bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring the refolding of β-sheets with different turn sequences on a nanosecond time scale
Authors: Chen Rita P.-Y. , Huang Joseph J.-T. , Chen Hsin-Liang , Jan Howard , Velusamy Marappan , Lee Chung-Tien , Fann Wunshain , Larsen Randy W. , Chan Sunney I.
Published: May 2004

Whether turns play an active or passive role in protein folding remains a controversial issue at this juncture. Here we use a photolabile cage strategy in combination with laser-flash photolysis and photoacoustic calorimetry to study the effects of different turns on the kinetics of β-hairpin refolding on a nanosecond time scale. This strategy opens up a temporal window to allow the observation of early kinetic events in the protein refolding process at ambient temperature and pH without interference from any denaturants. Our results provide direct evidence demonstrating that even a one-residue difference in the turn region can change the refolding kinetics of a peptide. This observation suggests an active role for turn formation in directing protein folding.
Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation
Authors: Kondo Yutaka , Shen Lanlan , Yan Pearlly S. , Huang Tim Hui-Ming , Issa Jean-Pierre J.
Published: May 2004

Switching from acetylation to methylation at histone H3 lysine 9 (K9) has recently been shown to contribute to euchromatin gene silencing. To identify genes silenced by K9 modifications, we probed a human CpG island microarray with DNA obtained by chromatin immunoprecipitation (ChIP) in a cancer cell line using an anti-H3-K9 methylated antibody or an anti-H3-K9 acetylated antibody. Of the 27 clones with the highest signal ratio of K9 methylation over acetylation (Me/Ac), 13 contained repetitive sequences. Among 14 nonrepetitive clones, we identified 11 genes (seven known and four previously undescribed), one EST, and two unknown fragments. Using ChIP-PCR, all 18 examined clones showed higher ratios of H3-K9 Me/Ac than the active gene control,
P21
, thus confirming the microarray data. In addition, we found a strong correlation between the K9 Me/Ac ratio and CpG island DNA methylation (
R
= 0.92,
P
< 0.01), and five of seven genes examined (
megalin
, thrombospondin-4,
KR18
, latrophilin-3, and phosphatidylinositol-3-OH kinase
P101
subunit) showed lack of expression by RT-PCR and reactivation by DNA methylation and/or histone deacetylase inhibition, suggesting that these genes are true targets of silencing through histone modifications. All five genes also showed significant DNA methylation in a cell line panel and in primary colon cancers. Our data suggest that CpG island microarray coupled with ChIP can identify novel targets of gene silencing in cancer. This unbiased approach confirms the tight coupling between DNA methylation and histone modifications in cancer and could be used to probe gene silencing in nonneoplastic conditions as well.
Paracrine regulation of mammalian oocyte maturation and male germ cell survival
Authors: Kawamura Kazuhiro , Kumagai Jin , Sudo Satoko , Chun Sang-Young , Pisarska Margareta , Morita Hiroki , Toppari Jorma , Fu Ping , Wade John D. , Bathgate Ross A. D. , Hsueh Aaron J. W.
Published: May 2004

Mammalian oocytes are arrested at the prophase of meiosis before induction of maturation by the preovulatory luteinizing hormone (LH) surge. LH also promotes the survival of meiotic male germ cells in the testis. Because LH binds somatic cells, the mechanism underlying its regulation of germ cell function is unclear. We found that LH stimulates Leydig insulin-like 3 (INSL3) transcripts in ovarian theca and testicular Leydig cells. INSL3, in turn, binds a G protein-coupled receptor, LGR8 (leucine-rich repeat-containing G protein-coupled receptor 8), expressed in germ cells to activate the inhibitory G protein, thus leading to decreases in cAMP production. Treatment with INSL3 initiates meiotic progression of arrested oocytes in preovulatory follicles
in vitro
and
in vivo
and suppresses male germ cell apoptosis
in vivo
, thus demonstrating the importance of the INSL3-LGR8 paracrine system in mediating gonadotropin actions.
Carbon nutrition of
Escherichia coli
in the mouse intestine
Authors: Chang Dong-Eun , Smalley Darren J. , Tucker Don L. , Leatham Mary P. , Norris Wendy E. , Stevenson Sarah J. , Anderson April B. , Grissom Joe E. , Laux David C. , Cohen Paul S. , Conway Tyrrell
Published: May 2004

