Antibacterial activity of Arthrobacter strains isolated from Great Gobi A Strictly Protected Area, Mongolia

Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 Arthrobacter strains from topsoil samples collected from the Great Gobi A Strictly Protected Area in the Gobi Desert, were characterized by a combination of different techniques. The phylogenetic analysis, performed using their 16S rDNA sequences and the most similar Arthrobacter sequences found in databases, revealed that most of them were close to A. crystallopoietes, while others joined a sister group to the clade formed by A. humicola, A. pascens, and A. oryzae. The resistance of each strain to different antibiotics, heavy-metals, and NaCl was also tested as well as the inhibitory potential against human pathogens (i.e., Burkholderia ssp., Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus ssp.) via cross-streaking, to check the production of metabolites with antimicrobial activity. Data obtained revealed that all strains were resistant to heavy metals and were able to strongly interfere with the growth of many of the human pathogens tested. The volatile organic compounds (VOCs) profile of the 11 Arthrobacter strains was also analyzed. A total of 16 different metabolites were found, some of which were already known for having an inhibitory action against different Gram-positive and Gram-negative bacteria. Isolate MS-3A13, producing the highest quantity of VOCs, is the most efficient against Burkholderia cepacia complex (Bcc), K. pneumoniae, and coagulase-negative Staphylococci (CoNS) strains. This work highlights the importance of understanding microbial populations' phenotypical characteristics and dynamics in extreme environments to uncover the antimicrobial potential of new species and strains.

Characterization of Trichoderma species from forest ecosystems by high-throughput phenotypic microarray

The use of beneficial organisms for the biocontrol of soil-borne pathogens in forestry is still poor explored. In this work, the nutritional demands of 10 previously selected isolates of Trichoderma for the biocontrol of forest soil-borne pathogens have been tested by Phenotype Microarray technology, to investigate about their C-source utilization and exploring the possibility to obtain a microbial consortia (SynCom), an innovative strategy for the biocontrol of plant disease. All Trichoderma isolates tested in this study showed a high spore germination percentage within 3 d and evidenced nutritional preference regardless of the species they belong to, and unrelated to their soil of origin. Results of growth curve analysis and MANOVA test revealed that all isolates assimilate a broad range of substrates, generally preferring complex compounds such as monosaccharides related compounds, nitrogen compounds, carboxylic acids and esters. No evidence of competition for nutritional resources have been observed among isolates of this study. As a result, a combination of different isolates could be proposed to obtain a SynCom useful for the practice of phytopathogen biocontrol in forestry. The addition of i-erythritol, adenosine and turanose to a growth substrate could be suggested as stimulating compounds for the growth of the selected Trichoderma isolates.

Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil

Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.

Wood-Decaying Fungi: From Timber Degradation to Sustainable Insulating Biomaterials Production

Addressing the impacts of climate change and global warming has become an urgent priority for the planet's well-being. In recent decades the great potential of fungal-based products with characteristics equal to, or even outperforming, classic petroleum-derived products has been acknowledged. These new materials present the added advantage of having a reduced carbon footprint, less environmental impact and contributing to the shift away from a fossil-based economy. This study focused on the production of insulation panels using fungal mycelium and lignocellulosic materials as substrates. The process was optimized, starting with the selection of Trametes versicolor, Pleurotus ostreatus, P. eryngii, Ganoderma carnosum and Fomitopsis pinicola isolates, followed by the evaluation of three grain spawn substrates (millet, wheat and a 1:1 mix of millet and wheat grains) for mycelium propagation, and finishing with the production of various mycelium-based composites using five wood by-products and waste materials (pine sawdust, oak shavings, tree of heaven wood chips, wheat straw and shredded beech wood). The obtained biomaterials were characterized for internal structure by X-ray micro-CT, thermal transmittance using a thermoflowmeter and moisture absorption. The results showed that using a wheat and millet 1:1 (w/w) mix is the best option for spawn production regardless of the fungal isolate. In addition, the performance of the final composites was influenced both by the fungal isolate and the substrate used, with the latter having a stronger effect on the measured properties. The study shows that the most promising sustainable insulating biomaterial was created using T. versicolor grown on wheat straw.

