bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling induced polarization effects due to pyrite in geochemical alteration zones above hydrocarbon accumulations
Authors: Veeken P. C. H. , Kudryavceva E. O. , Putikov O. F. , Legeydo P. Y. , Ivanov S. A.
Published: March 2012

Geoelectrical methods measure resistivity and induced polarization (IP) effects in the subsurface. The differentially normalized electromagnetic method (DNME) detects geochemical alteration zones due to anomalous electrical responses which are often located above a hydrocarbon accumulation. Leakage above a non-perfect top seal is postulated to change the pH in the overlying sediments where a shallower mobility barrier is encountered. Epigenetic pyrite mineral growth is stimulated when iron and sulfur ions are available. Leakage and mineral growth are modelled by mathematical formulae assuming diffusion migration through the overburden. Effects of time and tectonic faulting are examined. Pyrite is highly polarizable and easily detected by an electrical IP survey in the field, whereby a current is introduced into the ground and subsequently turned off. Decay of the potential difference over the receiver electrodes is monitored in time. Special parameters facilitate detection of IP anomalies related to the presence of hydrocarbons. An inverted electrical depth model is computed using the Cole–Cole formula. The impact of geochemical modelling and predicted epigenetic mineral growth is demonstrated for the Severo-Gulyaevskaya dataset (Siberia). The overall DNME track record shows a reduced risk attached to hydrocarbon prospects, with a more reliable ranking at reasonable costs.
The third porosity system
Authors: Corbett P. W. M. , Geiger S. , Borges L. , Garayev M. , Valdez C.
Published: March 2012

Well testing is a critical part of any evaluation of a carbonate reservoir discovery. Well-test interpretation in carbonate reservoirs poses additional challenges to those normally faced in the interpretation process in clastic reservoirs. The range of different boundary and crossflow relationships that are generated during well testing by the complex porosity systems are often poorly quantified and understood. The volume over which the pressure response is effective is also a source of great uncertainty and could be critical at the exploration/appraisal stage in any project.

In this paper, which describes a generic modelling approach, we consider carbonate reservoirs which contain three pore sytems (or porosity types): (1) microporosity (end-member) with low permeability and high porosity; (2) macroporosity (end-member) with high permeability and high porosity; and (3) fracture porosity with high permeability and low porosity. These occur in various nested geometrical distributions and varying contrasts. The observed well-test responses (i.e. fracture flow, fracture–matrix interactions) tend to ‘obscure’ one of these systems when compared with theoretical models. Micro- (meso-) and macroporosity can merge into a single matrix porosity system where the permeability contrasts are not great and the correlation lengths short (which can often be the case in carbonates). Macroporosity can also appear in well testing to ‘merge’ with the fracture response, i.e. the contributions of flow in the fractures and (high-permeability) porous matrix are indistinguishable. As a result of the homogenizing attributes of pressure dissipation away from the well, it is not generally possible to see the effects of a ‘triple-porosity’ response (i.e. where three different pore systems have a separate and identifiable signature on the well-test response) and a classical double-porosity response in the well test, despite three different pore systems being present, is possible. The apparent double-porosity response, which might obscure a triple-porosity system, therefore needs careful interpretation in order to attribute the appropriate properties during reservoir characterization in carbonates.

In this work we use ‘geological’ well testing (i.e. well testing through numerical simulation of hypothetical geological models) to systematically analyse the effects of microporosity, macroporosity and fracture porosity on pressure dissipation and their apparent homogenization. While recent studies have proposed that a triple-porosity system should result in a ‘W-shaped’ response, we do not observe this behaviour in our simulations, although we specifically designed our geological models with a triple-porosity system. Instead we observe how macroporosity merges with the fractures or micro- and macroporosity merge, creating a ‘sub-dominant’ matrix or a ‘dominant’ fracture system, respectively and follow a traditional ‘V-shaped’ double-porosity response.
Heavy mineral stratigraphic analysis on the Clair Field, UK, west of Shetlands
Authors: Morton Andrew , Milne Alex
Published: March 2012

Hydrocarbons in the Clair Field, west of the Shetland Islands, are hosted by Devonian–Carboniferous clastic red beds deposited in a non-marine fluviolacustrine setting. The succession is almost entirely biostratigraphically barren and, hence, alternative approaches to reservoir correlation are required. Heavy mineral analysis (HMA), which subdivides clastic successions on the basis of changes in provenance and sediment transport history, has proven successful in establishing a high-resolution correlation framework for the Clair Field. Since the technique offers a reliable and rapid method for monitoring the stratigraphy of the Clair reservoir succession, HMA has been undertaken on a real-time basis at well site for virtually all development wells during Phase 1 of the Clair Field development, and for all Phase 2 appraisal wells. Heavy mineral data can be acquired in less than 2 hours from receipt of sample. Consequently, owing to the relatively slow penetration rates frequently associated with Clair drilling, stratigraphic information is usually acquired ahead of logging while drilling. Heavy mineral data are used in the decision-making process in a variety of situations, including picking of casing and coring points, whether to maintain or alter well trajectory, and when to terminate drilling. In the Clair Field, formation tops can be subtle and, since HMA can establish trends and predict formation changes before they are encountered, they are critical in aiding geosteering decisions. HMA has also been used to monitor stratigraphy and to pick formation tops when logging tools have failed, allowing drilling to continue and avoiding tripping to change the bottom-hole assembly. The application of HMA to the Clair Field development is illustrated by reference to a number of wells drilled on the field since 2005.
A new method for top seals predictions in high-pressure hydrocarbon plays
Authors: Casabianca Davide , Cosgrove John
Published: March 2012

The current model describing the sealing mechanism of high-pressure hydrocarbon traps and the ensuing methodology for predicting top seal integrity and capacity in high-pressure plays assumes that the caprock, defined as the low matrix permeability formation immediately overlying the reservoir, is the seal.