Whole-genome expression profiling revealed
Escherichia coli
MG1655 genes induced by growth on mucus, conditions designed to mimic nutrient availability in the mammalian intestine. Most were nutritional genes corresponding to catabolic pathways for nutrients found in mucus. We knocked out several pathways and tested the relative fitness of the mutants for colonization of the mouse intestine in competition with their wild-type parent. We found that only mutations in sugar pathways affected colonization, not phospholipid and amino acid catabolism, not gluconeogenesis, not the tricarboxylic acid cycle, and not the pentose phosphate pathway. Gluconate appeared to be a major carbon source used by
E. coli
MG1655 to colonize, having an impact on both the initiation and maintenance stages.
N
-acetylglucosamine and
N
-acetylneuraminic acid appeared to be involved in initiation, but not maintenance. Glucuronate, mannose, fucose, and ribose appeared to be involved in maintenance, but not initiation. The
in vitro
order of preference for these seven sugars paralleled the relative impact of the corresponding metabolic lesions on colonization: gluconate >
N
-acetylglucosamine >
N-
acetylneuraminic acid = glucuronate > mannose > fucose > ribose. The results of this systematic analysis of nutrients used by
E. coli
MG1655 to colonize the mouse intestine are intriguing in light of the nutrient-niche hypothesis, which states that the ecological niches within the intestine are defined by nutrient availability. Because humans are presumably colonized with different commensal strains, differences in nutrient availability may provide an open niche for infecting
E. coli
pathogens in some individuals and a barrier to infection in others.
Short amino acid stretches can mediate amyloid formation in globular proteins: The Src homology 3 (SH3) case
Authors: Ventura Salvador , Zurdo Jesús , Narayanan Saravanakumar , Parreño Matilde , Mangues Ramón , Reif Bernd , Chiti Fabrizio , Giannoni Elisa , Dobson Christopher M. , Aviles Francesc X. , Serrano Luis
Published: May 2004

Protein misfolding and deposition underlie an increasing number of debilitating human disorders. We have shown that model proteins unrelated to disease, such as the Src homology 3 (SH3) domain of the p58α subunit of bovine phosphatidyl-inositol-3′-kinase (PI3-SH3), can be converted
in vitro
into assemblies with structural and cytotoxic properties similar to those of pathological aggregates. By contrast, homologous proteins, such as α-spectrin-SH3, lack the capability of forming amyloid fibrils at a measurable rate under any of the conditions we have so far examined. However, transplanting a small sequence stretch (6 aa) from PI3-SH3 to α-spectrin-SH3, comprising residues of the diverging turn and adjacent RT loop, creates an amyloidogenic protein closely similar in its behavior to the original PI3-SH3. Analysis of specific PI3-SH3 mutants further confirms the involvement of this region in conferring amyloidogenic properties to this domain. Moreover, the inclusion in this stretch of two consensus residues favored in SH3 sequences substantially inhibits aggregation. These findings show that short specific amino acid stretches can act as mediators or facilitators in the incorporation of globular proteins into amyloid structures, and they support the suggestion that natural protein sequences have evolved in part to code for structural characteristics other than those included in the native fold, such as avoidance of aggregation.
The DNA-unwinding mechanism of the ring helicase of bacteriophage T7
Authors: Jeong Yong-Joo , Levin Mikhail K. , Patel Smita S.
Published: May 2004

Helicases are motor proteins that use the chemical energy of NTP hydrolysis to drive mechanical processes such as translocation and nucleic acid strand separation. Bacteriophage T7 helicase functions as a hexameric ring to drive the replication complex by separating the DNA strands during genome replication. Our studies show that T7 helicase unwinds DNA with a low processivity, and the results indicate that the low processivity is due to ring opening and helicase dissociating from the DNA during unwinding. We have measured the single-turnover kinetics of DNA unwinding and globally fit the data to a modified stepping model to obtain the unwinding parameters. The comparison of the unwinding properties of T7 helicase with its translocation properties on single-stranded (ss)DNA has provided insights into the mechanism of strand separation that is likely to be general for ring helicases. T7 helicase unwinds DNA with a rate of 15 bp/s, which is 9-fold slower than the translocation speed along ssDNA. T7 helicase is therefore primarily an ssDNA translocase that does not directly destabilize duplex DNA. We propose that T7 helicase achieves DNA unwinding by its ability to bind ssDNA because it translocates unidirectionally, excluding the complementary strand from its central channel. The results also imply that T7 helicase by itself is not an efficient helicase and most likely becomes proficient at unwinding when it is engaged in a replication complex.
Chlamydial histone-DNA interactions are disrupted by a metabolite in the methylerythritol phosphate pathway of isoprenoid biosynthesis
Authors: Grieshaber Nicole A. , Fischer Elizabeth R. , Mead David J. , Dooley Cheryl A. , Hackstadt Ted
Published: May 2004

The chlamydial developmental cycle is characterized by an intracellular replicative form, termed the reticulate body, and an extracellular form called the elementary body. Elementary bodies are characterized by a condensed chromatin, which is maintained by a histone H1-like protein, Hc1. Differentiation of elementary bodies to reticulate bodies is accompanied by dispersal of the chromatin as chlamydiae become transcriptionally active, although the mechanisms of Hc1 release from DNA have remained unknown. Dissociation of the nucleoid requires chlamydial transcription and translation with negligible loss of Hc1. A genetic screen was therefore designed to identify chlamydial genes rescuing
Escherichia coli
from the lethal effects of Hc1 overexpression. CT804, a gene homologous to
ispE
, which encodes an intermediate enzyme of the non-mevalonate methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis, was selected.
E. coli
coexpressing CT804 and Hc1 grew normally, although they expressed Hc1 to a level equivalent to that which condensed the chromatin of parent Hc1-expressing controls. Inhibition of the MEP pathway with fosmidomycin abolished IspE rescue of Hc1-expressing
E. coli
. Deproteinated extract from IspE-expressing bacteria caused dispersal of purified chlamydial nucleoids, suggesting that chlamydial histone-DNA interactions are disrupted by a small metabolite within the MEP pathway rather than by direct action of IspE. By partial reconstruction of the MEP pathway, we determined that 2-
C
-methylerythritol 2,4-cyclodiphosphate dissociated Hc1 from chlamydial chromatin. These results suggest that chlamydial histone-DNA interactions are disrupted upon germination by a small metabolite in the MEP pathway of isoprenoid biosynthesis.
Identification of hepoxilin A3in inflammatory events: A required role in neutrophil migration across intestinal epithelia
Authors: Mrsny Randall J. , Gewirtz Andrew T. , Siccardi Dario , Savidge Tor , Hurley Bryan P. , Madara James L. , McCormick Beth A.
Published: May 2004

