<i>De novo</i> design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of 4-fold symmetrical (β/α)(8)-barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of sidechain-backbone hydrogen bonding for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical with the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has only sampled a subset of the sequence space available to the TIM-barrel fold. The ability to de novo design TIM-barrels opens new possibilities for custom-made enzymes

[Possibilities in the differential diagnosis of brain neoplasms using the long and short time sequences of proton magnetic resonance spectroscopy]

Currently to perform proton magnetic resonance spectroscopy (1H MRS) with single voxel spectroscopy (SVS) technique long and/or short echo time sequences are used in order to provide complementary information. PURPOSE: The aim of the study was to compare the usefulness of STEAM (time echo, TE, 20 ms) and PRESS (TE 136 ms) sequences in the evaluation of brain neoplasms. MATERIALS AND METHOD: 15 healthy volunteers and 19 patients with brain tumors were examined using 1, 5 T MR scanner. MRI was performed with a standard protocol for brain neoplasms. 1H MRS with the SVS technique was performed after magnetic resonance imaging (MRI) using STEAM 20 and PRESS 136 sequences (voxel size 1 to 8 cc). RESULTS: In the STEAM sequence besides basic metabolites visible in PRESS as N-acetylaspartate, choline and creatine peaks of myoinositol and glutamate were visualized. Data obtained with short TE sequences in conjunction with long TE data were useful and in 5 cases necessary to identify the tumor type. These results were confirmed by pathology. CONCLUSIONS: The use of short TE sequences enables to visualize metabolites important for the diagnosis and differentiation of the tumor type. The combined information drawn out from both long and short TE spectra is also important

[Possibilities in the differential diagnosis of brain neoplasms using the long and short time sequences of proton magnetic resonance spectroscopy]

Item does not contain fulltextCurrently to perform proton magnetic resonance spectroscopy (1H MRS) with single voxel spectroscopy (SVS) technique long and/or short echo time sequences are used in order to provide complementary information. PURPOSE: The aim of the study was to compare the usefulness of STEAM (time echo, TE, 20 ms) and PRESS (TE 136 ms) sequences in the evaluation of brain neoplasms. MATERIALS AND METHOD: 15 healthy volunteers and 19 patients with brain tumors were examined using 1, 5 T MR scanner. MRI was performed with a standard protocol for brain neoplasms. 1H MRS with the SVS technique was performed after magnetic resonance imaging (MRI) using STEAM 20 and PRESS 136 sequences (voxel size 1 to 8 cc). RESULTS: In the STEAM sequence besides basic metabolites visible in PRESS as N-acetylaspartate, choline and creatine peaks of myoinositol and glutamate were visualized. Data obtained with short TE sequences in conjunction with long TE data were useful and in 5 cases necessary to identify the tumor type. These results were confirmed by pathology. CONCLUSIONS: The use of short TE sequences enables to visualize metabolites important for the diagnosis and differentiation of the tumor type. The combined information drawn out from both long and short TE spectra is also important

Transformation of methane in peatlands environments

Wetlands and particularly peatlands are the main natural source of methane. Data indicate that 10–45% of methane emission comes from these sources. Methane emission from wetlands is the result of the balance between methanogenesis and methanotrophic processes and is actively affected by the wetland plant community composition. There are many factors affecting the balance of CH4: for instance, vegetation has a strong effect on CH4 emissions from wetland ecosystems by influencing methane production, consumption and transport in the soil. The effects of plants on methane fluxes may be mediated by: molecular diffusion, internal transport through plant aerenchyma tissues and ebullition. Methane is formed in the process of methanogenesis under anaerobic conditions. It may then be emitted into the atmosphere directly from the soil or by internal transport through the plant. Alternatively, it may undergo methane oxidation by methanotrophic bacteria, both free-living in the root zone and associated with the host plant in symbiosis. Sphagnum moss is of particular importance for this processes as it contains methanotrophic bacteria in its endophytic system. Methanotrophic bacteria live inside the dead hyaline cells or on the surface of Sphagnum leaves and are able to oxidise methane produced in the soil during methanogenesis, making peatlands a natural biofilter for methane, one of the main greenhouse gases

[Brain metabolism alterations in patients with anorexia nervosa observed in 1H-MRS]

