Phylogenetic heterogeneity within the genus Herpetosiphon: Transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen, nov. in the Flexibacter-Bacteroides-Cytophaga phylum

Analysis of the 16S rDNA sequences of species currently assigned to the genus Herpetosiphon revealed intrageneric phylogenetic heterogeneity. The thermotolerant freshwater species Herpetosiphon geysericola is most closely related to the type species Herpetosiphon aurantiacus in the Chloroflexus Subdivision of the green non-sulfur bacteria, The marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus, on the other hand, were found to form a cluster with the sheathed bacterium Haliscomenobacter hydrossis in the Saprospira group of the Flexibacter-Bacteroides-Cytophaga (FBC) phylum. A proposal is made to transfer these marine species to the genus Lewinella gen. nov. as Lewinella cohaerens comb, nov., Lewinella nigricans comb. nov, and Lewinella persica comb. nov. The marine sheathed gliding bacterium Flexithrix dorotheae was also found to be a member of the FBC phylum but on a separate phylogenetic line to the marine herpetosiphons now assigned to the genus Lewinella.

Expokit: A software package for computing matrix exponentials

Expokit provides a set of routines aimed at computing matrix exponentials. More precisely, it computes either a small matrix exponential in full, the action of a large sparse matrix exponential on an operand vector, or the solution of a system of linear ODEs with constant inhomogeneity. The backbone of the sparse routines consists of matrix-free Krylov subspace projection methods (Arnoldi and Lanczos processes), and that is why the toolkit is capable of coping with sparse matrices of large dimension. The software handles real and complex matrices and provides specific routines for symmetric and Hermitian matrices. The computation of matrix exponentials is a numerical issue of critical importance in the area of Markov chains and furthermore, the computed solution is subject to probabilistic constraints. In addition to addressing general matrix exponentials, a distinct attention is assigned to the computation of transient states of Markov chains.

Localisation of gelatinase activity in epidermal hoof lamellae by in situ zymography

In situ gelatin zymography is a technique, which utilises a gelatin-based emulsion overlay to detect and, more importantly, localise the gelatinase activity in underlying tissue. Gelatinase A [matrix metalloproteinase-2 (MMP-2)] and gelatinase B [matrix metalloproteinase-9 (MMP-9)] are present in equine hoof homogenates and supernatants from cultured hoof explants by SDS-PAGE gelatin zymography, and it has been assumed that the enzymes are derived solely from matrix and epithelia and not from other sources such as leucocytes. Using in situ zymography, gelatinases are shown to be localised within the equine epidermal hoof lamellae and, more specifically, are apparently produced by epidermal basal and/or parabasal cells. The pattern of expression correlates with that expected based on the progression of pathological changes observed during the onset of laminitis, thus providing further evidence that laminitis pathology probably arises as a result of inadequate local MMP regulation.

Transfer of a supernumerary chromosome between vegetatively incompatible biotypes of the fungus Colletotrichum gloeosporioides

Two biotypes (A and B) of Colletotrichum gloeosporioides infect the tropical legumes Stylosanthes spp. in Australia. These biotypes are asexual and vegetatively incompatible. However, field isolates of biotype B carrying a supernumerary 2-Mb chromosome, thought to originate from biotype A, have been reported previously. We tested the hypothesis that the 2-Mb chromosome could be transferred from biotype A to biotype B under laboratory conditions. Selectable marker genes conferring resistance to hygromycin and phleomycin were introduced into isolates of biotypes A and B, respectively. A transformant of biotype A, with the hygromycin resistance gene integrated on the 2-Mb chromosome, was cocultivated with phleomycin-resistant transformants of biotype B. Double antibiotic-resistant colonies were obtained from conidia of these mixed cultures at a frequency of approximately 10(-7). Molecular analysis using RFLPs, RAPDs, and electrophoretic karyotypes showed that these colonies contained the 2-Mb chromosome in a biotype B genetic background. In contrast, no double antibiotic colonies developed from conidia obtained from mixed cultures of phleomycin-resistant transformants of biotype B with biotype A transformants carrying the hygromycin resistance gene integrated in chromosomes >2 Mb in size. The results demonstrated that the 2-Mb chromosome was selectively transferred from biotype A to biotype B. The horizontal transfer of specific chromosomes across vegetative incompatibility barriers may explain the origin of supernumerary chromosomes in fungi.

