Evaluation of the Rothman Index in Predicting Readmission after Colorectal Resection

The Rothman Index (RI) is a real-time health indicator score that has been used to quantify readmission risk in several fields but has never been studied in gastrointestinal surgery. In this retrospective single-institution study, the association between RI scores and readmissions after unplanned colectomy or proctectomy was evaluated in 427 inpatients. Patient demographics and perioperative measures, including last RI, lowest RI, and increasing/decreasing RI score, were collected. In the selected cohort, 12.4% of patients were readmitted within 30 days of their initial discharge. Last RI, lowest RI, decreasing RI, and increasing RI scores remained significant after controlling for covariates in separate multivariate regression analyses. The last RI score at the time of discharge was found to be the most strongly associated with 30-day readmission risk following colorectal resection. These findings support the RI as a potential tool in the inpatient management of postoperative patients to identify those at high risk of readmission.

Evaluation of Metarhizium brunneum- and Metarhizium-Derived VOCs as Dual-Active Biostimulants and Pest Repellents in a Wireworm-Infested Potato Field

Wireworm, the larval stages of click beetles, are a serious pest of tubers, brassicas and other important commercial crops throughout the northern hemisphere. No effective control agent has been developed specifically for them, and many of the pesticides marketed as having secondary application against them have been withdrawn from EU and Asian markets. Metarhizium brunneum, an effective entomopathogenic fungus, and its derived volatile metabolites are known to be effective plant biostimulants and plant protectants, although field efficacy has yet to be validated. Field validation of a combined M. brunneum and derived VOC treatments was conducted in Wales, UK, to assess the effects of each as a wireworm control agent and biostimulant. Plots were treated with Tri-Soil (Trichoderma atroviridae), M. brunneum, 1-octen-3-ol or 3-octanone, or combinations thereof. Treatments were applied subsurface during potato seeding (n = 52), and potatoes were harvested at the end of the growing season. Each potato was weighed individually and scored for levels of wireworm damage. Applications of both the VOCs and the M. brunneum individually were found to significantly decrease wireworm burden (p < 0.001). Combinations of M. brunneum and 3-octanone were also found to significantly decrease wireworm damage (p < 0.001), while no effect on yield was reported, resulting in an increased saleable mass over controls (p < 0.001). Herein, we present a novel 'stimulate and deter' wireworm control strategy that can be used to significantly enhance saleable potato yields and control wireworm populations, even under high pest pressure densities.

Antimicrobial Volatiles of the Insect Pathogen Metarhizium brunneum

Fungal volatile organic compounds (VOCs) represent promising candidates for biopesticide fumigants to control crop pests and pathogens. Herein, VOCs produced using three strains of the entomopathogenic fungus Metarhizium brunneum were identified via GC-MS and screened for antimicrobial activity. The VOC profiles varied with fungal strain, development state (mycelium, spores) and culture conditions. Selected VOCs were screened against a range of rhizosphere and non-rhizosphere microbes, including three Gram-negative bacteria (Escherichia coli, Pantoea agglomerans, Pseudomonas aeruginosa), five Gram-positive bacteria (Micrococcus luteus, Staphylococcus aureus, Bacillus subtilis, B. megaterium, B. thuringiensis), two yeasts (Candida albicans, Candida glabrata) and three plant pathogenic fungi (Pythium ultimum, Botrytis cinerea, Fusarium graminearum). Microbes differed in their sensitivity to the test compounds, with 1-octen-3-ol and isovaleric acid showing broad-spectrum antimicrobial activity. Yeasts and bacteria were inhibited by the same VOCs. Cryo-SEM showed that both yeasts and bacteria underwent some form of “autolysis”, where all components of the cell, including the cell wall, disintegrated with little evidence of their presence in the clear, inhibition zone. The oomycete (P. ultimum) and ascomycete fungi (F. graminearum, B. cinerea) were sensitive to a wider range of VOCs than the bacteria, suggesting that eukaryotic microbes are the main competitors to M. brunneum in the rhizosphere. The ability to alter the VOC profile in response to nutritional cues may assist M. brunneum to survive among the roots of a wide range of plant species. Our VOC studies provided new insights as to how M. brunneum may protect plants from pathogenic microbes and correspondingly promote healthy growth.

