The Agilent in situ-synthesized microarray platform

Microarray technology has become a standard tool in many laboratories. Agilent Technologies manufactures a variety of catalog and custom long-oligonucleotide (60-mer) microarrays that can be used in multiple two-color microarray applications. Optimized methods and techniques have been developed for two such applications: gene expression profiling and comparative genomic hybridization. Methods for a third technique, location analysis, are evolving rapidly. This chapter outlines current best methods for using Agilent microarrays, provides detailed instructions for the most recently developed techniques, and discusses solutions to common problems encountered with two-color microarrays.

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats

The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species.

The purification and characterisation of novel dipeptidyl peptidase IV-like activity from bovine serum

The discovery of a potentially novel proline-specific peptidase from bovine serum is presented which is capable of cleaving the dipeptidyl peptidase IV (DPIV) substrate Gly-Pro-MCA. The enzyme was isolated and purified with the use of Phenyl Sepharose Hydrophobic Interaction, Sephacryl S-300 Gel Filtration, and Q-Sephacryl Anion Exchange, producing an overall purification factor of 257. SDS PAGE resulted in a monomeric molecular mass of 158kDa while size exclusion chromatography generated a native molecular mass of 328kDa. The enzyme remained active over a broad pH range with a distinct preference for a neutral pH range of 7-8.5. Chromatofocusing and isoelectric focusing (IEF) revealed the enzyme's isoelectric point to be 4.74. DPIV-like activity was not inhibited by serine protease inhibitors but was by the metallo-protease inhibitors, the phenanthrolines. The enzyme was also partially inhibited by bestatin. Substrate specificity studies proved that the enzyme is capable of sequential cleavage of bovine beta-Casomorphin and Substance P. The peptidase cleaved the standard DPIV substrate, Gly-Pro-MCA with a K(M) of 38.4 microM, while Lys-Pro-MCA was hydrolysed with a K(M) of 103 microM. The DPIV-like activity was specifically inhibited by both Diprotin A and B, non-competitively, generating a K(i) of 1.4 x 10(-4) M for both inhibitors. Ile-Thiazolidide and Ile-Pyrrolidide both inhibited competitively with an inhibition constant of 3.7 x 10(-7) and 7.5 x 10(-7) M, respectively. It is concluded that bovine serum DPIV-like activity share many biochemical properties with DPIV and DPIV-like enzymes but not exclusively, suggesting that the purified peptidase may play an important novel role in bioactive oligopeptide degradation.

Purification, identification and characterisation of seprase from bovine serum

The study and identification for the first time of a soluble form of a seprase activity from bovine serum is presented. To date, this activity has only been reported to be an integral membrane protease but has been known to shed from its membrane. The activity was purified 30,197-fold to homogeneity, using a combination of column chromatographies, from bovine serum. Inhibition by DFP, resulting in an IC(50) of 100:nM confirms classification as a serine protease. The protease after separation and visualisation by native PAGE was subjected to tryptic digestion and the subsequent peptides sequenced. Each peptide sequenced was found to be present in the primary structure of seprase/fibroblast activation protein (FAP), a serine gelatinase specific for proline-containing peptides and macromolecules. Substrate specificity studies using kinetic, RP-HPLC and LC-MS analysis of synthetic peptides suggest that this peptidase has an extended substrate-binding region in addition to the primary specificity site S(1). This analysis revealed at least five subsites to be involved in enzyme-substrate binding, with the smallest peptide cleaved being a tetrapeptide. A proline residue in position P(1) was absolutely necessary therefore showing high primary substrate specificity for the Pro-X bond, while a preference for a hydrophobic residue at the C-terminal end of the scissile bond (P'(1)) was evident. The enzyme also showed complete insensitivity to the prolyl oligopeptidase specific inhibitors, JTP-4819, Fmoc-Ala-pyrrCN and Z-Phe-Pro-BT. To date, no physiological substrate has clearly been defined for this protease but its ability to effectively degrade gelatin suggests a candidate protein substrate in vivo and a possible role in extracellular matrix protein degradation.

Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit

Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.

