A pleiotropy scan to discover new susceptibility loci for pancreatic ductal adenocarcinoma

Pleiotropic variants (i.e., genetic polymorphisms influencing more than one phenotype) are often associated with cancer risk. A scan of pleiotropic variants was successfully conducted ten years ago in relation to pancreatic ductal adenocarcinoma susceptibility. However, in the last decade, genetic association studies performed on several human traits have greatly increased the number of known pleiotropic variants. Based on the hypothesis that variants already associated with a least one trait have a higher probability of association with other traits, 61,052 variants reported to be associated by at least one genome wide association study (GWAS) with at least one human trait were tested in the present study consisting of two phases (discovery and validation), comprising a total of 16,055 pancreatic ductal adenocarcinoma (PDAC) cases and 212,149 controls. The meta-analysis of the two phases showed two loci (10q21.1-rs4948550 (P=6.52×10-5) and 7q36.3-rs288762 (P=3.03×10-5) potentially associated with PDAC risk. 10q21.1-rs4948550 shows a high degree of pleiotropy and it is also associated with colorectal cancer risk while 7q36.3-rs288762 is situated 28,558 base pairs upstream of the Sonic Hedgehog (SHH) gene, which is involved in the cell differentiation process and PDAC etiopathogenesis. In conclusion, none of the single nucleotide polymorphisms (SNPs) showed a formally statistically significant association after correction for multiple testing. However, given their pleiotropic nature and association with various human traits including colorectal cancer, the two SNPs showing the best associations with PDAC risk merit further investigation through fine mapping and ad hoc functional studies.

Bayesian Vancomycin Model Selection for Therapeutic Drug Monitoring in Neonates

BACKGROUND AND OBJECTIVE

Pharmacokinetic models can inform drug dosing of vancomycin in neonates to optimize therapy. However, the model selected needs to describe the intended population to provide appropriate dose recommendations. Our study aims to identify the population pharmacokinetic (PopPK) model(s) with the best performance to predict vancomycin exposure in neonates in our hospital.

METHODS

Relevant published PopPK models for vancomycin in neonates were selected based on demographics and vancomycin dosing strategy. The predictive performance of the models was evaluated in Tucuxi using a local cohort of 69 neonates. Mean absolute error (MAE), relative bias (rBias) and relative root mean square error (rRMSE) were used to quantify the accuracy and precision of the predictive performance of each model for three different approaches: a priori, a posteriori, and Bayesian forecasting for the next course of therapy based on the previous course predictions. A PopPK model was considered clinically acceptable if rBias was between ± 20 and 95% confidence intervals included zero.

RESULTS

A total of 25 PopPK models were identified and nine were considered suitable for further evaluation. The model of De Cock et al. 2014 was the only clinically acceptable model based on a priori [MAE 0.35 mg/L, rBias 0.8 % (95% confidence interval (CI) - 7.5, 9.1%), and rRMSE 8.9%], a posteriori [MAE 0.037 mg/L, rBias - 0.23% (95% CI - 1.3, 0.88%), and rRMSE 6.02%] and Bayesian forecasting for the next courses [MAE 0.89 mg/L, rBias 5.45% (95% CI - 8.2, 19.1%), and rRMSE 38.3%) approaches.

CONCLUSIONS

The De Cock model was selected based on a comprehensive approach of model selection to individualize vancomycin dosing in our neonates.

Is there a need to optimise pyrazinamide doses in patients with tuberculosis? A systematic review

Pyrazinamide (PZA) is a first-line antituberculosis drug with potent sterilising activity. Variability in drug exposure may translate into suboptimal treatment responses. This systematic review, conducted according to PRISMA guidelines, aimed to evaluate the concentration-effect relationship. In vitro/in vivo studies had to contain information on the infection model, PZA dose and concentration, and microbiological outcome. Human studies had to present information on PZA dose, measures of drug exposure and maximum concentration, and microbiological response parameter or overall treatment outcome. A total of 34 studies were assessed, including in vitro (n = 2), in vivo (n = 3) and clinical studies (n = 29). Intracellular and extracellular models demonstrated a direct correlation between PZA dose of 15-50 mg/kg/day and reduction in bacterial count between 0.50-27.7 log10 CFU/mL. Consistent with this, higher PZA doses (>150 mg/kg) were associated with a greater reduction in bacterial burden in BALB/c mice models. Human pharmacokinetic studies displayed a linear positive correlation between PZA dose (i.e. 21.4-35.7 mg/kg/day) and drug exposure (AUC range 220.6-514.5 mg·h/L). Additionally, human studies confirmed a dose-effect relationship, with an increased 2-month sputum culture conversion rate at AUC/MIC targets of 8.4-11.3 with higher exposure/susceptibility ratios leading to greater efficacy. A 5-fold variability in AUC was observed at PZA dose of 25 mg/kg. A direct concentration-effect relationship and increased treatment efficacy with higher PZA exposure to susceptibility ratios was observed. Taking into account variability in drug exposure and treatment response, further studies on dose optimisation are justified.

