Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.

The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species.

Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species.

To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species.

Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi.

The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.

Correction to: Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger

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Deletion of homologs of the SREBP pathway results in hyper-production of cellulases in Neurospora crassa and Trichoderma reesei

BACKGROUND

The filamentous fungus Neurospora crassa efficiently utilizes plant biomass and is a model organism for genetic, molecular and cellular biology studies. Here, a set of 567 single-gene deletion strains was assessed for cellulolytic activity as compared to the wild-type parental strain. Mutant strains included were those carrying a deletion in: (1) genes encoding proteins homologous to those implicated in the Saccharomyces cerevisiae secretion apparatus; (2) genes that are homologous to those known to differ between the Trichoderma reesei hyper-secreting strain RUT-C30 and its ancestral wild-type strain; (3) genes encoding proteins identified in the secretome of N. crassa when cultured on plant biomass and (4) genes encoding proteins predicted to traverse the secretory pathway.

RESULTS

The 567 single-gene deletion collection was cultured on crystalline cellulose and a comparison of levels of secreted protein and cellulase activity relative to the wild-type strain resulted in the identification of seven hyper-production and 18 hypo-production strains. Some of these deleted genes encoded proteins that are likely to act in transcription, protein synthesis and intracellular trafficking, but many encoded fungal-specific proteins of undetermined function. Characterization of several mutants peripherally linked to protein processing or secretion showed that the hyper- or hypo-production phenotypes were primarily a response to cellulose. The altered secretome of these strains was not limited to the production of cellulolytic enzymes, yet was part of the cellulosic response driven by the cellulase transcription factor CLR-2. Mutants implicated the loss of the SREBP pathway, which has been found to regulate ergosterol biosynthesis genes in response to hypoxic conditions, resulted in a hyper-production phenotype. Deletion of two SREBP pathway components in T. reesei also conferred a hyper-production phenotype under cellulolytic conditions.

CONCLUSIONS

These studies demonstrate the utility of screening the publicly available N. crassa single-gene deletion strain collection for a particular phenotype. Mutants in a predicted E3 ligase and its target SREBP transcription factor played an unanticipated role in protein production under cellulolytic conditions. Furthermore, phenotypes similar to those observed in N. crassa were seen following the targeted deletion of orthologous SREBP pathway loci in T. reesei, a fungal species commonly used in industrial enzyme production.

A xylosylphosphotransferase of Cryptococcus neoformans acts in protein O-glycan synthesis

Cryptococcal meningoencephalitis is an AIDS-defining illness caused by the opportunistic pathogen Cryptococcus neoformans. This organism possesses an elaborate polysaccharide capsule that is unique among pathogenic fungi, and the glycobiology of C. neoformans has been a focus of research in the field. The capsule and other cellular glycans and glycoconjugates have been described, but the machinery responsible for their synthesis remains largely unexplored. We recently discovered Xpt1p, an enzyme with the unexpected activity of generating a xylose-phosphate-mannose linkage. We now demonstrate that this novel activity is conserved throughout the C. neoformans species complex, localized to the Golgi apparatus, and functions in the O-glycosylation of proteins. We also present the first survey of O-glycans from C. neoformans.

Clinical trial: the effects of certolizumab pegol therapy on work productivity in patients with moderate-to-severe Crohn's disease in the PRECiSE 2 study

BACKGROUND

The effect of certolizumab pegol on employment status and work productivity has not been previously assessed.

AIM

To assess the impact of treatment with certolizumab pegol, the only PEGylated, Fab' TNF antagonist, on work productivity in patients with active Crohn's disease (CD) from the PRECiSE 2 study.

METHODS

Patients (n = 668) with active disease [CD activity index (CDAI) score of 220-450] were treated with open-label subcutaneous certolizumab pegol 400 mg (week 0, 2, 4). Responders (n = 425) (> or = 100-point decrease in CDAI from baseline) were randomized to receive certolizumab pegol 400 mg or placebo every 4 weeks until week 24, with final evaluation at week 26. Patients completed the Work Productivity and Activity Impairment for CD questionnaire (WPAI:CD) and the Inflammatory Bowel Disease Questionnaire (IBDQ) at weeks 0, 6, 16 and 26 and at the withdrawal visit.

