Subunit distribution of calcium-binding sites in Lumbricus terrestris hemoglobin

The giant, 3.6-MDa hexagonal bilayer hemoglobin (Hb) of Lumbricus terrestris consist of twelve 213-kDa globin subassemblies, each comprised of three disulfide-bonded trimers and three monomer globin chains, tethered to a central scaffolding of 36–42 linkers L1–L4 (24–32 kDa). It is known to contain 50–80 Ca and 2–4 Cu and Zn; the latter are thought to be responsible for the superoxide dismutase activity of the Hb. Total reflection X-ray fluorescence spectrometry was used to determine the Ca, Cu, and Zn contents of the Hb dissociated at pH 2.2, the globin dodecamer subassembly, and linker subunits L2 and L4. Although the dissociated Hb retained 20 Ca²⁺ and all the Cu and Zn, the globin subassembly had 0.4 to 3 Ca²⁺, depending on the method of isolation, and only traces of Cu and Zn. The linkers L2 and L4, isolated by reversed-phase high-pressure liquid chromatography at pH 2.2, had 1 Ca per mole and very little Cu and Zn. Electrospray ionization mass spectrometry of linker L3 at pH 2.2 and at neutral pH demonstrated avid binding of 1 Ca²⁺ and additional weaker binding of 7 Ca²⁺ in the presence of added Ca²⁺. Based on these and previous results which document the heterogeneous nature of the Ca²⁺-binding sites in Lumbricus Hb, we propose three classes of Ca²⁺-binding sites with affinities increasing in the following order: (i) a large number of sites (>100) with affinities lower than EDTA associated with linker L3 and dodecamer subassembly, (ii) 30 sites with affinities higher than EDTA occurring within the cysteine-rich domains of linker L3 and dodecamer subassembly, and (iii) 25 very high affinity sites associated with the linker subunits L1, L2, and L4. It is likely that the low-affinity type (i) sites are the ones involved in the effects of 1–100 mM Group IIA cations on Lumbricus Hb structure and function, namely increased stability of its quaternary structure and increased affinity and cooperativity of its oxygen binding.     

Single-channel K+ currents inDrosophila muscle and their pharmacological block

Summary Four types of nonvoltage-activated potassium channels in the body-wall muscles ofDrosophila third instar larvae have been identified by the patch-clamp technique. Using the inside-out configuration, tetraethylammonium (TEA). Ba²⁺, and quinidine were applied to the cytoplasmic face of muscle membranes during steady-state channel activation. The four channels could be readily distinguished on the basis of their pharmacological sensitivities and physiological properties. The K_ST channel was the only type that was activated by stretch. It had a high unitary conductance (100 pS in symmetrical 130/130mm KCl solution), was blocked by TEA (K _d 35mm), and was the most sensitive to Ba²⁺ (complete block at 10^–4 m). A Ca²⁺-activated potassium channel. K_CF 72pS (130/130mm KCl), was gated open at>10^–8 m Ca²⁺, was the least sensitive to Ba²⁺ (K _d of 3mm) and TEA (K _d of 100mm), and was not affected by quinidine. K₂ was a small conductance channel of 11 pS (130/2 KCl, pipette/bath), and was very sensitive to quinidine, being substantially blocked at 0.1mm. It also exhibited a half block at 0.3mm Ba²⁺ and 25mm TEA. A fourth channel type, K₃, was the most sensitive to TEA (half block<1mm). It displayed a partial block to Ba²⁺ at 10mm, but no block by 0.1mm quinidine. The blocking effects of TEA, Ba²⁺ and quinidine were reversible in all channels studied. The actions of TEA and Ba²⁺ appeared qualitatively different: in all four channels. TEA reduced the apparent unitary conductance, whereas Ba²⁺ decreased channel open probability.     

