bluuebunny/crossref_metadata_2025_split huggingface dataset:
CBFβ is a facultative Runx partner in the sea urchin embryo
Authors: Robertson Anthony J , Dickey-Sims Carrie , Ransick Andrew , Rupp Dawn E , McCarthy John J , Coffman James A 
Published: February 2006

Abstract

Background

Runx proteins are developmentally important metazoan transcription factors that form a heterodimeric complex with the non-homologous protein Core Binding Factor β (CBFβ). CBFβ allosterically enhances Runx DNA binding but does not bind DNA itself. We report the initial characterization of SpCBFβ, the heterodimeric partner of SpRunt-1 from the sea urchin Stronylocentrotus purpuratus.

Results

SpCBFβ is remarkably similar to its mammalian homologues, and like them it enhances the DNA binding of the Runt domain. SpCBFβ is entirely of zygotic provenance and its expression is similar that of SpRunt-1, accumulating globally at late blastula stage then later localizing to endoderm and oral ectoderm. Unlike SpRunt-1, however, SpCBFβ is enriched in the endodermal mid- and hindgut of the pluteus larva, and is not highly expressed in the foregut and ciliated band. We showed previously that morpholino antisense-mediated knockdown of SpRunt-1 leads to differentiation defects, as well as to extensive post-blastula stage apoptosis caused by under-expression of the Runx target gene SpPKC1. In contrast, we show here that knockdown of SpCBFβ does not negatively impact cell survival or SpPKC1 expression, although it does lead to differentiation defects similar to those associated with SpRunt-1 deficiency. Moreover, SpRunt-1 containing a single amino acid substitution that abolishes its ability to interact with SpCBFβ retains the ability to rescue cell survival in SpRunt-1 morphant embryos. Chromatin immunoprecipitation shows that while the CyIIIa promoter engages both proteins, the SpPKC1 promoter only engages SpRunt-1.

Conclusion

SpCBFβ is a facultative Runx partner that appears to be required specifically for cell differentiation.
Patterns of evolution of host proteins involved in retroviral pathogenesis
Authors: Ortiz Millan , Bleiber Gabriela , Martinez Raquel , Kaessmann Henrik , Telenti Amalio 
Published: February 2006

Abstract

Background
Evolutionary analysis may serve as a useful approach to identify and characterize host defense and viral proteins involved in genetic conflicts. We analyzed patterns of coding sequence evolution of genes with known (TRIM5α and APOBEC3G) or suspected (TRIM19/PML) roles in virus restriction, or in viral pathogenesis (PPIA, encoding Cyclophilin A), in the same set of human and non-human primate species.

Results and conclusion
This analysis revealed previously unidentified clusters of positively selected sites in APOBEC3G and TRIM5α that may delineate new virus-interaction domains. In contrast, our evolutionary analyses suggest that PPIA is not under diversifying selection in primates, consistent with the interaction of Cyclophilin A being limited to the HIV-1M/SIVcpz lineage. The strong sequence conservation of the TRIM19/PML sequences among primates suggests that this gene does not play a role in antiretroviral defense.
Chemical immobilization of adult female Weddell seals with tiletamine and zolazepam: effects of age, condition and stage of lactation
Authors: Wheatley Kathryn E , Bradshaw Corey JA , Harcourt Robert G , Davis Lloyd S , Hindell Mark A 
Published: February 2006

AbstractBackgroundChemical immobilization of Weddell seals (Leptonychotes weddellii) has previously been, for the most part, problematic and this has been mainly attributed to the type of immobilizing agent used. In addition to individual sensitivity, physiological status may play an important role. We investigated the use of the intravenous administration of a 1:1 mixture of tiletamine and zolazepam (Telazol®) to immobilize adult females at different points during a physiologically demanding 5–6 week lactation period. We also compared performance between IV and IM injection of the same mixture.ResultsThe tiletamine:zolazepam mixture administered intravenously was an effective method for immobilization with no fatalities or pronounced apnoeas in 106 procedures; however, there was a 25 % (one animal in four) mortality rate with intramuscular administration. Induction time was slightly longer for females at the end of lactation (54.9 ± 2.3 seconds) than at post-parturition (48.2 ± 2.9 seconds). In addition, the number of previous captures had a positive effect on induction time. There was no evidence for effects due to age, condition (total body lipid), stage of lactation or number of captures on recovery time.ConclusionWe suggest that intravenous administration of tiletamine and zolazepam is an effective and safe immobilizing agent for female Weddell seals. Although individual traits could not explain variation in recovery time, we suggest careful monitoring of recovery times during longitudinal studies (> 2 captures). We show that physiological pressures do not substantially affect response to chemical immobilization with this mixture; however, consideration must be taken for differences that may exist for immobilization of adult males and juveniles. Nevertheless, we recommend a mass-specific dose of 0.50 – 0.65 mg/kg for future procedures with adult female Weddell seals and a starting dose of 0.50 mg/kg for other age classes and other phocid seals.
Randomization in substance abuse clinical trials
Authors: Hedden Sarra L , Woolson Robert F , Malcolm Robert J 
Published: February 2006