Therapeutic drug monitoring practices of anti-infectives: An Asia-wide cross-sectional survey

Objectives: The current practice of therapeutic drug monitoring (TDM) in Asia is poorly documented. Our aim was to capture and describe TDM services delivered in hospitals across Asia, including aspects such as assay availability, interpretation of results and clinical decision-making. Methods: An online survey about anti-infective TDM practices, available in English and involving 50 questions, was promoted to people involved in TDM in Asia. The survey was open for responses from September to November 2021. Results: Of 207 responses from participants working in 14 Asian countries, 150 responses from 10 countries could be included. TDM services are available for many anti-infectives, providing assays based on chromatographic assays (100.0%) or immunoassays (39.3%). Clinicians (82.6%) and pharmacists (86.8%) were responsible for ordering and interpreting TDM. Most services provided reference targets and dose recommendations. Interpretative support was available to a varying degree. Assay results were available and clinical decision-making could be completed within 24 h in most hospitals (87.9% and 88.9% respectively). As the turnaround time of assay results decreased, the proportion of clinical decision-making completed within 8 h increased. Barriers to implementation of TDM included lack of funding or equipment (71.1%), lack of clinician interest or cooperation (47.0%), and lack of expertise (42.3%). Lack of expertise was the primary barrier for using precision dosing software (50.5%). Conclusion: There are significant differences and challenges in the development and practice of anti-infective TDM in Asian countries.

Detection of Ganciclovir-Resistant Cytomegalovirus in a Prospective Cohort of Kidney Transplant Recipients Receiving Subtherapeutic Valganciclovir Prophylaxis

Cytomegalovirus infection during antiviral prophylaxis occurs in transplant recipients despite individualized regimens based on renal function. Fifty kidney transplant recipients were assessed between 2016 and 2019 for valganciclovir dosing, ganciclovir exposure, cytomegalovirus infection, and genotypic resistance markers during the first year posttransplant. Ganciclovir plasma concentrations were measured using mass spectrometry. Population pharmacokinetics was used to determine individual ganciclovir exposure and to evaluate the ability of manufacturer dosing guidelines to meet therapeutic target daily area under the curve (AUC24) of 40 to 50 μg·h/mL. Full-length UL54 and UL97 were assessed using high-throughput sequencing in cytomegalovirus DNA-positive patient specimens. Valganciclovir doses administered to recipients with creatinine clearance of <40 mL/min were higher than specified by guidelines, and they were lower for recipients with creatinine clearance of ≥40 mL/min. The mean ganciclovir AUC24 was 33 ± 13 μg·h/mL, and 82% of subjects did not attain the therapeutic target. Pharmacokinetic simulations showed that the guidelines similarly could not attain the therapeutic target in 79% of individuals. Cytomegalovirus breakthrough occurred in 6% (3/50) of recipients, while 12% (6/50) developed late-onset infection. The mean AUC24s of recipients with (n = 3) and without (n = 47) infection were not significantly different (P = 0.528). However, one recipient with an AUC24 of 20 μg·h/mL acquired two UL97 ganciclovir resistance mutations. Current prophylaxis guidelines resulted in subtherapeutic ganciclovir exposure in several study recipients, including the emergence of resistance genotypes. IMPORTANCE This study examined the pharmacokinetics and viral genomic data from a prospective cohort of kidney transplant recipients undergoing valganciclovir prophylaxis for cytomegalovirus (CMV) prevention. We showed for the first time using high-throughput sequencing the detection of ganciclovir resistance mutations in breakthrough CMV infection during subtherapeutic plasma ganciclovir as indicated by the pharmacokinetic parameter daily area under the curve (AUC24). In addition, we found that current valganciclovir dosing guidelines for CMV prophylaxis are predicted to attain therapeutic targets in only 21% of recipients, which is consistent with previous pharmacokinetic studies. The novel findings of resistance mutations during subtherapeutic ganciclovir exposure presented here can inform future studies investigating the dynamics of drug selection pressure and the emergence of resistance mutations in vivo.

Pharmacogenomic testing: perception of clinical utility, enablers and barriers to adoption in Australian hospitals

Background

Despite healthcare professionals (HCP) endorsing the clinical utility of pharmacogenomics testing, use in clinical practice is limited.

Aims

To assess HCP' perceptions of pharmacogenomic testing and identify barriers to implementation.

Methods

HCP involved in prescribing decisions at three hospitals in Sydney, Australia, were invited to participate. The online survey assessed perceptions of pharmacogenomic testing, including: (i) demographic and practice variables; (ii) use, knowledge and confidence; (iii) perceived benefits; (iv) barriers to implementation; and (v) operational and/or system changes and personnel required to implement on site.

Results

HCP were predominantly medical practitioners (75/107) and pharmacists (25/107). HCP perceived pharmacogenomic testing was beneficial to identify reasons for drug intolerance (85/95) and risk of side‐effects (86/95). Although testing was considered relevant to their practice (79/100), few HCP (23/100) reported past or intended future use (26/100). Few HCP reported confidence in their ability to identify indications for pharmacogenomic testing (14/107), order tests (19/106) and communicate results with patients (16/107). Lack of clinical practice guidelines (62/79) and knowledge (54/77) were identified as major barriers to implementation of pharmacogenomics. Comprehensive reimbursement for testing and clinical practice guidelines, alongside models‐of‐care involving multidisciplinary teams and local clinical champions were suggested as strategies to facilitate implementation of pharmacogenomic testing into practice.

Conclusions

Pharmacogenomic testing was considered important to guide drug selection and dosing decisions. However, limited knowledge, low confidence and an absence of guidelines impede the use of pharmacogenomic testing. Establishment of local resources including multidisciplinary models‐of‐care was suggested to facilitate implementation of pharmacogenomics.

Therapeutic Drug Monitoring of the Echinocandin Antifungal Agents: Is There a Role in Clinical Practice? A Position Statement of the Anti-Infective Drugs Committee of the International Association of Therapeutic Drug Monitoring and Clinical Toxicology

PURPOSE

Reduced exposure to echinocandins has been reported in specific patient populations, such as critically ill patients; however, fixed dosing strategies are still used. The present review examines the accumulated evidence supporting echinocandin therapeutic drug monitoring (TDM) and summarizes available assays and sampling strategies.