The mechanism by which neutrophils [polymorphonuclear leukocyte (PMNs)] are stimulated to move across epithelial barriers at mucosal surfaces has been basically unknown in biology. IL-8 has been shown to stimulate PMNs to leave the bloodstream at a local site of mucosal inflammation, but the chemical gradient used by PMNs to move between adjacent epithelial cells and traverse the tight junction at the apical neck of these mucosal barriers has eluded identification. Our studies not only identify this factor, previously termed pathogen-elicited epithelial chemoattractant, as the eicosanoid hepoxilin A3(hepA3) but also demonstrate that it is a key factor promoting the final step in PMN recruitment to sites of mucosal inflammation. We show that hepA3is synthesized by epithelial cells and secreted from their apical surface in response to conditions that stimulate inflammatory events. Our data further establish that hepA3acts to draw PMNs, via the establishment of a gradient across the epithelial tight junction complex. The functional significance of hepA3to target PMNs to the lumen of the gut at sites of inflammation was demonstrated by the finding that disruption of the 12-lipoxygenase pathway (required for hepA3production) could dramatically reduce PMN-mediated tissue trauma, demonstrating that hepA3is a key regulator of mucosal inflammation.
Identification of core amino acids stabilizing rhodopsin
Authors: Rader A. J. , Anderson Gülsüm , Isin Basak , Khorana H. Gobind , Bahar Ivet , Klein-Seetharaman Judith
Published: May 2004

Rhodopsin is the only G protein-coupled receptor (GPCR) whose 3D structure is known; therefore, it serves as a prototype for studies of the GPCR family of proteins. Rhodopsin dysfunction has been linked to misfolding, caused by chemical modifications that affect the naturally occurring disulfide bond between C110 and C187. Here, we identify the structural elements that stabilize rhodopsin by computational analysis of the rhodopsin structure and comparison with data from previous
in vitro
mutational studies. We simulate the thermal unfolding of rhodopsin by breaking the native-state hydrogen bonds sequentially in the order of their relative strength, using the recently developed Floppy Inclusion and Rigid Substructure Topography (FIRST) method [Jacobs, D. J., Rader, A. J., Kuhn, L. A. & Thorpe, M. F. (2001)
Proteins
44, 150-165]. Residues most stable under thermal denaturation are part of a core, which is assumed to be important for the formation and stability of folded rhodopsin. This core includes the C110–C187 disulfide bond at the center of residues forming the interface between the transmembrane and the extracellular domains near the retinal binding pocket. Fast mode analysis of rhodopsin using the Gaussian network model also identifies the disulfide bond and the retinal ligand binding pocket to be the most rigid region in rhodopsin. Experiments confirm that 90% of the amino acids predicted by the FIRST method to be part of the core cause misfolding upon mutation. The observed high degree of conservation (78.9%) of this disulfide bond across all GPCR classes suggests that it is critical for the stability and function of GPCRs.
The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold
Authors: Corbett Kevin D. , Shultzaberger Ryan K. , Berger James M.
Published: May 2004

DNA gyrase is unique among enzymes for its ability to actively introduce negative supercoils into DNA. This function is mediated in part by the C-terminal domain of its A subunit (GyrA CTD). Here, we report the crystal structure of this ≈35-kDa domain determined to 1.75-Å resolution. The GyrA CTD unexpectedly adopts an unusual fold, which we term a β-pinwheel, that is globally reminiscent of a β-propeller but is built of blades with a previously unobserved topology. A large, conserved basic patch on the outer edge of this domain suggests a likely site for binding and bending DNA; fluorescence resonance energy transfer-based assays show that the GyrA CTD is capable of bending DNA by ≥180° over a 40-bp region. Surprisingly, we find that the CTD of the topoisomerase IV A subunit, which shares limited sequence homology with the GyrA CTD, also bends DNA. Together, these data provide a physical explanation for the ability of DNA gyrase to constrain a positive superhelical DNA wrap, and also suggest that the particular substrate preferences of topoisomerase IV might be dictated in part by the function of this domain.
The diploid genome sequence of
Candida albicans
Authors: Jones Ted , Federspiel Nancy A. , Chibana Hiroji , Dungan Jan , Kalman Sue , Magee B. B. , Newport George , Thorstenson Yvonne R. , Agabian Nina , Magee P. T. , Davis Ronald W. , Scherer Stewart
Published: May 2004

