bluuebunny/crossref_metadata_2025 huggingface dataset:
Bicarbonate transport proteins
Authors: Sterling Deborah , Casey Joseph R
Published: October 2002

Bicarbonate is not freely permeable to membranes. Yet, bicarbonate must be moved across membranes, as part of CO2metabolism and to regulate cell pH. Mammalian cells ubiquitously express bicarbonate transport proteins to facilitate the transmembrane bicarbonate flux. These bicarbonate transporters, which function by different transport mechanisms, together catalyse transmembrane bicarbonate movement. Recent advances have allowed the identification of several new bicarbonate transporter genes. Bicarbonate transporters cluster into two separate families: (i) the anion exachanger (AE) family of Cl/HCO[Formula: see text] exchangers is related in sequence to the NBC family of Na+/HCO[Formula: see text] cotransporters and the Na+-dependent Cl/HCO[Formula: see text] exchangers and (ii) some members of the SLC26a family of sulfate transporters will also transport bicarbonate but are not related in sequence to the AE/NBC family of transporters. This review summarizes our understanding of the mammalian bicarbonate transporter superfamily.Key words: bicarbonate transport, anion exchange, pH regulation, sodium/bicarbonate co-transport, chloride/bicarborate exchange, carbonic anhydrase.
Molecular biology and regulation of nucleoside and nucleobase transporter proteins in eukaryotes and prokaryotes
Authors: Cabrita Miguel A , Baldwin Stephen A , Young James D , Cass Carol E
Published: October 2002

The molecular cloning of cDNAs encoding nucleoside transporter proteins has greatly advanced understanding of how nucleoside permeants are translocated across cell membranes. The nucleoside transporter proteins identified thus far have been categorized into five distinct superfamilies. Two of these superfamilies, the equilibrative and concentrative nucleoside transporters, have human members and these will be examined in depth in this review. The human equilibrative nucleoside transporters translocate nucleosides and nucleobases bidirectionally down their concentration gradients and are important in the uptake of anticancer and antiviral nucleoside drugs. The human concentrative nucleoside transporters cotranslocate nucleosides and sodium unidirectionally against the nucleoside concentration gradients and play a vital role in certain tissues. The regulation of nucleoside and nucleobase transporters is being studied more intensely now that more tools are available. This review provides an overview of recent advances in the molecular biology and regulation of the nucleoside and nucleobase transporters.Key words: nucleoside transporter, nucleoside transport, nucleobase transporter, nucleobase transport, regulation of nucleoside and nucleobase transport, nucleoside drugs.
Structure determination of membrane proteins by NMR spectroscopy
Authors: Opella S J , Nevzorov A , Mesleh M F , Marassi F M
Published: October 2002

Current strategies for determining the structures of membrane proteins in lipid environments by NMR spectroscopy rely on the anisotropy of nuclear spin interactions, which are experimentally accessible through experiments performed on weakly and completely aligned samples. Importantly, the anisotropy of nuclear spin interactions results in a mapping of structure to the resonance frequencies and splittings observed in NMR spectra. Distinctive wheel-like patterns are observed in two-dimensional 1H15N heteronuclear dipolar/15N chemical shift PISEMA (polarization inversion spin-exchange at the magic angle) spectra of helical membrane proteins in highly aligned lipid bilayer samples. One-dimensional dipolar waves are an extension of two-dimensional PISA (polarity index slant angle) wheels that map protein structures in NMR spectra of both weakly and completely aligned samples. Dipolar waves describe the periodic wave-like variations of the magnitudes of the heteronuclear dipolar couplings as a function of residue number in the absence of chemical shift effects. Since weakly aligned samples of proteins display these same effects, primarily as residual dipolar couplings, in solution NMR spectra, this represents a convergence of solid-state and solution NMR approaches to structure determination.Key words: NMR spectroscopy, protein structure, dipolar couplings, membrane proteins, structure determination.
Activation of the glucose transporter GLUT4 by insulin
Authors: Furtado L Michelle , Somwar Romel , Sweeney Gary , Niu Wenyan , Klip Amira
Published: October 2002

The transport of glucose into cells and tissues is a highly regulated process, mediated by a family of facilitative glucose transporters (GLUTs). Insulin-stimulated glucose uptake is primarily mediated by the transporter isoform GLUT4, which is predominantly expressed in mature skeletal muscle and fat tissues. Our recent work suggests that two separate pathways are initiated in response to insulin: (i) to recruit transporters to the cell surface from intracellular pools and (ii) to increase the intrinsic activity of the transporters. These pathways are differentially inhibited by wortmannin, demonstrating that the two pathways do not operate in series. Conversely, inhibitors of p38 mitogen-activated protein kinase (MAPK) imply that p38 MAPK is involved only in the regulation of the pathway leading to the insulin-stimulated activation of GLUT4. This review discusses the evidence for the divergence of GLUT4 translocation and activity and proposed mechanisms for the regulation of GLUT4.Key words: glucose transporter 4 (GLUT4), glucose uptake, p38 MAPK, GLUT4 activity.
Role of bicarbonate in the regulation of intracellular pH in the mammalian ventricular myocyte
Authors: Vaughan-Jones Richard D , Spitzer Kenneth W
Published: October 2002

