Structural Biology of Peanut Allergens

Peanuts are a cause of one of the most common food allergies. Allergy to peanuts not only affects a significant fraction of the population, but it is relatively often associated with strong reactions in sensitized individuals. Peanut and tree nut allergies, which start in childhood are often persistent and continue through life, as opposed to other food allergies that resolve with age. Cherefore, peanut allergens are one of the most intensively studied food allergens. In this review we focus on the structural studies of peanut allergens. Despite the fact that these allergens are attracting a lot of interest and several of them have had their structures experimentally determined, still some molecular properties of peanut allergens are not well understood. Peanut allergens like other allergens belong to just a few protein families. Allergens from the cupin superfamily (Ara h 1 and Ara h 3), 2S albumins (Arah 2 and Ara h 6), Ara h 8 (pathogenesis related class-10 protein) and Ara h 5 (profilin) are relatively well characterized in terms of their 3D structures. However some peanut allergens like Ara h 7 (2S albumin), Ara h 9 (nonspecific lipid-transfer protein), and especially oleosins (Ara h 10 and Ara h 11) and defensins (Ara h 12 and Ara h 13), still are waiting for such characterization

To automate or not to automate: this is the question

New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected

Allergic sensitization: screening methods

Experimental in silico, in vitro, and rodent models for screening and predicting protein sensitizing potential are discussed, including whether there is evidence of new sensitizations and allergies since the introduction of genetically modified crops in 1996, the importance of linear versus conformational epitopes, and protein families that become allergens. Some common challenges for predicting protein sensitization are addressed: (a) exposure routes; (b) frequency and dose of exposure; (c) dose-response relationships; (d) role of digestion, food processing, and the food matrix; (e) role of infection; (f) role of the gut microbiota; (g) influence of the structure and physicochemical properties of the protein; and (h) the genetic background and physiology of consumers. The consensus view is that sensitization screening models are not yet validated to definitively predict the de novo sensitizing potential of a novel protein. However, they would be extremely useful in the discovery and research phases of understanding the mechanisms of food allergy development, and may prove fruitful to provide information regarding potential allergenicity risk assessment of future products on a case by case basis. These data and findings were presented at a 2012 international symposium in Prague organized by the Protein Allergenicity Technical Committee of the International Life Sciences Institute’s Health and Environmental Sciences Institute

High-Throughput NMR Assessment of the Tertiary Structure of Food Allergens

In vitro component-resolved diagnosis of food allergy requires purified allergens that have to meet high standards of quality. These include the authentication of their conformation, which is relevant for the recognition by specific IgE antibodies from allergic patients. Therefore, highly sensitive and reliable screening methods for the analysis of proteins/allergens are required to assess their structural integrity. In the present study one-dimensional 1H Nuclear Magnetic Resonance (1D 1H-NMR) analysis was adopted for the assessment of overall structural and dynamic properties and authentication of a set of relevant food allergens, including non-specific lipid transfer proteins from apple, peach and hazelnut, 7/8S seed storage globulins from hazelnut and peanut, 11S seed storage globulins from hazelnut and peanut, caseins from cows' and goats' milk and tropomyosin from shrimp.Two sets of 1D 1H-NMR experiments, using 700 MHz and 600 MHz instruments at 298 K were carried out to determine the presence and the extent of tertiary structure. Structural similarity among members of the individual allergen families was also assessed and changes under thermal stress investigated. The nuclear magnetic resonance (NMR) results were compared with structural information available either from the literature, Protein Data Bank entries, or derived from molecular models.1D (1)H-NMR analysis of food allergens allowed their classification into molecules with rigid, extended and ordered tertiary structures, molecules without a rigid tertiary structure and molecules which displayed both features. Differences in thermal stability were also detected. In summary, 1D (1)H-NMR gives insights into molecular fold of proteins and offers an independent method for assessing structural properties of proteins

Raman optical activity of biological samples

In this Chapter, the fundamentals and instrumentation of vibrational Raman optical activity are briefly presented. Next, we describe selected examples of successful applications of computational approaches to the analysis of ROA spectra of biomolecules showing that such calculations are an important aspect of this incisive structural technique

