MoRFPred-plus: Computational Identification of MoRFs in Protein Sequence using physicochemical properties and HMM profiles

Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences. Two separate independent propensity scores are computed via incorporating physicochemical properties and HMM profiles, these scores are combined to predict final MoRF propensity score for a given residue. The first score reflects the characteristics of a query residue to be part of MoRF region based on the composition and similarity of assumed MoRF and flank regions. The second score reflects the characteristics of a query residue to be part of MoRF region based on the properties of flanks associated around the given residue in the query protein sequence. The propensity scores are processed and common averaging is applied to generate the final prediction score of MoRFpred-plus. Performance of the proposed predictor is compared with available MoRF predictors, MoRFchibi, MoRFpred, and ANCHOR. Using previously collected training and test sets used to evaluate the mentioned predictors, the proposed predictor outperforms these predictors and generates lower false positive rate. In addition, MoRFpred-plus is a downloadable predictor, which makes it useful as it can be used as input to other computational tools

Antioxidant properties of pancreatic hydrolysates from various protein sources

Antioxidant activity of pancreatic hydrolysates of casein, spent brewer’s yeast, bovine liver and tendon was evaluated in comparison to unhydrolised substrates by ABTS assay. In the result of enzymic treatment ABTS cation radical scavenging activity of spent brewer’s yeast, bovine liver and bovine tendon was increased in 4.8, 3.3, and 2.3 times respectively, except casein.  The IC50 values of ABTS cation radical scavenging for casein and it’s hydrolysate were similar. The IC50 values of DPPH radical scavenging activity for pancreatic hydrolysates of casein, spent brewer’s yeast, bovine liver and tendon  were 1.8±0.1 mg/ml,  1.3±0.1 mg/ml, 1.7±0.1 mg/ml, and 6.2±0.1 mg/ml respectively. Above mentioned hydrolysates of various origin were produced at the same conditions (temperature 50oC, pH 7.5-8.9, duration 5 hours) using fresh bovine pancreatic tissue as an enzyme source. The extent of hydrolysis expressed as AN/TN (amino nitrogen/total nitrogen) for hydrolysates had  values from 0.36±0.02 to 0.46±0.04.DOI: http://doi.dx.org/10.5564/mjc.v15i0.321 Mongolian Journal of Chemistry 15 (41), 2014, p43-4

Antioxidative activity of Silibum marianum cultivated in Mongolia

Silibum marianum (Milk thistle) contains high amount of phenolic compounds with antioxidant properties. The aim of this work was to evaluate the antioxidant activity of  phenolic compounds included in Milk thistle. The  antioxidant properties of the leaves and seeds of milk thistle were examined by determining its ability to scavenge the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical. The results obtained from DPPH assay confirm that Milk thistle extracts have high antioxidative activity.DOI: http://doi.dx.org/10.5564/mjc.v15i0.323 Mongolian Journal of Chemistry 15 (41), 2014, p53-5

Utilization of spent brewer’s yeast Saccharomyces cerevisiae for the production of yeast enzymatic hydrolysate

Spent brewer’s yeast (Saccharomyces cerevisiae) is a rich source of protein, vitamins and widely used as a raw material for production of food supplements. The autolysis and enzymatic treatment of spent brewer’s yeast using Pancreatin (2.5%) and Flavourzyme (2.5%) were performed at 45 °C and 50 °C, respectively. The autolysis and hydrolysis processes were evaluated by determining a soluble solids, soluble protein concentration and α-amino nitrogen content in a reaction mixture. The yield of pancreatic digest and α-amino nitrogen content was high in comparison with autolysis and Flavourzyme treatment. The total solids recovery in dry Yeast hydrolysate was about 50%, a protein and α-amino nitrogen content was 55.9 and 4.8%, respectively. These results show the possibility of utilizing the spent brewer’s yeast as hydrolysate using hydrolytic enzymes and use it as a food supplement after biological experiments.DOI: http://dx.doi.org/10.5564/mjc.v12i0.179 Mongolian Journal of Chemistry Vol.12 2011: 88-9

Order and Disorder in Mixed (Si, P)–N Networks Sr2SiP2N6:Eu2+ and Sr5Si2P6N16:Eu2+

In the field of nitride phosphors, which are crucial for phosphor-converted light-emitting diodes, mixed tetrahedral networks hold a significant position. With respect to the wide range of compositions, the largely unexplored (Si, P)–N networks are investigated as potential host structures. In this work, two highly condensed structures, namely Sr2SiP2N6 and Sr5Si2P6N16 are reported to address the challenges that arise from the similarities of the network-forming cations Si4+ and P5+ in terms of charge, ionic radius, and atomic scattering factor, a multistep workflow is employed to elucidate their structure. Using single-crystal X-ray diffraction, energy-dispersive X-ray spectroscopy (EDX), atomic-resolution scanning transmission electron microscopy (STEM)-EDX maps, and straightforward crystallographic calculations, it is found that Sr2SiP2N6 is the first ordered, and Sr5Si2P6N16 the first disordered, anionic tetrahedral (Si, P)–N network. After doping with Eu2+, Sr2SiP2N6:Eu2+ shows narrow cyan emission (λmax = 506 nm, fwhm = 60 nm/2311 cm−1), while for Sr5Si2P6N16:Eu2+ a broad emission with three maxima at 534, 662, and 745 nm upon irradiation with ultraviolet light is observed. An assignment of Sr sites as probable positions for Eu2+ and their relation to the emission bands of Sr5Si2P6N16:Eu2+ is discussed