METHODS

A literature search was conducted using PubMed in December 2020, with search terms such as echinocandins, anidulafungin, caspofungin, micafungin, or rezafungin with pharmacology, pharmacokinetics (PKs), pharmacodynamics (PDs), drug-drug interactions, TDM, resistance, drug susceptibility testing, toxicity, adverse drug reactions, bioanalysis, chromatography, and mass spectrometry. Data on PD/PD (PK/PD) outcome markers, drug resistance, PK variability, drug-drug interactions, assays, and TDM sampling strategies were summarized.

RESULTS

Echinocandins demonstrate drug exposure-efficacy relationships, and maximum concentration/minimal inhibitory concentration ratio (Cmax/MIC) and area under the concentration-time curve/MIC ratio (AUC/MIC) are proposed PK/PD markers for clinical response. The relationship between drug exposure and toxicity remains poorly clarified. TDM could be valuable in patients at risk of low drug exposure, such as those with critical illness and/or obesity. TDM of echinocandins may also be useful in patients with moderate liver impairment, drug-drug interactions, hypoalbuminemia, and those undergoing extracorporeal membrane oxygenation, as these conditions are associated with altered exposure to caspofungin and/or micafungin. Assays are available to measure anidulafungin, micafungin, and caspofungin concentrations. A limited-sampling strategy for anidulafungin has been reported.

CONCLUSIONS

Echinocandin TDM should be considered in patients at known risk of suboptimal drug exposure. However, for implementing TDM, clinical validation of PK/PD targets is needed.

Model-Optimized Fluconazole Dose Selection for Critically Ill Patients Improves Early Pharmacodynamic Target Attainment without the Need for Therapeutic Drug Monitoring

Fluconazole has been associated with higher mortality compared with the echinocandins in patients treated for invasive candida infections. Underexposure from current fluconazole dosing regimens may contribute to these worse outcomes, so alternative dosing strategies require study. The objective of this study was to evaluate fluconazole drug exposure in critically ill patients comparing a novel model-optimized dose selection method with established approaches over a standard 14-day (336-h) treatment course. Target attainment was evaluated in a representative population of 1,000 critically ill adult patients for (i) guideline dosing (800-mg loading and 400-mg maintenance dosing adjusted to renal function), (ii) guideline dosing followed by therapeutic drug monitoring (TDM)-guided dose adjustment, and (iii) model-optimized dose selection based on patient factors (without TDM). Assuming a MIC of 2 mg/liter, free fluconazole 24-h area under the curve (fAUC24) targets of ≥200 mg · h/liter and <800 mg · h/liter were used for assessment of target attainment. Guideline dosing resulted in underexposure in 21% of patients at 48 h and in 23% of patients at 336 h. The TDM-guided strategy did not influence 0- to 48-h target attainment due to inherent procedural delays but resulted in 37% of patients being underexposed at 336 h. Model-optimized dosing resulted in ≥98% of patients meeting efficacy targets throughout the treatment course, while resulting in less overexposure compared with guideline dosing (7% versus 14%) at 336 h. Model-optimized dose selection enables fluconazole dose individualization in critical illness from the outset of therapy and should enable reevaluation of the comparative effectiveness of this drug in patients with severe fungal infections.

Out-of-pocket spending among a cohort of Australians living with gout

OBJECTIVE

To measure the direct and indirect out-of-pocket (OOP) costs borne by Australians with gout.

METHODS

A cross-sectional, Australia-wide, web-based survey was conducted over 12 months between May 2017 and April 2018. Participants were recruited via advertisements in doctors' clinics and healthcare organizations' websites, and social media platforms such as Facebook and Twitter. Survey questions collected information about participants' OOP spending on direct medical and non-medical gout-related healthcare costs. Participant demographics, gout status, healthcare sought, workdays lost to due gout and health-related quality of life were also collected.

RESULTS

Seventy-nine patients with gout completed the survey; 70 (89%) were male, and on average were 56 (SD 16) years of age and had gout for 14 (SD 12) years. For this cohort, the median total OOP direct medical cost was AU$200 per year (interquartile range [IQR]: AU$60-AU$570). Sixty (76%) people with gout reported being affected by gout during work; however, only 0.25 (IQR: 0-3) days of work (approximately $60) were lost due to gout in a year. Nine percent (n = 7) of participants experienced cost-related treatment attrition and 33% reported economic hardship (n = 26). Participants who experienced economic hardship or cost-related treatment attrition had higher median total gout-related direct costs than those who did not.

CONCLUSION

In Australia, gout has an OOP financial cost and reduces work productivity. The presence of cost-related treatment attrition among people with gout indicates that financial costs may be a significant barrier to seeking treatment for a subset of patients with gout.

Rebranding Gout: Could a Name Change for Gout Improve Adherence to Urate-Lowering Therapy?

Gout is the most common form of inflammatory arthritis in men, yet both patients and the public often do not recognise gout as a form of arthritis. Instead, due to historical misconceptions, gout is typically seen as a lifestyle disease caused by poor diet. In reality, there are a number of risk factors that contribute to gout, including genetic factors. Views of gout as precipitated by lifestyle alone can lead to stigma, and maladaptive beliefs that it should be treated primarily through dietary changes. This is thought to contribute to poor uptake of, and adherence to, effective pharmaceutical treatments. Gout has some of the poorest medication adherence rates of any chronic disease, contributing to suboptimal health outcomes for patients. Recent research suggests that when gout is referred to as 'urate crystal arthritis' (a rarely used name for gout), the perception of the disease by members of the public was more accurate. It was viewed as being less under personal control (i.e. less appropriately managed by behaviours such as dietary intake), and more appropriately managed by long-term medical treatment. This finding raises the possibility that patients themselves might also benefit from gout being explicitly labelled as arthritis. Indeed, parallels can be drawn between this case and other diseases that have recently had their names changed to improve outcomes, namely primary biliary cirrhosis and schizophrenia. A movement away from the term gout may benefit those living with the disease by changing illness perceptions and increasing uptake of, and adherence to, guideline-recommended treatment(s).

