bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Insights into the Catalytic Mechanism of Escherichia coli Selenophosphate Synthetase
Authors: Noinaj Nicholas , Wattanasak Rut , Lee Duck-Yeon , Wally Jeremy L. , Piszczek Grzegorz , Chock P. Boon , Stadtman Thressa C. , Buchanan Susan K. 
Published: November 2011

ABSTRACT

Selenophosphate synthetase (SPS) catalyzes the synthesis of selenophosphate, the selenium donor for the biosynthesis of selenocysteine and 2-selenouridine residues in seleno-tRNA. Selenocysteine, known as the 21st amino acid, is then incorporated into proteins during translation to form selenoproteins which serve a variety of cellular processes. SPS activity is dependent on both Mg
2+
and K
+
and uses ATP, selenide, and water to catalyze the formation of AMP, orthophosphate, and selenophosphate. In this reaction, the gamma phosphate of ATP is transferred to the selenide to form selenophosphate, while ADP is hydrolyzed to form orthophosphate and AMP. Most of what is known about the function of SPS has derived from studies investigating
Escherichia coli
SPS (EcSPS) as a model system. Here we report the crystal structure of the C17S mutant of SPS from
E. coli
(EcSPS
C17S
) in apo form (without ATP bound). EcSPS
C17S
crystallizes as a homodimer, which was further characterized by analytical ultracentrifugation experiments. The glycine-rich N-terminal region (residues 1 through 47) was found in the open conformation and was mostly ordered in both structures, with a magnesium cofactor bound at the active site of each monomer involving conserved aspartate residues. Mutating these conserved residues (D51, D68, D91, and D227) along with N87, also found at the active site, to alanine completely abolished AMP production in our activity assays, highlighting their essential role for catalysis in EcSPS. Based on the structural and biochemical analysis of EcSPS reported here and using information obtained from similar studies done with SPS orthologs from
Aquifex aeolicus
and humans, we propose a catalytic mechanism for EcSPS-mediated selenophosphate synthesis.
In the NadR Regulon, Adhesins and Diverse Meningococcal Functions Are Regulated in Response to Signals in Human Saliva
Authors: Fagnocchi Luca , Pigozzi Eva , Scarlato Vincenzo , Delany Isabel 
Published: November 2011

ABSTRACT

The
Neisseria meningitidis
regulator NadR was shown to repress expression of the NadA adhesin and play a major role in NadA phase-variable expression. In this study, we identified through microarray analysis over 30 genes coregulated with
nadA
in the NadR mutant and defined members of the NadR regulon through
in vitro
DNA-binding assays. Two distinct types of promoter architectures (I and II) were identified for NadR targets, differing in both the number and position of NadR-binding sites. All NadR-regulated genes investigated were found to respond to 4-hydroxyphenylacetic acid (4HPA), a small molecule secreted in human saliva, which was previously demonstrated to induce
nadA
expression by alleviating NadR-dependent repression. Interestingly, two types of NadR 4HPA responsive activities were found on different NadR targets corresponding to the two types of genes identified by different promoter architectures: while NadA and the majority of NadR targets (type I) are induced, only the MafA adhesins (type II) are corepressed in response to the same 4HPA signal. This alternate behavior of NadR was confirmed in a panel of strains in response to 4HPA and after incubation in saliva. The
in vitro
NadR binding activity at type I and type II promoter regions is differentially affected by 4HPA, suggesting that the nature of the NadR binding sites may define the regulation to which they will be subjected. We conclude that NadR coordinates a broad transcriptional response to signals present in human saliva, mimicked
in vitro
by 4HPA, enabling the meningococcus to adapt to the relevant host niche.
The Major Autolysin Acm2 from Lactobacillus plantarum Undergoes Cytoplasmic O-Glycosylation
Authors: Fredriksen Lasse , Mathiesen Geir , Moen Anders , Bron Peter A. , Kleerebezem Michiel , Eijsink Vincent G. H. , Egge-Jacobsen Wolfgang 
Published: November 2011