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Saddle block anesthetic technique for benign outpatient anorectal surgery

BACKGROUND

Current American Society of Colorectal Surgery Clinical Practice Guidelines for Ambulatory Anorectal Surgery endorse use of monitored anesthesia care, general anesthesia, or spinal anesthesia based on physician and patient preference. Although several studies support the use of monitored anesthesia care over general anesthesia, the literature regarding spinal anesthesia is limited and heterogenous due to small sample sizes and disparate spinal anesthesia techniques. Saddle block anesthesia is a form of spinal anesthesia that localizes to the lowermost sacral spinal segments allowing for preservation of lower extremity motor function and faster recovery. We accrued one of the largest reported cohort of anorectal procedures using saddle block anesthesia, as such, we sought to evaluate our institutional 12-year experience.

METHODS

Patients who underwent a benign anorectal procedure at our outpatient surgery center between July 2008-2020 were retrospectively reviewed. Demographics, surgical factors, perioperative times, and adverse events were collected from the electronic medical records. Saddle block anesthesia was generally performed in the preoperative area using a spinal needle (25-27 gauge) and a single injection technique of a 1:1 ratio local anesthetic mixed with 10% dextrose solution. Between 2.5-5 mg of hyperbaric anesthetic was injected intrathecally in the sitting position and the patient remained upright for 3-10 minutes. This technique of saddle block anesthesia provides analgesia for approximately 1-3 hours.

RESULTS

In the study, 859 saddle block anesthesia patients were identified, with a mean age of 44.6 years and American Society of Anesthesia score of 1.9; 609 (70.9%) were male. Surgical indications included lesion removal (27.1%), anal fistula (25.8%), hemorrhoidectomy (24.7%), pilonidal disease (6.3%), anal fissure (5.8%), and a combination of prior (10.2%). Prone jackknife positioning was used in 91.6% of procedures. Saddle block anesthesia most often was performed with bupivacaine (48.9%) or ropivacaine (41.7%). The median procedural saddle block anesthesia time was 11 minutes, surgery time was 17 minutes, anesthesia time was 42 minutes, and recovery time was 91 minutes. Patients spent a median of 3 hours and 53 minutes in the facility. Adverse events included urinary retention (1.9%), conversion to general anesthesia (1.8%), spinal headache (1.5%), hemodynamic instability (0.9%), and injection site reaction (0.3%).

CONCLUSION

Demonstrated using the largest known cohort of anorectal patients with saddle block anesthesia, saddle block anesthesia provides an effective method of analgesia to avoid general anesthesia with a low rate of adverse events.

Space and patchiness affects diversity-function relationships in fungal decay communities

The space in which organisms live determines health and physicality, shaping the way in which they interact with their peers. Space, therefore, is critically important for species diversity and the function performed by individuals within mixed communities. The biotic and abiotic factors defined by the space that organisms occupy are ecologically significant and the difficulty in quantifying space-defined parameters within complex systems limits the study of ecological processes. Here, we overcome this problem using a tractable system whereby spatial heterogeneity in interacting fungal wood decay communities demonstrates that scale and patchiness of territory directly influence coexistence dynamics. Spatial arrangement in 2- and 3-dimensions resulted in measurable metabolic differences that provide evidence of a clear biological response to changing landscape architecture. This is of vital importance to microbial systems in all ecosystems globally, as our results demonstrate that community function is driven by the effects of spatial dynamics.

Biochemical characterization of Serpula lacrymans iron-reductase enzymes in lignocellulose breakdown

Putative iron-reductase (IR) genes from Serpula lacrymans with similarity to the conserved iron-binding domains of cellobiose dehydrogenase (CDH) enzymes have been identified. These genes were cloned and expressed to functionally characterize their activity and role in the decomposition of lignocellulose. The results show that IR1 and IR2 recombinant enzymes have the ability to depolymerize both lignin and cellulose, are capable of the reduction of ferric iron to the ferrous form, and are capable of the degradation of nitrated lignin. Expression of these genes during wheat straw solid-state fermentation was shown to correlate with the release of compounds associated with lignin decomposition. The results suggest that both IR enzymes mediate a non-enzymatic depolymerisation of lignocellulose and highlight the potential of chelator-mediated Fenton systems in the industrial pre-treatment of biomass.

