bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence anomalies in the Cag7 gene of the
Helicobacter pylori
pathogenicity island
Authors: Liu Guoying , McDaniel Timothy K. , Falkow Stanley , Karlin Samuel
Published: July 2002

The severity of
Helicobacter pylori
-related disease is correlated with a pathogenicity island (the Cag region of about 26 genes) whose presence is associated with the up-regulation of an IL-8 cytokine inflammatory response in gastric epithelial cells. Statistical analysis of the Cag gene sequences calculated from the complete genome of strain 26695 revealed several unusual features. The Cag7 sequence (1,927 aa) has two repeat regions. Repeat region I runs 317 aa in a form of 𝒜𝒜𝒜 proximal to the protein N terminal; repeat region II extends 907 aa in the middle of the protein sequence consisting of 74 contiguous segments composed from selections among six consensus sequences and includes 58 regularly distributed cysteine residues with consecutive cysteines mostly 12, 18, or 24 aa apart. This “regular” cysteine arrangement may provide a scaffolding of linker elements stabilized by disulfide bridges. When Cag7 homologues from different strains are compared, differences were found almost exclusively in the repeat regions, resulting from deletion and/or insertion of repeating units. These observations suggest that the anomalous repetitive structure of the sequence plays an important role in the conformation of Cag7 gene product and potentially in the function of the pathogenicity island. Other facets of the Cag7 sequence show significant charge clusters, high multiplet count, and extremes of amino acid usage.
Divergent evolution of membrane protein topology: The
Escherichia coli
RnfA and RnfE homologues
Authors: Sääf Annika , Johansson Marie , Wallin Erik , von Heijne Gunnar
Published: July 2002

Although the molecular evolution of protein tertiary structure and enzymatic activity has been studied for decades, little attention has been paid to the evolution of membrane protein topology. Here, we show that two closely related polytopic inner membrane proteins from
Escherichia coli
have evolved opposite orientations in the membrane, which apparently has been achieved by the selective redistribution of positively charged amino acids between the polar segments flanking the transmembrane stretches. This example of divergent evolution of membrane protein topology suggests that a complete inversion of membrane topology is possible with relatively few mutational changes even for proteins with multiple transmembrane segments.
Direct crosslinking of the antitumor antibiotic sparsomycin, and its derivatives, to A2602 in the peptidyl transferase center of 23S-like rRNA within ribosome-tRNA complexes
Authors: Porse Bo T. , Kirillov Stanislav V. , Awayez Mariana J. , Ottenheijm Harry C. J. , Garrett Roger A.
Published: July 2002

The antitumor antibiotic sparsomycin is a universal and potent inhibitor of peptide bond formation and selectively acts on several human tumors. It binds to the ribosome strongly, at an unknown site, in the presence of an N-blocked donor tRNA substrate, which it stabilizes on the ribosome. Its site of action was investigated by inducing a crosslink between sparsomycin and bacterial, archaeal, and eukaryotic ribosomes complexed with P-site-bound tRNA, on irradiating with low energy ultraviolet light (at 365 nm). The crosslink was localized exclusively to the universally conserved nucleotide A2602 within the peptidyl transferase loop region of 23S-like rRNA by using a combination of a primer extension approach, RNase H fragment analysis, and crosslinking with radioactive [
125
I]phenol-alanine-sparsomycin. Crosslinking of several sparsomycin derivatives, modified near the sulfoxy group, implicated the modified uracil residue in the rRNA crosslink. The yield of the antibiotic crosslink was weak in the presence of deacylated tRNA and strong in the presence of an N-blocked P-site-bound tRNA, which, as was shown earlier, increases the accessibility of A2602 on the ribosome. We infer that both A2602 and its induced conformational switch are critically important both for the peptidyl transfer reaction and for antibiotic inhibition. This supposition is reinforced by the observation that other antibiotics that can prevent peptide bond formation
in vitro
inhibit, to different degrees, formation of the crosslink.
Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone
Authors: Street Arthur G. , Mayo Stephen L.
Published: July 2002

The intrinsic secondary structure-forming propensities of the naturally occurring amino acids have been measured both experimentally in host–guest studies and statistically by examination of the protein structure databank. There has been significant progress in understanding the origins of intrinsic α-helical propensities, but a unifying theme for understanding intrinsic β-sheet propensities has remained elusive. To this end, we modeled dipeptides by using a van der Waals energy function and derived Ramachandran plots for each of the amino acids. These data were used to determine the entropy and Helmholtz free energy of placing each amino acid in the β-sheet region of φ—ψ space. We quantitatively establish that the dominant cause of intrinsic β-sheet propensity is the avoidance of steric clashes between an amino acid side chain and its local backbone. Standard implementations of coulombic and solvation effects are seen to be less important.
Early hominid biogeography
Authors: Strait David S. , Wood Bernard A.
Published: July 2002

We examined the biogeographic patterns implied by early hominid phylogenies and compared them to the known dispersal patterns of Plio-Pleistocene African mammals. All recent published phylogenies require between four and seven hominid dispersal events between southern Africa, eastern Africa, and the Malawi Rift, a greater number of dispersals than has previously been supposed. Most hominid species dispersed at the same time and in the same direction as other African mammals. However, depending on the ages of critical hominid specimens, many phylogenies identify at least one hominid species that dispersed in the direction opposite that of contemporaneous mammals. This suggests that those hominids may have possessed adaptations that allowed them to depart from continental patterns of mammalian dispersal.
Dynamic visualization of nervous system in live
Drosophila
Authors: Sun Banghua , Xu Peizhang , Salvaterra Paul M.
Published: July 2002

