Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

9 pages, 13 figures.-- PACS nrs.: 05.45.Yv, 87.15.-v.-- PMID: 15783440 [PubMed].We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons. The soliton phenomena described in the simulations of alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.Peer reviewe

Mandibular nerve block in juvenile Nile crocodile: a cadaveric study

Study design Experimental cadaveric study. Animals A group of 16 juvenile Nile crocodile heads. Methods To study the course of the mandibular nerve, one head was dissected. Computed tomography (CT) examination was performed in two heads to identify useful landmarks. Thereafter, a hypodermic needle was inserted through the external mandibular fenestra of 17 hemimandibles (13 heads) and a mixture of methylene blue and iohexol was injected. Injection volumes were 0.5 (n = 7) and 1.0 mL (n = 10) for hemimandibles < 15 and ≥ 15 cm long, respectively. Iohexol spread and nerve staining with methylene blue were assessed with CT and anatomical dissection, respectively. Data were analysed with either one sample t-test or Mann-Whitney Rank Sum test. p < 0.05 Results Both anatomical dissection and imaging confirmed the external mandibular fenestra as a useful anatomical landmark for needle insertion. The CT images acquired after needle positioning confirmed that its tip was located on the medial bony mandibular surface formed by the fusion of the angular and coronoid bone in 100% of the cases. In all the hemimandibles, the rostro-caudal spread of contrast was greater than 23 mm. The length of the stained mandibular nerve in the temporal region and of the stained medial branch of the mandibular nerve, as well as the dorso-ventral and medio-lateral spread of iohexol, was greater in group 1.0 than in group 0.5 (p < 0.001). The caudal spread of iohexol was greater in group 1.0 than in group 0.5 (p = 0.01). Conclusions and clinical relevance The technique developed in this study is feasible. Both injection volumes resulted in staining of the mandibular nerve. The spread of contrast in the anatomical region of interest may result in successful sensory block

Controlling chaotic transients: Yorke's game of survival

5 pages, 4 figures.-- PACS nr.: 05.45.Gg, 05.45.Pq.-- PMID: 14995689 [PubMed].We consider the tent map as the prototype of a chaotic system with escapes. We show analytically that a small, bounded, but carefully chosen perturbation added to the system can trap forever an orbit close to the chaotic saddle, even in presence of noise of larger, although bounded, amplitude. This problem is focused as a two-person, mathematical game between two players called "the protagonist" and "the adversary." The protagonist's goal is to survive. He can lose but cannot win; the best he can do is survive to play another round, struggling ad infinitum. In the absence of actions by either player, the dynamics diverge, leaving a relatively safe region, and we say the protagonist loses. What makes survival difficult is that the adversary is allowed stronger "actions" than the protagonist. What makes survival possible is (i) the background dynamics (the tent map here) are chaotic and (ii) the protagonist knows the action of the adversary in choosing his response and is permitted to choose the initial point x(0) of the game. We use the "slope 3" tent map in an example of this problem. We show that it is possible for the protagonist to survive.J.A. and M.S.J. acknowledge financial support from the Spanish Ministry of Science and Technology under project BFM2000-0967, and from the Universidad Rey Juan Carlos under projects URJC-PGRAL-2001/02 and URJC-PIGE-02-04. F.d'O. acknowledges financial support from MCyT (Spain) and FEDER, project REN2001-0802-C02-01/MAR (IMAGEN).Peer reviewe

Population dynamics in compressible flows

Organisms often grow, migrate and compete in liquid environments, as well as on solid surfaces. However, relatively little is known about what happens when competing species are mixed and compressed by fluid turbulence. In these lectures we review our recent work on population dynamics and population genetics in compressible velocity fields of one and two dimensions. We discuss why compressible turbulence is relevant for population dynamics in the ocean and we consider cases both where the velocity field is turbulent and when it is static. Furthermore, we investigate populations in terms of a continuos density field and when the populations are treated via discrete particles. In the last case we focus on the competition and fixation of one species compared to anotherComment: 16 pages, talk delivered at the Geilo Winter School 201

Risk assessment for the spread of Serratia marcescens within dental-unit waterline systems using Vermamoeba vermiformis

