Monocot chimeric jacalins: a novel subfamily of plant lectins

Abstract

Monocot chimeric jacalins are a small group of lectins (currently with nine members), each typically consisting of a dirigent domain and a jacalin-related lectin domain. This unique module structure, along with their limited taxonomic distribution and short time window in molecular evolution, makes them a novel family of lectins. Recent studies have shown that these proteins play important roles in plant stress responses and development. Our knowledge of these proteins in functional domain and evolution has also made significant progress.     

Some Evidence for Aquatic Macrophytes as Repellents for a Limnetic Species of Daphnia

Under controlled laboratory conditions Daphnia rosea SARS is strongly repelled by substances secreted by Elodea, Nitella, and Myriophyllum. This phenomenon can be easily demonstrated in a large glass U-tube having a small sprig of hydrophyte at the surface of the water on one side of the U-tube. It can also be demonstrated in a long narrow aquarium having an incomplete vertical plastic divider at the center, and with the hydrophyte on one side of the divider. Simulated plastic aquarium vegetation in control aquaria has only a slight repellent or „shading”︁ effect. The implications of this phenomenon in the hydrophyte zone of lakes and ponds are discussed.     

Studies of a Murine Monoclonal Antibody Directed against DARC: Reappraisal of Its Specificity

Duffy Antigen Receptor for Chemokines (DARC) plays multiple roles in human health as a blood group antigen, a receptor for chemokines and the only known receptor for Plasmodium vivax merozoites. It is the target of the murine anti-Fy6 monoclonal antibody 2C3 which binds to the first extracellular domain (ECD1), but exact nature of the recognized epitope was a subject of contradictory reports. Here, using a set of complex experiments which include expression of DARC with amino acid substitutions within the Fy6 epitope in E. coli and K562 cells, ELISA, surface plasmon resonance (SPR) and flow cytometry, we have resolved discrepancies between previously published reports and show that the basic epitope recognized by 2C3 antibody is ²²FEDVW²⁶, with ²²F and ²⁶W being the most important residues. In addition, we demonstrated that ³⁰Y plays an auxiliary role in binding, particularly when the residue is sulfated. The STD-NMR studies performed using 2C3-derived Fab and synthetic peptide corroborated most of these results, and together with the molecular modelling suggested that ²⁵V is not involved in direct interactions with the antibody, but determines folding of the epitope backbone.     

Reconsideration of Phylogenetic Relationships of the Subclass Peritrichia (Ciliophora, Oligohymenophorea) Based on Small Subunit Ribosomal RNA Gene Sequences, with the Establishment of a New Subclass Mobilia Kahl, 1933

ABSTRACT. Based on its characteristic oral apparatus, the ciliate subclass Peritrichia has long been recognized as a monophyletic assemblage composed of the orders Mobilida and Sessilida. Following the application of molecular methods, the monophyly of Peritrichia has recently been questioned. We investigated the phylogenetic relationships of the peritrichous ciliates based on four further complete small subunit ribosomal RNA sequences of mobilids, namely Urceolaria urechi, Trichodina meretricis, Trichodina sinonovaculae , and Trichodina ruditapicis . In all phylogenetic trees, the mobilids never clustered with the sessilids, but instead formed a monophyletic assemblage related to the peniculines. By contrast, the sessilids formed a sister clade with the hymenostomes at a terminal position within the Oligohymenophorea. We therefore formally separate the mobilids from the sessilids (Peritrichia sensu stricto) and establish a new subclass, Mobilia Kahl, 1933 , which contains the order Mobilida Kahl, 1933 . We argue that the oral apparatus in the mobilians and sessilid peritrichs is a homoplasy, probably due to convergent evolution driven by their similar life-styles and feeding strategies. Morphologically, the mobilians are distinguished from all other oligohymenophoreans by the presence of the adhesive disc, this character being a synapomorphy for the Mobilia.     