Immunohistochemical distinction of metastases of renal cell carcinoma to the adrenal from primary adrenal nodules, including oncocytic tumor

Metastases of clear cell renal cell carcinoma to the adrenal can mimic primary adrenal cortical neoplasms or normal adrenal, especially in biopsy material. We compared 34 cases of clear cell renal cell carcinoma metastasis to the adrenal with 49 primary adrenal lesions (16 carcinoma, 22 adenoma, 9 oncocytic tumor, and 2 hyperplasia). Normal adrenal was available in 59 cases. Each entity was represented on tissue microarrays by duplicate-triplicate evaluable spots taken from spatially separate areas. Two pathologists evaluated all reactivity from 0 to 3+. A panel of 12 immunohistochemical stains was performed, including the first diagnostic uses of steroid receptor coactivator (SRC1) and equilibrative nucleoside transporter 1 (ENT1). The most sensitive and specific renal cell carcinoma markers were membranous reactivity for carbonic anhydrase IX (CAIX) and RCC marker and nuclear reactivity for PAX8. For adrenal cortical carcinomas, best markers were synaptophysin, SRC1, and MelanA; and for adrenal oncocytic tumor, synaptophysin and ENT1. Optimal markers for adrenal cortical adenoma and normal adrenal were ENT1 (more specific) and either MelanA or SRC1 (more sensitive). Calretinin, cytokeratin 34βE12 and CAM5.2, inhibin, and steroidogenic factor 1 (SF1) proved less valuable to the panel. Nonspecific cytoplasmic biotin reactivity was frequent for CAIX and PAX8. Tumors with high-grade cytology should be worked up with 2 of the 3 stains: CAIX, PAX8, or RCC marker; and either SRC1 or MelanA. Adrenal adenoma, or normal adrenal, versus low-grade renal cell carcinoma are distinguished by a panel of: CAIX, PAX8, or RCC Marker; ENT1 and either SRC1 or MelanA.

Limited utility of routine surveillance imaging for classical Hodgkin lymphoma patients in first complete remission

BACKGROUND

The objective of this study was to compare the outcomes of patients with classical Hodgkin lymphoma (cHL) who achieved complete remission with frontline therapy and then underwent either clinical surveillance or routine surveillance imaging.

METHODS

In total, 241 patients who were newly diagnosed with cHL between January 2000 and December 2010 at 3 participating tertiary care centers and achieved complete remission after first-line therapy were retrospectively analyzed. Of these, there were 174 patients in the routine surveillance imaging group and 67 patients in the clinical surveillance group, based on the intended mode of surveillance. In the routine surveillance imaging group, the intended plan of surveillance included computed tomography and/or positron emission tomography scans; whereas, in the clinical surveillance group, the intended plan of surveillance was clinical examination and laboratory studies, and scans were obtained only to evaluate concerning signs or symptoms. Baseline patient characteristics, prognostic features, treatment records, and outcomes were collected. The primary objective was to compare overall survival for patients in both groups. For secondary objectives, we compared the success of second-line therapy and estimated the costs of imaging for each group.

RESULTS

After 5 years of follow-up, the overall survival rate was 97% (95% confidence interval, 92%-99%) in the routine surveillance imaging group and 96% (95% confidence interval, 87%-99%) in the clinical surveillance group (P = .41). There were few relapses in each group, and all patients who relapsed in both groups achieved complete remission with second-line therapy. The charges associated with routine surveillance imaging were significantly higher than those for the clinical surveillance strategy, with no apparent clinical benefit.

CONCLUSIONS

Clinical surveillance was not inferior to routine surveillance imaging in patients with cHL who achieved complete remission with frontline therapy. Routine surveillance imaging was associated with significantly increased estimated imaging charges.

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

BACKGROUND

Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present.

RESULTS

In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies.

CONCLUSIONS

The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.

Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO₂

Reproductive phase change from vegetative mycelium to the initiation of fruiting in Agaricus bisporus is regulated in large part by the sensing of environmental conditions. A model is proposed in which three separate environmental factors exert control at different stages of the reproductive developmental process change. The eight carbon volatile 1-octen-3-ol controls the early differentiation from vegetative hyphae to multicellular knots; temperature reduction is essential for the later differentiation of primodia; and carbon dioxide level exerts quantitative control on the number of fruiting bodies developed. Analysis of transcriptomic changes during the reproductive phase change was carried out with initiation-specific microarrays, and the newly published A. bisporus genome was used to analyse the promoter regions of differentially regulated genes. Our studies have shown there to be both early and late initiation responses relating to sensing of eight carbon volatiles and temperature respectively. A subset of 45 genes was transcriptionally regulated during the reproductive phase change which exhibited a range of functions including cell structure, nitrogen and carbon metabolism, and sensing and signalling. Three gene clusters linking increased transcription with developmental stage were identified. Analysis of promoter regions revealed cluster-specific conserved motifs indicative of co-ordinated regulation of transcription.

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

Genome organization and transcription response to harvest of two metallothionein-like genes in Agaricus bisporus fruiting bodies

Metallothioneins are a class of small cysteine-rich proteins that have been associated with increased tolerance to metal and oxidative stresses in animals, plants, and fungi. We investigated a metallothionein-like (mt-like) gene shown previously to be upregulated in fruiting bodies of the fungus Agaricus bisporus in response to post-harvest storage. Analysis of an A. bisporus genomic DNA cosmid library identified two similar mt-like genes (met1 and met2) arranged as a bidirectional gene pair transcribed from the same promoter region. The promoter contained regulatory elements including 9 metal responsive elements and a CAAT box region 220 bp downstream of met1 that showed striking similarity to a feature in Coprinopsis cinerea mt-like gene promoters. Transcriptional analysis showed that both met genes are significantly and rapidly (within 3 hours) upregulated during post-harvest storage and expression is significantly greater in stipe and cap tissues compared with the gills. However, a strong directionality of the promoter was demonstrated, as transcript levels of met1 were at least two orders of magnitude greater than those of met2 in all samples tested.

The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi

Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.

Repeatability and sources of variability in multi-center assessment of segmental foot kinematics in normal adults

Multi-site application of biomechanical models can be a powerful tool as quantitative methods are employed to improve clinical care and to assess larger populations for research purposes. However, the use of such models depends on adequate validation to assure reliability in inter-site measures. We assessed repeatability and sources of variability associated with the assessment of segmental foot kinematics using the Milwaukee Foot Model during multiple testing sessions at two sites. Six healthy ambulators were instrumented and tested during comfortable ambulation; data were analyzed with variance components analysis using a mixed effects linear model. Results indicated that the largest source of variability was inter-subject; measurement error associated with Site and Session fell below 3.5 degrees in over 80% of position measurements and below 2.5 degrees in over 80% of ROM measurements. These findings support the continued use of the segmental foot model at multiple sites for clinical and research purposes.

Factors associated with recurrent bacterial vaginosis

OBJECTIVE

To determine whether menstrual abnormalities, multiple personal behaviors and some contraceptive methods, all of which have been described as potential causes of single episodes of bacterial vaginosis (BV), are associated with recurrent bacterial vaginosis (RBV).

STUDY DESIGN

This was a retrospective, case-controlled study performed in an urban setting. Women with RBV and matched controls were mailed a survey that included multiple questions about potential risk factors for BV. Four-to-one matching of age groups was performed, with 28 RBV cases matched to 112 controls.

RESULTS

Among multiple possible predisposing factors, only African American ethnicity (p < 0.001) and > 1 male sex partner in the previous 2 years (p = 0.007) were strongly associated with RBV. Abnormal uterine bleeding, frequent intercourse without a condom or withdrawal, anal intercourse, menstrual hygiene product use, tub baths, back-to-front wiping after using the toilet, smoking, choice of contraceptive method (including condoms, the combination oral contraceptive, injectable medroxyprogesterone acetate or an intrauterine device) and douching were not associated with RBV.

CONCLUSION

Providers should counsel women with RBV to minimize their number of male sex partners. There are few data to support the recommendation of other behavioral changes.

The effect of obesity on neuraxial technique difficulty in pregnant patients: a prospective, observational study

BACKGROUND

Practitioners often presuppose that obesity will increase neuraxial technique difficulty in pregnant patients, but few investigators have systematically examined this population for risk factors associated with difficult epidural or spinal needle placement. We designed this study to prospectively identify factors that predict neuraxial technique difficulty in pregnant patients.

