GPS: a comprehensive www server for phosphorylation sites prediction

Protein phosphorylation plays a fundamental role in most of the cellular regulatory pathways. Experimental identification of protein kinases' (PKs) substrates with their phosphorylation sites is labor-intensive and often limited by the availability and optimization of enzymatic reactions. Recently, large-scale analysis of the phosphoproteome by the mass spectrometry (MS) has become a popular approach. But experimentally, it is still difficult to distinguish the kinase-specific sites on the substrates. In this regard, the in silico prediction of phosphorylation sites with their specific kinases using protein's primary sequences may provide guidelines for further experimental consideration and interpretation of MS phosphoproteomic data. A variety of such tools exists over the Internet and provides the predictions for at most 30 PK subfamilies. We downloaded the verified phosphorylation sites from the public databases and curated the literature extensively for recently found phosphorylation sites. With the hypothesis that PKs in the same subfamily share similar consensus sequences/motifs/functional patterns on substrates, we clustered the 216 unique PKs in 71 PK groups, according to the BLAST results and protein annotations. Then, we applied the group-based phosphorylation scoring (GPS) method on the data set; here, we present a comprehensive PK-specific prediction server GPS, which could predict kinase-specific phosphorylation sites from protein primary sequences for 71 different PK groups. GPS has been implemented in PHP and is available on a www server at

Orbit- and Atom-Resolved Spin Textures of Intrinsic, Extrinsic and Hybridized Dirac Cone States

Combining first-principles calculations and spin- and angle-resolved photoemission spectroscopy measurements, we identify the helical spin textures for three different Dirac cone states in the interfaced systems of a 2D topological insulator (TI) of Bi(111) bilayer and a 3D TI Bi2Se3 or Bi2Te3. The spin texture is found to be the same for the intrinsic Dirac cone of Bi2Se3 or Bi2Te3 surface state, the extrinsic Dirac cone of Bi bilayer state induced by Rashba effect, and the hybridized Dirac cone between the former two states. Further orbit- and atom-resolved analysis shows that s and pz orbits have a clockwise (counterclockwise) spin rotation tangent to the iso-energy contour of upper (lower) Dirac cone, while px and py orbits have an additional radial spin component. The Dirac cone states may reside on different atomic layers, but have the same spin texture. Our results suggest that the unique spin texture of Dirac cone states is a signature property of spin-orbit coupling, independent of topology

Primary productivity dynamics in the summer Arctic Ocean confirms broad regulation of the electron requirement for carbon fixation by light-phytoplankton community interaction

© 2019 Zhu, Suggett, Liu, He, Lin, Le, Ishizaka, Goes and Hao. Predicting conversion of photosynthetic electron transport to inorganic carbon uptake rates (the so-called electron requirement for carbon fixation, KC) is central to the broad scale deployment of Fast Repetition Rate fluorometry (FRRf) for primary productivity studies. However, reconciling variability of KC over space and time to produce robust algorithms remains challenging, given the large number of factors that influence KC. We have previously shown that light appears to be a proximal driver of Kc in several ocean regions and we therefore examined whether and how light similarly regulated KC variability in the Arctic Ocean, during a summer cruise in 2016. Sampling transited ice-free and ice-covered waters, with temperature, salinity and Chl-a concentrations all higher for the ice-free than ice covered surface waters. Micro- and pico-phytoplankton generally dominated the ice-free and ice-covered waters, respectively. Values of KC, determined from parallel measures of daily integrated electron transport rates and 14C-uptake, were overall lower for the ice-covered vs. ice-free stations. As in our previous studies, KC was strongly linearly correlated to daily PAR (r = 0.68, n = 46, p < 0.001) and this relationship could be further improved (r = 0.84, n = 46, p < 0.001) by separating samples into ice-free (micro-phytoplankton dominated) vs. ice-covered (Nano- and Pico-phytoplankton dominated water. We subsequently contrasted the PAR-KC relationship form the Arctic waters with the previous relationships from the Ariake Bay and East China Sea and revealed that these various PAR-KC relationships can be systematically explained across regions by phytoplankton community size structures. Specifically, the value of the linear slope describing PAR-KC decreases as water bodies have an increasing fraction of larger phytoplankton. We propose that this synoptic trend reflects how phytoplankton community structure integrates past and immediate environmental histories and hence may be a better broad-scale predictor of KC than specific environmental factors such as temperature and nutrients. We provide a novel algorithm that may enable broad-scale retrieval of CO2 uptake from FRRf with knowledge of light and phytoplankton community size information