We present the diploid genome sequence of the fungal pathogen
Candida albicans
. Because
C. albicans
has no known haploid or homozygous form, sequencing was performed as a whole-genome shotgun of the heterozygous diploid genome in strain SC5314, a clinical isolate that is the parent of strains widely used for molecular analysis. We developed computational methods to assemble a diploid genome sequence in good agreement with available physical mapping data. We provide a whole-genome description of heterozygosity in the organism. Comparative genomic analyses provide important clues about the evolution of the species and its mechanisms of pathogenesis.
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
Authors: Mathews David H. , Disney Matthew D. , Childs Jessica L. , Schroeder Susan J. , Zuker Michael , Turner Douglas H.
Published: May 2004

A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method,
in vivo
modification was performed on 5S rRNA in both
Escherichia coli
and
Candida albicans
with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-
p
-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the
E. coli
sequence by using modification constraints. For
C. albicans
, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs.
Influences of a rider on the rotation of the horse–rider system during jumping
Authors: Powers PNR , Harrison AJ
Published: May 2004

This study examined the effects of a rider on the angular momentum and angular velocity of the jumping horse, particularly during the flight phase. Sagittal plane video recordings were digitized of eight horses jumping a vertical fence (1 m high) under two conditions: Loose and Ridden. An experienced rider rode the horses during the Ridden condition. Using appropriate segmental inertial data for the horse and rider, angular momentum and angular velocity were calculated for the Loose and Ridden conditions. Estimates of the various rider effects on angular momentum and angular velocity were obtained by comparison of Loose and Ridden conditions and examination of the contributions of the horse and rider segments to the total angular momentum. The results showed that the rider's effect on angular momentum was significant but that the rider's segmental contribution to the angular momentum of the horse–rider system was minimal. Repeated-measures ANOVA revealed that the rider had a significant effect on the angular momentum and angular velocity of the horse during the flight phase (P<0.01). However, the rider did not have a significant effect on the transfer of angular momentum during the flight. We concluded that the rider's instruction has a greater influence on the horse's motion than the mechanical transfer between rider and horse.
When Two Limbs are Weaker than One: Sensorimotor Syncopation with Alternating Hands
Authors: Keller Peter E. , Repp Bruno H.
Published: April 2004

This study addresses the demands of alternating bimanual syncopation, a coordination mode in which the two hands move in alternation while tapping in antiphase with a metronomic tone sequence. Musically trained participants were required to engage in alternating bimanual syncopation and five other coordination modes: unimanual syncopation where taps are made (with the left or right hand) after every tone; unimanual syncopation where taps are made after every other tone; bimanual synchronization with alternating hands; unimanual synchronized tapping with every tone; and unimanual tapping with every other tone. Variability in tap timing was greatest overall for alternating bimanual syncopation, indicating that it is the most difficult. This appears to be due to instability arising from the simultaneous presence of two levels of antiphase coordination (one between the pacing sequence and the hands, the other between the two hands) rather than factors relating to movement frequency or dexterity limits of the nonpreferred hand.
Report of diffusion‐weighted MRI in two cases with different cerebral hydatid disease
Authors: Kitis O. , Calli C. , Yunten N.
Published: April 2004

Purpose: To present MRI findings in two cases of cerebral hydatid disease with an emphasis on diffusion‐weighted imaging (DWI) findings of Echinococcus granulosus (EG) versus Echinococcus alveolaris (EA).

Results: EG lesions were isointense with cerebrospinal fluid in all sequences including DWI. On DWI, EA lesions remained hypointense on b=1000 s/mm2 diffusion‐weighted images. Apparent diffusion coefficient (ADC) values of EG and EA lesions were completely different from each other, 2.88±0.24×10−3 s/mm2 and 1.33±0.15×10−3 s/mm2, respectively.

Conclusion: The ADC values could not be used to discriminate from other differential diagnoses.
Social capital, the miniaturization of community and assessment of patient satisfaction in primary healthcare: a population-based study
Authors: Lindström Martin , Axén Elin
Published: April 2004

Aims: A study was undertaken to assess the impact of social participation, trust and the miniaturization of community, i.e. high social participation/low trust, on two measures of patient dissatisfaction in primary healthcare. Methods: The Scania 2000 public-health survey is a cross-sectional, postal questionnaire study. A total of 3,456 persons aged 18 - 80 years who had a regular doctor within the primary healthcare system were included. A logistic regression model was used to investigate the association between the social capital variables and dissatisfaction. Multivariate analysis analysed the importance of confounders on the differences in lack of general openness and lack of information concerning treatment in accordance with social capital variables. Results: Lack of openness is positively associated with low trust, the miniaturization of community and low social capital, while lack of information is not significantly associated with the miniaturization of community, but to a lesser extent with low trust and low social capital. Conclusions: Low levels of trust and the miniaturization of community may enhance non-specific patient dissatisfaction such as experience of lack of openness by the patient. In contrast, the miniaturization of community was not significantly associated with the more specific "lack of information''. The results have implications for the evaluation of patient dissatisfaction.
Prevalence and regional differences in overweight in 2001 and trends in BMI distribution in Swedish children from 1987 to 2001
Authors: Ekblom Örjan B. , Oddsson Kristjan , Ekblom Björn T.
Published: April 2004