Oropharyngeal Scintigraphy: A Reliable Technique for the Quantitative Evaluation of Oral–Pharyngeal Swallowing

A valid and reliable technique to quantify the efficiency of the oral-pharyngeal phase of swallowing is needed to measure objectively the severity of dysphagia and longitudinal changes in swallowing in response to intervention. The objective of this study was to develop and validate a scintigraphic technique to quantify the efficiency of bolus clearance during the oral-pharyngeal swallow and assess its diagnostic accuracy. To accomplish this, postswallow oral and pharyngeal counts of residual for technetium-labeled 5- and 10-ml water boluses and regional transit times were measured in 3 separate healthy control groups and in a group of patients with proven oral-pharyngeal dysphagia. Repeat measures were obtained in one group of aged (> 55yr) controls to establish test-retest reliability. Scintigraphic transit measures were validated by comparison with radiographic temporal measures. Scintigraphic measures in those with proven dysphagia were compared with radiographic classification of oral vs. pharyngeal dysfunction to establish their diagnostic accuracy. We found that oral ( p = 0.04), but not pharyngeal, isotope clearance is swallowed bolus-dependently. Scintigraphic transit times do not differ from times derived radiographically. All scintigraphic measures have extremely good test-retest reliability. The mean difference between test and retest for oral residual was -1% (95% CI -3%-1%) and for pharyngeal residual it was -2% (95% CI -5%-1%). Scintigraphic transit times have very poor diagnostic accuracy for regional dysfunction. Abnormal oral and pharyngeal residuals have positive predictive values of 100% and 92%, respectively, for regional dysfunction. We conclude that oral-pharyngeal scintigraphic clearance is highly reliable, bolus volume-dependent, and has a high predictive value for regional dysfunction. It may prove useful in assessment of dysphagia severity and longitudinal change.

Inhibition of egg development by phosphine in the cosmopolitan pest of stored products Liposcelis bostrychophila (Psocoptera: Liposcelididae)

Phosphine-induced delay in development of eggs was investigated as a mechanism of resistance to this fumigant in Liposcelis bostrychophila Badonnel. One-day-old eggs of a susceptible and a strongly resistant strain of L bostrychophila were exposed to a range of phosphine concentrations for 6days at 30 (+/- 1) degrees C and 70 (+/- 2)% RH. Delay in mean hatching period occurred in both susceptible and resistant eggs, although it was more pronounced in the latter. A maximum delay of 2.65 days was recorded for eggs of the susceptible strain at 0.01 mg litre(-1) (the highest concentration at which eggs survived) and 13.39 days for the resistant strain at 1 mg litre(-1) (the highest concentration tested). Delay in egg development time was positively correlated with increasing phosphine concentration. Our results reveal that the most successful strategy to control resistant L bostrychophila is to apply relatively low concentrations of phosphine for extended exposure times (eg 0.05 mg litre(-1) for 16 days) that allow all eggs to hatch to the much less tolerant nymph stage.

Caenorhabditis elegans mutants resistant to phosphine toxicity show increased longevity and cross-resistance to the synergistic action of oxygen

Phosphine (hydrogen phosphide, PH3) is the fumigant most widely used to protect stored products from pest infestation. Despite the importance of this chemical, little is known about its mode of action. We have created three phosphine-resistant lines (pre-1, pre-7, pre-33) in the model organism C. elegans, with LC50 values 2, 5, and 9 times greater than the fully susceptible parental strain. Molecular oxygen was shown to be an extremely effective synergist with phosphine as, under hyperoxic conditions, 100% mortality was observed in wild-type nematodes exposed to 0.1 mg/l phosphine, a nonlethal concentration in air. All three mutants were resistant to the synergistic effects of oxygen in proportion to their resistance to phosphine with one mutant, pre-33, showing complete resistance to this synergism. We take the proportionality of cross-resistance between phosphine and the synergistic effect of oxygen to imply that all three mutants circumvent a mechanism of phosphine toxicity that is directly coupled to oxygen metabolism. Compared with the wild-type strain, all three mutants have an extended average life expectancy of from 12.5 to 25.3%. This is consistent with the proposed involvement of oxidative stress in both phosphine toxicity and ageing. Because the wild-type and mutant nematodes develop at the same rate, the longevity is unlikely to be caused by a clk-type reduction in oxidative metabolism, a potential alternative mechanism of phosphine resistance.