Bicarbonate is important for pHicontrol in cardiac cells. It is a major part of the intracellular buffer apparatus, it is a substrate for sarcolemmal acid-equivalent transporters that regulate intracellular pH, and it contributes to the pHosensitivity of steady-state pHi, a phenomenon that may form part of a whole-body response to acid/base disturbances. Both bicarbonate and H+/OHtransporters participate in the sarcolemmal regulation of pHi, namely Na+HCO3cotransport (NBC), ClHCO3exchange (i.e., anion exchange, AE), Na+H+exchange (NHE), and ClOHexchange (CHE). These transporters are coupled functionally through changes of pHi, while pHiis linked to [Ca2+]ithrough secondary changes in [Na+]imediated by NBC and NHE. Via such coupling, decreases of pHoand pHican ultimately lead to an elevation of [Ca2+]i, thereby influencing cardiac contractility and electrical rhythm. Bicarbonate is also an essential component of an intracellular carbonic buffer shuttle that diffusively couples cytoplasmic pH to the sarcolemma and minimises the formation of intracellular pH microdomains. The importance of bicarbonate is closely linked to the activity of the enzyme carbonic anhydrase (CA). Without CA activity, intracellular bicarbonate-dependent buffering, membrane bicarbonate transport, and the carbonic shuttle are severely compromised. There is a functional partnership between CA and HCO3transport. Based on our observations on intracellular acid mobility, we propose that one physiological role for CA is to act as a pH-coupling protein, linking bulk pH to the allosteric H+control sites on sarcolemmal acid/base transporters.Key words: bicarbonate transporter, pHi, heart, ventricular.
Iron transport: emerging roles in health and disease
Authors: Goswami Tapasree , Rolfs Andreas , Hediger Matthias A
Published: October 2002

In the theater of cellular life, iron plays an ambiguous and yet undoubted lead role. Iron is a ubiquitous core element of the earth and plays a central role in countless biochemical pathways. It is integral to the catalysis of the redox reactions of oxidative phosphorylation in the respiratory chain, and it provides a specific binding site for oxygen in the heme binding moiety of hemoglobin, which allows oxygen transport in the blood. Its biological utility depends upon its ability to readily accept or donate electrons, interconverting between its ferric (Fe3+) and ferrous (Fe2+) forms. In contrast to these beneficial features, free iron can assume a dangerous aspect catalyzing the formation of highly reactive compounds such as cytotoxic hydroxyl radicals that cause damage to the macromolecular components of cells, including DNA and proteins, and thereby cellular destruction. The handling of iron in the body must therefore be very carefully regulated. Most environmental iron is in the Fe3+ state, which is almost insoluble at neutral pH. To overcome the virtual insolubility and potential toxicity of iron, a myriad of specialized transport systems and associated proteins have evolved to mediate regulated acquisition, transport, and storage of iron in a soluble, biologically useful, non-toxic form. We are gradually beginning to understand how these proteins individually and in concert serve to maintain cellular and whole body homeostasis of this crucial yet potentially harmful metal ion. Furthermore, studies are increasingly implicating iron and its associated transport in specific pathologies of many organs. Investigation of the transport proteins and their functions is beginning to unravel the detailed mechanisms underlying the diseases associated with iron deficiency, iron overload, and other dysfunctions of iron metabolism.Key words: iron, transporter, transferrin, hemochromatosis, anemia, DCT1.
Assessing the structure of membrane proteins: combining different methods gives the full picture
Authors: Stahlberg Henning , Engel Andreas , Philippsen Ansgar
Published: October 2002

The rotor stoichiometry of F-ATPases has been revealed by the combined approaches of X-ray diffraction (XRD), electron crystallography, and atomic force microscopy (AFM). XRD showed the rotor from the yeast mitochondrial F-ATPase to contain 10 subunits. AFM was used to visualize the tetradecameric chloroplast rotors, and electron crystallography and AFM together revealed the rotors from Ilyobacter tartaricus to be composed of 11 subunits. While biochemical methods had determined an approximate stoichiometric value, precise measurements and new insights into a species-dependent rotor stoichiometry became available by applying the three structural tools together. The structures of AQP1, a water channel, and GlpF, a glycerol channel, were determined by electron crystallography and XRD. The combination of both of these structural tools with molecular dynamics simulations gave a differentiated description of the mechanisms determining the selectivity of water and glycerol channels. This illustrates that the combination of different methods in structural biology reveals more than each method alone.Key words: AQP1, GlpF, F-ATPase, XRD, electron crystallography, AFM.
TGF-β and the Smad signal transduction pathway
Authors: Mehra Arun , Wrana Jeffrey L
Published: October 2002

Transforming growth factor β (TGF-β) superfamily members are important regulators of many diverse developmental and homeostatic processes and disruption of their activity has been implicated in a variety of human diseases ranging from cancer to chondrodysplasias and pulmonary hypertension. TGF-β family members signal through transmembrane SerThr kinase receptors that directly regulate the intracellular Smad pathway. Smads are a unique family of signal transduction molecules that can transmit signals directly from the cell surface receptors to the nucleus, where they regulate transcription by interacting with DNA binding partners as well as transcriptional coactivators and corepressors. In addition, more recent evidence indicates that Smads can also function both as substrates and adaptors for ubiquitin protein ligases, which mediate the targeted destruction of intracellular proteins. Smads have thus emerged as multifunctional transmitters of TGF-β family signals that play critical roles in the development and homeostasis of metazoans.Key words: TGF-β, Smads, receptors, ubiquitin ligase, signal transduction.
Meeting report: membrane proteins in health and disease
Authors: Young James D , Casey Joseph R , Reithmeier Reinhart A.F
Published: October 2002

