The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.

MOTIVATION: Next generation sequencing (NGS) technologies allow a rapid and cost-effective compilation of large RNA sequence datasets in model and non-model organisms. However, the storage and analysis of transcriptome information from different NGS platforms is still a significant bottleneck, leading to a delay in data dissemination and subsequent biological understanding. Especially database interfaces with transcriptome analysis modules going beyond mere read counts are missing. Here, we present the Transcriptome Analysis and Comparison Explorer (T-ACE), a tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily exported for external analysis. We developed T-ACE for laboratory environments, which have only a limited amount of bioinformatics support, and for collaborative projects in which different partners work on the same dataset from different locations or platforms (Windows/Linux/MacOS). For laboratories with some experience in bioinformatics and programming, the low complexity of the database structure and open-source code provides a framework that can be customized according to the different needs of the user and transcriptome project.

In vivo seizure induction and affinity studies of domoic acid and isodomoic acids-D, -E and -F.

Domoic acid and its isomers are produced via algal blooms and are found in high concentrations in shellfish. Here, we assessed the acute seizurogenic potencies of isomers-D, -E and -F and their binding affinities at heterogeneous populations of KA receptors from rat cerebrum. In addition, binding affinities of all six isomers (Iso-A through -F) were assessed at AMPA receptors. Radioligand displacement studies indicated that the seizurogenic potency of Iso-F (E-configuration) closely correlates with its affinities at both KA and AMPA receptors, whereas isomers-D (Z) and -E (E), which exhibit distinctly lower seizurogenic potencies, are quite weak displacers. Previously observed functional potencies for isomers-A, -B and -C (Sawant et al., 2008) correlated with AMPA receptor affinities observed here. Taken together, these findings call into question previous structure-activity rules. Significantly, in our hands, Iso-D was ten-fold less potent than Iso-F. To further explain observed links between structural conformation and functional potency, molecular modeling was employed. Modeling results closely matched the rank order of potency and binding data observed. We further assessed the efficacy of isomers-D, -E and -F as pharmacological preconditioning agents. Acute preconditioning with low-dose Iso-D, -E or -F, before high-dose DA failed to impart behavioural tolerance. This study has shed new light on structural conformations affecting non-NMDA ionotropic glutamate receptor binding and functional potency, and provides a foundation for future work in areas of AMPA and KA receptor modeling.

Spectral analysis of electrocorticographic activity during pharmacological preconditioning and seizure induction by intrahippocampal domoic acid.

Previously we have shown that low-dose domoic acid (DA) preconditioning produces tolerance to the behavioral effects of high-dose DA. In this study, we used electrocorticography (ECoG) to monitor subtle CNS changes during and after preconditioning. Young adult male Sprague-Dawley rats were implanted with a left cortical electrode, and acute recordings were obtained during preconditioning by contralateral intrahippocampal administration of either low-dose DA (15 pmoles) or saline, followed by a high-dose DA (100 pmoles) challenge. ECoG data were analyzed by fast Fourier transformation to obtain the percentage of baseline power spectral density (PSD) for delta to gamma frequencies (range: 1.25-100 Hz). Consistent with previous results, behavioral analysis confirmed that low-dose DA preconditioning 60 min before a high-dose DA challenge produced significant reductions in cumulative seizure scores and high level seizure behaviors. ECoG analysis revealed significant reductions in power spectral density across all frequency bands, and high-frequency/high-amplitude spiking in DA preconditioned animals, relative to saline controls. Significant correlations between seizure scores and ECoG power confirmed that behavioral analysis is a reliable marker for seizure analysis. The reduction of power in delta to gamma frequency bands in contralateral cortex does not allow a clear distinction between seizure initiation and seizure propagation, but does provide objective confirmation that pharmacological preconditioning by DA reduces network seizure activity.

In vivo seizure induction and pharmacological preconditioning by domoic acid and isodomoic acids A, B and C.

