bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of physical factors affecting the production of thermo-stable organic solvent-tolerant protease from a newly isolated halo tolerant Bacillus subtilis strain Rand
Authors: Abusham Randa A , Rahman Raja Noor Zaliha RA , Salleh Abu Bakar , Basri Mahiran 
Published: April 2009

Abstract

Background
Many researchers have reported on the optimization of protease production; nevertheless, only a few have reported on the optimization of the production of organic solvent-tolerant proteases. Ironically, none has reported on thermostable organic solvent-tolerant protease to date. The aim of this study was to isolate the thermostable organic solvent-tolerant protease and identify the culture conditions which support its production. The bacteria of genus Bacillus are active producers of extra-cellular proteases, and the thermostability of enzyme production by Bacillus species has been well-studied by a number of researchers. In the present study, the Bacillus subtilis strain Rand was isolated from the contaminated soil found in Port Dickson, Malaysia.

Results
A thermostable organic solvent-tolerant protease producer had been identified as Bacillus subtilis strain Rand, based on the 16S rRNA analysis conducted, as well as the morphological characteristics and biochemical properties. The production of the thermostable organic solvent-tolerant protease was optimized by varying various physical culture conditions. Inoculation with 5.0% (v/v) of (AB600 = 0.5) inoculum size, in a culture medium (pH 7.0) and incubated for 24 h at 37°C with 200 rpm shaking, was the best culture condition which resulted in the maximum growth and production of protease (444.7 U/ml; 4042.4 U/mg). The Rand protease was not only stable in the presence of organic solvents, but it also exhibited a higher activity than in the absence of organic solvent, except for pyridine which inhibited the protease activity. The enzyme retained 100, 99 and 80% of its initial activity, after the heat treatment for 30 min at 50, 55, and 60°C, respectively.

Conclusion
Strain Rand has been found to be able to secrete extra-cellular thermostable organic solvent-tolerant protease into the culture medium. The protease exhibited a remarkable stability towards temperature and organic solvent. This unique property makes it attractive and useful to be used in industrial applications.
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
Authors: Merhej Vicky , Royer-Carenzi Manuela , Pontarotti Pierre , Raoult Didier 
Published: April 2009

Abstract

Background
Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles.

Results
Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways.

Conclusion
Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution.

Reviewers
This article was reviewed by Eugene V. Koonin, Nicolas Galtier, and Jeremy Selengut.
Does training improve understanding of core concepts in cognitive behaviour therapy by people with intellectual disabilities? A randomized experiment
Authors: Bruce Melanie , Collins Suzanne , Langdon Peter , Powlitch Stephanie , Reynolds Shirley 
Published: April 2009

Background. People with intellectual disabilities (ID) experience similar or even higher rates of mental health problems than the general population and there is a need to develop appropriate treatments. Cognitive behaviour therapy (CBT) is effective for a wide range of disorders in the general population. However, there is some evidence that people with ID may lack the cognitive skills needed to take part in CBT.Aims. To test if people with ID can learn skills required for CBT, specifically the ability to distinguish between thoughts, feelings, and behaviours and to link thoughts and feelings (cognitive mediation).Method. A randomized independent groups design was used to examine the effect of training in CBT on two tasks measuring CBT skills. Thirty‐four adults with ID were randomly allocated to the experimental condition (N=18) or to the control condition (N=16). CBT skills were assessed blind at baseline and after the intervention.Results. The training led to significant improvements in participants' ability to link thoughts and feelings, and this skill was generalized to new material. There was no effect of training on participants' ability to distinguish amongst thoughts, feelings, and behaviours. People with ID can, therefore, learn some skills required for CBT. This implies that preparatory training for CBT might be useful for people with ID. The results might be applicable to other groups who find aspects of CBT difficult.
Thermodynamic and thermophysical properties of the reference ionic liquid: 1-Hexyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide (including mixtures). Part 2. Critical evaluation and recommended property values (IUPAC Technical Report)
Authors: Chirico Robert D. , Diky Vladimir , Magee Joseph W. , Frenkel Michael , Marsh Kenneth N. 
Published: April 2009

Abstract
This article is a product of IUPAC Project 2002-005-1-100 (Thermodynamics of ionic liquids, ionic liquid mixtures, and the development of standardized systems). Experimental results of thermodynamic, transport, and phase equilibrium studies made on a reference sample of the ionic liquid 1-hexyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide are summarized, compared, and critically evaluated to provide recommended values with uncertainties for the properties measured. Properties measured included thermal properties (triple-point temperature, glass-transition temperature, enthalpy of fusion, heat capacities of condensed states), volumetric properties, speeds of sound, viscosities, electrolytic conductivities, relative permittivities, as well as properties for mixtures, such as gas solubilities (solubility pressures), solute activity coefficients at infinite dilution, and liquid-liquid equilibrium temperatures. Recommended values with uncertainties are provided for the properties studied experimentally. The effect of the presence of water on the property values is discussed.
Dual Antiplatelet Drug Resistance Is a Risk Factor for Cardiovascular Events after Percutaneous Coronary Intervention
Authors: Ivandic Boris T , Sausemuth Mareike , Ibrahim Hesham , Giannitsis Evangelos , Gawaz Meinrad , Katus Hugo A 
Published: April 2009