Pressure-induced charge ordering transition in CaMn7O12

We use high-pressure resistivity and single crystal x-ray diffraction at ambient and low temperature to investigate the charge ordering phase transition of CaMn 7 O 12 . We have found that at ambient temperature the Jahn-Teller distortion of the Mn 3 + O 6 octahedra rapidly decreases above 20 GPa, and vanishes at 28 GPa, when two Mn octahedral sites initially occupied by Mn 3 + and Mn 4 + become regular and equivalent as the result of a charge delocalization. Such a change correlates with a two orders of magnitude drop in the resistivity and a symmetry increase from the low-pressure rhombohedral R ¯ 3 phase to the cubic Im ¯ 3 structure, the same as one found at ambient pressure above 440 K. This yields the slope of the charge ordering phase boundary of d T c / d p ? ? 6 K/GPa. This result is further supported by the lack of a structural phase transition up to the maximum measured pressure of 30 GPa when the experiment is performed at 70 K. The satellite reflections of the structural modulation of the multiferroic phase of CaMn 7 O 12 observed at 70 K were found to hold up to 25 GPa with the structure keeping a constant modulation vector k = ( 0 0 0.925 ) with pressure. The average structure at 70 K does not show other indications of further phase transition.Y. Li and X. Du from Peking University are greatly acknowledged for growing and providing the CaMn7O12 crystals. D. Spahr and J. König from Goethe University are acknowledged for help with the single-crystal diffraction experiments. M.S. would like to acknowledge the financial support under the DFG-ANR Grant No. WI1232/41-1 and DFG GACR Project No. WI3320/3-1. V.M. and J.R.-F. thank the financial support from the Spanish Ministerio de Ciencia e Innovación (MICINN) for the Beatriz Galindo Program (BG20/000777) and for the Project No. PGC2018-097520- A-I00, respectively. DESY Photon Science is gratefully acknowledged. PETRA III at DESY is a member of the Helmholtz Association (HGF)

Ferroelectric soft mode of polar ZnTiO3 investigated by Raman spectroscopy at high pressure

We explore the vibrational behavior and stability of ferroelectric ZnTiO3 under high pressure by Raman spectroscopy and second-harmonic-generation (SHG) measurements. Ab initio lattice-dynamics calculations have been employed to solve a controversy concerning the phonon-dispersion relations of ZnTiO3 and to carry out an assignment of the Raman modes. A ferroelectric to paraelectric phase transition has been observed both by Raman spectroscopy and SHG at 20.8 GPa. Contrary to LiNbO3, the ferroelectric soft mode of ZnTiO3 has been found to be the A1(2) and not the A1(1) mode. The calculated eigenvectors show that the A1(2) mode of ferroelectric ZnTiO3 is an antiphase vibration of the Ti atom against the oxygen framework, similar to the soft modes observed in ferroelectric perovskites. The SHG signal of ZnTiO3 has been found to be independent of the grain size below the phase transition, indicating that ZnTiO3 is a phase-matchable compound

The use of NDVI and its Derivatives for Monitoring Lake Victoria’s Water Level and Drought Conditions

Normalized Difference Vegetation Index (NDVI), which is a measure of vegetation vigour, and lake water levels respond variably to precipitation and its deficiency. For a given lake catchment, NDVI may have the ability to depict localized natural variability in water levels in response to weather patterns. This information may be used to decipher natural from unnatural variations of a given lake’s surface. This study evaluates the potential of using NDVI and its associated derivatives (VCI (vegetation condition index), SVI (standardised vegetation index), AINDVI (annually integrated NDVI), green vegetation function (F g ), and NDVIA (NDVI anomaly)) to depict Lake Victoria’s water levels. Thirty years of monthly mean water levels and a portion of the Global Inventory Modelling and Mapping Studies (GIMMS) AVHRR (Advanced Very High Resolution Radiometer) NDVI datasets were used. Their aggregate data structures and temporal co-variabilities were analysed using GIS/spatial analysis tools. Locally, NDVI was found to be more sensitive to drought (i.e., responded more strongly to reduced precipitation) than to water levels. It showed a good ability to depict water levels one-month in advance, especially in moderate to low precipitation years. SVI and SWL (standardized water levels) used in association with AINDVI and AMWLA (annual mean water levels anomaly) readily identified high precipitation years, which are also when NDVI has a low ability to depict water levels. NDVI also appears to be able to highlight unnatural variations in water levels. We propose an iterative approach for the better use of NDVI, which may be useful in developing an early warning mechanisms for the management of lake Victoria and other Lakes with similar characteristics

Polar nanoregions of Ca0.28Ba0.72Nb2O6 probed by second harmonic generation and Raman spectroscopy at high pressure

The pressure-induced ferroelectric phase transition of calcium barium niobate Ca0.28Ba0.72Nb2O6 is studied by second harmonic generation (SHG) and Raman spectroscopy. We observe the ferroelectric to paraelectric phase transition at P-c = 4 GPa and evidence for two additional local changes at 8.5 and 11.5 GPa that are interpreted as the characteristic intermediate P* and the Burns pressure P-B of a relaxor phase. The pressure dependence of the SHG intensity has a Landau critical exponent of gamma = 1.3 between 4 and 8.5 GPa, indicating the presence of static polar nanoregions. At higher pressures, from 8.5 to 11.5 GPa, these nanoregions become dynamic, with gamma = 2.4, and disappear at 11.5 GPa. The polar nanoregions appear when only one of the two non-equivalent octahedral positions of Nb is centrosymmetric. A Landau exponent of gamma = 1 above 11.5 GPa together with a change in the compression mechanism indicates that the system completes a phase transformation to a centrosymmetric space group and the polar nanoregions vanish. (C) 2014 AIP Publishing LLC