To date, nothing is known of the pharmacological properties of isomers of domoic acid (DA) in vivo in mammals. Here we assessed the acute seizurogenic and toxic properties of DA, isodomoic acids A, B and C (Iso-A, -B, -C), and the therapeutic potential of these compounds as pharmacological preconditioning agents. DA, Iso-A, Iso-B, and Iso-C all produced significant dose-dependent increases in seizure activity following intrahippocampal administration; doses producing half maximal cumulative seizure scores (ED50) were 137 pmol, 171 pmol, 13,000 pmol, and 3150 pmol, respectively. Pharmacological preconditioning with low-dose DA or Iso-A, 60 min before a high test dose of DA produced a significant reduction in seizure scores. In contrast, Iso-B and Iso-C each failed to induce any detectable tolerance to high-dose DA. Radioligand binding indicated a significant correlation between seizurogenic potency and kainate receptor affinity with KIs of 2.4 nM, 4.4 nM, 4990 nM and 170 nM for DA, Iso-A, Iso-B and Iso-C, respectively. Our in vivo results indicate that DA and Iso-A are functionally equipotent in acute seizure induction by direct intrahippocampal administration, while Iso-B and Iso-C are distinctly less potent.

Assessment of protein phosphatase in a re-usable rapid assay format in detecting microcystins and okadaic acid as a precursor to biosensor development.

The feasibility of developing an immobilised protein phosphatase (PP) biosensor was tested by immobilising PP onto CNBr-activated Sepharose beads placed in Millipore microfilter plate wells. Under optimised immobilised enzyme assay conditions, okadaic acid (OA) and microcystin LR (MC-LR) inhibited Upstate Biotechnology PP (PP-2A), with IC50 values of 12.5 and 11nM respectively. Similarly, immobilised recombinant PP type 1 (rec PP-1) was inhibited by MC-LR and OA, with IC50 values of 150 and >1000nM respectively. The IC50 values for free PP-2A against OA and MC-LR were 2.5 and 3.5nM, and 0.7nM and 200nM for rec PP-1 against the same substrates respectively. For free and immobilised Neptunea arthritic PP (PP-2Ana) against OA the IC50 values were 0.45 and >1000nM respectively. Of the three immobilised enzyme systems, PP-2A showed greatest sensitivity to OA and MC-LR followed by rec PP-1 and PP-2Ana. In assessments for re-usability (determined by removal of > or =70% OA or MC-LR inhibition of PP-2A by washing), <50% of the original activity remained after 20 washings. Including 1M NaCl in the wash buffer did not increase enzyme activity with wash frequency, but rather "salted in" the inhibitor. The LoD of immobilised PP-2A to MC-LR meets the WHO guideline of 1microgl(-1) for drinking water, and the sensitivity to OA (3.5microgl(-1)) would allow detection of DSP during the peak of some phytoplankton blooms.

Isodomoic acids A and C exhibit low KA receptor affinity and reduced in vitro potency relative to domoic acid in region CA1 of rat hippocampus.

Several natural isomers of the seizurogenic neurotoxin domoic acid (DA) have been found to occur at up to mg/kg levels in shellfish. The aim of the current study was to assess the neurotoxic potency of isodomoic acids A and C (Iso-A and Iso-C), recently isolated from commercial shellfish. Hippocampal slices were obtained from young adult rats and maintained in a tissue recording chamber. Synaptically evoked population spikes were recorded in region CA1 before and after exposure to DA or its isomers. Both Iso-A and Iso-C produced transient neuronal hyperexcitability followed by a dose-dependent suppression of population spikes, but were, respectively, 4- and 20-fold less potent than DA (spike area: EC50 DA=237 nM; Iso-A=939 nM; Iso-C=4.6 microM). In the hippocampus, DA preconditioning induces tolerance to subsequent DA toxicity. However, in the present study neither Iso-A nor Iso-C were effective as preconditioning agents. Competitive binding studies using homomeric GluR6 kainate (kainic acid, KA) receptors showed the affinity of Iso-A to be 40-fold lower than DA (Ki DA=3.35 nM; Iso-A=130 nM). Together with earlier work showing Iso-C affinity at GluR6 receptors to be 240-fold lower than DA, our results suggest that neuroexcitatory effects of Iso-A in CA1 may involve both alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) and KA receptors, while Iso-C likely involves the activation of AMPA receptors alone.

Contrasting digestive strategies in four New Zealand herbivorous fishes as reflected by carbohydrase activity profiles.

