bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure–function relationship in annexin A13, the founder member of the vertebrate family of annexins
Authors: Turnay Javier , Lecona Emilio , Fernández-Lizarbe Sara , Guzmán-Aránguez Ana , Fernández María Pilar , Olmo Nieves , Lizarbe Ma Antonia 
Published: July 2005

Annexin A13 is considered the original progenitor of the 11 other members of vertebrate annexins, a superfamily of calcium/phospholipid-binding proteins. It is highly tissue-specific, being expressed only in intestinal and kidney epithelial cells. Alternative splicing generates two isoforms, both of which bind to rafts. In view of the lack of structural information supporting the physiological role of this annexin subfamily, we have cloned, expressed and purified human annexin A13b to investigate its structural and functional properties. The N-terminus of annexin A13b: (i) destabilizes the conserved protein core, as deduced from the low melting temperature in the absence (44 °C) or presence of calcium (55 °C), and (ii) impairs calcium-dependent binding to acidic phospholipids, requiring calcium concentrations &gt;400 μM. Truncation of the N-terminus restores thermal stability and decreases the calcium requirement for phospholipid binding, confirming its essential role in the structure–function relationship of this annexin. Non-myristoylated annexin A13b only binds to acidic phospholipids at high calcium concentrations. We show for the first time that myristoylation of annexin A13b enables the direct binding to phosphatidylcholine, raft-like liposomes and acidic phospholipids in a calcium-independent manner. The conformational switch induced by calcium binding, from a ‘closed’ to an ‘open’ conformation with exposure of Trp227, can be mimicked by a decrease in pH, a process that may be relevant for membrane interactions. Our studies confirm that the common structural and functional characteristics that are dependent on the protein core of vertebrate annexins are likely to be common conserved features, whereas their variable N-termini confer distinct functional properties on annexins, as we report for myristoylation of annexin A13b.
Molecular action of 1,25-dihydroxyvitamin D3 and phorbol ester on the activation of the rat cytochrome P450C24 (CYP24) promoter: role of MAP kinase activities and identification of an important transcription factor binding site
Authors: Nutchey Barbara K. , Kaplan Josef S. , Dwivedi Prem P. , Omdahl John L. , Ferrante Antonio , May Brian K. , Hii Charles S. T. 
Published: July 2005

Although investigations of the transcriptional regulation of the rat cytochrome P450C24 [CYP24 (25-hydroxyvitamin D3 24-hydroxylase)] gene by 1,25D (1,25-dihydroxyvitamin D3) at either the genomic, or more recently at the non-genomic, level have provided insight into the mechanism of control of 1,25D levels, this regulation is still poorly characterized. Using HEK-293T cells (human embryonic kidney 293T cells), we reported that 1,25D induction of CYP24 requires JNK (c-Jun N-terminal kinase) but not the ERK1/2 (extracellular-signal-regulated kinase 1/2). The phenomenon of synergistic up-regulation of CYP24 expression by PMA and 1,25D is well known and was found to be protein kinase C-dependent. Whereas ERK1/2 was not activated by 1,25D alone, its activation by PMA was potentiated by 1,25D also. The importance of ERK1/2 for transcriptional synergy was demonstrated by transfection of a dominant-negative ERK1(K71R) mutant (where K71R stands for Lys71→Arg), which resulted in a reduced level of synergy on a CYP24 promoter-luciferase construct. JNK was also shown to be required for synergy. We report, in the present study, the identification of a site located at −171/−163, about 30 bp upstream of the vitamin D response element-1 in the CYP24 proximal promoter. This sequence, 5′-TGTCGGTCA-3′, is critical for 1,25D induction of CYP24 and is therefore termed the vitamin D stimulatory element. The vitamin D stimulatory element, a target for the JNK module, and an Ets-1 binding site were shown to be vital for synergy between PMA and 1,25D. This is the first report to identify the DNA binding sequences required for the synergy between PMA and 1,25D and a role for JNK on the CYP24 gene promoter.
The iron–siderophore transporter FhuA is the receptor for the antimicrobial peptide microcin J25: role of the microcin Val11–Pro16 β-hairpin region in the recognition mechanism
Authors: Destoumieux-Garzón Delphine , Duquesne Sophie , Peduzzi Jean , Goulard Christophe , Desmadril Michel , Letellier Lucienne , Rebuffat Sylvie , Boulanger Pascale 
Published: July 2005

