A broad mercury resistant strain of <Emphasis Type="Italic">Pseudomonas putida</Emphasis> secretes pyoverdine under limited iron conditions and high mercury concentrations

The Pseudomonas putida FB1, known as a broad-spectrum mercury resistant strain, becomes yellow-green due to the secretion of pyoverdine (PVDs) under limited iron conditions and high mercury concentrations. Different modified Nelson’s media were obtained by adding mercury, iron, and the complexing agent nitrilotriacetic acid to demonstrate that the strain produces only the highest concentrations of PVDs due to the induction with 25 µM Hg²⁺. An amount of 250 mg PVDs was purified from the supernatant of 1 litre culture. The various forms of PVDs were characterized using different techniques such as fluorescence spectroscopy, high performance liquid chromatography coupled with high resolution mass spectrometry, and scanning electron microscope equipped with energy dispersive X-ray analyser. A set of “in vivo” experiments demonstrated that additions of Hg²⁺ to the cultures from 10 to 25 µM Hg²⁺ stimulate an over secretion of PVDs suggesting that the toxic cation strongly reduces the availability of apo-PVDs, because the complex mercuric-pyoverdine is very stable at neutral pH, and hinder the formation of PVDs-Fe(III).     

Biogeochemical,Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation

We explore the possibility of tracing routes of dense waters toward and within the ocean abyss by the use of an extended set of observed physical and biochemical parameters. To this purpose, we employ mercury, isotopic oxygen, biopolymeric carbon and its constituents, together with indicators of microbial activity and bacterial diversity found in bottom waters of the Eastern Mediterranean. In this basin, which has been considered as a miniature global ocean, two competing sources of bottom water (one in the Adriatic and one in the Aegean seas) contribute to the ventilation of the local abyss. However, due to a recent substantial reduction of the differences in the physical characteristics of these two water masses it has become increasingly complex a water classification using the traditional approach with temperature, salinity and dissolved oxygen alone. Here, we show that an extended set of observed physical and biochemical parameters allows recognizing the existence of two different abyssal routes from the Adriatic source and one abyssal route from the Aegean source despite temperature and salinity of such two competing sources of abyssal water being virtually indistinguishable. Moreover, as the near-bottom development of exogenous bacterial communities transported by convectively-generated water masses in the abyss can provide a persistent trace of episodic events, intermittent flows like those generating abyssal waters in the Eastern Mediterranean basin may become detectable beyond the availability of concomitant measurements.     

Leaching of Pyrites of Various Reactivities by Thiobacillus ferrooxidans

Wide variations were found in the rate of chemical and microbiological leaching of iron from pyritic materials from various sources. Thiobacillus ferrooxidans accelerated leaching of iron from all of the pyritic materials tested in shake flask suspensions at loadings of 0.4% (wt/vol) pulp density. The most chemically reactive pyrites exhibited the fastest bioleaching rates. However, at 2.0% pulp density, a delay in onset of bioleaching occurred with two of the pyrites derived from coal sources. T. ferrooxidans was unable to oxidize the most chemically reactive pyrite at 2.0% pulp density. No inhibition of pyrite oxidation by T. ferrooxidans occurred with mineral pyrite at 2.0% pulp density. Experiments with the most chemically reactive pyrite indicated that the leachates from the material were not inhibitory to iron oxidation by T. ferrooxidans.     

How sensory maps could enhance resolution through ordered arrangements of broadly tuned receivers

We investigate the properties of a model recently introduced by Heiligenberg (1987) for an array of sensors tuned to progressively higher ranges of a continuous stimulus variablex and with bell shaped single response curve with width parameterd. The main result is that asd increases, the overall response rapidly becomes almost linear in a very smooth and robust fashion. Biological relevance and implications of the model and of its extensions are discussed together with a few examples.