Aims: This study was undertaken to assess current prevalence and regional differences of overweight in 2001 and changes in body mass index (BMI) distribution between 1987 and 2001 in Swedish adolescents. Methods: Comparison was made of two independent samples. For assessment of prevalence and regional differences in 2001, a total of 1732 subjects were used. For trend analyses a total of 1,949 children (516 and 1,470 in 1987 and 2001, respectively), aged 10, 13, and 16 years. Results: The prevalence of overweight in 2001 was between 21.7% and 13.3% for boys and girls aged 10 to 16 years and the prevalence of obesity was between 2.9% and 6.2%. Mean BMI as well as prevalence of overweight and obesity was higher in subjects from schools in smaller towns or from the countryside. Median BMI among adolescents changed from 1987 to 2001, most notably in 13- and 16-year-old children. The prevalence of overweight and obesity combined has changed more than 2.5-fold in children aged 10 to 16 years. In this study, the most pronounced elevation in BMI is found in the upper part of the BMI spectrum. This change is especially apparent in girls. Conclusion: The change in mean BMI and prevalence of overweight and obesity in children in this study is mainly due to the pronounced change in BMI at the upper end of the spectrum, indicating that the factors leading to overweight or obesity have changed in only a subgroup of the child population.
Intracellular Trafficking of Bile Salt Export Pump (ABCB11) in Polarized Hepatic Cells: Constitutive Cycling between the Canalicular Membrane and rab11-positive Endosomes
Authors: Wakabayashi Yoshiyuki , Lippincott-Schwartz Jennifer , Arias Irwin M.
Published: May 2004

The bile salt export pump (BSEP, ABCB11) couples ATP hydrolysis with transport of bile acids into the bile canaliculus of hepatocytes. Its localization in the apical canalicular membrane is physiologically regulated by the demand to secrete biliary components. To gain insight into how such localization is regulated, we studied the intracellular trafficking of BSEP tagged with yellow fluorescent protein (YFP) in polarized WIF-B9 cells. Confocal imaging revealed that BSEP-YFP was localized at the canalicular membrane and in tubulo-vesicular structures either adjacent to the microtubule-organizing center or widely distributed in the cytoplasm. In the latter two locations, BSEP-YFP colocalized with rab11, an endosomal marker. Selective photobleaching experiments revealed that single BSEP-YFP molecules resided in canalicular membranes only transiently before exchanging with intracellular BSEP-YFP pools. Such exchange was inhibited by microtubule and actin inhibitors and was unaffected by brefeldin A, dibutyryl cyclic AMP, taurocholate, or PI 3-kinase inhibitors. Intracellular carriers enriched in BSEP-YFP elongated and dissociated as tubular elements from a globular structure adjacent to the microtubule-organizing center. They displayed oscillatory movement toward either canalicular or basolateral membranes, but only fused with the canalicular membrane. The pathway between canalicular and intracellular membranes that BSEP constitutively cycles within could serve to regulate apical pools of BSEP as well as other apical membrane transporters.
Estradiol Abrogates Apoptosis in Breast Cancer Cells through Inactivation of BAD: Ras-dependent Nongenomic Pathways Requiring Signaling through ERK and Akt
Authors: Fernando Romaine Ingrid , Wimalasena Jay
Published: May 2004

Estrogens such as 17-β estradiol (E2) play a critical role in sporadic breast cancer progression and decrease apoptosis in breast cancer cells. Our studies using estrogen receptor-positive MCF7 cells show that E2abrogates apoptosis possibly through phosphorylation/inactivation of the proapoptotic protein BAD, which was rapidly phosphorylated at S112 and S136. Inhibition of BAD protein expression with specific antisense oligonucleotides reduced the effectiveness of tumor necrosis factor-α, H2O2, and serum starvation in causing apoptosis. Furthermore, the ability of E2to prevent tumor necrosis factor-α-induced apoptosis was blocked by overexpression of the BAD S112A/S136A mutant but not the wild-type BAD. BAD S112A/S136A, which lacks phosphorylation sites for p90RSK1and Akt, was not phosphorylated in response to E2in vitro.E2treatment rapidly activated phosphatidylinositol 3-kinase (PI-3K)/Akt and p90RSK1to an extent similar to insulin-like growth factor-1 treatment. In agreement with p90RSK1activation, E2also rapidly activated extracellular signal-regulated kinase, and this activity was down-regulated by chemical and biological inhibition of PI-3K suggestive of cross talk between signaling pathways responding to E2. Dominant negative Ras blocked E2-induced BAD phosphorylation and the Raf-activator RasV12T35S induced BAD phosphorylation as well as enhanced E2-induced phosphorylation at S112. Chemical inhibition of PI-3K and mitogen-activated protein kinase kinase 1 inhibited E2-induced BAD phosphorylation at S112 and S136 and expression of dominant negative Ras-induced apoptosis in proliferating cells. Together, these data demonstrate a new nongenomic mechanism by which E2prevents apoptosis.
Multiple Interactions of Rad23 Suggest a Mechanism for Ubiquitylated Substrate Delivery Important in Proteolysis
Authors: Kim Ikjin , Mi Kaixia , Rao Hai
Published: May 2004