This study challenges this assumption and proposes the existence within the caprock of a fluid waste zone consisting of a system of fractures cutting from the reservoir upwards into the caprock and, therefore, charged with reservoir fluids. Because of the waste zone fractures the reservoir fluids are not sealed at the base of the caprock. Instead the seal coincides with the fracture waste zone tip point, which occurs at an important stress and stratigraphic boundary termed the ultimate seal. Six case studies demonstrate that in the UK Central Graben the top seal for Mesozoic high pressure hydrocarbon accumulations lies between the Base Cretaceous Unconformity and the base of the Chalk Group and that the Jurassic Kimmeridge Clay Formation is not necessarily the seal for these traps. The data used for the construction of structural and stress models for the case studies include pore pressure measurements, formation integrity measurements, well logs and reflection seismic profiles.

An important conclusion of this study is that the shorter the waste zone the higher the chance of finding a hydrocarbon column in the reservoir.
Free/Libre open-source software development
Authors: Crowston Kevin , Wei Kangning , Howison James , Wiggins Andrea
Published: March 2012

We review the empirical research on Free/Libre and Open-Source Software (FLOSS) development and assess the state of the literature. We develop a framework for organizing the literature based on the input-mediator-output-input (IMOI) model from the small groups literature. We present a quantitative summary of articles selected for the review and then discuss findings of this literature categorized into issues pertaining to inputs (e.g., member characteristics, technology use, and project characteristics), processes (software development practices, social processes, and firm involvement practices), emergent states (e.g., social states and task-related states), and outputs (e.g. team performance, FLOSS implementation, and project evolution). Based on this review, we suggest topics for future research, as well as identify methodological and theoretical issues for future inquiry in this area, including issues relating to sampling and the need for more longitudinal studies.
Proximity measures for rank join
Authors: Martinenghi Davide , Tagliasacchi Marco
Published: March 2012

We introduce the proximity rank join problem, where we are given a set of relations whose tuples are equipped with a score and a real-valued feature vector. Given a target feature vector, the goal is to return the
K
combinations of tuples with high scores that are as close as possible to the target and to each other, according to some notion of distance or dissimilarity. The setting closely resembles that of traditional rank join, but the geometry of the vector space plays a distinctive role in the computation of the overall score of a combination. Also, the input relations typically return their results either by distance from the target or by score. Because of these aspects, it turns out that traditional rank join algorithms, such as the well-known
HRJN
, have shortcomings in solving the proximity rank join problem, as they may read more input than needed. To overcome this weakness, we define a tight bound (used as a stopping criterion) that guarantees instance optimality, that is, an I/O cost is achieved that is always within a constant factor of optimal. The tight bound can also be used to drive an adaptive pulling strategy, deciding at each step which relation to access next. For practically relevant classes of problems, we show how to compute the tight bound efficiently. An extensive experimental study validates our results and demonstrates significant gains over existing solutions.
Identifying Web Spam with the Wisdom of the Crowds
Authors: Liu Yiqun , Chen Fei , Kong Weize , Yu Huijia , Zhang Min , Ma Shaoping , Ru Liyun
Published: March 2012

Combating Web spam has become one of the top challenges for Web search engines. State-of-the-art spam-detection techniques are usually designed for specific, known types of Web spam and are incapable of dealing with newly appearing spam types efficiently. With user-behavior analyses from Web access logs, a spam page-detection algorithm is proposed based on a learning scheme. The main contributions are the following. (1) User-visiting patterns of spam pages are studied, and a number of user-behavior features are proposed for separating Web spam pages from ordinary pages. (2) A novel spam-detection framework is proposed that can detect various kinds of Web spam, including newly appearing ones, with the help of the user-behavior analysis. Experiments on large-scale practical Web access log data show the effectiveness of the proposed features and the detection framework.
Quality and Leniency in Online Collaborative Rating Systems
Authors: Lauw Hady W. , Lim Ee-Peng , Wang Ke
Published: March 2012

The emerging trend of social information processing has resulted in Web users’ increased reliance on user-generated content contributed by others for information searching and decision making. Rating scores, a form of user-generated content contributed by reviewers in online rating systems, allow users to leverage others’ opinions in the evaluation of objects. In this article, we focus on the problem of summarizing the rating scores given to an object into an overall score that reflects the object’s quality. We observe that the existing approaches for summarizing scores largely ignores the effect of reviewers exercising different standards in assigning scores. Instead of treating all reviewers as equals, our approach models the leniency of reviewers, which refers to the tendency of a reviewer to assign higher scores than other coreviewers. Our approach is underlined by two insights: (1) The leniency of a reviewer depends not only on how the reviewer rates objects, but also on how other reviewers rate those objects and (2) The leniency of a reviewer and the quality of rated objects are mutually dependent. We develop the
leniency-aware quality
, or
LQ
model, which solves leniency and quality simultaneously. We introduce both an exact and a ranked solution to the model. Experiments on real-life and synthetic datasets show that
LQ
is more effective than comparable approaches.
LQ
is also shown to perform consistently better under different parameter settings.
A Declarative Language Approach to Device Configuration
Authors: Schüpbach Adrian , Baumann Andrew , Roscoe Timothy , Peter Simon
Published: March 2012