AbstractBackgroundA well designedrandomizedclinical trial rates as the highest level of evidence for a particular intervention's efficacy. Randomization, a fundamental feature of clinical trials design, is a process invoking the use of probability to assign treatment interventions to patients. In general, randomization techniques pursue the goal of providing objectivity to the assignment of treatments, while at the same time balancing for treatment assignment totals and covariate distributions. Numerous randomization techniques, each with varying properties of randomness and balance, are suggested in the statistical literature. This paper reviews common randomization techniques often used in substance abuse research and an application from a National Institute on Drug Abuse (NIDA)-funded clinical trial in substance abuse is used to illustrate several choices an investigator faces when designing a clinical trial.ResultsComparisons and contrasts of randomization schemes are provided with respect to deterministic and balancing properties. Specifically, Monte Carlo simulation is used to explore the balancing nature of randomization techniques for moderately sized clinical trials. Results demonstrate large treatment imbalance for complete randomization with less imbalance for the urn or adaptive scheme. The urn and adaptive randomization methods display smaller treatment imbalance as demonstrated by the low variability of treatment allocation imbalance. For all randomization schemes, covariate imbalance between treatment arms was small with little variation between adaptive schemes, stratified schemes and unstratified schemes given that sample sizes were moderate to large.ConclusionWe develop this paper with the goal of reminding substance abuse researchers of the broad array of randomization options available for clinical trial designs. There may be too quick a tendency for substance abuse researchers to implement the fashionable urn randomization schemes and other highly adaptive designs. In many instances, simple or blocked randomization with stratification on a major covariate or two will accomplish the same objectives as an urn or adaptive design, and it can do so with more simply implemented schedules and without the dangers of overmatching. Furthermore, the proper analysis, fully accounting for the stratified design, can be conducted.
CD147 overexpression on synoviocytes in rheumatoid arthritis enhances matrix metalloproteinase production and invasiveness of synoviocytes
Authors: Zhu Ping , Lu Ning , Shi Zhan-guo , Zhou Jun , Wu Zhen-biao , Yang Yong , Ding Jin , Chen Zhi-nan 
Published: February 2006

AbstractMacrophage-like synoviocytes and fibroblast-like synoviocytes (FLS) are known as the most active cells of rheumatoid arthritis (RA) and are close to the articular cartilage in a position enabling them to invade the cartilage. Macrophage-like synoviocytes and FLS expression of matrix metalloproteinases (MMPs) and their interaction has aroused great interest. The present article studied the expression of CD147, also called extracellular matrix metalloproteinase inducer, on monocytes/macrophages and FLS from RA patients and its potential role in enhancing MMPs and the invasiveness of synoviocytes. Expression of CD147 on FLS derived from RA patients and from osteoarthritis patients, and expression of CD147 on monocytes/macrophages from rheumatic synovial fluid and healthy peripheral blood were analyzed by flow cytometry. The levels of CD147, MMP-2 and MMP-9 mRNA in FLS were detected by RT-PCR. The role of CD147 in MMP production and the cells' invasiveness in vitro were studied by the co-culture of FLS with the human THP-1 cell line or monocytes/macrophages, by gel zymography and by invasion assay. The results showed that the expression of CD147 was higher on RA FLS than on osteoarthritis FLS and was higher on monocytes/macrophages from rheumatic synovial fluid than on monocytes/macrophages from healthy peripheral blood. RT-PCR showed that the expressions of CD147, MMP-2 and MMP-9 mRNA was higher in RA FLS than in osteoarthritis FLS. A significantly elevated secretion and activation of MMP-2 and MMP-9 were observed in RA FLS co-cultured with differentiated THP-1 cells or RA synovial monocytes/macrophages, compared with those co-cultured with undifferentiated THP-1 cells or healthy control peripheral blood monocytes. Invasion assays showed an increased number of invading cells in the co-cultured RA FLS with differentiated THP-1 cells or RA synovial monocytes/macrophages. CD147 antagonistic peptide inhibited the MMP production and the invasive potential. Our studies demonstrated that the CD147 overexpression on monocytes/macrophages and FLS in RA patients may be responsible for the enhanced MMP secretion and activation and for the invasiveness of synoviocytes. These findings suggest that CD147 may be one of the important factors in progressive joint destruction of RA and that CD147 may be a potential therapeutic target in RA treatment.
Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress
Authors: Aragon Anthony D , Quiñones Gabriel A , Thomas Edward V , Roy Sushmita , Werner-Washburne Margaret 
Published: February 2006

Abstract
Background
As carbon sources are exhausted, Saccharomyces cerevisiae cells exhibit reduced metabolic activity and cultures enter the stationary phase. We asked whether cells in stationary phase cultures respond to additional stress at the level of transcript abundance.

