Correlation between Physico-Chemical Characteristics of Particulated ß-Lactoglobulin and Its Behavior at Air/Water and Oil/Water Interfaces.

It is widely accepted that protein-based particles can efficiently stabilize foams and emulsions. However, it is not fully elucidated which particle properties are decisive for the stabilization of air/water and oil/water interfaces. To unravel this correlation, selected properties of nano-sized soluble ß-lactoglobulin particles were changed one at a time. Therefore, particles of (1) variable size but similar zeta potential and degree of cross-linking and (2) similar size but different further properties were produced by heat treatment under a specific combination of pH value and NaCl concentration and then analyzed for their interfacial behavior as well as foaming and emulsifying properties. On the one hand, it was found that the initial phase of protein adsorption at both the air/water and the oil/water interface was mainly influenced by the zeta potential, independent of the particle size. On the other hand, foam stability as resolved from the time-dependent evolution of mean bubble area negatively correlated with disulfide cross-linking, whereas emulsion stability in terms of oil droplet flocculation showed a positive correlation with disulfide cross-linking. In addition, flocculation was more pronounced for larger particles. Concluding from this, foam and emulsion stability are not linked to the same particle properties and, thus, explanatory approaches cannot be used interchangeably.

Scalable Electron Correlation Methods. 6. Local Spin-Restricted Open-Shell Second-Order Møller-Plesset Perturbation Theory Using Pair Natural Orbitals: PNO-RMP2.

We present a (near) linear scaling implementation of high-spin open-shell Møller-Plesset perturbation theory using pair natural orbitals (PNO-RMP2). The theory is based on a new variant of open-shell MP2 which is fully spin-adapted and uses a single set of spin-free amplitudes, as in closed-shell MP2. This method, denoted SROMP2, is invariant to unitary orbital transformations within the closed, open, and virtual orbital subspaces. Accordingly, only a single set of PNOs per spatial orbital pair is needed, and the efficiency is similar to closed-shell calculations. The PNOs are obtained using a semicanonical approximation with large domains of projected atomic orbitals (PAOs). Linear scaling is achieved provided that the open-shell orbitals are local, and distant pairs are treated by multipole approximations. The method is efficiently parallelized. The convergence of ionization and reaction energies as a function of the PAO and PNO domain sizes is demonstrated and found to be very similar as for closed-shell calculations. The suitability of the PNOs for explicitly correlated PNO-RCCSD-F12 calculations is also tested. So far, this method is only simulated using a conventional program with appropriate projections to the PAO and PNO subspaces. It is demonstrated for radical stabilization energies as well as ionization potentials that the errors caused by the local domain approximations with our default thresholds are negligible.

The ABCs of RSV.

Respiratory syncytial virus (RSV) is a common viral infection affecting many children in the United States. This seasonal virus is the leading cause of hospitalization of infants and neonates. This article reviews the current recommendations for diagnostic testing, treatment options, and prevention of RSV.

Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers.

The existence of a 30-nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg(2+)-dependent self-association of linear 12-mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call "oligomers", are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10-nm fibers, rather than folded 30-nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2, but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro These results indicate that a 10-nm array of nucleosomes has the intrinsic ability to self-assemble into large chromatin globules stabilized by nucleosome-nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.

Scalable electron correlation methods I.: PNO-LMP2 with linear scaling in the molecular size and near-inverse-linear scaling in the number of processors.

We propose to construct electron correlation methods that are scalable in both molecule size and aggregated parallel computational power, in the sense that the total elapsed time of a calculation becomes nearly independent of the molecular size when the number of processors grows linearly with the molecular size. This is shown to be possible by exploiting a combination of local approximations and parallel algorithms. The concept is demonstrated with a linear scaling pair natural orbital local second-order Møller-Plesset perturbation theory (PNO-LMP2) method. In this method, both the wave function manifold and the integrals are transformed incrementally from projected atomic orbitals (PAOs) first to orbital-specific virtuals (OSVs) and finally to pair natural orbitals (PNOs), which allow for minimum domain sizes and fine-grained accuracy control using very few parameters. A parallel algorithm design is discussed, which is efficient for both small and large molecules, and numbers of processors, although true inverse-linear scaling with compute power is not yet reached in all cases. Initial applications to reactions involving large molecules reveal surprisingly large effects of dispersion energy contributions as well as large intramolecular basis set superposition errors in canonical MP2 calculations. In order to account for the dispersion effects, the usual selection of PNOs on the basis of natural occupation numbers turns out to be insufficient, and a new energy-based criterion is proposed. If explicitly correlated (F12) terms are included, fast convergence to the MP2 complete basis set (CBS) limit is achieved. For the studied reactions, the PNO-LMP2-F12 results deviate from the canonical MP2/CBS and MP2-F12 values by <1 kJ mol(-1), using triple-ζ (VTZ-F12) basis sets.