This article summarizes the scientific presentations made at a Canadian Society of Biochemistry and Molecular & Cellular Biology Symposium on "Membrane Proteins in Health and Diseases" and two satellite meetings on "Bicarbonate Transporters" and "Nucleoside Transporters" held in Banff, Alberta, 2024 March 2002. Membrane proteins are encoded by about 1/3 of genes and are involved in a wide range of essential functions, including the transport of nutrients, ions, and waste products across biological membranes. Mutations or changes in the expression of these genes cause an equally wide range of diseases. Membrane proteins are also common drug targets or provide drug entry mechanisms. The importance of membrane proteins in biology and medicine was highlighted by the presentations made at this exciting meeting by an international group of experts.Key words: bicarbonate, genomics, inherited disease, nucleosides, organelles, pH regulation, structural biology, trafficking, transporters.
Laminar hydromagnetic natural convection flow along a heated vertical surface in a stratified environment with internal heat absorption
Authors: Chamkha A J
Published: October 2002

The problem of steady, laminar, natural convection flow along a vertical permeable surface immersed in a thermally stratified environment in the presence of magnetic-field and heat-absorption effects is studied numerically. Conditions for similarity solutions are determined for arbitrary stable and unstable thermal environment stratification. Numerical solution of the similarity equations is performed using an implicit, iterative, tri-diagonal finite-difference method. Comparison with previously published work is performed and the results are found to be in excellent agreement. The effects of Hartmann number, heat-absorption coefficient, and the wall mass-transfer parameter on the velocity and temperature profiles as well as the skin-friction coefficient and Nusselt number are presented graphically and discussed. It is found that both the magnetic-field and heat-absorption effects eliminate the occurrence of the fluid backflow and temperature deficit in the outer part of the boundary layer predicted for the nonmagnetic case.

PACS Nos.: 44.20, 44.25, 47.65
State space formulation for boundary-layer magneto-hydrodynamic free convection flow with one relaxation time
Authors: Ezzat M A , Samaan A A , Bary A Abd-El
Published: October 2002

We introduce a magnetohydrodynamic model of a boundary-layer equation for a conducting viscous fluid. The state space approach is adopted for one-dimensional problems including heat sources with one relaxation time. The resulting formulation is applied to a problem for the whole space with a plane distribution of heat sources. The reflection method together with the solution obtained for the whole space is applied to a semi-space problem with a plane distribution of heat sources located inside the fluid. Numerical results for the velocity, temperature, and induced-magnetic- and induced-electric-field distributions are given and illustrated graphically for both problems.

PACS No.: 47.65+a
Studies on muonic dynamics of liquid DTH in dtμ muonic-molecule resonance formation and its comparison with a DT system
Authors: Eskandari M R , Hoseini-Motlagh S N , Rezaie B
Published: October 2002

Recent experimental and theoretical studies on muon-catalyzed fusion in a mixture of three gases, DTH, have shown that the muon-cycling-rate changes obtained are mostly in contradiction with each other and depend strongly on the physical conditions of the system. In this paper, we have considered the muon-cycling rate and its relevant nonlinear dynamical equations for mixtures of DT and DTH in practical conditions where the muon-cycling rate is temperature; density of the mixture; and relative-particle concentration (deuterium, tritium, and hydrogen) dependent. Our theoretical method has shown that addition of protium to a DT mixture leads to a significant decrease in the cycling rate, namely, by a factor of more than 15 in the liquid mixture and more than three in the gaseous mixture at 300600 K. We show that the results obtained for given experimental conditions are in very good agreement with recent experimental values of Joint Institute for Nuclear Research in Dubna. The given reliable theoretical method leads us to determine the optimal condition of the muon-cycling rate such as relative-particle concentration in the resonance-temperature range at liquid hydrogen density, Φ = 1. It is shown that for a deuterium and tritium relative concentration of Cd = Ct = 0.45 with Cp = 0.1 and ωs = 0.0029, a muon-cycling rate of 199 in the dtμ branch at 800 K is achievable, which compared to the DT system in optimal conditions, still has a 29% enhancement. Finally, by energy-gain evaluation of resonance-muon-catalyzed fusion, we show that even this key step in high-yield μCF is far, far away from sufficiently minimal values to be of interest for practical applications of such a system. PACS No.: 25.30M
Transfer of the self energy into field energy of density E2/8π during assembly of a localized charge distribution from infinity
Authors: Favreau R F
Published: October 2002

Purcell proposes that the potential energy U of a localized distribution of electrostatic charge has physical significance only as the total energy of the whole configuration. Feynman, on the other hand, favors the idea that U be localized as field energy of density E2/8π however, he points out that the demonstration of E2/8π as localized energy remains ambiguous. The article shows that by calculating the work done by the Maxwell stresses during assembly from infinity of a charge distribution of density q(r), it may be demonstrated unambiguously how the Maxwell stresses create a flow of work that distributes U into localized field energy of density E2/8π. This result supports the Feynman point of view.