RESULTS

Work productivity improved following induction with certolizumab pegol. Between week 6 and 26, certolizumab pegol-treated patients experienced significant improvement in work productivity compared with placebo recipients (11% and 10% overall improvement in work and activity impairment, respectively). During the maintenance phase, impairments in productivity and activities due to CD were significantly less in the certolizumab pegol group than in the placebo group.

CONCLUSION

Induction and maintenance therapy with certolizumab pegol significantly improved the work productivity of patients with active CD compared with those in the placebo group.

A novel xylosylphosphotransferase activity discovered in Cryptococcus neoformans

Cryptococcus neoformans is a fungal pathogen that causes serious disease in immunocompromised individuals. The organism produces a distinctive polysaccharide capsule that is necessary for its virulence, a predominantly polysaccharide cell wall, and a variety of protein- and lipid-linked glycans. The glycan synthetic pathways of this pathogen are of great interest. Here we report the detection of a novel glycosylphosphotransferase activity in C. neoformans, identification of the corresponding gene, and characterization of the encoded protein. The observed activity is specific for UDP-xylose as a donor and for mannose acceptors and forms a xylose-alpha-1-phosphate-6-mannose linkage. This is the first report of a xylosylphosphotransferase activity in any system.

Glycosyltransferases and their products: cryptococcal variations on fungal themes

Glycosyltransferases are specific enzymes that catalyse the transfer of monosaccharide moieties to biological substrates, including proteins, lipids and carbohydrates. These enzymes are present from prokaryotes to humans, and their glycoconjugate products are often vital for survival of the organism. Many glycosyltransferases found in fungal pathogens such as Cryptococcus neoformans do not exist in mammalian systems, making them attractive potential targets for selectively toxic agents. In this article, we present the features of this diverse class of enzymes, and review the fungal glycosyltransferases that are involved in synthesis of the cell wall, the cryptococcal capsule, glycoproteins and glycolipids. We specifically focus on enzymes that have been identified or studied in C. neoformans, and we consider future directions for research on glycosyltransferases in the context of this opportunistic pathogen.

Systematic review: the impact of gastro-oesophageal reflux disease on work productivity

BACKGROUND

Gastro-oesophageal reflux disease has wide-ranging effects on patients' lives.

AIM

To review systematically the effects of gastro-oesophageal reflux disease on work productivity.

METHODS

Studies of gastro-oesophageal reflux disease and work productivity were identified in a systematic literature search and their results were valued in US dollars using the human capital method. Work productivity loss was defined as absence from work (absenteeism) plus reduced effectiveness while working (presenteeism).

RESULTS

Eight eligible studies were included. Reported work productivity loss among individuals with gastro-oesophageal reflux disease ranged from 6% to 42% and was primarily because of presenteeism (6-40%) rather than absenteeism (<1% to 7%). Reported losses were greatest in patients experiencing sleep disturbance because of gastro-oesophageal reflux disease, and lowest in individuals from the general population taking appropriate prescription medication. Work productivity impairment correlated with symptom severity and responded to acid-suppressive therapy. Assuming a 40-h working week and average wages in the US, the weekly mean productivity loss per employee with gastro-oesophageal reflux disease can be estimated between 2.4 (62 dollars) and 16.6 h (430 dollars), depending on the population studied.

CONCLUSIONS

Gastro-oesophageal reflux disease has a substantial impact on employee productivity, primarily by impairing productivity while working. Further studies are needed to confirm that this impact can be decreased by acid-suppressive therapy.

Effect of tegaserod on work and daily activity in irritable bowel syndrome with constipation

BACKGROUND

Tegaserod is a promotility agent with proven efficacy and safety in patients with irritable bowel syndrome with constipation.

AIM

To assess tegaserod's effect on work productivity and daily activity.

METHODS

Women, 18-65 years old and meeting Rome II criteria for irritable bowel syndrome with constipation, were randomized to a double-blind, placebo-controlled, multicentre study of tegaserod 6 mg b.d. or placebo. Productivity loss and daily activity impairment because of irritable bowel syndrome were measured with the Work Productivity and Activity Impairment questionnaire for irritable bowel syndrome, modified to exclude diarrhoea as a symptom. Assessments were made at baseline, weeks 2 and 4.