Localized stem heating from the rest to growth phase induces latewood-like cell formation and slower stem radial growth in Norway spruce saplings

Recent climate projections predict a more rapid increase of winter temperature than summer and global temperature averages in temperate and cold environments. As there is relatively little experimental knowledge on the effect of winter warming on cambium phenology and stem growth in species growing in cold environments, the setting of manipulative experiments is considered of primary importance, and they can help to decipher the effect of reduced winter chilling and increased forcing temperatures on cambium reactivation, growth and xylem traits. In this study, localized stem heating was applied to investigate the effect of warming from the rest to the growth phase on cambium phenology, intra-annual stem growth dynamics and ring wood features in Picea abies (L.) H.Karst. We hypothesized that reduced winter chilling induces a postponed cambium dormancy release and decrease of stem growth, while high temperature during cell wall lignification determines an enrichment of latewood-like cells. The heating device was designed to maintain a +5 °C temperature delta with respect to air temperature, thus allowing an authentic scenario of warming. Continuous stem heating from the rest (November) to the growing phase determined, at the beginning of radial growth, a reduction of the number of cell layers in the cambium, higher number of cell layers in the wall thickening phase and an asynchronous stem radial growth when comparing heated and ambient saplings. Nevertheless, heating did not induce changes in the number of produced cell layers at the end of the growing season. The analyses of two-photon fluorescence images showed that woody rings formed during heating were enriched with latewood-like cells. Our results showed that an increase of 5 °C of temperature applied to the stem from the rest to growth might not influence, as generally reported, onset of cambial activity, but it could affect xylem morphology of Norway spruce in mountain environments.

Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds

Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.

Localized reshaping of the fungal community in response to a forest fungal pathogen reveals resilience of Mediterranean mycobiota

Mediterranean forests are facing the impact of pests such as the soilborne Phytophthora cambivora, the causal agent of Ink disease, and this impact is made more severe by global changes. The status and resilience of the soil microbial ecosystem in areas with such a disturbance are little known; however, the assessment of the microbial community is fundamental to preserve the ecosystem functioning under emerging challenges. We profile soil fungal communities in a chestnut stand affected by ink disease in Italy using metabarcoding, and couple high-throughput sequencing with physico-chemical parameters and dendrometric measurements. Since the site also includes an area where the disease symptoms seem to be suppressed, we performed several analyses to search for determinants that may contribute to such difference. We demonstrate that neither pathogen presence nor trees decline associate with the reduction of the residing community diversity and functions, but rather with microbial network reshaping through substitutions and new interactions, despite a conservation of core taxa. We predict interactions between taxa and parameters such as soil pH and C/N ratio, and suggest that disease incidence may also relate with disappearance of pathogen antagonists, including ericoid- and ectomycorrhizal (ECM) fungi. By combining metabarcoding and field studies, we infer the resilient status of the fungal community towards a biotic stressor, and provide a benchmark for the study of other threatened ecosystems.

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission

BACKGROUND

The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission, six crewmembers lived completely isolated from the outer world for 520 days following standardized diet regimes. The mission constitutes the first spaceflight simulation to Mars and was a unique experiment to determine, in a longitudinal study design, the composition and importance of the resident vs. a more variable microbiota-the fraction of the human microbiota that changes in time and according to environmental conditions-in humans.

METHODS

Here, we report the characterization of the salivary microbiota from 88 samples taken during and after Mars500 mission for a total of 720 days. Amplicon sequencing of the V3-V4 regions of 16S rRNA gene was performed, and results were analyzed monitoring the diversity of the microbiota while evaluating the effect of the three main variables present in the experimental system: time, diet, and individuality of each subject.

RESULTS

Results showed statistically significant effects for either time, diet, and individuality of each subject. The main contribution came from the individuality of each subject, emphasizing salivary microbiota-personalized features, and an individual-based resilience of the microbiota.

CONCLUSIONS

The uniqueness of Mars500 mission, allowed to dampen the effect of environmental variables on salivary microbiota, highlighting its pronounced personalization even after sharing the same physical space for more than a year. Video abstract.

Can sugar metabolism in the cambial region explain the water deficit tolerance in poplar?

Drought dramatically affects wood production by adversely impacting cambial cells and their derivatives. Photosynthesis and assimilate transport are also affected by drought conditions. Two poplar genotypes, Populus deltoides 'Dvina' and Populus alba 'Marte', demonstrated contrasting growth performance and water-carbon balance strategies; a mechanistic understanding of the water deficit response was provided by these poplar species. 'Marte' was found to be more anisohydric than 'Dvina'. This characteristic was associated with the capacity to reallocate carbohydrates during water deficits. In contrast, 'Dvina' displayed more conservative water management; carbohydrates were preferably stored or used for cellulose production rather than to achieve an osmotic balance between the phloem and the xylem. Data confirmed that the more 'risk-taking' characteristic of 'Marte' allowed a rapid recovery following water deficit and was connected to a different carbohydrate metabolism.

Can Teledialysis Help in the Clinical Management of Patients on Remote Hemodialysis?