Hydrogeochemical Aspects Associated with the Mixing of Formation Waters Injected Into the Hydrocarbon Reservoir

Wody złożowe wydobywane razem z ropą naftową i gazem ziemnym, ze względu na ich ilość oraz skład chemiczny, stanowią problem dla firm naftowych eksploatujących złoża węglowodorów. Przeciętnie na świecie wydobywa się 2 do 3 razy więcej wody niż ropy. Ilość wydobywanych wód wzrasta wraz z czasem eksploatacji złóż, w przypadku złóż na końcowym etapie sczerpania ilość eksploatowanej wody jest 5 do 8 razy większa niż ropy naftowej. Wody złożowe wydobywane z węglowodorami to najczęściej solanki o wysokiej mineralizacji. Duże ilości wysoko zmineralizowanych wód wydobywanych wraz z ropą i gazem są w różny sposób zagospodarowywane lub unieszkodliwiane. Najbardziej powszechny sposób unieszkodliwiania tych wód to zatłaczanie ich do warstw chłonnych. W wyniku zatłaczania wód złożowych do złóż węglowodorów dochodzi do oddziaływania wód z formacją do składowania. W formacji tej mogą następować rozliczne reakcje wody złożowej ze środowiskiem skalnym. Zatłaczanie wód złożowych będzie powodowało również mieszanie wód, które naruszy stany równowagi reakcji chemicznych i wpłynie na zmianę chemizmu mieszających się wód. Przeanalizowano metodą modelowania geochemicznego oddziaływania wód złożowych zatłaczanych do złoża gazu ziemnego Przemyśl. Przy wykorzystaniu programu PHREEQC przebadano reakcje chemiczne związane z mieszaniem wód złożowych różnych typów chemicznych. Stwierdzono możliwość wytrącania się odpowiednich minerałów jako efekt mieszania wód o zróżnicowanym składzie chemicznym.Formation waters extracted with crude oil and natural gas, due to their amount and chemical composition can be a problem for petroleum companies operating hydrocarbon deposits. On average, the world generates 2 to 3 times more water than oil. On average, the world generates 2 to 3 times more water than crude oil. The amount of extracted water increases with the time of exploitation of the deposit, in the case of deposits at the final stage of depletion, the amount of extracted water is 5 to 8 times bigger than petroleum. Formation waters from hydrocarbons deposits are usually the highly mineralized brines. Large quantities of highly mineralized waters extracted with crude oil and gas are disposed of in various ways or neutralized. The most common way of disposing of these waters is by injecting them into rock mass. As a result of injection of reservoir waters into hydrocarbon deposits, the waters interact with the storage formations. In these formations, there may be numerous reactions of mineral water with the rock environment. The injection of reservoir waters will also cause mixing of waters that can disturb the state of thermodynamic equilibrium and will alter the chemistry of these waters. It was analyzed by the geochemical modeling of the interaction of the reservoir waters of Przemyśl natural gas field. Using the PHREEQC program, the chemical reactions related to the mixing of reservoir waters of different chemical types have been studied. It has been found that is possible to precipitation appropriated minerals as a result of mixing water with different chemical composition

Hydrogeochemical aspects associated with the mixing of formation waters injected into the hydrocarbon reservoir