We have constructed transgenic
Drosophila melanogaster
lines that express green fluorescent protein (GFP) exclusively in the nervous system. Expression is controlled with transcriptional regulatory elements present in the 5′ flanking DNA of the
Drosophila
Na
+
,K
+
-ATPase β-subunit gene
Nervana2
(
Nrv2
). This regulatory DNA is fused to the yeast transcriptional activator GAL4, which binds specifically to a sequence motif termed the UAS (upstream activating sequence).
Drosophila
lines carrying
Nrv2
-GAL4 transgenes have been genetically recombined with UAS–GFP (S65T) transgenes (
Nrv2-
GAL4+UAS–GFP) inserted on the same chromosomes. We observe strong nervous system-specific fluorescence in embryos, larvae, pupae, and adults. The GFP fluorescence is sufficiently bright to allow dynamic imaging of the nervous system at all of these developmental stages directly through the cuticle of live
Drosophila
. These lines provide an unprecedented view of the nervous system in living animals and will be valuable tools for investigating a number of developmental, physiological, and genetic neurobiological problems.
Crosstalk between Gα
i
- and Gα
q
-coupled receptors is mediated by Gβγ exchange
Authors: Quitterer Ursula , Lohse Martin J.
Published: July 2002

Activation of Gα
i
-coupled receptors often causes enhancement of the inositol phosphate signal triggered by Gα
q
-coupled receptors. To investigate the mechanism of this synergistic receptor crosstalk, we studied the Gα
i
-coupled adenosine A
1
and α
2C
adrenergic receptors and the Gα
q
-coupled bradykinin B
2
and a UTP-preferring P2Y receptor. Stimulation of either Gα
i
-coupled receptor expressed in COS cells increased the potency and the efficacy of inositol phosphate production by bradykinin or UTP. Likewise, overexpression of Gβ
1
γ
2
resulted in a similar increase in potency and efficacy of bradykinin or UTP. In contrast, these stimuli did not affect the potency of direct activators of Gα
q
; a truncated Gβ
3
mutant had no effect on the receptor-generated signals whereas signals generated at the G-protein level were still enhanced. This suggests that the Gβγ-mediated signal enhancement occurs at the receptor level. Almost all possible combinations of Gβ
1–3
with Gγ
2–7
were equally effective in enhancing the signals of the B
2
and a UTP-preferring P2Y receptor, indicating a very broad specificity of this synergism. The enhancement of the bradykinin signal by (
i
) Gα
i
-activating receptor ligands or (
ii
) cotransfection of Gβγ was suppressed when the B
2
receptor was replaced by a B
2
Gβ
2
fusion protein. Gβγ enhanced the B
2
receptor-stimulated activation of G-proteins as determined by GTPγS-induced decrease in high affinity agonist binding and by B
2
receptor-enhanced [
35
S]GTPγS binding. These findings support the concept that Gβγ exchange between Gα
i
- and Gα
q
-coupled receptors mediates this type of receptor crosstalk.
Interaction between cyclin-dependent kinases and human papillomavirus replication-initiation protein E1 is required for efficient viral replication
Authors: Ma Tianlin , Zou Nianxiang , Lin Biing Yuan , Chow Louise T. , Harper J. Wade
Published: July 2002

We have identified the human papillomavirus (HPV) DNA replication initiation protein E1 as a tight-binding substrate of cyclin E/cyclin-dependent kinase (Cdk) complexes by using expression cloning. E1, a DNA helicase, collaborates with the HPV E2 protein in ori-dependent replication. E1 formed complexes with cyclin E in insect and mammalian cells, independent of Cdks and E2. Additional cyclins, including A-, B-, and F-type (but not D-type), interacted with the E1/E2 complex, and A- and E-type cyclin kinases were capable of phosphorylating E1 and E2
in vitro
. Association with cyclins and efficient phosphorylation of E1 required the presence of a cyclin interaction motif (the RXL motif). E1 lacking the RXL motif displayed defects in E2-dependent HPV ori replication
in vivo
. Consistent with a role for Cdk-mediated phosphorylation in E1 function, an E1 protein lacking all four candidate Cdk phosphorylation sites still associated with E2 and cyclin E but was impaired in HPV replication
in vitro
and
in vivo
. Our data reveal a link between cyclin/Cdk function and activation of HPV DNA replication through targeting of Cdk complexes to the E1 replication-initiation protein and suggest a functional role for E1 phosphorylation by Cdks. The use of cyclin-binding RXL motifs is now emerging as a major mechanism by which cyclins are targeted to key substrates.
Galectin-7 overexpression is associated with the apoptotic process in UVB-induced sunburn keratinocytes
Authors: Bernerd Francoise , Sarasin Alain , Magnaldo Thierry
Published: July 2002