Contains fulltext : 48323.pdf (publisher's version ) (Open Access)The causes of metabolic brain changes in patients with anorexia nervosa are still not fully explained. The purpose of this study was to use the 1H-MRS method in investigating metabolic changes in the brain of patients with anorexia nervosa. We studied 10 patients for visible alternations in brain metabolism and compared the results to healthy controls. 1H-MRS was acquired by the method of single voxels in white and grey matter. Proton MRS was performed after image guided localization using stimulated echo acquisition mode (STEAM) sequence with a short echo time of 20 ms. For data evaluation we used standard Siemens software and the additional PC. Choosing of the MRS sequences was related with particular interest in metabolites of short time echo: myoinositol and lipids. Besides this we evaluated peaks of: N-acetylaspartate (NAN), creatine (Cr) and choline (Cho). The results show significant differences in the levels of metabolites connected with fatty metabolism. In white matter we observed the reduction of lip-peak. The data was evaluated approximately and presented as lip:Cr. We did not observe any differences in other metabolites. As far as we know similar results had been reported and our study confirmed significant disorders in metabolism of these chemicals in patients with anorexia nervosa

Influence of plant composition on methane emision from Moszne peatland

Methane is the second most important man-made greenhouse gas after carbon dioxide. For more than the last 20 years the increase of the rate of CH4 emission has been varying dramatically each year. This trend is common worldwide, though in different parts of the world unevenly intense, conditioned by the amount of emissions from natural and anthropogenic sources. Peatland ecosystems are one of the natural methane emitters, responsible for about 24% of the total CH4 emissions. Methane emission from wetlands is the balance between the processes of methanogenesis and methanotrophy with an active role of wetlands plants composition. Participation of vegetation in the reduction the emissions by 30-35% was confirmed. Association of methanotrophic bacteria with plants has been already recognized by Raghoebarsing and colleagues, who showed that methanotrophic bacteria, as endosymbionts and epibionts, live both inside and outside the cells of Sphagnum sp. The main aim of this study was to estimate methane emissions from Moszne peatland, dominated by: Sphagnum sp., Eriophorum vaginatum, Carex nigra and Vaccinium uliginosum

Elicitation of anthocyanin production in roots of Kalanchoe blossfeldiana by methyl jasmonate

The influence of methyl jasmonate on anthocyanin accumulation in roots of Kalanchoe blossfediana plants was studied. Methyl jasmonate (JA-Me), at a concentration of 5.0 to 40.0 mg.l-1, substantially increased anthocyanin accumulation in roots of intact plants, when it was applied as a solution under natural light conditions. The production of anthocyanin depended on the concentration of methyl jasmonate and the age of the plant. The stimulatory effect was higher in older plants of K. blossfeldiana than in younger ones. When leaves were removed methyl jasmonate slightly stimulated anthocyanin accumulation compared with intact plants. The obtained results indicate that leaves are necessary for the anthocyanin accumulation in the roots. In isolated roots methyl jasmonate did not affect the accumulation of anthocyanins in light conditions. Seven anthocyanins were documented in the roots of control plants and 8 anthocyanins in the roots of JA-Me treated ones. JA-Me increased the level of anthocyanins in roots of old K. blossfeldiana plants 6.8, 6.0 and 3.6-folds, after 4, 8 and 14-days of treatment, respectively

Dynamika zmiany stężenia atmosferycznego CH4, O3, NO2, SO2 w Lublinie w latach 2007-2009

