Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins

Aquaporin 1 (Aqp1) expression in healthy dog tears

Aquaporins (AQPs) are a family of thirteen membrane proteins that play an essential role in the transport of fluids across the cell plasma membrane. Recently, the expression of AQPs in dierent ocular tissues and their involvement in the pathophysiology of eye diseases, have garnered attention. Considering that literature on AQP expression in the lacrimal glands and their secretion is scarce, we aimed to characterise AQP1 expression in the tears of healthy dogs using two tear collection methods (Schirmer tear strips (STS) and ophthalmic sponges (OS)). Fifteen healthy dogs, free of ophthalmic diseases, were included in the study. Tear collection was performed by using STS in one eye and OS in the other. After the extraction of proteins from the tears, the expression of AQP1 was analysed by Western blotting. AQP1 was expressed as a band of 28 kDa. In addition, dierences were observed in the expression of AQP1 and in the correlation between tear volume and protein concentration, in tears collected by the two dierent methods. Our results suggest that AQP1 has a specific role in tear secretion; further research is required to assess its particular role in the function of the ocular surface in eye physiology and pathology

Automation of RNA-based biomarker extraction from dried blood spots for the detection of blood doping.

Aim: Transcriptomic biomarkers originating from reticulocytes measured in dried blood spots (DBSs) may be reliable indicators of blood doping. Methods/results: Here, we examined changes in the expression levels of the erythropoiesis-related ALAS2, CA1 and SLC4A1 genes in DBS samples from elite athletes and volunteers of clinical study with recombinant erythropoietin dose. Conclusion: By comparing the mean intraday coefficients of variation for ALAS2L, ALASLC, CA1 and SLC4A1 between manual and automated RNA extractions, an average improvement was observed, whereas the assessment of interday variability provided comparable results for both manual and automated approaches. Our results confirmed that RNA biomarkers on DBS support are efficient to detect blood doping

Energy and geotechnical behaviour of energy piles for different design solutions

Energy piles are heat capacity systems that have been increasingly exploited to provide both supplies of energy and structural support to civil structures. The energy and geotechnical behaviours of such foundations, which are governed by their response to thermo-mechanical loads, is currently not fully understood, especially considering the different design solutions for ground-coupled heat exchangers. This paper summarises the results of numerical sensitivity analyses that were performed to investigate the thermo-mechanical response of a full-scale energy pile for different (i) pipe configurations, (ii) foundation aspect ratios, (iii) mass flow rates of the fluid circulating in the pipes and (iv) fluid mixture compositions. This study outlines the impacts of the different solutions on the energy and geotechnical behaviour of the energy piles along with important forethoughts that engineers might consider in the design of such foundations. It was observed that the pipe configuration strongly influenced both the energy and the geotechnical performance of the energy piles. The foundation aspect ratio also played an important role in this context. The mass flow rate of the fluid circulating in the pipes remarkably influenced only the energy performance of the foundation. Usual mixtures of a water-antifreeze liquid circulating in the pipes did not markedly affect both the energy and the geotechnical performance of the pile

The interaction factor method for energy pile groups

Prior to this study, no simplified yet rational methods were available for estimating the vertical displacements of energy pile groups subjected to thermal loads. Observing such a challenge, the goal of this study has been threefold: (i) to extend the interaction factor concept from the framework of conventional pile groups to that of energy pile groups, (ii) to present charts for the analysis of the displacement interaction between two identical energy piles over a broad range of design conditions, and (iii) to propose, apply and validate the interaction factor method for the displacement analysis of energy pile groups

Optimisation of a one-step PCR assay for the diagnosis of Flavescence doreerelated phytoplasmas in field-grown grapevines and vector populations