This study investigated whether transmission of the parameters monitored from a remote center to the main center could improve the control of a dialysis session. The parameters of the computer connection module Monitral SC in remote and main centers, were transmitted by means of the Hospal data collection software (Demoplus) by modem, to the host computer. Each remote center can be temporarily disconnected, if necessary, from the telephone line and linked directly to a local computer. We checked 101 hemodialyses. The dialysis was monitored from filter washing to disconnection of the patients and the following parameters were selected: backfiltration during washing and hemodialysis: ultrafiltration, conductivity and temperature. From the sessions recorded (93%) we observed that backfiltration during the filter preparation phase was high (30%) in 28 sessions. Backfiltration during the preparatory phase is the major problem for correct management of dialysis sessions. The high percentage in which ultrafiltration had to be stopped shows that control of this parameter is still not ideal. Finally, the collection of monitor parameters and the comparative analysis of clinical data is useful for improving dialytic management.

Drought response of Mucuna pruriens (L.) DC. inoculated with ACC deaminase and IAA producing rhizobacteria

Drought is one of the major constraints limiting agricultural production worldwide and is expected to increase in the future. Limited water availability causes significant effects to plant growth and physiology. Plants have evolved different traits to mitigate the stress imposed by drought. The presence of plant growth-promoting rhizobacteria (PGPR) could play an important role in improving plant performances and productivity under drought. These beneficial microorganisms colonize the rhizosphere of plants and increase drought tolerance by lowering ethylene formation. In the present study, we demonstrate the potential to improve the growth of velvet bean under water deficit conditions of two different strains of PGPR with ACCd (1-Aminocyclopropane-1-Carboxylate deaminase) activity isolated from rainfed farming system. We compared uninoculated and inoculated plants with PGPR to assess: a) photosynthetic performance and biomass; b) ACC content and ethylene emission from leaves and roots; c) leaf isoprene emission. Our results provided evidence that under drought conditions inoculation with PGPR containing the ACCd enzyme could improve plant growth compared to untreated plants. Ethylene emission from roots and leaves of inoculated velvet bean plants was significantly lower than uninoculated plants. Moreover, isoprene emission increased with drought stress progression and was higher in inoculated plants compared to uninoculated counterparts. These findings clearly illustrate that selected PGPR strains isolated from rainfed areas could be highly effective in promoting plant growth under drought conditions by decreasing ACC and ethylene levels in plants.

A L-type lectin gene is involved in the response to hormonal treatment and water deficit in Volkamer lemon

Combination of biotic and abiotic stress is a major challenge for crop and fruit production. Thus, identification of genes involved in cross-response to abiotic and biotic stress is of great importance for breeding superior genotypes. Lectins are glycan-binding proteins with a functions in the developmental processes as well as in the response to biotic and abiotic stress. In this work, a lectin like gene, namely ClLectin1, was characterized in Volkamer lemon and its expression was studied in plants exposed to either water stress, hormonal elicitors (JA, SA, ABA) or wounding to understand whether this gene may have a function in the response to multiple stress combination. Results showed that ClLectin1 has 100% homology with a L-type lectin gene from C. sinensis and the in silico study of the 5'UTR region showed the presence of cis-responsive elements to SA, DRE2 and ABA. ClLectin1 was rapidly induced by hormonal treatments and wounding, at local and systemic levels, suggesting an involvement in defence signalling pathways and a possible role as fast detection biomarker of biotic stress. On the other hand, the induction of ClLectin1 by water stress pointed out a role of the gene in the response to drought. The simultaneous response of ClLectin1 expression to water stress and SA treatment could be further investigated to assess whether a moderate drought stress may be useful to improve citrus performance by stimulating the SA-dependent response to biotic stress.

Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene?

Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.

Preliminary data on antibacterial activity of Echinacea purpurea-associated bacterial communities against Burkholderia cepacia complex strains, opportunistic pathogens of Cystic Fibrosis patients

Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A source of such natural compounds is represented by medicinal plants and, in particular, by bacterial communities associated with these plants able to produce molecules with antimicrobial activity. In this work, a panel of 151 (endophytic) bacteria isolated from three different compartments (rhizospheric soil, roots, and stem/leaves) of the medicinal plant Echinacea purpurea were tested (using the cross-streak method) for their ability to inhibit the growth of 10 Bcc strains. Data obtained revealed that bacteria isolated from the roots of E. purpurea are the most active in the inhibition of Bcc strains, followed by bacteria isolated from the rhizospheric soil, and endophytes from stem/leaf compartment. At the same time, Bcc strains of environmental origin showed a higher resistance toward inhibition than the Bcc strains with clinical (i.e. CF patients) origin. Differences in the inhibition activity of E. purpurea-associated bacteria are mainly linked to the environment -the plant compartment- rather than to their taxonomical position.