The mechanism underlying the delivery of ubiquitylated substrates to the proteasome is poorly understood. Rad23 is a putative adaptor molecule for this process because it interacts with ubiquitin chains through its ubiquitin-associated motifs (UBA) and with the proteasome through a ubiquitin-like element (UBL). Here, we demonstrate that the UBL motif of Rad23 also binds Ufd2, an E4 enzyme essential for ubiquitin chain assembly onto its substrates. Mutations in the UBL of Rad23 alter its interactions with Ufd2 and the proteasome, and impair its function in the UFD proteolytic pathway. Furthermore, Ufd2 and the proteasome subunit Rpn1 compete for the binding of Rad23, suggesting that Rad23 forms separate complexes with them. Importantly, we also find that the ability of other UBL/UBA proteins to associate with Ufd2 correlates with their differential involvement in the UFD pathway, suggesting that UBL-mediated interactions may contribute to the substrate specificity of these adaptors. We propose that the UBL motif, a protein-protein interaction module, may be used to facilitate coupling between substrate ubiquitylation and delivery, and to ensure the orderly handoff of the substrate from the ubiquitylation machinery to the proteasome.
Sorting Nexin 17 Accelerates Internalization Yet Retards Degradation of P-selectin
Authors: Williams Ross , Schlüter Thomas , Roberts Marnie S. , Knauth Peter , Bohnensack Ralf , Cutler Daniel F.
Published: May 2004

The transient appearance of P-selectin on the surface of endothelial cells helps recruit leukocytes into sites of inflammation. The tight control of cell surface P-selectin on these cells depends on regulated exocytosis of Weibel-Palade bodies where the protein is stored and on its rapid endocytosis. After endocytosis, P-selectin is either sorted via endosomes and the Golgi apparatus for storage in Weibel-Palade bodies or targeted to lysosomes for degradation. A potential player in this complex endocytic itinerary is SNX17, a member of the sorting nexin family, which has been shown in a yeast two-hybrid assay to bind P-selectin. Here, we show that overexpression of SNX17 in mammalian cells can influence two key steps in the endocytic trafficking of P-selectin. First, it promotes the endocytosis of P-selectin from the plasma membrane. Second, it inhibits the movement of P-selectin into lysosomes, thereby reducing its degradation.
YAdumper: extracting and translating large information volumes from relational databases to structured flat files
Authors: Fernández José M. , Valencia Alfonso
Published: May 2004

Summary: Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Availability: YAdumper is freely available.
Class discovery and classification of tumor samples using mixture modeling of gene expression data—a unified approach
Authors: Alexandridis Roxana , Lin Shili , Irwin Mark
Published: May 2004

Motivation: The DNA microarray technology has been increasingly used in cancer research. In the literature, discovery of putative classes and classification to known classes based on gene expression data have been largely treated as separate problems. This paper offers a unified approach to class discovery and classification, which we believe is more appropriate, and has greater applicability, in practical situations.

Results: We model the gene expression profile of a tumor sample as from a finite mixture distribution, with each component characterizing the gene expression levels in a class. The proposed method was applied to a leukemia dataset, and good results are obtained. With appropriate choices of genes and preprocessing method, the number of leukemia types and subtypes is correctly inferred, and all the tumor samples are correctly classified into their respective type/subtype. Further evaluation of the method was carried out on other variants of the leukemia data and a colon dataset.

Supplementary information: The program implementing the method and additional details and figures are at http://www.stat.ohio-state.edu/~statgen/PAPERS/DNC-MIX.html.
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
Authors: Barth Sandra , Fischer Markus , Schmid Rolf D. , Pleiss Jürgen
Published: May 2004

Summary: The epoxide hydrolases and haloalkane dehalogenases database (EH/HD) integrates sequence and structure of a highly diverse protein family, including mainly the Asp-hydrolases of EHs and HDs but also proteins, such as Ser-hydrolases non-heme peroxidases, prolyl iminopetidases and 2-hydroxymuconic semialdehyde hydrolases. These proteins have a highly conserved structure, but display a remarkable diversity in sequence and function. A total of 305 protein entries were assigned to 14 homologous families, forming two superfamilies. Annotated multisequence alignments and phylogenetic trees are provided for each homologous family and superfamily. Experimentally derived structures of 19 proteins are superposed and consistently annotated. Sequence and structure of all 305 proteins were systematically analysed. Thus, deeper insight is gained into the role of a highly conserved sequence motifs and structural elements.

