Induction of transgenic hairy roots in soybean genotypes by Agrobacterium rhizogenes‑mediated transformation

The objective of this work was to perform the screening of soybean genotypes as to their ability to respond to the induction of hairy roots by Agrobacterium rhizogenes‑mediated transformation. Four Brazilian soybean cultivars (BRSMG 68 Vencedora, BRS 137, Embrapa 48, and MG/BR 46 Conquista) and two North American ones adapted to Brazilian cropping conditions (Bragg and IAS‑5) were screened for their capacity to respond to A. rhizogenes in protocols for in vitro hairy root culture and ex vitro composite plant production. Four‑day‑old seedlings with uniform size were injected with A. rhizogenes harboring the plasmid p35S‑GFP. Seedlings expressing green fluorescent protein (GFP) in at least one hairy root were used to determine the transformation frequency. Using an axenic in vitro protocol, excised cotyledons from four‑day‑old seedlings were infected with A. rhizogenes harboring the pCAMBIA1301 plasmid, containing the gusA reporter gene. The transformation frequency and the number of days for hairy root emergence after bacterial infection (DAI) were evaluated. The transformation frequency and DAI varied according to the genotype. Cultivars MG/BR 46 Conquista and BRSMG 68 Vencedora are more susceptible to A. rhizogenes and can be recommended for transformation experiments.

Amoebal pathogens as emerging causal agents of pneumonia.

Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella-like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.).

Maitikkauute-aineiden vaikutus tervasroson (Cronartium flaccidum ja Peridermium pini) rihmastoviljelmien kasvuun keinoalustoilla

Seloste artikkelista: Effects of Melampyrum extracts on the growth of axenic cultures of Cronartium flaccidum and Peridermium pini / Juha Kaitera & Heikki Nuorteva. - Julkaisussa: Silva Fennica 44 (2010) : 2, s. 197-202.

Sinningia allagophylla(Gesneriaceae): in vitro cultivation of a native plant of the Brazilian cerrado

We used axillary buds as initial explants for hormone interaction studies required for in vitro cultivation of S. allagophylla. Callus production was achieved on gelled Murashige & Skoog medium (MS) supplemented with indole-3-acetic acid (IAA= 0.1 and 0.5 mg.l­1 alone or combined with 6 benzylaminopurine) (BA= 0.01 and 0.1 mg.l-1). A hormone balance between IAA and BA that would encourage shoot bud development was not found. Nodal segments from axenic cultures grown in the presence of cytokinin (0.1 mg.1­1 of BA) without any auxin on MS medium with half-strength macronutrients were used as a standard explant source for subsequent experiments on optimum mineral culture media composition for S. allagophylla in vitro cultivation. We found that explants kept in vitro on gelled Gamborg et al. (B5) mineral composition culture medium showed better shoot and specially root growth than on MS medium. Comparisons of the ammonium and nitrate ratios of MS and B5 media indicate that B5 medium has a substantial reduced ammonium ion when compared to MS medium, as well as a lower total nitrogen level. The growth response pattern obtained in vitro may be evidence of the adaptation of this species to soils of poor mineral composition as found in the Brazilian cerrado, as well as an indication that nitrogen levels play a key role for S. allagophylla growth.