The role of the outer-membrane iron transporter FhuA as a potential receptor for the antimicrobial peptide MccJ25 (microcin J25) was studied through a series of in vivo and in vitro experiments. The requirement for both FhuA and the inner-membrane TonB–ExbB–ExbD complex was demonstrated by antibacterial assays using complementation of an fhuA− strain and by using isogenic strains mutated in genes encoding the protein complex respectively. In addition, MccJ25 was shown to block phage T5 infection of Escherichia coli, in vivo, by inhibiting phage adhesion, which suggested that MccJ25 prevents the interaction between the phage and its receptor FhuA. This in vivo activity was confirmed in vitro, as MccJ25 inhibited phage T5 DNA ejection triggered by purified FhuA. Direct interaction of MccJ25 with FhuA was demonstrated for the first time by size-exclusion chromatography and isothermal titration calorimetry. MccJ25 bound to FhuA with a 2:1 stoichiometry and a Kd of 1.2 μM. Taken together, our results demonstrate that FhuA is the receptor for MccJ25 and that the ligand–receptor interaction may occur in the absence of other components of the bacterial membrane. Finally, both differential scanning calorimetry and antimicrobial assays showed that MccJ25 binding involves external loops of FhuA. Unlike native MccJ25, a thermolysin-cleaved MccJ25 variant was unable to bind to FhuA and failed to prevent phage T5 infection of E. coli. Therefore the Val11–Pro16 β-hairpin region of MccJ25, which is disrupted upon cleavage by thermolysin, is required for microcin recognition.
Characterization of mouse amino acid transporter B0AT1 (slc6a19)
Authors: Böhmer Christoph , Bröer Angelika , Munzinger Michael , Kowalczuk Sonja , Rasko John E. J. , Lang Florian , Bröer Stefan 
Published: July 2005

The mechanism of the mouse (m)B0AT1 (slc6a19) transporter was studied in detail using two electrode voltage-clamp techniques and tracer studies in the Xenopus oocyte expression system. All neutral amino acids induced inward currents at physiological potentials, but large neutral non-aromatic amino acids were the preferred substrates of mB0AT1. Substrates were transported with K0.5 values ranging from approx. 1 mM to approx. 10 mM. The transporter mediates Na+–amino acid co-transport with a stoichiometry of 1:1. No other ions were involved in the transport mechanism. An increase in the extracellular Na+ concentration reduced the K0.5 for leucine, and vice versa. Moreover, the K0.5 values and Vmax values of both substrates varied with the membrane potential. As a result, K0.5 and Vmax values are a complex function of the concentration of substrate and co-substrate and the membrane potential. A model is presented assuming random binding order and a positive charge associated with the ternary [Na+–substrate–transporter] complex, which is consistent with the experimental data.
Membrane binding of β2-glycoprotein I can be described by a two-state reaction model: an atomic force microscopy and surface plasmon resonance study
Authors: Gamsjaeger Roland , Johs Alexander , Gries Anna , Gruber Hermann J. , Romanin Christoph , Prassl Ruth , Hinterdorfer Peter 
Published: July 2005

Complexes formed between β2GPI (β2-glycoprotein I), a human plasma protein, and biological membranes are considered to be targets of macrophages and antiphospholipid autoantibodies involved in autoimmune diseases, such as antiphospholipid syndrome or systemic lupus erythematosus. The positively charged lysine-rich fifth domain of β2GPI facilitates its interaction with phospholipid membranes containing acidic phospholipids, which normally become exposed by apoptotic processes. In the present study, atomic force microscopy was applied to visualize the binding of β2GPI to a mixed phospholipid model membrane at physiological ionic strength. On supported lipid bilayers the formation of supramolecular assemblies of the protein with a height of approx. 3.3 nm was observed, suggesting a lateral agglomeration of β2GPI. Detailed analysis of kinetic constants using surface plasmon resonance revealed that the binding can be described by a two-state reaction model, i.e. a very fast interaction step, depending on the content of acidic phospholipids in the bilayer, and a second step with significantly lower kon and koff values. Taken together, our results suggest a biphasic interaction mechanism: a fast step of β2GPI binding to negatively charged lipids, mainly based on electrostatic interactions, and a slower phase of agglomeration of the protein on the bilayer surface accompanied by a protein-induced rigidification of the membrane, as revealed by electron paramagnetic resonance.
Novel variants of human SCaMC-3, an isoform of the ATP-Mg/Pi mitochondrial carrier, generated by alternative splicing from 3′-flanking transposable elements
Authors: del Arco Araceli 
Published: July 2005