Biochemical differentiation of two groups within the species-complex Henricia Gray, 1840 (Echinodermata, Asteroidea) using starch-gel electrophoresis

Eighteen specimens from the Henricia pertusa group and 12 from the H. perforata group were examined for biochemical differences at the glucose-1-phosphate isomerase (GPI^* locus). Six alleles were found. Neither group showed deviations from Hardy Weinberg equilibrium (HW) (H. pertusa group: P1, H. perforata group: P=0.07, confidence interval=0.066–0.076). Significant differences in allele frequencies between the two groups (P0), supported previous assertions of reproductive isolation between the two groups based on morphological differences. However, near significance in HW disequilibrium in the H. perforata group indicates possible substructure in this group.     

Characterization of the photosynthetic electron transport chain in normal and photobleachedAnabaena cylindrica by flash spectroscopy

Electron transport of normal and photobleachedAnabaena cylindrica was studied using spectral and kinetic analyses of absorbance transients induced by single turnover flashes. Between 500 and 600 nm two positive bands (540 and 566 nm) and two negative bands (515 and 554 nm) were found. Absorbance changes at 515 and 540 nm were partly characterized. None of these absorbance changes represent an electrochromic shift. Absorbance changes at 554 and 566 nm correspond to the oxidation of cytochromef and the reduction of cytochromeb ₅₆₃, respectively. We found a very slight 3-(3,4-dichlorophenyl)-1, 1-dimethylurea (DCMU) sensitivity of cytochromef in normal cells, while DCMU was completely ineffective for cytochromef reduction in photobleached cells. The absorbance change of cytochromeb ₅₆₃ increased, while the absorbance change of cytochromef was smaller than in normal cells. The increased O₂ evolution in photobleached cells and the negligible electron transport via cytochromef suggest the participation of other electron acceptor(s) in the electron-transport chain of photobleachedAnabaena cylindrica.     

Effects of an exotic bivalve mollusc on benthic invertebrates and food quality in the Ohio River

Effects of zebra mussels (Dreissena polymorpha) on populations of amphipods (Gammarus fasciatus) and prosobranch snails (Lithasia obovata) and on nutritional quality of benthic organic matter were examined in 20 artificial streams receiving Ohio River water and containing either mussels or small gravel. Twenty individually-marked snails were placed in each trough, and streams were allowed to colonize with other benthic species for 28 days.Dreissenids positively affected other benthic invertebrates in our stream channels. Compared to gravel channels, Gammarus biomass was significantly higher (P<0.01) in mussel channels, amphipod densities increased 300%, and snail growth rates were 50% greater. Food quality of fine benthic organic matter (FBOM) was greater in mussel channels (i.e. lower C:N), and FBOM was carbon depleted (lower ¹³C) but nitrogen enriched (higher ¹⁵N). Isotope data suggest that detrital FBOM was not the sole food source for snails and amphipods in our channels and that they were assimilating a higher quality portion of this BOM. The overall influence of dreissenids on particular benthic invertebrates may depend on the response and/or susceptibility of those species to biofouling, increased habitat heterogeneity, and changes in the quality and quantity of nutrients.     

Hydrocarbon production from secondarily treated piggery wastewater by the green alga Botryococcus braunii

A laboratory study was conducted on the removal of nitrogen and phosphorus from piggery wastewater during growth of Botryococcus braunii UTEX 572, together with measurements of hydrocarbon formation by the alga. The influence was tested of the initial nitrogen and phosphorus concentration on the optimum concentration range for a culture in secondarily treated piggery wastewater. A high cell density (> 7 g L^–1 d. wt) was obtained with 510 mg L^–1 NO₃-N. Growth increased with nitrogen concentration at the basal phosphorus concentration (14 mg P L^–1). The growth rate was nearly independent ( = 0.027 0.030 h^–1) of the initial phosphate concentration, except under conditions of phosphate deficiency ( = 0.019 h^–1). B. braunii grew well in piggery wastewater pretreated by a membrane bioreactor (MBR) with acidogenic fermentation. A dry cell weight of 8.5 mgL^–1 and hydrocarbon level of 0.95 gL^–1 were obtained, and nitrate was removed at a rate of 620 mg NL^–1. These results indicate that pretreated piggery wastewater provides a good culture medium for the growth and hydrocarbon production by B. braunii.     