Proteomic characterization of the nucleolar linker histone H1 interaction network.

To investigate the relationship between linker histone H1 and protein-protein interactions in the nucleolus, we used biochemical and proteomics approaches to characterize nucleoli purified from cultured human and mouse cells. Mass spectrometry identified 175 proteins in human T cell nucleolar extracts that bound to Sepharose-immobilized H1 in vitro. Gene ontology analysis found significant enrichment for H1 binding proteins with functions related to nucleolar chromatin structure and RNA polymerase I transcription regulation, rRNA processing, and mRNA splicing. Consistent with the affinity binding results, H1 existed in large (400 to >650kDa) macromolecular complexes in human T cell nucleolar extracts. To complement the biochemical experiments, we investigated the effects of in vivo H1 depletion on protein content and structural integrity of the nucleolus using the H1 triple isoform knockout (H1ΔTKO) mouse embryonic stem cell (mESC) model system. Proteomic profiling of purified wild-type mESC nucleoli identified a total of 613 proteins, only ~60% of which were detected in the H1 mutant nucleoli. Within the affected group, spectral counting analysis quantitated 135 specific nucleolar proteins whose levels were significantly altered in H1ΔTKO mESC. Importantly, the functions of the affected proteins in mESC closely overlapped with those of the human T cell nucleolar H1 binding proteins. Immunofluorescence microscopy of intact H1ΔTKO mESC demonstrated both a loss of nucleolar RNA content and altered nucleolar morphology resulting from in vivo H1 depletion. We conclude that H1 organizes and maintains an extensive protein-protein interaction network in the nucleolus required for nucleolar structure and integrity.

Comparison of explicitly correlated local coupled-cluster methods with various choices of virtual orbitals.

Explicitly correlated local coupled-cluster (LCCSD-F12) methods with pair natural orbitals (PNOs), orbital specific virtual orbitals (OSVs), and projected atomic orbitals (PAOs) are compared. In all cases pair-specific virtual subspaces (domains) are used, and the convergence of the correlation energy as a function of the domain sizes is studied. Furthermore, the performance of the methods for reaction energies of 52 reactions involving 58 small and medium sized molecules is investigated. It is demonstrated that for all choices of virtual orbitals much smaller domains are needed in the explicitly correlated methods than without the explicitly correlated terms, since the latter correct a large part of the domain error, as found previously. For PNO-LCCSD-F12 with VTZ-F12 basis sets on the average only 20 PNOs per pair are needed to obtain reaction energies with a root mean square deviation of less than 1 kJ mol(-1) from complete basis set estimates. With OSVs or PAOs at least 4 times larger domains are needed for the same accuracy. A new hybrid method that combines the advantages of the OSV and PNO methods is proposed and tested. While in the current work the different local methods are only simulated using a conventional CCSD program, the implications for low-order scaling local implementations of the various methods are discussed.

Integrating an internet-mediated walking program into family medicine clinical practice: a pilot feasibility study.

BACKGROUND: Regular participation in physical activity can prevent many chronic health conditions. Computerized self-management programs are effective clinical tools to support patient participation in physical activity. This pilot study sought to develop and evaluate an online interface for primary care providers to refer patients to an Internet-mediated walking program called Stepping Up to Health (SUH) and to monitor participant progress in the program. METHODS: In Phase I of the study, we recruited six pairs of physicians and medical assistants from two family practice clinics to assist with the design of a clinical interface. During Phase II, providers used the developed interface to refer patients to a six-week pilot intervention. Provider perspectives were assessed regarding the feasibility of integrating the program into routine care. Assessment tools included quantitative and qualitative data gathered from semi-structured interviews, surveys, and online usage logs. RESULTS: In Phase I, 13 providers used SUH and participated in two interviews. Providers emphasized the need for alerts flagging patients who were not doing well and the ability to review participant progress. Additionally, providers asked for summary views of data across all enrolled clinic patients as well as advertising materials for intervention recruitment. In response to this input, an interface was developed containing three pages: 1) a recruitment page, 2) a summary page, and 3) a detailed patient page. In Phase II, providers used the interface to refer 139 patients to SUH and 37 (27%) enrolled in the intervention. Providers rarely used the interface to monitor enrolled patients. Barriers to regular use of the intervention included lack of integration with the medical record system, competing priorities, patient disinterest, and physician unease with exercise referrals. Intention-to-treat analyses showed that patients increased walking by an average of 1493 steps/day from pre- to post-intervention (t = (36) = 4.13, p < 0.01). CONCLUSIONS: Providers successfully referred patients using the SUH provider interface, but were less willing to monitor patient compliance in the program. Patients who completed the program significantly increased their step counts. Future research is needed to test the effectiveness of integrating SUH with clinical information systems over a longer evaluation period.