ABSTRACT

The major autolysin Acm2 from the probiotic strain
Lactobacillus plantarum
WCFS1 contains high proportions of alanine, serine, and threonine in its N-terminal so-called AST domain. It has been suggested that this extracellular protein might be glycosylated, but this has not been experimentally verified. We used high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the possible occurrence of glycans on peptides generated from lactobacillary surface proteins by protease treatment. This approach yielded five glycopeptides in various glycoforms, all derived from the AST domain of Acm2. All five glycopeptides contained the hydroxy-amino acids serine and threonine, suggesting that Acm2 is O-glycosylated. By using lectin blotting with succinylated wheat germ agglutinin, and by comparing the wild-type strain with an Acm2-negative derivative (NZ3557), we found that the attached
N
-acetylhexosamines are most likely
N
-acetylglucosamines (GlcNAc). NZ3557 was further used as a genetic background to express an Acm2 variant lacking its secretion signal, resulting in intracellular expression of Acm2. We show that this intracellular version of Acm2 is also glycosylated, indicating that the GlcNAc modification is an intracellular process.
Pim Kinase Inhibitors Sensitize Prostate Cancer Cells to Apoptosis Triggered by Bcl-2 Family Inhibitor ABT-737
Authors: Song Jin H. , Kraft Andrew S. 
Published: November 2011

Abstract
Pim serine/threonine kinases contribute to prostate tumorigenesis and therapeutic resistance, yet Pim kinase inhibitors seem to have only limited effects on prostate cancer cell survival. Because overexpression of Bcl-2 family members are implicated in chemotherapeutic resistance in prostate cancer, we investigated the cooperative effects of Pim kinase inhibition with ABT-737, a small molecule antagonist of Bcl-2 family members. Strikingly, the addition of ABT-737 to Pim inhibitors triggered a robust apoptosis of prostate cancer cells in vitro and in vivo. Pim inhibitors decreased levels of the Bcl-2 family member Mcl-1, both by blocking 5′-cap dependent translation and decreasing protein half life. In addition, Pim inhibition transcriptionally increased levels of the BH3 protein Noxa by activating the unfolded protein response (UPR), lead to eIF-2α phosphorylation and increased expression of CHOP. Increased levels of Noxa also inactivated the remaining levels of Mcl-1 protein activity. Notably, these specific protein changes were essential to the apoptotic process because ABT-737 did not inhibit Mcl-1 protein activity and Mcl-1 overexpression blocked the apoptotic activity of ABT-737. Our results therefore suggest that this combination treatment could be developed as a potential therapy for human prostate cancer where overexpression of Pim kinases and antiapoptotic Bcl-2 family members drives tumor cell resistance to current anticancer therapies. Cancer Res; 72(1); 294–303. ©2011 AACR.
STEAP1 Is Associated with the Invasive and Oxidative Stress Phenotype of Ewing Tumors
Authors: Grunewald Thomas G.P. , Diebold Isabel , Esposito Irene , Plehm Stephanie , Hauer Kristina , Thiel Uwe , da Silva-Buttkus Patricia , Neff Frauke , Unland Rebekka , Müller-Tidow Carsten , Zobywalski Colette , Lohrig Katharina , Lewandrowski Urs , Sickmann Albert , da Costa Olivia Prazeres , Görlach Agnes , Cossarizza Andrea , Butt Elke , Richter Günther H.S. , Burdach Stefan 
Published: November 2011

Abstract
Ewing tumors comprise the second most common type of bone-associated cancer in children and are characterized by oncogenic EWS/FLI1 fusion proteins and early metastasis. Compelling evidence suggests that elevated levels of intracellular oxidative stress contribute to enhanced aggressiveness of numerous cancers, possibly including Ewing tumors. Using comprehensive microarray analyses and RNA interference, we identified the six-transmembrane epithelial antigen of the prostate 1 (STEAP1)—a membrane-bound mesenchymal stem cell marker of unknown function—as a highly expressed protein in Ewing tumors compared with benign tissues and show its regulation by EWS/FLI1. In addition, we show that STEAP1 knockdown reduces Ewing tumor proliferation, anchorage-independent colony formation as well as invasion in vitro and decreases growth and metastasis of Ewing tumor xenografts in vivo. Moreover, transcriptome and proteome analyses as well as functional studies revealed that STEAP1 expression correlates with oxidative stress responses and elevated levels of reactive oxygen species that in turn are able to regulate redox-sensitive and proinvasive genes. In synopsis, our data suggest that STEAP1 is associated with the invasive behavior and oxidative stress phenotype of Ewing tumors and point to a hitherto unanticipated oncogenic function of STEAP1. Mol Cancer Res; 10(1); 52–65. ©2011 AACR.
Reduced Ventricular Proarrhythmic Potential of the Novel Combined Ion-Channel Blocker AZD1305 Versus Dofetilide in Dogs With Remodeled Hearts
Authors: Johnson Daniel M. , de Jong Monique M.J. , Crijns Harry J.G.M. , Carlsson Leif G. , Volders Paul G.A. 
Published: November 2011

