Vegetative anatomy and morphology of Amentiferae

Some of the important vegetative characters of amentiferous families described in research papers concerned with interfamilial relationships and published since 1947–1948 are briefly summarized. Important conclusions by the writers are also reviewed. Thus, Bataceae are considered derivatives of the Centrospermae ; Betulaceae, Casuarinaceae, and Ulmaceae are hamamelidaceous derivatives; Garryaceae and Cornaceae are closely related; and Julianiaceae and Anacardiaceae are plausible relatives. A more extensive tabulation of vegetative characters of essentially all amentiferous and ranalean families and Dilleniaceae is also presented, and the data are utilized to compare the percentages of advanced and primitive characters in these same taxa. The logic for considering trends whose evolutionary directions were initiated previous or incidental to angiospermous origin as more valid than other evolutionary trends is offered. The following principal conclusions are based upon the analysis of the tabulation: (1) the Amentiferae have sufficient advanced vegetative characters to preclude consideration of them as earliest angiosperms or their direct derivatives unless a large number of primitive features of other sorts offers strong counter evidence; (2) they also have sufficient primitive characters to discount the concept that they are highly evolved; (3) most Amentiferae clearly possess many more advanced vegetative characters than do most Magnoliales, Laurales, Trochodendrales, or Dilleniaceae ; and (4) relationships of several Amentiferae to various, unrelated angiospermous families have been demonstrated.     

Fossil forms of Amentiferae

Review of the procedures used in determining fossil plant organs indicates that the many Cretaceous records of extant genera of “Amentiferae” based on leaves should be rejected as theoretically unreliable. Palynological data, in combination with some valid megafossil data, indicate that most recognizable members of “Amentiferae” are no older than the later part of the Late Cretaceous. Juglandales appear to be derivatives of the ancient Normapolles complex and unrelated to other “Amentiferae.” A preliminary account of some of the comparative foliar morphology of extant “Amentiferae” indicates that some—particularly Betulaceae and Fagaceae—are closely related to Hamamelidales but that other families—notably Rhoipteleaceae, Juglandaceae, Didymelaceae, and Leitneriaceae—are unrelated to this order.     

Development of the amentiferous concept

The amentiferous concept developed in pre-Linnaean times, and early botanists clearly recognized the topical similarities among plants bearing aments. Among the amentiferous plants placed side by side in early times were many that would not be so situated today—e.g., gymnosperms intermixed with dicotyledons. By the time of Linnaeus, only dicotyledons were included among the ament-bearing groups. J. G. Gmelin was first to recognize ament-bearing plants (including some gymnosperms) under a single category, “Amentaceae.” Linnaeus, A. L. de Jussieu, W. J. Hooker, Lindley, and Eichler, at one time or another, placed these plants in a separate amentaceous category, but never under the term “Amentiferae.” The name was never used by Engler although he did place the ament-bearing plants among the first families of his Archichlamydeae. The category “Amentiferae” appears to have entered the literature in British publications and through British/English translations from the German.     

INVESTIGATIONS OF ANGIOSPERMS FROM THE MIDDLE EOCENE OF NORTH AMERICA: FLOWERS OF THE CELTIDOIDEAE

Flowers from the Middle Eocene Claiborne Formation of western Tennessee have both floral and palynological features suggestive of affinities with the subfamily Celtidoideae of the Ul-maceae. Floral size, pollen size, and exine structure suggest that these flowers are intermediate between insect-pollinated ancestors and the modern wind-pollinated Celtidoideae. Thus, they represent the first direct fossil evidence supporting the widespread notion that at least some of the Amentiferae have been derived from insect-pollinated ancestors.     

Protein-translocating outer membrane porins of Gram-negative bacteria

Five families of outer membrane porins that function in protein secretion in Gram-negative bacteria are currently recognized. In this report, these five porin families are analyzed from structural and phylogenetic standpoints. They are the fimbrial usher protein (FUP), outer membrane factor (OMF), autotransporter (AT), two-partner secretion (TPS) and outer membrane secretin (Secretin) families. All members of these families in the current databases were identified, and all full-length homologues were multiply aligned for structural and phylogenetic analyses. The organismal distribution of homologues in each family proved to be unique with some families being restricted to proteobacteria and others being widespread in other bacterial kingdoms as well as eukaryotes. The compositions of and size differences between subfamilies provide evidence for specific orthologous relationships, which agree with available functional information and intra-subfamily phylogeny. The results reveal that horizontal transfer of genes encoding these proteins between phylogenetically distant organisms has been exceptionally rare although transfer within select bacterial kingdoms may have occurred. The resultant in silico analyses are correlated with available experimental evidence to formulate models relevant to the structures and evolutionary origins of these proteins.     