C remains the language of choice for hardware programming (device drivers, bus configuration, etc.): it is fast, allows low-level access, and is trusted by OS developers. However, the algorithms required to configure and reconfigure hardware devices and interconnects are becoming more complex and diverse, with the added burden of legacy support, “quirks,” and hardware bugs to work around. Even programming PCI bridges in a modern PC is a surprisingly complex problem, and is getting worse as new functionality such as hotplug appears. Existing approaches use relatively simple algorithms, hard-coded in C and closely coupled with low-level register access code, generally leading to suboptimal configurations.

We investigate the merits and drawbacks of a new approach: separating hardware configuration
logic
(algorithms to determine configuration parameter values) from
mechanism
(programming device registers). The latter we keep in C, and the former we encode in a declarative programming language with constraint-satisfaction extensions. As a test case, we have implemented full PCI configuration, resource allocation, and interrupt assignment in the Barrelfish research operating system, using a concise expression of efficient algorithms in constraint logic programming. We show that the approach is tractable, and can successfully configure a wide range of PCs with competitive runtime cost. Moreover, it requires about half the code of the C-based approach in Linux while offering considerably more functionality. Additionally it easily accommodates adaptations such as hotplug, fixed regions, and “quirks.”
Moving From Paper to E-Book Reading
Authors: Vinall-Cox Joan
Published: March 2012

Reading in the digital world has both similarities and differences from reading on paper. Books as tangible objects elicit powerful responses linked to the pleasures felt in reading them. Although our eyes scan differently when reading online, reading e-versions of books initially seems similar to reading on paper. However digital books have some significantly different aspects that will be especially powerful in academic work.
1H‐NMR study of some new acetyl dimethylbiphenyls: unambiguous signal assignment for the methyl groups
Authors: Kamounah Fadhil S. , Titinchi Salam J.
Published: March 2012

The abundance 1H‐NMR spectra of some new mono‐ and diacetyl compounds derived from 2,2′‐dimethyl‐, 3,3′‐dimethyl‐, and 4,4′‐dimethylbiphenyls were recorded. Unambiguous signal assignment of the methyl groups of the aromatic biphenyl rings were made for the structure elucidation.
Catalyzed asymmetric hydrolysis of fluorinated chiral esters in locust haemolymph. In vitro19F NMR monitoring
Authors: Menguy L. , Hamm S. , Cherton J. C.
Published: March 2012

19F NMR is used for monitoring the In vitro behaviour in locust organs or tissues of an ester with a fluorinated alkoxy structure and a chiral acyl moiety. In carrying out analysis directly in the biological media, the problematic extraction of polar metabolites is avoided, contributing to an easier and more reliable monitoring. Thus, in diluted haemolymph a remarkable enantioselectivity of the transformation is evidenced. Over a four hour period the ester R remains unalterated, while the S enantiomer is completely hydrolyzed. This enantioselectivity is the reverse of the trend which is generally observed in the hydrolysis of esters by lipases.
A fast screening method for tricyclic antidepressants and their urinary metabolites by FAB‐tandem mass spectrometry
Authors: Schäfer M. , Budzikiewicz H. , Brzezinka H. , Schifferdecker M.
Published: March 2012

A screening method for tricyclic antidepressants (TCA) and their urinary metabolites by FAB tandem mass spectrometry (FAB MS/MS) is presented. The collision induced dissociation (CID) behavior of pure dibenzocycloheptadienes (amitriptyline 1, nortriptyline 2), dibenzoxepines (doxepine 3, dosulepine 4), dibenzazepines (imipramine 5, desipramine 6, trimipramine 7) and the iminostilbene derivative opipramol 8 is described and used for the specific determination of these tricyclics by MS/MS.

For the screening procedure a methanolic extract of the urine sample is passed through a XAD‐2 column and the eluate is examined without further purification after evaporation of the solvent. Identification of the TCA is achieved by constant neutral loss (CNL) scans for 173 u, 195 u and 193 u and subsequent daughter ion spectra of the molecular ions [M+H]+. Glucuronide conjugate metabolites of the tricyclic antidepressants 1, 2, 3, 6, 8 could be identified by CNL‐scans (176 u) and the assignments were confirmed by daughter ion mass spectra. A urine sample of a fatal 1, 2, 8 overdose and samples of three patients under therapeutic dosage with 1, 3 or 6 are presented as examples for application.
Compositional analysis of the leaf oils of Piper callosum Ruiz & Pav. from Peru and Michelia montana Blume from India
Authors: Marcel H. P. van Genderen , Leclercq Piet A. , Delgado Hermann Silva , Kanjilal Purnendu B. , Singh Ramesh S.
Published: March 2012