Usability of Reports Generated by a Computerised Dose Prediction Software

Computerised dose prediction software assist clinicians in undertaking therapeutic drug monitoring by providing individualised dosing recommendations, typically communicated to prescribers in the form of a report. These software are highly sophisticated and accurate in predicting individualised dosage regimens, but if the information contained in the report is not understood by prescribers, the benefits of the software are not achieved. In this study, we set out to assess the perceived usability of a report generated from a dose prediction system. Fifteen prescribers were presented with a mock report and asked a number of questions to elicit their views of the report's content and design. Overall, we found that the mock report was effective in communicating the recommended dose of a drug, but this recommendation was presented alongside information that was not understood or was unlikely to be utilised by prescribers. In particular, the aspects of the report viewed negatively by end-users largely related to a lack of familiarity with the pharmacological terminology used in the report, which hindered understanding and caused confusion. Involving prescribers early on in the process of designing decision support systems is likely to result in systems and outputs that are more useful, usable and accessible to users.

Genetic variants in transcription factors are associated with the pharmacokinetics and pharmacodynamics of metformin

One-third of type 2 diabetes patients do not respond to metformin. Genetic variants in metformin transporters have been extensively studied as a likely contributor to this high failure rate. Here, we investigate, for the first time, the effect of genetic variants in transcription factors on metformin pharmacokinetics (PK) and response. Overall, 546 patients and healthy volunteers contributed their genome-wide, pharmacokinetic (235 subjects), and HbA1c data (440 patients) for this analysis. Five variants in specificity protein 1 (SP1), a transcription factor that modulates the expression of metformin transporters, were associated with changes in treatment HbA1c (P < 0.01) and metformin secretory clearance (P < 0.05). Population pharmacokinetic modeling further confirmed a 24% reduction in apparent clearance in homozygous carriers of one such variant, rs784888. Genetic variants in other transcription factors, peroxisome proliferator-activated receptor-α and hepatocyte nuclear factor 4-α, were significantly associated with HbA1c change only. Overall, our study highlights the importance of genetic variants in transcription factors as modulators of metformin PK and response.

Evaluation of methods to identify the Klebsiella pneumoniae carbapenemase in Enterobacteriaceae

The Klebsiella pneumoniae carbapenem (KPC) beta-lactamase occurs in Enterobacteriaceae and can confer resistance to all beta-lactam agents including carbapenems. The enzyme may confer low-level carbapenem resistance, and the failure of susceptibility methods to identify this resistance has been reported. Automated and nonautomated methods for carbapenem susceptibility were evaluated for identification of KPC-mediated resistance. Ertapenem was a more sensitive indicator of KPC resistance than meropenem and imipenem independently of the method used. Carbapenemase production could be confirmed with the modified Hodge test.

Intralesional radioimmunotherapy in the treatment of malignant glioma: clinical and experimental findings

In the last two decades radioimmunotherapy has been used as an additional treatment option for malignant glioma in several centers. More than 400 patients have been reported, who were treated in the framework of different studies. Most of them received labelled antibodies to tenascin, an extracellular matrix-glycoprotein, which is expressed in high amounts in malignant gliomas. We report side effects and survival time of 46 patients, treated after surgical resection and conventional radiotherapy with intralesionally injected labelled (131-Iodine) antibodies to tenascin. Despite the fact, that many treatments have been performed, little is known about the distribution properties of labelled antibodies after injection in the tumour cavity. For an optimal effect labelled antibodies should be able to reach tumour cells, which have migrated into the surrounding tissue. We investigated the propagation velocity and area of distribution of labelled antibodies and their considerably smaller fragments after the injection in C6-gliomas of Wistar rats. Propagation increased with time and was significantly greater after injection of labelled fragments than after injection of labelled antibodies. According to our results labelled fragments might be better able to reach distant tumour cells in the peritumoural tissue of malignant gliomas than labelled antibodies.

Traffic hypoglycaemias and accidents in patients with diabetes mellitus treated with different antidiabetic regimens

OBJECTIVES

Insulin-treated patients with diabetes are at a higher risk than the general population in causing traffic accidents due to hypoglycaemias. Preceding investigations focused on insulin-treated patients and hypoglycaemia-induced accidents as "end-points". We studied the incidence of symptomatic hypoglycaemia and hypoglycaemia-induced accidents during driving and put it in relation to the different treatment modes of insulin therapy (Conventional Insulin Treatment = CT, Intensified Conventional Insulin Treatment = ICT, Continuous Subcutaneous Insulin Infusion = CSII) as well as to patients treated with oral hypoglycaemia-inducing agents and the two main types of diabetes mellitus.

SUBJECTS AND SETTING

We investigated 450 patients (122 treated with sulphonylureas, 151 with CT, 143 with ICT and 34 with CSII) by an anonymous questionnaire at different locations to avoid bias. A total of 176 persons had type 1 diabetes, 243 persons had type 2 diabetes, 31 subjects could not be classified.