Instrument and methods for surface dilatational rheology measurements.

We describe an instrument combining the advantages of two methods, axisymmetric drop shape analysis for well-deformed drops and capillary pressure tensiometry for spherical drops, both used for measuring the interfacial tension and interfacial rheological parameters. The rheological parameters are the complex interfacial elasticity, and the surface elasticity and viscosity of Kelvin-Voigt and Maxwell rheological models. The instrument is applicable for investigation of the effect of different types of surfactants (nonionic, ionic, proteins, and polymers) on the interfacial rheological properties both of air/water and oil/water interfaces, and of interfaces between liquids with equal mass densities. A piezodriven system and a specially designed interface unit, implemented in the instrument, ensure precise control for standard periodic waveforms of surface deformation (sine, square, triangle, and sawtooth) at a fixed frequency, or produce surface deformation at constant rate. The interface unit ensures accurate synchronization between the pressure measurement and the surface control, which is used for real-time data processing and feedback control of drop area in some of the applications.

The silent information regulator 3 protein, SIR3p, binds to chromatin fibers and assembles a hypercondensed chromatin architecture in the presence of salt.

The telomeres and mating-type loci of budding yeast adopt a condensed, heterochromatin-like state through recruitment of the silent information regulator (SIR) proteins SIR2p, SIR3p, and SIR4p. In this study we characterize the chromatin binding determinants of recombinant SIR3p and identify how SIR3p mediates chromatin fiber condensation in vitro. Purified full-length SIR3p was incubated with naked DNA, nucleosome core particles, or defined nucleosomal arrays, and the resulting complexes were analyzed by electrophoretic shift assays, sedimentation velocity, and electron microscopy. SIR3p bound avidly to all three types of templates. SIR3p loading onto its nucleosomal sites in chromatin produced thickened condensed fibers that retained a beaded morphology. At higher SIR3p concentrations, individual nucleosomal arrays formed oligomeric suprastructures bridged by SIR3p oligomers. When condensed SIR3p-bound chromatin fibers were incubated in Mg(2+), they folded and oligomerized even further to produce hypercondensed higher-order chromatin structures. Collectively, these results define how SIR3p may function as a chromatin architectural protein and provide new insight into the interplay between endogenous and protein-mediated chromatin fiber condensation pathways.

Domain organization and quaternary structure of the Saccharomyces cerevisiae silent information regulator 3 protein, Sir3p.

The silent information regulator protein 3 (Sir3p) functions in the initiation, propagation, and maintenance of transcriptionally silenced chromatin in Saccharomyces cerevisiae. To better understand the physicochemical basis for its effects on chromatin architecture, recombinant full-length S. cerevisiae Sir3p has been purified to near homogeneity on the large-scale and characterized by circular dichroism, limited protease digestion, and analytical ultracentrifugation. Results indicate that the Sir3p monomer has a unique tripartite domain organization, including a nearly 300-amino-acid residue stretch of intrinsically disordered residues that lies internal to its structured N- and C-terminal regions. Sir3p self-associates extensively in moderate salt and at micromolar protein concentrations producing a broad range of oligomers that sediment from 8 to in excess of 85 S. These results provide new insight into Sir3p domain organization and quaternary structure and support a nucleosome bridging model for Sir3p-dependent regulation of chromatin architecture.

A database for therapy evaluation in neurological disorders: application in epilepsy.

Due to the high diversity of cases and the variety of treatment modalities, the information to be managed and processed in therapy evaluation is excessive in many neurological diseases. Additionally, in order to gain more insight into, not only the disorders, but also the applied therapies, more objectivity is requested in clinical practice. Therefore, in this study, a database system is designed for assisting therapy evaluation in neurological diseases. A sample implementation is accomplished for structuring and managing the information accessible for different treatment modalities available for epilepsy. The first application of the developed database system for clinical use in epilepsy is tested with selected quantitative parameters extracted from electrophysiological signals of epilepsy patients who receive neurotherapy as a complementary treatment to the pharmacological therapy, as well as of voluntary control subjects. The system contributes to the automation of statistical analysis for therapy planning, monitoring, and evaluation. It is extendible for other disorders such as attention deficit hyperactivity disorder, depression, and sleep disorders.