision repair
Authors: Glassner Brian J. , Rasmussen Lene Juel , Najarian Mark T. , Posnick Lauren M. , Samson Leona D.
Published: July 2002

Increased spontaneous mutation is associated with increased cancer risk. Here, by using a model system, we show that spontaneous mutation can be increased several hundred-fold by a simple imbalance between the first two enzymes involved in DNA base excision repair. The
Saccharomyces cerevisiae MAG1
3-methyladenine (3MeA) DNA glycosylase, when expressed at high levels relative to the apurinic/apyrimidinic endonuclease, increases spontaneous mutation by up to ≈600-fold in
S. cerevisiae
and ≈200-fold in
Escherichia coli
. Genetic evidence suggests that, in yeast, the increased spontaneous mutation requires the generation of abasic sites and the processing of these sites by the
REV1
/
REV3
/
REV7
lesion bypass pathway. Comparison of the mutator activity produced by Mag1, which has a broad substrate range, with that produced by the
E. coli Tag
3MeA DNA glycosylase, which has a narrow substrate range, indicates that the removal of endogenously produced 3MeA is unlikely to be responsible for the mutator effect of Mag1. Finally, the human
AAG
3-MeA DNA glycosylase also can produce a small (≈2-fold) but statistically significant increase in spontaneous mutation, a result which could have important implications for carcinogenesis.
Hippocampal morphometry in schizophrenia by high dimensional brain mapping
Authors: Csernansky John G. , Joshi Sarang , Wang Lei , Haller John W. , Gado Mokhtar , Miller J. Philip , Grenander Ulf , Miller Michael I.
Published: July 2002

Theories of the pathophysiology of schizophrenia have implicated the hippocampus, but controversy remains regarding hippocampal abnormalities in patients with schizophrenia.In vivostudies of hippocampal anatomy using high resolution magnetic resonance scanning and manual methods for volumetric measurement have yielded inconclusive results, perhaps because of the normal variability in hippocampal volume and the error involved in manual measurement techniques. To resolve this controversy, high dimensional transformations of a computerized brain template were used to compare hippocampal volumes and shape characteristics in 15 matched pairs of schizophrenia and control subjects. The transformations were derived from principles of general pattern matching and were constrained according to the physical properties of fluids. The analysis and comparison of hippocampal shapes based on these transformations were far superior to the comparison of hippocampal volumes or other global indices of hippocampal anatomy in showing a statistically significant difference between the two groups. In the schizophrenia subjects, hippocampal shape deformations were found to be localized to subregions of the structure that send projections to prefrontal cortex. The results of this study demonstrate that abnormalities of hippocampal anatomy occur in schizophrenia and support current hypotheses that schizophrenia involves a disturbance of hippocampal–prefrontal connections. These results also show that comparisons of neuroanatomical shapes can be more informative than volume comparisons for identifying individuals with neuropsychiatric diseases, such as schizophrenia.
Elucidation of conditions allowing conversion of penicillin G and other penicillins to deacetoxycephalosporins by resting cells and extracts of
Streptomyces clavuligerus
NP1
Authors: Cho Hiroshi , Adrio José L. , Luengo José M. , Wolfe Saul , Ocran Simeon , Hintermann Gilberto , Piret Jacqueline M. , Demain Arnold L.
Published: July 2002

Using resting cells and extracts of
Streptomyces clavuligerus
NP1, we have been able to convert penicillin G (benzylpenicillin) to deacetoxycephalosporin G. Conversion was achieved by increasing by 45× the concentration of FeSO
4
(1.8 mM) and doubling the concentration of α-ketoglutarate (1.28 mM) as compared with standard conditions used for the normal cell-free conversion of penicillin N to deacetoxycephalosporin C. ATP, MgSO
4
, KCl, and DTT, important in cell-free expansion of penicillin N, did not play a significant role in the ring expansion of penicillin G by resting cells or cell-free extracts. When these conditions were used with 14 other penicillins, ring expansion was achieved in all cases.
Creation of RNA molecules that recognize the oxidative lesion 7,8-dihydro-8-hydroxy-2′-deoxyguanosine (8-oxodG) in DNA
Authors: Rink Stacia M. , Shen Jiang-Cheng , Loeb Lawrence A.
Published: July 2002

We used
in vitro
evolution to obtain RNA molecules that specifically recognize and bind with high affinity to the oxidative lesion 7,8-dihydro-8-hydroxy-2′-deoxyguanosine (8-oxodG) in DNA. A pool of ≈10
15
RNA molecules containing a random insert of 45 nucleotides in length was subject to 10 successive rounds of chromatographic enrichment using an 8-oxodG affinity matrix, reverse transcription, PCR amplification, and RNA synthesis. Selected RNA molecules bind to 8-oxodG located at the 3′ terminus (
K
d
≤ 270 nM) or in the center (
K
d
≤ 2.8 μM) of a 19-nt strand of DNA, with no detectable affinity for the corresponding dG-containing DNA sequences. These 8-oxodG-binding RNAs will be used to monitor levels of 8-oxodG in DNA from biological sources and should provide a unique method for evaluating oxygen-mediated DNA damage. This approach should be applicable for the creation of RNA molecules that can bind to and identify the different modifications of DNA produced by a variety of environmental agents.
Use of intrinsic modes in biology: Examples of indicial response of pulmonary blood pressure to ± step hypoxia
Authors: Huang Wei , Shen Zheng , Huang Norden E. , Fung Yuan Cheng
Published: July 2002