Monitoring intra-annual dynamics of wood formation with microcores and dendrometers in Picea abies at two different altitudes

Seasonal analyses of cambial cell production and day-by-day stem radial increment can help to elucidate how climate modulates wood formation in conifers. Intra-annual dynamics of wood formation were determined with microcores and dendrometers and related to climatic signals in Norway spruce (Picea abies (L.) Karst.). The seasonal dynamics of these processes were observed at two sites of different altitude, Savignano (650 m a.s.l.) and Lavazè (1800 m a.s.l.) in the Italian Alps. Seasonal dynamics of cambial activity were found to be site specific, indicating that the phenology of cambial cell production is highly variable and plastic with altitude. There was a site-specific trend in the number of cells in the wall thickening phase, with the maximum cell production in early July (DOY 186) at Savignano and in mid-July (DOY 200) at Lavazè. The formation of mature cells showed similar trends at the two sites, although different numbers of cells and timing of cell differentiation were visible in the model shapes; at the end of ring formation in 2010, the number of cells was four times higher at Savignano (106.5 cells) than at Lavazè (26.5 cells). At low altitudes, microcores and dendrometers described the radial growth patterns comparably, though the dendrometer function underlined the higher upper asymptote of maximum growth in comparison with the cell production function. In contrast, at high altitude, these functions exhibited different trends. The best model was obtained by fitting functions of the Gompertz model to the experimental data. By combining radial growth and cambial activity indices we defined a model system able to synchronize these processes. Processes of adaptation of the pattern of xylogenesis occurred, enabling P. abies to occupy sites with contrasting climatic conditions. The use of daily climatic variables in combination with plant functional traits obtained by sensors and/or destructive sampling could provide a suitable tool to better investigate the effect of disturbances on response strategies in trees and, consequently, contribute to improving our prediction of tree growth and species resilience based on climate scenarios.

Endophytic and rhizospheric bacterial communities isolated from the medicinal plants Echinacea purpurea and Echinacea angustifolia

In this work we analyzed the composition and structure of cultivable bacterial communities isolated from the stem/leaf and root compartments of two medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC.) Hell, grown in the same soil, as well as the bacterial community from their rhizospheric soils. Molecular PCR-based techniques were applied to cultivable bacteria isolated from the three compartments of the two plants. The results showed that the two plants and their respective compartments were characterized by different communities, indicating a low degree of strain sharing and a strong selective pressure within plant tissues. Pseudomonas was the most highly represented genus, together with Actinobacteria and Bacillus spp. The presence of distinct bacterial communities in different plant species and among compartments of the same plant species could account for the differences in the medicinal properties of the two plants.

Physiological and metabolomic analysis of Punica granatum (L.) under drought stress

Punica granatum has a noticeable adaptation to drought stress. The levels of the green leaf volatile trans-2-hexenal increased in response to drought stress suggesting a possible role of this compound in drought stress response in pomegranate. Punica granatum (L.) is a highly valued fruit crop for its health-promoting effects and it is mainly cultivated in semi-arid areas. Thus, understanding the response mechanisms to drought stress is of great importance. In the present research, a metabolomics analysis was performed to evaluate the effects of drought stress on volatile organic compounds extracted from the leaves of pomegranate plants grown under water shortage conditions. The time course experiment (7 days of water deprivation and 24-h recovery) consisted of three treatments (control, drought stress, and rehydration of drought-stressed plants). Plant weights were recorded and control plants were irrigated daily at pot capacity to provide the lost water. Fraction of transpirable soil water has been evaluated as indicator of soil water availability in stressed plants. The levels of proline, hydrogen peroxide and lipid peroxidation as well as of the photosynthetic parameters such as photosynthesis rate (A), stomatal conductance (g s), photosynthetic efficiency of photosystem II, and photochemical quenching were monitored after the imposition of drought stress and recovery as markers of plant stress. Constitutive carbon volatile components were analyzed in the leaf of control and drought-stressed leaves using Head Space Solid Phase Micro Extraction sampling coupled with Gas Chromatography Mass Spectrometry. A total of 12 volatile compounds were found in pomegranate leaf profiles, mainly aldehydes, alcohols, and organic acids. Among them, the trans-2-hexenal showed a significant increase in water-stressed and recovered leaves respect to the well-watered ones. These data evidence a possible role of the oxylipin pathway in the response to water stress in pomegranate plants.

Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

BACKGROUND

Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species.

RESULTS

We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population.

CONCLUSIONS

The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.