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Originally known as la définition mathématique de la femme     

Exploiting the past and the future in protein secondary structure prediction

MOTIVATION: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network architectures with a fixed, and relatively short, input window of amino acids, centered at the prediction site. Although a fixed small window avoids overfitting problems, it does not permit capturing variable long-rang information. RESULTS: We introduce a family of novel architectures which can learn to make predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary information, expressed in terms of multiple alignments, both at the input and output levels. While our system currently achieves an overall performance close to 76% correct prediction--at least comparable to the best existing systems--the main emphasis here is on the development of new algorithmic ideas. AVAILABILITY: The executable program for predicting protein secondary structure is available from the authors free of charge. CONTACT: pfbaldi@ics.uci.edu, gpollast@ics.uci.edu, brunak@cbs.dtu.dk, paolo@dsi.unifi.it.     

Improved podophyllotoxin production by transformed cultures of Linum album

Various cell and hairy root cultures of L. album were developed and analyzed for podophyllotoxin content. Transformed callus and hairy root cultures developed from infection of stem portions of in vitro-germinated L. album plant with Agrobacterium rhizogenes NCIM 5140 strain were selected on the basis of high podophyllotoxin content and growth. Based on the integration of Ri T(L)-DNA and T(R)-DNA, integration of only the ags and not the rol gene in transformed cell culture indicated fragmented integration pattern. The effect of different cultivation media and carbon source on growth and podophyllotoxin production were studied in shake-flask suspension cultures. Detailed batch growth and production kinetics with sugar consumption profile were also established. Maximum volumetric productivity of 4.40 and 2.75 mg/L per day was obtained in cell suspension and hairy root cultures, respectively.     

Changes in laboratory and clinical parameters in subjects with chronic brucellosis treated with an immunomodulator: methisoprinol

In order to evaluate the immunomodulating activity of isoprinosine in chronic infections, 7 patients with chronic brucellosis unresponsive to antibiotic and corticosteroid therapy were treated with 4 g/die of isoprinosine in association with antibiotic therapy from 3 to 6 months. Immunoserologic and clinical evaluation were obtained at regular intervals from each patient. The treatment induced a significant increase of E rosette formation, reduction of erythrocyte sedimentation rate, associated with improvement or disappearance of clinical symptoms. These data suggest that isoprinosine may favourably influence the clinical course of chronic brucellosis, probably modifying host cell-mediated immune response.     

Tolerance to mercury chloride in Scenedesmus strains

Mercury chloride toxicity was investigated in two strains of Chlorella and in a strain of Scenedesmus isolated from polluted areas in Tuscany (Italy). No Hg resistance was found in the autotrophic microorganisms isolated, but Scenedesmus sp. strain AR-2489, isolated from the Arno river, was able to grow at concentrations of up to 5 mg ml1 of Hg. This concentration was twice that which inhibited growth of the two Chlorella strains and Scenedesmus acutus 8M, the reference strain from a culture collection. Photosynthesizing cells of Scenedesmus sp. AR-2489 showed reduced Hg uptake, with the highest percentage of Hg removal from the medium. Loss of Hg was not due to Hg(0) volatilization, as shown by a comparison test with the broad-spectrum Hg-resistant Pseudomonas putida FB1. The metabolic differences between Scenedesmus sp. strain AR-2489 and Siacatus strain 8M were: (1) higher growth rate (doubling time of 6.0h versus 10.6 h); (2) higher O2 production rate (maximum 2 mmol h mg dry weight); and (3) higher intracellular pH during growth. The latter was imaged with a green fluorescence molecular probe (BCEFC–AM) and observed by scanning confocal laser microscopy (SCLM). The distribution of red-autofluorescence chlorophyll-a showed that strain AR-2489 had a rougher and hence more extended specific chloroplast surface than strain 8M. Hg tolerance in strain AR-2489 was related to the rapid increase in dissolved O in the medium and in intracellular pH; this caused a loss of soluble mercury transformed to insoluble mercury hydroxide, which is thermodynamically more stable at alkaline pH in highly oxygenated systems.