mRNA differential display of 2-amino-1-methyl-6-phenylinlidazo[4,5-b]pyridine-induced rat mammary gland tumors

The mRNA differential display technique was used to compare mRNAs between normal mammary gland and turner-derived epithelial cells from female Sprague-Dawley rat mammary gland tumors induced by the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) and promoted by a high-fat diet (23.5% corn oil). Two genes, beta-casein and transferrin, were identified as differentially expressed. The expression of these genes was examined across a bank of rat mammary gland tumors derived from animals on a low-fat diet (5% corn oil) or the high-fat diet. Carcinomas had over a 10- and 50-fold lower expression of beta-casein and transferrin, respectively than normal mammary gland. In addition, carcinomas from animals on the high-fat diet showed on average a 5-fold higher expression of beta-casein, and transferrin than carcinomas from animals on the low-fat diet. The results indicate the process of mammary gland tumorigenesis alters the expression of certain genes in the mammary gland, and that the level of dietary fat further modulates the expression of these genes.

A numerical study of large sparse matrix exponentials arising in Markov chains

Krylov subspace techniques have been shown to yield robust methods for the numerical computation of large sparse matrix exponentials and especially the transient solutions of Markov Chains. The attractiveness of these methods results from the fact that they allow us to compute the action of a matrix exponential operator on an operand vector without having to compute, explicitly, the matrix exponential in isolation. In this paper we compare a Krylov-based method with some of the current approaches used for computing transient solutions of Markov chains. After a brief synthesis of the features of the methods used, wide-ranging numerical comparisons are performed on a power challenge array supercomputer on three different models. (C) 1999 Elsevier Science B.V. All rights reserved.AMS Classification: 65F99; 65L05; 65U05.

Efficient transformation and regeneration of diverse cultivars of peanut (Arachis hypogaea L.) by particle bombardment into embryogenic callus produced from mature seeds

Peanut, one of the world's most important oilseed crops, has a narrow germplasm base and lacks sources of resistance to several major diseases. The species is considered recalcitrant to transformation, with few confirmed transgenic plants upon particle bombardment or Agrobacterium treatment. Reported transformation methods are limited by low efficiency, cultivar specificity, chimeric or infertile transformants, or availability of explants. Here we present a method to efficiently transform cultivars in both botanical types of peanut, by (1) particle bombardment into embryogenic callus derived from mature seeds, (2) escape-free (not stepwise) selection for hygromycin B resistance, (3) brief osmotic desiccation followed by sequential incubation on charcoal and cytokinin-containing media; resulting in efficient conversion of transformed somatic embryos into fertile, non-chimeric, transgenic plants. The method produces three to six independent transformants per bombardment of 10 cm(2) embryogenic callus. Potted, transgenic plant lines can be regenerated within 9 months of callus initiation, or 6 months after bombardment. Transgene copy number ranged from one to 20 with multiple integration sites. There was ca. 50% coexpression of hph and luc or uidA genes coprecipitated on separate plasmids. Reporter gene (luc) expression was confirmed in T-1 progeny from each of six tested independent transformants. Insufficient seeds were produced under containment conditions to determine segregation ratios. The practicality of the technique for efficient cotransformation with selected and unselected genes is demonstrated using major commercial peanut varieties in Australia (cv. NC-7, a virginia market type) and Indonesia (cv. Gajah, a spanish market type).