Host-parasite relationships in mycoparasite /

A mycoparasite, Piptocephalis virginiana ^ shows a resemblance to fungal parasites of higher plants in the fine structure of hyphae and haustoria. The morphology and fine structure of host and parasitic fungi have been described. The mode of penetration of the host cell, Choanephora cucurbitarum , probably involves mechanical forces. Although the presence of cell wall degrading enzyme was not detected by conventional techniques, its role in penetration can't be ruled out. A collar around the haustorial neck is formed as an extension of the host cell wall. No papilla was detected although appressorixim was seen during penetration. The young haustorium is enclosed in highly invaginating plasmalemma of the host cell and n\imerous cisternae of endoplasmic reticulum. Appearance of an electron—dense sheath around the mature haustorium seems to coincide with the disappearance of cisternae of endoplasmic reticulum from the host cystoplasm in the vicinity of the haustorium. The role of host cytoplasm particularly of endoplasmic reticulum in the development of the sheath is discussed. Extensive accumulation of spherosomes-like bodies, containing lipids, is found in haustorium, parasite and host hypha. Electron microscope revealed the parasiticculture spore has more lipid content than the axenic culture spore of P. virginiana . The biochemical and cytochemical tests also support these results. The mature spore of C. cucurbitarum possesses a thick three-layered cell wall, different from the hyphal wall. Its germination is accompanied by the formation of an elastic thin inner layer which surrounds the emerging germ tube and the growing hypha. High resolution autoradiography showed that H N-acetyl-glucosamine , a precursor of chitin, was incorporated preferentially in the thin inner layer of the spore wall and also in the cell wall of the growing hypha. When the label was fed to the infected cells, at different intervals after inoculation, grains were observed on the sheath which developed around the haustorium of P. virginiana , 30 hours after inoculation. The significance of these results in relation to the origin and composition of the sheath is discussed.

Syntrophic relationships between algae and bacteria in a fresh-water stream and in culture /

Interactions between freshwater algae and bacteria were examined in a natural stream habitat and a laboratory model. Field observations provided circumstantial evidence, in statistical correlation for syntrophy between the microbial populations. This relation is probably subject to control by the temperature and pH of the aquatic environment. Several species of a pond community were isolated in axenic culture and tests were performed to determine the nature of mixed species interactions. Isolation procedures and field studies indicated that selected strains of Chlorella and Azotobacter were closely associated in their natural habitat. With the suspected controlling parameters, pH and temperature, held constant, mixed cultures of algae and bacteria were compared to axenic cultures of the same organisms, and a mutual stimulation of growth was observed. A mixed pure culture apparatus was designed in this laboratory to study the algal-bacterial interaction and to test the hypothesis that such an interaction may take place through a diffusable substance or through certain medium-borne conditions, Azotobacter was found to take up a Chlorella-produced exudate, to stimulate protein synthesis, to enhance chlorophyll production and to cause a numerical increase in the interacting Chlorella population. It is not clear whether control is at the environmental, cellular or genetic level in these mixed population interactions. Experimental observations in the model system, taken with field correlations allow one to state that there may be a direct relationship governing the population fluctuations of these two organisms in their natural stream surroundings.

Molecular studies on a Dictyostelium homolog of the tafazzin gene, the cause of Barth syndrome in humans

