Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes

Chimeric RNAs have been reported in varieties of organisms and are conventionally thought to be produced by trans-splicing of two or more distinct transcripts. Here, we conducted a large-scale search for chimeric RNAs in the budding yeast, fruit fly, mous

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Recombination Yet Inefficient Selection along the Drosophila melanogaster Subgroup's Fourth Chromosome

A central goal of evolutionary genetics is an understanding of the forces responsible for the observed variation, both within and between species. Theoretical and empirical work have demonstrated that genetic recombination contributes to this variation by breaking down linkage between nucleotide sites, thus allowing them to behave independently and for selective forces to act efficiently on them. The Drosophila fourth chromosome, which is believed to experience no-or very low-rates of recombination has been an important model for investigating these effects. Despite previous efforts, central questions regarding the extent of recombination and the predominant modes of selection acting on it remain open. In order to more comprehensively test hypotheses regarding recombination and its potential influence on selection along the fourth chromosome, we have resequenced regions from most of its genes from Drosophila melanogaster, D. simulans, and D. yakuba. These data, along with available outgroup sequence, demonstrate that recombination is low but significantly greater than zero for the three species. Despite there being recombination, there is strong evidence that its frequency is low enough to have rendered selection relatively inefficient. The signatures of relaxed constraint can be detected at both the level of polymorphism and divergence.

Tetranorclerodanes and clerodane-type diterpene glycosides from Dicranopteris dichotoma

The acetone extract of Dicranopteris dichotoma afforded two new tetranorclerodanes, 18-hydroxyaylthonic acid (1) and 18-oxo-aylthonic acid (2), and four new clerodane-type diterpene glycosides, (6S,13S)-6-O-[6-O-acetyl-beta-D-glucopyranosyl-(1 -> 4)-alpha

Przewalskin B, a novel diterpenoid with an unprecedented skeleton from Salvia przewalskii maxim

[GRAPHIC] Przewalskin B (1), a novel diterpenoid possessing a unique skeleton, was isolated from a Chinese medicinal plant Salvia przewalskii. Its structure and relative stereochemistry were elucidated by extensive NMR analysis and a single-crystal X-ray

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

Aim: To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide, N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide, as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) bindi

Three new compounds from Kadsura longipedunculata

Two new tetrahydrofuran lignans, kadlongirins A and B (1, 2), a new cadinane-type sesquiterpenoid, 2,7-dihydroxy-1 1,1 2-dehydrocalamenene (3), together with seven known lignans, grandisin, fragransin B-1, vladirol F, kadsuralignan C, otobaphenol, isoanwu

Piezo-assisted nuclear transfer affects cloning efficiency and may cause apoptosis

Even though it generates healthy adults, nuclear transfer in mammals remains an inefficient process. Mainly attributed to abnormal reprograming of the donor chromatin, this inefficiency may also be caused at least partly by a specific effect of the clonin

HSPC117 deficiency in cloned embryos causes placental abnormality and fetal death

Somatic cell nuclear transfer (SCNT) has been successfully used in many species to produce live cloned offspring, albeit with low efficiency. The low frequency of successful development has usually been ascribed to incomplete or inappropriate reprogramming of the transferred nuclear genome. Elucidating the genetic differences between normal fertilized and cloned embryos is key to understand the low efficiency of SCNT. Here, we show that expression of HSPC117, which encodes a hypothetical protein of unknown function, was absent or very low in cloned mouse blastocysts. To investigate the role of HSPC117 in embryo development, we knocked-down this gene in normal fertilized embryos using RNA interference. We assessed the post-implantation survival of HSPC117 knock-down embryos at 3 stages: E9 (prior to placenta formation); E12 (after the placenta was fully functional) and E19 (post-natal). Our results show that, although siRNA-treated in vivo fertilized/produced (IVP) embryos could develop to the blastocyst stage and implanted without any difference from control embryos, the knock-down embryos showed substantial fetal death, accompanied by placental blood clotting, at E12. Furthermore, comparison of HSPC117 expression in placentas of nuclear transfer (NT), intracytoplasmic sperm injection (ICSI) and IVP embryos confirmed that HSPC117 deficiency correlates well with failures in embryo development: all NT embryos with a fetus, as well as IVP and ICSI embryos, had normal placental HSPC117 expression while those NT embryos showing reduced or no expression of HSPC117 failed to form a fetus. In conclusion, we show that HSPC117 is an important gene for post-implantation development of embryos, and that HSPC117 deficiency leads to fetal abnormalities after implantation, especially following placental formation. We suggest that defects in HSPC117 expression may be an important contributing factor to loss of cloned NT embryos in vivo. (C) 2010 Elsevier Inc. All rights reserved.

Velleratretraol, an unusual highly functionalized lactarane sesquiterpene from Lactarius vellereus

An unusual highly functionalized lactarane sesquiterpene, named velleratretraol (1), was isolated from the ethanol extract of the fruiting body of the mushroom Lactarius vellereus. Its structure was determined through spectroscopic analysis and single-cry

Lycojapodine A, a Novel Alkaloid from Lycopodium japonicum

Lycojapodine A, a novel C16N-type Lycopodium alkaloid with an unprecedented 6/6/6/7 tetracyclic ring system, was isolated from the club moss Lycopodium japonicum. The structure and relative stereochemistry were elucidated on the basis of spectroscopic dat

Anti-HIV-1 Activity of Lignans from the Fruits of Schisandra rubriflora

This study investigated the 70% aqueous acetone extract of the fruits of Schisandra rubriflora which led to the isolation of eight lignans, including a new isolate, rubrisandrin C (1), and seven known lignans (2-8). The structure of 1 was established by extensive 1D and 2D NMR spectroscopy and its absolute stereochemistry was determined by CD spectrum. Compounds 1-5 and 7-8 were evaluated for their anti-HIV-1 activity that showed inhibitory activity on HIV-1(IIIB) induced syncytium formation with EC50 values in the range of 2.26 similar to 20.4 mu g/mL. Compounds 1 and 7 exerted their obvious protection of HIV-1(IIIB) inducted MT-4 host cells lytic effects with a selectivity index of 15.4 and 24.6, respectively.

Chemical Constituents from the Leaves and Stems of Schisandra rubriflora

Six new nortriterpenoids, schirubridilactones A-F (1-6). as well as 14 known compounds, were isolated from the leaves and stems of Schisandra rubriflora. The Structures of 1-6 were elucidated oil the basis of spectroscopic methods including HSQC, HMBC, H-1-H-1 COSY, and ROESY NMR experiments. The relative stereochemistry of I was confirmed through single-crystal X-ray analysis. In addition, compounds 1-6 showed anti-HIV-1 activity with EC50 values in the range 14.3-80.8 mu g/mL and Selectivity indices in the range 2.2-9.0.

Assessing functioning of the prefrontal cortical subregions with auditory evoked potentials in sleep-wake cycle

Our previously observations showed that the amplitude of cortical evoked potentials to irrelevant auditory stimulus (probe) recorded from several different cerebral areas was differentially modulated by brain states. At present study, we simultaneously re