The leaf oils of Piper callosum from Peruvian Amazon and Michelia montana from Assam, India, were prepared by hydrodistillation and analyzed by a combination of GC and GC/MS. Twenty five and thirty components have been identified, representing 96.3 and 100.0% of the respective oils. The major constituents were found to be asaricin (syn. sarisan) (35.9 and 81.8%, respectively) and safrole (20.2 and 13.0%). The oil of P. callosum contained in addition eugenyl methyl ether (9.7%) and (E)‒asarone (7.8%), compounds not detected in the M. montana oil. The identity of the principal compound, an isomer of myristicin, was unequivocally established by 13C‒NMR spectrometric techniques, especially long‒range 1H–13C correlation.
Mass spectrometric fragmentation reactions of dialkylselenides1
Authors: Filsak G. , Budzikiewicz H.
Published: March 2012

Mass spectrometric fragmentation and especially rearrangement reactions of dialkyl selenides after electron ionization will be discussed.
The investigation of N‒dinitrophenyl derivatives of amino acids by electron/chemical ionization using a particle beam interface1
Authors: Kaußmann M. , Budzikiewicz H.
Published: March 2012

The EI and CI mass spectra of DNP‒amino acids and oligopeptides give characteristic mass spectra when a particle beam interface is used for introduction. They differ from mass spectra obtained after direct insertion into the ion source: In the particle beam interface the major part of the molecules suffers degradation by contact with metal surfaces such as decarboxylation and reduction of the nitro groups. The final products are benzimidazole derivatives carrying in 2‒position the residue of the respective amino acid. These products show characteristic fragmentation reactions which allow to identify isomeric amino acids. For DNP‒di‒ and oligopeptides an identification of the N‒terminal amino acid is always possible, that of the C‒terminus with restrictions.
A revision of the 13C NMR spectral assignment of globulol
Authors: Toyota Masao , Tanaka Masami , Asakawa Yoshinori
Published: March 2012

Complete assignment of the 13C NMR spectrum of the aromadendrane‒type sesquiterpene alcohol, globulol was reported, however, it still remained to be ambiguous. We report here the unambiguous and complete assignment of the 1>H and 13C NMR spectra of (+)‒globulol, which was isolated from the liverworts Plagiochila ovalifolia, Neotrichocolea bissetii and Pallavicinia subciliata
A new program to 13C NMR spectrum prediction based on tridimensional models
Authors: Magri Fátima M. M. , Militão Júlio S. L. , Ferreira Marcelo J. P. , Brant Antônio J. C. , Emerenciano Vicente P.
Published: March 2012

This work describes a new program creation, written for Windows environment for 13C NMR spectrum prediction based on interatomic distances and types of atoms. It has shown to be more efficient on forecast of natural product spectra than some commercial programs such as ACD and DENDRAL. Predictions of spectra of molecules with great conformational variations, as, for example, sesquiterpene lactones, are given.
Direct determination of naturally occurring biologically active compound–serum albumin conjugate by matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Tanaka H. , Xuan L.J. , Morimoto S. , Shoyama Y. , Isobe R. , Nojima K.
Published: March 2012

Opium alkaloids were conjugated with bovine serum albumin (BSA) to give individual antigen conjugates which were analyzed using BSA as an internal standard by matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry. It became clear that 9 molecules of thebaine were conjugated in a thebaine–BSA conjugate. Codeine and morphine contents in individual conjugates were determined to be 12 and 6 molecules, respectively. Using a relative molecular mass of BSA, 11.5 molecules of forskolin conjugated with BSA. Tetrahydrocannabinolic acid (THCA)–carrier protein conjugates using β‐alanine or without β‐alanine as a linker were analyzed. From these results it became evident that the hapten molecules of THCA–β‐alanine–BSA, THCA–BSA, THCA–β‐alanine–human serum albumin (HSA) and THCA–HSA were 17.2, 12.7, 27.8 and 54.4, respectively. Crocin–HSA conjugates were synthesized by two methods using succinate and NaIO4 cleavage of sugar moiety. A broad molecular peak of crocin–HSA conjugate appeared at around m/z 98,342 resulting in 30 molecules of crocin‐hemisuccinate conjugated with HSA. The crocin–HSA synthesized via NaIO4 oxidation showed a sharp molecular peak around 69,504 compared to that of hemisuccinate preparation. The number of crocin combined with HSA was, however, smaller 3.1 molecules.

Analysis of monoclonal antibody by MALDI mass spectrometry determined the exact molecular weight and their purities.
The structural and spectroscopic basis for modelling prion protein interactions
Authors: Warwicker Jim , Cole Chris
Published: March 2012

Mammalian prion diseases are characterised by an α‐helical to β‐sheet conformational change within the prion protein, that was originally established with circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy. Since prion disease is transmissible, significant effort has been aimed at establishing the molecular details of conformational change and the specificity that underpins infectivity. The structure determined for the carboxy‐terminal domain of the predominantly α‐helical form by nuclear magnetic resonance (NMR) provides a starting point for considering questions at the molecular level. However, elucidation of atomic detail for the β‐rich form is complicated by problems of protein solubility, and regions other than the carboxy‐terminal domain of the α‐rich form are likely to possess functionally significant, ordered domains in the presence of suitable ligands and solution conditions. Further spectroscopic analysis, particularly of polypeptide secondary structure, is playing a key role in constraining molecular modelling studies of prion protein folding and interactions. We present a review of this area of prion research.
Biomolecule structure characterization in the gas phase using mass spectrometry
Authors: Bothner Brian , Carmitchel Laurie , Staniszewski Kristin , Sonderegger Martin , Siuzdak Gary
Published: March 2012

