A rapid method to screen fungi for resistance to toxic chemicals

Although many species of fungi are able to degrade highly toxic chemicals, only a few species have been evaluated for resistance to toxic effects of these chemicals. In this paper we demonstrate the successful application of a method to rapidly screen several species of fungi for toxicity to chemicals or mixtures of chemicals using pentachlorophenol (PCP) as a model toxic compound. Cellulose antibiotic assay disks were soaked in solutions containing different concentrations of PCP (5, 10, 25, 50, and 80 mg l^–1) and then placed in a triangular pattern outside the growing edge of the mycelia of eighteen species of white rot fungi. The plates were incubated and observed for development of inhibition zones (non-growth areas) around the disks. The short-term (24 h) growth of all eighteen species of fungi was inhibited by 5–10 mg-PCP l^–1, a range similar to that observed using previously reported techniques. Long-term growth studies using this screening method were not useful since PCP diffused from the disk into the agar, decreasing the applied dose.     

Enzymatic Dehalogenation of Pentachlorophenol by <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> of the Microbial Community from Tannery Effluent

Four different bacterial isolates obtained from a stable bacterial consortium were capable of utilizing pentachlorophenol (PCP) as sole carbon and energy source. The consortium was developed by continuous enrichment in the chemostat. The degradation of PCP by bacterial strain was preceded through an oxidative route as indicated by accumulation of tetrachloro-ρ-hydroquinone and dichlorohydroquinone as determined by high performance liquid chromatography (HPLC). Among the four isolates, Pseudomonas fluorescens exhibited maximum degradation capability and enzyme production. PCP-monooxygenase enzyme was extracted from culture extract and fractionated by DEAE-cellulose ion exchange chromatography. The molecular weight of the enzyme, purified from Pseudomonas fluorescens, determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and gel filtration chromatography was found to be 24,000 Da. Received: 22 July 2002 / Accepted: 23 September 2002     

Phencyclidine

Phenycyclidine (PCP) produces many profound effects in the central nervous system. PCP has numerous behavioral and neurochemical effects such as inhibiting the uptake and facilitating the release of dopamine, serotonin, and norepinephrine. PCP also interacts with sigma, mu opioid, muscarinic, and nicotinic receptors. However, the psychotomimetic effects induced by PCP are believed to be mediated by specific PCP receptors, where PCP binds with greater potency than sigma compounds. Electrophysiological, behavioral, and neuro-chemical evidence strongly suggests that at least some of the many PCP actions result from antagonism of excitatory amino acid-induced responses via PCP receptors. The recent isolation and partial characterization of the alpha and beta endopsychosins and the identification of other endogenous ligands for the PCP and sigma receptors, is another promising area of research in the elucidation of the physiological role of an endogenous PCP and sigma system.     

Sudden challenges in teaching ecology and aligned disciplines during a global pandemic: Reflections on the rapid move online and perspectives on moving forward

The challenges facing higher education in response to COVID‐19 are significant and possibly none more so than in ecology and aligned disciplines. Not only did most ecology lecturers have to rush lectures and tutorials online, but also laboratory and field classes. We reflect on our experience of this move and also consider those of 30 other ecology‐aligned teaching academics to summarize the challenges faced in the move online early in 2020 and the developing plans for adapting ecology teaching and learning going into the 2020/21 academic year. The move online had the most significant impact on field classes, with more of these canceled than lectures or laboratory classes. Most respondents to an online poll also highlighted that many respondents (~45%) felt that ecology was more impacted by COVID‐19 that even other STEM disciplines. The availability of technological solutions is key to moving forward and will hopefully enhance the teaching and learning experience for many beyond the current crisis.     