Background—
AZD1305 is an investigational antiarrhythmic agent for management of atrial fibrillation. It blocks various cardiac ion currents at different potencies and has atrial-predominant electrophysiological effects. We investigated the electrophysiological and proarrhythmic effects of AZD1305 versus dofetilide in dogs with chronic complete atrioventricular block and myocardial hypertrophic remodeling.

Methods and Results—

AZD1305 was administered to anesthetized mongrel dogs before and >2 weeks after the induction of atrioventricular block and ventricular and atrial electrophysiological parameters were assessed. In all dogs, the selective I
Kr
blocker dofetilide was used to examine susceptibility to acquired torsades de pointes in chronic atrioventricular block and for comparison. At normal sinus rhythm, AZD1305 increased QT and RR intervals from 290±7 to 397±15 ms (+37%,
P
<0.0001) and from 603±22 to 778±32 ms (+29%,
P
=0.002), respectively. In the same animals at chronic atrioventricular block, AZD1305 increased the QT interval from 535±28 to 747±36 ms (+40%,
P
<0.0001), similar to the QT prolongation by dofetilide (511±22 to 703±45 ms [+38%,
P
<0.0001]). AZD1305 slightly slowed the idioventricular rhythm. Whereas all (n=14) chronic atrioventricular block animals exhibited torsades de pointes on dofetilide, the arrhythmia was induced in only 4 of 11 dogs after AZD1305. Beat-to-beat variability of left-ventricular monophasic-action-potential duration increased after dofetilide (2.3±0.2 to 6.3±0.7 ms;
P
<0.0001) but not after AZD1305 (2.8±0.3 to 3.7±0.3 ms;
P
=0.20) despite similar left-ventricular monophasic-action-potential duration prolongations.

Conclusions—

Despite causing similar degrees of repolarization delay as the selective I
Kr
blocker dofetilide, the combined ion-channel blocker AZD1305 induces less repolarization instability and has a lower ventricular proarrhythmic potential in the remodeled dog heart.
Probucol alleviates atherosclerosis and improves high density lipoprotein function
Authors: Zhong Jian-Kai , Guo Zhi-Gang , Li Chen , Wang Zhen-Kun , Lai Wen-Yan , Tu Yan 
Published: November 2011

Abstract

Background
Probucol is a unique hypolipidemic agent that decreases high density lipoprotein cholesterol (HDL-C). However, it is not definite that whether probucol hinders the progression of atherosclerosis by improving HDL function.

Methods
Eighteen New Zealand White rabbits were randomly divided into the control, atherosclerosis and probucol groups. Control group were fed a regular diet; the atherosclerosis group received a high fat diet, and the probucol group received the high fat diet plus probucol. Hepatocytes and peritoneal macrophages were isolated for [3H] labeled cholesterol efflux rates and expression of ABCA1 and SR-B1 at gene and protein levels; venous blood was collected for serum paraoxonase 1, myeloperoxidase activity and lipid analysis. Aorta were prepared for morphologic and immunohistochemical analysis after 12 weeks.

Results
Compared to the atherosclerosis group, the paraoxonase 1 activity, cholesterol efflux rates, expression of ABCA1 and SR-BI in hepatocytes and peritoneal macrophages, and the level of ABCA1 and SR-BI in aortic lesions were remarkably improved in the probucol group, But the serum HDL cholesterol concentration, myeloperoxidase activity, the IMT and the percentage plaque area of aorta were significantly decreased.

