A multiscale orchestrated computational framework to reveal emergent phenomena in neuroblastoma

Neuroblastoma is a complex and aggressive type of cancer that affects children. Current treatments involve a combination of surgery, chemotherapy, radiotherapy, and stem cell transplantation. However, treatment outcomes vary due to the heterogeneous nature of the disease. Computational models have been used to analyse data, simulate biological processes, and predict disease progression and treatment outcomes. While continuum cancer models capture the overall behaviour of tumours, and agent-based models represent the complex behaviour of individual cells, multiscale models represent interactions at different organisational levels, providing a more comprehensive understanding of the system. In 2018, the PRIMAGE consortium was formed to build a cloud-based decision support system for neuroblastoma, including a multi-scale model for patient-specific simulations of disease progression. In this work we have developed this multi-scale model that includes data such as patient's tumour geometry, cellularity, vascularization, genetics and type of chemotherapy treatment, and integrated it into an online platform that runs the simulations on a high-performance computation cluster using Onedata and Kubernetes technologies. This infrastructure will allow clinicians to optimise treatment regimens and reduce the number of costly and time-consuming clinical trials. This manuscript outlines the challenging framework's model architecture, data workflow, hypothesis, and resources employed in its development.

A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources

OBJECTIVE

The Genomic Medicine Working Group of the National Advisory Council for Human Genome Research virtually hosted its 13th genomic medicine meeting titled "Developing a Clinical Genomic Informatics Research Agenda". The meeting's goal was to articulate a research strategy to develop Genomics-based Clinical Informatics Tools and Resources (GCIT) to improve the detection, treatment, and reporting of genetic disorders in clinical settings.

MATERIALS AND METHODS

Experts from government agencies, the private sector, and academia in genomic medicine and clinical informatics were invited to address the meeting's goals. Invitees were also asked to complete a survey to assess important considerations needed to develop a genomic-based clinical informatics research strategy.

RESULTS

Outcomes from the meeting included identifying short-term research needs, such as designing and implementing standards-based interfaces between laboratory information systems and electronic health records, as well as long-term projects, such as identifying and addressing barriers related to the establishment and implementation of genomic data exchange systems that, in turn, the research community could help address.

DISCUSSION

Discussions centered on identifying gaps and barriers that impede the use of GCIT in genomic medicine. Emergent themes from the meeting included developing an implementation science framework, defining a value proposition for all stakeholders, fostering engagement with patients and partners to develop applications under patient control, promoting the use of relevant clinical workflows in research, and lowering related barriers to regulatory processes. Another key theme was recognizing pervasive biases in data and information systems, algorithms, access, value, and knowledge repositories and identifying ways to resolve them.

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Background

Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology.

Results

We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified.

Conclusions

We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01108-y.

Abstract 439: Trajectory Analysis of Left Ventricular Dimensions From Biobank Data Uncovers Novel Genetic Associations

Background: Approximately 6 million adults in the United States have heart failure. The progression of heart failure is variable arising from differences in sex, age, genetic background including ancestry, and medication response. Many population-based genetic studies of heart failure have been cross-sectional in nature, failing to gain additional power from longitudinal analyses. As heart failure is known to change over time, using longitudinal data trajectories as a quantitative trait will increase power in genome wide association studies (GWAS).

Methods: We used the electronic health record in a racially and ethnically diverse medical biobank from a single, metropolitan US center. We used whole genome data from 896 unrelated participants analyzed, including 494 who had at least 1 electrocardiogram and 324 who had more than 1 echocardiogram (average of 3 observations per person). A mixture model based semiparametric latent growth curve model was used to cluster outcome measures used for genome-wide analyses.

Results: GWAS on the trajectory probability of QTc interval identified significant associations with variants in regulatory regions proximal to the WLS gene, which encodes Wntless, a Wnt ligand secretion mediator. WLS was previously associated with QTc and myocardial infarction, thus confirming the power of the method. GWAS on the trajectory probability of left ventricular diameter (LVIDd) identified significant associations with variants in regulatory regions near MYO10 , which encodes unconventional Myosin-10. MYO10 was previously associated with obesity and metabolic syndrome.

Conclusions: This is the first study to show an association with variants in or near MYO10 and left ventricular dimension changes over time. Further, we found that using trajectory probabilities can provide increased power to find novel associations with longitudinal data. This reduces the need for larger cohorts, and increases yield from smaller, well-phenotyped cohorts, such as those found in biobanks. This approach should be useful in the study of rare diseases and underrepresented populations.