Carbohydrate/cation interactions were examined in the gas phase using mass spectrometry and the results were compared with computer generated models of the complexes. Monosaccharide/alkali cation complexes of five carbohydrates, D‐fructose, D‐glucose, D‐galactose, D‐mannose, and a deuterated analog of D‐glucose, 6,6‐D‐glucose‐d2, were studied. Among the technuques used in this effort were electrospray ionization (ESI), desorption/ionization on silicon (DIOS), matrix‐assisted laser desorption/ionization (MALDI) and fast atom/ion bombardment (FAB) mass spectrometry. A series of ESI, DIOS, MALDI and FAB‐MS experiments were used to obtain relative cation binding preferences of each monosaccharide. Heterodimers of 6,6‐D‐glucose‐d2 formed with each of the monosaccharides show that Na+ binding for D‐fructose, D‐mannose and D‐galactose is similar, while D‐glucose was 25% weaker. Modeling studies and energy minimization calculations on the alpha and beta forms of the monosaccharide alkali cation complexes are consistent with the experimental data and indicate that D‐fructose, D‐galactose, and D‐mannose undergo tridentate and tetradentate binding with Na+ and Li+ while D‐glucose would only form a bidentate complex.
In situ Characterisation of Living Cells by Raman Spectroscopy
Authors: Notingher I. , Verrier S. , Romanska H. , Bishop A. E. , Polak J. M. , Hench L. L.
Published: March 2012

We report the first Raman spectra of individual living and dead cells (MLE‐12 line) cultured on bioinert standard poly‐L‐lysine coated fused silica and on bioactive 45S5 Bioglass® measured at 785 nm laser excitation. At this excitation wavelength no damage was induced to the cells even after 40 minutes irradiation at 115 mW power, as indicated by cell morphology observation and trypan blue viability test. We show that shorter wavelength lasers, 488 nm and 514 nm, cannot be used because they induce damage to the cells at very low laser powers (5 mW) and short irradiation times (5–20 minutes). The most important differences between the spectra of living and dead cells are in the 1530–1700 cm−1 range, where the dead cells have strong peaks at 1578 cm−1 and 1607 cm−1. Other differences occur around the DNA peak at 1094 cm−1. Our study establishes the feasibility of using the 785 nm laser for an in situ real‐time non‐invasive method to follow biological events (proliferation, differentiation, cell death, etc.) within individual cells cultured on bioactive scaffolds in their physiologic environment over long periods of time.
Dynamics and Protein–Solvent Interactions of Hemoglobin in T and R Quaternary Conformation
Authors: Caronna Chiara , Cupane Antonio
Published: March 2012

In this work we report the thermal behaviour of the amide I′ band of carbonmonoxy and deoxy hemoglobin in 65% v/v glycerolD8/D2O solutions and in the temperature interval 10–295 K. Following recent suggestions in the literature, we analyze the amide I′ band in terms of two components, one at about 1630 cm−1 and the other at about 1650 cm−1, that are assigned to solvent‒exposed and buried α‒helical regions, respectively.

For deoxy hemoglobin (in T quaternary structure) both components are narrower with respect to carbonmonoxy hemoglobin (in R quaternary structure), while the peak frequency blue shift observed, upon increasing temperature, for the component at about 1630 cm−1 is smaller. The reported data provide evidence of the dependence of hemoglobin dynamic properties upon the protein quaternary structure and suggest a more compact α‒helical structure of hemoglobin in T conformation, with reduced population of low‒frequency modes involving the solvent and protein.
Use of Synchrotron Radiation SAXS to Study the First Steps of the Interaction between Sodium Dodecyl Sulfate and Charged Liposomes
Authors: López O. , Cócera M. , Pons R. , Amenitsch H. , Caelles J. , Parra J. L. , Coderch L. , de la Maza A.
Published: March 2012

The technique of time resolved small angle X–ray scattering (SAXS) using a synchrotron radiation source was used to study the structural transformations as well as the kinetic associated with the first steps of the solubilization of liposomes induced by the anionic surfactant sodium dodecyl sulfate (SDS). Neutral and electrically charged (anionic and cationic) liposomes were used to investigate the effect of the electrostatic charges on these initial steps. The mechanism that induces the solubilization process consisted in an adsorption of surfactant on the bilayers and a desorption of mixed micelles from the liposomes surface to the aqueous medium. Regardless of the type of charge of the liposome the time needed for the desorption of the first mixed micelles was shorter than that for the complete adsorption of the surfactant on the liposomes surface. The present work demonstrates that the adsorption of the SDS molecules on liposomes was slower when the charges of surfactant and lipids were the same. As for the release of mixed micelles from the surface of these liposomes, this process was slower when the charges of surfactant and lipids were opposite.
Protein Dynamics Measurements by 3D HNCO Based NMR Experiments
Authors: Xia Youlin , Sze Kong Hung , Li Ning , Shaw Pang Chui , Zhu Guang
Published: March 2012