RESULTS

Symptomatic hypoglycaemias during driving were rare events with an occurrence of 0.19-8.26 (minimal and maximal mean, depending on the mode of treatment), if given as hypoglycaemias per 100 000 km on one treatment regimen, or 0.02-0.63, if given as events per year driven. Their incidence increased significantly with the degree of "strictness" between the treatment groups, except between the patients treated with ICT and CSII. Hypoglycaemia-induced accidents are rare with 0.01-0.49, if given as events per 100 000 km and 0.007-0.01, if given as events per year driven. These differences were not significant. Significant confounders influencing the traffic safety of the patients were age, duration of diabetes and concomitant antihypertensive medication. Analysing the data in accordance with the type of diabetes revealed a significantly higher rate of hypoglycaemic events in patients with type 1 diabetes. The number of hypoglycaemia-induced accidents was considerably higher in this group, but failed slightly to reach statistical significance.

CONCLUSIONS

Hypoglycaemias during driving are rare events, their occurrence is significantly influenced by the treatment regimen and type of diabetes. Hypoglycaemia-induced accidents are extremely rare, presumably as a positive effect of patient education in our group.

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum

Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees C and pH 2, which was isolated from self-heating coal refuse piles and solfatara fields. Species of the genus Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. Our interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism. Here we have sequenced the 1,564,905-base-pair genome in just 7,855 sequencing reactions by using a new strategy. The 1,509 open reading frames identify Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related genes; however, evidence indicates that there has been much lateral gene transfer between Thermoplasma and Sulfolobus solfataricus, a phylogenetically distant crenarchaeon inhabiting the same environment. At least 252 open reading frames, including a complete protein degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.

MIPS: a database for genomes and protein sequences

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried, near Munich, Germany, continues its longstanding tradition to develop and maintain high quality curated genome databases. In addition, efforts have been intensified to cover the wealth of complete genome sequences in a systematic, comprehensive form. Bioinformatics, supporting national as well as European sequencing and functional analysis projects, has resulted in several up-to-date genome-oriented databases. This report describes growing databases reflecting the progress of sequencing the Arabidopsis thaliana (MATDB) and Neurospora crassa genomes (MNCDB), the yeast genome database (MYGD) extended by functional analysis data, the database of annotated human EST-clusters (HIB) and the database of the complete cDNA sequences from the DHGP (German Human Genome Project). It also contains information on the up-to-date database of complete genomes (PEDANT), the classification of protein sequences (ProtFam) and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database. These databases can be accessed through the MIPS WWW server (http://www. mips.biochem.mpg.de).

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Phototactic migration of Dictyostelium cells is linked to a new type of gelsolin-related protein

The molecular and functional characterization of a 125-kDa Ca2+-extractable protein of the Triton X-100-insoluble fraction of Dictyostelium cells identified a new type of a gelsolin-related molecule. In addition to its five gelsolin segments, this gelsolin-related protein of 125 kDa (GRP125) reveals a number of unique domains, two of which are predicted to form coiled-coil regions. Another distinct attribute of GRP125 concerns the lack of sequence elements known to be essential for characteristic activities of gelsolin-like proteins, i.e. the severing, capping, or nucleation of actin filaments. The subcellular distribution of GRP125 to vesicular compartments suggests an activity of GRP125 different from actin-binding, gelsolin-related proteins. GRP125 expression is tightly regulated and peaks at the transition to the multicellular pseudoplasmodial stage of Dictyostelium development. GRP125 was found indispensable for slug phototaxis, because slugs fail to correctly readjust their orientation in the absence of GRP125. Analysis of the GRP125-deficient mutant showed that GRP125 is required for coupling photodetection to the locomotory machinery of slugs. We propose that GRP125 is essential in the natural environment for the propagation of Dictyostelium spores. We also present evidence for further representatives of the GRP125 type in Dictyostelium, as well as in heterologous cells from lower to higher eukaryotes.

MIPS: a database for genomes and protein sequences

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database.

In vitro and in vivo porphyrin accumulation by C6 glioma cells after exposure to 5-aminolevulinic acid

Several malignant tissues synthesize endogenous porphyrins after exposure to 5-aminolevulinic acid (5-ALA). The present experiments have been designed to elucidate whether the C6 glioma cell, a model cell for human malignant glioma, similarly synthesizes porphyrins when exposed to 5-ALA, and whether specific synthesis occurs when C6 cells are inoculated into rat brains to form a tumor. In this situation the blood-brain barrier may interfere with 5-ALA availability, and spreading of porphyrins with edema outside the tumor may occur. Flow cytometry is used to determine the course of cell volume and porphyrin fluorescence intensities in cultured C6 cells which are incubated in 1 mM 5-ALA. For the induction of experimental brain tumors, 10(4) untreated C6 cells are inoculated into the brains of rats. After 9 days animals receive 100 mg 5-ALA/kg body weight. Brains are removed after 3, 6, or 9 h and frozen coronal sections obtained for H/E staining or fluorescence spectography. Cultured C6 cells show a linear increase of protoporphyrin IX fluorescence after exposure to 5-ALA, which begins to plateau after 85 min. Marked fluorescence is also observed in solid and infiltrating experimental tumor. However, faint fluorescence also occurs in normal tissue, basal pia, choroid plexus, and, more obviously, in white-matter tracts bordering the tumor (maximal distance: 1.5 +/- 0.7 mm). The observations demonstrate that C6 cells synthesize protoporphyrin IX after exposure to 5-ALA in vitro and in vivo. However, when utilizing 5-ALA for fluorescence detection or photodynamic therapy of brain tumors, attention should be paid to the possibility of protoporphyrin IX occurring outside the tumor.

Intraoperative detection of malignant gliomas by 5-aminolevulinic acid-induced porphyrin fluorescence

OBJECTIVE

Survival after surgery and radiotherapy for the treatment of malignant gliomas is linked to the completeness of tumor removal. Therefore, methods that permit intraoperative identification of residual tumor tissue may be of benefit. In a preliminary investigation, we have studied the value of fluorescent porphyrins that accumulate in malignant tissue after administration of a precursor (5-aminolevulinic acid) for labeling of malignant gliomas in nine patients.