Recently, a new method to analyze biological nonstationary stochastic variables has been presented. The method is especially suitable to analyze the variation of one biological variable with respect to changes of another variable. Here, it is illustrated by the change of the pulmonary blood pressure in response to a step change of oxygen concentration in the gas that an animal breathes. The pressure signal is resolved into the sum of a set of oscillatory intrinsic mode functions, which have zero “local mean,” and a final nonoscillatory mode. With this device, we obtain a set of “mean trends,” each of which represents a “mean” in a definitive sense, and together they represent the mean trend systematically with different degrees of oscillatory content. Correspondingly, the oscillatory content of the signal about any mean trend can be represented by a set of partial sums of intrinsic mode functions. When the concept of “indicial response function” is used to describe the change of one variable in response to a step change of another variable, we now have a set of indicial response functions of the mean trends and another set of indicial response functions to describe the energy or intensity of oscillations about each mean trend. Each of these can be represented by an analytic function whose coefficients can be determined by a least-squares curve-fitting procedure. In this way, experimental results are stated sharply by analytic functions.
cDNA cloning of
Batis maritima
methyl chloride transferase and purification of the enzyme
Authors: Ni Xinhai , Hager Lowell P.
Published: July 2002

Methyl chloride transferase catalyzes the synthesis of methyl chloride from
S
-adenosine-
l
-methionine and chloride ion. This enzyme has been purified 2,700-fold to homogeneity from
Batis maritima,
a halophytic plant that grows abundantly in salt marshes. The purification of the enzyme was accomplished by a combination of ammonium sulfate fractionation, column chromatography on Sephadex G100 and adenosine-agarose, and TSK-250 size-exclusion HPLC. The purified enzyme exhibits a single band on SDS/PAGE with a molecular mass of approximately 22.5 kDa. The molecular mass of the purified enzyme was 22,474 Da as determined by matrix-associated laser desorption ionization mass spectrometry. The methylase can function in either a monomeric or oligomeric form. A 32-aa sequence of an internal fragment of the methylase was determined (GLVPGCGGGYDVVAMANPER FMVGLDIXENAL, where X represents unknown residue) by Edman degradation, and a full-length cDNA of the enzyme was obtained by rapid amplification of cDNA ends–PCR amplification of cDNA oligonucleotides. The cDNA gene contains an ORF of 690 bp encoding an enzyme of 230 aa residues having a predicted molecular mass of 25,761 Da. The disparity between the observed and calculated molecular mass suggests that the methylase undergoes posttranslational cleavage, possibly during purification. Sequence homologies suggest that the
B. maritima
methylase defines a new family of plant methyl transferases. A possible function for this novel methylase in halophytic plants is discussed.
Identification of a structural determinant for resistance to β-lactam antibiotics in Gram-positive bacteria
Authors: Mouz N. , Gordon E. , Di Guilmi A.-M. , Petit I. , Pétillot Y. , Dupont Y. , Hakenbeck R. , Vernet T. , Dideberg O.
Published: July 2002

Streptococcus pneumoniae
is the main causal agent of pathologies that are increasingly resistant to antibiotic treatment. Clinical resistance of
S. pneumoniae
to β-lactam antibiotics is linked to multiple mutations of high molecular mass penicillin-binding proteins (H-PBPs), essential enzymes involved in the final steps of bacterial cell wall synthesis. H-PBPs from resistant bacteria have a reduced affinity for β-lactam and a decreased hydrolytic activity on substrate analogues. In
S. pneumoniae
, the gene coding for one of these H-PBPs, PBP2x, is located in the cell division cluster (DCW). We present here structural evidence linking multiple β-lactam resistance to amino acid substitutions in PBP2x within a buried cavity near the catalytic site that contains a structural water molecule. Site-directed mutation of amino acids in contact with this water molecule in the “sensitive” form of PBP2x produces mutants similar, in terms of β-lactam affinity and substrate hydrolysis, to altered PBP2x produced in resistant clinical isolates. A reverse mutation in a PBP2x variant from a clinically important resistant clone increases the acylation efficiency for β-lactams and substrate analogues. Furthermore, amino acid residues in contact with the structural water molecule are conserved in the equivalent H-PBPs of pathogenic Gram-positive cocci. We suggest that, probably via a local structural modification, the partial or complete loss of this water molecule reduces the acylation efficiency of PBP2x substrates to a point at which cell wall synthesis still occurs, but the sensitivity to therapeutic concentrations of β-lactam antibiotics is lost.
Mechanisms of β cell death in diabetes: A minor role for CD95
Authors: Allison Janette , Strasser Andreas
Published: July 2002

Insulin-dependent diabetes mellitus is an autoimmune disease, under polygenic control, manifested only when >90% of the insulin-producing β cells are destroyed. Although the disease is T cell mediated, the demise of the β cell results from a number of different insults from the immune system. It has been proposed that foremost amongst these effector mechanisms is CD95 ligand-induced β cell death. Using the nonobese diabeticlprmouse as a model system, we have found, to the contrary, that CD95 plays only a minor role in the death of β cells. Islet grafts from nonobese diabetic mice that carry thelpr mutation and therefore lack CD95 were protected only marginally from immune attack when grafted into diabetic mice. An explanation to reconcile these differing results is provided.
Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase α subunit
Authors: Aiyar Sarah E. , Gourse Richard L. , Ross Wilma
Published: July 2002