RESULTS

A total of 2660 women were randomized and, of these, 1675 [tegaserod (n = 1363), placebo (n = 312)] were employed and completed Work Productivity and Activity Impairment for irritable bowel syndrome questionnaires. Compared with placebo, tegaserod significantly reduced work and daily activity impairment at weeks 2 and 4. Tegaserod reduced absenteeism by 2.6% (P = 0.004), presenteeism by 5.4% (P < 0.0001), overall work productivity loss by 6.3% (P < 0.0001), and activity impairment by 5.8% (P < 0.0001) at week 4 (vs. baseline). Assuming a 40-h workweek, tegaserod reduced work productivity loss by 2.5 h/week.

CONCLUSIONS

Tegaserod significantly reduced work productivity loss and daily activity impairment at 2 weeks, and this benefit was maintained at 4 weeks.

The validity and accuracy of the Work Productivity and Activity Impairment questionnaire--irritable bowel syndrome version (WPAI:IBS)

BACKGROUND

Irritable bowel syndrome is a common chronic functional gastrointestinal disorder characterized by recurrent abdominal pain and discomfort associated with alterations in bowel habit. Irritable bowel syndrome affects patients' quality of life and increases productivity loss.

AIM

To assess validity and accuracy of the Work Productivity and Activity Impairment questionnaire in irritable bowel syndrome as a tool for quantifying the effects of irritable bowel syndrome on productivity and daily activities.

METHODS

Validity and accuracy were evaluated in 135 irritable bowel syndrome patients relative to three measures of irritable bowel syndrome disease severity; a debriefing questionnaire; retrospective diary; Work Limitations Questionnaire, and an activity impairment measure (Dimensions of Daily Activities).

RESULTS

Symptom severity scores, diary scores, Work Limitations Questionnaire and Dimensions of Daily Activities were significant predictors of work productivity and activity impairment questionnaire in irritable bowel syndrome measures of work time missed, and work and activity productivity loss (P = 0.04 to < 0.0001). Impairment due to irritable bowel syndrome was estimated to be 2.9-4.3% for work time missed and 22-32% for impairment at work, the equivalent of 9.7 -14 h lost productivity per week. Activity impairment was 24-41%.

CONCLUSIONS

Discriminative validity of the Work Productivity and Activity Impairment questionnaire in irritable bowel syndrome was established, making it the only validated tool for measuring the relative differences between disease severity groups and quantifying work productivity loss and activity impairment in irritable bowel syndrome patients.

Percutaneous methods of tibial plateau fixation

Various methods of percutaneous fixation of tibial plateau fractures are available. The optimal method of fixation is dictated by soft tissue injury, fracture characteristics, and functional demands of the patient. Unicondylar fractures are amenable to percutaneous stabilization with screws or plates although some fractures are best approached with open techniques. Hybrid and ring external fixators are most appropriate for patients with bicondylar injuries who have severe soft tissue trauma. Use of intramedullary nails to align ipsilateral shaft fractures adjacent to percutaneously fixed plateau injuries remains controversial but may be indicated for some patients with bicondylar lesions and combined plateau and shaft fractures.

Superior gluteal artery in the extended iliofemoral approach

OBJECTIVE

To determine the incidence of superior gluteal artery injury following fracture of the acetabulum and to determine whether the combination of a superior gluteal artery injury and the use of an extended iliofemoral approach to the acetabulum creates abductor muscle necrosis.

DESIGN

Prospective protocol, consecutive cases.

SETTING

A consecutive series from the referral practice of the senior author plus seven cases from the practices of two other authors.

PATIENTS

Two hundred twenty-seven patients with fractures of the acetabulum were treated operatively between November 1992 and January 1995. Forty-one were treated with the use of the extended iliofemoral approach. Preoperative angiograms were not performed for any of the patients. All fractures involved the posterior column, and all but two fractures had displacement of the greater sciatic notch. The average displacement of the notch was 2.5 centimeters (range 6 to 60 millimeters).

INTERVENTION

All patients were treated with open reduction and internal fixation via the extended iliofemoral approach. Intraoperative Doppler examination of the superior gluteal artery was performed before and after reduction and fixation of the posterior column.

MAIN OUTCOME MEASURE

Wound complications, abductor manual muscle testing, hip range of motion.