生态化学计量学在水生态系统中的研究与应用

生态化学计量学主要是研究碳、氮、磷等元素在各种生态过程中平衡的一门科学,其核心问题是揭示生物体元素组成的差异对生态功能的影响。由于生态化学计量学研究可以把生态实体的各个层次在元素水平上统一起来,因此生态化学计量学已成为许多生态系统的新兴研究工具。目前,生态化学计量学的研究与应用已深入到生态学的各个层次(分子、细胞、个体、种群、群落、生态系统及区域等不同尺度)。该文围绕生态化学计量学的两个重要组成理论,并结合笔者近年来的研究,归纳总结了生态化学计量学在水生态系统中的研究与应用及未来研究重点,希望有助于推动我国生态化学计量学在水生态系统中的应用研究。     

Phylogenetic Reappraisal of the Genus Monomorphina (Euglenophyceae) Based on Molecular and Morphological Data

A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakry?, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

Surface Printing of Plant Leaves for Phylogenetic Studies

A solution of plastic consisting of toluene, 720 ml; methanol, 180 ml; ethyl cellulose (Ethocel, standard 7 CPS), 250 gm; and Dow resin 276 V-2, 75 gm is applied to a leaf surface which has been dampened with toluene. The plastic is spread to a thin film with the edge of a card and allowed to dry. After drying, the plastic may be peeled from the leaf surface and either stored dry in a small envelope or mounted permanently on a microscope slide. Permanent mounts are prepared by placing a small section of the peel from the upper and lower surfaces of the leaf on a microscope slide and covering with a No. 1 cover glass. A small spot of balsam on each corner of the cover glass secures the glass in position. This air mount has proved to be superior to water, glycerol or balsam mounts. Fresh leaves are washed with a mild detergent before application of the plastic. Herbarium specimens are soaked in water overnight to restore the leaf to a semiturgid condition. Five species of different plant families have been illustrated to show the diagnostic features of the surface of the cuticle. An isolated layer of epidermal cells obtained by chemical maceration permitted cell and imprint comparison. The remarkable amount of detail shown by the prints is an aid for phylogenetic studies and may make the recognition of fossil cuticles possible.     

Reappraisal of the Genus Tapirus (Perissodactyla, Tapiridae): Systematics and Phylogenetic Affinities of the South American Tapirs

The record of the genus Tapirus in South America is associated with the faunistic events of the Great American Biotic Interchange (GABI). The taxon is considered an immigrant of Holarctic origin. Although remains are scarce and incomplete during the Pleistocene, an analysis of these materials allowed us to consider valid seven fossil species : Tapirus tarijensis, T. cristatellus, T. greslebini, T. rioplatensis, T. oliverasi, T. mesopotamicus, and T. rondoniensis. A phylogenetic analysis was carried out in order to elucidate the relationships of the American fossil and extant species. Our result is consistent with a paraphyletic hypothesis for South American tapirs and suggests that a second dispersal event would have occurred from South America to North America, of a form closely related to T. cristatellus, resulting in the derived forms of North America.     

Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence

A highly resolved primate cladogram based on DNA evidence is congruent with extant and fossil osteological evidence. A provisional primate classification based on this cladogram and the time scale provided by fossils and the model of local molecular clocks has all named taxa represent clades and assigns the same taxonomic rank to those clades of roughly equivalent age. Order Primates divides into Strepsirhini and Haplorhini. Strepsirhines divide into Lemuriformes and Loriformes, whereas haplorhines divide into Tarsiiformes and Anthropoidea. Within Anthropoidea when equivalent ranks are used for divisions within Platyrrhini and Catarrhini, Homininae divides into Hylobatini (common and siamang gibbon) and Hominini, and the latter divides into Pongina forPongo(orangutans) and Hominina forGorillaandHomo. Homoitself divides into the subgeneraH.(Homo) for humans andH.(Pan) for chimpanzees and bonobos. The differences between this provisional age related phylogenetic classification and current primate taxonomies are discussed.     