Identification of the key factors affecting composting of a weathered hydrocarbon-contaminated soil

The batch culture degradation of NASA wastewater containing mixtures of citric acid, methylhydrazine, and their reaction product was studied. The organic contaminants present in the NASA wastewater were degraded by Achromobacter sp., Rhodococcus B30 and Rhodococcus J10. While the Achromobacter sp. showed a preference for the degradation of the citric acid, the Rhodococcus species were most effective in reducing the methylhydrazine and the reaction product. Removals of more than 50% were observed for citric acid, methylhydrazine and the reaction product when the NASA wastewater was inoculated with the microbes in batch cultures. Simulation and chemical characterization of citric acid and hydrazine mixtures show that the interaction is partly of a chemical nature and leads to the formation of a conjugated UV/Visible absorbing compound. An 'azo' carbonyl derivative of the citric acid, consistent with the spectral data obtained from the investigation, has been proposed as the possible product.     

Release of carboxylic anions and protons by tomato roots in response to ammonium nitrate ratio and pH in nutrient solution

The exudation of certain organic anions and protons by roots which may affect solubility of metals and P and uptake by plants, is affected by nitrogen form and pH. The objective of this work was to study exudation of carboxylates and H⁺/OH^– by tomato plants in response to NH₄/NO₃ ratio and pH in nutrient solution. Four NH₄/(NH₄+NO₃) ratios (R= 0, 0.33, 0.67 and 1) and constant vs. variable solution pH treatments were investigated. The sum of the exudation rates of all carboxylates tended to decline with increasing R, particularly tri- and dicarboxylates. The molar fraction of the exuded tri- and dicarboxylates, averaged over all treatments and plant ages, increased in the order tartarate 2%), malate (6%), succinate (15%), citrate (26%) and fumarate (46%). At R=1 the solution pH dropped from 5.2 to 3 and at R=0 increased to 8. The R corresponding to the pH stat of tomato plant was 0.3. For the constant solution pH treatment, the effect of solution pH on carboxylate exudation rate was small as compared to the effect of R. The exudation of citrate and H⁺ efflux which were initiated when NO₃ and NH₄ uptake rates per plant exceeded certain threshold values, increased with plant age.     

Nucleotide sequence and expression of the two genes encoding D2 protein and the single gene encoding the CP43 protein of Photosystem II in the cyanobacterium synechococcus sp. PCC 7002

The unicellular photoheterotrophic cyanobacterium Synechococcus sp. PCC 7002 was shown to encode two genes for the Photosystem II reaction center core protein D2 and one gene for the reaction center chlorophyhll-binding protein CP43. These three genes were cloned and their DNA sequences determined along with their flanking DNA sequences. Northern hybridization experiments show that both genes which encode D2, psbD1 and psbD2, are expressed at roughly equivalent levels. For each of the two psbD genes, there are 18 nucleotide differences among the 1059 nucleotides which are translated. The DNA sequences surrounding the coding sequences are nearly 70% divergent. Despite the DNA sequence differences in the genes, the proteins encoded by the two genes are predicted to be identical. The proteins encoded by psbD1 and psbD2 are 92% homologous to other sequenced cyanobacterial psbD genes and 86% homologous to sequenced chloroplast-encoded psbD genes.The single gene for CP43, psbC, overlaps the 3 end of psbD1 and is co-transcribed with it. Results from previous sequencing of psbC genes encoded by chloroplasts suggest that the 5 end of the psbC gene overlaps the 3 end of the coding sequence of psbD by 50 nucleotides. In Synechococcus sp. PCC 7002, the methionine codon previously proposed to be the start codon for psbC is replaced by an ACG (threonine) codon. We propose an alternative start for the psbC gene at a GTG codon 36 nucleotides downstream from the threonine codon. This GTG codon is preceded by a consensus E. coli-like ribosome binding sequence. Both the GTG start codon and its preceding ribosome binding sequence are conserved in all psbC genes sequenced from cyanobacteria and chloroplasts. This suggests that all psbC genes start at this alternative GTG codon. Based on this alternative start codon, the gene product is 85% identical to other cyanobacterial psbC gene products and 77% identical to eucaryotic chloroplast-encoded psbC gene products.     