Population studies in Artemisia tridentata ssp. vaseyana: Chromosome numbers and sesquiterpene lactone races

The sesquiterpene lactones and chromosome numbers for three chemical races of Artemisia tridentata ssp. vaseyana have been examined from four populations in western Montana. TLC analysis of the sesquiterpene lactones in the seeds and seed producing parents demonstrated that genetic exchange does occur between sympatric sesquiterpene lactone chemical races. However, other evidence suggests that introgression between these races is restricted to zones of sympatry. There appears to be no correlation between chromosome numbers and sesquiterpene lactone races.     

On the evolutionary relationship of the 4-alpha-helical heme proteins. The comparison of cytochrome b562 and cytochrome c'

The atomic models of the cytochrome b562 and cytochrome c' monomers have been compared. When the respective heme groups are superimposed, the four alpha-helices of each nearly coincide. Four aromatic side chains, including the heme ligands, and a methionine occur in spatially equivalent positions in contact with the heme groups. This structural evidence suggests that the two cytochrome families may have diverged from a common molecular ancestor.     

The biochemistry and biology of extracellular plant lipid-transfer proteins (LTPs)

Plant lipid-transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a role in intracellular lipid transport is considered unlikely, based on their extracellular localization. A number of other biological roles, including antimicrobial defense, signaling, and cell wall loosening, have been proposed, but conclusive evidence is generally lacking, and these functions are not well correlated with in vitro activity or structure. A survey of sequenced plant genomes suggests that the two biochemically characterized families of LTPs are phylogenetically restricted to seed plants and are present as substantial gene families. This review aims to summarize the current understanding of LTP biochemistry, as well as the evidence supporting the proposed in vivo roles of these proteins within the emerging post-genomic framework.     

Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling

Cell-cell communication via the production and detection of chemical signal molecules has been the focus of a great deal of research over the past decade. One class of chemical signals widely used by proteobacteria consists of N-acyl-homoserine lactones, which are synthesized by proteins related to LuxI of Vibrio fischeri and are detected by proteins related to the V. fischeri LuxR protein. A related marine bacterium, Vibrio harveyi, communicates using two chemical signals, one of which, autoinducer-2 (AI-2), is a furanone borate diester that is synthesized by the LuxS protein and detected by a periplasmic protein called LuxP. Evidence from a number of laboratories suggests that AI-2 may be used as a signal by diverse groups of bacteria, and might permit intergeneric signalling. These two families of signalling systems have been studied from the perspectives of physiology, ecology, biochemistry, and more recently, structural biology. Here, we review the biochemistry and structural biology of both acyl-homoserine-lactone-dependent and AI-2-dependent signalling systems.     

Sensing embolism in xylem vessels: the role of sucrose as a trigger for refilling

Refilling of embolized vessels requires a source of water and the release of energy stored in xylem parenchyma cells. Past evidence suggests that embolism presence can trigger a biological response that is switched off upon successful vessel refilling. As embolism formation is a purely physical process and most biological triggers rely on chemical sensors, we hypothesized that accumulation of osmotic compounds in walls of embolized vessels are involved in the embolism sensing mechanism. Analysis of Populus trichocarpa's response to infiltration of sucrose, monosaccharides, polyethylene glycol and potassium chloride into the xylem revealed that only presence of sucrose resulted in a simultaneous physiological and molecular response similar to that induced by embolism. This response included reduction of the starch pool in xylem parenchyma cells and significant correlation of gene expression from aquaporins, amylases and sugar transporter families. The work provides evidence of the ability of plants to sense embolism and suggests that sucrose concentration is the stimulus that allows plants to trigger a biological response to embolism.     

The importance of structural complexity in coral reef ecosystems

The importance of structural complexity in coral reefs has come to the fore with the global degradation of reef condition; however, the limited scale and replication of many studies have restricted our understanding of the role of complexity in the ecosystem. We qualitatively and quantitatively (where sufficient standardised data were available) assess the literature regarding the role of structural complexity in coral reef ecosystems. A rapidly increasing number of publications have studied the role of complexity in reef ecosystems over the past four decades, with a concomitant increase in the diversity of methods used to quantify structure. Quantitative analyses of existing data indicate a strong negative relationship between structural complexity and algal cover, which may reflect the important role complexity plays in enhancing herbivory by reef fishes. The cover of total live coral and branching coral was positively correlated with structural complexity. These habitat attributes may be creating much of the structure, resulting in a collinear relationship; however, there is also evidence of enhanced coral recovery from disturbances where structural complexity is high. Urchin densities were negatively correlated with structural complexity; a relationship that may be driven by urchins eroding reef structure or by their gregarious behaviour when in open space. There was a strong positive relationship between structural complexity and fish density and biomass, likely mediated through density-dependent competition and refuge from predation. More variable responses were found when assessing individual fish families, with all families examined displaying a positive relationship to structural complexity, but only half of these relationships were significant. Although only corroborated with qualitative data, structural complexity also seems to have a positive effect on two ecosystem services: tourism and shoreline protection. Clearly, structural complexity is an integral component of coral reef ecosystems, and it should be incorporated into monitoring programs and management objectives.     