Enzymatic degradation of algal carbohydrates was examined in the New Zealand herbivorous fishes Parma alboscapularis (Pomacentridae), Aplodactylus etheridgii (Aplodactylidae), Girella tricuspidata and G. cyanea (Girellidae). Enzyme extract taken from the anterior gut wall, gut fluid and microbial pellet from sections sampled along the gut were tested for activity against starch, carrageenan, agarose and carboxymethylcellulose. Hydrolysis of starch was greater than for all other substrates tested. Endogenous (host-produced) activity in the anterior gut fluid varied between species in the order G. tricuspidata (7700 units mL(-1))>G. cyanea (2300 units mL(-1))>P. alboscapularis (2000)>A. etheridgii (1400 units mL(-1)) where one unit is equivalent to 1 mug of reducing sugar released per minute. Activity decreased markedly along the gut in all cases, so that at the posterior end of the gut only 0.3-8% of the anterior activity remained in the gut fluid. Enzyme activity against structural carbohydrates was lower than that against starch, and was of exogenous (produced by resident microbiota) origin in all species although the location of activity along the gut differed. The microbial extract of A. etheridgii displayed the highest activity against carrageenan and agarose in all gut sections, reaching maxima of 47 units mL(-1) against carrageenan and 35 units mL(-1) against agarose in the mid-gut microbial extract. Carrageenase and agarase activity in the other three species was <10 units mL(-1) for all gut sections. Results suggest that carrageenan and agarose are potentially important substrates for microbial fermentation, particularly in A. etheridgii, and that there is microbial activity in the mid-gut of this species, rather than primarily in the hind-gut as in other herbivorous species.

Gut carbohydrases from the New Zealand marine herbivorous fishes Kyphosus sydneyanus (Kyphosidae), Aplodactylus arctidens (Aplodactylidae) and Odax pullus (Labridae).

Carbohydrase activities were examined in Odax pullus (Labridae), Kyphosus sydneyanus (Kyphosidae) and Aplodactylus arctidens (Aplodactylidae) collected from subtidal reefs in northeastern New Zealand. Enzyme extracts were prepared using two methods from gut wall, gut fluid and microbial pellet samples taken serially along the gut, and assayed against the substrates starch, laminarin, carrageenan, alginate and agarose. In all three fish species, starch degradation activity was substantially higher than for any other substrate tested. Activities of 500, 1294 and 3326 units g tissue(-1) were measured in anterior gut wall extracts of O. pullus, K. sydneyanus and A. arctidens, respectively. Starch degrading activity in gut fluid declined from 37, 313 and 284 units ml(-1) in anterior gut sections of O. pullus, K. sydneyanus and A. arctidens, respectively, to less than 50 units ml(-1) in terminal gut section of each species. Activity against structural polysaccharides was much lower than against starch and was detected mainly in posterior gut sections. The two methods of sample preparation differed little in enzyme activities; however, method of sample preparation did affect isoform patterns as displayed by zymogram analysis. Results suggest that these fish species fall on a continuum from maximizing throughput and digesting easily hydrolysed substrates in the foregut in A. arctidens to relying more heavily on microbial fermentation in the hindgut in K. sydneyanus.

Protein phosphatase inhibition assay adapted for determination of total DSP in contaminated mussels.

The fluorescence protein phosphatase (PP-2A) inhibition assay detects okadaic acid (OA) and DTX-1 in mussels down to 1 microg/100 g of mussel tissue. It is more sensitive than the mouse bioassay (detection limit, 20 microg/100 g) or ELISA using the SCETI DSP check kit (detection limit, 10 microg/100 g). A drawback of the PP-2A assay method has been its lack of sensitivity towards the ester derivatives of OA and DTX-1. This has been addressed by including a hydrolysis step in the pretreatment of extracts which allows these derivatives to be converted to either okadaic acid or DTX-1 prior to the DSP assay. The method has been applied to the analysis of DSP in 19 samples of naturally contaminated mussels and the results from the PP-2A inhibition assay compared to those for HPLC. A good correlation was obtained for OA determined by the two methods in both unhydrolysed and hydrolysed samples. The new procedure will substantially reduce the incidence of false negatives in the DSP assay.