Abstract
Background: Nonresponsiveness to clopidogrel and acetylsalicylic acid (ASA), a frequent result of platelet aggregometry studies, has unclear clinical and prognostic significance.
Methods: We performed impedance aggregometry in 182 patients 12–24 h after percutaneous coronary intervention (PCI) and a 600-mg loading dose of clopidogrel, adding 5 μmol/L ADP and 1 mg/L collagen to diluted whole blood to determine platelet inhibition by clopidogrel and ASA, respectively. Samples from nonresponders were incubated in vitro with methyl-S-adenosine monophosphate or ASA to distinguish between pharmacodynamic and pharmacokinetic types of resistance. We assessed a combined primary endpoint of myocardial infarction, target vessel revascularization, late stent thrombosis, or cardiac death.
Results: Nineteen patients (10.4%) were dual nonresponders (nonresponsive to both ASA and clopidogrel), and 163 patients (89.6%) were designated responders. The latter group also included 15 and 14 single nonresponders (responsive to either clopidogrel or ASA, respectively), who exhibited endpoint frequencies comparable to those of full responders (n = 134). Pharmacokinetic resistance was most prevalent. Primary endpoints occurred more frequently in dual nonresponders (n = 6, 31.6%) than in responders (n = 20, 12.3%) (relative risk 2.57; 95% CI 1.18–5.61; log-rank P = 0.03). Multivariate analysis confirmed dual nonresponsiveness (hazard ratio 2.9; 95% CI 1.17–7.2; P = 0.02) as an independent risk factor.
Conclusions: Dual nonresponders carry a high cardiovascular risk after PCI and should obtain intensified antiplatelet therapy and follow-up.
Measurement of Aldosterone in Human Plasma by Semiautomated HPLC–Tandem Mass Spectrometry
Authors: Taylor Paul J , Cooper Donald P , Gordon Richard D , Stowasser Michael 
Published: April 2009

Abstract
Background: Reliable measurement of aldosterone with less interlaboratory variation than RIA would help standardize testing for primary aldosteronism. We set out to validate a high-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS) method for aldosterone in human plasma.
Methods: We prepared samples (EDTA plasma, lithium heparin plasma, and serum from separator and plain clot tubes) and measured aldosterone using online HPLC-MS/MS with d7-aldosterone as internal standard. We also analyzed EDTA plasma samples by immunoassay. We established a reference range for HPLC-MS/MS aldosterone by analyzing blood collected midmorning from 97 normotensive seated subjects.
Results: The linear range was 69.4–5548.0 pmol/L (2.5–200 ng/dL) (r2 &gt; 0.994, n = 14). Inter- and intraday analytical recovery and imprecision for quality control samples of 166.4, 1109.6, and 4161.0 pmol/L (6.0, 40.0, and 150.0 ng/dL) were 92.2%–102.0% and &lt;6.3%, respectively (n = 5). The lower limit of quantification was 69.4 pmol/L (2.5 ng/dL), with inter- and intraday analytical recovery and imprecision of 91.4%–94.5% and &lt;9.5% (n = 5). No interferences were observed in plasma from Addison’s disease patients (n = 5). Comparison of collection tubes, using EDTA as the reference, revealed similar aldosterone results. Comparison of HPLC-MS/MS with immunoassay gave an acceptable mean bias (0.83%) but wide range (−44.8% to 39.7%) of differences. HPLC-MS/MS aldosterone concentrations in normotensive subjects ranged from &lt;69.4 to 635.2 pmol/L (&lt;2.5 to 22.9 ng/dL).
Conclusions: This first reported aldosterone method using online HPLC-MS/MS is precise across the clinically relevant range, not influenced by collection tube type, and offers semiautomated sample preparation and high throughput.
Ultraperformance Liquid Chromatography–Tandem Mass Spectrometry Assay for Iohexol in Human Serum
Authors: Annesley Thomas M , Clayton Larry T 
Published: April 2009

