Derivative Process of Inversion of Kirkwood-Buff Theory in Binary Liquid Mixtures

The Kirkwood-Buff (KB) integrals are calculated using thermodynamic properties such as isothermal compressibilities, partial molar volumes (or excess molar volumes), and partial vapor pressures (or activity coefficients, or excess molar Gibbs energies) with the help of the inversion of the KB theory about liquid mixtures. Matteoli and Lepoli have already proposed the useful formulae with which the KB integrals are easily estimated in binary liquid mixtures. However, the derivative process of these formulae is still obscure. In this paper, the Matteoli-Lepoli formulae are obtained from the modified KB equations by Ben-Nairn via Donkersloot equations, and consequently the detailed derivative process is clarified

Heterologous production of asperipin-2a: proposal for sequential oxidative macrocyclization by a fungi-specific DUF3328 oxidase

Asperipin-2a is a ribosomally synthesized and post-translationally modified peptide isolated from Asperigillus flavus. Herein, we report the heterologous production of asperipin-2a and determination of its absolute structure. Notably, the characteristic bicyclic structure was likely constructed by a single oxidase containing the DUF3328 domain

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data.

A hybrid de novo assembly pipeline was constructed to utilize both MiSeq and SOLiD short read data in combination in the assembly. The short read data were converted to a standard format of the pipeline, and were supplied to the pipeline components such as ABySS and SOAPdenovo. The assembly pipeline proceeded through several stages, and either MiSeq paired-end data, SOLiD mate-paired data, or both of them could be specified as input data at each stage separately. The pipeline was examined on the filamentous fungus Aspergillus oryzae RIB40, by aligning the assembly results against the reference sequences. Using both the MiSeq and the SOLiD data in the hybrid assembly, the alignment length was improved by a factor of 3 to 8, compared with the assemblies using either one of the data types. The number of the reproduced gene cluster regions encoding secondary metabolite biosyntheses (SMB) was also improved by the hybrid assemblies. These results imply that the MiSeq data with long read length are essential to construct accurate nucleotide sequences, while the SOLiD mate-paired reads with long insertion length enhance long-range arrangements of the sequences. The pipeline was also tested on the actinomycete Streptomyces avermitilis MA-4680, whose gene is known to have high-GC content. Although the quality of the SOLiD reads was too low to perform any meaningful assemblies by themselves, the alignment length to the reference was improved by a factor of 2, compared with the assembly using only the MiSeq data

R50 and N50 values with different k-mer sizes.

<p>(a) The R50 and (b) the N50 values for lib2.8.qv10 (closed square) and lib1.9.qv10 (open square). The R50 value corresponds to N50 using sequence fragments of the reference genome covered by highly accurate sequences of assembled scaffolds.</p

Libraries, data filtering, and k-mer size used for the series of <i>de novo</i> assemblies.

a<p>Standard deviation of the library insert size.</p>b<p>Meaning all bases have QVs of >10 or 90% base-level accuracy.</p