Toxin production in cyanobacterial mats from ponds on the McMurdo ice shelf, Antarctica.

Cyanobacteria are known to produce hepatotoxic substances, the functional and ecological role of these toxins, however, remains largely unclear. Toxic properties of cyanobacteria collected in Antarctica were investigated to determine whether toxin-producing species can also be found under these environmental conditions. Samples were collected from meltwater ponds on the McMurdo Ice Shelf, Antarctica in the summers of 1997 to 1999. These ponds are colonized by benthic algae and cyanobacterial mats. Oscillatoriales, Nodularia sp., and Nostoc sp. constituted the major taxa in freshwater ponds, while Nostoc sp. was missing from brackish and saline ponds. Samples were taken from either floating, submerged or benthic mats, and extracted for in vitro toxicity testing. The presence of toxins was determined by the phosphatase-inhibition assay and by high performance liquid chromatography. The cytotoxic properties of the extracts were investigated in hepatocytes determining 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide metabolism and trypan blue dye exclusion. The results show that all cyanobacterial extracts display phosphatase-inhibiting activity, of which approximately half had significantly greater than 50% inhibiting activity. The presence of nodularin and microcystin-LR was established by high performance liquid chromatography. Cytotoxic properties, independent of the phosphatase inhibiting activity, were also detected. Toxic strains of cyanobacteria can therefore also be found in Antarctica and this finding may lead to further insight into potential ecological roles of cyanobacterial phosphatase inhibiting toxins.

Partitioning effects during terminal carbon and electron flow in sediments of a low-salinity meltwater pond near Bratina Island, McMurdo Ice Shelf, Antarctica.

A study of anaerobic sediments below cyanobacterial mats of a low-salinity meltwater pond called Orange Pond on the McMurdo Ice Shelf at temperatures simulating those in the summer season (<5 degrees C) revealed that both sulfate reduction and methane production were important terminal anaerobic processes. Addition of [2-(14)C]acetate to sediment samples resulted in the passage of label mainly to CO(2). Acetate addition (0 to 27 mM) had little effect on methanogenesis (a 1.1-fold increase), and while the rate of acetate dissimilation was greater than the rate of methane production (6.4 nmol cm(-3) h(-1) compared to 2.5 to 6 nmol cm(-3) h(-1)), the portion of methane production attributed to acetate cleavage was <2%. Substantial increases in the methane production rate were observed with H(2) (2.4-fold), and H(2) uptake was totally accounted for by methane production under physiological conditions. Formate also stimulated methane production (twofold), presumably through H(2) release mediated through hydrogen lyase. Addition of sulfate up to 50-fold the natural levels in the sediment (interstitial concentration, approximately 0.3 mM) did not substantially inhibit methanogenesis, but the process was inhibited by 50-fold chloride (36 mM). No net rate of methane oxidation was observed when sediments were incubated anaerobically, and denitrification rates were substantially lower than rates for sulfate reduction and methanogenesis. The results indicate that carbon flow from acetate is coupled mainly to sulfate reduction and that methane is largely generated from H(2) and CO(2) where chloride, but not sulfate, has a modulating role. Rates of methanogenesis at in situ temperatures were four- to fivefold less than maximal rates found at 20 degrees C.

Evaluation of the fluorometric protein phosphatase inhibition assay in the determination of okadaic acid in mussels.

