As an indispensable component of various living organisms, the antioxidant proteins have been studied for anti-aging and prevention of various diseases, such as altitude sickness, coronary heart ...disease, and even cancer. However, the traditional experimental methods for identifying the antioxidant proteins are very expensive and time-consuming. Thus, to address the challenge, a new predictor, named ANOX, was developed in this study. Multiple features, such as frequency matrix features (FRE), amino acid and dipeptide composition (AADP), evolutionary difference formula features (EEDP), k-separated bigrams (KSB), and PSI-PRED secondary structure (PRED), were extracted to generate the original feature space. To find the optimized feature subset, the Max-Relevance-Max-Distance (MRMD) algorithm was implemented for feature ranking and our model received the best performance with the top 1170 features. Rigorous tests were performed to evaluate the performance of ANOX, and the results showed that ANOX achieved a major improvement in the prediction accuracy of the antioxidant proteins (AUC:0.930 and 0.935 using 5-fold cross-validation or the jackknife test) compared to the state-of-the-art predictor AOPs-SVM (AUC:0.869 and 0.885). The dataset used in this study and the source code of ANOX are all available at https://github.com/NWAFU-LiuLab/ANOX.
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•An SVM-based model was proposed to identify the antioxidant proteins.•Multiple features were extracted to generate the original feature space.•The Max-Relevance-Max-Distance algorithm is implemented for feature selection.•Our model performs better than the state-of-the art predictor.
•Improvisers showed distinct network connectivity when categorizing musical structures.•Improvisers showed inter-network connectivity in the α-band before a motor-response.•Connectivity between DMN ...and VN was strongly linked to improvisation expertise.•More experienced musicians showed stronger connectivity between DMN, DAN and CCN.
Musical improvisers are trained to categorize certain musical structures into functional classes, which is thought to facilitate improvisation. Using a novel auditory oddball paradigm (Goldman et al., 2020) which enables us to disassociate a deviant (i.e. musical chord inversion) from a consistent functional class, we recorded scalp EEG from a group of musicians who spanned a range of improvisational and classically trained experience. Using a spatiospectral based inter and intra network connectivity analysis, we found that improvisers showed a variety of differences in connectivity within and between large-scale cortical networks compared to classically trained musicians, as a function of deviant type. Inter-network connectivity in the alpha band, for a time window leading up to the behavioural response, was strongly linked to improvisation experience, with the default mode network acting as a hub. Spatiospectral networks post response were substantially different between improvisers and classically trained musicians, with greater inter-network connectivity (specific to the alpha and beta bands) seen in improvisers whereas those with more classical training had largely reduced inter-network activity (mostly in the gamma band). More generally, we interpret our findings in the context of network-level correlates of expectation violation as a function of subject expertise, and we discuss how these may generalize to other and more ecologically valid scenarios.
Anti-prion systems in yeast Wickner, Reed B.
The Journal of biological chemistry,
02/2019, Letnik:
294, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Yeast prions have become important models for the study of the basic mechanisms underlying human amyloid diseases. Yeast prions are pathogenic (unlike the Het-s prion of Podospora anserina), and most ...are amyloid-based with the same in-register parallel β-sheet architecture as most of the disease-causing human amyloids studied. Normal yeast cells eliminate the large majority of prion variants arising, and several anti-prion/anti-amyloid systems that eliminate them have been identified. It is likely that mammalian cells also have anti-amyloid systems, which may be useful in the same way humoral, cellular, and innate immune systems are used to treat or prevent bacterial and viral infections.
None, as it is a short commentary, but if you need one, here it is.
This commentary places Alejandro Parra's very long list of plagiarisms and data missrepresentations within the context of Dante's ...classification of human foibles. The responses from two Argentinean universities are described, along with continuing examples of Parra's misrepresentations.
We provide a step-by-step analysis and discussion of the ‘PSI-based matrix approach’, a methodology employing ground deformation velocities derived through Persistent Scatterer Interferometry (PSI) ...for the assessment of the state of activity and intensity of extremely to very slow landslides. Two matrices based on PSI data are designed respectively for landslides already mapped in preexisting inventories and for newly identified phenomena. Conversely, a unique intensity scale is proposed indiscriminately for both. Major influencing factors of the approach are brought to light by the application in the 14 km
2
area of Verbicaro, in Northern Calabria (Italy). These include lack of PSI data within the landslide boundaries, temporal coverage of the available estimates, and need of field checks as well as the operative procedures to set the activity and intensity thresholds. For the area of Verbicaro, we exploit 1992–2011 PSI data from ERS1/2 and RADARSAT1/2 satellites, projecting them along the maximum slope directions. An activity threshold of ±5 mm/year is determined by applying the average projection factor of local slopes to the PSI data precision. The intensity threshold between extremely and very slow phenomena (16 mm/year) is reduced by ~20 % to account for temporal and spatial averages being applied to attribute representative velocities to each landslide. The methodology allows assessing the state of activity and the intensity for 13 of the 24 landslides premapped in the 2007 inventory and for two newly identified phenomena. Current limitations due to characteristics and spatial coverage of PSI data are critically tackled within the discussion, jointly with respective implications.
