A novel short neurotoxin, cobrotoxin c, from monocellate cobra (Naja kaouthia) venom: isolation and purification, primary and secondary structure determination, and tertiary structure modeling

A novel short neurotoxin, cobrotoxin c (CBT C) was isolated from the venom of monocellate cobra (Naja kaouthia) using a combination of ion-exchange chromatography and FPLC. Its primary structure was determined by Edman degradation. CBT C is composed of 61 amino acid residues. It differs from cobrotoxin b (CBT B) by only two amino acid substitutions, Thr/Ala11 and Arg/Thr56, which are not located on the functionally important regions by sequence similarity. However, the LD50 is 0.08 mg/g to mice, i.e. approximately five-fold higher than for CBT B. Strikingly, a structure-function relationship analysis suggests the existence of a functionally important domain on the outside of Loop III of CBT C. The functionally important basic residues on the outside of Loop III might have a pairwise interaction with alpha subunit, instead of gamma or delta subunits of the nicotinic acetylcholine receptor (nAChR). (C) 2002 Elsevier Science Inc. All rights reserved.

Molecular Phylogeny of Slow Lorises ( Nycticebus) Revealed by D2loop Sequences and Complete Cytochrome bGene Sequences of Mitochondrial DNA

本研究测定了懒猴属( Nycticebus) D 环的部分序列和细胞色素b 基因的全序列(1 140 bp) , 分析了 该属物种之间的系统发育进化关系。在DNA 水平上, 序列分析结果一致地提供了新的分类学证据: 支持Rata2 jszczak 和Groves 的观点, 即N1intermedus 只是N1 pygmaeus 的成体(Ratajszczak , 1998 ; Groves , 1971) 。对两种 序列的数据做了联合及个别分析, 获得相似的系统树, 支持懒猴属由两个单系群组成: 第一群由N1 pygmaeus 聚成, 第二群由N1coucang 聚成。该结果也提供了新的分子遗传证据, 支持懒猴属由N1coucang 和 N1 pygmaeus 两物种组成。

A Molecular Phylogeny of Macaca Based on Mitochondrial Control Region Sequences

通过线粒体部分控制区DNA 序列数据探讨7 种猕猴属物种的分子系统发育关系。结果表明熊猴的 核苷酸多样度最高, 而藏酋猴核苷酸多样度较低。基于控制区序列数据所构建的最大似然树, 不考虑食蟹猴的 位置, 7 种猕猴物种可粗略地分为3 个种组, 即狮尾猴组(包括北平顶猴) 、头巾猴组(包括红面猴、熊猴和藏 酋猴) 和食蟹猴组(包括恒河猴和台湾猴) 。与前人( Fooden & Lanyon , 1989 ; Tosi et al , 2003a ; Deinard & Smith , 2001 ; Evans et al , 1999 ; Hayasaka et al , 1996 ; Morales &Melnick , 1998) 的结果不同, 我们的结果支 持食蟹猴比北平顶猴分化早的假设; 东部恒河猴(相对于台湾猴) 和东部熊猴(相对于藏酋猴) 出现并系。与 Y染色体、等位酶、核基因以及部分形态学数据推测的结果(Delson , 1980 ; Fooden &Lanyon , 1989 ; Fooden , 1990 ; Tosi et al , 2000 , 2003a , b ; Deinard & Smith , 2001) 一致, 红面猴应归于头巾猴组, 但此结论与前人 (Hayasaka et al , 1996 ; Morales &Melnick , 1998 ; Tosi et al , 2003a) 依据线粒体得到的结果有较大分歧。

A phylogeny of Chinese leaf monkeys using mitochondrial ND3-ND4 gene sequences

The phylogeny of Chinese leaf monkeys, especially the snub-nosed monkeys (Rhinopithecus), has not been thoroughly investigated using molecular sequence data, perhaps due to their rarity in the wild and their poor representation in institutional collections. Despite several proposed classifications, systematic relationships of these species remain poorly defined and this has hindered their conservation. To clarify the phylogenetic relationships of the leaf monkey clade in China, we sequenced the mitochondrial ND3, ND4L, ND4, tRNA(Arg), tRNA(His), tRNA(Ser), and tRNA(Leu) genes for Rhinopithecus bieti, R. roxellana, Trachypithecus francoisi, T. f. leucocephalus, and T. phayrei as well as Pygathrix nemaeus and Colobus guereza. We included a rotal of 2252 characters for each individual, excluding gaps in primary sequences. Our interpretation of the results from character- and distance-based phylogenetic analyses suggest that (1) Pygathrix nemaeus is sister to Rhinopithecus rather than to Trachypithecus though it is quite divergent from the former; (2) the Yunnan snub-nosed monkey, Rhinopithecus bieti, represents a valid species; (3) the white-headed leaf monkey is not a distinct species, but instead is a subspecies of Trachypithecus francoisi (T. f. leucocephalus), though it should still be considered a separate evolutionarily significant unit (ESU); and (4) because two individuals of the Phayrei's leaf monkey, T. phayrei, are genetically distinct from one another, a more extensive revision of the taxonomy of this putative species in China is needed. These results, plus ongoing work on the molecular systematics of the entire Asian leaf monkey radiation, can provide a sound basis for identifying the appropriate units of conservation for this endangered group of primates.