Results
Microarrays were used to quantify changes in transcript abundance in cells from stationary phase cultures in response to stress. More than 800 mRNAs increased in abundance by one minute after oxidative stress. A significant number of these mRNAs encode proteins involved in stress responses. We tested whether mRNA increases were due to new transcription, rapid poly-adenylation of message (which would not be detected by microarrays), or potential release of mature mRNA present in the cell but resistant to extraction during RNA isolation. Examination of the response to oxidative stress in an RNA polymerase II mutant, rpb1-1, suggested that new transcription was not required. Quantitative RT-PCR analysis of a subset of these transcripts further suggested that the transcripts present in isolated total RNA from stationary phase cultures were polyadenylated. In contrast, over 2,000 transcripts increased after protease treatment of cell-free lysates from stationary phase but not exponentially growing cultures. Different subsets of transcripts were released by oxidative stress and temperature upshift, suggesting that mRNA release is stress-specific.

Conclusions
Cells in stationary phase cultures contain a large number of extraction-resistant mRNAs in a protease-labile, rapidly releasable form. The transcript release appears to be stress-specific. We hypothesize that these transcripts are associated with P-bodies.
Activation Function 1 of Glucocorticoid Receptor Binds TATA-Binding Protein in Vitro and in Vivo
Authors: Copik Alicja J. , Webb M. Scott , Miller Aaron L. , Wang Yongxin , Kumar Raj , Thompson E. Brad 
Published: February 2006

Abstract
The mechanism through which the glucocorticoid receptor (GR) stimulates transcription is still unclear, although it is clear that the GR affects assembly of the transcriptional machinery. The binding of the TATA-binding protein (TBP) to the TATA-box is accepted as essential in this process. It is known that the GR can interact in vitro with TBP, but the direct interaction of TBP with GR has not been previously characterized quantitatively and has not been appreciated as an important step in assembling the transcriptional complex. Herein, we demonstrate that the TBP-GR interaction is functionally significant by characterizing the association of TBP and GR in vitro by a combination of techniques and confirming the role of this interaction in vivo. Combined analysis, using native gel electrophoresis, sedimentation equilibrium, and isothermal microcalorimetry titrations, characterize the stoichiometry, affinity, and thermodynamics of the TBP-GR interaction. TBP binds recombinant GR activation function 1 (AF1) with a 1:2 stoichiometry and a dissociation constant in the nanomolar range. In vivo fluorescence resonance energy transfer experiments, using fluorescently labeled TBP and various GR constructs, transiently transfected into CV-1 cells, show GR-TBP interactions, dependent on AF1. AF1-deletion variants showed fluorescence resonance energy transfer efficiencies on the level of coexpressed cyan fluorescent protein and yellow fluorescent protein, indicating that the interaction is dependent on AF1 domain. To demonstrate the functional role of the in vivo GR-TBP interaction, increased amounts of TBP expressed in vivo stimulated expression of GR-driven reporters and endogenous genes, and the effect was also specifically dependent on AF1.
In Vitro Evidence that Upstream of N-ras Participates in the Regulation of Parathyroid Hormone Messenger Ribonucleic Acid Stability
Authors: Dinur Maya , Kilav Rachel , Sela-Brown Alin , Jacquemin-Sablon Helene , Naveh-Many Tally 
Published: February 2006