The water relations of Verna Lemon trees from flowering to the end of rapid fruit growth

Lemon plants (Citrus limonum L. cv. Verna) were grown in the field under two different flood irrigation treatments. The dry treatment received four irrigations per year (March, July, September and November) and the wet treatment one monthly. The amounts of water applied per year for dry and wet treatments were 340.0 mm and 1020.0 mm, respectively. The effects of the two treatments on certain aspects of the plant water relations during the period between flowering and the end of rapid fruit growth (critical period) were studied. Soil matric potential (ψm) and leaf water potential (ψi) values in the dry treatment revealed development of water stress during the experimental period. The water supply in the wet treatment seems sufficient to achieve the crop water requirements. The g₁ values in July were higher in the wet than dry treatments. Pronounced oscillations in g₁ from sunrise to afternoon were found especially in the dry treatment.     

Block by phencyclidine of acetylcholine and barium induced adrenal catecholamine secretion

Activation of the sympathetic system by phencyclidine (PCP) should result in catecholamine release from the adrenals. However, adrenalectomy does not reduce PCP-induced hypertension. In an attempt to rectify this inconsistency, the direct effects of PCP on the bovine adrenal medulla were examined. At (3×10^?6M), PCP reduced the acetylcholine-(ACh)-induced catecholamine release by 50%. Surprisingly, barium-induced secretion of catecholamines was also reduced by PCP. ACh-induced catecholamine release was not altered by 10^?3M 4-aminopyridine (4 AP), the potassium channel blocker. Thus, calcium antagonist actions of PCP and consequent block of catecholamine secretion from adrenal medulla may explain the lack of effect of adrenalectomy on PCP-induced hypertension. Possible contributions of calcium and/or potassium channel blockade to other manifestations of PCP overdosage are discussed.     

Revisiting planar cell polarity in the inner ear

Since the first implication of the core planar cell polarity (PCP) pathway in stereocilia orientation of sensory hair cells in the mammalian cochlea, much has been written about this subject, in terms of understanding how this pathway can shape the mammalian hair cells and using the inner ear as a model system to understand mammalian PCP signaling. However, many conflicting results have arisen, leading to puzzling questions regarding the actual mechanism and roles of core PCP signaling in mammals and invertebrates. In this review, we summarize our current knowledge on the establishment of PCP during inner ear development and revisit the contrast between wing epithelial cells in Drosophila melanogaster and sensory epithelia in the mammalian cochlea. Notably, we focus on similarities and differences in the asymmetric distribution of core PCP proteins in the context of cell autonomous versus non-autonomous role of PCP signaling in the two systems. Additionally, we address the relationship between the kinocilium position and PCP in cochlear hair cells and increasing results suggest an alternate cell autonomous pathway in regulating PCP in sensory hair cells.     

Bioremediation of pentachlorophenol-contaminated soil by bioaugmentation using activated soil

The use of an indigenous microbial consortium, pollutant-acclimated and attached to soil particles (activated soil), was studied as a bioaugmentation method for the aerobic biodegradation of pentachlorophenol (PCP) in a contaminated soil. A 125-l completely mixed soil slurry (10% soil) bioreactor was used to produce the activated soil biomass. Results showed that the bioreactor was very effective in producing a PCP-acclimated biomass. Within 30 days, PCP-degrading bacteria increased from 10⁵ cfu/g to 10⁸ cfu/g soil. Mineralization of the PCP added to the reactor was demonstrated by chloride accumulation in solution. The soil-attached consortium produced in the reactor was inhibited by PCP concentrations exceeding 250 mg/l. This high level of tolerance was attributed to the beneficial effect of the soil particles. Once produced, the activated soil biomass remained active for 5 weeks at 20 °C and for up to 3 months when kept at 4 °C. The activated attached soil biomass produced in the completely mixed soil slurry bioreactor, as well as a PCP-acclimated flocculent biomass obtained from an air-lift immobilized-soil bioreactor, were used to stimulate the bioremediation of a PCP-impacted sandy soil, which had no indigenous PCP-degrading microorganisms. Bioaugmentation of this soil by the acclimated biomass resulted in a 99% reduction (from 400 mg/kg to 5 mg/kg in 130 days) in PCP concentration. The PCP degradation rates obtained with the activated soil biomass, produced either as a biomass attached to soil particles or as a flocculent biomass, were similar. Received: 31 March 1997 / Received revision: 22 July 1997 / Accepted: 25 August 1997     