Field-infected grapevines and natural populations of Scaphoideus titanus have been analysed to detect group V phytoplasmas associated with flavescence doree in northwestern Italy using nested PCR. A first amplification driven by universal ribosomal primers R16SF2/R2 was followed by a second round assisted by R16(V)F1/R1 primers and subsequent RFLP analysis. To optimize the test, nested PCRs were compared with direct amplification assisted by the group V-specific fAY/rEY primer pair, directed towards other ribosomal sequences. In nested and direct PCRs, respectively, DNAs from 71 and 57 out of 96 grapevines (i.e. 73.9 and 59.3 %) and 51 and 50 out of 108 insects (i.e. 47.2 and 46.3 %) reacted positively. Although it was not possible to determine the subgroup of the phytoplasmas after fAY/rEY amplification, these primers could be used successfully in mass screening of plant material and insect populations. They could detect, in single-step amplification, the phytoplasmas in 80 and 98 % of the plant and insect samples, respectively, that were already indexed as positive using nested PCR. This strongly reduced the number of samples requiring the nested approach, with beneficial effects on costs, labour and risks of the analysis.

Leptin system in obese dog skin: A pilot study

Obesity predisposes to several health problems including skin diseases. However, information on the relationship between obesity and skin disorders in pets is very scarce. Leptin (LEP) is mainly produced by adipose tissue and has a prominent role in skin biology. This study evaluated the LEP system in the skin of obese dogs compared to normal-weight animals. The investigation was carried out on 10 obese (Obese group) and 10 normal-weight (Normal-weight group) dogs through Real-time PCR and immunohistochemistry. Cells of skin associated immune system were also evaluated. No differences were evidenced between the two groups as well as skin inflammation. LEP differences were no significant, while LEPR transcript appeared 10-fold higher in obesedogs than in normal-weight ones. Immunostaining for both molecules was observed in several skin structures such as the epidermis, hair follicles, and glands. No differences appeared in the skin associated immune system composition. This study is a preliminary report showing that LEP system changes in obese dog skin. The increased LEPR expression observed in the obese group suggests that the receptor plays a modulating role in the system control. However, the exact role of LEPin the skin under obesity conditions needs further elucidation

Plasmonic lenses for ultrafast electron nanoemission

We show the capability of plasmonic lenses for next-generation ultrafast electron sources. Using electromagnetic simulations, we design structures capable of femtosecond, nanoscale electron pulses. Plasmonic properties of template-stripped gold prototypes are characterized using cathodoluminescence spectromicroscopy

Total Degree Formula for the Generic Offset to a Parametric Surface

We provide a resultant-based formula for the total degree w.r.t. the spatial variables of the generic offset to a parametric surface. The parametrization of the surface is not assumed to be proper.Comment: Preprint of an article to be published at the International Journal of Algebra and Computation, World Scientific Publishing, DOI:10.1142/S021819671100680

Effects of obesity on adiponectin system skin expression in dogs: A comparative study

Obesity is an important health issue in dogs since it influences a plethora of associated pathologies, including dermatological disorders. Considering the scarcity of information in pets, this work aimed to evaluate the localization and expression of adiponectin (ADIPOQ) and its two receptors (ADIPOR1 and ADIPOR2) in the skin of 10 obese dogs, compared with serum ADIPOQ level. Through immunohistochemistry, ADIPOQ and ADIPOR2 were observed in the adipose tissue, sweat and sebaceous glands, endothelium, and some connective cells. Both receptors were observed in the epidermis and the hair follicles, other than in the sweat and sebaceous glands. Real-time PCR evidenced that the ADIPOQ and ADIPOR2 transcripts were expressed 5.4-fold (p < 0.01) and 2.3-fold less (p < 0.01), respectively, in obese than in normal weight dogs, while ADIPOR1 expression did not change. Obese dogs showed lower serum ADIPOQ levels than the normal weight group. Accordingly, ADIPOQ and ADIPOR2 expression in the skin appear negatively correlated with obesity in the same way as the serum ADIPOQ level. These findings evidence that ADIPOQ system changes in the skin of obese dogs and suggest that the ADIPOQ effect on the skin is at least in part regulated by the reduced expression of ADIPOR2