Changes in atmospheric concentrations of gases including CH4, O3, NO2, SO2 are one of the most current issues, due to the observed global warming. The concentration of atmos-pheric gases is being monitored by satellite measurements and also by tropospheric air monitoring stations located at various geographical latitudes. Polish law and EU Directives determine the limit values of concentrations of air pollutants established for the protection of human health: sulphur dioxide, nitrogen dioxide, benzene, carbon monoxide, ozone, PM10, lead, arsenic, cadmium, nickel and benzo(a)pyrene. The basic equipment of monitoring stations does not include methane analys-ers. Our monitoring station is one of two stations in Poland with a CH4 analyser. The sampling intake of the KUL monitoring station is located on the wall oriented perpendicularly to the Lublin-Krakow road, c.a. 41.5 m from this very frequently used road. The research, conducted for three years beginning from 2007 until 2009, showed significant variations in greenhouse gases (GHG) concentrations. The increase in mean annual methane concentration noted at the KUL station was 1.4 % for the years 2007-2008 and 1.7% for 2008-2009. The growth rate of ozone mixing ratio was 29% in the period of 2007-2009. Annual mean values of NO2 concentration in 2007 were 50.3% higher than in 2009. The growth rate of SO2 mixing ratio exceeded 65% between 2007 and 2008. The concentration levels of pollutants in the air were related directly with the emission of pollutants to the atmosphere and with the meteorological conditions.Zmiany stężenia gazów takich jak: CH4, O3, NO2, SO2 są jednym z najbardziej aktualnych problemów ze względu na obserwowane globalne ocieplenie. Stężenie tych gazów w atmosferze monitorowane jest satelitarnie lub poprzez stacje monitoringu powietrza troposferycznego zlokalizowane na różnych szerokościach geograficznych. Ustawodawstwo polskie i dyrektywy Unii Europejskiej określają wartości dopuszczalne stężenia zanieczyszczeń powietrza określone w celu ochrony ludzkiego zdrowia: ditlenek siarki, ditlenek azotu, benzen, tlenek węgla, ozon, PM10, ołów, arsen, kadm, nikiel i benzo(a)piren. Podstawowe wyposażenie stacji monitoringu nie zawiera analizatorów metanu. Stacja KUL jest jedną z dwóch stacji w Polsce posiadającą analizator CH4. Czerpnia prób gazowych w stacji monitoringu KUL zlokalizowana jest w odległości około 41,5 m od drogi krajowej Lublin-Kraków. Badania prowadzone przez trzy lata począwszy od 2007 do 2009 roku wykazują znaczne różnice w stężeniu analizowanych gazów cieplarnianych (GHG). Odnotowany w stacji monitoringu KUL wzrost średniej rocznej wartości stężenia metanu wynosił w latach 2007-2008 1,4%, w latach 2008-2009 1,7%. Wzrost stężenia ozonu w analizowanym okresie czasu utrzymywał się na poziomie 29%. Średnie roczne wartości stężenia NO2 w roku 2007 były o 50% wyższe niż w roku 2009. Dynamika zmian stężenia SO2 w latach 2007 i 2008 przekroczyła 65%. Poziom stężenia badanych zanieczyszczeń wynikał bezpośrednio z ich emisji do atmosfery oraz z warunków meteorologicznych

Effect of fluridone on the composition of fatty acids and other properties of tomato fruits

The effects of fluridone on the content and composition of fatty acids and some other properties of tomato fruits during a 14-day period of ripening were studied. Mature green tomato fruits were used for the experiments. Fluridone at a 1.0% concentration in lanolin paste was applied as a 2-3 mm stripe from the top to the base of a tomato fruit, and a stripe of lanolin was applied in the same way on the opposite side of the frui as control. After 14 days of the experiment, the treated (yellow) and untreated (red) halves of the tomato were separately freeze-dried and powdered before analysis. Determination of the profile and content of fatty acids was carried out in a micro-HPLC-MS/MS system including a 5600 QTOF mass spectrometer. Fatty acids were identified, based on retention times of available standards and the MS/MS spectra. The degree of lipid peroxidation, DPPH radical scavenging activity, proline and soluble protein content were determined using spectrophotometric methods. The use of fluridone did not cause significant changes in the content of unbound fatty acids, although there was a tendency to increased amounts of unsaturated acids. Concerning total fatty acids, the use of fluridone significantly increased the ratio of oleic acid to stearic, as well as the ratio of total unsaturated acids to saturated acids in the treated pericarp of tomato fruits. Fluridone had not effect on the content of proline, total phenolic acids, MDA and antioxidant activity, but inhibited soluble protein accumulation and enhanced the content of total flavonoids

Methanotroph-derived bacteriohopanepolyol signatures in sediments covering Miocene brown coal deposits

Methanotrophic bacteria (MB) are an important group of microorganisms, involved in the greenhouse gas (GHG) cycles. They are responsible for the utilization of methane, one of the main GHGs, which is released in large amounts (via biogenic and abiogenic processes) during coal formation. This study aimed to determine the main factors affecting the distribution of the MB in two lignite-bearing series of the Turów and Bełchatów coal basins. Distribution of MB in the lignite profiles was studied using methanotroph-specific lipid biomarkers such as amino-bacteriohopanepolyols (NH-BHPs) and C-3 methylated BHPs. BHP results were combined with physical and chemical properties of the studied sediments. In general, lignites were richer in BHPs than the mineral samples, which points to the important role of the intrinsic methane cycling. NH-BHP speciation confirmed that the methanotrophic community of the studied sediments was a combination of both type I and, especially, type II methanotrophs. Based on geological data, it was suggested that elevated temperature during diagenesis intensifies decomposition of methanotroph-specific biomarkers (aminopentol and 3-Me BHT). It was found that the tested BHPs can derive from both fossil and living MB. The presence of metabolically active methanotrophs should therefore be accounted for during studies aimed at using lignite deposits as a source of methane