Galectin-7 is a β-galactoside binding protein specifically expressed in stratified epithelia and notably in epidermis, but barely detectable in epidermal tumors and absent from squamous carcinoma cell lines. Galectin-7 gene is an early transcriptional target of the tumor suppressor protein P53 [Polyak, K., Xia, Y., Zweier, J., Kinzler, K. & Vogelstein, B. (1997)
Nature (London)
389, 300–305]. Because p53 transcriptional activity is increased by genotoxic stresses we have examined the possible effects of ultraviolet radiations (UVB) on galectin-7 expression in epidermal keratinocytes. The amounts of galectin-7 mRNA and protein are increased rapidly after UVB irradiation of epidermal keratinocytes. The increase of galectin-7 is parallel to P53 stabilization. UVB irradiation of skin reconstructed
in vitro
and of human skin
ex vivo
demonstrates that galectin-7 overexpression is associated with sunburn/apoptotic keratinocytes. Transfection of a galectin-7 expression vector results in a significant increase in terminal deoxynucleotidyltransferase-mediated UTP end labeling-positive keratinocytes. The present findings demonstrate a keratinocyte-specific protein involved in the UV-induced apoptosis, an essential process in the maintenance of epidermal homeostasis.
A quantitative analysis of the kinetics of the G
2
DNA damage checkpoint system
Authors: Aguda Baltazar D.
Published: July 2002

A detailed model of the G
2
DNA damage checkpoint (G2DDC) system is presented that includes complex regulatory networks of the mitotic kinase Cdc2, phosphatase Cdc25, Wee1 kinase, and damage signal transduction pathways involving Chk1 and p53. Assumptions on the kinetic equations of the G2DDC are made, and computer simulations are carried out to demonstrate how the various subsystems operate to delay or arrest cell cycle progression. The detailed model could be used to explain various experiments relevant to G2DDC reported recently, including the nuclear export of 14–3–3-bound Cdc25, the down-regulation of cyclin B1 expression by p53, the effect of Chk1 and p53 on Cdc25 levels, and Wee1 degradation. It also is shown that, under certain conditions, p53 is necessary to sustain a G
2
arrest.
Poly(ADP-ribose) polymerase gene disruption conferred mice resistant to streptozotocin-induced diabetes
Authors: Masutani Mitsuko , Suzuki Hiroshi , Kamada Nobuo , Watanabe Miho , Ueda Otoya , Nozaki Tadashige , Jishage Kou-ichi , Watanabe Takeshi , Sugimoto Tetsuro , Nakagama Hitoshi , Ochiya Takahiro , Sugimura Takashi
Published: July 2002

Streptozotocin (STZ), a glucose analogue known to induce diabetes in experimental animals, causes DNA strand breaks and subsequent activation of poly(ADPribose) polymerase (Parp). Because Parp uses NAD as a substrate, extensive DNA damage will result in reduction of cellular NAD level. In fact, STZ induces NAD depletion and cell death in isolated pancreatic islets
in vitro
. Activation of Parp therefore is thought to play an important role in STZ-induced diabetes. In the present study, we established Parp-deficient (

Parp
−/−

) mice by disrupting
Parp
exon 1 by using the homologous recombination technique. These mice were used to examine the possible involvement of
Parp
in STZ-induced β-cell damage
in vivo
. The wild-type (

Parp
+/+

) mice showed significant increases in blood glucose concentration from 129 mg/dl to 218, 370, 477, and 452 mg/dl on experimental days 1, 7, 21, and 60, respectively, after a single injection of 180 mg STZ/kg body weight. In contrast, the concentration of blood glucose in

Parp
−/−

mice remained normal up to day 7, slightly increased on day 21, but returned to normal levels on day 60. STZ injection caused extensive necrosis in the islets of

Parp
+/+

mice on day 1, with subsequent progressive islet atrophy and loss of functional β cells from day 7. In contrast, the extent of islet β-cell death and dysfunction was markedly less in

Parp
−/−

mice. Our findings clearly implicate Parp activation in islet β-cell damage and glucose intolerance induced by STZ
in vivo
.
Transfer of plastid RNA-editing activity to novel sites suggests a critical role for spacing in editing-site recognition
Authors: Hermann Marita , Bock Ralph
Published: July 2002

RNA editing in higher plant plastids alters mRNA sequences by C-to-U conversions at highly specific sites through an unknown mechanism. To elucidate how the cytidine residues to be edited are specifically recognized and distinguished from other cytidines in close proximity, we have changed
in vivo
the distances of two plastid RNA-editing sites from their essential upstream cis-acting sequence element. Analysis of RNA editing in transgenic chloroplasts revealed that reduction of this distance by 1 nt entirely abolishes RNA editing. Surprisingly, deletions or combinations of deletional and point mutations that shift a heterologous cytidine residue in the same distance from the upstream cis-element as the editing site in the wild type result in transfer of the RNA-editing activity to the heterologous cytidine whereas the wild-type site remains unedited. Our results suggest that the molecular identity of at least some editing sites in the chloroplast genome is defined by their distance from an essential upstream sequence element.
Phylogeny of Darwin’s finches as revealed by mtDNA sequences
Authors: Sato Akie , O’hUigin Colm , Figueroa Felipe , Grant Peter R. , Grant B. Rosemary , Tichy Herbert , Klein Jan
Published: July 2002

Darwin’s finches comprise a group of passerine birds first collected by Charles Darwin during his visit to the Galápagos Archipelago. The group, a textbook example of adaptive radiation (the diversification of a founding population into an array of species differentially adapted to diverse environmental niches), encompasses 14 currently recognized species, of which 13 live on the Galápagos Islands and one on the Cocos Island in the Pacific Ocean. Although Darwin’s finches have been studied extensively by morphologists, ecologists, and ethologists, their phylogenetic relationships remain uncertain. Here, sequences of two mtDNA segments, the cytochrome
b
and the control region, have been used to infer the evolutionary history of the group. The data reveal the Darwin’s finches to be a monophyletic group with the warbler finch being the species closest to the founding stock, followed by the vegetarian finch, and then by two sister groups, the ground and the tree finches. The Cocos finch is related to the tree finches of the Galápagos Islands. The traditional classification of ground finches into six species and tree finches into five species is not reflected in the molecular data. In these two groups, ancestral polymorphisms have not, as yet, been sorted out among the cross-hybridizing species.
Increased expression of preprotachykinin-I and neurokinin receptors in human breast cancer cells: Implications for bone marrow metastasis
Authors: Singh Deeppreet , Joshi Deval D. , Hameed Meera , Qian Jing , Gascón Pedro , Maloof Paul B. , Mosenthal Anne , Rameshwar Pranela
Published: July 2002