PACS No.: 03.50De
Spectroscopic theory for organic and organometallic conductors
Authors: Oza A T
Published: October 2002

Here the Gaussian distributions obtained in the UVvisible and infrared spectra of inclusion compounds and charge-transfer complexes are derived theoretically. In some organometallic conductors, log α (where α is the absorption coefficient) is normally distributed. This result and the Gaussian centre-split in a compound are explained theoretically.

PACS No.: 72.80Le
Eddy currents in the SternGerlach experiment
Authors: Sulcs S , Gilbert B C
Published: October 2002

We calculate the effects of Larmor precession in the two-state SternGerlach experiment performed with silver atoms. We compare the time constants and Q factors for an oscillating magnetic-dipole moment in free space and in close proximity to an iron magnet. Numerical modelling suggests that the original SternGerlach experiment was too dissipative to have eliminated classical explanations. A recent experiment, also admitting a classical interpretation, is discussed briefly. A new experiment is proposed that should be able to confirm quantum mechanics unequivocally.

PACS Nos.: 03.65Bz, 41.20Gz, 32.10Dk
Quantized form of electronnucleus interaction in laser fields
Authors: Kálmán Péter , Bükki Tamás
Published: October 2002

A general formalism for the treatment of electronnucleus laser-combined processes is presented in a quantized manner. The laser is described by a coherent state in one mode of the quantized electromagnetic field. The system is composed of one electron and A nucleons and it is handled with A + 1 particle quantum mechanics. As a first step, the coherent state is transformed into the vacuum state, while a classical external field corresponding to the laser field arises. The interaction with the laser beam is taken into account by transforming the system into an oscillating frame, called Henneberger picture, while the electronnucleus electromagnetic interaction is handled as photon exchange via quantized electromagnetic field and in the second order of perturbation theory. A general expression for the transition probability per unit time is given in the l photonic case.PACS Nos.: 23.20Nx, 32.80Wr
Disinfection assessment in full-scale chlorine contact chambers
Authors: Edwards E S , Anderson W B , Andrews S A , Huck P M
Published: October 2002

In 1998, the City of Brantford Water Purification Plant was retrofitted with an ultra-high-rate upflow clarification process and two post-clarification chlorine contact chambers. The objective of the work described herein was to assess the theoretical inactivation of Giardia lamblia cysts by free chlorine disinfection in the new chlorine contact chambers. At the time this research was conducted, Ontario drinking water disinfection requirements were not as comprehensive as they are now, following the Walkerton outbreak. In an effort to remain proactive with respect to potential new disinfection regulations in Canada, the 1989 United States Environmental Protection Agency Surface Water Treatment Rule (SWTR) was used to assess the disinfection capability of the City of Brantford chlorine contact chambers. The Ontario Ministry of the Environment promulgated the Ontario Drinking Water Protection Regulation (DWPR) shortly after this project was completed (using the SWTR as a model), reaffirming the relevance of the approach described herein. This study showed that the new chlorine contactors did not provide sufficient contact time to ensure the minimum 0.5-log inactivation of G. lamblia cysts under all potential adverse scenarios. Contactor modifications were made to correct design deficiencies. The comprehensive assessment of the disinfection strategies presented here may be useful to other utilities in Ontario that must now comply with newly implemented DWPRs as well as utilities in other provinces that wish to be proactive with respect to potential new regulations in Canada regarding pathogen control. Key words: surface water treatment rule (SWTR), disinfection, chlorine, Giardia lamblia, CT concept, tracer studies, T10 contact time, log inactivation.
Comparing crushed recycled glass to silica sand for dual media filtration
Authors: Rutledge S O , Gagnon G A
Published: October 2002

The objective of this project was to evaluate the performance of a pressure filter utilizing crushed glass as the filter media in a dual media anthraciteglass filter compared to a dual media anthracitesand filter. In general, the particle removal capabilities of the crushed-glass filter were slightly poorer than those of a sand filter, as quantified in a field application in the community of Orangedale, Nova Scotia. It was found that the crushed glass used in this project had a higher angularity and slightly higher uniformity coefficient then the sand tested. After 6 months of use the crushed-glass filter was able to produce a filter effluent of 5070 particles/mL (diameter >2 μμm), which is greater than the 2550 particles/mL (diameter >2 μμm) that was produced by sand filter. Over the course of the 6-month study the dual media crushed-glass filter was able to achieve a 1.4-log removal, which was only slightly greater than the dual media silica sand filter that achieved a 1.6-log removal of particles with diameters >2 μμm. Key words: filtration, drinking water, recycled glass, sustainability, particle counting.
Soil nitric and nitrous oxide emissions from agricultural and tidal flat fields in southwestern Korea
Authors: Kim D -S , Kim J -C
Published: October 2002