Effects of long-term ambient ozone exposure on biomass and wood traits in poplar treated with ethylenediurea (EDU)

This is the longest continuous experiment where ethylenediurea (EDU) was used to protect plants from ozone (O3). Effects of long-term ambient O3 exposure (23 ppm h AOT40) on biomass of an O3 sensitive poplar clone (Oxford) were examined after six years from in-ground planting. Trees were irrigated with either water or 450 ppm EDU. Above (-51%) and below-ground biomass (-47%) was reduced by O3 although the effect was significant only for stem and coarse roots. Ambient O3 decreased diameter of the lower stem, and increased moisture content along the stem of not-protected plants (+16%). No other change in the physical wood structure was observed. A comparison with a previous assessment in the same experiment suggested that O3 effects on biomass partitioning to above-ground organs depend on the tree ontogenetic stage. The root/shoot ratios did not change, suggesting that previous short-term observations of reduced allocation to tree roots may be overestimated.

Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome

Using a computational pipeline based on similarity networks reconstruction we analysed the 1133 genes of the Burkholderia vietnamiensis (Bv) G4 five plasmids, showing that gene and operon duplication played an important role in shaping the plasmid architecture. Several single/multiple duplications occurring at intra- and/or interplasmids level involving 253 paralogous genes (stand-alone, clustered or operons) were detected. An extensive gene/operon exchange between plasmids and chromosomes was also disclosed. The larger the plasmid, the higher the number and size of paralogous fragments. Many paralogs encoded mobile genetic elements and duplicated very recently, suggesting that the rearrangement of the Bv plastic genome is ongoing. Concerning the "molecular habitat" and the "taxonomical status" (the Preferential Organismal Sharing) of Bv plasmid genes, most of them have been exchanged with other plasmids of bacteria belonging (or phylogenetically very close) to Burkholderia, suggesting that taxonomical proximity of bacterial strains is a crucial issue in plasmid-mediated gene exchange.

A census of RND superfamily proteins in the Burkholderia genus

Aim: The aim of this work was to analyze the eight resistance–nodulation–cell division (RND) families (a group of proteins mainly involved in multidrug resistance of Gram-negative bacteria) in 26 Burkholderia genomes in order to gain knowledge regarding their presence and distribution, to obtain a platform for future experimental tests aimed to identify new molecular targets to be used in antimicrobial therapy against Burkholderia species and to refine the annotation of RND-like sequences in these genomes. Materials & methods: A total of 417 coding sequences were retrieved and analyzed using different bioinformatics tools. Results & conclusion: A complex pattern of RND presence and distribution in the different Burkholderia species was disclosed and a core of proteins represented in all 26 genomes was identified. These ‘core’ proteins might represent useful targets of new synthetic antimicrobial compounds. Furthermore, the annotation of RND-like sequences in Burkholderia was refined.

Transcript Accumulation Dynamics of Phenylpropanoid Pathway Genes in the Maturing Xylem and Phloem of Picea abies during Latewood Formation

In temperate regions, latewood is produced when cambial activity declines with the approach of autumnal dormancy. The understanding of the temporal (cambium activity vs dormancy) and spatial (phloem, cambial region, maturing xylem) regulation of key genes involved in the phenylpropanoid pathway during latewood formation represents a crucial step towards providing new insights into the molecular basis of xylogenesis. In this study, the temporal pattern of transcript accumulation of 12 phenylpropanoid genes (PAL1, C4H3/5, C4H4, 4CL3, 4CL4, HCT1, C3H3, CCoAOMT1, COMT2, COMT5, CCR2) was analyzed in maturing xylem and phloem of Picea abies during latewood formation. Quantitative reverse transcription-polymerase chain reaction analyses revealed a well-defined RNA accumulation pattern of genes involved in the phenylpropanoid pathway during latewood formation. Differences in the RNA accumulation patterns were detected between the different tissue types analyzed. The results obtained here demonstrated that the molecular processes involved in monolignol biosynthesis are not restricted to the cambial activity timeframe but continued after the end of cambium cell proliferation. Furthermore, since it has been shown that lignification of maturing xylem takes place in late autumn, we argue on the basis of our data that phloem could play a key role in the monolignol biosynthesis process.

