Karyotype Differentiation in Newly Discovered Members of the Drosophila obscura Species Group from Yunnan , China

观察了新近发现于我国云南的果蝇属暗果蝇种组( Drosophila obscura species group ) 种类 D1luguensis 、D1 dianensis 和D1limingi 的有丝分裂中期核型, 并将3 个种的核型与各自的近缘种类进行了比较。 D1luguensis 具2n = 12 条染色体, 包括3 对中央着丝粒(V 形) 染色体、2 对近端着丝粒(棒状) 染色体以及1 对微小(点状) 染色体。其中X 和Y染色体均为中央着丝粒染色体。D1 dianensis 和D1limingi 具2n = 10 条染 色体, 包括1 对大的V 形常染色体, 1 对小的V 形常染色体, 2 对J 形(亚中着丝粒型) 常染色体和1 对点状染 色体。其中X 染色体为J 形, Y染色体为短棒状。基于核型比较的结果以及D1sinobscura 亚组地理分布的资料, 结合种间系统发育关系研究结果, 认为D1 luguensis 可能保留了该亚组祖先种类的核型。D1sinobscura 的核型(2n = 12 : 2V , 1J , 2R , 1D) 可能由一个pre2“sinobscura2hubeiensis”谱系的一个分支通过臂间倒位演化而来, 而D1 hubeiensis 的核型(2n = 10 : 4V , 1D) 可能由该谱系的另一分支通过着丝粒融合(2 对近端着丝粒常染色 体的融合) 而形成。推测在D1 dianensis 和近缘欧洲种D1subsilvestris (2n = 12 : 3V , 2R , 1D) 间、D1limingi 和 东亚近缘种D1tsukubaensis (2n = 12 : 3V , 2R , 1D) 间的物种分化过程中, 可能有相似的染色体变异类型发生。

X(3915) and X(4350) as New Members in the P-Wave Charmonium Family

The analysis of the mass spectrum and the calculation of the strong decay of P-wave charmonium states strongly purport to explain the newly observed X(3915) and X(4350) as new members in the P-wave charmonium family, i.e., chi'(c0) for X(3915) and chi ''(c2) for X(4350). Under the P-wave charmonium assignment to X(3915) and X(4350), the J(PC) quantum numbers of X(3915) and X(4350) must be 0(++) and 2(++) respectively, which provide important criteria to test the P-wave charmonium explanation for X(3915) and X(4350) proposed by this Letter. The decay behavior of the remaining two P-wave charmonium states with the second radial excitation is predicted, and an experimental search for them is suggested.

Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities

Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by extracting diagnostic molecular species such as fatty acids and nucleic acids from the community and determining which specific molecules have incorporated the isotope. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. Stable isotope probing allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This short review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

A novel family of antimicrobial peptides from the skin of Amolops loloensis

While conducting experiments to investigate antimicrobial peptides of amphibians living in the Yunnan-Sichuan region of southwest China, a new family of antimicrobial peptides was identified from skin secretions of the rufous-spotted torrent frog, Amolops loloensis. Members of the new peptide family named amolopins are composed of 18 amino acids with a unique sequence, for example, NILSSIVNGINRALSFFG. By BLAST search, amolopins did no show similarity to any known peptides. Among the tested microorganisms, native and synthetic peptides only showed antimicrobial activities against Staphylococcus aureus ATCC2592 and Bacillus pumilus, no effects on other microorganisms. The CD spectroscopy showed that it adopted a structure of random combined with beta-sheet in water, Tris-HCl or Tris-HCl-SDS. Several cDNAs encoding amolopins were cloned from the skin cDNA library of A. loloensis. The precursors of amolopin are composed of 62 amino acid residues including predicted signal peptides, acidic propieces, and mature antimicrobial peptides. The preproregion of amolopin precursor comprises a hydrophobic signal peptide of 22 residues followed by an 18 residue acidic propiece which terminates by a typical prohormone processing signal Lys-Arg. The preproregions of precursors are very similar to other amphibian antimicrobial peptide precursors but the mature amolopins are different from other antimicrobial peptide families. The remarkable similarity of preproregions of precursors that give rise to very different antimicrobial peptides in distantly related frog species suggests that the corresponding genes form a multigene family originating from a common ancestor. (C) 2008 Elsevier Masson SAS. All rights reserved.

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.

On the origin of new genes in Drosophila

Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns

A review of the Chinese species of Crossocheilus, with description of a new species (Ostariophysi : Cyprinidae)

Fishes of the genus Crossocheilus in China is reviewed on the basis of specimens in Kunming Institute of Zoology, Chinese Academy of Sciences. Crossocheilus multirastellus is described from the upper Irrawaddy and upper Salween rivers. It is distinguished from all of its congeners by having two black longitudinal stripes on sides of body, 36-38 lateral line scales, 18-25 gill rakers, anus at midpoint between ventral fin and anal fin insertions, ventral fin extending over anus, a large deep blue rhomboid spot above the pectoral fin, and a straight mouth gape almost equal to head width. There are presently two species of Crossocheilus fishes in China. Crossocheilus bamaensis Fang and Crossocheilus liuchengensis Liang, Liu & Wu are recognized here as members of the genus Sinocrossocheilus.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Molecular phylogenetics of the family Cyprinidae (Actinopterygii : Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichotvensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages. (c) 2008 Published by Elsevier Inc.