METHODS

Using a prospective, observational format, pregnant patients were examined for multiple potential risk factors for neuraxial technique difficulty, including current body mass index, ability to palpate spinous processes, maximum back flexion, scoliosis, and experience of the practitioner. Neuraxial technique difficulty was then assessed using two measures: 1) the number of needle passes needed to reach the desired space, and 2) the placement time from skin infiltration to either spinal injection or epidural catheter threading. Predictors of total needle passes were determined by fitting the data to a generalized linear model with negative binomial error. Predictors of neuraxial anesthetic time were determined by fitting a linear model to the log of neuraxial anesthetic placement time. A survival model was used to account for bias introduced when attending physicians intervened in resident physician procedures.

RESULTS

Neuraxial procedures in 427 pregnant patients were studied. For both the number of needle passes and the neuraxial anesthetic placement time, the significant predictors of difficulty were the practitioner's ability to palpate the patient's bony landmarks and the patient's ability to flex her back. Obesity, as measured by body mass index, was not an independent predictor of either end point. Obesity did, however, strongly predict both the ability to palpate landmarks and flex the back.

CONCLUSIONS

Despite concerns that obesity may cause difficulty with neuraxial technique, some obese patients have surprisingly easy neuraxial block placements. When approaching any neuraxial anesthetic in a pregnant patient, and especially in the obese parturient, back flexion and landmark palpation predict neuraxial technique difficulty.

Influence of sporophore development, damage, storage, and tissue specificity on the enzymic formation of volatiles in mushrooms (Agaricus bisporus)

The enzymic oxidation of the polyunsaturated fatty acid-linoleic acid leads, in fungi, to the formation of a unique class of nonconjugated hydroperoxides, which are cleaved to form eight-carbon volatiles characteristic of mushroom and fungal flavor. However, the enzymes involved in this biosynthetic pathway, the bioavailability of the fatty acid substrate, and the occurrence of the reaction products (hydroperoxides and eight-carbon volatiles) are not fully understood. This study investigated the lipids, fatty acids, and hydroperoxide levels, as well as eight-carbon volatile variations in the fungal model Agaricus bisporus, according to four parameters: sporophore development, postharvest storage, tissue type, and damage. Eight-carbon volatiles were measured using solid phase microextraction and gas chromatography-mass spectrometry. Tissue disruption had a major impact on the volatile profile, both qualitatively and quantitatively; 3-octanone was identified as the main eight-carbon volatile in whole and sliced sporophore, an observation overlooked in previous studies due to the use of tissue disruption and solvent extraction for analysis. Fatty acid oxidation and eight-carbon volatile emissions decreased with sporophore development and storage, and differed according to tissue type. The release of 1-octen-3-ol and 3-octanone by incubation of sporophore tissue homogenate with free linoleic acid was inhibited by acetylsalicylic acid, providing evidence for the involvement of a heme-dioxygenase in eight-carbon volatile production.

Statistical modelling of transcript profiles of differentially regulated genes

BACKGROUND

The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression.

RESULTS

Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Split-line" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t) = A + (B + Ct)Rt + epsilon. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data allowed 11% of the Escherichia coli features to be fitted by an exponential function, and 25% of the Rattus norvegicus features could be described by the critical exponential model, all with statistical significance of p < 0.05.

CONCLUSION

The statistical non-linear regression approaches presented in this study provide detailed biologically oriented descriptions of individual gene expression profiles, using biologically variable data to generate a set of defining parameters. These approaches have application to the modelling and greater interpretation of profiles obtained across a wide range of platforms, such as microarrays. Through careful choice of appropriate model forms, such statistical regression approaches allow an improved comparison of gene expression profiles, and may provide an approach for the greater understanding of common regulatory mechanisms between genes.

Hairpin-mediated down-regulation of the urea cycle enzyme argininosuccinate lyase in Agaricus bisporus

A double-stranded (ds) RNA hairpin-mediated down-regulation system was developed for the cultivated mushroom Agaricus bisporus, and the role of the urea cycle enzyme argininosuccinate lyase (asl) in mushroom post-harvest development was investigated. Hairpin expression vectors were constructed to initiate down-regulation of asl and introduced into A. bisporus by Agrobacterium tumefaciens-mediated transformation. Transcripts of asl were significantly reduced (93.1 and 99.9%) in two transformants and hairpin vector transgene sequences were maintained throughout sporophore development. Single and multiple hairpin integration events were observed in Southern analysis. Transformants with down-regulated asl exhibited reduced yield and cap expansion during post-harvest sporophore development. There were no detectable differences in urea levels between the hairpin-transformed and control strains. This is the first report of reduced gene expression resulting from the introduction of dsRNA hairpins in A. bisporus and the applications of this technology will facilitate functional studies in the mushroom.