AbstractBackground: Iohexol is an iodinated contrast dye that has been shown to be useful in the estimation of glomerular filtration rate (GFR) in patients with suspected renal insufficiency. We developed and validated an ultraperformance liquid chromatography (UPLC)–triple quadrupole mass spectrometry (MS/MS) assay for quantifying iohexol in human serum.Methods: Sample preparation involved dilution of 50 μL serum with 400 μL water, followed by protein precipitation with zinc sulfate and methanol containing the structural analog ioversol as the internal standard. After 1:20 dilution of the supernatant with water, 5 μL was injected into the UPLC-MS/MS system. Chromatography was performed using a Waters Oasis HLB 5-μm particle size, 2.1 × 20 mm column maintained at 50 °C. We used a 1-step acetonitrile/0.1% formic acid gradient to elute the compounds of interest at a common retention time of 0.96 min. The multiple reaction monitoring transitions used for integration and quantification were m/z 821.7→803.7 for iohexol and m/z 807.9→589.0 for ioversol in the electrospray positive ionization mode.Results: The assay was linear from 2.5 mg/L (lower limit of quantification) to 1500 mg/L iohexol, with a mean extraction efficiency of &gt;99%. Recovery of nominal target concentrations was 99%–102%. Interassay imprecision ranged from 7.9% at a concentration of 2.5 mg/L to 4.1% at 1000 mg/L. Ion suppression studies showed no matrix effects on the ionization of the 2 compounds.Conclusions: This rapid UPLC-MS/MS method can be successfully used for quantifying iohexol in human serum. .
Characterization of NT-proBNP in Human Urine
Authors: Palmer Suetonia C , Endre Zoltan H , Richards A Mark , Yandle Timothy G 
Published: April 2009

Abstract
Background: Urine amino-terminal probrain natriuretic peptide (NT-proBNP) concentrations may exclude the presence of heart failure and provide insight into renal clearance mechanisms for human NT-proBNP. We characterized the molecular forms of urine NT-proBNP detected by immunoassay.
Methods: Urine from patients with heart failure was subjected to HPLC and analyzed using immunoassays specific toward different epitopes of NT-proBNP. We assessed urine NT-proBNP immunoreactivity in healthy subjects and patients with heart failure.
Results: Size-exclusion chromatography of heart failure urine identified no NT-proBNP immunoreactivity coeluting with NT-proBNP(1–76); multiple immunoreactive NT-proBNP fragments were present. The absence of intact urinary NT-proBNP was supported by reversed-phase HPLC. Urine NT-proBNP immunoreactivity was higher in patients with acute [median 192 (interquartile range 108–1445) pg/mg creatinine] and chronic [52 (15–118) pg/mg creatinine] heart failure than in healthy subjects [4.2 (2.6–5.8) pg/mg creatinine] (P &lt; 0.001). In 40 patients with heart failure, urine NT-proBNP immunoreactivity correlated with plasma NT-proBNP (r = 0.72, P &lt; 0.001) and inversely with left ventricular ejection fraction (r = −0.33, P = 0.04).
Conclusions: Our findings clarify previous reported relationships of urine NT-proBNP–like immunoreactivity with plasma NT-proBNP concentrations and the diagnosis of heart failure. As urine NT-proBNP immunoreactivity is not intact NT-proBNP(1–76), but rather reflects assorted metabolites, the diagnostic performance of NT-proBNP assays in urine may be assay specific, necessitating validation of biomarker performance on an assay-by-assay basis. .
From the Sec complex to the membrane insertase YidC
Authors: Kuhn Andreas 
Published: April 2009

Abstract
The key enzymes that catalyze the insertion of proteins into membranes are the Sec translocase and the YidC membrane insertase. Recent insights into the structure and functional intermediates of these enzymes have provided a first molecular glimpse of how they help the newly synthesized proteins to enter the membrane bilayer. In this process, the new proteins undergo a number of specific interactions in the cytoplasm and at the membrane surface before they insert into the bilayer and translocate their external domains across the membrane. The components involved in this pathway recognize each other at the molecular level, forming a route the membrane protein can move along.
Cooperative effects in the substrate specificity of the complement protease C1s
Authors: Boyd Sarah E. , Kerr Felicity K. , Albrecht David W. , de la Banda Maria Garcia , Ng Natasha , Pike Robert N. 
Published: April 2009

Abstract
Complement is a key component of the immune system, but can contribute to inflammatory diseases. The substrate specificity of C1s protease has been successfully investigated using a combinatorial approach, while a positional scanning method failed. The lack of success of the latter approach is possibly due to cooperativity in the active site, which could confound such analyses. With a panel of peptides devised using factorial design, we show pronounced cooperativity between the S4 and S1′ subsites in the active site of the enzyme, and weaker cooperativity between the S1′ and S3′ subsites. The use of factorial design has promise as a methodology for determining cooperativity in protease active sites.
Subsite cooperativity in protease specificity
Authors: Ng Natasha M. , Pike Robert N. , Boyd Sarah E. 
Published: April 2009