Der eukaryotische Mikroorganismus Dictyostelium discoideum lebt als einzellige Amöbe solange ausreichende Nahrungsressourcen zur Verfügung stehen. Sobald Nahrungsmangel eintritt, entwickeln sich die Zellen von einem einzelligen zu einem mehrzelligen Zustand, der mit einem multizellulären Fruchtkörper abschließt. Dieser Prozess wird durch eine Reihe aufeinanderfolgender Signale organisiert, die eine differentielle Genexpression regulieren. Die Gene der Discoidin I Familie gehören zu den Ersten, die im Laufe des Wachstums-Differenzierungs-Übergangs (engl. GDT) aktiviert werden. Sie eignen sich daher vorzüglich als Marker für den Beginn der Entwicklung. Mit Hilfe einer REMI-Mutagenese und Discoidin I als molekularem Marker sind verschiedene Komponenten des Wachstums-Differenzierungs-Übergangs in unserer Arbeitsgruppe identifiziert worden (Zeng et al., 2000 A und B; Riemann und Nellen, persönliche Mitteilung). Mit demselben Ansatz wurde in der vorliegenden Arbeit eine REMI-Mutante identifiziert, die eine Fehl-Expression von Discoidin zeigte und einen axenischen Wachstumsdefekt bei 15 °C aufwies. Das Gen wurde als Homolog zum humanen Tafazzin-Gen identifiziert. Dieses Gen wurde zur Rekonstruktion des Phänotyps über homologe Rekombination erneut disruptiert, was wie erwartet zu dem zuerst beschriebenen Phänotyp führte. Folgerichtig ergab eine Überexpression des Gens in den Mutanten eine Komplementation des Phänotyps. Immunfluoreszenz-Experimente zeigten eine mitochondriale Lokalisation des Dictyostelium discoideum Taffazzin Proteins. Dass ein mitochondriales Protein in Zusammenhang mit dem Wachstums-Differenzierungs-Übergang steht, ist ein unerwarteter Befund, der aber als Hinweis darauf gewertet werden kann, dass Mitochondrien einen direkten Einfluss auf die entwicklungsspezifische Signaltransduktion ausüben. Die Taffazzin Disruptions-Mutante in Dictyostelium führte zu einem abnormalen Cardiolipin Metabolismus. Dieses Phospholipid ist ein charakteristischer Bestandteil der inneren Mitochondrienmembran und für die Funktion verschiedener Enzyme erforderlich. Unsere vorläufigen Analysen des Phospholipid-Gehalts zeigten Übereinstimmung mit Daten von Patienten mit Barth-Syndrom, einer humanen Erkrankung, bei der das Taffazzin-Gen Mutationen aufweist, und mit Hefe-Mutanten dieses Gens. Dies zeigt den Wert von Dictyostelium discoideum als einen weiteren Modelorganismus zur Untersuchung des Barth-Syndroms und zur Erprobung möglicher Therapieansätze.

Heterochromatin und epigenetische Kontrolle der Centromere in Dictyostelium discoideum