Upstream A-tracts stimulate transcription from a variety of bacterial promoters, and this has been widely attributed to direct effects of the intrinsic curvature of A-tract-containing DNA. In this work we report experiments that suggest a different mechanism for the effects of upstream A-tracts on transcription. The similarity of A-tract-containing sequences to the adenine- and thymine-rich upstream recognition elements (UP elements) found in some bacterial promoters suggested that A-tracts might increase promoter activity by interacting with the α subunit of RNA polymerase (RNAP). We found that an A-tract-containing sequence placed upstream of the
Escherichia coli lac
or
rrnB
P1 promoters stimulated transcription both
in vivo
and
in vitro
, and that this stimulation required the C-terminal (DNA-binding) domain of the RNAP α subunit. The A-tract sequence was protected by wild-type RNAP but not by α-mutant RNAPs in footprints. The effect of the A-tracts on transcription was not as great as that of the most active UP elements, consistent with the degree of similarity of the A-tract sequence to the UP element consensus. A-tracts functioned best when positioned close to the −35 hexamer rather than one helical turn farther upstream, similar to the positioning optimal for UP element function. We conclude that A-tracts function as UP elements, stimulating transcription by providing binding site(s) for the RNAP αCTD, and we suggest that these interactions could contribute to the previously described wrapping of promoter DNA around RNAP.
A decrease of reelin expression as a putative vulnerability factor in schizophrenia
Authors: Impagnatiello Francesco , Guidotti Alessandro R. , Pesold Christine , Dwivedi Yogesh , Caruncho Hector , Pisu Maria G. , Uzunov Doncho P. , Smalheiser Neil R. , Davis John M. , Pandey Ghanshyam N. , Pappas George D. , Tueting Patricia , Sharma Rajiv P. , Costa Erminio
Published: July 2002

Postmortem prefrontal cortices (PFC) (Brodmann’s areas 10 and 46), temporal cortices (Brodmann’s area 22), hippocampi, caudate nuclei, and cerebella of schizophrenia patients and their matched nonpsychiatric subjects were compared forreelin(RELN) mRNA and reelin (RELN) protein content. In all of the brain areas studied, RELN and its mRNA were significantly reduced (≈50%) in patients with schizophrenia; this decrease was similar in patients affected by undifferentiated or paranoid schizophrenia. To exclude possible artifacts caused by postmortem mRNA degradation, we measured the mRNAs in the same PFC extracts from γ-aminobutyric acid (GABA)Areceptors α1and α5and nicotinic acetylcholine receptor α7subunits. Whereas the expression of the α7nicotinic acetylcholine receptor subunit was normal, that of the α1and α5receptor subunits of GABAAwas increased when schizophrenia was present.RELNmRNA was preferentially expressed in GABAergic interneurons of PFC, temporal cortex, hippocampus, and glutamatergic granule cells of cerebellum. A protein putatively functioning as an intracellular target for the signal-transduction cascade triggered by RELN protein released into the extracellular matrix is termed mouse disabled-1 (DAB1) and is expressed at comparable levels in the neuroplasm of the PFC and hippocampal pyramidal neurons, cerebellar Purkinje neurons of schizophrenia patients, and nonpsychiatric subjects; these three types of neurons do not express RELN protein. In the same samples of temporal cortex, we found a decrease in RELN protein of ≈50% but no changes in DAB1 protein expression. We also observed a large (up to 70%) decrease of GAD67 but only a small decrease of GAD65 protein content. These findings are interpreted within a neurodevelopmental/vulnerability “two-hit” model for the etiology of schizophrenia.
Tissues of MSH2-deficient mice demonstrate hypermutability on exposure to a DNA methylating agent
Authors: Andrew Susan E. , McKinnon Margaret , Cheng Benjamin S. , Francis Agnes , Penney Janice , Reitmair Armin H. , Mak Tak W. , Jirik Frank R.
Published: July 2002

The mutational response of mismatch repair-deficient animals to the alkylating agent
N
-methyl-
N
-nitrosourea was evaluated by using a transgenic
lacI
reporter system. Although the mutations detected in
MSH2
heterozygotes were similar to those of controls,
MSH2
−/−
animals demonstrated striking increases in mutation frequency in response to this agent. G:C to A:T transitions at GpG sites, as opposed to CpG sites, dominated the mutational spectrum of both
MSH2
+/+
and
MSH2
−/−
N
-methyl-
N
-nitrosourea -treated animals. Extrapolating to humans with hereditary non-polyposis colorectal cancer, the results suggest that
MSH2
heterozygotes are unlikely to be at increased risk of mutation, even when exposed to potent DNA methylating agents. In contrast, mismatch repair-deficient cells spontaneously arising within individuals with hereditary non-polyposis colorectal cancer would likely exhibit hypermutability in response to such mutagens, an outcome predicted to accelerate the pace of tumorigenesis.
Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2
Authors: Lin Chentao , Yang Hongyun , Guo Hongwei , Mockler Todd , Chen Jeff , Cashmore Anthony R.
Published: July 2002