Description of Skermanella parooensis gen. nov., sp. nov. to accommodate Conglomeromonas largomobilis subsp. parooensis following the transfer of Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum

As a consequence of the transfer of the type species Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum, the name of the genus Conglomeromonas must be changed in accordance with Rule 37a(1) of the International Code of Nomenclature of Bacteria. Consequently, it is proposed that the subspecies Conglomeromonas largomobilis subsp, parooensis be transferred to the genus Skermanella gen, nov. as the type species Skermanella parooensis gen, nov., sp, nov. This taxon belongs to an isolated subline of descent in the Azospirillum branch of the alpha-Proteobacteria. The spelling of the specific epithet of Azospirillum largomobile is corrected to Azospirillum largimobile.

Effects of medium thermoelasticity on high Rayleigh number steady-state heat transfer and mineralization in deformable fluid-saturated porous media heated from below

In this paper, a solution method is presented to deal with fully coupled problems between medium deformation, pore-fluid flow and heat transfer in fluid-saturated porous media having supercritical Rayleigh numbers. To validate the present solution method, analytical solutions to a benchmark problem are derived for some special cases. After the solution method is validated, a numerical study is carried out to investigate the effects of medium thermoelasticity on high Rayleigh number steady-state heat transfer and mineralization in fluid-saturated media when they are heated from below. The related numerical results have demonstrated that: (1) medium thermoelasticity has a little influence on the overall pattern of convective pore-fluid flow, but it has a considerable effect on the localization of medium deformation, pore-fluid flow, heat transfer and mineralization in a porous medium, especially when the porous medium is comprised of soft rock masses; (2) convective pore-fluid flow plays a very important role in the localization of medium deformation, heat transfer and mineralization in a porous medium. (C) 1999 Elsevier Science S.A. All rights reserved.

New techniques in nutritional assessment: body composition methods

New techniques in air-displacement plethysmography seem to have overcome many of the previous problems of poor reproducibility and validity. These have made body-density measurements available to a larger range of individuals, including children, elderly and sick patients who often have difficulties in being submerged underwater in hydrodensitometry systems. The BOD POD air-displacement system (BOD POD body composition system; Life Measurement Instruments, Concord, CA, USA) is more precise than hydrodensitometry, is simple and rapid to operate (approximately 1 min measurements) and the results agree closely with those of hydrodensitometry (e.g. +/-3.4% for estimation of body fat). Body line scanners employing the principles of three-dimensional photography are potentially able to measure the surface area and volume of the body and its segments even more rapidly (approximately 10 s), but the validity of the measurements needs to be established. Advances in i.r. spectroscopy and mathematical modelling for calculating the area under the curve have improved precision for measuring enrichment of (H2O)-H-2 in studies of water dilution (CV 0.1-0.9% within the range of 400-1000 mu l/l) in saliva, plasma and urine. The technique is rapid and compares closely with mass spectrometry (bias 1 (SD 2) %). Advances in bedside bioelectrical-impedance techniques are making possible potential measurements of skinfold thicknesses and limb muscle mass electronically. Preliminary results suggest that the electronic method is more reproducible (intra-and inter-individual reproducibility for measuring skinfold thicknesses) and associated with less bias (+ 12%), than anthropometry (+ 40%). In addition to these selected examples, the 'mobility' or transfer of reference methods between centres has made the distinction between reference and bedside or field techniques less distinct than in the past.

The crack tip strain field of AISI 4340 - Part I - Measurement technique

This is the first paper in a study on the influence of the environment on the crack tip strain field for AISI 4340. A stressing stage for the environmental scanning electron microscope (ESEM) was constructed which was capable of applying loads up to 60 kN to fracture-mechanics samples. The measurement of the crack tip strain field required preparation (by electron lithography or chemical etching) of a system of reference points spaced at similar to 5 mu m intervals on the sample surface, loading the sample inside an electron microscope, image processing procedures to measure the displacement at each reference point and calculation of the strain field. Two algorithms to calculate strain were evaluated. Possible sources of errors were calculation errors due to the algorithm, errors inherent in the image processing procedure and errors due to the limited precision of the displacement measurements. Estimation of the contribution of each source of error was performed. The technique allows measurement of the crack tip strain field over an area of 50 x 40 mu m with a strain precision better than +/- 0.02 at distances larger than 5 mu m from the crack tip. (C) 1999 Kluwer Academic Publishers.

