Genetic diversity analysis of grapevine rupestris stem pitting-associated virus from grapevine by colony PCR-SSCP and -RFLP.

We have developed methods for detecting the genetic diversity of grapevine rupestris stem pitting-associated virus (GRSPaV) based on restriction fragment length polymorphism (RFLP) and single stranded conformational polymorphism (SSCP) in the 905 nt 3' sequence. The amplicons were cloned from six grapevine cultivars, and colony polymerase chain reaction (colony PCR) using recombination bacteria was subsequently analyzed by RFLP and SSCP. Four haplotypes of SSCP and six haplotypes of Sac I RFLPs were defined. The two methods had a 40% discrepancy rate in showing the degree of diversity. All clones were sequenced and were used to construct a phylogenetic tree with seven previously reported GRSPaV sequences. In the tree, all the newly acquired sequences were divided into three clusters, I, II, and III, which corresponded to haplotypes I, II, and III of SSCP, respectively. Haplotype IV of SSCP was grouped into cluster II. A recombination analysis showed that haplotype IV has undergone a recombination event. Together, these results indicate that the SSCP assay is useful for the rapid identification of genetic diversity of GRSPaV. This is the first report of an analysis of the large fragment of GRSPaV by colony PCR-SSCP. Keywords: grapevine; grapevine rupestris stem pitting-associated virus (GRSPaV); RFLP; SSCP; genetic diversity analysis.

Self-assemblies of TTF derivatives programmed by alkyl chains and functional groups.

Tetrathiafulvalenes (TTFs) are a class of important functional materials whose intermolecular interaction, which will contribute to constructing a supramolecular structure, still needs further understanding. In this study, the self-assembly behavior and structure of a series of TTFs bearing different alkyl chains and substituents were investigated by scanning tunneling microscopy (STM) in combination with density functional theory (DFT) calculations. Contrary to previous reports, herein, a series of benzoic acid-functionalized TTFs (CnTTFCOOH) and pyridine-functionalized TTFs (CnTTFN) with different lengths of alkyl chains have been substituted on the sulfur atom, where n is equal to 8, 10, 14, or 16. Due to the weak intra- and intermolecular interactions, CnTTFN (n = 8 and 10) molecules cannot be observed during STM scanning. For other cases, various self-assembled monolayers with different nanostructures were observed depending on different substituents. The results reveal that the alkyl chains and functional groups on the TTF skeleton synergistically affect the molecular self-assembly process, which results from the synergism of van der Waals, hydrogen bonding, and SS interactions. These results not only help to explain the relationship between structures and properties, but also help to design better molecular structures for various fields.

Occurrence and genetic diversity analysis of apple stem pitting virus isolated from apples in China.

Two primer pairs were used to detect apple stem pitting virus (ASPV) using a reverse transcription (RT)-PCR test. 82 out of the 141 randomly collected samples, from ten orchards in five provinces and regions of China, tested positive. In the positive samples forty-five (55%) were infected by ASPV and two other viruses. The full coat protein (CP) and the triple gene block (TGB) gene 1, 2 and 3 of partial ASPV isolates were subsequently cloned. The nucleotide and amino acid identities of 39 CP sequence variants from 31 Chinese apple samples were compared with that of previously reported ASPV isolates and were 67.4-96.0% and 68.4-97.7%, respectively. All ASPV sequence variants from Chinese apples separated into two clades with CP- and TGB-based phylogenetic trees, whilst the grouping of TGB2 and TGB3 trees was the same. Three recombinants (FS06-2, X5-2, and XLF-C-2) for CP and six (TH2-5, X8-2, FS05-2, X6-2 and XLF-A-1) recombinants for TGB were identified from the Chinese apple isolates. Two recombinants were found in the TGB sequence of isolate XLF-A-1. The results presented here may assist in the development of a more comprehensive screening tool for apple viruses.

Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♀ × E. lanceolatus♂).