The “Amentiferae” or Hamamelidae as an artificial group: A summary statement

The various contributions to this symposium on the “Amentiferae” reach the general conclusion that the group is an artificial aggregation of taxa of diverse origin that have converged to a common evolutionary plateau in possessing a large syndrome of characteristics that adapt them for successful cross-pollination by wind. Aside from those few families (Eucommiaceae, Casuarinaceae, Fagaceae, and Betulaceae) that apparently do have close relationships (close common origin) with each other and with the Hamamelidales, the following taxa should be removed from the Hamamelidae: Juglandales (Juglandaceae and Rhoipteleaceae) to the Rutales as the Juglandineae near the Anacardiineae; Myricaceae and Leitneriaceae respectively to the Myricales and Leitneriales near the Rutales in the Rutiflorae; Urticales (excludingBarbeya andEucommia) to the Malviflorae near the Malvales and Euphorbiales;Picrodendron to the Euphorbiaceae; Didymelaceae to the Euphorbiales; Myrothamnaceae to the Brunineae of the Pittosporales; andBalanops, Barbeya, andCanacomyrica, along withBatis, to “taxa incertae sedis.”     

Structural and functional implications of a restricted antibody response to a defined antigenic region on the influenza virus hemagglutinin.

A group of hybridoma antibodies that recognize structurally overlapping epitopes on the influenza virus hemagglutinin have been analyzed for the sequence of their immunoglobulin heavy and light chain variable regions. All VH regions derive from the same gene family, and only two Vk genes, from different families, are involved. The repetitive and restricted use of these variable region genes indicates that considerable structural requirements influence the generation of antibodies specific for this region of the hemagglutinin. The degree of amino acid variability which is permissive for interaction with this region suggests that two thirds of the possible replacement mutations may abolish either antibody function or specificity. Analysis of the somatic mutation which occurred in the individual antibodies indicates that the light chains acquired replacement mutations at the rate predicted for random mutation. The heavy chains, however, accumulated a 3-fold excess of replacement mutations over that predicted for random accumulation, correlating with the dominant role they apparently play in determining fine differences in the specificity of these antibodies. The effect of somatic mutation on the clonal amplification and diversification of these B cell lineages is discussed.     

Chromosomal localizations by in situ hybridization of the repetitious human DNA families and evidence of their satellite DNA equivalents

Four of the five major repetitious human DNA families, have been mapped by the in situ hybridization technique at their T_OPT values. Two of the lighter density DNA families have autoradiographic grain patterns over heterochromatic chromosomal regions that resemble those of known satellite DNAs. The two heaviest density DNA families have autoradiographic grain patterns of middle repetitious DNAs, with all chromosomes showing labelling. Some evidence suggests that one of these DNA families is concentrated in certain chromosomal regions. Both DNA families exhibit biphasic T_OPT curves. The presence of two thermal stability classes of hybrids suggests sequence interspersion. By co-enrichment studies in Ag⁺-Cs₂SO₄ gradients, evidence suggests the origin of the three lightest density renaturated human DNA families to be satellites I, II and III.     

The helical character of the S6 segment of TRPV1 channels

The era of the molecular structure of ion channels has revealed that their transmembrane segments are alpha helices, as was suspected from hydropathy analysis and experimental data. TRP channels are recent additions to the known families of ion channels and little structural data is available. In a recent work, we explored the conformational changes occurring at the putative S6 segment of TRPV1 channels and observed a periodicity of chemical modification of residues suggestive of an alpha helical structure. Further analysis of the periodicity of the disposition of hydrophobic residues in the S6 segment, suggests that the general architecture of the TRPV1 S6 segment, is very similar to that of voltage-dependent channels of known structure—an aqueous cavity lined by an amphipathic alpha helix, with most of the hydrophobic residues pointing into it.     

FSSA: a novel method for identifying functional signatures from structural alignments

MOTIVATION: It is commonly believed that sequence determines structure, which in turn determines function. However, the presence of many proteins with the same structural fold but different functions suggests that global structure and function do not always correlate well. RESULTS: We propose a method for accurate functional annotation, based on identification of functional signatures from structural alignments (FSSA) using the Structural Classification of Proteins (SCOP) database. The FSSA method is superior at function discrimination and classification compared with several methods that directly inherit functional annotation information from homology inference, such as Smith-Waterman, PSI-BLAST, hidden Markov models and structure comparison methods, for a large number of structural fold families. Our results indicate that the contributions of amino acid residue types and positions to structure and function are largely separable for proteins in multi-functional fold families.