Gene transfer and expression of a non-viral polycation-based vector in CD4(+) cells

CD4-selective targeting of an antibody-polycation-DNA complex was investigated The complex was synthesized with the anti-CD4 monoclonal antibody B-F5, polylysine(268) (pLL) and either the pGL3 control vector containing the luciferase reporter gene or the pGeneGrip vector containing the green fluorescent protein (GFP) gene. B-F5-pLL-DNA complexes inhibited the binding of I-125-B-F5 to CD4(+) Jurkat cells, while complexes synthesised either without B-F5 or using a non-specific mouse IgG1 antibody had little or no effect Expression of the luciferase reporter gene was achieved in Jurkat cells using the B-F5-pLL-pGL3 complex and was enhanced in the presence of PMA. Negligible luciferase activity was defected with the non-specific antibody complex in Jurkat cells or with the B-F5-pLL-pGL3 complex in the CD4(-) K-562 cells. Using complexes synthesised with the pGeneGrip vector, the transfection efficiency in Jurkat and K-562 cells was examined using confocal microscopy. More than 95% of Jurkat cells expressed GFP and the level of this expression was markedly enhanced by PMA. Negligible GFP expression was seen in K-562 cells or when B-F5 was replaced by a nonspecific antibody. Using flow cytometry, fluorescein-labelled complex showed specific targeting to CD4(+) cells in a mixed cell population from human peripheral blood. These studies demonstrate the selective transfection of CD4(+) T-lymphoid cells using a polycation-based gene delivery system. The complex may provide a means of delivering anti-HIV gene therapies to CD4(+) cells in vivo.

PAM chlorophyll fluorometry: a new in situ technique for stress assessment in scleractinian corals, used to examine the effects of cyanide from cyanide fishing

Sodium cyanide is being used on reefs in the Asia-Pacific region to capture live fish for the aquarium industry, and to supply a rapidly growing, restaurant-based demand, The effects of cyanide on reef biota have not been fully explored. To investigate its effect on hard corals, we exposed small branch lips of Stylophora pistillata and Acropora aspera to cyanide concentrations estimated to occur during cyanide fishing. Pulse amplitude modulation (PAM) chlorophyll fluorescence techniques were used to examine photoinhibition and photosynthetic electron transport in the symbiotic algae (zooxanthellae) in the tissues of the corals, These measurements were made in situ and in real time using a recently developed submersible PAM fluorometer. In S. pistillata. exposure to cyanide resulted in an almost complete cessation in photosynthetic electron transport rate. Both species displayed marked decreases in the ratio of variable fluorescence (F-v) to maximal fluorescence (F-m) (dark-adapted F-v/F-m), following exposure to cyanide, signifying a decrease in photochemical efficiency. Dark-adapted F-v/F-m recovered to normal levels in similar to 6 d, although intense tissue discolouration, a phenomenon well-recognised as coral 'bleaching' was observed during this period, Bleaching was caused by loss of zooxanthellae from the coral tissues, a well-recognised sub-lethal stress response of corals. Using the technique of chlorophyll fluorescence quenching analysis, corals exposed to cyanide did not show light activation of Calvin cycle enzymes and developed high levels of non-photochemical quenching (q(N)), signifying the photoprotective dissipation of excess light as heat, These features are symptomatic of the known properties of cyanide as an inhibitor of enzymes of the Calvin cycle. The results of this in situ study show that an impairment of zooxanthellar photosynthesis is; the site of cyanide-mediated toxicity, and is the cue that causes corals to release their symbiotic zooxanthellac following cyanide exposure. This study demonstrates the efficacy of PBM fluorometry as a new tool for in situ stress assessment in zooxanthellate scleractinian corals. (C) 1999 Elsevier Science Ltd. All rights reserved.