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1.  Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes 
Nature Communications  2014;5:5896.
Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.
The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.
PMCID: PMC4284660  PMID: 25523484
2.  Carbon inverse opal entrapped with electrode active nanoparticles as high-performance anode for lithium-ion batteries 
Scientific Reports  2013;3:2317.
Enhancing ion and electron transport kinetics together with improving cycle life are important issues to be considered when developing high-performance Li ion batteries. Here we demonstrate a three dimensional ordered macroporous conductive electrode concept by entrapping electrode active nanoparticles in an interpenetrating macroporous carbon inverse opal. The electrodes are featured with simultaneously enhanced ion and electron transport kinetics as well as geometrically constrained active nanoparticles. The electrode can deliver up to 94.17% of theoretical capacity over 1000 discharge/charge cycles at a current density of 2.0 A g−1, and exhibits good rate capability in the high current density range of 1.0–10.0 A g−1. We hope that our findings will help pave the way for tailored design of many other sophisticated electrode materials in electrochemistry.
PMCID: PMC3727061  PMID: 23897089
3.  HTS-PEG: A Method for High Throughput Sequencing of the Paired-Ends of Genomic Libraries 
PLoS ONE  2012;7(12):e52257.
Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.
PMCID: PMC3527410  PMID: 23284958
4.  A facile approach to nanoarchitectured three-dimensional graphene-based Li–Mn–O composite as high-power cathodes for Li-ion batteries 
We report a facile method to prepare a nanoarchitectured lithium manganate/graphene (LMO/G) hybrid as a positive electrode for Li-ion batteries. The Mn2O3/graphene hybrid is synthesized by exfoliation of graphene sheets and deposition of Mn2O3 in a one-step electrochemical process, which is followed by lithiation in a molten salt reaction. There are several advantages of using the LMO/G as cathodes in Li-ion batteries: (1) the LMO/G electrode shows high specific capacities at high gravimetric current densities with excellent cycling stability, e.g., 84 mAh·g−1 during the 500th cycle at a discharge current density of 5625 mA·g−1 (~38.01 C capacity rating) in the voltage window of 3–4.5 V; (2) the LMO/G hybrid can buffer the Jahn–Teller effect, which depicts excellent Li storage properties at high current densities within a wider voltage window of 2–4.5 V, e.g., 93 mAh·g−1 during the 300th cycle at a discharge current density of 5625 mA·g−1 (~38.01 C). The wider operation voltage window can lead to increased theoretical capacity, e.g., 148 mAh·g−1 between 3 and 4.5 V and 296 mAh·g−1 between 2 and 4.5 V; (3) more importantly, it is found that the attachment of LMO onto graphene can help to reduce the dissolution of Mn2+ into the electrolyte, as indicated by the inductively coupled plasma (ICP) measurements, and which is mainly attributed to the large specific surface area of the graphene sheets.
PMCID: PMC3458596  PMID: 23019546
cathode; graphene; Li-ion battery; lithium manganate
5.  Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries 
The ISME journal  2010;5(3):414-426.
Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.
PMCID: PMC3105715  PMID: 20927138
metagenomics; deep sea; chimney; fosmid; pyrosequencing
6.  Comparative studies on single-layer reduced graphene oxide films obtained by electrochemical reduction and hydrazine vapor reduction 
Nanoscale Research Letters  2012;7(1):161.
The comparison between two kinds of single-layer reduced graphene oxide (rGO) sheets, obtained by reduction of graphene oxide (GO) with the electrochemical method and hydrazine vapor reduction, referred to as E-rGO and C-rGO, respectively, is systematically studied. Although there is no morphology difference between the E-rGO and C-rGO films adsorbed on solid substrates observed by AFM, the reduction process to obtain the E-rGO and C-rGO films is quite different. In the hydrazine vapor reduction, the nitrogen element is incorporated into the obtained C-rGO film, while no additional element is introduced to the E-rGO film during the electrochemical reduction. Moreover, Raman spectra show that the electrochemical method is more effective than the hydrazine vapor reduction method to reduce the GO films. In addition, E-rGO shows better electrocatalysis towards dopamine than does C-rGO. This study is helpful for researchers to understand these two different reduction methods and choose a suitable one to reduce GO based on their experimental requirements.
PMCID: PMC3309976  PMID: 22373422

Results 1-6 (6)