Aluminum current collectors are widely used in nonaqueous batteries owing to their cost-effectiveness, lightweightness, and ease of fabrication. However, they are excluded from aqueous batteries due ...to their severe corrosion in aqueous solutions. Here, we propose hydrolyzation-type anodic additives to form a robust passivation layer to suppress corrosion. These additives dramatically lower the corrosion current density of aluminum by nearly three orders of magnitude to ~10
A cm
. In addition, realizing that electrochemical corrosion accompanies anode prelithiation, we propose a prototype of self-prolonging aqueous Li-ion batteries (Al ||LiMn
O
||TiO
), whose capacity retention rises from 49.5% to 70.1% after 200 cycles. A sacrificial aluminum electrode where electrochemical corrosion is utilized is introduced as an electron supplement to prolong the cycling life of aqueous batteries. Our work addresses the short-life issue of aqueous batteries resulting from the corrosion of the current collector and lithium loss from side reactions.
The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using ...short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
The ion transportation mechanism in a high-concentration solution remains unclear due to the complexity of the strong ion–ion/ion–solvent interaction, resulting in the invalidation of most ionic ...conducting theories based on diluted solutions. Here, a superconcentrated electrolyte (water-in-salt) is investigated by multiple experimental techniques, including advanced tools (NMR, synchrotron X-ray diffraction, and spallation neutron scattering), combined with molecular dynamics (MD) simulation to draw out its unique microstructure and uncover its intrinsic relationship with the ionic transportation. Based on the results, we firstly proposed the ionic transport model for the water-in-salt electrolyte, where the solid-like nano-anion clusters construct a superfluid framework and the lithium ion is able to move freely like in an ionic atmosphere. Our model gives a unified explanation to the unique phenomena previously discovered in water-in-salt electrolytes, including the decoupling of conductivity–viscosity and the nanophase separation between the anion and water. Our findings on the microstructure of the super-high-concentrated electrolyte and the involved unique Li-conducting mechanism can fill in the gap between a solid-state conductor and a dilute liquid electrolytic solution.
There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be ...efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.
To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover ...approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art ...programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.
The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that ...can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development and study designing of sequencing projects.
We provide a software package, pIRS (profile-based Illumina pair-end reads simulator), which simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. The error and quality distributions as well as coverage bias patterns of simulated reads using pIRS fit the properties of real sequencing data better than existing simulators. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes.
pIRS is written in C++ and Perl, and is freely available at ftp://ftp.genomics.org.cn/pub/pIRS/.
The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the ...genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3' ends of each read pair, one is able to construct longer reads for assembling. However, effectively joining two overlapped pair-end reads remains a challenging task.
In this article, we present an efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.
COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope.
twlam@cs.hku.hk or luoruibang@genomics.org.cn
Thellungiella salsuginea, a close relative of Arabidopsis , represents an extremophile model for abiotic stress tolerance studies. We present the draft sequence of the T. salsuginea genome, assembled ...based on ∼134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. This genome provides resources and evidence about the nature of defense mechanisms constituting the genetic basis underlying plant abiotic stress tolerance. Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments.
The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza ...brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.
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