The protein phosphatase inhibition assay for okadaic acid, the major DSP toxin, modified to use the fluorescence substrates methylumbelliferyl phosphate (MUP) and fluorescein diphosphate (FDP), was compared to the assay using p-nitrophenylphosphate (p-NPP) and the bioluminescence assay using luciferin phosphate (L-P). Under the standard assay conditions used okadaic acid inhibited the enzyme activity dose-dependently with IC50 values of 1.5 nM (MUP) and 1.2 nM (FDP). This compares to IC50 values of 0.9 and 6 nM using L-P and p-NPP respectively. CDP-star, a chemiluminescence substrate, was not hydrolysed by the enzyme. Decreasing the enzyme concentration lowered the IC50 for the colorimetric method (IC50=2 nM [p-NPP], 0.75 nM enzyme) but no shift was observed with fluorimetry. However at enzyme concentrations < 1.5 nM (standard assay) the error margin was too great for routine analysis. The method using fluorimetry allowed detection of okadaic acid concentrations to levels < or = 1 microg/100 g of mussel tissue which is well below the limit of 20 microg/100 g (mouse bioassay) set by some regulatory agencies. Determination of the toxin content in naturally contaminated mussels in three separate experiments gave coefficients of variance ranging from 16 to 29% (MUP) and from 8 to78% (p-NPP). Multicomparison studies showed that concentrations of okadaic acid in naturally contaminated mussel samples determined by fluorescence generally agreed with those obtained using ELISA and LC-MS procedures, and with the mouse bioassay. However using the mouse bioassay as the standard, values determined by the ELISA, PP-2A and LC-MS all scored false negative results compared to those for the mouse bioassay in the range 20-40 microg/100 g mussel, and at the limit of the mouse bioassay the values by the other three methods were substantially less. With few exceptions the methods scored okadaic acid with highest to lowest values in the following order: mouse bioassay > ELISA > PP-2A > LC-MS. The fluorimetric assay was both more sensitive and accurate than the colorimetric assay (the latter showed a propensity towards false positives in the region 20 microg/100 g), and the moderate increase in equipment cost appears to be outweighed by the performance of the method.

Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica.

A gram-positive, motile, rod-shaped, strictly anaerobic bacterium was isolated from an enrichment initiated with sediment taken from below the cyanobacterial mat of a low-salinity pond on the McMurdo Ice Shelf, Antarctica. The organism grew optimally at 12 degrees C, at pH 6.5, and at an NaCl concentration of< 0.5% (w/v). It survived freeze-thawing at low salt concentrations,but not exposure to temperatures over 25 degrees C for more than 20 h or short-term exposure to temperatures> 50 degrees C. Out of a variety of polysaccharides tested as growth substrates, only xylan supported growth. The organism also grew on a variety of mono- and disaccharides including the cyanobacterial cell wall constituent, N-acetyl glucosamine. Fermentation products on a mol product per 100 mol of hexose monomer fermented basis were: acetate, 72; formate, 72; butyrate, 55; hydrogen, 114; and CO2, 100. Not detectable in the culture medium(< 2 mol per 100 mol of monomer) were lactate, propionate, ethanol,n-propanol, n-butanol, and succinate. The G+C content of the DNA from the bacterium was 33 mol%, and a phylogenetic analysis indicated that it grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. It differed from other species of this genus with regard to growth temperature optimum, substrate range, and fermentation pattern, and is therefore designated as a new species of Clostridium for which the name Clostridium vincentii is proposed. The type strain is lac-1 (DSM 10228).

Clostridium grantii sp. nov., a new obligately anaerobic, alginolytic bacterium isolated from mullet gut.

A gram-positive, motile, rod-shaped, strictly anaerobic, sporulating bacterium was isolated from an enrichment initiated with mullet gut contents. The organism grew optimally at 30 degrees C and pH 6.5, and at a salinity of 1/10(3). Out of a variety of polysaccharides tested as growth substrates, only alginate supported growth in either semidefined or complex culture medium. The organism also grew on a variety of mono- and disaccharides. Moles product per 100 mol of alginate monomer degraded were: acetate, 186; ethanol, 19; formate, 54; and CO2, 0.19. Moles product per 100 mol of hexose in cellobiose or glucose degraded were: acetate, 135; ethanol, 61; formate, 63; and CO2, 61. Hydrogen was not detectable during the incubations (detection limit, < 10(-5) atm) and propionate, butyrate, lactate, or succinate were not produced as fermentation end products (< 2 mol per 100 mol of monomer). The G+C content of DNA from the bacterium was 30.2 +/- 0.3 mol%, and the cell walls contained the peptidoglycan component meso-diaminopimelic acid. A phylogenetic analysis of the 16S rDNA sequence indicated that the organism grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. However, it differed from other species of the genus with regard to morphology, growth temperature optimum, substrate range, and fermentation pattern and is therefore designated as a new species of Clostridium; the type strain is A-1 (DSM 8605).