Availability: The EH/HD database is available at http://www.led.uni-stuttgart.de
Convergence of ethics?
Authors: Richter Ewa Maria , Buttery Ernest Alan
Published: April 2004

Two pillars of Western culture are the free market doctrine and democracy. The ability of these pillars to generate behavior that converges to a global ethical system is investigated. The market mechanism is no longer as described by Adam Smith, it is oligopolistic. Strategic architecture is outside the resources of many firms, a value free morality prevails, and government intervenes in the market. People believe that they are better off than in the past. However, the gap between the “haves” and “have‐nots” is widening. Market doctrine does not conform to ethical principles. Market freedom requires choice; it benefits corporations giving rise to three diverging classes in society. This type of imperialism potentially contains the seeds of its own destruction.
Recent trends in library services for ethnic minorities – the Danish experience
Authors: Berger Ågot
Published: April 2004

Outlines the experiences of the author in studying library services in multiethnic societies in several countries in Western Europe. This led to a comprehensive survey, carried out in 2001, into how the ethnic minorities in Denmark use public libraries. The historical context to immigration to Denmark and changing government policies are described, together with the development of public library services. The work of the Danish Central Library of Immigrant Literature is reviewed. The methodology and main findings are provided, together with recommendations. Two main lessons emerged: that public libraries have something both unique and essential to offer as a part of a national policy towards immigration and ethnic minorities; and that success lies in combining different service elements and ensuring that libraries are perceived and used as friendly meeting places.
Optimal shielding of low frequency fields
Authors: Canova Aldo , Gruosso Giambattista , Repetto Maurizio
Published: April 2004

Shielding of electromagnetic low frequency field can be performed by means of conductive sheets. These sheets have a thickness which is usually two or three orders of magnitude lower than their other dimensions, thus their effects must be modeled by means of special numerical techniques. In this paper, two integral formulations for the analysis of conductive shields are presented: one is two‐dimensional and is based on a multiconductor system, while the other, three‐dimensional, is based on a finite formulation of electromagnetic fields. Once these analysis tools have been introduced, this paper presents the study of different shielding systems and a problem of optimal exploitation of conductive material.
Nonlinear model of linear synchronous reluctance motor for real time applications
Authors: Štumberger Gorazd , Štumberger Bojan , Dolinar Drago , Težak Oto , Hameyer Kay
Published: April 2004

The finite element (FE) method calculations are used to improve dynamic behavior of the two‐axis linear synchronous reluctance motor (LSRM) model, which is appropriate for the control design, the real time applications and the low speed servo applications. By the FE method, calculated current and position dependent flux linkages, their partial derivatives and motor thrust are approximated by the continuous functions and incorporated into the dynamic LSRM model as a nonlinear iron core model. The agreement between the calculated and the measured flux linkages, their partial derivatives and the motor thrust is very good. The agreement between all trajectories calculated by the improved dynamic LSRM model and measured during the experiment in the case of kinematic control is very good as well.
Fourier and wavelet transform analysis of moire fringe patterns in electronic packaging
Authors: Xiong C.Y. , Zhang J. , Li M. , Fang J. , Yi S.
Published: April 2004

In this paper, two transform methods, the Fourier transform (FT) and the wavelet transform (WT) methods, are utilized to process moiré fringes for the strain analysis of electronic packaging. With the introduction of fringe carriers, those transform techniques need only one fringe pattern for each deformation state. The strain modulation to the carrier frequency can be subtracted by filtering as the pattern is transformed into spectrum domain by the fast‐FT processing, and the deformation field can thus be restored by the inverse FT transform after spectral shifting. The WT method expands the pattern information involved in the fringe carrier in both spatial domain and spectral domain to analyze the deformation distribution in this combined space. By changing the transform scales in the processing, the wavelet transform offers multi‐resolution analysis for the deformation field with high gradients.
The nature of hospital prescribing errors
Authors: Dobrzanski S. , Hammond I. , Khan G. , Holdsworth H.
Published: April 2004

A study was carried out to determine the nature of medical prescribing errors identified by pharmacists in an NHS Hospital Trust. From the 587 errors detected in a one‐month period, eight were potentially grave, 151 were potentially very serious, 351 were potentially moderately serious and 77 were comparatively minor. This extrapolated to 7,044 prescribing problems a year and an estimated detected prescribing error rate of approximately 0.35 to 0.7 per cent. Pharmacists detected 63 per cent of these errors while working on wards and 36 per cent while in dispensaries. The main causes of errors were failure to obtain an accurate medication history, oversight and prescribing uncertainty. In the absence of guidelines, there was a tendency for the isolated hard‐pressed prescriber to guess or prescribe on a “that looks about right somehow” basis. This study has made medical staff more aware of the areas where they are most vulnerable to making prescribing errors. In addition, greater support is now being offered to junior doctors in checking medication histories and in creating prescribing guidelines.
Power in the union?
Authors: Broadbent Kaye
Published: April 2004