Strongly exciton-coupled BChle chromophore system in the chlorosomal antenna of intact cells of the green bacteriumChlorobium phaeovibrioides: A spectral hole burning study

Spectral hole burning studies of intact cells of the green bacteriumChlorobium phaeovibrioides have proven that the Q_y-absorption system of antenna bacteriochlorophylle (BChle) should be interpreted in terms of the delocalized exciton level structure of an aggregate. For the first time the 0-0 band of the lowest exciton state of BChle aggregates has been directly detected as the lowest energy inhomogeneously broadened band (FWHM 100 cm^–1; position of maximum, at 739 nm) of the near-infrared BChle band in the 1.8 K excitation spectrum (FWHM=750 cm^–1; position of maximum, at 715 nm). The comparative analysis of the hole spectra, measured for the three species of BChlc- ande-containing green bacteria, has shown that the 0-0 transition bands of the lowest exciton state of BChlc ande aggregates display fundamentally similar spectral features: (1) the magnitude of inhomogeneous broadening of these bands is about 100 cm^–1; (2) at the wavelength of the maximum of each band, the amplitude of the preburnt excitation spectrum makes up 20% of the maximum amplitude of the spectrum; (3) the spectral position of each band coincides with the spectral position of the longest wavelength band of the circular dichroism spectrum; (4) the width of these bands is 2.3-times less than that of monomeric BChl in vitro.     

rDNA targeted oligonucleotide primers for the identification of pathogenic yeasts in a polymerase chain reaction

Summary Species-specific oligonucleotide primers were designed for PCR identification of the basidiomycetous yeastsCryptococcus neoformans, Trichosporon cutaneum andRhodotorula mucilaginosa. The procedure uses standard PCR components including DNA from the test species and three primers: two universal external (upstream and downstream) limiting primers and a species-specific internal primer. Species identification requires the formation of a species-specific rDNA nucleotide segment that is significantly smaller (200 bp) than a non-target segment (600 bp). The procedure can be used to identify yeasts from single and mixed populations.This paper is dedicated to Professor Herman Jan Phaff in honor of his 50 years of active research which still continues.     

The identification of a Caenorhabditis elegans homolog of p34cdc2 kinase

We have identified a Caenorhabditis elegans homolog of p34^cdc2 kinase. The C. elegans homolog, ncc-1, is -60% identical to p34^cdc2 of Homo sapiens. When expressed from a constitutive yeast promoter, ncc-1 is capable of complementing a conditional lethal mutation in the CDC28 gene of Saccharomyces cerevisiae, indicating that this C. elegans homolog can properly regulate the cell cycle.     

Spirulina cultivation in digested sago starch factory wastewater

Wastewater arising from the production of sago starchhas a high carbon to nitrogen ratio, which is improvedwith anaerobic fermentation in an upflow packed beddigester. The digested effluent with an average C: N:P ratio of 24: 0.14: 1 supported growth of Spirulina platensis (Arthrospira) with anaverage specific growth rate () of 0.51day^-1 compared with the average of 0.54day^-1 in the inorganic Kosaric Medium in a highrate algal pond. Supplementation with 6 mM urea and2.1 mM K₂HPO₄ produced gross biomassproductivity of 14.4 g m^-2 day^-1. Aflow-rate of 24 cm s^-1 increased the andgross biomass productivity (18 g m^-2 day^-1). The highest crude protein, carbohydrate and lipidcontents of the biomass were 68%, 23% and 11%,respectively. Percentage reductions in chemicaloxygen demand, ammoniacal-nitrogen and phosphatelevels of the digested effluent reached 98.0%, 99.9%and 99.4% respectively. The HRAP offers a goodtreatment system for sago starch factory wastewater.     