Conclusion
Probucol alleviated atherosclerosis by improving HDL function. The mechanisms include accelerating the process of reverse cholesterol transport, improving the anti-inflammatory and anti-oxidant functions.
Energy-loss function of TTF-TCNQ
Authors: Lošić Željana 
Published: November 2011

Abstract
We investigate the energy-loss function for a previously developed model of quasi-one-dimensional metals with two one-dimensional electron bands per donor and acceptor chains and the three-dimensional long-range Coulomb electron-electron interaction within the random phase approximation. It is essentially influenced by two hybridized collective modes which result from the strong coupling of the intraband plasmon and the interband dipolar modes. Our calculations show that the spectral weights of the renormalized plasmon and the dipolar mode dominate within the long wavelength limit, while for large longitudinal wave vectors the intraband electron-hole quasi-continuumgains some experimentally observable spectral weight as the second mode approaches it. The function obtained is brought into correspondence with the data of the quasi-one-dimensional organic conductor tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ) obtained from electron energy-loss spectroscopy (EELS) measurements.
Revisiting the Hypothesis-Driven Interview in a Contemporary Context
Authors: Holmes Alex , Singh Bruce , Mccoll Geoff 
Published: November 2011

Objective: The “hypothesis-driven interview” was articulated by George Engel as a method of raising and testing hypotheses in the process of building a biopsychosocial formulation and determining the most likely diagnosis. This interview was a forerunner of the modern medical interview as well as the contemporary psychiatric assessment. The objective of this article is to describe the hypothesis-driven interview and to explore its relationship with the contemporary medical interview. Method: The literature on the medical and hypothesis-driven interview was reviewed. Key features of each were identified. Results: The hypothesis-driven interview shares much with the contemporary medical interview. In addition, it enhances the application of communication skills and allows the interviewer to develop a formulation during the course of the assessment. Conclusion: The hypothesis-driven interview is well suited to the aims of a contemporary psychiatric assessment.
The Validity and Utility of Risk Assessment for Inpatient Suicide
Authors: Large Matthew , Ryan Christopher , Nielssen Olav 
Published: November 2011

Objective: It is widely assumed that identifying clinical risk factors can allow us to determine which patients are at high risk of suicide while in hospital, and that identifying those patients can help prevent inpatient suicide. We aimed to examine the validity and utility of categorizing psychiatric patients to be at either high or low risk of committing suicide while in hospital. Method: The assumption that high-risk categorizations are valid was examined by comparing factors included in high-risk models derived from individual studies of inpatient suicide with the results of a meta-analysis of factors associated with inpatient suicide. A valid high-risk model was then applied to a hypothetical clinical setting in order to test the assumption that high-risk categorizations are useful. Results: The existing models for assessing whether inpatients are at high risk of suicide all include one or more factors that were not found to be associated with inpatient suicide by meta-analysis and were probably chance associations. Depressed mood and a prior history of self-harm are the only well-established independent risk factors for inpatient suicide. Using these risk factors to classify patients as being at high or low risk would prevent few, if any, suicides, and would come at a considerable cost in terms of more restrictive care of many patients and the reduced level of care available to the remaining patients. Conclusions: Risk categorization of individual patients has no role to play in preventing the suicide of psychiatric inpatients.
The Youth Criminal Justice Act: New Directions and Implementation Issues
Authors: Barnhorst Richard 
Published: November 2011

This article explains some of the Youth Criminal Justice Act's key provisions and policy directions. It also identifies implementation issues that can significantly influence how the youth justice system operates under the YCJA. Major objectives of the act include reducing the use of the youth court and reducing the use of incarceration. The YCJA emphasizes restraint, accountability, proportionality, and greater structuring of the discretion of decision makers. It contains provisions to encourage the use of extrajudicial measures, including a presumption that non-violent first offenders should be dealt with through extrajudicial measures. Conferences are recognized as a potentially useful means of improving decision making. Pre-trial detention is prohibited for child welfare purposes and presumed to be unnecessary if the youth could not be sentenced to custody. The sentencing principles set out a new approach to sentencing. Sentences must be proportionate to the seriousness of the offence and, within the limits of proportionality, must promote rehabilitation. The sentencing provisions also place specific restrictions on the use of custody. Implementation issues include appropriate use of available funding, the risk of net-widening, the adequacy of provincial policies and guidelines for police and prosecutors, conditions of release, and the interpretation of provisions related to proportionality, rehabilitation, and restrictions on custody.
The Freedom of Information Act as a Methodological Tool: Suing the Government for Data
Authors: Yeager Matthew 
Published: November 2011