The role of ornithine aminotransferase in fruiting body formation of the mushroom Agaricus bisporus

The complete oat gene and cDNA from the commercial mushroom, Agaricus bisporus, encoding ornithine aminotransferase (OAT) was characterized. The gene encodes a 466 amino acid protein and provides the first fully reported homobasidiomycete OAT protein sequence. The gene is interrupted by ten introns, and no mitochondrial targeting motif was present pointing to a cytoplasmic localization. The function of the gene was demonstrated by complementation of a Saccharomyces cerevisiae mutant unable to utilize ornithine as a sole source of nitrogen with an A. bisporus oat cDNA construct. Northern analysis of the oat gene together with the pruA gene (encoding Delta(1)-pyrroline-5-carboxylate dehydrogenase) showed that transcripts of both genes were lower during the first stages of fruiting body development. The higher expression of the oat gene in later stages of development, suggests the importance of ornithine metabolism for the redistribution of metabolites in the developing mushroom. Hplc analysis of all amino acids revealed that ornithine levels increased during fruiting body development whereas proline levels fell.

Argininosuccinate synthetase and argininosuccinate lyase: two ornithine cycle enzymes from Agaricus bisporus

Accumulation of high quantities of urea in fruiting bodies is a known feature of larger basidiomycetes. Argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL) are two ornithine cycle enzymes catalysing the last two steps in the arginine biosynthetic pathway. Arginine is the main precursor for urea formation. In this work the nucleotide sequences of the genes and corresponding cDNAs encoding argininosuccinate synthetase (ass) and argininosuccinate lyase (asl) from Agaricus bisporus were determined. Eight and six introns were present in the ass and asl gene, respectively. The location of four introns in the asl gene were conserved among vertebrate asl genes. Deduced amino acid sequences, representing the first homobasidiomycete ASS and ASL protein sequences, were analysed and compared with their counterparts in other organisms. The ass ORF encoded for a protein of 425 amino acids with a calculated molecular mass of 47266Da. An alignment with ASS proteins from other organisms revealed high similarity with fungal and mammalian ASS proteins, 61-63% and 51-55% identity, respectively. The asl open reading frame (ORF) encoded a protein of 464 amino acids with an calculated mass of 52337Da and similar to ASS shared the highest similarity with fungal ASL proteins, 59-60% identity. Northern analyses of ass and asl during fruiting body formation and post-harvest development revealed that expression was significantly up-regulated from developmental stage 3 on for all the tissues studied. The expression reached a maximum at the later stages of fruiting body growth, stages 6 and 7. Both ass and asl genes were up-regulated within 3h after harvest showing that the induction mechanism is very sensitive to the harvest event and emphasizes the importance of the arginine biosynthetic pathway/ornithine cycle in post-harvest physiology.

Expression of the urease gene of Agaricus bisporus: a tool for studying fruit body formation and post-harvest development

Fruit body initials of Agaricus bisporus contain high levels of urea, which decrease in the following developmental stages until stage 4 (harvest) when urea levels increase again. At storage, the high urea content may affect the quality of the mushroom, i.e. by the formation of ammonia from urea through the action of urease (EC 3.5.1.5). Despite the abundance of urea in the edible mushroom A. bisporus, little is known about its physiological role. The urease gene of A. bisporus and its promoter region were identified and cloned. The coding part of the genomic DNA was interrupted by nine introns as confirmed by cDNA analysis. The first full homobasidiomycete urease protein sequence obtained comprised 838 amino acids (molecular mass 90,694 Da, pI 5.8). An alignment with fungal, plant and bacterial ureases revealed a high conservation. The expression of the urease gene, measured by Northern analyses, was studied both during normal development of fruit bodies and during post-harvest senescence. Expression in normal development was significantly up-regulated in developmental stages 5 and 6. During post-harvest senescence, the expression of urease was mainly observed in the stipe tissue; expression decreased on the first day and remained at a basal level through the remaining sampling period.