Growth and laccase production kinetics of <Emphasis Type="Italic">Trametes versicolor</Emphasis> in a stirred tank reactor

White rot fungi are a promising option to treat recalcitrant organic molecules, such as lignin, polycyclic aromatic hydrocarbons, and textile dyes, because of the lignin-modifying enzymes (LMEs) they secrete. Because knowledge of the kinetic parameters is important to better design and operate bioreactors to cultivate these fungi for degradation and/or to produce LME(s), these parameters were determined using Trametes versicolor ATCC 20869 (ATCC, American Type Culture Collection) in a magnetic stir bar reactor. A complete set of kinetic data has not been previously published for this culture. Higher than previously reported growth rates with high laccase production of up to 1,385 U l⁻¹ occurred during growth without or glucose limitation. The maximum specific growth rate averaged 0.94 ± 0.23 day⁻¹, whereas the maximum specific substrate consumption rates for glucose and ammonium were 3.37 ± 1.16 and 0.15 ± 0.04 day⁻¹, respectively. The maximum specific oxygen consumption rate was 1.63 ± 0.36 day⁻¹.     

Desulfurization of light gas oil by a novel recombinant strain from Pseudomonas aeruginosa

The dsz desulfurization gene cluster from Rhodococcus erythropolis KA2-5-1 was transferred into the chromosomes of Pseudomonas aeruginosa NCIMB 9571 by using a transposon vector. Resting cells of the recombinant strain, PAR41, desulfurized 63 mg sulfur l^–1 of light gas oil (LGO) containing 360 mg S l^–1. The desulfurization activity for LGO by the resting cells of strain PAR41 grown with n-tetradecane (50% v/v) was much higher (1018-fold) than in glucose-grown cells. P. aeruginosa NCIMB 9571 is able to take up water-insoluble compounds from an oil phase which is enhanced by n-alkane.     

Secretion of Escherichia coli DsbA and DsbC proteins from Brevibacillus choshinensis: stimulation of human epidermal growth factor production

DsbA and DsbC, members of the thioredoxin super-family of redox proteins, which are expressed in the periplasmic space of Escherichia coli, were cloned into and successfully secreted from Brevibacillus choshinensis at 100 g ml^–1. Both proteins were active in exchanging disulfide bonds of bovine insulin in vitro. Furthermore, DsbA secreted by B. choshinensis promoted the conversion of non-native human epidermal growth factor to the native form.     

Effect of temperature on infection, development and reproduction of the parasitic nematode Thripinema nicklewoodi in Frankliniella occidentalis

The parasitic nematodeThripinema nicklewoodi Siddiqi (Tylenchida:Allantonematidae) is currently underinvestigation for use in inoculative releasestrategies against western flower thrips (WFT),Frankliniella occidentalis Pergande(Thysanoptera: Thripidae) infesting greenhousefloricultural crops. The aim was to determinewhether temperatures within greenhouses wouldpermit the establishment of T.nicklewoodi. The abilities of T.nicklewoodi to infect, develop and reproducein WFT were assessed under a range of constantand fluctuating temperatures in the laboratory.At constant temperatures, T. nicklewoodiinfected WFT over the range of 1–30 °C,although the temperature-related infectionprofile followed an asymmetric distributionaround an optimum 20 °C (80%infection). The lower and upper thresholds forT. nicklewoodi in vivo development andreproduction were higher than for infection, at10 °C and 35 °C, respectively.Climate data recorded over 1999–2000 in acommercial greenhouse (Texas) revealed atemperature range of 15 °C to31 °C from early March through mid June,when WFT were most abundant. While low(nighttime) greenhouse temperatures areconducive for T. nicklewoodi, upperdaytime temperatures are close to the upperthreshold for infection and may reducereproductive output. However, fluctuatingtemperature bioassays in the laboratorydemonstrated that T. nicklewoodimaintained separately at the upper thresholdtemperatures for infection (30 °C) anddevelopment (35 °C) readily infected anddeveloped in WFT when they were allowedintermittent (10 h daily) exposure to apermissive temperature in the range10–20 °C. Drawing on the results, thediurnal temperature-fluctuations of variousgreenhouses growing ornamentals would permitthe establishment of T. nicklewoodi.     

