Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.ImportanceTo fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available

Computation-Performance Optimization of Convolutional Neural Networks with Redundant Kernel Removal

Deep Convolutional Neural Networks (CNNs) are widely employed in modern computer vision algorithms, where the input image is convolved iteratively by many kernels to extract the knowledge behind it. However, with the depth of convolutional layers getting deeper and deeper in recent years, the enormous computational complexity makes it difficult to be deployed on embedded systems with limited hardware resources. In this paper, we propose two computation-performance optimization methods to reduce the redundant convolution kernels of a CNN with performance and architecture constraints, and apply it to a network for super resolution (SR). Using PSNR drop compared to the original network as the performance criterion, our method can get the optimal PSNR under a certain computation budget constraint. On the other hand, our method is also capable of minimizing the computation required under a given PSNR drop.Comment: This paper was accepted by 2018 The International Symposium on Circuits and Systems (ISCAS

Ab initio study of the giant ferroelectric distortion and pressure induced spin-state transition in BiCoO3

Using configuration-state-constrained electronic structure calculations based on the generalized gradient approximation plus Hubbard U method, we sought the origin of the giant tetragonal ferroelectric distortion in the ambient phase of the potentially multiferroic material BiCoO3 and identified the nature of the pressure induced spin-state transition. Our results show that a strong Bi-O covalency drives the giant ferroelectric distortion, which is further stabilized by an xy-type orbital ordering of the high-spin (HS) Co3+ ions. For the orthorhombic phase under 5.8 GPa, we find that a mixed HS and low-spin (LS) state is more stable than both LS and intermediate-spin (IS) states, and that the former well accounts for the available experimental results. Thus, we identify that the pressure induced spin-state transition is via a mixed HS+LS state, and we predict that the HS-to-LS transition would be complete upon a large volume decrease of about 20%.Comment: 6 pages, 6 figures, 2 table

A MIXED PERMIAN–TRIASSIC BOUNDARY BRACHIOPOD FAUNA FROM GUIZHOU PROVINCE, SOUTH CHINA

Although many studies have been concerned with Changhsingian brachiopod faunas in South China, brachiopod faunas of the mixed nearshore clastic–carbonate facies have not been studied in detail. In this paper, a brachiopod fauna collected from the Changhsingian Wangjiazhai Formation and the Griesbachian Yelang Formation at the Liuzhi section (Guizhou Province, South China) is described. The Liuzhi section represents mixed clastic–carbonate facies and yields 30 species of 16 genera of brachiopod. Among the described and illustrated species, new morphological features of genera Peltichia, Prelissorhynchia and Spiriferellina are provided. Because of limited materials, four undetermined species instead of new species from these three genera are proposed. The Liuzhi brachiopod fauna from lower part of the Wangjiazhai Formation shares most genera with fauna of carbonate facies in South China, and the fauna from the upper part is similar to that from the Zhongzhai and Zhongying sections, representative shallow-water clastic facies sections in Guizhou Province. Consistent with the lithological feature of the Wangjiazhai Formation at the Liuzhi section, the Liuzhi brachiopod fauna shows similar changing pattern with fauna from sections of shallow-water clastic and carbonate facies, and all present a sudden decline of diversity prior to the Permian–Triassic boundary

Loss of vesicular dopamine release precedes tauopathy in degenerative dopaminergic neurons in a Drosophila model expressing human tau.

While a number of genome-wide association studies have identified microtubule-associated protein tau as a strong risk factor for Parkinson's disease (PD), little is known about the mechanism through which human tau can predispose an individual to this disease. Here, we demonstrate that expression of human wild-type tau is sufficient to disrupt the survival of dopaminergic neurons in a Drosophila model. Tau triggers a synaptic pathology visualized by vesicular monoamine transporter-pHGFP that precedes both the age-dependent formation of tau-containing neurofibrillary tangle-like pathology and the progressive loss of DA neurons, thereby recapitulating the pathological hallmarks of PD. Flies overexpressing tau also exhibit progressive impairments of both motor and learning behaviors. Surprisingly, contrary to common belief that hyperphosphorylated tau could aggravate toxicity, DA neuron degeneration is alleviated by expressing the modified, hyperphosphorylated tau(E14). Together, these results show that impairment of VMAT-containing synaptic vesicle, released to synapses before overt tauopathy may be the underlying mechanism of tau-associated PD and suggest that correction or prevention of this deficit may be appropriate targets for early therapeutic intervention

Effects of Ox-LDL on Macrophages NAD(P)H Autofluorescence Changes by Two-photon Microscopy

Ox-LDL uptakes by macrophage play a critical role in the happening of atherosclerosis. Because of its low damage on observed cells and better signal-to- background ratio, two-photon excitation fluorescence microscopy is used to observe NAD(P)H autofluorescence of macrophage under difference cultured conditions- bare cover glass, coated with fibronectin or poly-D-lysine. The results show that the optimal condition is fibronectin coated surface, on which, macrophages profile can be clearly identified on NAD(P)H autofluorescence images collected by two-photon microscopy. Moreover, different morphology and intensities of autofluorescence under different conditions were observed as well. In the future, effects of ox-LDL on macrophages will be investigated by purposed system to research etiology of atherosclerosis.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions