Folding and function of the myelin proteins from primary sequence data.

To explain how the myelin proteins are involved in the organization and function of the myelin sheath requires knowing their molecular structures. Except for P2 basic protein of PNS myelin, however, their structures are not yet known. As an aid to predicting their molecular folding and possible functions, we have developed a FORTRAN program to analyze the primary sequence data for proteins, and have applied this to the myelin proteins in particular. In this program, propensities for the secondary structure conformations as well as physical-chemical parameters are assigned to the amino acids and the pattern of these parameters is examined by calculating their average values, autocorrelation functions and Fourier transforms. To compare two proteins, their sequences are aligned using a unitary scoring matrix, and homologies are searched by plotting a two-dimensional map of the correlation coefficients. Comparison of the corresponding myelin basic proteins (MBP) and P0 glycoproteins (P0) for rodent and shark showed that the conserved residues included most of the amino acids which were predicted to form the alpha or beta conformations, while the altered residues were mainly in the hydrophilic and turn or coil regions. In both rodent and shark the putative extracellular domain of P0 glycoprotein displayed consecutive peaks of beta propensity similar to that for the immunoglobulins, while the cytoplasmic domain showed alpha-beta-alpha folding. To trace the immunoglobulin fold along the P0 sequence, we compared the beta propensity curve of P0 with that of the immunoglobulin M603, whose three-dimensional structure has been determined. We propose that the flat beta-sheets of P0 are orientated parallel to the membrane surface to facilitate their homotypic interaction in the extracellular space. An extra beta-fold in the extracellular domain of shark P0 compared with rodent P0 was found, and this may result in a greater attraction between the apposed extracellular surfaces and may account for a smaller extracellular space as measured by x-ray diffraction. A computer search of the myelin protein sequences for functional motifs revealed sites for N-glycosylation, phosphorylation, nucleotide binding, and certain enzyme activities. We note especially that there are potential nucleotide binding sites in proteolipid protein (PLP), MBP and 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). This is consistent with the experimental observations that PLP acts like an ionophore or proton channel when reconstituted into planar lipid bilayers, MBP binds GTP, and CNP catalyzes in vitro the hydrolysis of 2',3'-nucleotides into corresponding 2'-nucleotides.     

Postembryonic development of tapeworms — source of novel phylogenetic characters for analysis of cestode evolution: comparative TEM studies

Summary Ultrastructural features of juvenile cestodes (metacestodes) can provide useful characters for phylogenetic and evolutionary analyses. Until now, however, they have been relatively little utilised (Beveridge 2001, Chervy 2002). The postembryonic development and structure of fully formed metacestodes were examined in two cyclophyllideans: Taenia parva Baer, 1926 (Taeniidae); and Sobolevitaenia verulamii (Mettrick, 1958) Korniushin, 1972 (Dilepididae). In T. parva, three developmental stages were recognized: (1) an early stage of exogenous budding at the surface of the central vesicle; (2) a stage of polycephalic cyst development accompanied by segmentation of the growing metacestode strobila and an obvious decrease in the size of the central vesicle; (3) a fully formed metacestode of the strobilocercus type with 14–24 invaginated scoleces. The tegument, scolex, subtegumental musculature of the strobilar segments, protonephridial system, calcareous corpuscles and medullary parenchyma of larvae exhibit general similarity to the same structures in adults at both LM and TEM levels. The morphogenesis of the metacestode of T. parva is compared with that of polycephalic metacestodes of other Taenia spp. (T. krepkogorski, T. twitchelli and T. endothoracica) and with other asexually multiplying metacestodes (Mesocestoides vogae, hymenolepidids and dilepidids). In S. verulamii, the body of the cysticercoid with invaginated scolex armed with a double crown of rostellar hooks was completely surrounded by the cercomer, which appears to be separated from the cyst and scolex. The surface of the suckers is covered with a thick layer of glycocalyx. Five cell types were distinguished in the sections: (1) perikarya of metacestode tegument; (2) glycolgen-storing parenchymal cells; (3) glandular-type cells with large, electron-dense secretory-like granules; (4) flame cells; and (5) calcareous corpuscle-forming cells. The surface of the cercomer is covered by elongated microvilli, which evidently differ from characteristic microtriches covering all other parts of the metacestode surface. The ultrastructure of S. verulamii evidently differs from that of the other dilepidid cestode examined to date, Lateriporus geographicus, the cyst wall of which more resembles cysticercoids of Hymenolepididae than those of Dilepididae. Concluding remarks: Ultrastructural studies on metacestodes have considerable promise for providing important new characters for phylogenetic analysis. New TEM data on a great variety of cestode species are urgently needed. Until now, this field has not been exploited in a systematic fashion. Until more comprehensive studies become available, the current data are not yet amenable to analysis.     

The periodontal differentiation in the phylogeny of teeth–an overview

During the evolution of teeth, different types of periodontal attachment have been developed. On the basis of the comparative histology of periodontal tissues, protoacrodontal, acrodontal, acro-protothecodontal, pleurodontal and thecodontal structures can be distinguished that depend upon the area of attachment (crestal, marginal or socketed type) and the mode of attachment (ankylosis, fibrous or combined type). Due to "phylogenetic memory", changes of the periodontium in health and disease could be interpreted as copies of phylogenetically older patterns. The greatest variations in tooth attachment have originated in acrodont bony fishes and in pleurodont reptiles, whereas the selection for a single thecodont or socketed type was an important event in the evolution of mammals. The detailed structures of cementum, of the fiber apparatus and of the junctional epithelium vary from type to type and within one type. These principal structures are decisive for reaction patterns of degeneration and regeneration. Therefore, comparative periodontology could be an important adjunct to help interpret the natural history of periodontal diseases, to help in the selection of experimental animals and to help provide treatment strategies in both human and veterinary situations.     

Evolution of North American PVYNTN Strain Tu 660 from Local PVYN by Mutation rather than Recombination

A North American (NA) isolate of tobacco veinal necrotic strain of Potato virus Y (PVY^N) (N-Jg) and a NA isolate of potato tuber necrotic strain of Potato virus Y (PVY^NTN) (Tu 660) were tested for their phenotypes by inoculation to potato plants of three potato cultivars. Upon inoculation with Tu 660, tubers of the cultivars Norchip and Ranger Russet developed potato tuber necrotic ringspot disease (PTNRD) but not the tubers of Russet Burbank. N-Jg failed to induce PTNRD in the tested cultivars. The genomic RNAs of both strains were completely sequenced and analysed. High homology (98% and 99% identity on nucleotide and polyprotein, respectively) was found between Tu 660 and N-Jg. When polyproteins were compared with other isolates, high identity was observed between Tu 660 and an European (Eu) PVY^N-605 (98%) and with an Eu-PVY^NTN-H (96%). However, when individual mature proteins were compared, much lower identities (86.5–94%) were found between Tu 660 and PVY^NTN-H compared to 98–99.5% between Tu 660 and PVY^N-605 in the P3, 6K1 and CI regions. Further sequence analysis indicated that the PVY^NTN-H is a hybrid molecule of the genomic RNA recombination of PVY^O and Eu-PVY^N as shown by Glais et al. (Arch Virol 147, 363–378), whereas NA-PVY^NTN Tu 660 is free of recombination points. Phylogenetic analysis confirmed this observation, and suggested that, in light of high homology, the Tu 660 might have evolved from NA-PVY^N by mutations rather than the genome recombinations. The non-recombinant nature of NA-PVY^NTN Tu 660 strongly suggests that the recombinant structure of genome is not a necessary prerequisite for the PTNRD phenotype.     

Hantaviruses in Central South America: phylogenetic analysis of the S segment from HPS cases in Paraná, Brazil

We sequenced the complete S segments of hantaviruses detected from 12 HPS patients living in southern of Brazil. Samples were obtained from patients diagnosed in different years, in distinct areas, and with a broad spectrum of clinical signs. Despite these differences, all the S proteins of hantavirus from Paraná were identical, except for one amino acid substitution. Phylogenetic analyses of the complete S segment nucleotide and amino acid sequences indicated that hantaviruses from Paraná form a distinct clade from those circulating in South and North America. Other hantaviruses from Brazil were not placed in the same clade. The Oligoryzomys nigripes-associated strains ITA37 and ITA38 from Paraguay were found to belong to the same clade as the hantaviruses from Paraná. Paraguay and Paraná state are located at the same latitude and some ecosystems are similar in both places. The geographic position and common rodent hosts could explain this phylogenetic relationship.     