Long-term effectiveness of grain protectants and structural treatments against Liposcelis decolor (Pearman) (Psocoptera: Liposcelididae), a pest of stored products

Numerous strains of the psocid pest, Liposcelis decolor (Pearman) were collected from farms and central storages and interbred to form three representative strains from three major grain-growing states of Australia: Queensland, South Australia and New South Wales. These were tested against the grain protectants and structural treatments currently registered for use in Australia. Recently, L decolor has become an important pest of stored grain in Australia, particularly in the eastern and southern parts. There is no published information available on management of this pest and the current pest-management strategy, based predominantly on phosphine fumigation, has failed to control infestations of this pest in numerous grain storages in Australia. Alternative methods of control such as use of contact insecticides were explored in the present work to supplement phosphine fumigation to manage this new pest. From eight grain protectants tested as admixtures, only chlorpyrifos-methyl, bioresmethrin plus piperonyl butoxide, and fenitrothion were found to provide long term (3-9 months) protection against all three strains of L decolor. Chlorpyrifos-methyl gave the best protection, providing a minimum of 7.5 to a maximum of 9 months protection, depending on the strains tested. Three structural treatments, azamethiphos, azamethiphos plus carbaryl and permethrin provided long-term control (8-9 months) of all three strains of L decolor on galvanised steel surfaces, with permethrin delivering 9 months protection against all strains. However, all of these treatments failed to provide long-term control of any strains on concrete surfaces. We conclude that chlorpyrifos-methyl as a grain admixture can be incorporated into fumigation strategies to optimise the control of L decolor infestations. Structural treatments, such as permethrin can be used to support a fumigation strategy in storages made of galvanised steel.

Effects of time and concentration on mortality of phosphine-resistant Sitophilus oryzae (L) fumigated with phosphine

The effects of exposure period and phosphine concentration on mortality of susceptible and resistant Sitophilus oryzae (L) were investigated. Although S oryzae is one of the world's most serious pests of stored grain there are few data on the practical significance of phosphine resistance in this species. The strains investigated were an Australian susceptible strain, a homozygous resistant strain exhibiting a level of resistance common in Australia and an unselected field strain from China with a much stronger resistance. Fumigations were carried out at 25 degrees C on adults and mixed-age cultures. For adults of all three strains and mixed-age cultures of the susceptible and resistant Australian strains, the relationship between concentration and time could be described by equations of the form Cnt = k. In all cases n < 1, indicating that time was a more important variable than concentration. In all fumigations of adults the resistant strains were harder to kill than the susceptible strain. However, in fumigations of mixed-age cultures, which contained the tolerant pupal stage, the difference between susceptible and resistant strains was more pronounced at lower concentrations than higher concentrations. For example, at 0.02 mg litre-1 the estimated LT99.9 for mixed-age cultures of the Australian resistant strain (27 days) is 3.4 times that of the susceptible strain (8 days), but at 1 mg litre-1 there is no difference between the two strains (4 days). Limited data on the Chinese resistant strain supported this finding. Twenty-three days exposure at 0.02 mg litre-1 had no effect on mixed-age cultures of this strain, but there were no survivors after 5 days exposure to 1 mg litre-1.

Genetics of resistance to phosphine in Rhyzopertha dominica (Coleoptera: Bostrichidae)

