Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

This chapter will be presented as follow. First, a brief introduction to structure and characterization of lignin and its derivatives is presented, as well as their importance as chemical scaffolds for obtaining value-added products in chemical, food, pharmaceutical and agriculture industry. Second, an extensive review of different reports using computational modeling methods—like molecular dynamics simulations, quantum mechanics and hybrid calculation methods, among others—in the understanding of enzyme-substrate interaction and biocatalysis will be presented. Third, and as last part of chapter, some hand picked examples from literature will be chosen as successful cases where the interplay between experiment and computation has given as a result protein engineered oxidoreductases with improved catalytic capabilities

A Tri-National program for estimating the link between snow resources and hydrological droughts

To evaluate how summer low flows and droughts are affected by the winter snowpack, a Tri-National effort will analyse data from three catchments: Alpbach (Prealps, central Switzerland), Gudjaretis-Tskali (Little Caucasus, central Georgia), and Kamenice (Jizera Mountains, northern Czech Republic). Two GIS-based rainfall-runoff models will simulate over 10 years of runoff in streams based on rain and snowfall measurements, and further meteorological variables. The models use information on the geographical settings of the catchments together with knowledge of the hydrological processes of runoff generation from rainfall, looking particularly at the relationship between spring snowmelt and summer droughts. These processes include snow accumulation and melt, evapotranspiration, groundwater recharge in spring that contributes to (the) summer runoff, and will be studied by means of the environmental isotopes 18O and 2H. Knowledge about the isotopic composition of the different water sources will allow to identify the flow paths and estimate the residence time of snow meltwater in the subsurface and its contribution to the stream. The application of the models in different nested or neighbouring catchments will explore their potential for further development and allow a better early prediction of low-flow periods in various mountainous zones across Europe. The paper presents the planned activities including a first analysis of already available dataset of environmental isotopes, discharge, snow water equivalent and modelling experiments of the (already) available datasets

Risk management and communication in informal dairy sector in Côte d’Ivoire: Options for sustainable livelihoods

Intervention in food and nutrition was the best investment for our collective future in terms of managing co-morbidity in population. This investment should combine agricultural system with health and education. Fermented dairy products (FDP) played an important role for prolonged shelf life, microbial safety and nutrition. FDP was proved to be contaminated in Kenya, Somalia, Mali and Côte d'Ivoire by foodborne pathogens including Staphylococcus aureus and Escherichia coli. Recently, it was showed that FDP was predominated by a novel Streptococcus infantarius subsp. infantarius (Sii) variant. Sii-produced bacteriocin and fermentation activity could contribute to the suppression of pathogens and possibly mitigate socioeconomic and health risks. However, Sii as member of Streptococcus bovis group was associated with human and animal infections. Therefore, a potential application of Sii as adapted African starter culture for enhanced food safety required a thorough safety assessment. In order to improve hygiene and quality as well as to increase production for school canteens, urban consumption and sustainable livelihoods, a cross-sectional study was conducted in Korhogo (Côte d’Ivoire) from May to August 2014. The objective was to assess local technologies and the dairy value chain in relation to Sii prevalence, followed by a participatory stakeholder workshop to validate findings and derive adapted interventions. The study showed that the dairy value chain contributed to livelihoods and household income. About 90% of milk produced (range: 12-44 liters/collector) were sold via collectors, generating 6-20 Euros per day shared among herder, collector and vendor. The remaining 10% were consumed within the household. However, dairy production was low and scattered due to informal practices resulting in poor quality product. Basic hygiene such as cleaning, washing, disinfecting was lacking. Milk quality depreciated with the local practices, access to clean water and energy. Future interventions identified by stakeholders comprised (i) awareness on local dairy hygiene and nutritional value for the population especially school children, (ii) stakeholders organization around cooperative to develop sustainable dairy model (public dairy with private management); (iii) promote healthy milk products for school canteen programme in Korhogo through adapted local dairy technology

Brauer-Thrall for totally reflexive modules over local rings of higher dimension

Let $R$ be a commutative Noetherian local ring. Assume that $R$ has a pair $\{x,y\}$ of exact zerodivisors such that $\dim R/(x,y)\ge2$ and all totally reflexive $R/(x)$-modules are free. We show that the first and second Brauer--Thrall type theorems hold for the category of totally reflexive $R$-modules. More precisely, we prove that, for infinitely many integers $n$, there exists an indecomposable totally reflexive $R$-module of multiplicity $n$. Moreover, if the residue field of $R$ is infinite, we prove that there exist infinitely many isomorphism classes of indecomposable totally reflexive $R$-modules of multiplicity $n$.Comment: to appear in Algebras and Representation Theor