Opacification of the genitourinary collecting system during MDCT urography with enhanced CT digital radiography: nonsaline versus saline bolus

OBJECTIVE

The purpose of this study was to determine whether a saline bolus during CT urography improves urinary collecting system opacification and whether the addition of enhanced CT digital radiography (CTDR) improves urinary collecting system visualization with or without a saline bolus.

MATERIALS AND METHODS

One hundred eight CT urography and enhanced CTDR examinations were reviewed. Fifty-four patients were given a saline bolus during CT urography, and 54 patients underwent CT urography without a saline bolus. Urinary collecting system opacification was evaluated by group (saline vs nonsaline), imaging technique (CT urography alone vs CT urography plus enhanced CTDR), number of enhanced CTDR images, and site of nonopacified urinary segments. Using a multivariate logistic regression model, we determined significance of variables and odds of complete opacification.

RESULTS

In the saline group, 248 nonopacified sites were identified on CT urography alone and 95 sites with CT urography plus enhanced CTDR. In the nonsaline group, 185 nonopacified sites were identified on CT urography alone and 59 sites with CT urography plus enhanced CTDR. Combining both groups, 433 nonopacified sites were identified with CT urography alone and 154 sites with CT urography plus enhanced CTDR. Multivariate logistic regression showed significance for group (p = 0.010), imaging method (p < 0.0001), number of enhanced CTDR images (p = 0.048), and site of segment opacification (p < 0.0001). The renal pelvis shows the greatest odds and the distal ureter the lowest odds for complete opacification by group or imaging method.

CONCLUSION

The addition of a saline bolus offers no improvement, whereas the addition of enhanced CTDR offers significant improvement in collecting system opacification during CT urography.

Differential expression of a putative riboflavin-aldehyde-forming enzyme (raf) gene during development and post-harvest storage and in different tissue of the sporophore in Agaricus bisporus

Cloning and characterisation of a putative riboflavin-aldehyde-forming enzyme gene (raf) from the cultivated mushroom Agaricus bisporus and its expression during morphogenesis are described. Three cDNA clones were isolated following differential screening of cDNA libraries from rapidly expanding sporophores and post-harvest stored sporophores. The cDNA sequence and predicted translation analysis revealed an open reading frame (ORF) of 348 nucleotides encoding a polypeptide of 115 amino acids, with three introns (56-66 bases) interrupting the genomic ORF. Blast X searches of the databases with the gene sequence showed homology (40% identity and 56% similarity) to the riboflavin-aldehyde-forming enzyme gene from Schizophyllum commune. In A.bisporus, the raf gene sequence upstream of the ORF contained a large CT-rich putative regulatory element (-64 to -24 bases) found in highly expressed genes in various mushrooms, and a 6-base motif present in the 3' end of the genomic sequence, but not in the corresponding 3' non-coding part of the cDNA, was identified. The raf gene transcripts increased abundantly in rapidly developing sporophores as well in post-harvest stored sporophores. Differential expression of the raf gene transcripts in different tissues of the sporophore was also observed, with higher levels in the stipe compared with the cap and gills. The temporal and spatial expression patterns observed suggest transcriptional regulation of the raf gene during A. bisporus morphogenesis.

Cloning and postharvest expression of serine proteinase transcripts in the cultivated mushroom Agaricus bisporus

Increases in both the levels and the activity of serine proteinase have been previously described in the senescing mushroom Agaricus bisporus. cDNA encoding serine proteinase was amplified by reverse transcriptase-polymerase chain reaction using a degenerate primer based on the N-terminal sequence of a previously isolated A. bisporus serine proteinase and then cloned. The cDNA was sequenced and shown to be homologous to those of other fungal serine proteinases. Northern analysis showed that this serine proteinase gene (Spr1) was not expressed in freshly harvested sporophores but was strongly up-regulated postharvest and found almost entirely in the stipe of the sporophore (approximately 0.08% of mRNAs 2 days after harvest). Low-level expression was detectable in the flesh (pileus trama) and gill (lamellae) tissues of the cap, but none was detected in the skin (pilei pellis). In three of the cloned cDNAs, sequence analysis showed that the poly(A) tail starts at different positions. Expression of Spr1 in Escherichia coli caused restricted colony growth.