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies have focused on establishing when these events occurred and on elucidating their functional and evolutionary consequences, but we still lack sufficient understanding of how genome duplications first originated. We used phylogenomics to study the ancient genome duplication occurred in the yeast Saccharomyces cerevisiae lineage and found compelling evidence for the existence of a contemporaneous interspecies hybridization. We propose that the genome doubling was a direct consequence of this hybridization and that it served to provide stability to the recently formed allopolyploid. This scenario provides a mechanism for the origin of this ancient duplication and the lineage that originated from it and brings a new perspective to the interpretation of the origin and consequences of whole-genome duplications.     

Strongest Evidence: Maximum Apparent Phylogenetic Signal as a New Cladistic Optimality Criterion

A new method for phylogenetic inference, Strongest Evidence (SE), is described. In this method, a character's support for a phylogenetic hypothesis, its apparent phylogenetic signal, is greatest when the amount of implied homoplasy is most remarkably small given background knowledge alone. Because evolutionary rates are not assumed to be slow, background expectations for character length can be derived through modeling complete dissociation between branching pattern and character state assignments. As in unweighted parsimony, SE holds that fewer required evolutionary steps in a character indicates stronger support for a tree. However, in SE, the relationship between steps and support differs by unlabeled tree topology and character state distribution. Strongest evidence is contrasted in detail with both unweighted parsimony and Goloboff's method of implied weights. An iterative process is suggested for incrementally resolving a phylogenetic hypothesis while conducting cladistic analyses at increasingly local levels.     

Phylogenetic relationships in the Hamamelidaceae: Evidence from the nucleotide sequences of the plastid genematK

The Hamamelidaceae is a family that bridges the basal elements of the Rosidae and the lower Hamamelidae, thus a better understanding of the phylogeny of the family is important for clarifying evolutionary patterns in the diversification of eudicots. However, subfamilial as well as tribal relationships in the Hamamelidaceae have been controversial. Nucleotide sequences of the chloroplast genematK were used to study the intergeneric relationships of the family. In the phylogenetic trees, constructed using parsimony analysis, the clade containingAltingia andLiquidambar (Altingioideae) is sister to a clade that includes all other Hamamelidaceae.Exbucklandia andRhodoleia form a clade, suggesting a close relationship between the two genera.Disanthus is sister to the monophyletic Hamamelidoideae. The paraphyletic arrangement ofDisanthus, Mytilaria andExbucklandia with respect to the Hamamelidoideae does not support the combination of these genera in one subfamily. In the Hamamelidoideae, thematK phylogeny supports the monophyly of several previously recognized groups with modifications, including the tribes Eustigmateae (incl.Molinadendron), Fothergilleae (excl.Molinadendron andMatudaea), and the subtribe Dicoryphinae. However, the Hamamelideae as traditionally circumscribed is polyphyletic. Apetaly has evolved three times independently in the Hamamelidoideae.     

Evidence for Polyphyly of the Genus Scrupocellaria (Bryozoa: Candidae) Based on a Phylogenetic Analysis of Morphological Characters

The bryozoan genus Scrupocellaria comprises about 80 species in the family Candidae. We propose a hypothesis for the phylogenetic relationships among species assigned to Scrupocellaria to serve as framework for a phylogenetic classification using 35 morphological characters. Our results suggest that the genus Scrupocellaria is polyphyletic. Scrupocellaria s. str. is redefined according to four morphological features: vibracular chamber with a curved setal groove, ooecium with a single ectooecial fenestra, two axillary vibracula, and a membranous operculum with a distinct distal rim. Thus, the genus includes only 11 species: Scrupocellaria aegeensis, Scrupocellaria delilii, Scrupocellaria harmeri, Scrupocellaria incurvata, Scrupocellaria inermis, Scrupocellaria intermedia, Scrupocellaria jullieni, Scrupocellaria minuta, Scrupocellaria puelcha, Scrupocellaria scrupea, and Scrupocellaria scruposa. The monophyly of Cradoscrupocellaria is supported and five new genera are erected: Aquiloniella n. gen., Aspiscellaria n. gen., Paralicornia n. gen., Pomocellaria n. gen. and Scrupocaberea n. gen. Two other new genera, Bathycellaria n. gen. and Sinocellaria n. gen., are erected to accommodate two poorly known species, Scrupocellaria profundis Osburn and Scrupocellaria uniseriata Liu, respectively. Scrupocellaria congesta is tentatively assigned to Tricellaria. Fifteen species are reassigned to Licornia: Licornia cookie n. comb., Licornia micheli n. comb., Licornia milneri n. comb., Licornia curvata n. comb., Licornia diegensis n. comb., Licornia drachi n. comb., Licornia mexicana n. comb., Licornia pugnax n. comb., Licornia raigadensis n. comb., Licornia regularis n. comb., Licornia resseri n. comb., Licornia securifera n. comb., Licornia spinigera n. comb., Licornia tridentata n. comb., and Licornia wasinensis n. comb. Notoplites americanus n. name is proposed as a replacement name for Scrupocellaria clausa Canu & Bassler. Three fossil species are reassigned to Canda: Canda rathbuni n. comb., Canda triangulata n. comb. and Canda williardi n. comb. A species is reassigned to Notoplites, Notoplites elegantissima n. comb. The generic assignment of eleven species of Scrupocellaria, including Scrupocellaria macandrei, remains uncertain.     