Protein dynamics can be characterized by relaxation parameters obtained from traditional 2D HSQC based NMR experiments. This approach is hampered when applied to proteins with severe spectral overlap. In the present work, several novel 3D TROSY‐HNCO and 3D HSQC‐HNCO based NMR experiments were applied for measuring 15N T1, T2 and 1H‐15N NOE with improved spectral dispersion by introducing a third 13C dimension. The number of phase cycling steps in these 3D pulse sequences was restricted to two in order to minimize the time required to perform the dynamics measurements. For a uniformly 100% 15N, 100% 13C, and 70%2H‐labelled trichosanthin sample (~27 kDa, 1.0 mM) at 30°C, the sensitivity of 3D TROSY‐HNCO based experiment was, on the average, enhanced by 72% compared to that of 3D HSQC‐HNCO based experiments. However, the 3D HSQC‐HNCO based experiments should be more effective for non‐deuterated proteins with smaller molecular weights and seriously overlapped 2D HSQC spectra. Results from the 3D TROSY‐HNCO and 3D HSQC‐HNCO based experiments were in good agreement with those obtained from traditional 2D HSQC based experiments.
Protein characterization using Liquid Chromatography Desorption Ionization on Silicon Mass Spectrometry (LC‐DIOS‐MS)
Authors: Prenni Jessica E. , Shen Zhouxin , Trauger Sunia , Chen Wei , Siuzdak Gary
Published: March 2012

This paper presents a novel combination of of‐line liquid chromatography (LC) separation with desorption ionization on silicon mass spectrometry (DIOS‐MS) as an alternative to the traditional on‐line coupling of LC and electrospray ionization (ESI). In this work, electrospray deposition is used to generate a spatially preserved linear track of the separated sample on a specially designed DIOS chip. The total sequence coverage analysis of two model protein systems was evaluated by both LC‐DIOS‐MS and nanoLC ESI tandem MS (MS/MS). LC‐DIOS‐MS yielded improved sequence coverage for both of the model systems (between 99.5 and 100%) compared with traditional LC‐ESI‐MS/MS analysis (between 82 and 87.6%). In addition to improved sequence coverage determination, LC‐DIOS‐MS also offers the potential for high‐throughput protein characterization.
Discovery of a Tat HIV‐1 Inhibitor through Computer‐Aided Drug Design
Authors: Esquieu Didier , Péloponèse Jean-Marie , Opi Sandrine , Gregoire Catherine , de Mareuil Jean , Watkins Jennifer , Campbell Grant , Dunot Jean-Pierre , Sturgis James , Witvrouw Myriam , Pannecouque Christophe , de Clercq Erik , Montembault Mickaël , Giang Vo-Thanh , Villiéras Monique , Fargeas Valérie , Lebreton Jacques , Loret Erwann P.
Published: March 2012

Tat is a regulatory HIV‐1 protein, which has the particularity to be secreted very early by HIV‐infected cells. The extra cellular roles of Tat are suspected to be the main cause of the maintenance of reservoirs of HIV‐infected cells and the failure of actual AIDS therapies to eradicate HIV. This study describes the rationale used to design molecules that bind to a target area containing an hydrophobic pocket identified in the 2D‐NMR structure of Tat. Molecules were synthesized and the derivative named TDS2 was shown to be a Tat inhibitor. Fluorescence revealed that TDS2 binds in the target area, which is conserved across five different Tat variants representative of the main HIV‐1 subtypes. TDS2 inhibited in vitro HIV‐1 replication in human T‐cells. Further chemical modifications remain necessary to enhance affinity to Tat and reduce cytotoxicity.
Solid state 13C and 1H MAS NMR investigations of C60(ferrocene‒d10)2 complex
Authors: Shabanova E. , Schaumburg K. , Kamounah F. S.
Published: March 2012

The article presents NMR investigations of a molecular crystalline material C60(ferrocene‒d10)2, which consists of two highly mobile molecules. 13C and 1H NMR line shapes and T1 relaxation times are discussed and compared with results obtained for the undeuteriated compound. The mobilities of C60 and ferrocene molecules were found to increase in the complex in comparison with the two components as crystalline materials.
Mass spectrometry in nucleic acid, carbohydrate and steroid analysis
Authors: Compton Bruce Jon , Siuzdak Gary
Published: March 2012

Mass spectrometry is now widely used in many areas of biomolecule analysis and this diversity is well represented by the analysis of oligonucleotides, carbohydrates and steroids. In this paper an overview of the common techniques used for analysis of these biomolecules is presented, including electrospray ionization (ESI), matrix‐assisted laser desorption/ionization (MALDI), desorption/ionization on silicon (DIOS), and negative chemical ionization gas chromatography mass spectrometry (NCI GC/MS). Additionally, important aspects of biomolecule analysis, such as molecular weight determination, sequencing using tandem mass spectrometry and enzymes, precursor ion scanning, noncovalent interactions, and sensitivity, will be discussed.
FTIR spectroscopic studies and AM1 semi‒empirical calculations of some hydrogen‒bonded complexes of 2,5‒dihydroxy‒3,6‒dichlorobenzoquinone and anilines
Authors: Habeeb Moustafa M. , Gohar Gamal A.
Published: March 2012