Vermamoeba vermiformis is associated with the biofilm ecology of dental-unit waterlines (DUWLs). This study investigated whether V. vermiformis is able to act as a vector for potentially pathogenic bacteria and so aid their dispersal within DUWL systems. Clinical dental water was initially examined for Legionella species by inoculating it onto Legionella selective-medium plates. The molecular identity/profile of the glassy colonies obtained indicated none of these isolates were Legionella species. During this work bacterial colonies were identified as a non-pigmented Serratia marcescens. As the water was from a clinical DUWL which had been treated with Alpron™ this prompted the question as to whether S. marcescens had developed resistance to the biocide. Exposure to Alpron™ indicated that this dental biocide was effective, under laboratory conditions, against S. marcescens at up to 1x108 colony forming units/millilitre (cfu/ml). V. vermiformis was cultured for eight weeks on cells of S. marcescens and Escherichia coli. Subsequent electron microscopy showed that V. vermiformis grew equally well on S. marcescens and E. coli (p = 0.0001). Failure to detect the presence of S. marcescens within the encysted amoebae suggests that V. vermiformis is unlikely to act as a vector supporting the growth of this newly isolated, nosocomial bacterium

Characterisation and radioimmunotherapy of L19-SIP, an anti-angiogenic antibody against the extra domain B of fibronectin, in colorectal tumour models

Angiogenesis is a characteristic feature of tumours and other disorders. The human monoclonal antibody L19- SIP targets the extra domain B of fibronectin, a marker of angiogenesis expressed in a range of tumours. The aim of this study was to investigate whole body distribution, tumour localisation and the potential of radioimmunotherapy with the L19-small immunoprotein (SIP) in colorectal tumours. Two colorectal tumour models with highly different morphologies, the SW1222 and LS174T xenografts, were used in this study. Localisation and retention of the L19-SIP antibody at tumour vessels was demonstrated using immunohistochemistry and Cy3-labelled L19-SIP. Whole body biodistribution studies in both tumour models were carried out with 125I-labelled L19-SIP. Finally, 131I-labelled antibody was used to investigate the potential of radioimmunotherapy in SW1222 tumours. Using immunohistochemistry, we confirmed extra domain B expression in the tumour vasculature. Immunofluorescence demonstrated localisation and retention of injected Cy3-labelled L19-SIP at the abluminal side of tumour vessels. Biodistribution studies using a 125I-labelled antibody showed selective tumour uptake in both models. Higher recorded values for localisation were found in the SW1222 tumours than in the LS174T (7.9 vs 6.6 %ID g−1), with comparable blood clearance for both models. Based on these results, a radioimmunotherapy study was performed in the SW1222 xenograft using 131I-Labelled L19-SIP (55.5 MBq), which showed selective tumour uptake, tumour growth inhibition and improved survival. Radio- and fluorescence-labelled L19-SIP showed selective localisation and retention at vessels of two colorectal xenografts. Furthermore, 131I-L19-SIP shows potential as a novel treatment of colorectal tumours, and provides the foundation to investigate combined therapies in the same tumour models

A catalogue of Triticum monococcum genes encoding toxic and immunogenic peptides for celiac disease patients

The celiac disease (CD) is an inflammatory condition characterized by injury to the lining of the small-intestine on exposure to the gluten of wheat, barley and rye. The involvement of gluten in the CD syndrome has been studied in detail in bread wheat, where a set of “toxic” and “immunogenic” peptides has been defined. For wheat diploid species, information on CD epitopes is poor. In the present paper, we have adopted a genomic approach in order to understand the potential CD danger represented by storage proteins in diploid wheat and sequenced a sufficiently large number of cDNA clones related to storage protein genes of Triticum monococcum. Four bona fide toxic peptides and 13 immunogenic peptides were found. All the classes of storage proteins were shown to contain harmful sequences. The major conclusion is that einkorn has the full potential to induce the CD syndrome, as already evident for polyploid wheats. In addition, a complete overview of the storage protein gene arsenal in T. monococcum is provided, including a full-length HMW x-type sequence and two partial HMW y-type sequences

Milan: A City Lost in the Transition from the Growth Machine Paradigm Towards a Social Innovation Approach

Milan can be described as a city lost in transition. For more than two decades, Milan has been ruled by a system of strongly market-oriented governance, following the rhetoric that creating a "good business climate" is an effective way to not only foster growth and innovation but also eradicate poverty and deliver higher standards of living. This approach has led to: (a) a disinvestment in welfare services directly provided by the municipality, in favour of a more residual welfare system based on non-profit and private involvement; (b) a huge investment in neo-liberal tools of government for the economic development of the city, such as the promotion of international events (Expo 2015) and large real estate investments through public–private partnerships. After some scandals as well as a huge increase of social inequalities, municipal elections rewarded a new coalition following a style of governance oriented to a social innovation approach. However, the difficult financial situation of the municipality has reduced ambitions of the current government