Cryptochrome is a group of flavin-type blue light receptors that regulate plant growth and development. The function of Arabidopsis cryptochrome 2 in the early photomorphogenesis of seedlings was studied by using transgenic plants overexpressing CRY2 protein, and
cry2
mutant plants accumulating no CRY2 protein. It is found that cryptochrome 2 mediates blue light-dependent inhibition of hypocotyl elongation and stimulation of cotyledon opening under low intensities of blue light. In contrast to CRY1, the expression of CRY2 is rapidly down-regulated by blue light in a light-intensity dependent manner, which provides a molecular mechanism to explain at least in part that cryptochrome 2 functions primarily under low light during the early development of seedlings.
A conotoxin from
Conus textile
with unusual posttranslational modifications reduces presynaptic Ca
2+
influx
Authors: Rigby Alan C. , Lucas-Meunier Estelle , Kalume Dário E. , Czerwiec Eva , Hambe Björn , Dahlqvist Ingrid , Fossier Philippe , Baux Gérard , Roepstorff Peter , Baleja James D. , Furie Barbara C. , Furie Bruce , Stenflo Johan
Published: July 2002

Cone snails are gastropod mollusks of the genus
Conus
that live in tropical marine habitats. They are predators that paralyze their prey by injection of venom containing a plethora of small, conformationally constrained peptides (conotoxins). We report the identification, characterization, and structure of a γ-carboxyglutamic acid-containing peptide, conotoxin ɛ-TxIX, isolated from the venom of the molluscivorous cone snail,
Conus textile
. The disulfide bonding pattern of the four cysteine residues, an unparalleled degree of posttranslational processing including bromination, hydroxylation, and glycosylation define a family of conotoxins that may target presynaptic Ca
2+
channels or act on G protein-coupled presynaptic receptors via another mechanism. This conotoxin selectively reduces neurotransmitter release at an
Aplysia
cholinergic synapse by reducing the presynaptic influx of Ca
2+
in a slow and reversible fashion. The three-dimensional structure, determined by two-dimensional
1
H NMR spectroscopy, identifies an electronegative patch created by the side chains of two γ-carboxyglutamic acid residues that extend outward from a cavernous cleft. The glycosylated threonine and hydroxylated proline enclose a localized hydrophobic region centered on the brominated tryptophan residue within the constrained intercysteine region.
Intermediates can accelerate protein folding
Authors: Wagner Clemens , Kiefhaber Thomas
Published: July 2002

The effect of intermediates on the rate of protein folding is explored by applying Kramers’ theory of diffusive barrier crossing in the high friction limit. Intermediates are represented as local minima in the transition barrier. We observe that very large or very small additional barriers created by the intermediates slow down the folding process. The rate of folding markedly increases, however, when the additional barriers become >1

k
B
T

but leave the overall barrier height unchanged. This rate-enhancing effect is caused by a favorable entropic contribution to the free energy of activation, and it increases with the number of intermediates up to a limiting value. From these calculations, we conclude that optimized transition barriers should contain partially folded high energy intermediates.
Functional dissection of the transmitter module of the histidine kinase NtrB in
Escherichia coli
Authors: Kramer Günter , Weiss Verena
Published: July 2002

Signal transduction by two-component systems involves phosphorylation and thereby activation of the response regulator by the cognate histidine kinase. Bifunctional histidine kinases have two opposing activities: depending on the environmental stimuli they either promote phosphorylation or stimulate the rapid dephosphorylation of the response regulator. To determine the mechanism of this switch, we analyzed the domain organization of the bifunctional histidine kinase NtrB. Based on sequence alignments with other histidine kinases and a deletion analysis, we defined three separate subdomains of the transmitter module, the H domain (amino acids 123–221), the N domain (amino acids 221–269), and the G domain (amino acids 269–349). The transmitter module, when separately expressed, exhibited a constitutive positive phenotype. In contrast, in the absence of the G domain, the H domain exhibits a constitutive negative phenotype. This negative regulatory activity of the H domain is inhibited by the G domain. The G domain could be physically uncoupled; when coexpressed with the H–N fragment, the constitutive positive phenotype of the transmitter was restored. We demonstrate,
in vitro
, that the constitutive negative phenotype of the fragments lacking the G domain is caused by stimulation of dephosphorylation of the response regulator NtrC-P. Based on our analysis, we suggest that the function of the sensor domain is to control the interaction of the H and G domains. If these subdomains interact, NtrB acts as a positive regulator; if they cannot interact, NtrB acts as a negative regulator.
Chaperone rings in protein folding and degradation
Authors: Horwich Arthur L. , Weber-Ban Eilika U. , Finley Daniel
Published: July 2002

Chaperone rings play a vital role in the opposing ATP-mediated
processes of folding and degradation of many cellular proteins, but the
mechanisms by which they assist these life and death actions are only
beginning to be understood. Ring structures present an advantage to
both processes, providing for compartmentalization of the substrate
protein inside a central cavity in which multivalent, potentially
cooperative interactions can take place between the substrate and a
high local concentration of binding sites, while access of other
proteins to the cavity is restricted sterically. Such restriction
prevents outside interference that could lead to nonproductive fates of
the substrate protein while it is present in non-native form, such as
aggregation. At the step of recognition, chaperone rings recognize
different motifs in their substrates, exposed hydrophobicity in the
case of protein-folding chaperonins, and specific “tag” sequences
in at least some cases of the proteolytic chaperones. For both folding
and proteolytic complexes, ATP directs conformational changes in the
chaperone rings that govern release of the bound polypeptide. In the
case of chaperonins, ATP enables a released protein to pursue the
native state in a sequestered hydrophilic folding chamber, and, in the
case of the proteases, the released polypeptide is translocated into a
degradation chamber. These divergent fates are at least partly governed
by very different cooperating components that associate with the
chaperone rings: that is, cochaperonin rings on one hand and
proteolytic ring assemblies on the other. Here we review the structures
and mechanisms of the two types of chaperone ring system.
Restriction of major surface protein 2 (MSP2) variants during tick transmission of the ehrlichiaAnaplasma marginale
Authors: Rurangirwa Fred R. , Stiller David , French Dorothy M. , Palmer Guy H.
Published: July 2002