The inheritance of resistance to phosphine was studied in two strains of the lesser grain borer, Rhyzopertha dominica (F.), labeled 'Weak-R' and 'Strong-R'. These strains were purified versions of field-selected populations collected in Queensland, Australia. Weak-R and Strong-R were, respectively, 23.4 times (20-h exposure) and 600 times (48-h exposure) resistant to phosphine compared with a reference susceptible strain (S-strain). Each -R strain was crossed with the S-strain and the response to phosphine was measured in their respective F1, F2, and F1-backcross (F1-BC) progenies. Data from testing of reciprocal F1 progeny indicated that resistance in Weak-R was autosomal and incompletely recessive with a degree of dominance -0.96. Modified chi-square analysis and contingency analysis of the observed response to phosphine of F1-BC and F2 progenies rejected the hypothesis of single gene inheritance of resistance. Analysis of the response of the F1, F2, and F1-BC progeny from the Strong-R x S-strain cross also rejected the null hypothesis for single gene resistance. Resistance in the Strong-R strain was autosomal and incompletely recessive with a degree of dominance of -0.64. The Weak-R and Strong-R strains were then crossed. Analysis ofthe F1 and F2 progenies of this reciprocal cross revealed that the strong resistance phenotype was coded by a combination of the genes already present in the Weak-R genotype plus an extra major, incompletely recessive gene. There was also evidence of a minor dominant gene present in approximately 5% of Strong-R individuals.

Genetic linkage analysis of the lesser grain borer Rhyzopertha dominica identifies two loci that confer high-level resistance to the fumigant phosphine

High levels of inheritable resistance to phosphine in Rhyzopertha dominica have recently been detected in Australia and in an effort to isolate the genes responsible for resistance we have used random amplified DNA fingerprinting (RAF) to produce a genetic linkage map of R. dominica. The map consists of 94 dominant DNA markers with an average distance between markers of 4.6 cM and defines nine linkage groups with a total recombination distance of 390.1 cM. We have identified two loci that are responsible for high-level resistance. One provides approximately 50x resistance to phosphine while the other provides 12.5x resistance and in combination, the two genes act synergistically to provide a resistance level 250x greater than that of fully susceptible beetles. The haploid genome size has been determined to be 4.76 x 10(8) bp, resulting in an average physical distance of 1.2 Mbp per map unit. No recombination has been observed between either of the two resistance loci and their adjacent DNA markers in a population of 44 fully resistant F5 individuals, which indicates that the genes are likely to reside within 0.91 cM (1.1 Mbp) of the DNA markers.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

High incidence of micrometastases in breast cancer sentinel nodes

BACKGROUND

Sentinel lymph node biopsy (SLNB) is being investigated as an alternative to formal axillary dissection in early breast cancer. Avoiding the morbidity of unnecessary axillary dissection is seen as the main potential benefit of SLNB. Sentinel lymph node biopsy also allows enhanced pathological analysis. A series of 62 sentinel node (SN) biopsies demonstrating a high incidence of micrometastases is presented here.

METHODS

All SN were initially examined and reported by H&E staining. All negative SN were analysed after staining with polyclonal anticytokeratin antibody.

RESULTS

Sixty-two patients underwent SLNB at Royal Melbourne Hospital between May 1998 and February 2000. One or more SN was identified in 51/62 patients. A total of 10/51 contained metastases identified after H&E staining. There was one false negative. A total of 10/41 patients with H&E-negative SN had micrometastases identified on immunohistochemistry (IHC). Micrometastases were more common in patients with larger tumours, with disease found in the H&E-negative SN of 1/17 T1a and T1b (1-10 mm), 4/15 T1c (11-20 mm), and 5/9 T2 (20-50 mm) tumours.

CONCLUSION

Sentinel lymph node biopsy can accurately assess the axilla in most patients with early breast cancer. A significant proportion of histologically negative SN will have micrometastases identifiable with IHC. Although the clinical significance of such metastases is uncertain, the available evidence suggests that these patients have a poorer prognosis than other patients with negative lymph nodes.

Residual efficacy of four organophosphate insecticides on concrete and galvanized steel surfaces against three liposcelid psocid species (Psocoptera: Liposcelidae) infesting stored products