Neuropeptides are implicated in many tumors, breast cancer (BC) included. Preprotachykinin-I (PPT-I) encodes multiple neuropeptides with pleiotropic functions such as neurotransmission, immune/hematopoietic modulation, angiogenesis, and mitogenesis.PPT-Iis constitutively expressed in some tumors. In this study, we investigated a role forPPT-Iand its receptors, neurokinin-1 (NK-1) andNK-2, in BC by using quantitative reverse transcription–PCR, ELISA, andin situhybridization. Compared with normal mammary epithelial cells (n= 2) and benign breast biopsies (n= 21), BC cell lines (n= 7) and malignant breast biopsies (n= 25) showed increased expression ofPPT-IandNK-1. NK-2 levels were high in normal and malignant cells. Specific NK-1 and NK-2 antagonists inhibited BC cell proliferation, suggesting autocrine and/or intercrine stimulation of BC cells by PPT-I peptides. NK-2 showed no effect on the proliferation of normal cells but mediated the proliferation of BC cells. Cytosolic extracts from malignant BC cells enhanced PPT-I translation whereas extracts from normal mammary epithelial cells caused no change. These enhancing effects may be protein-specific because a similar increase was observed for IL-6 translation and no effect was observed for IL-1α and stem cell factor. The data suggest that PPT-I peptides and their receptors may be important in BC development. Considering that PPT-I peptides are hematopoietic modulators, these results could be extended to understand early integration of BC cells in the bone marrow, a preferred site of metastasis. Molecular signaling transduced by PPT-I peptides and the mechanism that enhances translation of PPT-I mRNA could lead to innovative strategies for BC treatments and metastasis.
A deletion in a photoreceptor-specific nuclear receptor mRNA causes retinal degeneration in the
rd7
mouse
Authors: Akhmedov Novrouz B. , Piriev Natik I. , Chang Bo , Rapoport Ana Lia , Hawes Norman L. , Nishina Patsy M. , Nusinowitz Steven , Heckenlively John R. , Roderick Thomas H. , Kozak Christine A. , Danciger Michael , Davisson Muriel T. , Farber Debora B.
Published: July 2002

The
rd7
mouse, an animal model for hereditary retinal degeneration, has some characteristics similar to human flecked retinal disorders. Here we report the identification of a deletion in a photoreceptor-specific nuclear receptor (mPNR) mRNA that is responsible for hereditary retinal dysplasia and degeneration in the
rd7
mouse. mPNR was isolated from a pool of photoreceptor-specific cDNAs originally created by subtractive hybridization of mRNAs from normal and photoreceptorless
rd
mouse retinas. Localization of the gene corresponding to mPNR to mouse Chr 9 near the
rd7
locus made it a candidate for the site of the
rd7
mutation. Northern analysis of total RNA isolated from
rd7
mouse retinas revealed no detectable signal after hybridization with the mPNR cDNA probe. However, with reverse transcription–PCR, we were able to amplify different fragments of mPNR from
rd7
retinal RNA and to sequence them directly. We found a 380-nt deletion in the coding region of the
rd7
mPNR message that creates a frame shift and produces a premature stop codon. This deletion accounts for more than 32% of the normal protein and eliminates a portion of the DNA-binding domain. In addition, it may result in the rapid degradation of the
rd7
mPNR message by the nonsense-mediated decay pathway, preventing the synthesis of the corresponding protein. Our findings demonstrate that mPNR expression is critical for the normal development and function of the photoreceptor cells.
Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from
Methanobacterium thermoautotrophicum
Authors: Mackereth Cameron D. , Arrowsmith Cheryl H. , Edwards Aled M. , McIntosh Lawrence P.
Published: July 2002

The RNA polymerase subunit RPB10 displays a high level of
conservation across archaea and eukarya and is required for cell
viability in yeast. Structure determination of this RNA polymerase
subunit from
Methanobacterium thermoautotrophicum
reveals a topology, which we term a zinc-bundle, consisting of
three α-helices stabilized by a zinc ion. The metal ion is bound
within an atypical CX
2
CX
n
CC sequence motif and
serves to bridge an N-terminal loop with helix 3. This represents an
example of two adjacent zinc-binding Cys residues within an α-helix
conformation. Conserved surface features of RPB10 include discrete
regions of neutral, acidic, and basic residues, the latter being
located around the zinc-binding site. One or more of these regions may
contribute to the role of this subunit as a scaffold protein within the
polymerase holoenzyme.
Gene genealogies and population variation in plants
Authors: Schaal Barbara A. , Olsen Kenneth M.
Published: July 2002