The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary

Fluorescencein situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescencein situ hybridization and comparative mapping of the chromosomes of human, great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus) and Old World monkeys (Macaca fuscata andCercopithecus aethiops). Inversions were found in the pericentric region of the primate chromosome 2p homologs in great apes, and the hybridization pattern demonstrates the known phylogenetically derived telomere fusion in the line that leads to human chromosome 2. The hybridization of the 2q microlibrary to chromosomes of Old World monkeys gave a different pattern from that in the gorilla and the orang-utan, but a pattern similar to that of chimpanzees. This suggests convergence of chromosomal rearrangements in different phylogenetic lines.     

Phylogenomics of the dog and fox family (Canidae,Carnivora) revealed by chromosome painting

Canid species (dogs and foxes) have highly rearranged karyotypes and thus represent a challenge for conventional comparative cytogenetic studies. Among them, the domestic dog is one of the best-mapped species in mammals, constituting an ideal reference genome for comparative genomic study. Here we report the results of genome-wide comparative mapping of dog chromosome-specific probes onto chromosomes of the dhole, fennec fox, and gray fox, as well as the mapping of red fox chromosome-specific probes onto chromosomes of the corsac fox. We also present an integrated comparative chromosome map between the species studied here and all canids studied previously. The integrated map demonstrates an extensive conservation of whole chromosome arms across different canid species. In addition, we have generated a comprehensive genome phylogeny for the Canidae on the basis of the chromosome rearrangements revealed by comparative painting. This genome phylogeny has provided new insights into the karyotypic relationships among the canids. Our results, together with published data, allow the formulation of a likely Canidae ancestral karyotype (CAK, 2n = 82), and reveal that at least 6–24 chromosomal fission/fusion events are needed to convert the CAK karyotype to that of the modern canids. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Intra- or inter-specific difference in genotypes of Caligus elongatus Nordmann 1832?

Two mitochondrial and one nuclear genetic marker were used to study the phylogenetic position of the two reported CO1-genotypes of Caligus elongatus in a group of closely related caligid parasites. Molecular analysis of the two mitochondrial genes (CO1 and 16S), indicate genetic distances of the two C. elongatus genotypes in the lower range of distances previously reported between other crustacean species, but higher than comparable reported within-species differences. Analyses of nuclear 18S sequences indicate no detectable differentiation between these genotypes, but may be due to expected differences in the resolution of these genetic markers. Investigation of two of three selected morphological characters reveals phenotypes supporting the division based on the molecular division. The species status on the two C. elongatus genotypes cannot be drawn conclusively, although the molecular and morphological data presented here suggests the presence of sibling species.     

基于PacBio测序的对叶百部叶绿体基因组结构及系统发育分析

目的：获得对叶百部Stemona tuberosa高质量叶绿体基因组信息,明确其结构、序列特征,同时确定对叶百部的系统发育地位。方法：采用Illumina NovaSeq 6000和PacBio RSⅡ平台对对叶百部分别进行建库测序,利用生物信息软件将2个测序平台的数据进行混合组装和碱基校正,最终获得高质量叶绿体基因组,随后对其序列特征、重复序列、基因多样性和系统发育进行分析。结果：对叶百部叶绿体基因组大小为154 379 bp,叶绿体基因组结构为典型环状四段式,1对27 074 bp的反向重复区（IR）,1个大小为17 924 bp的小单拷贝区（SSC）和1个82 307 bp的大单拷贝区（LSC）,平均鸟嘌呤和肥嘧啶所占的比率（GC）含量为37.86%;共注释得到121个基因,包括30个tRNA基因,4个rRNA基因和87蛋白编码基因,其中6个tRNA基因和12个蛋白质编码基因中存在内含子;对叶百部叶绿体基因组中共发现49个长重复序列和59个单核苷酸简单重复序列（SSR）;4个百部属的叶绿体基因组比较分析表明ycf1和ndhF基因具有高度多样性;基于叶绿体基因组构建的系统发育树与对...