Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation

A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base. A new program called MS2Links was developed for the automated reduction and interpretation of fragmentation data obtained from modified nucleic acids. Based on an algorithm that searches for plausible isotopic patterns, the data reduction module is capable of discriminating legitimate signals from noise spikes of comparable intensity. The fragment identification module calculates the monoisotopic mass of ion products expected from a certain sequence and user-defined covalent modifications, which are finally matched with the signals selected by the data reduction program. Considering that MS2Links can generate similar fragment libraries for peptides and their covalent conjugates with other peptides or nucleic acids, this program provides an integrated platform for the structural investigation of protein-nucleic acid complexes based on cross-linking strategies and top-down ESI-FTMS.     

The cumulative advance of human know-how

Modern humans possess an enormous amount of 'know-how' that enables them to do things that early humans could not dream of doing. This paper explores some promising connections between two bodies of empirical research and theorizing that bear on technological know-how and its advance. Cognitive science is concerned with the nature and mechanisms of human knowing. The focus traditionally has not been on the knowledge involved in complex technologies, nor on the processes through which human know-how has advanced over time. However, certain recent developments in this field provide a nice linkage with the implicit cognitive theorizing used by scholars who study the advance of technology. And a number of the debates in the two fields are similar.     

Fluoxetine, smoking, and history of major depression: A randomized controlled trial.

The study was a randomized placebo-controlled trial testing whether fluoxetine selectively enhances cessation for smokers with a history of depression. Euthymic smokers with (H+, n = 109) or without (H-, n = 138) a history of major depression received 60 mg fluoxetine or placebo plus group behavioral quit-smoking treatment for 12 weeks. Fluoxetine initially enhanced cessation for H+ smokers (p = .02) but subsequently impaired cessation regardless of depressive history. Six months after quit date, fluoxetine-treated participants were 3.3 times more likely to be smoking (p = .02). Further research is warranted to determine why high-dose fluoxetine produces continuing effects that oppose tobacco abstinence. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Long-term follow-up of physical activity behavior in older adults.

Objective: To examine the contribution of social-cognitive factors (self-efficacy and affect) in predicting long-term physical activity in a sample of older adults (N = 174). Design: A prospective design assessed physical activity and psychosocial variables at 2 and 5 years following a 6-month randomized, controlled exercise trial. Main Outcome Measures: The primary outcome variable was self-reported physical activity, with previous behavior, self-efficacy, and affect assessed as determinants of physical activity. Results: Covariance modeling analyses indicated that physical activity at Year 2 was the strongest predictor of physical activity at 5-year follow-up. Both self-efficacy and affect at Year 2 were also associated with physical activity at Year 5, as was original treatment condition. Variables accounted for 35% of the variance in Year 5 activity. Conclusion: Older adults with higher levels of physical activity, more positive affect, and higher self-efficacy at Year 2 were more likely to continue to be active at Year 5. This study is one of the longest follow-ups of exercise behavior in older adults and has implications for structuring environments to maximize the maintenance of physical activity. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Investigation of the ceramifying process of modified silicone–silicate compositions

Glass frits were added into silicone-based composites with the aim to improve low temperature ceramification at elevated temperatures. The effect of glass frits on the properties of ceramic residue is investigated. Field emission scanning electron microscopy (FESEM), electron probe microchemical analysis (EPMA) and X-ray diffraction analysis (XRD) showed that glass frits reacted via a eutectic reaction with mica and silica. Electrical conductivity measurements at elevated temperatures showed a decline in volume resistivity with glass frit addition. It was concluded that increased conductivity is a result of ionic conduction of the glass phase produced by eutectic reactions between frits, silica and mica at high temperatures. Thermal mechanical analysis (TMA) was used to explore the dimensional changes of these composites during programmed heat treatment.     

DNA double-strand break repair: a theoretical framework and its application

DNA double-strand breaks (DSBs) are formed as a result of genotoxic insults, such as exogenous ionizing radiation, and are among the most serious types of DNA damage. One of the earliest molecular responses following DSB formation is the phosphorylation of the histone H2AX, giving rise to γH2AX. Many copies of γH2AX are generated at DSBs and can be detected in vitro as foci using well-established immuno-histochemical methods. It has previously been shown that anti-γH2AX antibodies, modified by the addition of the cell-penetrating peptide TAT and a fluorescent or radionuclide label, can be used to visualize and quantify DSBs in vivo. Moreover, when labelled with a high amount of the short-range, Auger electron-emitting radioisotope, ¹¹¹In, the amount of DNA damage within a cell can be increased, leading to cell death. In this report, we develop a mathematical model that describes how molecular processes at individual sites of DNA damage give rise to quantifiable foci. Equations that describe stochastic mean behaviours at individual DSB sites are derived and parametrized using population-scale, time-series measurements from two different cancer cell lines. The model is used to examine two case studies in which the introduction of an antibody (anti-γH2AX-TAT) that targets a key component in the DSB repair pathway influences system behaviour. We investigate: (i) how the interaction between anti-γH2AX-TAT and γH2AX effects the kinetics of H2AX phosphorylation and DSB repair and (ii) model behaviour when the anti-γH2AX antibody is labelled with Auger electron-emitting ¹¹¹In and can thus instigate additional DNA damage. This work supports the conclusion that DSB kinetics are largely unaffected by the introduction of the anti-γH2AX antibody, a result that has been validated experimentally, and hence the hypothesis that the use of anti-γH2AX antibody to quantify DSBs does not violate the image tracer principle. Moreover, it provides a novel model of DNA damage accumulation in the presence of Auger electron-emitting ¹¹¹In that is supported qualitatively by the available experimental data.     