Early in the development of plant evolutionary biology, genetic
drift, fluctuations in population size, and isolation were identified
as critical processes that affect the course of evolution in plant
species. Attempts to assess these processes in natural populations
became possible only with the development of neutral genetic markers in
the 1960s. More recently, the application of historically ordered
neutral molecular variation (within the conceptual framework of
coalescent theory) has allowed a reevaluation of these
microevolutionary processes. Gene genealogies trace the evolutionary
relationships among haplotypes (alleles) with populations. Processes
such as selection, fluctuation in population size, and population
substructuring affect the geographical and genealogical relationships
among these alleles. Therefore, examination of these genealogical data
can provide insights into the evolutionary history of a species. For
example, studies of
Arabidopsis thaliana
have suggested
that this species underwent rapid expansion, with populations showing
little genetic differentiation. The new discipline of phylogeography
examines the distribution of allele genealogies in an explicit
geographical context. Phylogeographic studies of plants have documented
the recolonization of European tree species from refugia subsequent to
Pleistocene glaciation, and such studies have been instructive in
understanding the origin and domestication of the crop cassava.
Currently, several technical limitations hinder the widespread
application of a genealogical approach to plant evolutionary studies.
However, as these technical issues are solved, a genealogical approach
holds great promise for understanding these previously elusive
processes in plant evolution.
A deoxyribonucleotidase in mitochondria: Involvement in regulation of dNTP pools and possible link to genetic disease
Authors: Rampazzo Chiara , Gallinaro Lisa , Milanesi Eva , Frigimelica Elisabetta , Reichard Peter , Bianchi Vera
Published: July 2002

Three cytosolic and one plasma membrane-bound 5′-nucleotidases have been cloned and characterized. Their various substrate specificities suggest widely different functions in nucleotide metabolism. We now describe a 5′-nucleotidase in mitochondria. The enzyme, named dNT-2, dephosphorylates specifically the 5′- and 2′(3′)-phosphates of uracil and thymine deoxyribonucleotides. The cDNA of human dNT-2 codes for a 25.9-kDa polypeptide with a typical mitochondrial leader peptide, providing the structural basis for two-step processing during import into the mitochondrial matrix. The deduced amino acid sequence is 52% identical to that of a recently described cytosolic deoxyribonucleotidase (dNT-1). The two enzymes share many catalytic properties, but dNT-2 shows a narrower substrate specificity. Mitochondrial localization of dNT-2 was demonstrated by the mitochondrial fluorescence of 293 cells expressing a dNT-2-green fluorescent protein (GFP) fusion protein. 293 cells expressing fusion proteins without leader peptide or with dNT-1 showed a cytosolic fluorescence. Duringin vitroimport into mitochondria, the preprotein lost the leader peptide. We suggest that dNT-2 protects mitochondrial DNA replication from overproduction of dTTP, in particular in resting cells. Mitochondrial toxicity of dTTP can be inferred from a severe inborn error of metabolism in which the loss of thymidine phosphorylase led to dTTP accumulation and aberrant mitochondrial DNA replication. We localized the gene for dNT-2 on chromosome 17p11.2 in the Smith–Magenis syndrome-critical region, raising the possibility that dNT-2 is involved in the etiology of this genetic disease.
Mosaicism in the alpha-like protein genes of group B streptococci
Authors: Lachenauer C. S. , Creti R. , Michel J. L. , Madoff L. C.
Published: July 2002

Members of a family of repeat-containing surface proteins of group B streptococci (GBS) defined by the alpha C and Rib proteins exhibit size variability and cross-reactivity and have been studied as potential vaccine components. We report evidence of horizontal DNA transfer with subsequent recombination as a mechanism generating diversity within this antigen family. Alp2 and Alp3 are additional members of the alpha C protein family identified in strains of the emerging GBS serotypes V and VIII. Each contains an overall genetic organization highly similar to that of the alpha C and Rib proteins, including a tandem repeat region and conserved N- and C-terminal regions. Among different strains, protein size varies according to the number of tandem repeats within the corresponding gene. Unlike the alpha C and Rib proteins, however, the newly described alpha-like proteins contain other regions, including one similar to the IgA-binding region of the GBS beta C protein, a nontandem repeat region, and an isolated repeat highly homologous to the alpha C repeat. Sequence analysis of the regions flanking the alpha C protein gene on a 13.7-kb insert reveals several ORFs that are likely to be involved in basic metabolic pathways. Analysis of corresponding flanking regions in other GBS strains, including the parent strains of the newly described alpha-like proteins, shows striking conservation among all strains studied. These findings indicate that the alpha-like proteins are encoded by mosaic variants at a single genomic locus and suggest that recombination after horizontal DNA transfer is a means of generating diversity within this protein family.
Aortic wall damage in mice unable to synthesize ascorbic acid
Authors: Maeda Nobuyo , Hagihara Hiroyuki , Nakata Yukiko , Hiller Sylvia , Wilder Jennifer , Reddick Robert
Published: July 2002

By inactivating the gene for
l
-gulono-γ-lactone oxidase, a key enzyme in ascorbic acid synthesis, we have generated mice that, like humans, depend on dietary vitamin C. Regular chow, containing about 110 mg/kg of vitamin C, is unable to support the growth of the mutant mice, which require
l
-ascorbic acid supplemented in their drinking water (330 mg/liter). Upon withdrawal of supplementation, plasma and tissue ascorbic acid levels decreased to 10–15% of normal within 2 weeks, and after 5 weeks the mutants became anemic, began to lose weight, and die. Plasma total antioxidative capacities were approximately 37% normal in homozygotes after feeding the unsupplemented diet for 3–5 weeks. As plasma ascorbic acid decreased, small, but significant, increases in total cholesterol and decreases in high density lipoprotein cholesterol were observed. The most striking effects of the marginal dietary vitamin C were alterations in the wall of aorta, evidenced by the disruption of elastic laminae, smooth muscle cell proliferation, and focal endothelial desquamation of the luminal surface. Thus, marginal vitamin C deficiency affects the vascular integrity of mice unable to synthesize ascorbic acid, with potentially profound effects on the pathogenesis of vascular diseases. Breeding the vitamin C-dependent mice with mice carrying defined genetic mutations will provide numerous opportunities for systematic studies of the role of antioxidants in health and disease.
Modulation of nucleotide sensitivity of ATP-sensitive potassium channels by phosphatidylinositol-4-phosphate 5-kinase
Authors: Shyng S.-L. , Barbieri A. , Gumusboga A. , Cukras C. , Pike L. , Davis J. N. , Stahl P. D. , Nichols C. G.
Published: July 2002

