The Impacts of Read Length and Transcriptome Complexity for <i>De Novo</i> Assembly: A Simulation Study

<div><p>Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve transcriptome assembly, but it is unknown whether the read length really matters. In addition, though many assembly tools are available now, it is unclear whether the existing assemblers perform well enough for all data with different transcriptome complexities. In this paper, we studied these two open problems using two high-performing assemblers, Velvet/Oases and Trinity, on several simulated datasets of human, mouse and S.cerevisiae. The results suggest that (1) the read length of paired reads does not matter once it exceeds a certain threshold, and interestingly, the threshold is distinct in different organisms; (2) the quality of <i>de novo</i> assembly decreases sharply with the increase of transcriptome complexity, all existing <i>de novo</i> assemblers tend to corrupt whenever the genes contain a large number of alternative splicing events.</p></div

Comparison of <i>de novo</i> assemblies on five human datasets with different numbers of spliced isoforms.

<p>Comparison of <i>de novo</i> assemblies on five human datasets with different numbers of spliced isoforms.</p

Analyses of five human datasets with different numbers of spliced isoforms.

<p>(A) Boxplot of exon number of each gene. (B) Boxplot of spliced isoform length.</p

Four assessment metrics of assemblies on S.cerevisiae datasets with different lengths.

<p>Four assessment metrics of assemblies on S.cerevisiae datasets with different lengths.</p

Comparison of <i>de novo</i> assemblies on S.cerevisiae datasets with different sequencing error rates (the read length is 75 bp).

a<p>Full-length Percentage: the percentage of full-length reconstructed reference transcripts.</p

Distribution of sequencing errors.

<p>(A) shows the sequencing errors occur randomly across one read and B) shows the error rate is almost the same among six human datasets with different read lengths.</p

Statistics of five human datasets with different numbers of spliced isoforms.

<p>Statistics of five human datasets with different numbers of spliced isoforms.</p

Co₃O₄@MWCNT Nanocable as Cathode with Superior Electrochemical Performance for Supercapacitors

Using a simple hydrothermal procedure, cobalt oxide (Co₃O₄) with preferred orientation along (220) planes is in situ prepared and coated on MWCNT. The prepared Co₃O₄@MWCNT nanocable shows superior electrochemical performance as cathode material for aqueous supercapacitors in 0.5 M KOH solution. Its redox peaks retain the well-defined shapes even when the scan rate increases to 200 mV/s. Its specific capacitance is high, 590 F/g at 15 A/g and 510 F/g even at 100 A/g within the potential range from −0.2 to 0.58 V (vs SCE). There is no capacitance fading after 2000 full cycles. This excellent performance is superior to the pristine and the reported Co₃O₄, which is ascribed to the unique nanocable structure with orientation

Polymer Dehalogenation-Enabled Fast Fabrication of N,S-Codoped Carbon Materials for Superior Supercapacitor and Deionization Applications

Doped carbon materials (DCM) with multiple heteroatoms hold broad interest in electrochemical catalysis and energy storage but require several steps to fabricate, which greatly hinder their practical applications. In this study, a facile strategy is developed to enable the fast fabrication of multiply doped carbon materials via room-temperature dehalogenation of polyvinyl dichloride (PVDC) promoted by KOH with the presence of different organic dopants. A N,S-codoped carbon material (NS-DCM) is demonstratively synthesized using two dopants (dimethylformamide for N doping and dimethyl sulfoxide for S doping). Afterward, the precursive room-temperature NS-DCM with intentionally overdosed KOH is submitted to inert annealing to obtain large specific surface area and high conductivity. Remarkably, NS-DCM annealed at 600 °C (named as 600-NS-DCM), with 3.0 atom % N and 2.4 atom % S, exhibits a very high specific capacitance of 427 F g^–1 at 1.0 A g^–1 in acidic electrolyte and also keeps ∼60% of capacitance at ultrahigh current density of 100.0 A g^–1. Furthermore, capacitive deionization (CDI) measurements reveal that 600-NS-DCM possesses a large desalination capacity of 32.3 mg g^–1 (40.0 mg L^–1 NaCl) and very good cycling stability. Our strategy of fabricating multiply doped carbon materials can be potentially extended to the synthesis of carbon materials with various combinations of heteroatom doping for broad electrochemical applications

Synthesis Mechanism Study of Layered Double Hydroxides Based on Nanoseparation

Colloidal layered double hydroxides (LDH) nanosheets were sorted by their lateral sizes using a density gradient ultracentrifuge separation technique. Composition investigations on these size-sorted nanosheets indicated that larger sheets had higher Mg:Al ratio than the smaller ones. Experiments using different Mg:Al feed ratios confirmed that high Mg:Al ratio induced fast sheet growth speed. Tracking the source of the Mg:Al spatial distribution difference in one batch of synthesis at the nucleation process revealed the coprecipitation-redissolution of Mg²⁺. Thus the discriminative separation of these nanosheets led to a new insight into the structure-composition relationship of LDH nanomaterials and more understanding on their formation mechanism