RESULTS

Pulsatile flow was confirmed in forty of forty-one patients. All patients were followed for a minimum of six months with an average follow-up of 1.4 years. At most recent follow-up, no patients had evidence of complete loss of abductor function. Sixty-three percent of patients had achieved Grade 4 of 5 motor strength, and 25 percent of them had achieved normal motor strength.

CONCLUSIONS

No instances of superior gluteal artery laceration and only one instance of superior gluteal artery thrombosis were encountered in these forty-one patients despite significant fracture displacement involving the sciatic notch. The incidence of superior gluteal artery injury was significantly less than would be expected from previous studies. Massive abductor necrosis resulting from superior gluteal artery injury combined with an extended approach has been described primarily in animal and cadaver studies. Although arteriograms are useful in the control of hemodynamic instability, we cannot support the recommendation of preoperative angiographic study of all patients undergoing acetabular fracture surgery via an extended approach. In one case, an extended iliofemoral approach was tolerated in a patient with absent superior gluteal artery flow.

'Floating pelvis'. A combination of bilateral hip dislocation with a lumbar ligamentous disruption

A patient is described with a ligamentous disruption at the L4/L5 level in association with bilateral, traumatic dislocations of the hip. The diagnostic evaluation, acute intervention, and definitive stabilisation are reported. The unstable spine posed a problem in treatment with regard to the timing and technique of the reduction of the hips.

Neurologic injuries in pelvic ring fractures

Unstable fractures of the pelvic ring are an increasingly frequent outcome of motor vehicle trauma. Neurologic injury after such injuries can be a cause of significant morbidity. The available literature on neurologic injuries was reviewed and compared with a clinical review of 90 unstable pelvic injuries treated during a 3-year period. Eighty-three patients were available for followup examination. Neurologic injuries were seen in 21 % of the patients. Thirty-seven percent of patients had sensory deficits alone whereas the remaining 63% had motor and sensory findings. All patients showed some evidence of neurologic recovery at an average or 24-months followup. At least 1 grade of muscle function improvement was consistently seen and 53% of patients had complete neurologic recovery. Improvement in function was seen as many as 24 months postinjury, but L5 function was least likely to progress to full recovery. The incidence of neurologic injuries and their distribution was similar to that reported in the literature, whereas the prognosis for neurologic recovery was significantly better. This may be related to techniques of early anatomic reduction and stabilization of unstable pelvic ring injuries.

Analytical characterization of peptide contaminants of L-tryptophan

Reversed-phase liquid chromatographic fractions of extracts of 2 preparations of eosinophilia-myalgia syndrome (EMS)-associated L-tryptophan were analyzed by proton nuclear magnetic resonance spectrometry, mass spectrometry, microbial-growth inhibition, and amino acid residue analyses. Fraction components demonstrated properties of an antibiotic peptide resembling bacitracin. Many peptide antibiotics like bacitracin are secondary metabolites of Bacillus species, genus of the tryptophan producer organism for the implicated manufacturer. In order to determine whether a correlation exists between individual EMS cases and the concentration of peptides or bacitracin consumed, reliable methods must be developed for quantification of the total of isoforms.

The validity and reproducibility of a work productivity and activity impairment instrument

The construct validity of a quantitative work productivity and activity impairment (WPAI) measure of health outcomes was tested for use in clinical trials, along with its reproducibility when administered by 2 different methods. 106 employed individuals affected by a health problem were randomised to receive either 2 self-administered questionnaires (self administration) or one self-administered questionnaire followed by a telephone interview (interviewer administration). Construct validity of the WPAI measures of time missed from work, impairment of work and regular activities due to overall health and symptoms, were assessed relative to measures of general health perceptions, role (physical), role (emotional), pain, symptom severity and global measures of work and interference with regular activity. Multivariate linear regression models were used to explain the variance in work productivity and regular activity by validation measures. Data generated by interviewer-administration of the WPAI had higher construct validity and fewer omissions than that obtained by self-administration of the instrument. All measures of work productivity and activity impairment were positively correlated with measures which had proven construct validity. These validation measures explained 54 to 64% of variance (p less than 0.0001) in productivity and activity impairment variables of the WPAI. Overall work productivity (health and symptom) was significantly related to general health perceptions and the global measures of interference with regular activity. The self-administered questionnaire had adequate reproducibility but less construct validity than interviewer administration. Both administration methods of the WPAI warrant further evaluation as a measure of morbidity.

