The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

The chloroplast genome of the moss Haplocladium microphyllum, first in family Thuidiaceae

Bryophytes are a highly diverse group containing more than 12,800 species. Haplocladium microphyllum is in a large moss belonging to the family Thuidiaceae. We report the complete chloroplast (124,478 bp) genome sequence of H. microphyllum, it includes a pair of inverted repeat regions (IRs, 9727 bp), one large single-copy (LSC, 86,528 bp) region, and one small single-copy (SSC, 18,496 bp) region. Besides, the complete chloroplast genome contains 134 genes in total, including 88 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that H. microphyllum has the closest relationship with Sanionia uncinata in Amblystegiaceae. Our study lays a foundation for further research like speciation of this species and the phylogeny of the Thuidiaceae family

Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants (<i>Rosa chinensis</i>)

The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development

Highly Electron-Deficient Hexaazapentacenes and Their Dihydro Precursors

Novel silylethynylated <i>N</i>-heteropentacenes that have three adjacent pyrazine rings at the center of a pentacene backbone are reported. These hexaazapentacenes exhibit a record low energy level of lowest unoccupied molecular orbital (LUMO) for <i>N</i>-heteropentacenes and thus are able to oxidize dihydroanthracene to anthracene. Their synthetic precursors are the corresponding dihydrohexaazapentacenes, which exhibit interesting H-bonding

Vinyl Phosphate-Functionalized, Magnetic, Molecularly-Imprinted Polymeric Microspheres’ Enrichment and Carbon Dots’ Fluorescence-Detection of Organophosphorus Pesticide Residues

The rapid detection of organophosphorus pesticide residues in food is crucial to food safety. One type of novel, magnetic, molecularly-imprinted polymeric microsphere (MMIP) was prepared with vinyl phosphate and 1-octadecene as a collection of dual functional monomers, which were screened by Gaussian09W molecular simulation. MMIPs were used to enrich organic phosphorus, which then detected by fluorescence quenching in vinyl phosphate-modified carbon dots (CDs@VPA) originated from anhydrous citric acid. MMIPs and CDs@VPA were characterized by TEM, particle size analysis, FT-IR, VSM, XPS, adsorption experiments, and fluorescence spectrophotometry in turn. Through the fitting data from experiment and Gaussian quantum chemical calculations, the molecular recognition properties and the mechanism of fluorescence detection between organophosphorus pesticides and CDs@VPA were also investigated. The results indicated that the MMIPs could specifically recognize and enrich triazophos with the saturated adsorption capacity 0.226 mmol g&minus;1, the imprinting factor 4.59, and the limit of recognition as low as 0.0006 mmol L&minus;1. Under optimal conditions, the CDs@VPA sensor has shown an extensive fluorescence property with a LOD of 0.0015 mmol L&minus;1 and the linear range from 0.0035 mmol L&minus;1 to 0.20 mmol L&minus;1 (R2 = 0.9988) at 390 nm. The mechanism of fluorescence detection of organic phosphorus with CDs@VPA sensor might be attributable to hydrogen bonds formed between heteroatom O, N, S, or P, and the O&minus;H group, which led to fluorescent quenching. Meanwhile, HN&minus;C=O and Si&minus;O groups in CDs@VPA system might contribute to cause excellent blue photoluminescence. The fluorescence sensor was thorough successfully employed to the detection of triazophos in cucumber samples, illustrating its tremendous value towards food sample analysis in complex matrix

Research Status and Prospect of Non-Viral Vectors Based on siRNA: A Review

Gene therapy has attracted much attention because of its unique mechanism of action, non-toxicity, and good tolerance, which can kill cancer cells without damaging healthy tissues. siRNA-based gene therapy can downregulate, enhance, or correct gene expression by introducing some nucleic acid into patient tissues. Routine treatment of hemophilia requires frequent intravenous injections of missing clotting protein. The high cost of combined therapy causes most patients to lack the best treatment resources. siRNA therapy has the potential of lasting treatment and even curing diseases. Compared with traditional surgery and chemotherapy, siRNA has fewer side effects and less damage to normal cells. The available therapies for degenerative diseases can only alleviate the symptoms of patients, while siRNA therapy drugs can upregulate gene expression, modify epigenetic changes, and stop the disease. In addition, siRNA also plays an important role in cardiovascular diseases, gastrointestinal diseases, and hepatitis B. However, free siRNA is easily degraded by nuclease and has a short half-life in the blood. Research has found that siRNA can be delivered to specific cells through appropriate vector selection and design to improve the therapeutic effect. The application of viral vectors is limited because of their high immunogenicity and low capacity, while non-viral vectors are widely used because of their low immunogenicity, low production cost, and high safety. This paper reviews the common non-viral vectors in recent years and introduces their advantages and disadvantages, as well as the latest application examples

Hydrogen-Bonded Dihydrotetraazapentacenes

Three new members of <i>N</i>-heteropentacenes explored herein have adjacent pyrazine and dihydropyrazine rings at one end of the pentacene backbone. Interesting findings from this study include self-complementary N–H···N H-bonds in the solid state, solvent-dependent UV–vis absorption caused by H-bonding, and new <i>p</i>-type organic semiconductors with field effect mobility up to 0.7 cm² V^–1 s^–1