Deciphering the role of RND efflux transporters in Burkholderia cenocepacia

Burkholderia cenocepacia J2315 is representative of a highly problematic group of cystic fibrosis (CF) pathogens. Eradication of B. cenocepacia is very difficult with the antimicrobial therapy being ineffective due to its high resistance to clinically relevant antimicrobial agents and disinfectants. RND (Resistance-Nodulation-Cell Division) efflux pumps are known to be among the mediators of multidrug resistance in Gram-negative bacteria. Since the significance of the 16 RND efflux systems present in B. cenocepacia (named RND-1 to -16) has been only partially determined, the aim of this work was to analyze mutants of B. cenocepacia strain J2315 impaired in RND-4 and RND-9 efflux systems, and assess their role in the efflux of toxic compounds. The transcriptomes of mutants deleted individually in RND-4 and RND-9 (named D4 and D9), and a double-mutant in both efflux pumps (named D4-D9), were compared to that of the wild-type B. cenocepacia using microarray analysis. Microarray data were confirmed by qRT-PCR, phenotypic experiments, and by Phenotype MicroArray analysis. The data revealed that RND-4 made a significant contribution to the antibiotic resistance of B. cenocepacia, whereas RND-9 was only marginally involved in this process. Moreover, the double mutant D4-D9 showed a phenotype and an expression profile similar to D4. The microarray data showed that motility and chemotaxis-related genes appeared to be up-regulated in both D4 and D4–D9 strains. In contrast, these gene sets were down-regulated or expressed at levels similar to J2315 in the D9 mutant. Biofilm production was enhanced in all mutants. Overall, these results indicate that in B. cenocepacia RND pumps play a wider role than just in drug resistance, influencing additional phenotypic traits important for pathogenesis.

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land

BACKGROUND

The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.

RESULTS

We have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PAL via horizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments.

CONCLUSION

Our results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.

The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis

BACKGROUND

It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution.

RESULTS

The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted.

CONCLUSION

The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.

[Long-term use of Profiler in patients with dialysis intolerance: 8 months follow-up]

PURPOSE

A new method of profiled dialysis has been set up for many years in the Department of Nephrology, Dialysis and Renal Transplantation at the University of Bologna. This profiled dialysis is based on the use of a new kinetic mathematical model, in collaboration with the Faculty of Engineering at the University of Bologna, for the elaboration of individual sodium and ultrafiltration profiles.

OBJECTIVE

The profiled dialysis aims are: 1) to stabilize the intradialytic blood volume, boosting the refilling of plasma water from the intracellular and the extravascular to the extracellular/intravascular compartments, to balance the ultrafiltration; 2) to counteract the disequilibrium syndrome reducing the shift of water from the extra to the intracellular compartment. The pre-dialysis elaboration of profiles is completely automatic and supported by a computerized programme, Profiler, which has been included in the software of the dialysis machine Bellco Formula 2000 Plus.

METHODS

In this prospective and multicenter study, this profiled dialysis, performed according to the Profiler, was continuously applied, for an 8-month period, in a group of 13 hemodialysis (HD) patients with an intolerance to previous dialysis treatment. During the study, the following parameters were evaluated, comparatively, with the patient's basal treatment: a) sodium and water balance; b) percentage incidence of intradialytic complications such as hypotensive events, cramps, headache, and vomiting and; c) metabolic and nutritional status.

RESULTS

Results evaluated in comparison with the patient's previous dialysis treatments, demonstrated: a) plasma sodium from 136.8 +/- 3 to 136.8 +/- 1.7 mEq/L (p=ns), dry body weight from 72.2 +/- 19.3 to 71.7 +/- 19.5 kg (p=ns), heart index from 3.7 +/- 0.7 to 3.1 +/- 0.5 L/min/m2 (p=ns), reactance from 5.3 +/- 15 to 4.9 +/- 11 ohm (p<0.05); b) incidence of intradialytic hypotensive events reduced from 64 to 4% (p<0.001), cramps reduced from 8 to 1% (p<0.01); c) plasma albumin from 3.5 +/- 0.2 to 3.7 +/- 0.3 g/dL (p=ns), Kt/Veq from 1.3 +/- 0.1 to 1.36 +/- 0.2 (p=ns).

CONCLUSIONS

Patients treated with profiled dialysis had a higher stability of intradialytic blood pressure (BP) achieving a reduction in the incidence of disequilibrium syndrome symptoms, in comparison with previous treatment. These clinical intradialytic improvements were not correlated to clinical, instrumental or biochemical indexes of sodium-water overload nor to a worst dialysis adequacy and nutritional state.

[On-line haemodiafiltration with sorbent-regenerated ultrafiltrate as replacement fluid: Beta2-microglobulin removal versus filtration fraction]

PURPOSE

In order to encourage the removal of middle molecules in hemodiafiltration (HDF) techniques an attempt is made to maximize convective clearance by increasing the ultrafiltration rate. However, convective clearance is limited by the maximum filtration fraction (FF%) obtainable, by the pre- or post reinfusion method and by the convective surface and the capacity of the filter used. This study aimed to evaluate the effect of the FF% in the removal of Beta2-microglobulin (Beta2-m) during hemodiafiltration reinfusion (HFR) to identify the best ultrafiltration strategies; and therefore, a better removal of medium molecular weight solutes in this hemodiafiltrative technique recently introduced in clinical practice.