Anaplasma marginaleis an ehrlichial pathogen of cattle that establishes lifelong persistent infection. Persistence is characterized by rickettsemic cycles in which newA. marginalevariant types, defined by the sequence of the expressedmsp2transcripts, emerge. The polymorphicmsp2transcripts encode structurally distinct MSP2 proteins and result in an antigenically diverse and continually changingA. marginalepopulation within the blood. In this manuscript, we used sequence analysis ofmsp2transcripts to show that a restricted repertoire of variant types, designated SGV1 and SGV2, is expressed within the tick salivary gland. The same SGV1 and SGV2 variant types were expressed in ticks regardless of the variant types expressed in the blood of infected cattle at the time of acquisition feeding by the ticks. Importantly, subsequent tick transmission to susceptible cattle resulted in acute rickettsemia composed of organisms expressing only the same SGV1 and SGV2 variant types. This indicates that themsp2expressed by organisms within the tick salivary gland predicts the variant type responsible for acute rickettsemia and disease. This restriction of transmittedA. marginalevariant types, in contrast to the marked diversity within persistently infected cattle, supports development of MSP2 vaccines to prevent acute rickettsemia in tick-transmitted infections.
Illite and hydrocarbon exploration
Authors: Pevear David R.
Published: July 2002

Illite is a general term for the dioctahedral mica-like clay mineral common in sedimentary rocks, especially shales. Illite is of interest to the petroleum industry because it can provide a K-Ar isotope date that constrains the timing of basin heating events. It is critical to establish that hydrocarbon formation and migration occurred after the formation of the trap (anticline, etc.) that is to hold the oil. Illite also may precipitate in the pores of sandstone reservoirs, impeding fluid flow. Illite in shales is a mixture of detrital mica and its weathering products with diagenetic illite formed by reaction with pore fluids during burial. K-Ar ages are apparent ages of mixtures of detrital and diagenetic end members, and what we need are the ages of the end members themselves. This paper describes a methodology, based on mineralogy and crystallography, for interpreting the K-Ar ages from illites in sedimentary rocks and for estimating the ages of the end members.
A modern human pattern of dental development in Lower Pleistocene hominids from Atapuerca-TD6 (Spain)
Authors: Bermúdez de Castro J. M. , Rosas A. , Carbonell E. , Nicolás M. E. , Rodríguez J. , Arsuaga J. L.
Published: July 2002

The study of life history evolution in hominids is crucial for the discernment of when and why humans have acquired our unique maturational pattern. Because the development of dentition is critically integrated into the life cycle in mammals, the determination of the time and pattern of dental development represents an appropriate method to infer changes in life history variables that occurred during hominid evolution. Here we present evidence derived from Lower Pleistocene human fossil remains recovered from the TD6 level (Aurora stratum) of the Gran Dolina site in the Sierra de Atapuerca, northern Spain. These hominids present a pattern of development similar to that of
Homo sapiens
, although some aspects (e.g., delayed M3 calcification) are not as derived as that of European populations and people of European origin. This evidence, taken together with the present knowledge of cranial capacity of these and other late Early Pleistocene hominids, supports the view that as early as 0.8 Ma at least one
Homo
species shared with modern humans a prolonged pattern of maturation.
Location of translational initiation factor IF3 on the small ribosomal subunit
Authors: McCutcheon John P. , Agrawal Rajendra K. , Philips Shibu M. , Grassucci Robert A. , Gerchman Sue Ellen , Clemons William M. , Ramakrishnan V. , Frank Joachim
Published: July 2002

The location of translational initiation factor IF3 bound to the 30S subunit of the
Thermus thermophilus
ribosome has been determined by cryoelectron microscopy. Both the 30S⋅IF3 complex and control 30S subunit structures were determined to 27-Å resolution. The difference map calculated from the two reconstructions reveals three prominent lobes of positive density. The previously solved crystal structure of IF3 fits very well into two of these lobes, whereas the third lobe probably arises from conformational changes induced in the 30S subunit as a result of IF3 binding. Our placement of IF3 on the 30S subunit allows an understanding in structural terms of the biochemical functions of this initiation factor, namely its ability to dissociate 70S ribosomes into 30S and 50S subunits and the preferential selection of initiator tRNA by IF3 during initiation.
Denaturant-induced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements
Authors: Pappenberger Günter , Saudan Christophe , Becker Michael , Merbach André E. , Kiefhaber Thomas
Published: July 2002