Toward a more International and Reputable Journal

Editors in 2004 In 2004 I, Hiroo Fukuda (University of Tokyo), was appointedto be the Editor-in-Chief of Plant and Cell Physiology (PCP).As my first task I have added four overseas and four domesticEditors: John Harada (University of California, Davis), FumihikoKatagiri (University of Minnesota, from July), Jiayang Li (ChineseAcademy of Science), Eberhard Schäfer (Freiburg University,from July), Ikuko Hara-Nishimura (Kyoto University), FumihikoSato (Kyoto University), Ichiro Terashima (Osaka University)and Hideyuki Takahashi (Tohoku University, from July). I would like to take     

Population growth kinetics and bulk membrane lipid alterations in Tetrahymena pyriformis: exposure to pentachlorophenol

This study describes effects of exposure of the freshwater ciliate Tetrahymena pyriformis to the "classic" weak acid respiratory uncoupler pentachlorophenol (PCP) on the population growth kinetics and membrane lipid profiles. The assessment of growth kinetics of naive populations exposed to PCP, at concentrations eliciting <50% growth inhibition, showed generation times of exposed cultures similar to generation times of controls but preceded by a short lag phase (<2 h). Assessment of exposed cultures exhibiting >50% growth inhibition revealed generation times that increased with increasing concentrations of toxicant. In addition, the relative percentages of selected fatty acid methyl esters (FAMEs) in both pellicle and mitochondrial membranes were examined. Upon exposure to PCP the relative percentages of FAMEs 12:0, 14:0, 16:0, 16:1, and 18:0 did not change. However, with exposure to PCP a decrease was observed for FAMEs 15:0 and 17:0. Conversely, with PCP exposure there was an increase in FAME 18:1. A comparison of these results with those elicited upon exposure to the model narcotic 1-octanol reveals marked differences in both growth kinetics and fatty acid shifts. This revised version was published online in July 2006 with corrections to the Cover Date.     

A Tribute to Leslie Nelson, Plant and Cell Physiology Production Manager

We regret to announce the sudden death of PCP production managerLeslie Nelson on June 16, 2004. Having energetically supportedthe online development of PCP, including the creation of anonline review system, Leslie made great     

Can sugars be produced from fatty acids? A test case for pathway analysis tools

Motivation: In recent years, several methods have been proposedfor determining metabolic pathways in an automated way basedon network topology. The aim of this work is to analyse thesemethods by tackling a concrete example relevant in biochemistry.It concerns the question whether even-chain fatty acids, beingthe most important constituents of lipids, can be convertedinto sugars at steady state. It was proved five decades agothat this conversion using the Krebs cycle is impossible unlessthe enzymes of the glyoxylate shunt (or alternative bypasses)are present in the system. Using this example, we can comparethe various methods in pathway analysis. Results: Elementary modes analysis (EMA) of a set of enzymescorresponding to the Krebs cycle, glycolysis and gluconeogenesissupports the scientific evidence showing that there is no pathwaycapable of converting acetyl-CoA to glucose at steady state.This conversion is possible after the addition of isocitratelyase and malate synthase (forming the glyoxylate shunt) tothe system. Dealing with the same example, we compare EMA withtwo tools based on graph theory available online, PathFindingand Pathway Hunter Tool. These automated network generatingtools do not succeed in predicting the conversions known fromexperiment. They sometimes generate unbalanced paths and revealproblems identifying side metabolites that are not responsiblefor the carbon net flux. This shows that, for metabolic pathwayanalysis, it is important to consider the topology (includingbimolecular reactions) and stoichiometry of metabolic systems,as is done in EMA. Contact: ldpf{at}minet.uni-jena.de; schuster{at}minet.uni-jena.de Supplementary information: Supplementary data are availableat Bioinformatics online. FOOTNOTES Associate Editor: Alfonso Valencia Received on July 24, 2008; revised on September 18, 2008; accepted on September 18, 2008     

