DISULFIND: a disulfide bonding state and cysteine connectivity prediction server

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Optionally, disulfide connectivity can be predicted from sequence and a bonding state assignment given as input. The output is a simple visualization of the assigned bonding state (with confidence degrees) and the most likely connectivity patterns. The server is available at

From naive to scientific understanding of motion and its causes

The difference in the descriptions of motion phenomena made by pupils in the first grades of secondary school and physicists is quite evident. Conceptual metaphors hidden in language suggest that there is continuity between the conceptual structure involved in the description and the interpretation of motion of experts and laypersons. In this paper the presence of such a continuity is shown through a metaphor analysis of linguistic expressions from both groups

From naive to scientific understanding of motion and its causes

The difference in the descriptions of motion phenomena made by pupils in the first grades of secondary school and physicists is quite evident. Conceptual metaphors hidden in language suggest that there is continuity between the conceptual structure involved in the description and the interpretation of motion of experts and laypersons. In this paper the presence of such a continuity is shown through a metaphor analysis of linguistic expressions from both kind of people

A high-sensitivity long-lifetime phosphorescent RIE additive to probe free volume-related phenomena in polymers

The photophysical behaviour of phosphorescent rigidification-induced emission (RIE) dyes is highly affected by their micro- and nanoenvironment. The lifetime measure of RIE dyes dispersed in polymers represents an effective approach to gain valuable information on polymer free volume and thus develop materials potentially able to self-monitor physical ageing and mechanical stresses

Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up

Background: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. Methods: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented. Single cell fluorescence values, acquired with a microscope set-up and processed with custom-made software, are compared with results that were obtained with a flow cytometer in a bacterial population transformed with the same gene circuitry. Results: The high correlation between data from the two experimental set-ups, with a correlation coefficient computed over the tested dynamic range > 0.99, proves that a standard optical microscope- when coupled with appropriate software for image processing- might be used for quantitative single-cell fluorescence measurements. The calibration of the set-up, together with its validation, is described. Conclusions: The experimental protocol described in this paper makes quantitative measurement of single cell fluorescence accessible to laboratories equipped with standard optical microscope set-ups. Our method allows for an affordable measurement/quantification of intercellular variability, whose better understanding of this phenomenon will improve our comprehension of cellular behaviors and the design of synthetic gene circuits. All the required software is freely available to the synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification)

Repair of composite-to-masonry bond using flexible matrix

The paper presents an experimental investigation on an innovative repair method, in which composite reinforcements, after debonding, are re-bonded to the substrate using a highly deformable polymer. In order to assess the effectiveness of this solution, shear bond tests were carried out on brick and masonry substrates within two Round Robin Test series organized within the RILEM TC 250-CSM: Composites for Sustainable strengthening of Masonry. Five laboratories from Italy, Poland and Portugal were involved. The shear bond performance of the reinforcement systems before and after repair were compared in terms of ultimate loads, load-displacement curves and strain distributions. The results showed that the proposed repair method may provide higher strength and ductility than stiff epoxy resins, making it an effective and cost efficient technique for several perspective structural applications

Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

Background : Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results: Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion: The predictive system are publicly available at the address http://distill.ucd.ieScience Foundation IrelandIrish Research Council for Science, Engineering and TechnologyHealth Research BoardUCD President's Award 2004au, da, ke, ab, sp - kpw30/11/1

Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities

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