The small all-β protein tendamistat folds and unfolds with
two-state kinetics. We determined the volume changes associated with
the folding process by performing kinetic and equilibrium measurements
at variable pressure between 0.1 and 100 MPa (1 to 1,000 bar).
GdmCl-induced equilibrium unfolding transitions reveal that the volume
of the native state is increased by 41.4 ± 2.0
cm
3
/mol relative to the unfolded state. This value is
virtually independent of denaturant concentration. The use of a
high-pressure stopped-flow instrument enabled us to measure the
activation volumes for the refolding
(Δ
V
f
0‡
) and unfolding reaction
(Δ
V
u
0‡
) over a broad range of GdmCl
concentrations. The volume of the transition state is 60% native-like
(Δ
V
f
0‡
= 25.0
± 1.2 cm
3
/mol) in the absence of denaturant, indicating
partial solvent accessibility of the core residues. The volume of the
transition state increases linearly with denaturant concentration and
exceeds the volume of the native state above 6 M GdmCl. This result
argues for a largely desolvated transition state with packing
deficiencies at high denaturant concentrations and shows that the
structure of the transition state depends strongly on the experimental
conditions.
Characterization of bacteriophage T4-coordinated leading- and lagging-strand synthesis on a minicircle substrate
Authors: Salinas Frank , Benkovic Stephen J.
Published: July 2002

The DNA replication complex of bacteriophage T4 has been assembled as a single unit on a minicircle substrate with a replication fork that permits an independent measurement of the amount of DNA synthesis on both the leading and lagging strands. The assembled replisome consists of the T4 polymerase [gene product 43 (gp43)], clamp protein (gp45), clamp loader (gp44/62), helicase (gp41), helicase accessory factor (gp59), primase (gp61), and single-stranded DNA binding protein (gp32). We demonstrate that on the minicircle the synthesis of the leading and lagging strands are coordinated and that the C-terminal domain of the gp32 protein regulates this coordination. We show that the reconstituted replisome encompasses two coupled holoenzyme complexes and present evidence that this coupling might include a gp43 homodimer interaction.
Prediction, identification, and artificial selection of DNA rearrangements in
Rhizobium
: Toward a natural genomic design
Authors: Flores Margarita , Mavingui Patrick , Perret Xavier , Broughton William J. , Romero David , Hernández Georgina , Dávila Guillermo , Palacios Rafael
Published: July 2002

Based on the DNA sequence of the symbiotic plasmid of
Rhizobium
strain NGR234, we predicted potential rearrangements generated by homologous recombination. All predicted rearrangements were identified experimentally by using a PCR-based methodology. Thus, the predicted and the actual dynamic maps of the replicon coincide. By using an approach that does not involve the introduction of exogenous genetic elements, derivative populations that are pure for specific rearrangements were obtained. We propose that knowledge of the DNA sequence of a genome offers the possibility of designing pathways of sequential rearrangements leading to alternative genomic structures. An experimental strategy to isolate bacterial populations containing the desired structures is discussed.
Mechanisms and streams for processing of “what” and “where” in auditory cortex
Authors: Rauschecker Josef P. , Tian Biao
Published: July 2002

The functional specialization and hierarchical organization of multiple areas in rhesus monkey auditory cortex were examined with various types of complex sounds. Neurons in the lateral belt areas of the superior temporal gyrus were tuned to the best center frequency and bandwidth of band-passed noise bursts. They were also selective for the rate and direction of linear frequency modulated sweeps. Many neurons showed a preference for a limited number of species-specific vocalizations (“monkey calls”). These response selectivities can be explained by nonlinear spectral and temporal integration mechanisms. In a separate series of experiments, monkey calls were presented at different spatial locations, and the tuning of lateral belt neurons to monkey calls and spatial location was determined. Of the three belt areas the anterolateral area shows the highest degree of specificity for monkey calls, whereas neurons in the caudolateral area display the greatest spatial selectivity. We conclude that the cortical auditory system of primates is divided into at least two processing streams, a spatial stream that originates in the caudal part of the superior temporal gyrus and projects to the parietal cortex, and a pattern or object stream originating in the more anterior portions of the lateral belt. A similar division of labor can be seen in human auditory cortex by using functional neuroimaging.
Plasticity in the neural coding of auditory space in the mammalian brain
Authors: King Andrew J. , Parsons Carl H. , Moore David R.
Published: July 2002

Sound localization relies on the neural processing of monaural and binaural spatial cues that arise from the way sounds interact with the head and external ears. Neurophysiological studies of animals raised with abnormal sensory inputs show that the map of auditory space in the superior colliculus is shaped during development by both auditory and visual experience. An example of this plasticity is provided by monaural occlusion during infancy, which leads to compensatory changes in auditory spatial tuning that tend to preserve the alignment between the neural representations of visual and auditory space. Adaptive changes also take place in sound localization behavior, as demonstrated by the fact that ferrets raised and tested with one ear plugged learn to localize as accurately as control animals. In both cases, these adjustments may involve greater use of monaural spectral cues provided by the other ear. Although plasticity in the auditory space map seems to be restricted to development, adult ferrets show some recovery of sound localization behavior after long-term monaural occlusion. The capacity for behavioral adaptation is, however, task dependent, because auditory spatial acuity and binaural unmasking (a measure of the spatial contribution to the “cocktail party effect”) are permanently impaired by chronically plugging one ear, both in infancy but especially in adulthood. Experience-induced plasticity allows the neural circuitry underlying sound localization to be customized to individual characteristics, such as the size and shape of the head and ears, and to compensate for natural conductive hearing losses, including those associated with middle ear disease in infancy.
On a classical limit for electronic degrees of freedom that satisfies the Pauli exclusion principle
Authors: Levine R. D.
Published: July 2002