Abstract
Proteases play vital roles in a range of biological processes, such as cell cycle, cell growth and differentiation, apoptosis, haemostasis and signalling. Fundamental to our knowledge of protease action is an understanding of how the active site operates; this has been examined through extensive studies of the substrate specificity of the enzymes. Kinetic and structural analyses have shown that the binding of a particular substrate residue at a protease subsite can have either a positive or negative influence on the binding of particular residues at other subsites. This phenomenon has been termed subsite cooperativity and has been observed in a wide range of proteases, often between non-adjacent subsites. This review aims to highlight studies where subsite cooperativity has been observed, experimental techniques used in the past and potential methods that can be employed to comprehensively examine this phenomenon. Further understanding of how the protease active site recognises and chooses its substrates for cleavage will have a significant impact on the development of pharmaceuticals that target these enzymes.
On-line nano-HPLC/ESI QTOF MS monitoring of α2–3 and α2–6 sialylation in granulocyte glycosphingolipidome
Authors: Kirsch Stephan , Müthing Johannes , Peter-Katalinić Jasna , Bindila Laura 
Published: April 2009

Abstract
A novel glycosphingolipidomic protocol using nano-high performance liquid chromatography coupled on-line to electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOF-MS) focusing on the separation of isomeric ganglioside structures is described here. A highly efficient separation of α2–3- and α2–6-sialylated ganglioside species of different carbohydrate chain length was achieved on an HILIC-amido column, followed by sensitive flow-through ESI-QTOF-MS detection and unambiguous structural identification by tandem MS experiments. The protocol was applied to encompass the glycosphingolipidome of human granulocytes, where 182 distinct components could be clearly identified and assigned regarding the ganglioside type and the isomer distribution.
An Attempt at Finding a Correlation Between Environmental and Accelerated RILEM TC 139-DBS Weathering for One-Component Polyurethane Sealants Applied on Mortar
Authors: Pozzi Enrico , Carcano Valerio , Ausilio Antonio 
Published: April 2009

Abstract
Two sets of butt joint test specimens (ISO 8339 type) with mortar substrate (ISO 13640, Method 1) were prepared without primer using eight one-component polyurethane sealants; four of low modulus (LM) type showing a movement capability of 25 % and four of high modulus (HM) type showing a movement capability of less than 12.5 % (nomenclature HM according to ISO 11600 as they show a secant modulus&gt;0.4 MPa at 23°C and&gt;0.6 MPa at −20°C, but the movement capability of these sealants does not comply with any of the HM classes stated by ISO 11600). All specimens were conditioned according to ISO 8339 Conditioning Method B. Afterwards the specimens were divided into two sets: the first set was exposed for 24 months in static conditions to the outdoor environment in the urban area of Milan, facing southeast at an angle of 45°. Periodically, i.e., every four months, they were evaluated by visual inspection of their exposed surface. The second set of joints was subjected to accelerated weathering according to RILEM TC 139 DBS in a light-exposure apparatus (xenon-arc type) with water spray. At the end of each RILEM cycle (eight weeks weathering plus one week thermo-mechanical cycling according to ISO 9047) the specimens were visually inspected. The authors found a good correlation between the results obtained in outdoor exposure and those observed after the RILEM durability cycling. In addition to tabulating the findings for crack density and size, the results are also presented as photographic documentation.
Enhanced Electrokinetic Remediation of Mercury-Contaminated Tailing Dam Sediments
Authors: Darban A. K. , Ayati B. , Yong R. N. , Khodadadi A. , Kiayee A. 
Published: April 2009

Abstract
This study evaluates the use of different extracting solutions at the cathode during electrokinetic remediation to optimize the removal of mercury from gold mine tailing dam sediments in Iran. The total mercury concentration of the soil was 210 mg/kg and the duration of this experiment was 4 weeks. Experiments were conducted on the mine tailing recovered sediments with two voltage gradients (1.0 VDC/cm and 1.5 VDC/cm) to assess the effect of the voltage gradient when employing 0.1M Na-EDTA, 0.1M, and 0.4M KI solutions and distilled water. The test conducted on the soil showed that when the 0.1M and 0.4M KI concentrations were employed with a voltage gradient of 1.0 VDC/cm, approximately 50 % and 70 %, respectively, of the mercury was removed from the sediment. Also, it is understood that when the 0.1M and 0.4M KI concentrations were used with a voltage gradient of 1.5 VDC/cm, 65 % and 56 %, respectively, of the mercury was removed from the contaminated soil. The tests showed that mercury removal from sediment was less with distilled water and Na-EDTA as the extracting agents. The results also indicated that electrokinetic remediation for the concentration of 0.4M KI and with a voltage gradient of 1.0 VDC/cm was optimal for the approximately 70 % removal of the initial contamination. The reason for the remaining mercury in the sediment could be the presence of CaO, other metals, and organic compounds.