Regulatory influences on the production of gamma-aminobutyric Acid by a marine pseudomonad.

A pseudomonad capable of producing gamma-aminobutyric acid (GABA) was isolated from seawater via an enrichment in which glutamate was the sole carbon and nitrogen source. The organism grew optimally at pH 7.3 and at 25 degrees C. Putrescine, alanine, and glucose-nitrate also served as effective growth substrates. The isolate grew poorly on GABA. Cell suspensions of the organism in 0.02 M phosphate buffer (pH 7.6) containing NaCl (19.4 g liter) and MgCl(2). 6H(2)O(3 g liter) produced GABA from succinic semialdehyde in combination with glutamate or alanine but not from any substrate alone. Little or no GABA was produced with putrescine or glucose-nitrate as substrates. GABA production in the amino acid cosubstrate systems was transitory with optimum levels occurring in the suspension fluid after 3 h of incubation (0.3 and 0.03 mM for glutamate and alanine cosubstrates, respectively). However, yields of GABA in the cell suspension fluid were low, and quantities near that predicted from stoichiometry could be obtained only by extracting cell suspensions with methanol. GABA release in the suspension fluid was increased with higher pH or by decreasing NaCl. Substitution of the salt by the equivalent Tris-HCl or KCl likewise resulted in increased GABA release. When nigericin (10 mug ml) was added to cell suspensions in which NaCl was not decreased, GABA release increased in a way similar to that observed in suspensions with decreased NaCl. The ionophore also decreased GABA uptake by cell suspensions of GABA-grown cells, and the effect was duplicated by lowering NaCl in cell suspensions. The results indicate a role for an Na-dependent transport system in GABA release.

Anaerobic Growth and Fermentation Characteristics of Paecilomyces lilacinus Isolated from Mullet Gut.

The anaerobic growth and fermentation of a marine isolate of Paecilomyces lilacinus is described. The fungus was isolated from mullet gut and grew optimally at 30 degrees C and at a salinity of >/=10%. The best growth was obtained with glucose or laminarin as substrate, and the growth yield was 5.0 g (dry weight of fungus) per mol of hexose fermented. Moles of products as a percentage of moles of hexose fermented were acetate, 29.0%; ethanol, 156.6%; CO(2), 108.0%; and lactate, 4.3%. Together these products accounted for >80% of hexose carbon. Hydrogen and formate were not detectable as fermentation end products (<0.5%). Other substrates utilized for growth, although less effectively than laminarin or glucose, included the monosaccharides galactose, fructose, arabinose, and xylose and the disaccharides maltose and cellobiose. No growth of the fungus occurred on cellulose, and of a variety of other polysaccharides tested only xylan supported growth.

Oxidation of aromatic alcohols by purified methanol dehydrogenase from Methylosinus trichosporium.

Methanol dehydrogenase was found to be present in subcellular preparations of methanol-grown Methylosinus trichosporium and occurred almost wholly in the soluble fraction of the cell. The enzyme, purified by DEAE-Sephadex and Sephadex G-100 chromatography, showed broad specificity toward different substrates and oxidized the aromatic alcohols benzyl, vanillyl, and veratryl alcohols in addition to a range of aliphatic primary alcohols. No enzyme activity was found toward the corresponding aldehydes of the alcohols tested. The Km for methanol was 50 microM, and that for the aromatic alcohols was in the range of 1 to 2 mM. EDTA and p-nitrophenylhydrazine, which are inhibitors of methanol oxidation in whole cells of methylotrophs, had little effect on activity of the purified enzyme. The results now extend the range of substrates oxidized by methanol dehydrogenase to include the aromatic alcohols.

Oxidation of Lignin-Related Aromatic Alcohols by Cell Suspensions of Methylosinus trichosporium.