Fermions need to satisfy the Pauli exclusion principle: no two can
be in the same state. This restriction is most compactly expressed in a
second quantization formalism by the requirement that the creation and
annihilation operators of the electrons satisfy anticommutation
relations. The usual classical limit of quantum mechanics corresponds
to creation and annihilation operators that satisfy commutation
relations, as for a harmonic oscillator. We discuss a simple classical
limit for Fermions. This limit is shown to correspond to an anharmonic
oscillator, with just one bound excited state. The vibrational quantum
number of this anharmonic oscillator, which is therefore limited to the
range 0 to 1, is the classical analog of the quantum mechanical
occupancy. This interpretation is also true for Bosons, except that
they correspond to a harmonic oscillator so that the occupancy is from
0 up. The formalism is intended to be useful for simulating the
behavior of highly correlated Fermionic systems, so the extension to
many electron states is also discussed.
An Experimental Study of Lexical Access in the Writing and Naming of Isolated Words
Authors: Bonin Patrick , Fayol Michel , Gombert Jean‐Emile
Published: July 2002

Unlike speech production, lexical access in written production has not systematically been investigated experimentally. Four experiments were run on literate adults to support the view that although the spoken and written language production systems may obviously share some processing levels, they also both have some specific processing components. The general findings provide evidence for such a view and are discussed in the framework of studies in verbal production conducted on normals and on brain‐damaged patients.
The Neuropsychology of Consciousness: The Mind‐Body Problem Re‐addressed
Authors: Pawlik Kurt
Published: July 2002

In this introductory contribution by the convenor of the 1996 Invited Presidential Symposium at the XXVI International Congress of Psychology, the recent renaissance of psychological, especially neuropsychological research into components and processes of consciousness is briefly reviewed. Conceptual dimensions of “consciousness” are distinguished, with an emphasis on consciousness in the sense of awareness, wakefulness, and control of overt behaviour, which are also central concepts in the subsequent symposium contributions.
Nature des représentations du langage écrit aux débuts de l'apprentissage de la lecture: un modèle interprétatif
Authors: Bastien‐Toniazzo Mireille , Magnan Annie , Bouchafa Houria
Published: July 2002

Ce travail vise à mettre à l'épreuve un modèle de simulation à base de connaissances élaboré dans une recherche longitudinale antérieure pour rendre compte des erreurs de lecture produites par des enfants en première année d'acquisition de la lecture. Ce modèle repose sur deux hypothèses: (1) au moment où se met en place l'apprentissage de la correspondance grapho‐phonologique, l'enfant cherche à extraire de la suite de lettres qui compose le mot, des configurations graphiques correspondant à des syllabes orales; (2) ces configurations graphiques peuvent ětre stockées soit sous forme de suites ordonnées de lettres soit sous forme d'ensembles non‐ordonnés de lettres. Les erreurs de permutations fréquemment observées dans cette période de l'acquistion de la lecture, seraient alors la trace d'une représentation non‐ordonnée des configurations graphiques. Deux expériences ont été conduites auprès d'un nouveau groupe d'enfants après six mois de cours préparatoire. Dans l'expérience 1, ils devaient détecter une syllabe orale dans un pseudo‐mot présenté visuellement et dont le premier trigramme correspondait ou non à l'ordre correct de transcription de la syllabe. Dans l'expérience 2, les enfants devaient lire des pseudo‐mots tri‐syllabiques dont le premier trigramme était présenté dans quatre ordres différents. Les erreurs de lecture produites en lecture correspondent aux prédictions que permettent de faire le modèle. Par ailleurs, l'absence de corrélation entre les deux épreuves, suggère que les connaissances activées sont de nature différente selon la tâche.
Manchester Plays Games: Exploring the Local Politics of Globalisation
Authors: Cochrane Allan , Peck Jamie , Tickell Adam
Published: July 2002

Using the example of Manchester's Olympic bidding process, the paper examines some of the links between globalisation and what has become known as the 'new urban politics'. The politics of the city's Olympic bids powerfully symbolise many of the supposedly transformative features of the new urban politics, British-style, as the old images of municipal welfarist (bureaucratic) politics have apparently been superseded by those of a dynamic and charismatic (entrepreneurial) business leadership. But while there are superficial similarities between these developments and those highlighted by analysts of US 'growth coalitions', the Manchester case reveals how they are as much about struggles over the role, meaning and structure of the state, as they are about urban growth. Manchester's Olympic bid committee resembles not so much a growth coalition as a grant coalition. This said, it is important not to underestimate the significance of the new urban imperative to talk about growth in order to get grants.
Monuments and Memory: Immortalizing Count M. N. Muraviev in Vilna, 1898
Authors: Weeks Theodore R.
Published: July 2002

Ernest Renan argued over a century ago that belonging to a nation entails forgetting just as much as it required remembering past events. Certainly this is the case in East Central Europe, where not infrequently different nationalities create out of a single historical event utterly opposing historical memories. In the western borderlands of the Russian Empire, one historical event that has been variously interpreted by different nationalities is the Insurrection of 1863. To simplify somewhat, prerevolutionary Russian historians generally interpreted this key event as a mutiny against the established legal order—the term miatezh (mutiny) was always used in such accounts—while the Poles interpreted the uprising as perhaps naive and foolish, but in any case a noble attempt to regain rights usurped by the Russian occupiers. With such a sharply opposed memory of the uprising as a whole, it comes as no surprise that the figure who did the most to crush the insurrection in the Northwest (Lithuanian and Belarusian) provinces, Count M. N. Muraviev, should also be a controversial figure, praised by conservative Russians and demonized by Poles, Lithuanians, and liberals of all nationalities.
‘This is Our School’: Provision, purpose and pedagogy of supplementary schooling in Leeds and Oslo
Authors: Hall Kathy A. , Özerk Kamil , Zulfiqar Mohsin , Tan Jon E. C.
Published: July 2002