Wody złożowe wydobywane razem z ropą naftową i gazem ziemnym, ze względu na ich ilość oraz skład chemiczny, stanowią problem dla firm naftowych eksploatujących złoża węglowodorów. Przeciętnie na świecie wydobywa się 2 do 3 razy więcej wody niż ropy. Ilość wydobywanych wód wzrasta wraz z czasem eksploatacji złóż, w przypadku złóż na końcowym etapie sczerpania ilość eksploatowanej wody jest 5 do 8 razy większa niż ropy naftowej. Wody złożowe wydobywane z węglowodorami to najczęściej solanki o wysokiej mineralizacji. Duże ilości wysoko zmineralizowanych wód wydobywanych wraz z ropą i gazem są w różny sposób zagospodarowywane lub unieszkodliwiane. Najbardziej powszechny sposób unieszkodliwiania tych wód to zatłaczanie ich do warstw chłonnych. W wyniku zatłaczania wód złożowych do złóż węglowodorów dochodzi do oddziaływania wód z formacją do składowania. W formacji tej mogą następować rozliczne reakcje wody złożowej ze środowiskiem skalnym. Zatłaczanie wód złożowych będzie powodowało również mieszanie wód, które naruszy stany równowagi reakcji chemicznych i wpłynie na zmianę chemizmu mieszających się wód. Przeanalizowano metodą modelowania geochemicznego oddziaływania wód złożowych zatłaczanych do złoża gazu ziemnego Przemyśl. Przy wykorzystaniu programu PHREEQC przebadano reakcje chemiczne związane z mieszaniem wód złożowych różnych typów chemicznych. Stwierdzono możliwość wytrącania się odpowiednich minerałów jako efekt mieszania wód o zróżnicowanym składzie chemicznym.Formation waters extracted with crude oil and natural gas, due to their amount and chemical composition can be a problem for petroleum companies operating hydrocarbon deposits. On average, the world generates 2 to 3 times more water than oil. On average, the world generates 2 to 3 times more water than crude oil. The amount of extracted water increases with the time of exploitation of the deposit, in the case of deposits at the final stage of depletion, the amount of extracted water is 5 to 8 times bigger than petroleum. Formation waters from hydrocarbons deposits are usually the highly mineralized brines. Large quantities of highly mineralized waters extracted with crude oil and gas are disposed of in various ways or neutralized. The most common way of disposing of these waters is by injecting them into rock mass. As a result of injection of reservoir waters into hydrocarbon deposits, the waters interact with the storage formations. In these formations, there may be numerous reactions of mineral water with the rock environment. The injection of reservoir waters will also cause mixing of waters that can disturb the state of thermodynamic equilibrium and will alter the chemistry of these waters. It was analyzed by the geochemical modeling of the interaction of the reservoir waters of Przemyśl natural gas field. Using the PHREEQC program, the chemical reactions related to the mixing of reservoir waters of different chemical types have been studied. It has been found that is possible to precipitation appropriated minerals as a result of mixing water with different chemical composition

Assessment of the quality of surface water from selected area of active oil exploitation

In this work, the studies of various physico-chemical parameters of surface waters originated from the selected area of oil exploitation in the south of Poland are presented. The water samples were collected from streams and ponds or directly from surface tanks situated in the vicinity of operating wells. The observed values of different parameters like pH, odór, color, turbidity, electroconductivity, concentration of sulfate, chloride, nitrate, iron, calcium, magnesium, ammonium, alkanity, dissolved oxygen or petroleum contamination of samples were compared with standard values recommended by the WHO (World Health Organization) and the relevant Polish Regulation. Preliminary studies show that investigated surface waters are slightly affected by anthropogenic pollution. The main two sources of contamination of water from the study area are agriculture and mining industry

Soil contamination by petroleum substances in the vicinity of oil production wells

The paper presents the study of various indicators of soil contamination by petroleum substances from the area of active exploitation of oil deposits in the south of Poland. Nineteen studied soil samples were taken directly around the production wells (0–1 m) or their vicinity (1–7 m) at a depth of 0.1 to 0.3 m. Collected samples were tested for the presence of benzene, toluene and xylene (BTX), and polycyclic aromatic hydrocarbons (PAHs) such as phenanthrene, anthracene, fluoranthene, fluorene, pyrene, benzo(a)anthracene, chrysene, benzo(a)pyrene, dibenz(a,h)anthracene and benzo(g,h,i)perylene. An analysis of the content of these chemical compounds in the soil samples was performed by gas chromatography. The observed results were interpreted to determine the hazard for the natural environment and human health. The evaluation of soil samples was based on the new Regulation of the Ministry of Environment of 1 September 2016 regarding the assessment of contamination of the surface of the earth (Journal of Laws 2016 Nr 0, item 1395) as well as guidelines presented by the Institute of Soil Science and Plant Cultivation (ISSPC)