Cell suspensions of Methylosinus trichosporium oxidized the aromatic alcohols benzyl alcohol, vanillyl alcohol, and veratryl alcohol to the corresponding aldehydes, and with the exception of vanillyl alcohol, the aldehydes were further oxidized to the corresponding aromatic acids. No other transformation was observed, and the methoxyl moieties attached to the aromatic nucleus remained intact. More than 70% of the alcohol oxidized could be accounted for by aldehyde and/or acid. Investigation of the inhibitor kinetics of EDTA or p-nitrophenylhydrazine (specific for NAD-independent methanol dehydrogenase in methylotrophs) on aromatic alcohol oxidation revealed noncompetitive inhibition in which the V(max) was decreased but the K(m) remained unchanged. The pattern of inhibition of aromatic alcohol oxidation matched that of methanol oxidation, and the K(m) values for all of the substrates were similar (12 to 16 mM). The results indicate that the initial step in the oxidation of aromatic alcohols was similar to that for methanol, and because oxidation was incomplete (i.e., only the corresponding aldehyde or acid was produced), there may be some biotechnological advantages in using whole cells of methylotrophs to facilitate aromatic biotransformations.

Production of xylanase by the ruminal anaerobic fungus Neocallimastix frontalis.

Xylanase (1,4-beta-D-xylan xylanohydrolase, EC 3.2.1.8) production was investigated in the ruminal anaerobic fungus Neocallimastix frontalis. The enzyme was released principally into the culture fluid and had pH and temperature optima of 5.5 and 55 degrees C, respectively. In the presence of low concentrations of substrate, the enzyme was stabilized at 50 degrees C. Xylobiose was the principal product of xylanase action, with lesser amounts of longer-chained xylooligosaccharides. No xylose was detected, indicating that xylobiase activity was absent. Activities of xylanase up to 27 U ml-1 (1 U represents 1 micromol of xylose equivalents released min-1) were obtained for cultures grown on xylan (from oat spelt) at 2.5 mg ml-1 in shaken cultures. No growth occurred in unshaken cultures. Xylanase production declined with elevated concentrations of xylan (less than 2.5 mg ml-1), and this was accompanied by an accumulation of xylose and, to a lesser extent, arabinose. Addition of either pentose to cultures grown on low levels of xylan in which neither sugar accumulated suppressed xylanase production, and in growth studies with the paired substrates xylan-xylose, active production of the enzyme occurred during growth on xylan only after xylose had been preferentially utilized. When cellobiose, glucose, and xylose were tested as growth substrates for the production of xylanase (each initially at 2.5 mg ml-1), they were found to be less effective than xylan, and use of xylan from different origins (birch wood or larch wood) as the growth substrate or in the assay system resulted in only marginal differences in enzyme activity. However, elevated production of xylanase occurred during growth on crude hemicellulose (barley straw leaf). The results are discussed in relation to the role of the anaerobic fungi in the ruminal ecosystem, and the possible application of the enzyme in bioconversion processes is also considered.

Production of alpha-Amylase by the Ruminal Anaerobic Fungus Neocallimastix frontalis.

alpha-Amylase production was examined in the ruminal anaerobic fungus Neocallimastix frontalis. The enzyme was released mainly into the culture fluid and had temperature and pH optima of 55 degrees C and 5.5, respectively, and the apparent K(m) for starch was 0.8 mg ml. The products of alpha-amylase action were mainly maltotriose, maltotetraose, and longer-chain oligosaccharides. No activity of the enzyme was observed towards these compounds or pullulan, but activity on amylose was similar to starch. Evidence for the endo action of alpha-amylase was also obtained from experiments which showed that the reduction in iodine-staining capacity and release in reducing power by action on amylose was similar to that for commercial alpha-amylase. Activities of alpha-amylase up to 4.4 U ml (1 U represents 1 mumol of glucose equivalents released per min) were obtained for cultures grown on 2.5 mg of starch ml in shaken cultures. No growth occurred in unshaken cultures. With elevated concentrations of starch (>2.5 mg ml), alpha-amylase production declined and glucose accumulated in the cultures. Addition of glucose to cultures grown on low levels of starch, in which little glucose accumulated, suppressed alpha-amylase production, and in bisubstrate growth studies, active production of the enzyme only occurred during growth on starch after glucose had been preferentially utilized. When cellulose, cellobiose, glucose, xylan, and xylose were tested as growth substrates for the production of alpha-amylase (initial concentration, 2.5 mg ml), they were found to be less effective than starch, but maltose was almost as effective. The fungal alpha-amylase was found to be stable at 60 degrees C in the presence of low concentrations of starch (