Heterochromatin Protein 1 (HP1) is an evolutionarily conserved protein required for formation of a higher-order chromatin structures and epigenetic gene silencing. The objective of the present work was to functionally characterise HP1-like proteins in Dictyostelium discoideum, and to investigate their function in heterochromatin formation and transcriptional gene silencing. The Dictyostelium genome encodes three HP1-like proteins (hcpA, hcpB, hcpC), from which only two, hcpA and hcpB, but not hcpC were found to be expressed during vegetative growth and under developmental conditions. Therefore, hcpC, albeit no obvious pseudogene, was excluded from this study. Both HcpA and HcpB show the characteristic conserved domain structure of HP1 proteins, consisting of an N-terminal chromo domain and a C-terminal chromo shadow domain, which are separated by a hinge. Both proteins show all biochemical activities characteristic for HP1 proteins, such as homo- and heterodimerisation in vitro and in vivo, and DNA binding activtity. HcpA furthermore seems to bind to K9-methylated histone H3 in vitro. The proteins thus appear to be structurally and functionally conserved in Dictyostelium. The proteins display largely identical subnuclear distribution in several minor foci and concentration in one major cluster at the nuclear periphery. The localisation of this cluster adjacent to the nucleus-associated centrosome and its mitotic behaviour strongly suggest that it represents centromeric heterochromatin. Furthermore, it is characterised by histone H3 lysine-9 dimethylation (H3K9me2), which is another hallmark of Dictyostelium heterochromatin. Therefore, one important aspect of the work was to characterise the so-far largely unknown structural organisation of centromeric heterochromatin. The Dictyostelium homologue of inner centromere protein INCENP (DdINCENP), co-localized with both HcpA and H3K9me2 during metaphase, providing further evidence that H3K9me2 and HcpA/B localisation represent centromeric heterochromatin. Chromatin immunoprecipitation (ChIP) showed that two types of high-copy number retrotransposons (DIRS-1 and skipper), which form large irregular arrays at the chromosome ends, which are thought to contain the Dictyostelium centromeres, are characterised by H3K9me2. Neither overexpression of full-length HcpA or HcpB, nor deletion of single Hcp isoforms resulted in changes in retrotransposon transcript levels. However, overexpression of a C-terminally truncated HcpA protein, assumed to display a dominant negative effect, lead to an increase in skipper retrotransposon transcript levels. Furthermore, overexpression of this protein lead to severe growth defects in axenic suspension culture and reduced cell viability. In order to elucidate the proteins functions in centromeric heterochromatin formation, gene knock-outs for both hcpA and hcpB were generated. Both genes could be successfully targeted and disrupted by homologous recombination. Surprisingly, the degree of functional redundancy of the two isoforms was, although not unexpected, very high. Both single knock-out mutants did not show any obvious phenotypes under standard laboratory conditions and only deletion of hcpA resulted in subtle growth phenotypes when grown at low temperature. All attempts to generate a double null mutant failed. However, both endogenous genes could be disrupted in cells in which a rescue construct that ectopically expressed one of the isoforms either with N-terminal 6xHis- or GFP-tag had been introduced. The data imply that the presence of at least one Hcp isoform is essential in Dictyostelium. The lethality of the hcpA/hcpB double mutant thus greatly hampered functional analysis of the two genes. However, the experiment provided genetic evidence that the GFP-HcpA fusion protein, because of its ability to compensate the loss of the endogenous HcpA protein, was a functional protein. The proteins displayed quantitative differences in dimerisation behaviour, which are conferred by the slightly different hinge and chromo shadow domains at the C-termini. Dimerisation preferences in increasing order were HcpA-HcpA << HcpA-HcpB << HcpB-HcpB. Overexpression of GFP-HcpA or a chimeric protein containing the HcpA C-terminus (GFP-HcpBNAC), but not overexpression of GFP-HcpB or GFP-HcpANBC, lead to increased frequencies of anaphase bridges in late mitotic cells, which are thought to be caused by telomere-telomere fusions. Chromatin targeting of the two proteins is achieved by at least two distinct mechanisms. The N-terminal chromo domain and hinge of the proteins are required for targeting to centromeric heterochromatin, while the C-terminal portion encoding the CSD is required for targeting to several other chromatin regions at the nuclear periphery that are characterised by H3K9me2. Targeting to centromeric heterochromatin likely involves direct binding to DNA. The Dictyostelium genome encodes for all subunits of the origin recognition complex (ORC), which is a possible upstream component of HP1 targeting to chromatin. Overexpression of GFP-tagged OrcB, the Dictyostelium Orc2 homologue, showed a distinct nuclear localisation that partially overlapped with the HcpA distribution. Furthermore, GFP-OrcB localized to the centrosome during the entire cell cycle, indicating an involvement in centrosome function. DnmA is the sole DNA methyltransferase in Dictyostelium required for all DNA(cytosine-)methylation. To test for its in vivo activity, two different cell lines were established that ectopically expressed DnmA-myc or DnmA-GFP. It was assumed that overexpression of these proteins might cause an increase in the 5-methyl-cytosine(5-mC)-levels in the genomic DNA due to genomic hypermethylation. Although DnmA-GFP showed preferential localisation in the nucleus, no changes in the 5-mC-levels in the genomic DNA could be detected by capillary electrophoresis.

Impact of chlorophenols and heavy metals on soil microbiota: their effects on activity and community composition, and resistant strains with potential for bioremetiation

Pollution by toxic compounds is one of the most relevant environmental damages to ecosystems produced by human activity and, therefore, it must be considered in environmental protection and restoration of contaminated sites. According to this purposes, the main goal of this doctoral thesis has been to analyse the impact of several chlorophenols and heavy metals on the microbial communities of two typical Mediterranean soils. The ecological risk concentrations of each pollutant, which have been determined according to respirometric activity and changes in the microbial community composition, and the factors that influence on their effective toxic concentrations (bioavailable pollutants) have been analysed in order to predict their potential impact on different soil ecosystems and provide scientific data for the regulation of the soil protection policies. Moreover, resistant microorganisms with pollutant removal capacities have been isolated from artificially contaminated soil microcosms and tested in axenic cultures, to infer their potential usefulness for bioremediation.