Phylogenetic relationships of the Subclass Peniculia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

Peniculine ciliates have been recognized as a distinct higher taxon of ciliates for almost 50 years. However, phylogenetic relationships within the Subclass Peniculia are still unsettled. To contribute to our understanding of their phylogeny and provide evidence for the position of Urocentrum turbo, we sequenced its small subunit (SS) rRNA gene and the SSrRNA genes from Lembadion bullinum, Frontonia sp., Paramecium caudatum, Paramecium multimicronucleatum, Paramecium putrinum, and Paramecium woodruffi. Urocentrum turbo was the only one of these species not to exhibit a shortened Helix E10_1, which we conclude characterizes the "higher" peniculines. Except for U. turbo, the peniculines are strongly supported as a monophyletic clade with Lembadion, Frontonia, and Paramecium species forming separate and strongly supported clades by bootstrap analysis using distance matrix, maximum parsimony, and maximum likelihood methods. Urocentrum turbo is associated with different lineages, depending upon the analysis used. The Paramecium species form at least four clades with the Paramecium aurelia subgroup being the most derived. We conclude that the Subclass Peniculia should be divided into two orders, the Order Urocentrida and Order Peniculida, with the latter order having two suborders, the Suborder Frontoniina and Peniculina. We place U. turbo with the peniculines because of shared morphological and stomatogenetic features.     

Further Evidence for a Role of Carbohydrates in Insulin Binding : Studies in Lectin-Purified Receptors

Abstract

Purification of liver membrane insulin receptors on concanavalin A-and ricin I-lectin columns gave a 15-fold enrichment in the insulin binding capacity per milligramm of protein. Final receptor and protein recoveries were 53 and 3.8 % respectively. Lectin-purification increased the receptor affinity for insulin, as indicated by a left-ward shift in the binding competition curve and a steeper slope in the Scatchard plot. Lectin-purification increased the receptor sensitivity towards the glycosidic probes. The maximal effects of β-galactosidase, ricin I (galactose-binding lectin) and α-mannosidase were markedly amplified : 80, 90 and 60 % inhibition, versus 45, 40 and 15 % with particulate membranes. The limulus polyphemus (LPA) and wheat germ (WGA) agglutinins (sialic acid- and N-acetyl-glucosaminyl-binding lectins) became effective in modifying the insulin binding : 45 and 80 % inhibition, respectively. The effects were dose-dependent, reversed by the monosaccharide competitors (lectin effects) and unrelated to the state of receptor occupancy. These findings indicate that, within the hormone recognition area, peptide chains containing galactose, mannose and N-acetyl-glucosamine are strictly required for insulin-receptor interaction and suggest that change in the receptor affinity is related to the role of carbohydrate in insulin binding.     

Phylogenetic and Molecular Epidemiological Studies Reveal Evidence of Multiple Past Recombination Events between Infectious Laryngotracheitis Viruses

In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV) have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field.