Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments

By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article (1). The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that long handles and soft laser traps represent the best conditions to extract rate estimates that are closest to the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.Comment: PDF file, 32 pages including 9 figures plus supplementary materia

Signal transduction pathways involved in proteolysis-inducing factor induced proteasome expression in murine myotubes

The proteolysis-inducing factor (PIF) is produced by cachexia-inducing tumours and initiates protein catabolism in skeletal muscle. The potential signalling pathways linking the release of arachidonic acid (AA) from membrane phospholipids with increased expression of the ubiquitin-proteasome proteolytic pathway by PIF has been studied using C2C12 murine myotubes as a surrogate model of skeletal muscle. The induction of proteasome activity and protein degradation by PIF was blocked by quinacrine, a nonspecific phospholipase A2 (PLA2) inhibitor and trifluroacetyl AA, an inhibitor of cytosolic PLA2. PIF was shown to increase the expression of calcium-independent cytosolic PLA2, determined by Western blotting, at the same concentrations as those inducing maximal expression of 20S proteasome α-subunits and protein degradation. In addition, both U-73122, which inhibits agonist-induced phospholipase C (PLC) activation and D609, a specific inhibitor of phosphatidylcholine-specific PLC also inhibited PIF-induced proteasome activity. This suggests that both PLA 2 and PLC are involved in the release of AA in response to PIF, and that this is important in the induction of proteasome expression. The two tyrosine kinase inhibitors genistein and tryphostin A23 also attenuated PIF-induced proteasome expression, implicating tyrosine kinase in this process. PIF induced phosphorylation of p44/42 mitogen-activated protein kinase (MAPK) at the same concentrations as that inducing proteasome expression, and the effect was blocked by PD98059, an inhibitor of MAPK kinase, as was also the induction of proteasome expression, suggesting a role for MAPK activation in PIF-induced proteasome expression. © 2003 Cancer Research UK

Validation of the Spanish version of the Multidimensional State Boredom Scale (MSBS)

BACKGROUND: Boredom, which is a common problem in the general population, has been associated with several psychiatric disorders. The Multidimensional State Boredom Scale (MSBS) was developed, based on a theoretically and empirically grounded definition of boredom, to assess this construct. The aim of the present study was to assess the psychometric properties of the Spanish validated version of the MSBS in a multi-age sample recruited from the general population. METHODS: The patients (N = 303) were recruited from primary care settings. In addition to the sociodemographic variables and the MSBS, the General Health Questionnaire 28 items (GHQ-28), Positive and Negative Affect Scale (PANAS), Negative subscale and the Mindful Attention Awareness Scale (MAAS) were administered. We used confirmatory factor analysis (CFA) to analyse the dimensionality of the MSBS. Cronbach’s α coefficient was used to analyse the internal consistency of the scale. The consistency of the MSBS over time (test-retest reliability) was assessed using the intra-class correlation coefficient. The construct validity was examined by calculating Pearson’s r correlations between the MSBS with theoretically related and unrelated constructs. Cronbach’s α for MSBS was 0.89 (95 % CI, 0.87–0.92), ranging from 0.75 to 0.83 for the 5 subscales. RESULTS: The characteristics of the final sample (N = 303) were that the participants were primarily female (66.77 %) with a mean age of 49.32 years (SD, 11.46) and primarily European (94.71 %). The CFA of the MSBS confirmed that the original five-factor model showed good fit indices: CFI = .96; GFI = .94; SRMR = .05; and RMSEA = .06 [.05–.08]. Cronbach’s α for MSBS was 0.89 (95 % CI, 0.87–0.92), ranging from 0.75 to 0.83 for the 5 subscales. The MSBS showed a test-retest coefficient measured with an ICC of 0.90 (95 % CI, 0.88–0.92). The ICC for the 5 subscales ranged from 0.81 to 0.89. The MSBS showed a significant negative correlation with MAAS and a significant positive correlation with the GHQ (total score and subscales) and PANAS-Negative Affect. CONCLUSIONS: The Spanish version of the MSBS has been validated as a reliable instrument for measuring boredom in the general population. This study will facilitate the assessment of boredom for clinical and research purposes in Spanish-speaking populations

Redefining innovation processes: The digital designers at work

As design in digital innovation has become a thing, we highlight the inconclusive concepts that describe design activity in innovation processes. Proposing an alternative theoretical lens - a sociomaterial practice lens - we claim that this view can reveal the contribution of digital designers to the work of innovation. This paper draws on a research study with digital designers in the UK. At the same time as we begin to reconceptualise the ways digital design activity can be described, we also illustrate a theoretical framework based on 1) action and knowing as ordered by collectively produced objects, 2) sociomateriality and the configuration of human bodies and materials in action, 3) the co-emergence of objects and sociomaterial configurations where each is the condition of the other. This alternative way of looking at design activity may pose some challenges to the theoretical traditions in the field. We however believe that it contains immense potential too

Finding-NEVO: toward radical design in HCI

Abstract. We address the methodology of design-oriented research in HCI, whereby researchers design and implement technology to test concepts. The task is to produce a testable prototype (that we call NEVO, Non-Embarrassing Version One) that faithfully embodies the concept. We probed leading HCI researchers and CHI authors about the challenge of Finding NEVO. We found uncertainty on how to design prototypes that allow for both design and scientific contributions. We propose the Finding-NEVO model that articulates a process yielding prototypes that are faithful to the rationale and idea being studied. We conclude by discussing our theoretical and methodological contributions