Increases in the number of jobs for part‐time workers has had little impact on the rate of unionisation for part‐time workers, the majority of whom are women. The argument run by union officials in Japan is that women, and thus part‐time workers, are not interested in industrial issues. This study explores an alternative explanation which is that union officials and “core” male workers are excluding women and part‐time workers in order to protect their own privileged position. Whilst it is acknowledged that the organisational structure of enterprise unions makes it difficult to incorporate the needs of part‐time workers, it is the attitudes of “core” male workers and union officials to women as paid workers that is the major hurdle to the non‐unionisation of part‐time workers. For women and part‐time workers there is no power in the union.
Revitalising new process development in the UK fine chemicals industry
Authors: Shaw N.E. , Burgess T.F. , Hwarng H.B. , de Mattos C.
Published: April 2004

Reports on one of the key developments made to date on a three‐year EPSRC IMI research project in the fine chemicals industry. The project, Batch Route Innovative Technology: Evaluation and Selection Techniques (BRITEST), began in late 1997 with the aim to research new methods to deliver substantial benefits associated with new product development. The project will deliver a methodology, models and a suite of decision support tools sustaining and improving the new product development process, enabling novel technical solutions to be developed more in line with, and evaluated more appropriately against, the business strategy and market characteristics. The specific deliverable presented in this paper is an action research‐derived framework that integrates the detailed processes, information requirements and decision making as a model of good practice for new product (or process) development (NPD) in the fine chemicals industry.
Bootstrapping knowledge representations
Authors: Heylighen Francis
Published: April 2004

The symbol‐based epistemology used in artificial intelligence is contrasted with the constructivist, coherence epistemology promoted by cybernetics. The latter leads to bootstrapping knowledge representations, in which different parts of the system mutually support each other. Gordon Pask’s entailment meshes are reviewed as a basic application of this approach, and then extended to entailment nets: directed graphs governed by the “bootstrapping axiom”, determining which concepts are to be distinguished or merged. This allows a constant restructuring of the conceptual network. Semantic networks and frame‐like representations can be expressed in this scheme by introducing a basic ontology of node and link types. Entailment nets are then generalized to associative networks with weighted links. Learning algorithms are presented which can adapt the link strengths, based on the frequency with which links are selected by hypertext users. It is argued that such bootstrapping methods can be applied to make the World Wide Web more intelligent, allowing it to self‐organize and support inferences.
Investigating resource utilization and product competence to improve production management
Authors: Chen Liang‐Hsuan , Liaw Shu‐Yi
Published: April 2004

Proposes an approach to improving production management (PM) of a firm through examining its resource utilization and product competence. To understand the status of PM in Taiwan, evaluates the achievement levels of 14 production management subjects from 50 large‐scale manufacturing firms. The subjects are further classified into four planning ranges of PM. Then productivity measures of these firms for resource utilization and product competence are determined. Two groups of patterns with distinct PM characteristics are found through a fuzzy clustering analysis based on resource utilization and product competence. Significant correlation has been found between resource utilization and product competence and PM. The PM patterns with good performance in terms of resource utilization and product competence are considered targets for firms of other patterns. The ways of adjusting PM for these firms of other patterns are then described in terms of the characteristics of the target patterns.
Work Life and Social Fulfillment: Does Social Affiliation at Work Reflect a Carrot or a Stick?*
Authors: Hodson Randy
Published: April 2004

Objectives.Work life and home life appear to be in increasing competition for scarce time and attention. Does the workplace offer a social haven for people? And if so, for whom is it most attractive? Or does the increasing affiliation with work life result from heightened job insecurity, which demands that employees focus on work in order to keep their jobs?

Methods.In this article we analyze a unique data set incorporating all book‐length workplace ethnographies (N=149) to address these questions. This data set provides rich measures of social life at work and related correlates.

Results.We find that rich social lives are common at work and that these correlate strongly with fulfillment, pride, and meaning in work. Well‐paid employees are much more likely to experience a rich social life at work than are lower‐level employees. Job security appears to be a relative constant, unrelated to the richness of social life on the job. Men are more socially involved at work than women, reflecting their greater average involvement in work life relative to family life. This relationship, however, does not hold net of controls, suggesting that it reflects underlying differences in the jobs men and women hold.

Conclusions.These findings suggest a bifurcated labor force in which upper‐status employees reap both greater material and greater social rewards from their jobs and, as a result, are more drawn to work, and to workaholism, than lower‐status workers.
Ideological Centrism and the Electoral Fortunes of U.S. Senate Candidates*
Authors: Gershtenson Joseph
Published: April 2004

Objective. The Downsian model of electoral competition with its individual‐level assumption of proximity voting by individuals implies that candidates in two‐party systems should perform better in elections when they adopt platforms more closely mirroring preferences of average constituents. Since extant analyses do not place candidates and constituents on a common ideological metric, they do not directly test the electoral consequences of proximity to voters. This study provides a direct test.

Methods. I use the NES Senate Election Study to locate candidates and constituents on a common ideological metric and use ordinary least squares regression models to analyze the effects of candidate positioning on electoral outcomes.

Results. Although stiff electoral competition may make it more likely that candidates gain votes by locating near average citizens, candidate proximity does not generally have a meaningful effect on Senate elections.

Conclusions. Insignificant electoral benefits from ideological centrism may help explain candidate divergence in elections and has important implications for the nature of representation.