Graphical comparison of resemblance measures in phytosociology

A simple graphical method, COREM, is described for the comparison of quantitative resemblance measures. The basis of the method is the ordered comparison case series (OCCAS) composed of relevé pairs ranked in decreasing order of similarity. For a given OCCAS, values of given resemblance functions are calculated and plotted in COREM.Delta resemblance (DR) is defined as the rate of change between two neighbouring relevé pairs in the OCCAS. High mean delta resemblance (% MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \]) of a resemblance measure indicates a high power of resolution and small standard deviation (SDDR) is indicative of linearity. A measure of efficiency combines % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \] and SDDR in the coefficient of variation for delta resemblance (CVDR). An efficient measure shows balanced sensitivity to the common and differential species. With the method COREM locally optimal resemblance measures may be selected for any given set of relevés which produce the sharpest separation of clusters. A reasonable compromise is to use types of measures, such as the similarity ratio (SIM6), Czekanowski coefficient (SIM8), or floristic similarity (SIM9), which have the best chance of being successful in most relevé sets. A study of transformation functions on Braun-Blanquet values with the help of COREM demonstrates that the combined transformation is the most advantageous for clustering. It is shown that standardization by relevés, or conversion to unit sum has undesirable effects.During the preparation of this paper the author was a recipient of a Postgraduate Scholarship, Deutscher Akademischer Austauschdients, Dortmund, KFA Abteilung Algenforschung, Germany. The author would like to thank L. Orlóci, P. Juhász-Nagy and E. van der Maarel for valuable suggestions, and comments.     

Characterization of isolated Fe-loaded rat hepatocytes prepared by collagenase perfusion

Summary Hepatocytes from livers of rats loaded by Fe-dextran treatment were isolated by an in situ collagenase perfusion technique and evaluated for their biochemical, cytochemical, and morphological characteristics in cell culture. Iron loads 15 times higher than in normal rat liver cells isolated in the same way were retained in the preparations with 40% present as hemosiderin. A simple centrifugation-mathematical approach is described for the calculation of Fe content in the hepatocyte (95%) and reticuloendothelial (5%) fractions in the isolates. The cells were cultured for 22 h without loss of protein synthesis capability or significant changes in cell count, viability, endogenous glutamate-oxaloacetate transaminase (GOT) or Fe and were morphologically similar in most respects to unloaded (normal) hepatocytes similarly cultured. Studies are in progress to assess the utility of these preparations as a model for Fe mobilization from Fe-loaded animals. This work is supported by National Institutes of Health Grants AM 25647-03 (M. Dawson, Principal Investigator) and GM 28158-01 (C. Tyson, Principal Investigator). The technical assistance of Mr. Jack E. Dabbs, Mr. Charles Hart, and Mr. Randy Douglas is acknowledged.     

Suppression of synthesis of immunoglobulin in mouse myeloma cells by alloantibody

Summary Alloantibody-containing globulins that can suppress the production of hemolytic antibody plaques by antigenically stimulated Balb/c spleen cells were tested for their effect on Balb/c plasmacytoma cells. Two plasmacytomas, MOPC 21 and MOPC 315, which normally produce IgGl and IgA, respectively, were treated with CBA anti-Balb/c globulin from which the cytotoxic antibody had been largely removed by differential absorption. The effects on synthesis of the Ig's were studied in three experimental modes.1. When the tumor cells were pretreated with the antibody before incubation with ³H-thymidine labeled aminoacids, there was suppression of the synthesis of immunoglobulins, as measured in both the cell contents and the medium. The suppression was most marked at the highest concentration of antibody and decreased progressively with dilution. In the case of other or smaller peptides not precipitated by anti-Ig but precipitable by TCA, this could be demonstrated only in the most recently synthesized peptides, those found within the cells.2. When the exposure to the suppressive antibody was simultaneous with the incubation of tumor cells and labeled aminoacids suppression was again demonstrated, indicating that the suppressive effect was expressed as early as the synthesis of the peptides.3. Even when the exposure to labeled aminoacids began before the incubation with antibody, the cell contents, which included the most recently synthesized peptides, still showed the same effects of the successive dilutions of the suppressive antibody as the cell contents from the other modes of exposure. In the medium, however, there was an additional effect under these experimental conditions. Labeled material appeared in amounts that increased with increasing concentration of the suppressive antibody, suggesting the release from the cells of the peptides whose synthesis was interrupted by the antibody.     

Growth effects of lithium chloride in BALB/c 3T3 fibroblasts and madin-darby canine kidney epithelial cells

The ability of LiCl to initiate DNA synthesis was studied in Madin-Darby canine kidney (MDCK) cells, and mouse BALB/c 3T3 fibroblasts. In a defined culture medium lacking serum, LiCl increased DNA synthesis in BALB/c 3T3 cells 100–200% over control values. Maximum DNA synthesis was observed with concentrations of LiCl between 10 and 25 mM and increases from 40–50% over control were observed with concentrations as low as 1 mM. Exposure of BALB/c 3T3 cultures to LiCl resulted in an increase in the percentage of cells initiating DNA synthesis, total DNA content and cell number. Lithium chloride, in combination with insulin or epidermal growth factor (EGF), had either an additive or synergistic effect upon the growth of BALB/c 3T3 fibroblasts. MDCK cells proved refractory to the growth actions of LiCl, although they responded to EGF and insulin with increased DNA synthesis. Lithium chloride appears to have a direct effect on cell proliferation in some but not all cell types.     

Vibrio communities along a salinity gradient within a marine saltern hypersaline environment (Saline di Tarquinia,Italy)

Vibrio species are ubiquitous in a number of different aquatic environments and promptly adapting to environmental changes due to high genome plasticity. The presence of these bacteria in marine salterns, in relation to a salinity gradient has been not investigated yet. Moreover, it is not clear if these hypersaline environments could represent a reservoir for Vibrio spp. This work investigated, through a metagenetic approach, the distribution of Vibrio (over 2 years) in different ponds along the salinity gradient within the ‘Saline di Tarquinia’ salterns, considering also the adjacent coastal waters and an isolated brine storage basin (BSB). Vibrio occurrence was higher in the sea than in the ponds and BSB, where it usually represented a rare taxon (abundance <1%). In the sea, it showed abundances in-between 1%–2.6% in 8 months out of 24. Four OTUs were assigned to the Vibrio genus; except for one that was more abundant in BSB, the others were much higher in the sea. Redundancy analysis (RDA) suggested a different distribution of the OTUs in relation to water temperature and salinity. Vibrio was found, even with low abundances, at the highest salinities also, suggesting the salterns as a possible reservoir for the bacterium.     

The plant landscape as inferred from a basket of the Roman town of Privernum (Latium,central Italy)

Abstract

Privernum was a rich Roman colony located 70 km southwest of Rome (southern Latium, central Italy). The archaeobotanical investigations focused on the garden and related structures of the luxury domus della Soglia nilotica. They are archaeologically and radiocarbon dated to the second half of the 1st century AD. The remains of a charred basket were found in the filling of the euripus, an ornamental water basin of the garden. The weaving was made with twisted strands of the leaves of Ampelodesmos mauritanicus (Poir.) T. Durand and Schinz; for the bottom and the handle/s of the basket, wood of evergreen oaks and ash and/or elm, respectively were probably used. The basket contained Pinus pinea seeds and cone scales, and Prunus persica endocarps, which were probably burnt in summer. The sediment in the drainage system and in the kitchen was processed for macro- and microremains. The results indicate the presence of spontaneous ruderal and weed flora elements, typical of human settlement areas, and crops.     

Characterization of a Small Auxin-Up RNA (SAUR)-Like Gene Involved in Arabidopsis thaliana Development

The root of Arabidopsis thaliana is used as a model system to unravel the molecular nature of cell elongation and its arrest. From a micro-array performed on roots that were treated with aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene, a Small auxin-up RNA (SAUR)-like gene was found to be up regulated. As it appeared as the 76th gene in the family, it was named SAUR76. Root and leaf growth of overexpression lines ectopically expressing SAUR76 indicated the possible involvement of the gene in the division process. Using promoter::GUS and GFP lines strong expression was seen in endodermal and pericycle cells at the end of the elongation zone and during several stages of lateral root primordia development. ACC and IAA/NAA were able to induce a strong up regulation of the gene and changed the expression towards cortical and even epidermal cells at the beginning of the elongation zone. Confirmation of this up regulation of expression was delivered using qPCR, which also indicated that the expression quickly returned to normal levels when the inducing IAA-stimulus was removed, a behaviour also seen in other SAUR genes. Furthermore, confocal analysis of protein-GFP fusions localized the protein in the nucleus, cytoplasm and plasma membrane. SAUR76 expression was quantified in several mutants in ethylene and auxin-related pathways, which led to the conclusion that the expression of SAUR76 is mainly regulated by the increase in auxin that results from the addition of ACC, rather than by ACC itself.