Abstract
Calcium and phosphate regulate PTH gene expression posttranscriptionally through the binding of trans-acting factors to a defined cis-acting instability element in the PTH mRNA 3′-untranslated region (UTR). We have previously defined AU-rich binding factor 1 as a PTH mRNA binding and stabilizing protein. We have now identified, by affinity chromatography, Upstream of N-ras (Unr) as another PTH mRNA 3′-UTR binding protein. Recombinant Unr bound the PTH 3′-UTR transcript, and supershift experiments with antibodies to Unr showed that Unr is part of the parathyroid RNA binding complex. Finally, because there is no parathyroid cell line, the functionality of Unr in regulating PTH mRNA levels was demonstrated in cotransfection experiments in heterologous human embryonic kidney 293 cells. Depletion of Unr by small interfering RNA decreased simian virus 40-driven PTH gene expression in human embryonic kidney 293 cells transiently cotransfected with the human PTH gene. Overexpression of Unr increased the rat full-length PTH mRNA levels but not a PTH mRNA lacking the terminal 60-nucleotide cis-acting protein binding region. Unr also stabilized a chimeric GH reporter mRNA that contained the rat PTH 63-nucleotide cis-acting element but not a truncated PTH element. Therefore, Unr binds to the PTH cis element and increases PTH mRNA levels, as does AU-rich binding factor 1. Our results suggest that Unr, together with the other proteins in the RNA binding complex, determines PTH mRNA stability.
High-Pressure 129Xe NMR Study of the Intermolecular Interaction of Xenon Confined in Activated Carbon Fiber (ACF)
Authors: Ueda Takahiro , Omi Hironori , Yukioka Takanori , Eguchi Taro 
Published: February 2006

Abstract
The pressure dependence of a 129Xe chemical shift (δ) and the local density of xenon adsorbed in activated carbon fiber (ACF) with slit-pore widths of 0.7–1.1 nm was investigated using in-situ high-pressure 129Xe NMR. 129Xe chemical shift values below 0.025 MPa change linearly with equilibrium pressure. The initial slope of the pressure dependence of δ led to a shift value at zero pressure, δS′, which approximately reflects the xenon–wall interaction. A statistical model incorporating the xenon–wall interaction well interprets the dependence of δS′ on the pore width. Furthermore, in a higher-pressure region, the density dependence of the chemical shift led to the xenon–xenon interaction via the virial coefficients of the chemical shift up to the second order on density (the third-virial coefficient). The second-virial coefficient (a coefficient for the linear term of density) depended on the pore width. Increasing the slit width from 0.7 to 1.1 nm increased the second-virial coefficient, δ1, from 42 × 10−3 to 78 × 10−3 ppm kg−1 m3, suggesting that the space accessible by the surrounding xenon atoms increases when the slit width increases. This aspect reveals the size effect of the xenon–xenon interaction in nanospace.
Intercalation of Glucosamine and Chitosan into Layered Zirconium Phosphates
Authors: Hayashi Aki , Nakabayashi Yui , Yasutomi Junko , Nakayama Hirokazu , Tsuhako Mitsutomo 
Published: February 2006

Abstract
Glucosamine was directly intercalated into γ-zirconium phosphate (γ-ZrP). The intercalation compound with a monolayer structure was obtained by the interaction between the 2-amino group of glucopyranose and the phosphate group in γ-ZrP. The uptake amount depended on the concentration of the glucosamine aqueous solution rather than reaction time, and reached 0.9 mmol per gram of γ-ZrP at the maximum. On the other hand, chitosan, polysaccharide of glucosamine, could be intercalated into alkylamine-intercalated γ-ZrP as the host compound. Chitosan-intercalated γ-ZrP showed two phases with different interlayer distances. It was confirmed from 13C CP/MAS NMR spectra that chitosan exists in the interlayer region of γ-ZrP for both phases.
Aluminium-27 NMR Investigation of the 2-Hydroxyethyl(trimethyl)ammonium Aluminosilicate Solution
Authors: Samadi-Maybodi Abdolraouf , Goudarzi Nasser , Naderi-Manesh Hossein 
Published: February 2006

Abstract
Alkaline solutions containing both silicate and aluminate ions are of considerable research interest inter alia because of their involvement in the synthesis of zeolites. 27Al NMR spectra of alkaline aluminosilicate solutions generally show a maximum of five broad bands. In the present work, we use 27Al NMR to characterize aluminosilicate solutions with different Al/Si ratios using 2-hydroxyethyl(trimethyl)ammonium as a cation template, no alkaline metals are used for preparation of aluminosilicate solutions. To understand the reaction between silicate and aluminate ions in this system, the evolutions of 27Al NMR spectra with time are investigated.
Luminescence of Copper(I) Dinuclear Complexes Bridged by Diphosphine Ligands
Authors: Tsukuda Toshiaki , Nakamura Ayaka , Arai Takashi , Tsubomura Taro 
Published: February 2006