Characterization of complete genome sequence of the spring viremia of carp virus isolated from common carp (Cyprinus carpio) in China

The complete genome of spring viraemia of carp virus (SVCV) strain A-1 isolated from cultured common carp (Cyprinus carpio) in China was sequenced and characterized. Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed and the DNA was sequenced. It showed that the entire genome of SVCV A-1 consists of 11,100 nucleotide base pairs, the predicted size of the viral RNA of rhabdoviruses. However, the additional insertions in bp 4633-4676 and bp 4684-4724 of SVCV A-1 were different from the other two published SVCV complete genomes. Five open reading frames (ORFs) of SVCV A-1 were identified and further confirmed by RT-PCR and DNA sequencing of their respective RT-PCR products. The 5 structural proteins encoded by the viral RNA were ordered 3'-N-P-M-G-L-5'. This is the first report of a complete genome sequence of SVCV isolated from cultured carp in China. Phylogenetic analysis indicates that SVCV A-1 is closely related to the members of the genus Vesiculovirus, family Rhabdoviridae.

Reevaluation of the phylogenetic relationship between Mobilid and Sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences

Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae.

Echolocation signals of the free-ranging Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientialis)

This paper describes the high-frequency echolocation signals from free-ranging Yangtze finless porpoise in the Tian-e-zhou Baiji National Natural Reserve in Hubei Province, China. Signal analysis showed that the Yangtze finless porpoise clicks are typical high-frequency narrow-band (relative width of the frequency spectrum Q=6.6 &PLUSMN; 1.56, N=548) ultrasonic pulses. The peak frequencies of the typical clicks range from 87 to 145 kHz with an average of 125 &PLUSMN; 6.92 kHz. The durations range from 30 to 122 μ s with an average of 68 &PLUSMN; 14.12 μ s. The characteristics of the signals are similar to those of other members of the Phocoenidae as well as the distantly related delphinids, Cephalorhynchus spp. Comparison of these signals to those of the baiji (Lipotes vexillifer), who occupies habitat similar to that of the Yangtze finless porpoise, showed that the peak frequencies of clicks produced by the Yangtze finless porpoise are remarkably higher than those produced by the baiji. Difference in peak frequency between the two species is probably linked to the different size of prefer-red prey fish. Clear double-pulse and multi-pulse reverberation structures of clicks are noticed, and there is no indication of any low-frequency (< 70 kHz) components during the recording period. © 2005 Acoustical Society of America.

New species of Doliodrilus and other Limnodriloidinae (Oligochaeta, Tubificidae) from Hainan and other parts of the north-west Pacific Ocean

Thirteen species of Limnodriloidinae (Tubificidae) are recorded from marine and brackish-water habitats of Hainan Island, southern China, including 11 species of Doliodrilus and two species belonging to Limnodriloides . Eight species are new to science: D. bisaccus sp. n. (types from Japan), D. longidentatus sp. n. (types from Hong Kong), D. ciliatus sp. n., D. adiacens sp. n., D. fibrisaccus sp. n. (also from Fiji), D. brachyductus sp. n., D. bidolium sp. n. and D. chinensis sp. n. In addition, material of D. puertoricensis Erseus and Milligan, 1988, from New Caledonia, is briefly described. This study shows that Doliodrilus is unexpectedly species-rich in Asian seas, in particular, around Hainan. Including an unnamed species from this island, the known members of this genus increase from three to 12.

PURIFICATION AND CHARACTERIZATION OF A KINASE SPECIFIC FOR THE SERINE-RICH AND ARGININE-RICH PRE-MESSENGER-RNA SPLICING FACTORS

Members of the SR family of pre-mRNA splicing factors are phosphoproteins that share a phosphoepitope specifically recognized by monoclonal antibody (mAb) 104. Recent studies have indicated that phosphorylation may regulate the activity and the intracellular localization of these splicing factors. Here, we report the purification and kinetic properties of SR protein kinase 1 (SRPK1), a kinase specific for SR family members. We demonstrate that the kinase specifically recognizes the SR domain, which contains serine/arginine repeats. Previous studies have shown that dephosphorylated SR proteins did not react with mAb 104 and migrated faster in SDS gels than SR proteins from mammalian cells. We show that SRPK1 restores both mobility and mAB 104 reactivity to a SR protein SF2/ASF (splicing factor 2/alternative splicing factor) produced in bacteria, suggesting that SRPK1 is responsible for the generation of the mAb 104-specific phosphoepitope in vivo. Finally, we have correlated the effects of mutagenesis in the SR domain of SF2/ASF on splicing with those on phosphorylation of the protein by SRPK1, suggesting that phosphorylation of SR proteins is required for splicing.