Assessing the responsiveness of a quality-of-life instrument and the measurement of symptom severity in essential hypertension

A pilot study was conducted to compare symptoms elicited with an open-ended question versus a checklist and to measure the responsiveness of quality-of-life measures to symptom severity. The pilot study was part of a multicentre, randomised, double-blind, placebo-controlled study of clentiazem, a calcium channel blocker, in the treatment of essential hypertension. Symptom and quality-of-life data were obtained from 88 patients at baseline and after 10 weeks of therapy by a trained telephone interviewer. Comparison of the symptom checklist and open-ended question method suggests that both methods are necessary to capture severe symptomatology. The 24-item checklist failed to elicit approximately 50% of the severe symptoms reported on the open question list. On the other hand, only 18% of the most severe symptoms subsequently reported on the checklist were first reported by the open question method. The responsiveness of quality-of-life measures to symptom severity was tested using a 20% change in symptom severity obtained from the checklist as the minimal clinically significant difference. Using Guyatt's formula, a minimum sample size of approximately 428 (alpha = 0.05, beta = 0.10) patients per treatment group is required to detect differences in measures of general health perception, anxiety, depression and limitations in social activities. A larger sample is required to show differences in leisure activities. Differences in limitations of the capability to perform house or yard work might be demonstrable with as few as 17 patients per group. This pilot study demonstrated that the severity of symptoms associated with hypertension, and the side effects of its treatment with drugs, are adequately captured by a symptom checklist preceded by an open-ended method of questioning. Responsiveness testing estimated the sample size required to show a statistically significant difference, assuming a 20% change in symptom severity.

The cost of outpatient physicians' services at a Veterans Administration hospital

The cost of an average outpatient visit to a physician at a Veterans Administration hospital in 1976 was estimated from hospital records to have been $80.35 ($104.46 in 1979 dollars). When productivity was used to measure relative cost, cost per visit ranged from a low of $32.66 (1979: $42.46) for hypertension clinic to a high of $243.48 (1979; $316.52) for hematology clinic. The average patient was seen 12.6 times annually at a cost of $1012 (1979: $1315). The major cost category for a physician visit was salaries, with nonphysician salaries costing twice as much as physician salaries. The cost of medical equipment was minimal. The findings suggest that the outpatient bookkeeping system was inadequate for cost accounting, the cost per visit was expensive, there were an excessive number of visits, and problems in the institutional delivery system of ambulatory care lowered productivity of physicians.

The place of sigmoid myotomy in diverticular disease

The place of longitudinal myotomy in the treatment of diverticular disease of the sigmoid colon is discussed, with passing reference to the drawbacks of transverse myotomy. The prime indication for longitudinal myotomy is in the longstanding uncomplicated case of troublesome diverticular disease that has not responded to correct medical treatment, which should include high-residue diet and bran. Such cases are usually over 50 years of age, when a functional and reversible obstruction has become organic and irreversible. They comprise 75% of a series of 104 cases described. A secondary indication is in cases of diverticular disease which have been complicated by perforation, abscess formation, acute intestinal obstruction or fistulae. Such cases comprise 25% of the present series. They may settle after drainage and/or defunctioning colostomy. Myotomy can be carried out later, with or without limited resection, provided that all signs of pus or peritonitis have disappeared. The technique of the operation is described and the results are analysed.

Individual and institutional variables which may serve as indicators of quality of medical care

This article is a critical review of empiric studies, in the medical care literature of the past two decades, that investigated associations between characteristics of physicians and medical care institutions and some measure of the quality of medical care given by them. The intention is to identify those characteristics of physicians and medical care institutions which can be considered the best indicators of the quality of performance to be expected, given the present state of knowledge. The analysis discusses 18 such characteristics but derives a list of 14 which appear to be the best choice of indicators on which further research might focus. It would be possible to design a survey instrument based on these characteristics, which, if upheld by empiric testing, could serve as a crude assessment tool for third parties needing to make quality comparisons between medical care institutions.

Budd-Chiari syndrome after oral contraceptives

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