A closed chamber system was used to measure fluxes of NO and N2O from soil surfaces. The research sites were located in southwestern Korea, and measurements were conducted during summer 2000 to assess the NO source strength of agricultural soils (upland and rice paddy) and tidal flats. Research for tidal flat soil fluxes was initially attempted to investigate their significance on the nitrogen budget in Korea. Soil samples were taken on each experimental day and analyzed for soil pH, soil moisture, and total Kjeldahl nitrogen (TKN = organic nitrogen + NH4-N + NO3-N). Soil nitrogen and NO flux increased significantly after applying nitrogen fertilizer to agricultural fields. Average NO and N2O fluxes were 84.8 ng N m2 s1 (range: 0.1~464.2 ng N m2 s1) and 67.8 ng N m2 s1 (range: 4.0~199.7 ng N m2 s1), respectively, from upland soils planted with green onions. Average N2O flux from soils planted with soybean was 52.5 ng N m2 s1 (range: 4.0~463.2 ng N m2 s1). Based on statistical test, no significant difference in N2O fluxes between green onion and soybean field was observed (t-statistic value = 1.2299; t98,0.05 = 1.6606). Soil NO and N2O fluxes from rice paddies and tidal flats were significantly lower than those from uplands; anoxic condition due to water saturation could limit the gas productions by processing nitrate reduction. Key words: NO and N2O flux, biogenic emission, closed chamber technology, agricultural soils, tidal flat nitrogen emission.
Slow sand filtration for small water systems
Authors: Logsdon G S , Kohne R , Abel S , LaBonde S
Published: October 2002

For over 150 years, slow sand filters have been an effective means of treating water for control of microbiological contaminants. Slow sand filters do not need constant operator attention, making them an appropriate technology for water systems that are small or that employ part-time operators. During the 1970s through the 1990s, research and field evaluations of slow sand filtration have demonstrated its efficacy for control of microbiological contaminants that were unknown in the 1800s. In addition, pretreatment processes such as roughing filters and pre-ozonation have been developed or adapted for use with slow sand filters, increasing the range of source waters that can be treated and the number of contaminants that can be removed in slow sand filters. Inclusion of a layer of granular-activated carbon in a slow sand filter bed has improved capability for control of synthetic organic chemicals. This paper reviews design concepts and process capabilities for slow sand filters and discusses recent innovations in slow sand filter design that now enable this technology to be applied more widely than would have been appropriate two decades ago. Key words: slow sand filter, design, operation and maintenance, microbiological contaminants, small systems, pretreatment.
Implementation of chlorine dioxide disinfection: Effects of the treatment change on drinking water quality in a full-scale distribution system
Authors: Volk C J , Hofmann R , Chauret C , Gagnon G A , Ranger G , Andrews R C
Published: October 2002

Drinking water utilities may have to consider changing disinfectant to improve water quality and meet more stringent disinfection regulations. The objective of this study was to evaluate the response of a full-scale drinking water distribution system to a change in disinfectant from chlorine to chlorine dioxide, in terms of its impact on microbiological stability and disinfection by-product formation. Chlorine dioxide residuals were consistently present above detection limits throughout the distribution system (>0.20 mg/L). Over a study period of 3.5 months, no degradation of bacterial water quality occurred after implementing the new disinfectant. Chlorine dioxide maintained total bacteria (microscopic counts) and heterotrophic plate count levels below 2 x 105 cells/mL and 1000 CFU/mL, respectively. The change in disinfectant from chlorine to chlorine dioxide led to an 85% reduction in trihalomethanes (i.e., from 30 to 5 μμg/L) and a 60% reduction in haloacetic acids (i.e., from 20 to 8 μμg/L). Chlorine dioxide represents a valuable tool to produce high quality water and is a strong alternative to chlorine for certain distribution systems. Key words: distribution system, chlorine dioxide, drinking water quality, disinfection by-products.
Effect of two different thermal units and three types of mulch on weeds in apple orchards
Authors: Rifai M N , Astatkie T , Lacko-Bartosova M , Gadus J
Published: October 2002

The effect of two different thermal units (flame and hot steam) and three types of mulch on the percentage of weeds killed was studied in a series of experiments over 2 years. The factors studied were driving speed (2, 3, 4 km/h), flame treatment (first, second, third), growth stage (<6, 68, >8 true leaves), hot steam treatment (single, double), mulch type (none, coarse bark, sawdust, hay), and chemical application. The results suggest that a driving speed of 2 km/h kills the highest percentage of weeds, and for weed species with unprotected growth points and thin leaves, the first flame application can completely kill weeds with <6 leaves. However, a second or third flame application is required for those with 6 or more leaves. The hot steam method is effective when it is applied twice, with the second application 1 week after the first. However, there is room for improving its technology to make it cost effective for large-scale applications. Mulches after chemical herbicide application are effective for controlling weeds. However, mulching cannot be recommended with flaming because of fire hazard. The effectiveness of herbicide depends on the weed species and on whether the same herbicide was used in the preceding years. Compared to using herbicide with mulching, herbicide alone was less effective in controlling weeds and more costly in terms of cost per hectare and the environment. Key words: thermal weed control, flame, hot steam, mulching, herbicides, apple orchard, logit models.
Effects of chloramination and site specific issues on nanofiltration flux loss and foulant characteristics
Authors: Speth Thomas F , Parrett Christopher J , Harmon Stephen M , Kelty Keith C
Published: October 2002