CaMCs (calcium-dependent mitochondrial carriers) represent a novel subfamily of metabolite carriers of mitochondria. The ATP-Mg/Pi co-transporter, functionally characterized more than 20 years ago, has been identified to be a CaMC member. There are three isoforms of the ATP-Mg/Pi carrier in mammals, SCaMC-1 (short CaMC-1), -2 and -3 (or APC-1, -3 and -2 respectively), corresponding to the genes SLC25A24, SLC25A25 and SLC25A23 respectively, as well as six N-terminal variants generated by alternative splicing for SCaMC-1 and -2 isoforms. In the present study, we describe four new variants of human SCaMC-3 generated by alternative splicing. The new mRNAs use the exon 9 3′-donor site and distinct 5′-acceptor sites from repetitive elements, in regions downstream of exon 10, the last exon in all SCaMCs. Transcripts lacking exon 10 (SCaMC-3b, -3b′, -3c and -3d) code for shortened proteins lacking the last transmembrane domain of 422, 456 and 435 amino acids, and were found in human tissues and HEK-293T cells. Mitochondrial targeting of overexpressed SCaMC-3 variants is incomplete. Surprisingly, the import impairment is overcome by removing the N-terminal extension of these proteins, suggesting that the hydrophilic N-terminal domain also participates in the mitochondrial import process, as shown for the CaMC members aralar and citrin [Roesch, Hynds, Varga, Tranebjaerg and Koehler (2004) Hum. Mol. Genet. 13, 2101–2111].
Identification of calcium-regulated heat-stable protein of 24 kDa (CRHSP24) as a physiological substrate for PKB and RSK using KESTREL
Authors: Auld Gillian C. , Campbell David G. , Morrice Nick , Cohen Philip 
Published: July 2005

A substrate for PKBα (protein kinase Bα) was detected in liver extracts, and was purified and identified as CRHSP24 (calcium-regulated heat-stable protein of apparent molecular mass 24 kDa). PKBα, as well as SGK1 (serum- and glucocorticoid-induced protein kinase 1) and RSK (p90 ribosomal S6 kinase), phosphorylated CRHSP24 stoichiometrically at Ser52in vitro and its brain-specific isoform PIPPin at the equivalent residue (Ser58). CRHSP24 became phosphorylated at Ser52 when HEK-293 (human embryonic kidney) cells were stimulated with IGF-1 (insulin-like growth factor-1) and this was prevented by inhibitors of PI3K (phosphoinositide 3-kinase), but not by rapamycin [an inhibitor of mTOR (mammalian target of rapamycin)] or PD 184352, an inhibitor of the classical MAPK (mitogen-activated protein kinase) cascade and hence the activation of RSK. IGF-1 induced a similar phosphorylation of CRHSP24 in ES (embryonic stem) cells from wild-type mice or mice that express the PDK1 (3-phosphoinositide-dependent kinase 1) mutant (PDK1[L155E]) that activates PKBα normally, but cannot activate SGK. CRHSP24 also became phosphorylated at Ser52 in response to EGF (epidermal growth factor) and this was prevented by blocking activation of both the classical MAPK cascade and the activation of PKBα, but not if just one of these pathways was inhibited. DYRK2 (dual-specificity tyrosine-phosphorylated and -regulated protein kinase 2) phosphorylated CRHSP24 at Ser30, Ser32 and Ser41in vitro, and Ser41 was identified as a site phosphorylated in cells. These and other results demonstrate that CRHSP24 is phosphorylated at Ser52 by PKBα in response to IGF-1, at Ser52 by PKBα and RSK in response to EGF, and at Ser41 in the absence of IGF-1/EGF by a DYRK isoform or another proline-directed protein kinase(s).
TileMap: create chromosomal map of tiling array hybridizations
Authors: Ji Hongkai , Wong Wing Hung 
Published: July 2005

Abstract
Motivation: Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is to develop effective statistical tools to identify genomic loci that show transcriptional or protein binding patterns of interest.
Results: A two-step approach is proposed and is implemented in TileMap. In the first step, a test-statistic is computed for each probe based on a hierarchical empirical Bayes model. In the second step, the test-statistics of probes within a genomic region are used to infer whether the region is of interest or not. Hierarchical empirical Bayes model shrinks variance estimates and increases sensitivity of the analysis. It allows complex multiple sample comparisons that are essential for the study of temporal and spatial patterns of hybridization across different experimental conditions. Neighboring probes are combined through a moving average method (MA) or a hidden Markov model (HMM). Unbalanced mixture subtraction is proposed to provide approximate estimates of false discovery rate for MA and model parameters for HMM.
Availability: TileMap is freely available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm
Contact: whwong@stanford.edu
Supplementary information: http://biogibbs.stanford.edu/~jihk/TileMap/index.htm (includes coloured versions of all figures)
BlastXtract—a new way of exploring translated searches
Authors: Claesson Marcus J. , van Sinderen Douwe 
Published: July 2005