Fourier transform infrared (FTIR) spectra of a series of 1 : 1 hydrogen‐bonded complexes between 2,5‐dihydroxy‐3,6‐dichlorobenzoquinone (chloranilic acid, CA) and anilines in the crystalline form were investigated. The correlation between the center of gravity of the protonic vibration bands (νcg, cm–1) and the calculated proton affinities of the investigated anilines (PA, kcal/mol) as well as the Hammett substituent constants, (σH) were presented. A deep minimum was located at PA = 210−211 kcal/mol and σH = 0.1 suggesting the existence of a critical behavior. The semi‒empiricalsemi‒empirical quantum mechanical method, AM1 was utilized to correlate the experimental FTIR data. The obtained data showed a reasonable consistency with the experimental results. An intersection point was recorded at PA = 210–211 kcal/mol in the correlations between the oxygen and nitrogen atomic charges, (q0 and qN, esu), the OH and NH bond distances (ROH and RNH, Å) and PA values of the substituted anilines. The strict correlation between the experimental and the calculated results confirmed the validity of the AM1 semi‐empirical method for studying chloranilic acid – anilines hydrogen‐bonded complexes.
Monitoring intracellular metabolites in neuroblastoma with 1H NMR spectroscopy: effects of growth factor withdrawal and modulation of lipid metabolism
Authors: Lindskog Magnus , Jarvet Jüri , Graslund Astrid , Kogner Per
Published: March 2012

1H NMR spectroscopy has previously been employed to detect and monitor changes in the lipid metabolism of neuroblastoma cells upon cytotoxic treatment. Here, we addressed the question whether altered growth conditions, by presence or absence of serum, would impact on the metabolites detectable with 1H NMR spectroscopy. Chronic serum deprivation of SH‒SY5Y human neuroblastoma cells resulted in a decrease in the intracellular content of several metabolites, in particular total choline. This metabolic effect was paralleled by significant growth inhibition. In addition, we investigated the potential functional origin of intracellular 1H NMR visible lipids in SH‒SY5Y cells. A drop in lipid methylene protons could be observed shortly after serum‒withdrawal. Contrary, removal of lipoproteins from the serum led to a pronounced increase in intracellular lipids, as did inhibition of de novo sterol synthesis by lovastatin. In conclusion, we demonstrate that intracellular total choline in neuroblastoma cells in vitro is highly dependent on the availability of growth factors. Furthermore, we show that 1H NMR visible lipids decrease upon serum‒withdrawal but are accumulated when cholesterol supply is abrogated. The biological and potential clinical implications of these findings are discussed.
Electrospray ion mobility spectrometry of intact viruses
Authors: Thomas John J. , Bothner Brian , Traina Joe , Benner W. Henry , Siuzdak Gary
Published: March 2012

Characterizing supramolecular interactions offers significant challenges using NMR or crystallographic techniques either because of size limitations or the difficulty in forming suitable crystals, while mass spectrometry is largely limited to low resolution mass information. Here we report gas phase measurements of intact virus particles using electrospray ion mobility spectrometry with an accuracy in radial measurements that were sufficient to differentiate closely related species. In addition, measured diameters indicate that iscosahedral virus particles retain their structure in the gas phase as well as undergoing a slight compaction in the absence of solvent. Analysis of the human pathogen adenovirus represents the largest and most sophisticated biomolecular complex detected in the gas phase to date. These results, on a diverse set of viral systems, suggest that ion mobility spectrometry may have broad applications for the analysis of biological complexes.
A two‒dimensional IR spectroscopic (2D‒IR) simulation of protein conformational changes
Authors: Arrondo José Luis R. , Iloro Ibon , Aguirre Julián , Goñi Félix M.
Published: March 2012

Two‒dimensional IR correlation spectroscopy (2D‒IR) is a novel method that provides the analysis of infrared spectra with the capacity to differentiate overlapping peaks and to distinguish between in‒phase and out‒of‒phase spectral responses. Artificial spectra originated from protein amide I band component parameters have been used to study their variation in the correlation maps. Using spectra composed of one, two or three Gaussian peaks, behaviour patterns of the bands in the synchronous and asynchronous maps have been originated, with changes in intensity, band position and bandwidth. Intensity changes produce high‒intensity spots in the synchronous spectra, whereas only noise is observed in the asynchronous spectra. Band shifting originates more complex patterns. In synchronous spectra, several spots are generated at the beginning and at the end of the shifting band. Also, characteristic asynchronous spectra with butterfly‒like shapes are formed showing the trajectory of the shift. Finally, synchronous maps corresponding to band broadening reveal several spots at peak inflection points, related to the zones with higher intensity variation. The asynchronous spectra are very complex but they follow a characteristic symmetric pattern. Furthermore, examples of maps obtained from polypeptides and proteins using temperature as the perturbing factor are interpreted in terms of the patterns obtained from artificial bands.
The use of high–sensitivity sapphire cells in high pressure NMR spectroscopy and its application to proteins
Authors: Kremer W. , Arnold M. R. , Kachel N. , Kalbitzer H. R.
Published: March 2012