Colonization-induced host-gut microbial metabolic interaction

The gut microbiota enhances the host's metabolic capacity for processing nutrients and drugs and modulate the activities of multiple pathways in a variety of organ systems. We have probed the systemic metabolic adaptation to gut colonization for 20 days following exposure of axenic mice (n = 35) to a typical environmental microbial background using high-resolution (1)H nuclear magnetic resonance (NMR) spectroscopy to analyze urine, plasma, liver, kidney, and colon (5 time points) metabolic profiles. Acquisition of the gut microbiota was associated with rapid increase in body weight (4%) over the first 5 days of colonization with parallel changes in multiple pathways in all compartments analyzed. The colonization process stimulated glycogenesis in the liver prior to triggering increases in hepatic triglyceride synthesis. These changes were associated with modifications of hepatic Cyp8b1 expression and the subsequent alteration of bile acid metabolites, including taurocholate and tauromuricholate, which are essential regulators of lipid absorption. Expression and activity of major drug-metabolizing enzymes (Cyp3a11 and Cyp2c29) were also significantly stimulated. Remarkably, statistical modeling of the interactions between hepatic metabolic profiles and microbial composition analyzed by 16S rRNA gene pyrosequencing revealed strong associations of the Coriobacteriaceae family with both the hepatic triglyceride, glucose, and glycogen levels and the metabolism of xenobiotics. These data demonstrate the importance of microbial activity in metabolic phenotype development, indicating that microbiota manipulation is a useful tool for beneficially modulating xenobiotic metabolism and pharmacokinetics in personalized health care. IMPORTANCE: Gut bacteria have been associated with various essential biological functions in humans such as energy harvest and regulation of blood pressure. Furthermore, gut microbial colonization occurs after birth in parallel with other critical processes such as immune and cognitive development. Thus, it is essential to understand the bidirectional interaction between the host metabolism and its symbionts. Here, we describe the first evidence of an in vivo association between a family of bacteria and hepatic lipid metabolism. These results provide new insights into the fundamental mechanisms that regulate host-gut microbiota interactions and are thus of wide interest to microbiological, nutrition, metabolic, systems biology, and pharmaceutical research communities. This work will also contribute to developing novel strategies in the alteration of host-gut microbiota relationships which can in turn beneficially modulate the host metabolism.

The endophytic fungus Piriformospora indica protects wheat from Fusarium crown rot disease in simulated UK autumn conditions

The root endophytic fungus Piriformospora indica (Sebacinacea) forms mutualistic symbioses with a broad range of host plants, increasing their biomass production and resistance to fungal pathogens. We evaluated the effect of P. indica on Fusarium crown rot disease of wheat, under in vitro and glasshouse conditions. Interaction of P. indica and Fusarium isolates under axenic culture conditions indicated no direct antagonistic activity of P. indica against Fusarium isolates. Seedlings of wheat were inoculated with P. indica and pathogenic Fusarium culmorum or F. graminearum and grown in sterilised soil-free medium or in a non-sterilised mix of soil and sand. Fusarium alone reduced emergence and led to visible browning and reduced root growth. Roots of seedlings in pots inoculated with both Fusarium isolates and P. indica were free of visible symptoms; seed emergence and root biomass were equivalent to the uninoculated. DNA was quantified by real-time polymerase chain reaction (qPCR). The ratio of Fusarium DNA to wheat DNA rose rapidly in the plants inoculated with Fusarium alone; isolates and species were not significantly different. P. indica inoculation reduced the ratio of Fusarium to host DNA in the root systems. The reduction increased with time. The ratio of P. indica to wheat DNA initially rose but then declined in root systems without Fusarium. With Fusarium, the ratio rose throughout the experiment. The absolute amount of Fusarium DNA in root systems increased in the absence of P. indica but was static in plants co-inoculated with P. indica.

Cell motility and SCAR localisation in axenically growing Dictyostelium cells.