METHODS

Ten chronic uremic patients (eight males, two females; age 66 +/- 18 yrs) already on renal dialysis therapy (RDT) for 80 +/- 36 months, were subjected to four HFR sessions, with Td=240 +/- 10 min, Qb=312 +/- 18 and Qd=500 mL/min; the reinfusion rates (Qr) used were 43.6 +/- 7.2 mL/min (25-58) with FF% rates varying from 20-34 (24.2 +/- 3.8) for hematocritic levels of 34.6 +/- 4.2% at the start of the dialysis session. For each session the intradialytic reduction rates (RR%) of urea, creatinine (Cr), phosphate, uric acid and Beta2-m and its average clearance (KBeta2-m mL/min) were evaluated.

RESULTS

The results obtained gave a RR% for urea of 69.4 +/- 5 (Kt/Veq=1.23 +/- 0.2) and for Cr, phosphate and uric acid values of, respectively, 61.2 +/- 5.4, 47.5 +/- 10 and 75.8 +/- 6.7. The intradialytic reductions in Beta2-m were 49.3 +/- 10.3% with a variability range from 29-69% and with average KBeta2-m values of 63.8 +/- 13.5 mL/min. The RR% of ss2-m and KBeta2-m were inversely correlated (p<0.01) to the FF% rate applied during the treatment; 75% of the HRF sessions in which we observed a reduction in Beta2-m levels >40% were those where a FF% between 20 and 26% was applied. CONCLUSIONS. From our study, it appears that in HFR the best ultrafiltration strategy from the convective sector in removing Beta2-m has FF% values in the range 20-26%. The occurrence of lower intradialytic reductions of Beta2-m with increasing FF% can be interpreted as a consequence of phenomena related to high intradialytic hemoconcentrations, to the excessive increase in the TMP and/or the increase in the protein cake with a consequent reduction in permeability and mass transfer. Although using a limited convective surface with a limited possibility of increasing the FF%, nevertheless, HFR seems capable of ensuring a satisfactory uremic toxin removal of low and medium molecular weight, which combined with the high biocompatibility deriving from the use of reinfused endogen, can be considered an effective dialytic strategy for preventing or retarding the complications in dialytic patients.

Longitudinal assessment of body composition in CAPD patients using bioelectric impedance analysis. A comparison with hemodialysis patients

The utility of bioelectric impedance analysis was assessed for longitudinal evaluation of body composition in two groups of uremic patients, one on CAPD and one on hemodialysis treatment, with no clinical marks of hyperhydration or infection. Nineteen CAPD patients (11 men 8 women) and 21 HD patients (12 men 9 women) were studied with bioelectric impedance analysis for a period of 12 months; total body water, fat free mass, and fat mass were calculated from bioelectric impedance analysis data of resistance and reactance at time 0 and 12 months later. No significant differences in body composition were found in the two groups at time 0 and 12 months later, with a similar trend for total body water, fat free mass, and fat mass. In CAPD, a significant increase in body weight was observed due mainly to a rise in fat mass, particularly evident in women with uremia. Bioelectric impedance analysis appears to be an instrument easily repeatable and reliable in CAPD and HD patients, reflecting at the same time body composition, the dialytic adequacy of a technique, and the patient's well being.

Laser mirrors with variable reflected intensity and uniform phase shift: design process

Optical coatings with circularly symmetric graded reflectance are used as laser mirrors in unstable resonators. A proper design of such coatings permits any maximum central reflectance to be obtained along with a null external reflectance. Different design approaches are discussed, and an optimized design that gives negligible distortion of the reflected and transmitted wave front is proposed. Coatings with super-Gaussian and step reflectance profiles are examined as two different solutions for improving laser beam quality.

[The disease of beta 2-amyloid deposition in the differential diagnosis of juxta-articular subchondral geode lesions]

Beta-2 amyloidosis deposition is a new type of amyloidosis recently observed in long-term hemodialysis patients. One of the major osteoarticular complications of this disease is the appearance of subchondral bone cysts. In this paper the radiologic features of such radiolucencies are described and the criteria are outlined of the differential diagnosis from the geodes found in other arthropathies or para-physiologic conditions. The importance of the status of the joint space is stressed: on the basis of its patterns, arthropathies may be grouped as follows: inhomogeneous space narrowing in degenerative arthritis; homogeneous space narrowing in inflammatory arthritis; normal or nearly normal joint space if there is no/not-prevalent involvement of articular cartilage.

Can teledialysis help in the clinical management of patients on remote hemodialysis?