METHODS

Three hours before the induction of anesthesia, 10 mg 5-aminolevulinic acid/kg body weight was administered orally. Intraoperatively, red porphyrin fluorescence was observed with a 455-nm long-pass filter after excitation with violet-blue (375-440 nm) xenon light and was verified by analysis of fluorescence spectra. Fluorescing and nonfluorescing samples taken from the tumor perimeters were examined histologically or used to study the photobleaching of porphyrins by excitation light and white light from the operating microscope. Plasma and erythrocyte porphyrin levels were determined by fluorescence photometry.

RESULTS

Normal brain tissue revealed no porphyrin fluorescence, whereas tumor tissue was distinguished by bright red fluorescence. For a total of 89 tissue biopsies, sensitivity was 85% and specificity was 100% for the detection of malignant tissue. For seven of nine patients, visible porphyrin fluorescence led to further resection of the tumor. Under operating light conditions, fluorescence decayed to 36% in 25 minutes for violet-blue light and in 87 minutes for white light. Plasma and erythrocyte porphyrin contents increased slightly, without exceeding normal levels.

CONCLUSION

Our observations suggest that 5-aminolevulinic acid-induced porphyrin fluorescence may label malignant gliomas safely and accurately enough to enhance the completeness of tumor removal.

DdLIM is a cytoskeleton-associated protein involved in the protrusion of lamellipodia in Dictyostelium

DdLim, a multi-domain member of the cysteine-rich family of LIM domain proteins, was isolated from Dictyostelium cells where it localizes in lamellipodia and at sites of membrane ruffling. The transcription and expression of DdLim are developmentally regulated, and the timing of its increased association with the actin cytoskeleton coincides with the acquisition in starved cells of a motile, chemotactic behavior. Vegetative cells that overexpress DdLim contain large lamella and exhibit ruffling at the cortex. The high frequency of large, multinucleated mutant cells found in suspension culture suggests that excess DdLim interferes with cytokinesis. DdLim was also identified as a protein in a Dictyostelium cell lysate that associated indirectly, but in a guanosine triphosphate-dependent manner, with a GST-rac1 fusion protein. The data presented suggest that DdLim acts as an adapter protein at the cytoskeleton-membrane interface where it is involved in a receptor-mediated rac1-signaling pathway that leads to actin polymerization in lamellipodia and ultimately cell motility.

Specific interaction of food proteins with apical membranes of the human intestinal cell lines Caco-2 and T84

A comparison between the intestinal epithelial cell lines Caco-2 and T84 was made to assess the influence of enterocytic differentiation on food protein binding capacities of the brush border membrane. Cell morphology and expression of brush border-associated enzymes were studied as differentiation markers. Food protein binding to isolated brush border membranes was measured with a dot blot chemiluminescence assay. Early at confluence, Caco-2 cells exhibited a more differentiated state compared to T84 cells. Brush border membranes of both cell lines bound gliadin peptides, beta-lactoglobulin and ovalbumin specifically. Binding capacities increased from gliadin peptides to ovalbumin to beta-lactoglobulin. There was correlation of membrane binding capacity with degree of cell differentiation. Due to their similarity to small intestinal epithelial cells, the colon carcinoma cell lines Caco-2 and T84 represent models for studying food protein-enterocytic brush border membrane interactions in relation to varying degrees of cell differentiation.

Myoelectric activity of the cecum and proximal loop of the ascending colon in cows after spontaneous cecal dilatation/dislocation

OBJECTIVE

To analyze myoelectric activity of the cecum and proximal loop of the ascending colon (PLAC) in cows after spontaneous cecal dilatation/dislocation (CDD) and compare it with that in healthy cows after surgical evacuation of the cecum.

ANIMALS

12 cows with spontaneous CDD and 6 healthy cows (group C). Cows with spontaneous CDD were retrospectively assigned to 2 groups: delayed recovery from surgery or recurrence (group A; n = 3), and normal recovery (group B; n = 9).

PROCEDURE

After surgical evacuation of the cecum, 8 pairs of bipolar, retrievable electrodes were implanted in the ileum, cecum, and PLAC. Cows were evaluated daily from postoperative day 1 to 7, using routine clinical methods and computer-based analysis of myoelectric activity of the cecum, and PLAC. Parameters of myoelectric activity included rate of spike bursts, duration of individual spike bursts, duration of overall spike burst activity per electrode, rate of propagated spike burst sequences, and ratio of orally propagated spike burst sequences.

RESULTS

Rate of spike bursts, duration of cecocolic spike burst activity, and ratio of orally to aborally propagated spike burst sequences did not vary among groups during the 7-day recording period. However, cows with delayed recovery had a typical, uniform pattern of myoelectric activity of the cecum and PLAC at days 1 and 2 after surgery that consisted of repeated, propagated spike burst sequences, made up of spike bursts of significantly (P < 0.05) increased duration at postsurgical day 1 and substantially prolonged duration at postsurgical day 2, interrupted by periods of little or no activity.

CONCLUSION

Delayed recovery and recurrence of CDD in cows after spontaneous CDD is not caused by hypomotility of the cecum and PLAC.

CLINICAL RELEVANCE

Postoperative treatment, intended to reduce recurrence of CDD or delayed recovery after surgical evacuation of the cecum, should address propagation of digesta in the spiral colon.

