BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

Epstein-Barr virus (EBV) infection is ubiquitous worldwide and is associated with multiple cancers, including nasopharyngeal carcinoma (NPC). The importance of EBV viral genomic variation in NPC development and its striking epidemic in southern China has been poorly explored. Through large-scale genome sequencing of 270 EBV isolates and two-stage association study of EBV isolates from China, we identified two non-synonymous EBV variants within BALF2 strongly associated with the risk of NPC (odds ratio (OR) = 8.69, P=9.69×10−25 for SNP 162476_C; OR = 6.14, P=2.40×10−32 for SNP 163364_T). The cumulative effects of these variants contributed to 83% of the overall risk of NPC in southern China. Phylogenetic analysis of the risk variants revealed a unique origin in Asia, followed by clonal expansion in NPC-endemic regions. Our results provide novel insights into NPC endemic in southern China and also enable the identification of high-risk individuals for NPC prevention.

Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcriptionfactor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality.mRNA localization | time series

Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input ''easy Hi-C'' protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. We used HiCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with a focus on neurogenesis and brain tissues. We found that dynamic chromatin loops are better hallmarks for cellular differentiation than compartment switching. HiCorr allowed direct observation of cell-type-and differentiation-specific E-P aggregates spanning large neighborhoods, suggesting a mechanism that stabilizes enhancer contacts during development. Interestingly, we concluded that Hi-C loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology.

sources. [1][2][3] To satisfy the requirements of upcoming large-scale energy storage applications, it is highly urgent to develop high-energy-density LIBs by elegantly configuring advanced electrode materials. The present commercial graphite anodes have a low theoretical capacity of 372 mA h g −1 , approaching the lithium storage limit. [4][5][6] Transition-metal oxides (TMOs) outperform graphite as anode alternatives, mechanistically operating through conversion reactions. [1] Notably, cobalt oxides (CoO or Co 3 O 4 ) can theoretically deliver as much as two to three times the specific capacity of graphite due to their multielectron conversion reaction upon electrochemical cycling. [5][6][7] However, the undesired volume expansion of cobalt oxides leads to the destruction of electrodes, accompanied by rapid capacity fading during repeated lithium ion insertion/extraction processes; additionally, their poor electrical conductivity causes weak rate capability. [8,9] Therefore, the lithium storage performance of materials that include cobalt oxides requires optimization of their composition and structure through engineering to achieve lithium storage performance suitable for practical applications. [4,[10][11][12] To this end, one of the most effective strategies is confining or embedding TMOs into a carbonaceous matrix to form hybrids, which can accommodate large volume changes, improve electrical conductivity, and maintain the integrity of the electrode. Generally, the sources of TMOs and carbon are separate, and the carbonization proceeds via a gas-solid reaction. However, another strategy wherein a single precursor was pyrolyzed to simultaneously generate the two components was also efficacious to create these hybrids. This method exhibits advantages including nanosized TMO particles and a highsurface-area carbon matrix. Despite recent advances, the search for suitable precursors for advantageous novel hybrid materials with enhanced performance remains challenging.Metal-organic frameworks (MOFs) are highly ordered crystalline polymers with tailorable voids constructed by the coordination of metal ions or polynuclear clusters with polytopic organic ligands. They serve as precursors for facile transformation into hybrid structures including composites of metal oxides/carbon, metal phosphides/carbon, or metal sulfides/carbon after thermal treatment under appropriate atmospheres. [13][14][15][16][17][18] As a Despite great breakthroughs, the search for anode materials with high performance for lithium-ion batteries (LIBs) remains challenging. Hence, engineering advantageous structures via effective routes can bring new possibilities to the development of the LIB field. Herein, the precise synthesis of three-dimensional (3D) hybrids of ultrathin carbon-wrapped CoO (CoO@C) dandelions is reported by the pyrolysis of two-dimensional (2D) Kagóme metal-organic layers (MOLs) at 400 °C under an Ar atmosphere. Due to the special coordination structure of the paternal MOLs, the resulting CoO nanowires show a small diameter ...

Engineering the interface between the perovskite absorber and the charge-transporting layers has become an important method for improving the charge extraction and open-circuit voltage ( V) of hybrid perovskite solar cells. Conjugated polymers are particularly suited to form the hole-transporting layer, but their hydrophobicity renders it difficult to solution-process the perovskite absorber on top. Herein, oxygen plasma treatment is introduced as a simple means to change the surface energy and work function of hydrophobic polymer interlayers for use as p-contacts in perovskite solar cells. We find that upon oxygen plasma treatment, the hydrophobic surfaces of different prototypical p-type polymers became sufficiently hydrophilic to enable subsequent perovskite junction processing. In addition, the oxygen plasma treatment also increased the ionization potential of the polymer such that it became closer to the valance band energy of the perovskite. It was also found that the oxygen plasma treatment could increase the electrical conductivity of the p-type polymers, facilitating more efficient charge extraction. On the basis of this concept, inverted MAPbI perovskite devices with different oxygen plasma-treated polymers such as P3HT, P3OT, polyTPD, or PTAA were fabricated with power conversion efficiencies of up to 19%.

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