The presence of chloramines or free ammonium ion was found to have little effect on the final specific flux and fouling cake-layer characteristics of nanofiltration membranes fed pretreated Little Miami Aquifer water. The system fed chloraminated water had the greatest amount of specific flux recovered with chemical cleaning; however, it also had the greatest flux decline within each operational cycle, resulting in a final flux that was similar to those from the other systems. The expected proteinaceous cake layer with chloramination was not observed in this study, indicating that this previously observed effect is a site and possibly seasonally specific issue. The membrane fouling at this location was found to have large seasonal variations with the greatest specific flux loss and cake-layer formation occurring during the October to December study. This was likely due to a change in the nature of the organic matter as indicated by differences in the cake layers between studies as determined by pyrolysis-gas chromatography/mass spectrometry (GC/MS). Key words: ammonia, biofouling, chloramination, chloramines, flux, fouling, groundwater, membranes, nanofiltration, and pyrolysis-GC/MS.
PCR and blot hybridization for rapid identification of Haloferax species
Authors: Asker Dalal , Ohta Yoshiyuki
Published: October 2002

Based on the amplification of a 16S rDNA, a PCR assay for the identification of species of Haloferax to genus level was performed. Two variable regions of the 16S rDNA in Haloferax spp. were selected as genus-specific primers for the PCR assay and hybridization probe. Five genera of halophilic Archaea and Escherichia coli were examined as outside groups. Using this approach, all strains of Haloferax spp. were positive. In contrast, all species belonging to the most closely related genera, including Natrinema, Halorubrum, Halobacterium, and Haloarcula, were negative. In addition, the mass bloom of halophilic Archaea that develops in the El-Mallahet saltern of Alexandria City was positive using the same approach. This assay, which does not require pure cultures of microorganisms, is a specific and rapid method for identifying Haloferax spp. in hypersaline environments.Key words: Haloferax spp., 16S rDNA, PCR, blot hybridization, El-Mallahet saltern.
Diversity of antifungal actinomycetes in various vegetative soils of Korea
Authors: Lee Jung Yeop , Hwang Byung Kook
Published: October 2002

Diversity of actinomycetes and their antifungal activities against some plant pathogenic fungi were examined in various vegetative soils from 14 different sites in the western part of Korea. Actinomycete counts ranged from 1.17 × 106to 4.20 × 106cfu·g-1dried soil. A total of 1510 actinomycetes were isolated from the soil samples. Streptomyces was predominant in soils with a pH range of 5.1-6.5, 9.1-13.0% moisture, and 9.1-11.0% organic matter. Most Micromonospora, Dactylosporangium, and Streptosporangium were distributed in soils with pH 4.0-5.0, 2.0-9.0% moisture, and 4.0-7.0% organic matter. Actinomadura and nocardioform actinomycetes were abundant in soils with pH 4.0-5.0 and 13.1-20.0% moisture and with 9.1-11.0 and 4.0-7.0% organic matter, respectively. Populations of Streptomyces were predominant in all the soils, but were highest in grassland and lowest in mountain-forest soils. Micromonospora was most abundant in pepper-field soil and nocardioform actinomycetes were highest in rice paddy field soil. Dactylosporangium was predominant in lake-mud sediments and pepper-field soil, Streptosporangium in lake-mud sediments, and Actinomadura in mountain-forest soil. Antifungal actinomycetes were abundant in orchard soil and lake mud. More than 50% of antifungal isolates from most soils were classified as genus Streptomyces. Actinomycete isolates that showed strong antifungal activity against Alternaria mali, Colletotrichum gloeosporioides, Fusarium oxysporum f.sp. cucumerinum, and Rhizoctonia solani were predominant in pepper-field soils, whereas those against Magnaporthe grisea and Phytophthora capsici were abundant in radish-field soils.Key words: actinomycetes, antifungal activity, plant pathogenic fungi, vegetative soils.
Molecular characterization of DNA encoding 16S23S rRNA intergenic spacer regions and 16S rRNA of pectolyticErwiniaspecies
Authors: Fessehaie A , De Boer S H , Lévesque C A
Published: October 2002

Sequences of 16S rDNAs and the intergenic spacer (IGS) regions between the 16S and 23S rDNA of bacterial strains from genus Erwinia were determined. Comparison of 16S rDNA sequences from different species and subspecies clearly revealed intraspeciessubspecies homology and interspecies heterogeneity. Phylogenetic analyses of 16S rDNA sequence data revealed that Erwinia spp. formed a discrete monophyletic clade with moderate to high bootstrap values. PCR amplification of the 16S23S rDNA regions using primers complementary to the 3' end of 16S and 5' end of 23S rRNA genes generated two DNA fragments. The small 16S23S rDNA IGS regions of Erwinia spp. examined in this study varied considerably in size and nucleotide sequence. Multiple sequence alignment and phylogenetic analysis of small IGS sequence data showed a consistent relationship among the test strains that was roughly in agreement with the 16S rDNA data that reflected the accepted species and subspecies structure of the taxon. Sequence data derived from the large IGS resolved the strains into coherent groups; however, the sequence information would not allow any phylogenetic conclusion, because it failed to reflect the accepted species structure of the test strains.Key words: Erwinia spp., 16S rDNA, intergenic spacer region, tRNA genes, phylogeny.
Physiological diversity and trehalose accumulation inSchizosaccharomyces pombestrains isolated from spontaneous fermentations during the production of the artisanal Braziliancachaça
Authors: Gomes Fátima C.O , Pataro Carla , Guerra Juliana B , Neves Maria J , Corrêa Soraya R , Moreira Elizabeth S.A , Rosa Carlos A
Published: October 2002