Performance of the LHCb Vertex Detector Alignment Algorithm determined with Beam Test Data

LHCb is the dedicated heavy flavour experiment at the Large Hadron Collider at CERN. The partially assembled silicon vertex locator (VELO) of the LHCb experiment has been tested in a beam test. The data from this beam test have been used to determine the performance of the VELO alignment algorithm. The relative alignment of the two silicon sensors in a module and the relative alignment of the modules has been extracted. This alignment is shown to be accurate at a level of approximately 2 micron and 0.1 mrad for translations and rotations, respectively in the plane of the sensors. A single hit precision at normal track incidence of about 10 micron is obtained for the sensors. The alignment of the system is shown to be stable at better than the 10 micron level under air to vacuum pressure changes and mechanical movements of the assembled system.Comment: accepted for publication in NIM

An Intact Kidney Slice Model to Investigate Vasa Recta Properties and Function in situ

Background: Medullary blood flow is via vasa recta capillaries, which possess contractile pericytes. In vitro studies using isolated descending vasa recta show that pericytes can constrict/dilate descending vasa recta when vasoactive substances are present. We describe a live kidney slice model in which pericyte-mediated vasa recta constriction/dilation can be visualized in situ. Methods: Confocal microscopy was used to image calcein, propidium iodide and Hoechst labelling in ‘live’ kidney slices, to determine tubular and vascular cell viability and morphology. DIC video-imaging of live kidney slices was employed to investigate pericyte-mediated real-time changes in vasa recta diameter. Results: Pericytes were identified on vasa recta and their morphology and density were characterized in the medulla. Pericyte-mediated changes in vasa recta diameter (10–30%) were evoked in response to bath application of vasoactive agents (norepinephrine, endothelin-1, angiotensin-II and prostaglandin E2) or by manipulating endogenous vasoactive signalling pathways (using tyramine, L-NAME, a cyclo-oxygenase (COX-1) inhibitor indomethacin, and ATP release). Conclusions: The live kidney slice model is a valid complementary technique for investigating vasa recta function in situ and the role of pericytes as regulators of vasa recta diameter. This technique may also be useful in exploring the role of tubulovascular crosstalk in regulation of medullary blood flow

Radiation damage in the LHCb vertex locator

The LHCb Vertex Locator (VELO) is a silicon strip detector designed to reconstruct charged particle trajectories and vertices produced at the LHCb interaction region. During the first two years of data collection, the 84 VELO sensors have been exposed to a range of fluences up to a maximum value of approximately 45 × 1012 1 MeV neutron equivalent (1 MeV neq). At the operational sensor temperature of approximately −7 °C, the average rate of sensor current increase is 18 μA per fb−1, in excellent agreement with predictions. The silicon effective bandgap has been determined using current versus temperature scan data after irradiation, with an average value of Eg = 1.16±0.03±0.04 eV obtained. The first observation of n+-on-n sensor type inversion at the LHC has been made, occurring at a fluence of around 15 × 1012 of 1 MeV neq. The only n+-on-p sensors in use at the LHC have also been studied. With an initial fluence of approximately 3 × 1012 1 MeV neq, a decrease in the Effective Depletion Voltage (EDV) of around 25 V is observed. Following this initial decrease, the EDV increases at a comparable rate to the type inverted n+-on-n type sensors, with rates of (1.43±0.16) × 10−12 V/ 1 MeV neq and (1.35±0.25) × 10−12 V/ 1 MeV neq measured for n+-on-p and n+-on-n type sensors, respectively. A reduction in the charge collection efficiency due to an unexpected effect involving the second metal layer readout lines is observed

Precision luminosity measurements at LHCb

Measuring cross-sections at the LHC requires the luminosity to be determined accurately at each centre-of-mass energy √s. In this paper results are reported from the luminosity calibrations carried out at the LHC interaction point 8 with the LHCb detector for √s = 2.76, 7 and 8 TeV (proton-proton collisions) and for √sNN = 5 TeV (proton-lead collisions). Both the "van der Meer scan" and "beam-gas imaging" luminosity calibration methods were employed. It is observed that the beam density profile cannot always be described by a function that is factorizable in the two transverse coordinates. The introduction of a two-dimensional description of the beams improves significantly the consistency of the results. For proton-proton interactions at √s = 8 TeV a relative precision of the luminosity calibration of 1.47% is obtained using van der Meer scans and 1.43% using beam-gas imaging, resulting in a combined precision of 1.12%. Applying the calibration to the full data set determines the luminosity with a precision of 1.16%. This represents the most precise luminosity measurement achieved so far at a bunched-beam hadron collider