The application of high pressure in bioscience and biotechnology has become an intriguing field in un/refolding and misfolding processes of proteins. NMR spectroscopy is the only generally applicable method to monitor pressure–induced structural changes at the atomic level in solution. Up to now the application of most of the multidimensional NMR experiments is impossible due to the restricted volume of the high pressure glass cells which causes a poor signal–to–noise ratio. Here we present high strength single crystal sapphire cells which double the signal–to–noise ratio. This increased signal–to–noise ratio is necessary to perform, for example, phophorus NMR spectroscopy under variable pressures. To understand the effect of pressure on proteins, we need to know the pressure dependence of 1H chemical shifts in random coil model tetrapeptides. The results allow distinguishing structural changes from the pressure dependence of the chemical shifts. In addition, the influence of pressure on the buffer system was investigated. Since high pressure was shown to populate intermediate amyloidogenic states of proteins the investigation of pressure effects on proteins involved in protein conformational disorders like Alzheimer′s Disease (AD) and Transmissible Spongiform Encephalopathies (TSE) is of keen interest. 1H–15N–TROSY–spectra were acquired to study the effects of pressure and temperature on chemical shifts and signal volumes of the human prion protein. These measurements show identical pressure sensitivity of huPrP(23–230) and huPrP(121–230). First results suggest a folding intermediate for the human prion protein which can be populated by high hydrostatic pressure.
Protein structure characterization with mass spectrometry
Authors: Kriwacki Richard , Reisdorph Nichole , Siuzdak Gary
Published: March 2012

Mass spectrometry is now commonly being used to determine both the primary and higher order structures of proteins. The basis for these investigations lies in the ability of mass analysis techniques to detect changes in protein conformation under differing conditions. These experiments can be conducted on proteins alone (with no modifying substance present) or in combination with proteolytic digestion or chemical modification. In addition to primary structure determination, proteases and chemical modification have long been used as probes of higher order structure, an approach that has been recently rejuvenated with the emergence of highly sensitive and accurate mass analysis techniques. Here, we review the application of proteases as probes of native structure and illustrate key concepts in the combined use of proteolysis, chemical modification, and mass spectrometry. For example, protein mass maps have been used to probe the structure of a protein/protein complex in solution (cell cycle regulatory proteins, p21 and Cdk2). This approach was also used to study the protein/protein complexes that comprise viral capsids, including those of the common cold virus where, in addition to structural information, protein mass mapping revealed mobile features of the viral proteins. Protein mass mapping clearly has broad utility in protein identification and profiling, yet its accuracy and sensitivity is also allowing for further exploration of protein structure and even structural dynamics.
Molecular events involved in the activation of calpain from human erythrocytes
Authors: Dainese Enrico , Sabatucci Annalaura , Minafra Roberto , Vachette Patrice , Melloni Edon , Cozzani Ivo
Published: March 2012

Calpains are intracellular cysteine endopeptidases that combine protease activity with a dependence on Ca2+ binding. Here we describe the conformational changes leading to the calpain activation, occurring in the enzyme purified from human erythrocytes, studied in solution using small angle X‐ray scattering (SAXS). Addition of Ca2+ determines the formation of large soluble aggregates that can be dissociated either chelating these ions or adding cahotropic salts in solution. On the other side, our SAXS studies revealed that the addition of Ca2+ in the presence of inhibitors as E64 or leupeptin triggers a reversible conformational transition leading to a proper assembly of the active site without any aggregation or dissociation process. It is suggested that the observed conformational changes can be considered as the early step in the sequence of molecular events leading to calpain activation.
Infrared spectroscopic study of triacetyl‒β‒cyclodextrin and its inclusion complex with nicardipine
Authors: Bratu I. , Veiga F. , Fernandes C. , Hernanz A. , Gavira J. M.
Published: March 2012

Infrared spectra of inclusion compounds of triacetyl‒β‒cyclodextrin with nicardipine hydrochloride were compared and analysed with those corresponding to their physical mixture and the pure compounds, respectively. Different O–H stretching vibrations, assigned to water molecules, were located in the Fourier Transform Infrared (FT IR) spectra of triacetyl‒β‒cyclodextrin, and its inclusion complex with nicardipine obtained by spray‒drying (SD) method. Water molecules involved in various hydrogen bonds environments change their status during complexation process. Evidences are observed of the formation of the complex especially in the spectral regions of the amino and carbonyl stretching vibrations.
The effect of glycerol on signal supression during electrospray ionization analysis of proteins
Authors: Mendes M. A. , Souza B. M. , Marques M. R. , Palma M. S.
Published: March 2012

The effect of salts, detergents and chaotropic agents on mass spectrometric analysis are relatively well understood, mainly due to their actions decreasing the performance of ESI interface in mass spectrometric analysis. However, there are few studies in the literature characterizing the effect of protein stabilization by glycerol, followed in some circumstances by the suppression of protein signal when ESI interface is used. The aim of the present research was to investigate in details the mass spectrometric behavior of some proteins in presence of high levels of glycerol during ESI–MS analysis. Thus, horse heart myoglobin and chicken ovalbumin were used as standard proteins. It was demonstrated that the presence of 1% (v/v) glycerol suppressed the signal of these proteins during the ESI–MS analysis, even when the sample nozzle potential was scanned from 28 to 80 V. However, when the glycerol concentration was decreased to 0.5% (v/v) and the sample cone voltage adjusted to 50 V, a perfect envelope of peaks was observed, allowing the spectrum deconvolution and the molecular mass determination with mass accuracy lower than 0.01% in each situation. A molecular explanation for this suppressive effect and for the analytical overcoming of this difficult is proposed.