Twenty-seven Schizosaccharomyces pombe isolates from seven cachaça distilleries were tested for maximum temperature of growth and fermentation, osmotolerance, ethanol resistance, invertase production, and trehalose accumulation. Two isolates were selected for studies of trehalose accumulation under heat shock and ethanol stress. The S. pombe isolates were also characterized by RAPD-PCR. The isolates were able to grow and ferment at 41°C, resisted concentrations of 10% ethanol, and grew on 50% glucose medium. Four isolates yielded invertase activity of more than 100 µmol of reducing sugar·mg1·min1. The S. pombe isolates were able to accumulate trehalose during stationary phase. Two isolates, strains UFMG-A533 and UFMG-A1000, submitted to a 15 min heat shock, were able to accumulate high trehalose levels. Strain UFMG-A533 had a marked reduction in viability during heat shock, but strain UFMG-A1000 preserved a viability rate of almost 20% after 15 min at 48°C. No clear correlation was observed between trehalose accumulation and cell survival during ethanol stress. Strain UFMG-A1000 had higher trehalose accumulation levels than strain UFMG-A533 under conditions of combined heat treatment and ethanol stress. Molecular analysis showed that some strains are maintained during the whole cachaça production period; using the RAPD-PCR profiles, it was possible to group the isolates according to their isolation sites.Key words: Schizosaccharomyces pombe, cachaça, fermentation, physiological tests, trehalose.
Use of PCRRFLP for genotyping 16S rRNA and characterizing bacteria cultured from halibut fry
Authors: Jensen Sigmund , Bergh Øivind , Enger Øivind , Hjeltnes Brit
Published: October 2002

Small subunit ribosomal genes were explored using PCRRFLP to facilitate the characterization of bacteria cultured from reared fry of the Atlantic halibut (Hippoglossus hippoglossus). Concern has been expressed about pathogen invasion in larvae lacking a counteracting normal flora that may aid the immune system in producing robust noninfected individuals. In this study, pure cultured representatives of normal flora that were previously found to be antagonistic towards a pathogenic Vibrio sp. were subjected to a whole cell PCR protocol amplifying ~1500 bp of 16S rDNA. Amplified DNA was digested by AluI, BstUI, CfoI, and RsaI, to generate restriction profiles. Before the isolates were characterized, a survey was performed to test the discriminative efficiency of the RFLP. Efficient detection of polymorphism and the resolution of species and subspecies were achieved. Using the RFLP on 103 isolates generated as many as 22 genotypes. Based on the restriction profiles, a taxonomic tree incorporating 19 reference strains was constructed. Partial sequencing found this tree to be dominated by γ-Proteobacteria in clusters of Vibrio-, Pseudomonas-, and Alteromonas-affiliated species. Only nine isolates fell outside these genera, including the three isolates Shewanella alga, Deleya marina, and Marinomonas protea. These species have not previously been reported as halibut flora. The most frequently isolated genotype resembled Vibrio salmonicida.Key words: halibut, Vibrio, RFLP, 16S rDNA, phylogeny.
Population structure and mating-type genes ofColletotrichum graminicolafromAgrostis palustris
Authors: Chen Fajun , Goodwin Paul H , Khan Adalat , Hsiang Tom
Published: October 2002

Eighty-seven isolates of Colletotrichum graminicola, mostly from Agrostis palustris, were collected in grass fields, most of which were in Ontario, Canada. Specific primers were designed to amplify the mating-type (MAT) genes and, among 35 isolates tested, all yielded a band of the expected size for MAT2. For six isolates, the MAT2 PCR products were sequenced and found to be similar to that reported for MAT2 of C. graminicola from maize. Based on 119 polymorphic bands from 10 random amplified polymorphic DNA primers, analyses of genetic distances were found to generally cluster isolates by host and geographic origin. Among 42 isolates from a grass field in Ontario, significant spatial autocorrelation was found to occur within a 20-m distance, implying that this is the effective propagule dispersal distance. Although clonal propagation was observed in the 87 isolates with 67 unique genotypes, the extent of genetic variation in local populations implies some occurrence of sexual or asexual recombination.Key words: anthracnose, turfgrass, RAPD, MAT, reproduction, fungi.
Characterization of two novel yeast strains used in mediated biosensors for wastewater
Authors: Trosok Steve P , Luong John H.T , Juck David F , Driscoll Brian T
Published: October 2002