ATP-sensitive potassium channels (K
ATP
channels) regulate cell excitability in response to metabolic changes. K
ATP
channels are formed as a complex of a sulfonylurea receptor (SURx), a member of the ATP-binding cassette protein family, and an inward rectifier K
+
channel subunit (Kir6.x). Membrane phospholipids, in particular phosphatidylinositol (PI) 4,5-bisphosphate (PIP
2
), activate K
ATP
channels and antagonize ATP inhibition of K
ATP
channels when applied to inside-out membrane patches. To examine the physiological relevance of this regulatory mechanism, we manipulated membrane PIP
2
levels by expressing either the wild-type or an inactive form of PI-4-phosphate 5-kinase (PIP5K) in COSm6 cells and examined the ATP sensitivity of coexpressed K
ATP
channels. Channels from cells expressing the wild-type PIP5K have a 6-fold lower ATP sensitivity (
K
1/2
, the half maximal inhibitory concentration, ≈ 60 μM) than the sensitivities from control cells (
K
1/2
≈ 10 μM). An inactive form of the PIP5K had little effect on the
K
1/2
of wild-type channels but increased the ATP-sensitivity of a mutant K
ATP
channel that has an intrinsically lower ATP sensitivity (from
K
1/2
≈ 450 μM to
K
1/2
≈ 100 μM), suggesting a decrease in membrane PIP
2
levels as a consequence of a dominant-negative effect of the inactive PIP5K. These results show that PIP5K activity, which regulates PIP
2
and PI-3,4,5-P
3
levels, is a significant determinant of the physiological nucleotide sensitivity of K
ATP
channels.
Identification of a third distinct estrogen receptor and reclassification of estrogen receptors in teleosts
Authors: Hawkins Mary Beth , Thornton Joseph W. , Crews David , Skipper James K. , Dotte Alyssa , Thomas Peter
Published: July 2002

This paper describes three distinct estrogen receptor (ER)
subtypes: ERα, ERβ, and a unique type, ERγ, cloned from a teleost
fish, the Atlantic croaker
Micropogonias undulatus
; the
first identification of a third type of classical ER in vertebrate
species. Phylogenetic analysis shows that ERγ arose through gene
duplication from ERβ early in the teleost lineage and indicates that
ERγ is present in other teleosts, although it has not been recognized
as such. The Atlantic croaker ERγ shows amino acid differences in
regions important for ligand binding and receptor activation that are
conserved in all other ERγs. The three ER subtypes are genetically
distinct and have different distribution patterns in Atlantic croaker
tissues. In addition, ERβ and ERγ fusion proteins can each bind
estradiol-17β with high affinity. The presence of three functional
ERs in one species expands the role of ER multiplicity in estrogen
signaling systems and provides a unique opportunity to investigate the
dynamics and mechanisms of ER evolution.
Constitutive expression of a complement-like protein in Toll and JAK gain-of-function mutants ofDrosophila
Authors: Lagueux Marie , Perrodou Emmanuel , Levashina Elena A. , Capovilla Maria , Hoffmann Jules A.
Published: July 2002

We show thatDrosophilaexpresses four genes encoding proteins with significant similarities with the thiolester-containing proteins of the complement C3/α2-macroglobulin superfamily. The genes are transcribed at a low level during all stages of development, and their expression is markedly up-regulated after an immune challenge. For one of these genes, which is predominantly expressed in the larval fat body, we observe a constitutive expression in gain-of-function mutants of the Janus kinase (JAK)hopand a reduced inducibility in loss-of-functionhopmutants. We also observe a constitutive expression in gain-of-functionTollmutants. We discuss the possible roles of these novel complement-like proteins in theDrosophilahost defense.
Replication by a single DNA polymerase of a stretched single-stranded DNA
Authors: Maier Berenike , Bensimon David , Croquette Vincent
Published: July 2002

A new approach to the study of DNA/protein interactions has been
opened through the recent advances in the manipulation of single DNA
molecules. These allow the behavior of individual molecular motors to
be studied under load and compared with bulk measurements. One example
of such a motor is the DNA polymerase, which replicates DNA. We
measured the replication rate by a single enzyme of a stretched single
strand of DNA. The marked difference between the elasticity of single-
and double-stranded DNA allows for the monitoring of replication in
real time. We have found that the rate of replication depends strongly
on the stretching force applied to the template. In particular, by
varying the load we determined that the biochemical steps limiting
replication are coupled to movement. The replication rate increases at
low forces, decreases at forces greater than 4 pN, and ceases when the
single-stranded DNA substrate is under a load greater than ≈20 pN.
The decay of the replication rate follows an Arrhenius law and
indicates that multiple bases on the template strand are involved in
the rate-limiting step of each cycle. This observation is
consistent with the induced-fit mechanism for error detection
during replication.
Hematopoietic reconstitution of SLP-76 corrects hemostasis and platelet signaling through αIIbβ3 and collagen receptors
Authors: Judd Barbi A. , Myung Peggy S. , Leng Lijun , Obergfell Achim , Pear Warren S. , Shattil Sanford J. , Koretzky Gary A.
Published: July 2002