Four organophosphate insecticides, azamethiphos, fenitrothion, chlorpyrifos-methyl, and pirimiphos-methyl, were tested as surface treatments on concrete (porous surface) and galvanized steel (nonporous surface) panels (0.3 by 0.3 m) against adults of three Liposcelid psocid spp.--Liposcelis bostrychophila Badonnel, Liposcelis entomophila (Enderlein), and Liposcelis paeta Pearman. Residual efficacy of these chemicals was assessed at 30 +/- 1 degrees C, 70 +/- 2% RH, and a photoperiod of 12:12 (L:D) h from 1 d after treatment (0 wk) and thereafter at weeks 1, 2, 4, 6, and 8, and then every 4 wk up to week 40. Mortality was recorded at exposure periods of 6 h and then every 24 h until end-point was achieved. L. bostrychophila was the most susceptible species to the organophosphates tested, followed by L. paeta and L. entomophila. We conclude that for long-term protection, azamethiphos is the preferred organophosphate against L. bostrychophila (up to 36 wk on steel and 24 wk on concrete storage surfaces) and L. paeta infestations only on steel surface (up to 28 wk). None of the four organophosphates tested, however, would provide long-term protection against L. paeta on concrete surface and against L. entomophila infestations on either concrete or steel storage surfaces.

Potential for integrating eleven agricultural insecticides with the predatory bug Pristhesancus plagipennis (Hemiptera: Reduviidae)

A problem for growers attempting to implement integrated pest management programs is the lack of information regarding the compatibility of insecticides with natural enemies. To provide information about this problem, we evaluated the acute and residual effects of 11 commonly used insecticides on nymphs of Pristhesancus plagipennis (Walker) under both laboratory and field conditions. For each insecticide, the length of time that weathering residues caused > 50% mortality was evaluated and compared against the LC50 (acute-toxicity) divided by the recommended field rate. Plots thus combined the acute and residual toxicity of each insecticide. Results suggested that carbaryl, esfenvalerate, endosulfan, and deltamethrin had low residual and acute toxicity to P. plagipennis, whereas chlorpyrifos, methomyl, and monocrotophos were highly toxic at low concentrations and left persistent harmful residues. Cypermethrin, methidathion, malathion, and dimethoate were moderately toxic. The potential use of these insecticides to supplement the control activity of P. plagipennis is discussed.

Sentinel node biopsy in breast cancer: recommendations for surgeons, pathologists, nuclear physicians and radiologists in Australia and New Zealand

BACKGROUND

Assessment of axillary lymph node status is necessary for patients with invasive breast cancer. Sentinel node biopsy is a new minimally invasive technique that may provide accurate assessment of regional lymph node status while limiting the morbidity associated with axillary clearance.

METHODS

A workshop conducted in Adelaide in November 1998 aimed to assess current sentinel node mapping and biopsy techniques, and make recommendations regarding its application in the surgical management of early breast cancer in Australia and New Zealand.

RESULTS

At the conclusion of the workshop, a consensus was reached regarding indications, exclusions, sentinel node mapping/biopsy technique, nuclear medicine requirements, pathology and safety of sentinel node biopsy in breast cancer. It was agreed that a feasibility study according to an agreed prospective protocol was necessary to validate the technique by breast surgeons. Surgeons that satisfied validation criteria for the feasibility study could then consider a prospective randomized study comparing sentinel node biopsy with standard axillary dissection.

CONCLUSIONS

Sentinel node biopsy in breast cancer involves close cooperation between members of a multidisciplinary team including surgeons, nuclear physicians, pathologists and radiologists. Although the technique has the potential to reduce morbidity associated with axillary surgery, surgical performance in this area will need to be closely monitored to ensure that the technique does not fall into disrepute by adversely affecting breast cancer prognosis.

Relationships between spatial patterns of colonic pressure and individual movements of content

The aim of this study was to examine the relationship between colonic pressure waves and movement of content. In 11 healthy subjects, pressures were recorded at 10-cm intervals from cecum to rectum for 32 h. In six subjects, transit was simultaneously measured for 8 h after direct cecal instillation of 1.5 mCi of (99m)Tc sulfur colloid. Thirty-two percent of isotope movements were related to nonpropagating activity and twenty-eight percent to propagating sequences. The extent of isotope movement related to propagating sequences (25.1 +/- 2.1 cm) was greater than that due to nonpropagating activity (12.8 +/- 0.7 cm; P = 0.0001). Propagating sequences originated significantly more frequently (P = 0.004) and propagated further (P = 0.0006) in the proximal compared with the distal colon. Only 36% of propagating sequences were propulsive of content, and compared with nonpropulsive sequences, these propagated further (41 +/- 6 vs. 27 +/- 2 cm; P < 0.05) and had a higher probability of originating proximally (P = 0.0003), a higher pressure wave amplitude (50 +/- 5 vs. 34 +/- 4 mmHg; P = 0.0001), and slower velocity (2.2 +/- 0.3 vs. 3.6 +/- 0.47 cm/s; P = 0.02). We conclude that most movements of colonic content are related to pressure waves. There is marked regional variation in the prevalence, velocity, and extent of propagation of propagating pressure wave sequences, which are an important mechanism for transporting content over long distances. The effectiveness of transport by a propagating sequence is influenced by its site of origin, amplitude, and velocity.