After isolation from a pulp mill wastewater treatment facility, two yeast strains, designated SPT1 and SPT2, were characterized and used in the development of mediated biochemical oxygen demand (BOD) biosensors for wastewater. 18S rRNA gene sequence analysis revealed a one nucleotide difference between the sequence of SPT1 and those of Candida sojae and Candida viswanthii. While SPT2 had the highest overall homology to Pichia norvegensis, at only 73.5%, it is clearly an ascomycete, based on BLAST comparisons and phylogenetic analyses. Neighbor-joining dendrograms indicated that SPT1 clustered with several Candida spp., and that SPT2 clustered with Starmera spp., albeit as a very deep branch. Physiological tests, microscopic observations, and fatty acid analysis confirmed that SPT1 and SPT2 are novel yeast strains. Physiological tests also indicated that both strains had potential for use in mediated biosensors for estimation of BOD in wastewater. The lower detection limits of SPT1- and SPT2-based K3Fe(CN)6-mediated biosensors for a pulp-mill effluent were 2 and 1 mg BOD/L, respectively. Biosensor-response times for effluents from eight different pulp mills were in the range of 5 min. Reliability and sensitivity of the SPT1- and SPT2-based biosensors were good, but varied with the wastewater.Key words: yeast characterization, 18S rRNA gene sequence, pulp-mill wastewater, BOD5, mediated BOD biosensor.
Some factors affecting the adherence of probiotic Propionibacterium acidipropionici CRL 1198 to intestinal epithelial cells
Authors: Zárate Gabriela , De Ambrosini Vilma Morata , Chaia Adriana Perez , González Silvia
Published: October 2002

Adhesion to the intestinal mucosa is generally considered an important property of probiotic microorganisms and has been related to many of their health benefits. This study investigated some factors that could affect or be involved in the adherence of Propionibacterium acidipropionici CRL 1198, a dairy strain with suggested probiotic effects and high adherence in vitro and in vivo to intestinal epithelial cells. In vitro adhesion of propionibacteria was decreased by gastric digestion but not affected by bile and pancreatic enzymes. Adherence was also decreased by pretreatment of bacterial cells with protease, sodium metaperiodate, and trichloroacetic acid, revealing that different features of the cell surface, like protein factors, carbohydrates, and teichoic acids, are involved in the process. Adherence to intestinal epithelial cells was enhanced by calcium and was dependent on other divalent cations. Adhesion to intestinal mucus was also demonstrated. The results should explain the metabolic effects in the host previously obtained with this strain and support the potential of Propionibacterium for development of new probiotics.Key words: propionibacteria, adhesion, probiotics.
Utilization and cell-surface binding of hemin byHistoplasma capsulatum
Authors: Foster Lisa-Anne Agiato
Published: October 2002

Histoplasma capsulatum, a dimorphic fungus capable of causing severe respiratory illness in immuno-compromised individuals, resides in macrophages during mammalian infection. Previous studies suggest that siderophore-mediated iron transport may be important for the acquisition of iron from transferrin while the organism resides in macrophages. However, iron is also present as hemin in the intracellular environment of the macrophage and may serve as a major source of iron during infection. Thus the ability of H. capsulatum to use hemin and heme-containing compounds was examined. Histoplasma capsulatum G217B was iron-starved by adding the iron chelator deferoxamine mesylate to the culture. The addition of 10 µM hemin in the presence of deferoxamine mesylate restored growth to the levels seen in the absence of the chelator. Histoplasma capsulatum was also cultivated in an iron-limited, chemically defined medium without the addition of chelators and it was determined that the organism could also use hemoglobin as a sole source of iron. The method of iron internalization from heme was examined by measuring hemin binding to the yeast-cell surface. The ability of H. capsulatum to bind hemin was related to the nutritional status of the cells. Cells grown under iron-limited conditions bound more heme to the cell surface than did cells grown in medium without chelator. Pretreatment of iron-starved cells with proteinase K eliminated the ability of the organism to bind hemin. Additionally, the pre-incubation of iron-starved H. capsulatum with hemin eliminated the ability of these cells to remove hemin from the solution, although pre-incubation of cells with the iron-free form of hemin, protoporphyrin IX, only modestly affected the ability of the organism to bind hemin. These results suggest that H. capsulatum uses hemin as a sole source of iron and that one mechanism of iron acquisition involves a cell-surface receptor for hemin.Key words: H. capsulatum, heme utilization, iron.
Transposition of pGh9:ISS1 is random and efficient in Streptococcus thermophilus CNRZ368
Authors: Thibessard Annabelle , Fernandez Annabelle , Gintz Brigitte , Decaris Bernard , Leblond-Bourget Nathalie
Published: October 2002

Streptococcus thermophilus bacteria are used as a starter in the fermentation of yogurts and many cheeses. To construct mutants of S. thermophilus CNRZ368, the use of the plasmid pGh9:ISS1 was considered. This plasmid is known to be a good tool for insertional mutagenesis in gram-positive bacteria, owing to its ability to integrate in the genome by a mechanism of replicative transposition. However, the presence of three endogenous ISS1 copies in the genome of S. thermophilus CNRZ368 and the possible occurrence of homologous recombination could reduce the efficiency of pGh9:ISS1 as a tool for generating mutants. To address this question, the ability of pGh9:ISS1 to transpose randomly in the genome of strain CNRZ368 was investigated. The results of our experiments indicated that: (i) the frequency of transposition of ISS1 was high, approximately 2 × 102, in S. thermophilus CNRZ368; (ii) the integration of multiple tandem copies of the plasmid was frequent; (iii) homologous recombination events between ISS1 were not predominant; and (iv) plasmid pGh9:ISS1 transposed randomly around the S. thermophilus CNRZ368 chromosome. In addition, we describe the strategy used to localize the pGh9:ISS1 insertion locus on the physical map of strain CNRZ368 and the method used to clone the regions flanking this insertion site, especially when multiple copies of the plasmid were integrated in tandem.Key words: insertional mutagenesis, random transposition, Streptococcus thermophilus, homologue recombination, ISS1.