(鱼兆)科鱼类细胞色素b基因片段的序列测定及其系统发育的初步研究

从9种(鱼兆)科鱼类的福尔马林标本中获得了333 bp的细胞色素b基因片段的序列.这9个种分别代表(鱼兆)科鱼类的8个属.333 bp的DNA序列经MUST软件排序后,有101个变异位点,其中有39个信息位点.序列在成对物种间的距离为8～48.平均遗传距离为2.4%～14.4%.简约分析产生了最大简约系统树,其步长是162(CI=0.735,RI=0.494).在该系统树上,Bagarius是最原始的属,并与所有其他的物种形成姊妹群.其余8个属形成一个单系类群并分为二个姊妹群.尽管在形态上具有13个离征,但在分子系统树上,(鱼宴)(鱼兆)鱼类并未形成一个单系类群.可能的原因是333 bp序列中的星系信息位点太少;另外单从福尔马林浸制标本获得的DNA序列的可靠性尚有待进一步验证.     

Analysing branching pattern in plantations of young red oak trees (Quercus rubra L., Fagaceae)

Branching patterns of the growth units of monocyclic or bicyclic annual shoots on the main axis of 5-year-old red oaks were studied in a plantation in south-western France. For each growth unit, the production of axillary structures associated with each node was described in the form of a sequence. For a given category of growth units, homogeneous zones (i.e. zones in which composition in terms of type of axillary production does not change substantially) were identified on such sequences using a dedicated statistical model called a hidden semi-Markov chain. For instance, on the first growth unit of bicyclic annual shoots, a zone with 1-year-delayed branches was found systematically below a zone with buds and one-cycle-delayed branches. Branching patterns shown by the growth unit of monocyclic annual shoots and on the second growth unit of bicyclic annual shoots were very similar. Branches with a 1-year delay in development tended to be polycyclic at the top of the growth unit and monocyclic lower down. The number of nodes shown by the branched zone of the growth unit of monocyclic annual shoots was stable, irrespective of the total number of nodes of the growth unit. In contrast, the second growth unit of bicyclic annual shoots exhibited a correlation between the number of nodes in the branching zone and the total number of nodes. The contribution made by this method to understanding plant functioning is discussed.     

Cathelicidin family of antimicrobial peptides: proteolytic processing and protease resistance

Cathelicidins are a gene family of antimicrobial peptides produced as inactive precursors. Signal peptidase removes the N-terminal signal sequence, while peptidylglycine alpha-amidating monooxygenase often amidates and cleaves the C-terminal region. Removal of the cathelin domain liberates the active antimicrobial peptide. For mammalian sequences, this cleavage usually occurs through the action of elastase, but other tissue-specific processing enzymes may also operate. Once released, these bioactive peptides are susceptible to proteolytic degradation. We propose that some mature cathelicidins are naturally resistant to proteases due to their unusual primary structures. Among mammalian cathelicidins, proline-rich sequences should resist attack by serine proteases because proline prevents cleavage of the scissile bond. In hagfish cathelicidins, the unusual amino acid bromotryptophan may make the active peptides less susceptible to proteolysis for steric reasons. Such protease resistance could extend the pharmacokinetic lifetimes of cathelicidins in vivo, sustaining antimicrobial activity.     

Equilibrium folding and stability of myotrophin: a model ankyrin repeat protein

Proteins containing stretches of repeating amino acid sequences are prevalent throughout nature, yet little is known about the general folding and assembly mechanisms of these systems. Here we propose myotrophin as a model system to study the folding of ankyrin repeat proteins. Myotrophin is folded over a large pH range and is soluble at high concentrations. Thermal and urea denaturation studies show that the protein displays cooperative two-state folding properties despite its modular nature. Taken together with previous studies on other ankyrin repeat proteins, our data suggest that the two-state folding pathway may be characteristic of ankyrin repeat proteins and other integrated alpha-helical repeat proteins in general.     

Identification and characterization of C6orf37, a novel candidate human retinal disease gene on chromosome 6q14

We have identified a novel human gene, chromosome 6 open reading frame 37 (C6orf37), that is expressed in the retina and maps to human chromosome 6q14, a genomic region that harbors multiple retinal disease loci. The cDNA sequence contains an open reading frame of 1314 bp that encodes a 437-amino acid protein with a predicted molecular mass of 49.2 kDa. Northern blot analysis indicates that this gene is widely expressed, with preferential expression observed in the retina compared to other ocular tissues. The C6orf37 protein shares homology with putative proteins in R. norvegicus, M. musculus, D. melanogaster, and C. elegans, suggesting evolutionary conservation of function. Additional sequence analysis predicts that the C6orf37 gene product is a soluble, globular cytoplasmic protein containing several conserved phosphorylation sites. Furthermore, we have defined the genomic structure of this gene, which will enable its analysis as a candidate gene for chromosome 6q-associated inherited retinal disorders.     

Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences

We estimated the genome size of Korean ginseng ( Panax ginseng C.A. Meyer), a medicinal herb, constructed a Hin dIII BAC library, and analyzed BAC-end sequences to provide an initial characterization of the library. The 1C nuclear DNA content of Korean ginseng was estimated to be 3.33 pg (3.12×10³ Mb). The BAC library consists of 106,368 clones with an average size of 98.61 kb, amounting to 3.34 genome equivalents. Sequencing of 2167 BAC clones generated 2492 BAC-end sequences with an average length of 400 bp. Analysis using BLAST and motif searches revealed that 10.2%, 20.9% and 3.8% of the BAC-end sequences contained protein-coding regions, transposable elements and microsatellites, respectively. A comparison of the functional categories represented by the protein-coding regions found in BAC-end sequences with those of Arabidopsis revealed that proteins pertaining to energy metabolism, subcellular localization, cofactor requirement and transport facilitation were more highly represented in the P. ginseng sample. In addition, a sequence encoding a glucosyltransferase-like protein implicated in the ginsenoside biosynthesis pathway was also found. The majority of the transposable element sequences found belonged to the gypsy type (67.6%), followed by copia (11.7%) and LINE (8.0%) retrotransposons, whereas DNA transposons accounted for only 2.1% of the total in our sequence sample. Higher levels of transposable elements than protein-coding regions suggest that mobile elements have played an important role in the evolution of the genome of Korean ginseng, and contributed significantly to its complexity. We also identified 103 microsatellites with 3–38 repeats in their motifs. The BAC library and BAC-end sequences will serve as a useful resource for physical mapping, positional cloning and genome sequencing of P. ginseng.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by M.-A. Grandbastien     

Phylogenetic relationships among genera of Massonieae (Hyacinthaceae) inferred from plastid DNA and seed morphology

The tribe Massonieae Baker (Hyacinthaceae-Hyacinthoideae) presently consists of about 19 genera and 230 species distributed from Africa (south of the Sahara) to Madagascar and India. Based on atpB and trnL-F DNA sequences the tribe is monophyletic only when the genus Pseudoprospero is excluded from Massonieae. In most trnL-F trees, this genus occupies a basal position within subfamily Hyacinthoideae and is sister to the rest of the subfamily. Molecular data suggest that the remaining genera of Massonieae do not share common ancestry with the Eurasian/North-African tribe Hyacintheae Dumort. (Scilla, Hyacinthus and allies), and thus a narrow concept of the essentially Eurasian genus Scilla is supported. Members of well-supported clades in Massonieae usually show similarities in seed characteristics as determined by scanning electron microscopy. Phylogenetic position and seed morphology indicate that Massonia angustifolia and M. zeyheri do not belong to the genus Massonia but fall into a clade together with Daubenya, Androsiphon and Amphisiphon. The genus Whiteheadia appears paraphyletic in the 50% majority rule trnL-F tree and occupies a basal position next to Massonia. However, in the strict consensus tree neither monophyly nor polyphyly can be excluded for this genus. Seed appendages are documented for members of the genera Ledebouria and Lachenalia. Within the genera of Massonieae there is a tendency towards bending of the seed axis. This phenomenon is most obvious within the genus Lachenalia. Delimitation of genera based on seed morphology largely agrees with the results of molecular studies. Correlation between number, size and color of seeds, geographical distribution and phylogenetic position of the genera are discussed. Electronic Publication     

GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations

A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods. The program and data can be downloaded from http://pondside.uchicago.edu/~lilab/ and http://webcollab.iis.sinica.edu.tw/~biocom.     

Molecular relatedness within the “Ascochyta pinodes-complex”

The morphological, molecular and pathological characters of 34 isolates identified as Ascochyta pinodes, A. phaseolorum, and Phoma medicaginis var. pinodella were determined. Initial molecular findings, based on PCR fragment size and RFLPs of sections of the mitochondrial genome, the rRNA gene cluster and the beta-tubulin gene complex, were further investigated by sequencing of the total rRNA ITS regions. Isolates were homogenous for all characteristics determined, with the exception of conidial size and septation, and RFLPs of AT rich (presumptive mitochondrial) DNA. The results suggest that the isolates represent host preferential forms of a single taxon, and this finding is discussed in relation to the known teleomorphs and reference material of the species studied.