Sox and Zfx genes in giant panda

By using PCR cloning techniques, the DNA sequences of the HMG box regions of six Sox genes (pSox) and the zinc finger domains of two Zfx genes (pZfx) in the giant panda were identified. The giant panda Sox genes fell into two subfamilies, SOX-S1 and SOX-S2. The pSox and pZfx genes of the giant panda were highly homologous to the corresponding genes in mammals and revealed close substitution rates to those in the primates.

Mitochondrial cytochrome b gene sequences of Old World monkeys: With special reference on evolution of Asian colobines

The classification and phylogenetic relationships of the Old World monkeys are still controversial. For Asian colobines, from three to nine genera were recognized by different primatologists. In the present study, we have sequenced a 424 bp mitochondrial tRNA(Thr) gene and cytochrome b gene fragment from Macaca mulatta, Mandrillus sphinx, Mandrillus leucophaeus, Semnopithecus entellus, Trachypithecus vetulus, T. johnii, T. phayrei, T. francoisi, Pygathrix nemaeus, Rhinopithecus roxellanae, R. bieti, R. avunculus, Nasalis larvatus, and Colobus polykomos in order to gain independent information on the classification and phylogenetic relationships of those species. Phylogenetic trees were constructed with parsimony analysis by weighting transversions 5 or 10 fold greater than transitions. Our results support the following conclusions: (1) the Old World monkeys are divided into two subfamilies; (2) that among the colobines, Colobus, the African group, diverged first, and Nasalis and Rhinopithecus form a sister clade to Pygathrix; (3) that there are two clades within leaf monkeys, i.e. 1) S. entellus, T. johnii, and T. vetulus, and 2) T, phayrei and T. francoisi; (4) that Rhinopithecus avunculus, R. roxellanae, and R. bieti are closely related to each other, and they should be placed into the same subgenus; (5) that Rhinopithecus is a distinct genus; and (6) that the ancestors of Asian colobines migrated from Africa to Asia during the late Pliocene or early Pleistocene.

Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genesis strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five, distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D, sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The Kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D.. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D, nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous. (C) 1999 Academic Press.

Mitochondrial cytochrome b sequences variation of Protura and molecular systematics of Apterygota

Mitochondrial cytochrome b genes of about 450 bp fragments from 3 proturan species, 5 collembolan species and 2 dipluran species have been sequenced. The number of nucleotide substitutions and Kimura 2-parameter distances have also been calculated, and a series of molecular phylogenetic trees reconstructed by using parsimony and distance methods. The proturan, collembolan and dipluran species have evolved monophyletic groups. The results suggest that Protura and Collembola are sister groups, while Diplura is more or less demonstrating a closer phylogenetic relationship to the pterygotan insects. The phylogeny and their systematic position of protura and other groups are also discussed.

Sequence evolution of the CCR5 chemokine receptor gene in primates

The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellanae, Rhinopithecus bieti, Rhinopithecus avunculus, Macaca assamensis, and Macaca arctoides. When compared with CCR5 sequences from humans and other primates, our results demonstrate that:(1) nucleotide and amino acid sequences of CCR5 among primates are highly homologous, with variations slightly concentrated on the amino and carboxyl termini; and (2) site Asp13, which is critical for CD4-independent binding of SIV gp120 to Macaca mulatta CCR5, was also present in all other nonhuman primates tested here, suggesting that those nonhuman primate CCR5s might also bind SIV gp120 without the presence of CD4. The topologies of CCR5 gene trees constructed here conflict with the putative opinion that the snub-nosed langurs compose a monophyletic group, suggesting that the CCR5 gene may not be a good genetic marker for low-level phylogenetic analysis. The evolutionary rate of CCR5 was calculated, and our results suggest a slowdown in primates after they diverged from rodents. The synonymous mutation rate of CCR5 in primates is constant, about 1.1 x 10(-9) synonymous mutations per site per year. Comparisons of K-a and K-s suggest that the CCR5 genes have undergone negative or purifying selection. K-a/K-s ratios from cercopithecines and colobines are significantly different, implying that selective pressures have played different roles in the two lineages.

Identification of Sarcocystis hominis-like (Protozoa : Sarcocystidae) cyst in water buffalo (Bubalus bubalis) based on 18S rRNA gene sequences

DNA templates were extracted from isolates of Sarcocystis hominis-like cysts collected from cattle and water buffalo, as well as from Sarcocystis fusiformis cysts and Sarcocystis suihominis cysts. The 18S rRNA genes were amplified using DNA from a single

Phylogeny of higher taxa of Hexapoda according to 12sRNA sequences

The phylogenetic relationship of Hexapoda has been debated for a long time, which will be resolved mainly depending on the settlement of monophyly, affinities and interrelationships among Protura, Collembola and Diplura. Mitochondrial 12sRNA gene about 35

Identification of native American founder mtDNAs through the analysis of complete mtDNA sequences: Some caveats

In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian-and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.