Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: ( 1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; ( 2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks ( Tamias sibiricus), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (order Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

Comparative study of three short-chain neurotoxins from the venom of Naja kaouthia (Yunnan, China)

Three short-chain neurotoxins named NT-I, NT-II, and NT-III were purified from the venom of Naja kaouthia, a snake distributed throughout the south of Yunnan province, China, by a series of chromatographic steps, including an FPLC Resource S column. Their molecular weights, determined by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS, were 6952.19 Da, 6854.92 Da, and 6828.80 Da, respectively. NT-I consisted of 62 amino acid residues, and the other two consisted of 61 amino acid residues, including 8 cysteines. After hydrolysis by endoproteinase Glu-C, their primary sequences were determined. A test of their activities demonstrated that they effectively inhibited muscle contractions induced by electric stimulation. Furthermore, the extent of inhibition caused by NT-II and NT-III was less than that of NT-I. The IC(50)s were 0.04 mug/ml, 0.20 mug/ml, and 0.23 mug/ml for NT-I, NT-II, and NT-III, respectively. Compared with NT-II and NT-III, the higher activity of NT-I may be a result of the amino acid residue substitution Ile36 to Arg36.

细胞色素b基因序列与11种熊蜂的系统进化

通过比较一段357bp的细胞色素b的序列,分析了熊蜂属5亚属11种熊蜂系统发育关系。5亚属包括Bombus(5种)、Thoracobombus(3种)、Mendacibombus(1种)、Fervidobombus(1种)和Pyrobombus(1种)。该序列有65个单变异多态位点和71个简约信息多态位点,翻译成119个氨基酸序列后有45个氨基酸变异位点。根据P-距离构建的邻接树(NJ tree)和最大简约树(MP tree)都显示同样的结果:Mendacibombus(B. avinovielllus)分化最早;Fervidobombus(B. pensylvanicus)次之;Pyrobombus(B. impatiens)和Bombus形成姊妹群;Bombus亚属是单系群,其中B. ignitus在所研究的5个种中分化最早。

Frequency of the mtDNA 9-bp deletion in Chinese ethnic groups

The 9-bp deletion in the COII/tRNA(Lys) intergenic region (region V) of human mitochondrial DNA was screened in 1521 Chinese from 16 ethnic groups and 9 Hen geographic groups. The highest frequency was found in populations of Miao (32.4%) and Bouyei (30.8

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

Background: Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported. Results:

Anti-HIV-1 Activities of Hemslecins A and B

目的:研究从药用植物金佛山雪胆分离的雪胆素A和雪胆素B两个三萜类化合物的体外抗HIV活性.方法:应用合胞体抑制实验、p24抗原产生的抑制实验、慢性感染细胞和正常细胞间的细胞融合抑制实验等技术检测化合物的体外抗HIV-l活性;利用HIV-l逆转录酶、蛋白酶抑制实验,NCp7锌离子逐出实验探讨化合物的作用机制.结果:雪胆素A和雪胆素B在体外有较好的抑制HIV-l活性,其活性主要表现为:(1)抑制HIV-l诱导合胞体形成,EC50值分别为3.09 μg·mL-1和2.53μg·mL-1;(2)抑制HIV- 急性感染的C8106细胞p24抗原产生,EC50值分别为3.97μg·mL-1和18.90μg·mL-1;(3)抑制HIV-1 慢性感染H9与正常C8166细胞间融合,EC50分别为1.76μg·mL-1和11.95μg·mL-1.雪胆素A和雪胆素B对HIV-l逆转录酶、蛋白酶、NCp7锌离子逐出均没有抑制作用.雪胆素A对HIV-1整合酶有微弱的结合活性,而雪胆素B对HIV-1整合酶没有结合活性.在共培养实验中,雪胆素A和雪胆素B预处理C8166细胞组比未经预处理细胞组能够更有效的抑制HIV-l活性.结论:化合物雪胆素A和雪胆素B体外有较好的抗HIV-1活性,可能主要作用于HIV-1病毒进入细胞阶段.

Two New Phenolic Glycosides from Viscum articulatum

Two new phenolic glycosides, 1-O-benzyl-[5-O-benzoyl-beta-D-apiofuranosyl (1. 2)]-beta-D-glucopyranoside (1), and 4'-hydroxy-7,3'-dimethoxyflavan-5-O-beta-D-glucopyranoside (2), together with nine known flavanones 3 -11, have been isolated from the dried

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

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.

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 Activities of the Compounds Isolated from Polygonum cuspidatum and Polygonum multiflorum

The 70% EtOH extract of Polygonum cuspidatum showed inhibitory action against HIV-1-induced syncytium formation at non-cytotoxic concentrations in vitro with a 50% effective concentration (EC50) of 13.94 +/- 3.41 mu g/mL. Through bioactivity-guided fractionation, 20 phenolic compounds, including eight stilbenoids, were isolated from the roots of Polygonum cuspidatum, and their anti-HIV-1 activities were evaluated. Results showed that compounds 1, 13, 14, and 16 demonstrated fairly strong antiviral activity against HIV-1-induced cytopathic effects in C8166 lymphocytes at non-cytotoxic concentrations, with EC50 values of 4.37 +/- 1.96 mu g/mL, 19.97 +/- 5.09, 14.4 +/- 1.34 mu g/mL, and 11.29 +/- 6.26 mu g/mL and therapeutic index (TI) values of 8.12, > 10.02, > 13.89, and > 17.71, respectively. Other compounds showed either weak or no effects. Compound 6 also showed weak inhibition (153.42 +/- 19.25 mu g/mL); however, it possesses very good water solubility and showed almost no cytotoxicity (> 2000 mu g/mL), therefore achieving a fairly good TI (13.04). The activities of the two compounds (3 and 18) from Polygonum multiflorum were also assayed. The relationship between molecular structures and their bioactivities was also discussed.

Two new species of Rhagophthalmus Motschulsky (Coleoptera : Rhagophthalmidae) from Yunnan, south-western China, with notes on known, species

Rhagophthalmus fugongensis Li & Liang and Rhagophthalmus lufengensis Li & Ohba are introduced as new to science. The first record of R. tonkineus in China is provided. The male genitalia of R. gibbosulus and R. giganteus are described and illustrated. The female and larva of R. giganteus and the female of R. semisulcatus are illustrated. The distribution of Rhagophthalmus is discussed and a rectification of the relative arrangement of different parts of the male genitalia is provided (the base-piece is on the ventral side of the male genitalia, and the parameres on the dorsal side).

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