Abstract
Mixed-ligand dinuclear Cu(I) complexes containing both diimine and diphosphine ligands have demonstrated interesting photophyisical properties; the complexes are emissive in solution at room temperature, even with 1,10-phenanthroline (phen) lacking a 2,9-substituted group.
Determination of the Solubility Product of CH3COONa in Propylene Carbonate and Standard Gibbs Energies of Ion Transfer Using a Poly(acrylamide) Membrane Ion-Selective Electrode Based on Benzo-15-crown-5
Authors: Ren Jujie , Nakashima Junichi , Nakamura Toshio 
Published: February 2006

Abstract
A Benzo-15-crown-5 modified poly(acrylamide) membrane coated platinum electrode is successfully used to determine the solubility product of CH3COONa in propylene carbonate. The standard Gibbs energies of Na+ and CH3COO− transfer from water to propylene carbonate are obtained. The datum of CH3COO− is reported for the first time.
Conversion of 2-Aminoethanethiolate (aet) to 2-Benzoylaminoethanethiolate (L) in a S-Bridged Diruthenium(II) Complex Composed of Two cis-[Ru(bpy)2] Units. Crystal Structures of ΔΔ/ΛΛ-[{Ru(bpy)2}2(μ-Haet)2]4+ and ΔΔ/ΛΛ-[{Ru(bpy)2}2(μ-L)2]2+
Authors: Matsuura Noriyuki , Kawamoto Tatsuya , Konno Takumi 
Published: February 2006

Abstract
A diruthenium(II) complex, ΔΔ/ΛΛ-[{Ru(bpy)2}2(μ-L)2]2+ (ΔΔ/ΛΛ-[2]2+), in which two cis-[Ru(bpy)2]2+ units are bridged by two S atoms from two 2-benzoylaminoethanethiolate (L) ligands, was synthesized by the reaction of ΔΔ/ΛΛ-[{Ru(bpy)2}2(μ-Haet)2]4+ (aet = 2-aminoethanethiolate; ΔΔ/ΛΛ-[1]4+) with benzoyl chloride in the presence of a base. The molecular structure and electrochemical properties of ΔΔ/ΛΛ-[2]2+ were discussed in comparison with those of ΔΔ/ΛΛ-[1]4+.
Chemical and Genetic Differentiation of Ligularia pleurocaulis in Northwestern Yunnan and Southwestern Sichuan Provinces of China
Authors: Nagano Hajime , Iwazaki Yukiko , Gong Xun , Shen Yuemao , Kuroda Chiaki , Hanai Ryo 
Published: February 2006

Abstract
Intra-specific diversity of Ligularia pleurocaulis was examined from both chemical and genetic aspects, using furanoeremophilanes as the chemical index and the nucleotide sequences in the atpB-rbcL and the ITS1 regions as the genetic index. Four samples of L. pleurocaulis were collected in northwestern Yunnan, and six in southwestern Sichuan. From the ethanol extracts of the roots of all of the samples, four compounds, 6β-angeloyloxy- and 6β-tigloyloxy-furanoeremophil-1(10)-enes, and 6β-angeloyloxy- and 6β-tigloyloxy-furanoeremophil-1(10)-en-3β-ols were isolated. Further, 3β-angeloyloxyfuranoeremophil-1(10)-en-6β-ol and furanoligularenone were isolated from the Yunnan and the Sichuan samples, respectively. Two variants were found for the atpB-rbcL sequence. Base multiplicity in the ITS1 region was observed at only a few positions in the Yunnan samples, whereas it was observed at about 10 positions for the Sichuan samples. These results show that L. pleurocaulis is diverse, both chemically and genetically, and that plants in northwestern Yunnan and those in southwestern Sichuan can be distinguished by their chemical and genetic indexes.
Substituent Effects on the Ground-State Properties of Naphthalene-Based Analogues of Salicylideneaniline in Solution
Authors: Ohshima Asuka , Momotake Atsuya , Arai Tatsuo 
Published: February 2006

Abstract
Substituent effects on the ground-state properties of seven naphthalene analogues of salicylideneaniline (1–7) were studied by comparison of both steady-state and transient absorption spectra. The naphthalene-based salicylideneanilines 1–5 were prepared from 2-hydroxy-1-naphthaldehyde and corresponding amines. The UV absorption spectra of 1–5 were largely dependent on the substituent group on the amino group. Transient absorption studies revealed that the introduced naphthyl group in 1–5 prolonged the lifetime of 1Ktrans in non-polar solvent probably due to the formation of intramolecular hydrogen bonding between nitrogen and C–H hydrogen on the naphthyl group. In acetonitrile, the lifetimes of 1–6 are much longer than those in benzene, probably because the zwitterionic forms are stabilized in polar solvents, whereas the much shorter lifetime in ethanol suggests that 1Ktrans undergoes the solvent assisted re-enolizaiton reaction in ethanol.