In vivo fluorescence kinetics of porphyrins following intravesical instillation of 5-aminolaevulinic acid in normal and tumour-bearing rat bladders

The fluorescence kinetics of protoporphyrin IX (PPIX) following intravesical instillation of 5-aminolaevulinic acid (5-ALA) have been studied in vivo in a rat bladder tumour model. 5-ALA dissolved in NaHCO3 was intravesically instilled for 60 min in tumour-bearing and normal bladders of Wistar rats. The fluorescence was excited with the violet lines of a Kr(+)-laser and recorded in vivo by means of a fibre coupled optical multichannel analyser. The fluorescence emission bands of PPIX at lambda = 636 nm and lambda = 708 nm were detected in normal and tumorous urothelium after only 30 min. The maximum fluorescence intensity was obtained in tumorous and normal urothelium 3-4 h after instillation. The ratio of the fluorescence intensity in tumorous to normal urothelium decreased continuously from four to about two during the time range of 6 h. PPIX fluorescence following 5-ALA instillation could also be observed in kidney and liver. Fluorescence from further porphyrin species with emission bands at lambda = 617 nm and lambda = 682 nm was detected in the bladder, indicating an efflux of hydrophilic porphyrins from the hepatic pathway.

Control of children's stuttering with response-contingent time-out: behavioral, perceptual, and acoustic data

Many stuttering treatments incorporate contingencies for stuttering that are thought to contribute to treatment effectiveness. One contingency used in a number of treatment programs for children is time-out (TO) from speaking. However, although TO has been shown to control stuttering in adults there are no clear demonstrations of this effect in children. One aim of the present study was to demonstrate in the laboratory that TO reduces stuttering in children. Three school-age children spoke in a single-subject ABA experiment. In the B phase, a red light was illuminated for 5 seconds when the subject stuttered, during which time the subject stopped talking. Two of the three children showed clear reductions in stuttering in response to TO. The second aim of the study was to detect whether the children who responded to To adopted an unusual speech pattern in order to control their stuttering. Listeners did not detect any differences between the perceptually stutter-free speech of baseline conditions and that of TO conditions, and a subsequent acoustic analysis revealed a reduction in the variability of vowel duration during TO in one subject and no changes in the other. The theoretical and clinical implications of the findings are discussed.

Interaction of a Dictyostelium member of the plastin/fimbrin family with actin filaments and actin-myosin complexes

A protein purified from cytoskeletal fractions of Dictyostelium discoideum proved to be a member of the fimbrin/plastin family of actin-bundling proteins. Like other family members, this Ca(2+)-inhibited 67-kDa protein contains two EF hands followed by two actin-binding sites of the alpha-actinin/beta-spectrin type. Dd plastin interacted selectively with actin isoforms: it bound to D. discoideum actin and to beta/gamma-actin from bovine spleen but not to alpha-actin from rabbit skeletal muscle. Immunofluorescence labeling of growth phase cells showed accumulation of Dd plastin in cortical structures associated with cell surface extensions. In the elongated, streaming cells of the early aggregation stage, Dd plastin was enriched in the front regions. To examine how the bundled actin filaments behave in myosin II-driven motility, complexes of F-actin and Dd plastin were bound to immobilized heavy meromyosin, and motility was started by photoactivating caged ATP. Actin filaments were immediately propelled out of bundles or even larger aggregates and moved on the myosin as separate filaments. This result shows that myosin can disperse an actin network when it acts as a motor and sheds light on the dynamics of protein-protein interactions in the cortex of a motile cell where myosin II and Dd plastin are simultaneously present.

Wavelength dependent photodynamic effects on chemically induced rat bladder tumors following intravesical instillation of 5-aminolevulinic acid

PURPOSE

The aim of the study was to determine photodynamic effects in chemically induced rat bladder tumors after intravesical instillations of 5-aminolevulinic acid (5-ALA) and PDT-dependence on laser wavelength and light dose.

MATERIAL AND METHODS

Following intravesical instillation of a 5-ALA solution (40 mg 5-ALA in isotonic saline and sodium-bicarbonate) rat bladder tumors have been treated with integral irradiation using laser light at wavelengths of lambda = 630 nm and lambda = 635 nm in a light dose range of 15 to 100 J/cm2.

RESULTS

A significantly higher amount of necrosis including damage of normal urothelium was obtained in rat bladder tumors using laser light at lambda = 635 nm.

CONCLUSIONS

For 5-ALA assisted photodynamic treatment of superficial bladder cancer in patients the irradiation wavelength of lambda = 635 nm is recommended.

[Retropharyngeal abscess in cattle. A case report]

This case report describes history, clinical, laboratory, radiographic, and endoscopic findings, therapy, and outcome of a 5-year-old cow, suffering from retropharyngeal abscessation. Clinical findings at admission included elevated body temperature, head and neck held in extended position, excessive salivation, swelling of the retropharyngeal area, and slight inspiratory noise. Radiographic and endoscopic examination confirmed the tentative diagnosis of retropharyngeal abscessation. Treatment consisted of parenteral application of procaine-penicillin for 10 days and local application of linseed rubefacients for 2 weeks. At that time, abscessation had developed. The abscess was subsequently surgically, approached by a modified Whitehouse approach. During this procedure, the abscess drained into the oropharynx, allowing interruption of surgery. Five months later, clinical, radiographic, and endoscopic follow-up examination revealed complete healing of the retropharyngeal abscess.