Rhythmic and Light-Inducible Appearance of Clock-Associated Pseudo-Response Regulator Protein PRR9 through Programmed Degradation in the Dark in Arabidopsis thaliana

The above article was published in Plant and Cell Physiology48(11): 1644–1651. Figure 1 was shown incorrectly online. The figure legend inFigure 1C was missing. The correct figure is given below. View larger version (26K):   Fig. 1 Construction     

The Bioinformatics Open Access option

We are pleased to report that July 2005 saw the launch of ournew Open Access option, part of the Oxford Open initiative (http://www.oxfordjournals.org/oxfordopen/).Bioinformatics authors can now choose to publish their work‘open access’ in an established, high-impact journal,under what we believe is a sustainable publication model. WHAT THIS MEANS FOR AUTHORS SUBMITTING TO BIOINFORMATICS The decision of whether to pay for open access is made by thecorresponding author upon acceptance (importantly this decisionis kept completely separate from the editorial review process).If a Bioinformatics author chooses to pay for the Open Accessoption, his or her paper will be made freely available onlineimmediately; if an author does not choose the option his orher     

A simple and rapid method for lithium acetate-mediated transformation of Kluyveromyces marxianus cells

Efficient plasmid transformation of Kluyveromyces marxianus cells of 1.9 × 10³ transformant μg⁻¹ DNA with an episomal plasmid was achieved by the use of a simple lithium acetate method with the addition of 10 mM DTT and an increased heat shock temperature of 47 °C. This method is shown to be also efficient for replicative plasmids. Therefore, we suggest its use as a routine method to transform K. marxianus cells. This revised version was published online in July 2006 with corrections to the Cover Date.     

Successive rapid reductive dehalogenation and mineralization of pentachlorophenol by the indigenous microflora of farmyard manure compost

AIMS: To determine whether composting with animal manure can be used to effectively remediate soil from a pentachlorophenol (PCP)-contaminated site, and to establish the fate of the degraded xenobiotic. METHODS AND RESULTS: Contaminated soil from a sawmill site was mixed with farm animal manure and composted in a 0.5 m3 silo under fully aerobic conditions. The disappearance and fate of PCP was monitored by gas chromatography (GC-ECD) and extensive mineralization confirmed in experiments with 14C-radiolabelled PCP. The disappearance of PCP was rapid and virtually complete within 6 days, prior to the onset of thermophilic conditions. Dechlorination of the PCP was found to be both reductive and sequential. CONCLUSIONS: PCP removal from contaminated soil by aerobic composting with animal manure is efficient and proceeds via reductive dechlorination to virtually complete mineralization. This contrasts with other chlorophenol composting regimes in which mineralization is achieved but dechlorination intermediates do not accumulate to detectable levels. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study demonstrate that anaerobic reductive dechlorination can proceed in an aerobic composting environment and contribute to efficient pentachlorophenol removal. Farmyard manure composts may represent a rapid, low-cost, low-technology option for treatment of chlorophenol-contaminated soils.     

Jacques Le Magnen (1916-2002)

View larger version (162K): [in this window] [in a new window]   Jacques Le Magnen with his wife Régine on July 14, 1976, the eve of ISOT VI, which he organized at Gif-sur-Yvette.   One of the pioneers in research on olfaction and taste, andon the regulation of water and food intake left us on Thursday,May 23, 2002, at the age of 85. Jacques Le Magnen was a discipleof the famous French physiologist Henri Piéron at theCollège de France, and from 1949 till 1989 developedhis own laboratory of sensory