Rational design of synthetic phage-displayed libraries requires the identification of the most appropriate positions for randomization using defined amino acid sets to recapitulate the natural ...occurrence. The present study uses position-specific scoring matrixes (PSSMs) for identifying and randomizing Camelidae nanobody (VHH) CDR3. The functionality of a synthetic VHH repertoire designed by this method was tested for discovering new VHH binders to recombinant coagulation factor VII (rfVII).
Based on PSSM analysis, the CDR3 of cAbBCII10 VHH framework was identified, and a set of amino acids for the substitution of each PSSM-CDR3 position was defined. Using the Rosetta design SwiftLib tool, the final repertoire was back-translated to a degenerate nucleotide sequence. A synthetic phage-displayed library was constructed based on this repertoire and screened for anti-rfVII binders.
A synthetic phage-displayed VHH library with 1 × 108 variants was constructed. Three VHH binders to rfVII were isolated from this library with estimated dissociation constants (KD) of 1 × 10−8 M, 5.8 × 10−8 M and 2.6 × 10-7 M.
PSSM analysis is a simple and efficient way to design synthetic phage-displayed libraries.
•Through Position Specific Scoring Matrixes (PSSMs), CDR3 hypervariable region was identified in the VHH scaffold cAbBCII10. The specified hypervariable region was in close conformity with the CDR3 region defined by the IMGT database.•Based on PSSM scores, a set of possible amino acid substitutions was defined for 13 positions at the CDR3 hypervariable region.•Specific VHH binders to recombinant coagulation factor VII were discovered through phage-displayed screening of the obtained library.
Photosynthesis fixes CO
and converts it to sugar, using chemical-energy compounds of both NADPH and ATP, which are produced in the photosynthetic electron transport system. The photosynthetic ...electron transport system absorbs photon energy to drive electron flow from Photosystem II (PSII) to Photosystem I (PSI). That is, both PSII and PSI are full of electrons. O
is easily reduced to a superoxide radical (O
) at the reducing side, i.e., the acceptor side, of PSI, which is the main production site of reactive oxygen species (ROS) in photosynthetic organisms. ROS-dependent inactivation of PSI in vivo has been reported, where the electrons are accumulated at the acceptor side of PSI by artificial treatments: exposure to low temperature and repetitive short-pulse (rSP) illumination treatment, and the accumulated electrons flow to O
, producing ROS. Recently, my group found that the redox state of the reaction center of chlorophyll P700 in PSI regulates the production of ROS: P700 oxidation suppresses the production of O
and prevents PSI inactivation. This is why P700 in PSI is oxidized upon the exposure of photosynthesis organisms to higher light intensity and/or low CO
conditions, where photosynthesis efficiency decreases. In this study, I introduce a new molecular mechanism for the oxidation of P700 in PSI and suppression of ROS production from the robust relationship between the light and dark reactions of photosynthesis. The accumulated protons in the lumenal space of the thylakoid membrane and the accumulated electrons in the plastoquinone (PQ) pool drive the rate-determining step of the P700 photo-oxidation reduction cycle in PSI from the photo-excited P700 oxidation to the reduction of the oxidized P700, thereby enhancing P700 oxidation.
A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate ...predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids.
The Lost Boys of Zeta Psitakes us inside the secret, amusing, and sometimes mundane world of a California fraternity around 1900. Gleaning history from recent archaeological excavations and from such ...intriguing sources as oral histories, architecture, and photographs, Laurie A. Wilkie uncovers details of everyday life in the first fraternity at the University of California, Berkeley, and sets this story into the rich social and historical context of West Coast America at the turn of the last century. In particular, Wilkie examines men's coming-of-age experiences in a period when gender roles and relations were undergoing dramatic changes. Her innovative study illuminates shifting notions of masculinity and at the same time reveals new insights about the inner workings of fraternal orders and their role in American society.
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