Age Is Important for the Early-Stage Detection of Breast Cancer on Both Transcriptomic and Methylomic Biomarkers

Patients at different ages have different rates of cell development and metabolisms. As a result, age should be an essential part of how a disease diagnosis model is trained and optimized. Unfortunately, most of the existing studies have not taken age into account. This study demonstrated that disease diagnosis models could be improved by merely applying individual models for patients of different age groups. Both transcriptomes and methylomes of the TCGA breast cancer dataset (TCGA-BRCA) were utilized for the analysis procedure of feature selection and classification. Our experimental data strongly suggested that disease diagnosis modeling should integrate patient age into the whole experimental design

Enhanced production of highly methylated brGDGTs linked to anaerobic bacteria from sediments of the Mariana Trench

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are widely used in terrestrial paleoclimatic reconstructions. Recent studies have reported that brGDGTs can also be produced by marine bacteria. However, the environmental factors influencing marine-derived brGDGTs and their source organisms remain largely unknown. Here, we investigated the distribution and composition of brGDGTs and a suite of their putative derivatives called overly branched GDGTs (obGDGTs) in the Mariana Trench core sediments (water depth 8300 m, core length 320 cm), as well as the composition of bacterial communities. The ratio of the branched over isoprenoid tetraethers (BIT) was 0.03-0.21 (average 0.07; SD = 0.04; n = 21) and the ratio ΣIIIa/ΣIIa of brGDGTs was 0.93-7.47 (average 3.39; SD = 1.73; n = 21), which support the in situ production of brGDGTs. Co-occurrence network analysis revealed that a total of 33 types of bacteria at the order level (e.g., Armatimonadota DG-56, Proteobacteria Rhodospirillales, Chloroflexi SAR202_clade) were closely related to the distribution of brGDGTs and obGDGTs, which could be potential sources for these compounds. The abrupt increase in brGDGT and obGDGT concentrations in deeper oxygen-depleted sediments and their good correlations with anaerobic bacterial abundances suggest that these brGDGTs and obGDGTs may be produced by anaerobic bacteria residing in the anoxic sediments. Considerable variation in the degrees of methylation and cyclization of brGDGTs (obGDGTs) under different redox conditions indicate that sediment oxygen levels may have a profound impact on the presence and abundance of brGDGTs and obGDGTs, which should be considered when applying them for paleo-temperature or pH reconstructions. This study shows that brGDGTs and obGDGTs obtained from the Mariana Trench were probably produced by a variety of bacterial phyla indigenous in the hadal ocean, which are different from Acidobacteria commonly considered to be major terrestrial sources of brGDGTs

The interplay of Dzyaloshinskii-Moriya and Kitaev interactions for magnonic properties of Heisenberg-Kitaev honeycomb ferromagnets

The properties of Kitaev materials are attracting ever increasing attention owing to their exotic properties. In realistic two-dimensional materials, Kitaev interaction is often accompanied by the Dzyloshinskii-Moriya interaction, which poses a challenge of distinguishing their magnitude separately. In this work, we demonstrate that it can be done by accessing magnonic transport properties. By studying honeycomb ferromagnets exhibiting Dzyaloshinskii-Moriya and Kitaev interactions simultaneously, we reveal non-trivial magnonic topological properties accompanied by intricate magnonic transport characteristics as given by thermal Hall and magnon Nernst effects. We also investigate the effect of a magnetic field, showing that it does not only break the symmetry of the system but also brings drastic modifications to magnonic topological transport properties, which serve as hallmarks of the relative strength of anisotropic exchange interactions. Based on our findings, we suggest strategies to estimate the importance of Kitaev interactions in real materials.Comment: 6 pages, 4 figure