Pharmacokinetics of 5-aminolevulinic-acid-induced porphyrins in tumour-bearing mice

Photodynamic therapy and photodynamic diagnosis help to support efficient treatment of superficial and early-stage cancer. During the last few years, 5-aminolevulinic acid (5-ALA), a precursor of haemoglobin in the haem biosynthetic pathway, was used to stimulate endogenous porphyrin production. In the following the time dependence of 5-ALA-induced porphyrin concentration will be investigated on several tissues in an in-vivo tumour model. 5-ALA was administered intravenously at a concentration of 50 mg-1 body weight. According to a certain time schedule the animals were sacrificed and 12 different organs as well as the tumour were removed. During excitation with the violet light of a Kr+ laser, porphyrin fluorescence spectra in the range 550-750 nm could be detected on the tissue samples. The intensity of the emission spectra at lambda = 635 +/- 2 nm was taken as a measure of the porphyrin concentration. All tissues showed porphyrin fluorescence. Brightest fluorescence was found on the tumour. A maximum contrast of the fluorescence intensity between the tumour and the non-malignant organs of up to 30 was observed at 4-6 h post-injection. The kinetics of the porphyrin concentration depend on the organ. Simple mathematical models will be derived and discussed.

Stress-induced tyrosine phosphorylation of actin in Dictyostelium cells and localization of the phosphorylation site to tyrosine-53 adjacent to the DNase I binding loop

Actin is known to be phosphorylated at tyrosine, serine, or threonine residues in various cells. In cells of Dictyostelium discoideum, a rise in the tyrosine phosphorylation of actin is observed in response to ATP depletion. An actin fraction rich in phosphotyrosine was obtained by chromatography on the weak anion exchanger Mono-P. Mass spectrometry and amino acid sequencing of protease cleavage products indicated that a single tyrosine residue was phosphorylated. Localization of this residue to position 53 of the actin sequence attributed the modification to a site that is critical for the capability of actin to polymerize. Induction of the tyrosine phosphorylation by heat shock and Cd2+ ions indicates that this modification of actin is implicated in the response of Dictyostelium cells to stress.

alpha-D-glucuronidases from the xylanolytic thermophiles Clostridium stercorarium and Thermoanaerobacterium saccharolyticum

alpha-D-Glucuronidases were purified from the xylanolytic thermophiles Clostridium stercorarium and Thermoanaerobacterium saccharolyticum. This enzyme activity was found to be intracellular in each organism, with T. saccharolyticum producing much greater total activity. The specific activities of the purified enzymes (10 U mg-1 T. saccharolyticum; 1.7 U mg-1 C. stercorarium) differed by a factor of approximately 5. For the determination of enzyme activities, 4-O-methyl-alpha-D-glucuronosyl-xylotriose was used as a substrate and the glucuronic acid released by alpha-D-glucuronidase action was quantified by a colorimetric procedure. 4-O-Methyl-alpha-D-glucuronosyl-xylotriose was the hydrolysis product that accumulated after exhaustive degradation of 4-O-methyl-alpha-D-glucuronoxylan with xylanases of C. stercorarium. Hydrolysis of side chains in high-molecular-mass glucuronoxylan could not be detected. Neither of the enzymes was able to hydrolyse the chromogenic aryl-substrate p-nitrophenyl-alpha-D-glucuronoside. Both alpha-D-glucuronidases have a dimeric structure, with monomeric molecular masses of 72 and 76 kDa for C. stercorarium and of 71 kDa for T. saccharolyticum. The pI was estimated to be 4.3 for each enzyme. While both enzymes exhibited a similar pH optimum (pH 5.5-6.5) they differed in their thermostabilities. At 60 degrees C, half-lives of 14 and 2.5 h, respectively, were determined for the alpha-D-glucuronidases of C. stercorarium and T. saccharolyticum. This description of alpha-D-glucuronidase activity in thermophilic anaerobic bacteria extends our knowledge of these enzymes, previously purified and characterized only in fungi.

Exogenous testosterone differentially affects myelination and neurone soma sizes in the brain of canaries

We assessed the temporal and functional relationship of myelin maturation and of neuronal development in the telencephalic song motor centres of the canary at different developmental stages. Brain differentiation was modulated by exogenous testosterone, its effects on song quality were also monitored. Myelin maturation was studied by using computer aided analysis of silver impregnated brain sections, whereas the differentiation of neurones was determined by measuring neuronal soma sizes. At an early developmental stage, testosterone triggers growth of neurones but does not affect myelination. At a later developmental stage, both neurone soma sizes and myelination are enhanced by testosterone.

Antioestrogen inhibits myelination in brains of juvenile Zebra finches

The effects of the antioestrogen Keoxifene on the ontogenetic process of myelination, on the differentiation of neurones of telencephalic song motor centres, on cerebellar structures and on behaviour were studied in male Zebra finches. Brain differentiation was studied by using computer aided analysis of silver impregnated brain sections and by measuring soma sizes of neurones after Nissl staining. An antioestrogen induced inhibition of myelination could be detected in the song motor centre robust nucleus of the archistriatum (RA) and in the cerebellum, whereas the region magnocellular nucleus of the anterior neostriatum (MAN) showed no difference between treated birds and controls.

Improving the diet of under fives in a deprived inner city practice

This paper reports the introduction of a programme of dietary education to a selected group of young mothers living in a deprived inner city area. The programme was devised by a general practitioner and practice health visitors in collaboration with two hospital dietitians. A diary was used to provide data on diet, food choice, shopping habits, eating together, and planning and frequency of meals. These were included in a list of twelve 'desirable' food groups and three organisational skills, thus providing an individual syllabus for teaching, and a means of assessing the intervention. At the start of the study milk, fruit, vegetables and protein containing iron were common dietary omissions. However, the results show that these foods were an established part of the children's diets following the intervention. The dietary diaries provided a successful means of analysis, and the teaching programme is continuing in this practice. The limitations of such a small study are acknowledged, and a long-term controlled study is suggested.