Abstract
Summary: Searches of translated, unannotated genomic DNA sequences against protein databases is a useful early-stage method for discovering protein homologues encoded by the sequence, but generates huge amounts of output data that quickly become impregnable. BlastXtract is a web-based tool for managing and visualizing results from large translated BLAST and FastA searches. It combines the speed and storage benefits of relational database management systems with an easy-to-use graphical navigation map, and greatly facilitates the early exploration of genomic sequence.
Availability: BlastXtract can be downloaded from http://bioinfo.ucc.ie/blastxtract/
Contact: mclaesson@bioinfo.ucc.ie
Efficacy and Safety of Heparinase I versus Protamine in Patients Undergoing Coronary Artery Bypass Grafting with and without Cardiopulmonary Bypass
Authors: Stafford-Smith Mark , Lefrak Edward A. , Qazi Anjum G. , Welsby Ian J. , Barber Linda , Hoeft Andreas , Dorenbaum Alejandro , Mathias Jasmine , Rochon James J. , Newman Mark F. 
Published: July 2005

Background
Hemodynamic protamine reactions with heparin reversal during cardiac surgery are common and associated with adverse outcomes. As an alternative to protamine, the authors examined heparinase I reversal of heparin after aortocoronary bypass graft surgery.

Methods
In a randomized, double-blind, double-dummy trial, 167 on- and off-pump aortocoronary bypass graft surgery patients received either heparinase I (maximum 35 microg/kg) or protamine (maximum 650 mg) for heparin reversal, monitored by activated clotting time values and clinical assessment. Hemodynamic parameters were recorded electronically; safety evaluation was to 30 days postoperatively. Noninferiority was predefined as 400 ml or less median 12-h chest tube drainage from intensive care unit arrival for heparinase I patients, after risk adjustment. Hemodynamic instability was defined as systemic hypotension (> or = 30 mmHg decrease) and/or pulmonary hypertension (> or = 40 mmHg with an increase > or = 10 mmHg) within 30 min of heparin reversal initiation.

Results
Patient enrollment was terminated on advisement of the Data Safety Monitoring Board. Although heparinase I was noninferior for 12-h chest tube drainage, protamine had a superior safety profile. Overall, heparinase I subjects had longer hospital stays (P = 0.04), were more likely to experience a serious adverse event (P = 0.01), and were less likely to avoid transfusion (P = 0.006). A composite morbidity score was not different (P = 0.24), and similar rates of hemodynamic instability were observed between groups. Findings were consistent in analyses stratified by on- and off-pump surgery.

Conclusions
Heparinase I reverses heparin anticoagulation after aortocoronary bypass graft surgery but is not equivalent to protamine because of its inferior safety profile.
Trends but Not Individual Values of Central Venous Oxygen Saturation Agree with Mixed Venous Oxygen Saturation during Varying Hemodynamic Conditions
Authors: Dueck Michael H. , Klimek Markus , Appenrodt Stefan , Weigand Christoph , Boerner Ulf 
Published: July 2005

Background
Previous studies found contradictory results regarding the question whether mixed venous oxygen saturation (Svo2) and central venous oxygen saturation (Scvo2) are equivalent. The inconsistency of study results may result from different study designs and different, partly questionable, statistical approaches.

Methods
The authors performed a prospective clinical trial comparing individual oxygen saturation values as well as the trend of values in blood from the superior vena cava (Scvo2), the right atrium (Srao2), and the pulmonary artery (Svo2) during varying hemodynamic situations. The subjects were 70 patients scheduled to undergo elective neurosurgical operations in the sitting position. Oxygen saturation was measured photospectrometrically in blood samples simultaneously taken at four different time points during supine and sitting positions. Statistical analysis was performed following the recommendations of Bland and Altman.

Results
Five hundred two comparative sets of measurements were obtained. Ninety-five percent limits of agreement ranging from +/-6.83 to +/-9.30% for single values were interpreted as clinically unacceptable. In contrast, correlations between changes of Svo2 and Scvo2 as well as of Svo2 and Srao2 were interpreted as clinically acceptable (R > or = 0.755, Pearson correlation coefficient; P < or = 0.0001).