BACKGROUND: Groupers (Epinephelus spp.) have been widely cultivated in China and South-East Asian countries. As a novel hybrid offspring crossed between E. fuscogutatus♀ and E. lanceolatus♂, Hulong grouper exhibits significant growth superiority over its female parent, which made it a promising farmed species in grouper aquaculture industry in China. Hulong grouper present a good combination of beneficial traits from both parent species, but the molecular mechanisms of its heterosis still remain poorly understood. RESULTS: Based on RNA sequencing and gene expression profiling, we conducted comparative transcriptome analyses between Hulong grouper and its parents E. fuscoguttatus & E. lanceolatus. Six hundred sixty-two and 5239 differentially expressed genes (DEGs) were identified in the brains and livers, respectively. GO enrichment analysis of these DEGs revealed that metabolic process and catalytic activity were the most enriched GO terms. Further analysis showed the expressions of GnRH1 and GnRH3 in the brain, and GH/IGF axis related genes such as IGF-1, IGF-2b, IGFBP-1, IGFBP-2, IGFBP-4 and IGFBP-5a in the liver of the hybrid F1 were significantly up-regulated, which is in accordance with the growth superiority of hybrid grouper. Meanwhile, expressions of genes related to the protein and glycogen synthesis pathway, such as PI3KC, PI3KR, Raptor, EIF4E3, and PP1 were up-regulated, while PYG expression was down-regulated. These changes might contribute to increased protein and glycogen synthesis in the hybrid grouper. CONCLUSIONS: We identified a number of differentially expressed genes such as GnRH1 and GnRH3, and genes involved in GH/IGF axis and its downstream signaling pathways for protein and glycogen synthesis in Hulong Grouper. These findings provided molecular basis underlying growth superiority of hybrid grouper, and comprehensive insights into better understanding the molecular mechanisms and regulative pathways regulating heterosis in fish.

Molecular characterizations of two grapevine rupestris stem pitting-associated virus isolates from China.

The complete nucleotide sequences of two isolates of grapevine rupestris stem pitting-associated virus (LSL and JF) collected from grapevine of Xingcheng in Liaoning Province, China, were determined. The genomes of both LSL and JF were found to contain five open reading frames (ORFs). Sequence alignments showed that the genomic sequences of JF were 76.1 %-83.5 % identical to the other ten GRSPaV isolates that have been reported previously and that the nucleotide sequence identity of isolate LSL to other isolates was no more than 78 %. Phylogenetic analysis based on the complete genome sequence indicated that JF belongs to group III and that LSL belongs to a new group (group IV). The average genetic distances of the new genetic lineage from groups I, II and III were 0.34, 0.32 and 0.33, respectively.

Association between reversal in the expression of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel and age-related atrial fibrillation.

BACKGROUND: We compared cardiac electrophysiological indicators and regional expression levels of cardiac hyperpolarization-activated cyclic nucleotide-gated (HCN) channels between adult and aged dogs to identify possible mechanisms of age-related atrial fibrillation. MATERIAL/METHODS: Corrected sinus node recovery time (SNRTc) and effective refractory period (ERP) of the atrium and pulmonary veins were measured in 10 adult (3-6 years old) and 10 aged dogs (>9 years old). Expression levels of HCN2 and HCN4 channel mRNAs and proteins were measured in the sinoatrial node, atrium, and pulmonary veins by real-time PCR and Western blotting. RESULTS: Aged dogs exhibited a higher induction rate of atrial fibrillation (AF) in response to electrical stimulation, longer AF duration after induction, longer SNRTc, longer right atrial effective refractory period (AERP), shorter left AERP, and increased AERP dispersion compared to adults. Expression levels of HCN2 and HCN4 channel mRNAs and proteins were lower in the sinoatrial node but higher in the atrium and pulmonary veins of aged dogs. CONCLUSIONS: Changes in atrial electrophysiological indicators in aged dogs revealed sinoatrial node dysfunction. There was a reversal in the local tissue distribution of HCN2 and HCN4 channel mRNA and protein, a decrease in sinoatrial node expression, and increase in atrial and pulmonary vein expression with age. Changes in atrial electrophysiological characteristics and regional HCN channel expression patterns were associated with the onset and maintenance of age-related atrial fibrillation.