Cloning and characterization of a cDNA encoding a novel extracellular peroxidase from Trametes versicolor

The white rot basidiomycete Trametes versicolor secretes a large number of peroxidases which are believed to be involved in the degradation of polymeric lignin. These peroxidases have been classified previously as lignin peroxidases or manganese peroxidases (MnP). We have isolated a novel extracellular peroxidase-encoding cDNA sequence from T. versicolor CU1, the transcript levels of which are repressed by low concentrations of Mn2+ and induced by nitrogen and carbon but not induced in response to a range of stresses which have been reported to induce MnP expression.

Analysis of forward scattering of diffuse photon-density waves in turbid media: a diffraction tomography approach to an analytic solution

We present a model of the forward problem for diffuse photon-density waves in a turbid medium containing a spherical inhomogeneity, using diffraction tomographic (DT) methods. Recently, by use of DT methods, the forward problem was investigated [Opt. Express 1, 6 (1997); www.osa.org] assuming weak perturbations from the background medium but an arbitrary inhomogeneity structure. We apply DT concepts to a forward problem solution that permits strong perturbations but requires a spherical inhomogeneity. We show that this model is consistent with previous DT results and discuss the application of this new model.

Regulation of Laccase Gene Transcription in Trametes versicolor

The expression of laccase in the white rot fungus Trametes versicolor is regulated at the level of gene transcription by copper and nitrogen. We used reverse transcription-PCR to demonstrate that as the concentration of copper or nitrogen in fungal cultures was increased, an increase in laccase activity, corresponding to increased laccase gene transcription levels, was observed. In addition, we demonstrated that the amounts of laccase mRNA and laccase activity in 10-day-old cultures were a direct function of the concentration of either 1-hydroxybenzotriazole, a previously described laccase substrate, or 2,5-xylidine, a well-known laccase inducer, in the medium. No induction was observed after the addition of two aromatic acids, ferulic acid and veratric acid, which have been shown to induce laccase production in other white rot fungi. When either copper, 2,5-xylidine, or both compounds were added to cultures grown in the absence of copper, increased laccase transcript levels were detected within 15 min. Corresponding increases in laccase activity were observed after 24-h incubation only when copper was present.

Stabilization of lignin peroxidases in white rot fungi by tryptophan

Supplementation of various cultures of white rot fungi with tryptophan was found to have a large stimulatory effect on lignin peroxidase activity levels. This enhancement was greater than that observed in the presence of the lignin peroxidase recycling agent veratryl alcohol. Using reverse transcription-PCR, we found that tryptophan does not act to induce lignin peroxidase expression at the level of gene transcription. Instead, the activity enhancement observed is likely to result from the protective effect of tryptophan against H2O2 inactivation. In experiments using a partially purified lignin peroxidase preparation, tryptophan and its derivative indole were determined to function in the same way as veratryl alcohol in converting compound II, an oxidized form of lignin peroxidase, to ferric enzyme, thereby completing the catalytic cycle. Furthermore, tryptophan was found to be a better substrate for lignin peroxidase than veratryl alcohol. Inclusion of either tryptophan or indole enhanced the oxidation of the azo dyes methyl orange and Eriochrome blue black. Stimulation of azo dye oxidations by veratryl alcohol has previously been shown to be due to its enzyme recycling function. Our data allow us to propose that tryptophan stabilizes lignin peroxidase by acting as a reductant for the enzyme.