Conclusions
In this sample of patients, exact numerical values of Scvo2 and Srao2 are not equivalent to those of Svo2 in varying hemodynamic conditions. However, for clinical purposes, the trend of Scvo2 may be substituted for the trend of Svo2. In addition, previous studies investigating the agreement between Svo2 and Scvo2 were found to be lacking in their chosen statistical approaches.
Sole Use of Dexmedetomidine Has Limited Utility for Conscious Sedation during Outpatient Colonoscopy
Authors: Jalowiecki Przemyslaw , Rudner Robert , Gonciarz Maciej , Kawecki Piotr , Petelenz Michal , Dziurdzik Piotr 
Published: July 2005

Background
This study evaluated the ability of dexmedetomidine to provide analgesia and sedation for outpatient colonoscopy, examining outcomes including cardiorespiratory variables, side effects, and discharge readiness.

Methods
Sixty-four patients were randomly assigned to one of three treatment regimens. In group D, patients received 1 microg/kg dexmedetomidine over 15 min followed by an infusion of 0.2 microg x kg x h. Group P received meperidine (1 mg/kg) with midazolam (0.05 mg/kg), and group F received fentanyl (0.1-0.2 mg intravenous) on demand. The assessment included measurements of heart rate, blood pressure, oxygen saturation, respiratory rate, quality of sedation/analgesia, and an evaluation of the recovery time.

Results
The study was terminated before the planned 90 patients had been recruited because of adverse events in group D. In all groups, negligible hemoglobin oxygen saturation and respiratory rate variations were observed. In group D, there was a significantly larger decrease in heart rate (to approximately 40 beats/min in 2 of 19 cases) and blood pressure (to less than 50% of the initial value in 4 of 19 patients). Supplemental fentanyl was required in 47% of patients receiving dexmedetomidine to achieve a satisfactory level of analgesia (vs. 42.8% of patients in group P and 79.2% of patients in group F). Vertigo (5 patients), nausea/vomiting (5 patients), and ventricular bigeminy (1 patient) were observed only in group D. Time to home readiness was longest in group D (85 +/- 74, 39 +/- 21, and 32 +/- 13 min in groups D, P and F, respectively; P = 0.007).

Conclusions
The use of dexmedetomidine to provide analgesia/sedation for colonoscopy is limited by distressing side effects, pronounced hemodynamic instability, prolonged recovery, and a complicated administration regimen.
Spectral Entropy Monitoring Is Associated with Reduced Propofol Use and Faster Emergence in Propofol–Nitrous Oxide–Alfentanil Anesthesia
Authors: Vakkuri Anne , Yli-Hankala Arvi , Sandin Rolf , Mustola Seppo , Høymork Siv , Nyblom Stina , Talja Pia , Sampson Timothy , van Gils Mark , Viertiö-Oja Hanna 
Published: July 2005

Background
This multicenter study evaluated the effect of a new depth of anesthesia-monitoring device based on time-frequency-balanced spectral entropy of electroencephalogram monitoring (GE Healthcare Finland, Helsinki, Finland) on consumption of anesthetic drugs and recovery times after anesthesia.

Methods
The study was a prospective, randomized, single-blind study performed in six hospitals in Finland, Sweden, and Norway. After institutional review board approval and written informed consent from each patient, the patients were randomly allocated to anesthesia with entropy values either shown (entropy group) or not shown (control group). Anesthesia was maintained with propofol, nitrous oxide, and alfentanil. In the entropy group, propofol was given to keep the state entropy value between 45 and 65, and alfentanil was given to keep the state entropy-response entropy difference below 10 units and heart rate and blood pressure within +/-20% of the baseline values. The control group patients were anesthetized to keep heart rate and blood pressure within +/-20% of the baseline values. Statistical methods included Mann-Whitney U test and unpaired t tests.

Results
A total of 368 patients were studied. In the entropy group, entropy values were higher during the whole operation and especially during the last 15 min (P < 0.001). Consequently, propofol consumption was smaller in the entropy group during the whole anesthesia period (P < 0.001) and especially during the last 15 min (P < 0.001). This shortened the time delay in the early recovery parameters in the entropy group.

Conclusion
Entropy monitoring assisted titration of propofol, especially during the last part of the procedures, as indicated by higher entropy values, decreased consumption of propofol, and shorter recovery times in the entropy group.