Semper's (zoanthid) larvae: pelagic life,parentage and other problems

Semper's larvae were obtained from <300 out of 1800 plankton tows taken in the world's oceans (1964–1993). Zoanthellae (larvae of Sphenopidae) occurred at 217 stations and zoanthinae (larvae of Zoanthidae) at 86, the two larval types showing distributions clearly delimited by a minimum sea temperature (22 °C for zoanthellae, 18 °C for zoanthinae; a statistically significant difference, P<0.001). Length of formalin-fixed zoanthellae was 2–8.6 mm and of zoanthinae 1.5–5.9 mm. Endodermal zooxanthellae were present in 9/24 zoanthinae but in no zoanthellae (of 19). Three larvae contained an endo-commensal/parasitic amphipod. Septa were externally visible in larger zoanthinae and were counted in transverse sections of other larvae, a majority of which (both kinds) had 12 septa, the normal maximum. The pattern was brachycnemic in 40/43 larvae and anomalous (but non-macrocnemic) in three. If macrocnemic genera reproduce by Semper's larvae, they should have been represented in such a large sample. The distribution of adult Epizoanthus was examined: many species are deep sea (recorded down to 5000 m) but shallow-water species are relatively plentiful in, for example, the Adriatic and North Seas. No Semper's larva has ever been recorded from either. Some Parazoanthus species also occur in shallow water, especially associated with western Atlantic reef sponges. If they produce Semper's larvae, these have never been found. It is probable that macrocnemic zoanthids settle from planulae that do not develop into recognizable zoanthellae or zoanthinae.     

High pressure studies of energy transfer and strongly coupled bacteriochlorophyll dimers in photosynthetic protein complexes

High pressure is used with hole burning and absorption spectroscopies at low temperatures to study the pressure dependence of the B800B850 energy transfer rate in the LH2 complex of Rhodobacter sphaeroides and to assess the extent to which pressure can be used to identify and characterize states associated with strongly coupled chlorophyll molecules. Pressure tuning of the B800–B850 gap from 750 cm^\s-1 at 0.1 MPa to 900 cm^-1 at 680 MPa has no measurable effect on the 2 ps energy transfer rate of the B800–850 complex at 4.2 K. An explanation for this resilience against pressure, which is supported by earlier hole burning studies, is provided. It is based on weak coupling nonadiabatic transfer theory and takes into account the inhomogeneous width of the B800–B850 energy gap, the large homogeneous width of the B850 band from exciton level structure and the Franck-Condon factors of acceptor protein phonons and intramolecular BChl a modes. The model yields reasonable agreement with the 4.2 K energy transfer rate and is consistent with its weak temperature dependence. It is assumed that it is the C₉-ring exciton levels which lie within the B850 band that are the key acceptor levels, meaning that BChl a modes are essential to the energy transfer process. These ring exciton levels derive from the strongly allowed lowest energy component of the basic B850 dimer. However, the analysis of B850s linear pressure shift suggests that another Förster pathway may also be important. It is one that involves the ring exciton levels derived from the weakly allowed upper component of the B850 dimer which we estimate to be quasi-degenerate with B800. In the second part of the paper, which is concerned with strong BChl monomer-monomer interactions of dimers, we report that the pressure shifts of B875 (LH2), the primary donor absorption bands of bacterial RC (P870 of Rb. sphaeroides and P960 of Rhodopseudomonas viridis) and B1015 (LH complex of Rps. viridis) are equal and large in value (-0.4 cm⁰¹/MPa at 4.2 K) relative to those of isolated monomers in polymers and proteins (< -0.1 cm⁰¹/MPa). The shift rate for B850 at 4.2 K is-0.28 cm^–1/MPa. A model is presented which appears to be capable of providing a unified explanation for the pressure shifts.Abbreviations B800 BChl antenna band absorbing (at room temperature) at 800 nm (B850, B875, B1015 are defined similarly) - CD circular dichroism - FC factor Franck-Condon factor - FMO comple Fenna-Matthews-Olson complex - L-S theory Laird-Skinner theory - LH1 core light-harvesting complex of the BChl antenna complexes - LH2 peripheral light-harvesting complex of the BChl antenna complexes - NPHB non-photochemical hole burning - P960 absorption band of special pair of Rhodopseudomonas viridis absorbing at 960 nm (room temperature). P870 of Rhodobacter sphaeroides is defined similarly - QM/MM results quantum mechanical/molecular mechanical results - RC reaction center - ZPH zero phonon hole