Mice deficient in the hematopoietic cell-specific adapter protein SLP-76 demonstrate a failure of T cell development and fetal hemorrhage. Although SLP-76-deficient platelets manifest defective collagen receptor signaling, this alone may not explain the observed bleeding diathesis. Because αIIbβ3, the platelet fibrinogen receptor, is required for normal hemostasis, we explored a potential role for SLP-76 in αIIbβ3 signaling. Interaction of soluble or immobilized fibrinogen with normal human or murine platelets triggers rapid tyrosine phosphorylation of SLP-76. Moreover, platelet adhesion to fibrinogen stimulates actin rearrangements, filopodial and lamellipodial extension, and localization of tyrosine phosphorylated proteins to the cell periphery. In contrast, SLP-76-deficient murine platelets bind fibrinogen normally, but spread poorly and exhibit reduced levels of phosphotyrosine. Thein vivobleeding diathesis as well as the defects in platelet responses to fibrinogen and collagen are reversed by retroviral transduction of SLP-76 into bone marrow derived from SLP-76-deficient mice. These studies establish that SLP-76 functions downstream of αIIbβ3 and collagen receptors in platelets. Furthermore, expression of SLP-76 in hematopoietic cells, including platelets, plays a necessary role in hemostasis.
Structural basis of the abscess-modulating polysaccharide A2 fromBacteroides fragilis
Authors: Wang Ying , Kalka-Moll Wiltrud M. , Roehrl Michael H. , Kasper Dennis L.
Published: July 2002

Zwitterionic capsular polysaccharides from pathogenic bacteria have peculiar immunological properties. They are capable of eliciting T-cell proliferation and modulating the course of abscess formation. To understand the molecular basis of this characteristic immune response, we are conducting detailed structure–function studies on these polysaccharides. We have identified, purified, and characterized an abscess-modulating polysaccharide, PS A2, from the clinical strainBacteroides fragilis638R. Here, we report the elucidation of both the chemical and three-dimensional structures of PS A2 by NMR spectroscopy, chemical methods, gas chromatography–mass spectrometry, and restrained molecular dynamics calculations. PS A2 consists of a pentasaccharide repeating unit containing mannoheptose,N-acetylmannosamine, 3-acetamido-3,6-dideoxyglucose, 2-amino-4-acetamido-2,4,6-trideoxygalactose, fucose, and 3-hydroxybutanoic acid. PS A2 is zwitterionic and carries one cationic free amine and one anionic carboxylate in each repeating unit. It forms an extended right-handed helix with two repeating units per turn and a pitch of 20 Å. Positive and negative charges are exposed on the outer surface of the polymer in a regularly spaced pattern, which renders them easily accessible to other molecules. The helix is characterized by repeated large grooves whose lateral boundaries are occupied by the charges. The three-dimensional structure of PS A2 explicitly suggests mechanisms of interaction between zwitterionic polysaccharides and proteins.
Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
Authors: Fersht Alan R.
Published: July 2002

I attempt to reconcile apparently conflicting factors and mechanisms that have been proposed to determine the rate constant for two-state folding of small proteins, on the basis of general features of the structures of transition states. Φ-Value analysis implies a transition state for folding that resembles an expanded and distorted native structure, which is built around an extended nucleus. The nucleus is composed predominantly of elements of partly or well-formed native secondary structure that are stabilized by local and long-range tertiary interactions. These long-range interactions give rise to connecting loops, frequently containing the native loops that are poorly structured. I derive an equation that relates differences in the contact order of a protein to changes in the length of linking loops, which, in turn, is directly related to the unfavorable free energy of the loops in the transition state. Kinetic data on loop extension mutants of CI2 and α-spectrin SH3 domain fit the equation qualitatively. The rate of folding depends primarily on the interactions that directly stabilize the nucleus, especially those in native-like secondary structure and those resulting from the entropy loss from the connecting loops, which vary with contact order. This partitioning of energy accounts for the success of some algorithms that predict folding rates, because they use these principles either explicitly or implicitly. The extended nucleus model thus unifies the observations of rate depending on both stability and topology.
How the “Iron Minister” Kaganovich Failed to Discipline Ukrainian Historians: A Stalinist Ideological Campaign Reconsidered
Authors: Yekelchyk Serhy
Published: July 2002

In late February 1947, Stalin's trusted troubleshooter Lazar' Kaganovich arrived in Kiev as the Ukrainian Communist Party's new first secretary. Having served consecutively as the Soviet People's Commissar of Railroad Transport, Heavy Industry, and Construction Materials, the notoriously heavy-handed Kaganovich had earned the epithet of zheleznyi narkom (“iron minister”). His tenure at the head of the Ukrainian party organization in March–December 1947 was marked by intensified coercive intervention in the economy and ideological purges in culture and scholarship. In Ukraine, Kaganovich's brief rule is remembered primarily for his relentless attacks on the alleged remnants of “Ukrainian bourgeois nationalism.” In the works of post-Soviet Ukrainian historians, the 1947 crusade against “nationalism” appears as a comprehensive campaign masterminded by Stalin, planned by his envoy Kaganovich, faithfully implemented by the servile republican functionaries, and submissively endured by the terrorized Ukrainian intellectuals. Clearly, modern Ukrainian historians have adopted the traditional Western concept of Stalinism as a successful totalitarian dictatorship, in which society was no more than a passive object of an all-powerful state.
Can Single‐sex Classes in Co‐educational Schools Enhance the Learning Experiences of Girls and/or Boys? An Exploration of Pupils' Perceptions
Authors: Jackson Carolyn
Published: July 2002

