Correction to: L_RNA_scaffolder: scaffolding genomes with transcripts.

Following the publication of this article [1], the authors reported that the link to the software described in the article is no longer valid.

Gold(III)-Catalyzed Selective Cyclization of Alkynyl Quinazolinone-Tethered Pyrroles: Synthesis of Fused Quinazolinone Scaffolds.

A series of 1,2- and 2,3-fused quinazolinones have been synthesized in good to excellent yields through gold-catalyzed selective hydroarylations of alkynyl quinazolinone-tethered pyrroles. The studies revealed that 1,2-fused quinazolinones were obtained through a 1,3-rearrangement and sequential 6- exo-trig cyclization of N1-alkynyl quinazolinone-tethered pyrroles, while N3-alkynyl quinazolinone-tethered pyrroles went through 6- exo-dig or 7- endo-dig cyclizations directly to afford 2,3-fused quinazolinones. The fused quinazolinones could be prepared at gram scale in three steps from commercial ortho-aminobenzamide.

Gold-Catalyzed Selective 6-exo-dig and 7-endo-dig Cyclizations of Alkyn-Tethered Indoles To Prepare Rutaecarpine Derivatives.

An efficient method to synthesize rutaecarpine derivatives via the gold-catalyzed selective cyclization of alkyn-tethered indoles under mild conditions is described. The alkyn-tethered indole can undergo 6-exo-dig cyclization by oxidation and sequential gold catalysis, while it goes through 7-endo-dig cyclization by gold catalysis and sequential oxidation. Substrate scope studies reveal that the selectivity of cyclization was controlled by the substrates with sp3 and sp2 hybridization of carbon at the 2 position in quinazolinone. Furthermore, the rutaecarpine scaffold was prepared in 67% yield at gram scale easily in four steps from isatoic anhydride.

Complete mitochondrial genome of the guppy (Poecilia reticulata).

The guppy (Poecilia reticulata), a member of the Poeciliidae family, is one of the most popular aquarium fish. Here, we reported the complete mitochondrial genome of P. reticulata. The genome is 16,570 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The structure of non-coding control region was also analyzed. Comparing the mitochondrial genome of P. reticulata with its congener Xiphophorus maculatus revealed the high sequence similarity and the identical gene structure. The complete mitochondrial genome of the guppy would help study the evolution of Poeciliidae family.

The Chondrogenic Induction Potential for Bone Marrow-Derived Stem Cells between Autologous Platelet-Rich Plasma and Common Chondrogenic Induction Agents: A Preliminary Comparative Study.

The interests in platelet-rich plasma (PRP) and their application in stem cell therapy have contributed to a better understanding of the basic biology of the prochondrogenesis effect on bone marrow-derived stem cells (BMSCs). We aimed at comparing the effect of autologous PRP with common chondrogenic induction agents (CCIAs) on the chondrogenic differentiation of BMSCs. Rabbit BMSCs were isolated and characterized by flow cytometry and differentiated towards adipocytes and osteoblasts. The chondrogenic response of BMSCs to autologous PRP and CCIAs which included transforming growth factor-ß1 (TGF-ß1), dexamethasone (DEX), and vitamin C (Vc) was examined by cell pellet culture. The isolated BMSCs after two passages highly expressed CD29 and CD44 but minimally expressed CD45. The osteogenic and adipogenic differentiation potentials of the isolated BMSCs were also confirmed. Compared with common CCIAs, autologous PRP significantly upregulated the chondrogenic related gene expression, including Col-2, AGC, and Sox-9. Osteogenic related gene expression, including Col-1 and OCN, was not of statistical significance between these two groups. Thus, our data shows that, compared with common chondrogenic induction agents, autologous PRP can be more effective in promoting the chondrogenesis of BMSCs.

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio).

Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Common carp had a very recent fourth round of WGD dated to 8 million years ago. It therefore constitutes an ideal model to study early-stage functional divergence and expression differentiation in vertebrates. We identified 1,757 pairs of recently duplicated genes (RDGs) originating from this specific WGD and found that most ancestral genes were retained in duplicate. Most RDGs were conserved and under selective pressure. Gene expression analysis across six tissues revealed that 92.5% of RDG pairs were co-expressed in at least one tissue and that the expression of nearly half pairs ceased to be strongly correlated, indicating slow spatial divergence but rapid expression dissociation. Functional comparison revealed that 25% of pairs had functional divergence, of which neo- and sub-functionalization were the main outcomes. Our analysis revealed slow gene loss but rapid and intense expression and function differentiation after WGD.

L_RNA_scaffolder: scaffolding genomes with transcripts.

BACKGROUND: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments. RESULTS: We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased. CONCLUSIONS: The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.

Complete mitochondrial genome of Chinese sleeper, Perccottus glenii.

Chinese sleeper (Perccottus glenii) belongs to the largest vertebrate order, Perciformes. In this study, the complete mitochondrial genome of P. glenii was determined to be 16,487 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. We also analysed the sequence structure of non-coding control region. Comparing the mitochondrial genome of P. glenii with its congener Rhyacichthys aspro showed sequence similarity and the identical gene arrangement. The complete mitochondrial genome of Chinese sleeper provides the basis for the studies in Perciformes evolution and conservation.

[Effect of diamond film on infrared absorption properties of potassium nitrate].

The influence of diamond film on potassium nitrate infrared absorption was studied. The diamond film was grown on silicon substrates by hot filament chemical vapor deposition (CVD) method. The infrared absorption of potassium nitrate shows that the antisymmetric stretching vibrations v1 and v2 of nitrate are red-shifted by 30 and 13 cm(-1) respectively. The red-shift of v1 vibration is mainly attributed to the combination of diamond film with potassium nitrate and phonon resonance effects, and the red-shift of v2 vibration mode is attributed to the influence of potassium nitrate's internal stress.

[Effect of silver/silcon dioxide film on the infrared absorption properties of sodium nitrate].

Silver/silicon dioxide (Ag/SiO2) film, which was used for surface enhanced infrared absorption spectroscopy, was made by mixing ammonia solution and SiO2 solution. Surface morphology of thin films was depicted by scanning electron microscopy, X-ray diffraction and ultraviolet-visible absorption spectrum. The present paper studies the spectroscopy of Ag/SiO2 film during the evaporation of water. Research results show that the anti-symmetric vibration absorption peak of nitrate is the function of solution concentration and the distances. Influence of surface enhanced infrared absorption spectroscopy in nitrate absorption peak is via the electromagnetic mechanism and increasing the effective surface area.

Gas gangrene without wound: both lower extremities affected simultaneously.

Gas gangrene is a necrotizing soft tissue infection characterized by muscular necrosis and gas formation. It develops quickly and can cause septic shock and death. In adults, gas gangrene used to be a well-known complication of war wounds. Recently, cases of spontaneous or nontraumatic gas gangrene have been reported in both adults and children. We report a case of nontraumatic gas gangrene involving both the lower extremities simultaneously. Pathogenesis of this fatal soft tissue infection is discussed.We also review the diagnosis and treatment aspects of this entity.