AbstractThe article examines supplementary schooling within ethnic minority communities in Leeds and Oslo. Through an analysis of original research involving visits to a sample of supplementary schools in both cities, interviews with teachers and pupils, and reviews of unpublished documentation, the article seeks to understand the scale of provision, variety of purpose and the nature of pedagogy in these schools. Following a brief account of contextualising literature, the article gives an overview of supplementary schooling in each country, and describes research design and the profile of the participating schools. The article analyses the case study data under the following themes: group solidarity as the overarching function; community vs. individual interests; and curriculum, pedagogy and links with mainstream schooling. It thus considers the positioning of supplementary schools, both in terms of their purpose and relationship with mainstream provision, and examines the assessments of value made by participants. In conclusion, the article discusses the implications for policy and the role of individuals and communities in negotiating social, cultural and educational frameworks.
Role of Thyroid Hormones in Hepatic Effects of Peroxisome Proliferators
Authors: Miller Richard T. , Scappino Lori A. , Long Sarah M. , Corton J. Christopher
Published: July 2002

Peroxisome proliferators are endocrine disrupting chemicals that cause liver tumors in rodents but not humans. Although the receptor that mediates key hepatic effects, the peroxisome proliferator-activated receptor alpha (PPAR-α), and its endogenous ligands have been identified, the mechanism whereby these commonly used chemicals cause liver tumors in rodents has yet to be elucidated. Species differences in PPAR-α and DNA response elements may explain some of the variability in response upon exposure to peroxisome proliferators. The possibility that thyroid-modulating effects of peroxisome proliferators may contribute to the hepatic effects of peroxisome proliferators has yet to be fully explored. When the potent peroxisome proliferator, WY-14,643, was given to hypothyroid rats, there was a blunting of the hepatomegaly and hepatocyte proliferative responses seen in thyroid-intact animals. Acyl-CoA oxidase activity was unaltered by changes in thyroid hormone status. In addition, preliminary evidence indicates that peroxisome proliferators increased hepatic thyroid receptor (TRα1) expression, but TRα1 levels in liver tumors were similar to those in unexposed animals. Significant differences between humans and rodents with respect to thyroid hormone physiology and metabolism, in conjunction with the results of these studies, may be indicative of yet another mechanism to explain differential sensitivity to hepatic effects of peroxisome proliferators.
SK&F 95654-Induced Acute Cardiovascular Toxicity in Sprague-Dawley Rats—Histopathologic, Electron Microscopic, and Immunohistochemical Studies
Authors: Jun Zhang  , Herman Eugene H. , Knapton Alan , Chadwick Douglas P. , Whitehurst Virgil E. , Koerner John E. , Papoian Thomas , Ferrans Victor J. , Sistare Frank D.
Published: July 2002

The characteristics and pathogenesis of the cardiovascular toxicity induced by the type III selective phosphodiesterase inhibitor SK&F 95654 were examined in 2 studies. Sprague—Dawley rats received either a single sc injection of 50, 100, or 200 mg/kg SK&F 95654 and were euthanized at 24 hours after administration of the drug (Study 1), or were given a single subcutaneous (sc) injection of 100 mg/kg SK&F 95654 and euthanized at 1, 2, 4, 6, 8, 12, 24 hours, or 2 weeks after treatment (Study 2). Control rats received either DMSO or saline. Myocardial lesions and vascular lesions of the mesentery, spleen, and pancreas were seen 24 hours after dosing with either 50, 100, or 200 mg/kg SK&F 95654. The frequency and severity of these lesions (evaluated after the 100 mg/kg dose) increased with time over a period of 1 to 24 hours. By 2 weeks, the lesions subsided. Cardiac lesions consisted of myocyte necrosis with hypercontraction bands, inflammatory cell infiltration, interstitial hemorrhage, and interstitial edema. Vascular lesions of the mesentery were most prominent and consisted of vasodilatation and inflammation in the small-sized vessels, arterial medial necrosis and hemorrhage, and venous thrombosis. The vascular lesions included: leukocyte adhesion to endothelial cells, transendothelial migration of leukocytes, and inflammatory cell infiltration into vessel walls. Affected vessels included arteries, terminal arterioles, capillaries, postcapillary venules, and veins. Apoptosis of endothelial and smooth muscle cells was detected in the mesenteric vasculature by both TUNEL assay and electron microscopy. Evidence of endothelial cell activation in the mesenteric arteries and veins was also observed by electron microscopy. Immunohistochemical staining detected enhanced endothelial cell expression of intercellular adhesion molecule-1 (ICAM-1) and von Willebrand factor (vWF) in the mesenteric arteries and veins. Mast cells were noted to be more prevalent in affected mesenteric tissue from drug-treated animals. The present findings suggest that apoptosis of endothelial and smooth muscle cells, activation of endothelial cells, recruitment of mast cells, and increased expression of adhesion molecules are important factors to the overall pathogenesis of SK&F 95654-induced vasculitis.