The U.S. Freedom of Information Act, enacted in 1966, and the corresponding Access to Information Act in Canada, circa 1983, were designed to make government more open and accountable to the general public. However, neither act has functioned that way, with most requests being made by lawyers, information professionals, corporations, and political parties. Academic researchers, including criminal justice types, have used the act to access a variety of information from government files. For instance, Alan Block (1975; 1980) used old FBI files for his study of Jewish gangsters in New York City. Ward Churchill and Jim Vander Wall (1990a; 1990b) used the act to illustrate government law breaking in the FBI COINTELPRO program, involving Native Americans, the Black Panthers, and other progressive groups. Only rarely, however, have academics elected to take the government to court and file for judicial review of the government's disclosure decisions. This article describes two lawsuits filed by the author, one under each act, and illustrates both the potential of those acts for obtaining data from the government and the pitfalls a potential plaintiff faces when prosecuting the state for a violation of the Freedom of Information Act. The two lawsuits in question are Yeager v. Drug Enforcement Administration (1982) and Yeager v. Canada (Correctional Service) [2003]. This methodological approach undoubtedly falls under more progressive theories of criminology, such as conflict, radical, or critical perspectives, since mainstream researchers rarely resort to this technique.
Establishing the phylogenetic origin, history, and age of the narrow endemic Viola guadalupensis (Violaceae)
Authors: Marcussen Thomas , Blaxland Kim , Windham Michael D. , Haskins Kristin E. , Armstrong Fred 
Published: November 2011

• Premise of the study: Climate change and shifts in land use are two major threats to biodiversity and are likely to disproportionately impact narrow endemics. Understanding their origins and the extent of their genetic diversity will enable land managers to better conserve these unique, highly localized gene pools. Viola guadalupensis is a narrow endemic of the Guadalupe Mountains (west Texas, USA). Its affinities within Viola section Chamaemelanium have been the subject of some debate. Furthermore, the polyploid and presumably reticulate relationships within this section remain largely unknown.• Methods: We counted chromosomes for V. guadalupensis. Phylogenies for the chloroplast trnL‐F region and the low‐copy nuclear gene GPI for 24 Viola taxa were generated and used to produce a polyploid phylogenetic network. Divergence dates were obtained by fossil calibration.• Key results: Meiotic chromosome counts revealed that V. guadalupensis is tetraploid (n = 12), and the presence of two GPI homoeologs further suggested allotetraploidy. Phylogenetic reconstructions showed that it originated through hybridization between unidentified members of subsection Canadenses (paternal parent) and subsection Nuttallianae (maternal parent). A fossil‐calibrated relaxed clock dating analysis of GPI estimated the maximum age of V. guadalupensis to be 8.6 (5.7–11.6) Myr, suggesting the species evolved after the Guadalupe Mountains formed 12–13 Ma.• Conclusions: Viola guadalupensis originated by intersubsectional hybridization followed by polyploidization. Within section Chamaemelanium, this phenomenon has occurred repeatedly in the last 9 Myr (at least for V. bakeri, V. douglasii, V. glabella, and V. sempervirens). Consequences for the systematics of the section are discussed.
Subcellular targeting and biosynthesis of cyclotides in plant cells
Authors: Conlan Brendon F. , Gillon Amanda D. , Barbeta Barbara L. , Anderson Marilyn A. 
Published: November 2011

• Premise of the study: The cyclotide kalata B1 is found in the leaves of Oldenlandia affinis and is a potent insecticidal and nematocidal molecule. This peptide is cleaved from a precursor protein, Oak1, and ligation of the N‐ and C‐termini occurs to form a continuous peptide backbone. The subcellular location of the excision and cyclization reactions is unknown, and there is debate as to which enzyme catalyzes the event. To determine where in the plant cell Oak1 is processed, we prepared constructs encoding GFP (green fluorescent protein) linked to the cyclotide precursor Oak1.• Methods: The GFP constructs were transiently expressed in the leaves of Nicotiana benthamiana, and GFP fluorescence was observed in living cells using confocal microscopy. A Fei Mao (FM) styryl dye was infiltrated into whole leaves that were still growing and expressing GFP constructs, enabling the plasma membrane and the tonoplast to be highlighted for visualization of the vacuole in living cells.• Key results: The full length Oak1 precursor directed GFP to the vacuole, suggesting that excision and cyclization of the cyclotide domain occurs in the vacuole where the cyclotides are then stored. The N‐terminal propeptide and N‐terminal repeat of Oak1 were both sufficient to target GFP to the vacuole, although the C‐terminal propeptide, which is essential for cyclization, was not a targeting signal.• Conclusions: The vacuolar location of cyclotides supports our hypothesis that the vacuolar processing enzyme, asparaginyl endoproteinase, has a pivotal role in excision and cyclization from cyclotide precursors.