Abstract The introduction of single‐sex classes within co‐educational schools is a strategy adopted by some schools to enhance the learning experiences of either the girls or the boys depending upon the educational climate of the time. In a period dominated by the ‘what about the boys?’ debate, this strategy is currently being introduced and advocated in a number of schools in an attempt to raise boys' achievement. This article explores the value of introducing single‐sex classes within co‐educational schools, and in doing so, it draws upon the perspectives of girls and boys involved in one such initiative. The article concludes that girls‐only classes may have positive effects for girls. However, curriculum‐as‐usual boys' classes do nothing to challenge the problematic macho male cultures inherent in schools; indeed, it may be the case that they actually exacerbate them.
Child Rearing, Prosocial Moral Reasoning, and Prosocial Behaviour
Authors: Janssens Jan M.A.M. , Deković Maja
Published: July 2002

This study examined the relations between child rearing, prosocial moral reasoning, and prosocial behaviour. The sample consisted of 125 children (6-11 years of age) and both their parents. Child-rearing behaviour was assessed by both observations at home and interviews with the parents; prosocial moral reasoning by interviews with the children, and prosocial behaviour by questionnaires filled in by their teachers and classmates. Positive relations were found between prosocial moral reasoning and prosocial behaviour, but only for the youngest children. Children growing up in a supportive, authoritative, and less restrictive environment behaved more prosocially and reasoned at a higher level about prosocial moral issues.
Detecting Bimodality in the Analogical Reasoning Performance of Elementary Schoolchildren
Authors: Hosenfeld Bettina , van der Maas Han L.J. , van den Boom Dymphna C.
Published: July 2002

This paper reports on modelling six frequency distributions representing the analogical reasoning performance of four different samples of elementary schoolchildren. A two-component model outperformed a one-component model in all investigated data sets, discriminating accurate performers with high success probabilities and inaccurate performers with low success probabilities, whereas for two data sets a three-component model provided the best fit. In a treatment-control group data set, the treatment group comprised a larger proportion of accurate performers than the control group, whereas the success probabilities of the two latent classes were nearly identical in both groups. In a repeated-measures data set, both the success probabilities of the two latent classes and the proportion of accurate performers increased from the first to the second test session. The results provided a first indication of a transition in the development of analogical reasoning in elementary schoolchildren.
Adults’ Expectations for Children’s Sibling Roles
Authors: Mendelson Morton J. , de Villa Eileen P. , Fitch Tamara A. , Goodman Francine G.
Published: July 2002

This study assesses generally shared norms for children’s sibling roles by examining adults’ role expectations for older brother, older sister, younger brother, and younger sister. Subjects listed prescriptions and proscriptions for each sibling in one of 12 two-child families with target children designated as 4 and 1, 7 and 4, or 10 and 7 years old for each of four sex compositions. Subjects had more, and relatively more positive, role expectations for older siblings than for younger siblings. Expectations differed qualitatively for the siblings (e.g. teaching, help, protection, and caretaking were associated with older siblings, learning, deference, and admiration with younger siblings). As the ages of the target children increased, role expectations for the siblings became more alike in some ways (e.g. affection and aggression) but less alike in others (e.g. respect and annoyance). The sex composition of the pair minimally influenced subjects’ responses; yet sibling roles for same-sex pairs were more differentiated than roles for mixed-sex pairs. Subjects’ sibling status did not affect their responses. The study provides a detailed description of children’s sibling roles and supported the prospect of using role theory as a framework for considering sibling relationships.
Partnership and Community Involvement: Institutional Morphing in Dundee
Authors: Fernie Keith , McCarthy John
Published: July 2002

In recent years, the policy agenda for urban regeneration in Scotland has focused on social justice and inclusion, reflecting the priorities of the New Labour government and the Scottish Parliament. In addition, there is now a national ‘community planning’ agenda in Scotland, aimed at improving service delivery by enhancing partnership between all relevant agencies, including local communities. This article examines how the regeneration partnership in Dundee - the ‘Dundee Partnership’ - has ‘morphed’ or evolved, in terms of institutional capacity, to respond to this changing context, as well as changing expectations in terms of community involvement. Firstly, critical concepts are set out; secondly, the evolution of the Dundee Partnership is considered; thirdly, the changing nature of community involvement within regeneration is highlighted; and finally, broad conclusions are proposed.
Augmentation of protective immune responses against viral infection by oral administration of schizophyllan
Authors: Itoh Wataru
Published: July 2002

An oral administration of fungal polysaccharide schizophyllan has augmented protective immune responses to Sendai virus infection in mice and the rodshaped DNA virus of Penaeus japonicus (RV‐PJ) infection in Kuruma shrimps. When schizophyllan was administered orally at a dose of 50 or 100 mg/kg body weight per day, the survival rates after virus challenge were significantly higher than those of the control groups. High phagocytic activities were observed in the haemocytes of the schizophyllan‐fed shrimps.These results suggest that schizophyllan confers effective protection against viral infection by increasing antiviral immune responses, and that it could be used to boost immunity to virus infection in animals or in invertebrates.