Dictyostelium is a popular experimental organism, in particular for studies of actin dynamics, cell motility and chemotaxis. We find that the motility of axenic cells is unexpectedly different from other strains during growth. In particular, vegetative AX3 cells do not show detectable localisation of SCAR and its regulatory complex to actin-rich protrusions such as filopodia and pseudopodia. Similarly, a range of different mutations, in particular knockouts of members of the SCAR complex and Ras proteins, cause different phenotypes during vegetative growth in different parental strains. Development reverses this unusual behaviour; aggregation-competent AX3 cells localise SCAR in the same way as cells of other strains and species. Studies on cell motility using vegetative cells should therefore be interpreted with caution.

Phosphate supply and arsenate toxicity in ectomycorrhizal fungi

Three species of ectomycorrhizal fungi (Hebeloma crustuliniforme, Suillus variegatus and Cenococcum geophilum) were grown in axenic culture amended with range of AsO43– concentration under three different PO43– regimes. The fungi exhibited different growth responses to AsO43– that varied with PO43– concentration. Suillus variegatus showed the greatest sensitivity to AsO43–, with growth almost completely inhibited in the presence of AsO43– under the lower two PO43– treatments. Under the highest PO43– treatment however, growth was enhanced and S. variegatus was able to persist at AsO43– concentrations of up to 4 mM. Hebeloma crustuliniforme also showed high sensitivity to AsO43– especially at low PO43– concentration. The two higher PO43– treatments had an ameliorating effect on AsO43– toxicity in H. crustuliniforme. This demonstrates the ability of PO43– to alleviate AsO43– toxicity. The response from S. variegatus and H. crustuliniforme, both basidiomycetes, was in contrast to the ascomycete C. geophilum. This fungus demonstrated tolerance to AsO43– when grown in culture solution and PO43– did not have an ameliorating effect on AsO43– toxicity in C. geophilum.

Low-temperature-induced changes in trehalose, mannitol and arabitol associated with enhanced tolerance to freezing in ectomycorrhizal basidiomycetes ( Hebeloma spp.)

Ectomycorrhizal fungi have been shown to survive sub-zero temperatures in axenic culture and in the field. However, the physiological basis for resistance to freezing is poorly understood. In order to survive freezing, mycelia must synthesise compounds that pro-tect the cells from frost damage, and certain fungal-spe-cific soluble carbohydrates have been implicated in this role. Tissue concentrations of arabitol, mannitol and trehalose were measured in axenic cultures of eight Hebeloma strains of arctic and temperate origin grown at 22, 12, 6 and 2°C. In a separate experiment, mycelia were frozen to –5°C after pre-conditioning at either 2°C or 22°C. For some, especially temperate strains, there was a clear increase in specific soluble carbohydrates at lower growth temperatures. Trehalose and mannitol were present in all strains and the highest concentrations (close to 2.5% and 0.5% dry wt.) were recorded only after a cold period. Arabitol was found in four strains only when grown at low temperature. Cold pre-condi-tioning enhanced recovery of mycelia following freez-ing. In four out of eight strains, this was paralleled by increases in mannitol and trehalose concentration at low temperature that presumably contribute towards cryopro-tection. The results are discussed in an ecological con-text with regard to mycelial overwintering in soil.

Utilization of organic nitrogen by ectomycorrhizal fungi (Hebeloma spp.) of arctic and temperate origin

Arctic and temperate strains of Hebeloma spp. were grown in axenic culture on glutamic acid, alanine, lysine and NH4+ as sole sources of nitrogen (N), with excess carbon (C) or deficient C (supplied as glucose). Their ability to utilize seed protein as a natural N source was also assessed. All strains tested had the capacity to assimilate amino acids and generally utilized alanine and glutamic acid more readily than NH4+. Some strains were able to utilize amino C when starved of glucose C, and could mineralize amino-N to NH3-N. Arctic strains, in particular, appeared to be pre-adapted to the utilization of seed protein N and glutamic acid N, which is often liberated in high concentrations after soil freezing. The results are discussed in relation to their possible ecological importance.