This study investigated whether transmission of the parameters monitored from a remote center to the main center could improve the control of a dialysis session. The parameters of the computer connection module Monitral SC in remote and main centers, were transmitted by means of the Hospal data collection software (Demoplus) by modem, to the host computer. Each remote center can be temporarily disconnected, if necessary, from the telephone line and linked directly to a local computer. We checked 101 hemodialyses. The dialysis was monitored from filter washing to disconnection of the patients and the following parameters were selected: backfiltration during washing and hemodialysis: ultrafiltration, conductivity and temperature. From the sessions recorded (93%) we observed that backfiltration during the filter preparation phase was high (30%) in 28 sessions. Backfiltration during the preparatory phase is the major problem for correct management of dialysis sessions. The high percentage in which ultrafiltration had to be stopped shows that control of this parameter is still not ideal. Finally, the collection of monitor parameters and the comparative analysis of clinical data is useful for improving dialytic management.

Characterization and calibration of a variable-angle absolute reflectometer

The instrument described is a newly designed reflectometer. Measurements are made with a polarized light beam as a function of wavelength and angle of incidence. Calibration tests have outlined the possibility of using the instrument for reflectance measurements on mirrors with good reproducibility (0.2%) and accuracy (better than 1%). This has been obtained by the alignment system of the sample and the absolute method used for the determination of its reflectance.

Optical coatings with variable reflectance for laser mirrors

Design procedures and fabrication techniques of variable reflectance dielectric mirrors for laser output couplers are proposed. The design criteria, based on the use of only one shaped layer in a multilayer structure, yield any peak value and shape of the reflectance profile. The deposition technique of the variable thickness layer consists of a sputtering process with a suitable mask interposed between the target and substrate. Results of a simple model that correlates the mirror parameters to mask diameter and position are presented. A few devices for a Nd:YAG laser have been proposed, characterized, and successfully tested in a laser resonator.

Technical and clinical evaluation of a new synthetic low flux polysulphon membrane for hemodialysis

New synthetic membranes have been developed to reduce the ultrafiltration coefficient (Kf) maintaining an adequate permeability to medium-large solutes and a good biocompatibility. The new Fresenius F6 Low Flux Polysulphon Membrane is studied in this paper as far as hydraulic and permeability properties are concerned. For this purpose in vitro and in vivo tests have been carried out in a series of different conditions. In vitro sieving coefficients were near 1 for solutes with molecular weight up to 5000 Daltons. The ultrafiltration coefficient of the device was 5.4 ml/h/mmHg while the value of Kf normalized per square meter was lower than 5 ml/h/mmHg. The geometry of the blood path was adequate even operating at high blood flows without excessive resistance and obligate filtration. This resulted in vivo in a good performance during short dialysis schedules with good clearances of small and large molecules and with no risks of backfiltration. In fact, the low permeability to water permits constant operation with positive transmembrane pressures without excessive ultrafiltration rates. The biocompatibility of the membrane was excellent and high capacity of adsorption for beta-2 microglobulin was demonstrated. These results suggest that these membranes seem to be able to join the advantages of the traditional cellulosic membranes and of the newer synthetic membranes reducing their relative disadvantages.

Comparison of clinical and neurological status in elderly patients treated with two different hemodialysis techniques

Five patients with a mean age of 63.4 years (range 62-67) who had frequent episodes of intradialytic intolerance during acetate hemodialysis (HDA) received biofiltration (BF). For each period of study (6 months on HDA and 6 months on BF), the patients underwent a complete clinical assessment, with evaluation of the electroencephalographic (EEG) pattern and acid-base status. During BF, we observed a reduction of hypotensive episodes (10% on BF vs. 26% on HDA) and EEG disturbances (18% on BF vs. 70% on HDA), with a more physiological correction of uremic acidosis. We conclude that BF improves clinical status and neurological tolerance with a better compensation of acidosis in the elderly.

All-oxide broadband antireflection coatings by reactive ion plating deposition

Coating experiments were made with reactive low-voltage ion plating to achieve the computer designed performance of all-oxide broadband antireflection systems on BK-7 glass. Reasonable accordance between calculated design and coating experiment as well as reliable production have been demonstrated.

The acid-base balance and the electroencephalographic pattern in patients on biofiltration treatment

Electroencephalogram (EEG) monitoring and arterial blood gases was performed during biofiltration (BF) treatment and during conventional acetate hemodialysis (HDA). Biofiltration is an ultrashort hemodiafiltration with 3 liters of substitution fluid (Na+ 145 mEq/l, HCO-3 100 mEq/l). Our data show a better correction of acid-base balance during BF than during HDA. Moreover, we observe a lower incidence of EEG disturbancies on BF, that suggests a better neurological tolerance of this treatment.