Asymmetric oscillation of adherent targeted ultrasound contrast agents

With a lipid shell containing biotin, micron-sized bubbles bound to avidin on a porous and flexible cellulose boundary were insonified by ultrasound. The oscillation of these targeted microbubbles was observed by high-speed photography and compared to the oscillation of free-floating microbubbles. Adherent microbubbles were observed to oscillate asymmetrically in the plane normal to the boundary, and nearly symmetrically in the plane parallel to the boundary, with a significantly smaller maximum expansion in each dimension for bound than free bubbles. With sufficient transmitted pressure, a jet was produced traveling toward the boundary.     

Effectiveness of partner social support predicts enduring psychological distress after hematopoietic stem cell transplantation.

Objective: Hematopoietic stem cell transplant (HSCT) survivors who are 1 to 3 years posttransplant are challenged by the need to resume valued social roles and activities—a task that may be complicated by enduring transplant-related psychological distress common in this patient population. The present study investigated whether transplant survivors who receive adequate social support from their spouse or intimate partner experience lower distress. Method: Effects of receiving a greater quantity of partner support (a common approach to studying enacted support) were compared with effects of receiving more effective partner support (i.e., support that more closely matches their needs in terms of its quantity and quality). Men and women (N = 230) who were 1 to 3 years posttransplant completed measures of partner support quantity (Manne & Schnoll, 2001), partner social support effectiveness (Rini & Dunkel Schetter, 2010), and psychological distress (Brief Symptom Inventory; Derogatis & Spencer, 1982). Potential medical and sociodemographic confounds were controlled in analyses. Results: As hypothesized, survivors reported less distress when they received more effective partner support (p     

Investigation of food products containing garlic or onion for a false positive sulphite response by LC-MS/MS

ABSTRACT

In the US, sulphites must be declared on the label if they are present in concentrations greater than 10 mg/kg (determined as) SO₂ because an allergic-like response has been reported in a small subset of the population upon consumption of sulphite-containing products. The most widely used method for sulphite determination, the optimised Monier-Williams (OMW), produces false positive results with vegetables from the Allium (garlic) and Brassica (cabbage) genera due to extraction conditions that are thought to cause endogenous sulphur compounds to release SO₂. Recently, an LC-MS/MS method was developed for sulphites but has only been tested with samples that are 100% Allium or Brassica. Since regulatory samples may contain these vegetables as ingredients, additional investigations were necessary to determine the potential extent of false positives. Four blank matrices, chips, phyllo shells, hummus, and quinoa were spiked with various concentrations of onion and garlic powders. The sulphite concentrations were determined using an LC-MS/MS method. The matrix is extracted with a buffered formaldehyde solution, converting free and reversibly bound sulphite to the stable formaldehyde adduct, hydroxymethylsulfonate (HMS). It was determined that even at concentrations up to 8% garlic powder or 2% onion powder, the measured sulphite concentration was below the 10 mg/kg SO₂ labelling threshold. Commercial dried garlic powders were evaluated to determine the variation in responses that might be encountered in future regulatory samples. Recovery studies were conducted to determine if these methods would detect added sulphite. The ability to eliminate false positives due to these ingredients will result in a greater reliability in the accurate determination of added sulphite to ensure compliance with labelling requirements.     

Lanthanide-binding tags as versatile protein coexpression probes

Comprehensive proteomic analyses require new methodologies to accelerate the correlation of gene sequence with protein function. Key tools for such efforts include biophysical probes that integrate into the covalent architecture of proteins. Lanthanide-binding tags (LBTs) are expressible, multitasking fusion partners that are optimized to bind lanthanide ions and have several desirable attributes, which include long-lived luminescence, excellent X-ray scattering power for phase determination, and magnetic properties to facilitate NMR spectroscopic structure elucidation. Herein, we present peptide sequences with a 40-fold higher affinity for Tb(3+) ions and significantly brighter luminescence intensity compared with existing peptides. Incorporation of an LBT onto ubiquitin as a prototype fusion protein allows the use of powerful protein-visualization techniques, which include rapid luminescence detection of LBT-tagged proteins in SDS-PAGE gels, as well as determination of protein concentrations in complex mixtures. The LBT strategy is a new alternative for expressing fluorescent fusion proteins by routine molecular biological techniques.