Pathogenic and Uncertain Genetic Variants Have Clinical Cardiac Correlates in Diverse Biobank Participants

Background

Genome sequencing coupled with electronic heath record data can uncover medically important genetic variation. Interpretation of rare genetic variation and its role in mediating cardiovascular phenotypes is confounded by variants of uncertain significance.

Methods and Results

We analyzed the whole genome sequence of 900 racially and ethnically diverse biobank participants selected from a single US center. Participants were equally divided among European, African, Hispanic, and mixed races/ethnicities. We evaluated the American College of Medical Genetics and Genomics medically actionable list of 59 genes, focusing on the cardiac genes. Variation was interpreted using the most recent reports in ClinVar, a database of medically relevant human variation. We identified 19 individuals with pathogenic or likely pathogenic variants in cardiac actionable genes (2%) and found evidence of related clinical correlates in the electronic health record. Participants of African ancestry, compared with those of European ancestry, had more variants of uncertain significance in the medically actionable genes including the 30 cardiac actionable genes, even when normalized to total variant count per person. Longitudinal measures of left ventricle size from ≈400 biobank participants (1723 patient‐years) were correlated with genetic findings. The presence of ≥1 uncertain variant in the actionable cardiac genes and a cardiomyopathy diagnosis correlated with increased left ventricular internal diameter in diastole and in systole. In particular, MYBPC3 was identified as a gene with excess variants of uncertain significance.

Conclusions

These data indicate that a subset of uncertain genetic variants may confer risk and should not be considered benign.

The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype

The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome‐wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single‐nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA‐B herpes zoster (shingles) association and discovered a novel zoster‐associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).

Assessment of myocardial metabolic flexibility and work efficiency in human type 2 diabetes using 16-[18F]fluoro-4-thiapalmitate, a novel PET fatty acid tracer

Altered myocardial fuel selection likely underlies cardiac disease risk in diabetes, affecting oxygen demand and myocardial metabolic flexibility. We investigated myocardial fuel selection and metabolic flexibility in human type 2 diabetes mellitus (T2DM), using positron emission tomography to measure rates of myocardial fatty acid oxidation {16-[(18)F]fluoro-4-thia-palmitate (FTP)} and myocardial perfusion and total oxidation ([(11)C]acetate). Participants underwent paired studies under fasting conditions, comparing 3-h insulin + glucose euglycemic clamp conditions (120 mU·m(-2)·min(-1)) to 3-h saline infusion. Lean controls (n = 10) were compared with glycemically controlled volunteers with T2DM (n = 8). Insulin augmented heart rate, blood pressure, and stroke index in both groups (all P < 0.01) and significantly increased myocardial oxygen consumption (P = 0.04) and perfusion (P = 0.01) in both groups. Insulin suppressed available nonesterified fatty acids (P < 0.0001), but fatty acid concentrations were higher in T2DM under both conditions (P < 0.001). Insulin-induced suppression of fatty acid oxidation was seen in both groups (P < 0.0001). However, fatty acid oxidation rates were higher under both conditions in T2DM (P = 0.003). Myocardial work efficiency was lower in T2DM (P = 0.006) and decreased in both groups with the insulin-induced increase in work and shift in fuel utilization (P = 0.01). Augmented fatty acid oxidation is present under baseline and insulin-treated conditions in T2DM, with impaired insulin-induced shifts away from fatty acid oxidation. This is accompanied by reduced work efficiency, possibly due to greater oxygen consumption with fatty acid metabolism. These observations suggest that improved fatty acid suppression, or reductions in myocardial fatty acid uptake and retention, could be therapeutic targets to improve myocardial ischemia tolerance in T2DM.

Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index

Phenome-wide association studies (PheWAS) have demonstrated utility in validating genetic associations derived from traditional genetic studies as well as identifying novel genetic associations. Here we used an electronic health record (EHR)-based PheWAS to explore pleiotropy of genetic variants in the fat mass and obesity associated gene (FTO), some of which have been previously associated with obesity and type 2 diabetes (T2D). We used a population of 10,487 individuals of European ancestry with genome-wide genotyping from the Electronic Medical Records and Genomics (eMERGE) Network and another population of 13,711 individuals of European ancestry from the BioVU DNA biobank at Vanderbilt genotyped using Illumina HumanExome BeadChip. A meta-analysis of the two study populations replicated the well-described associations between FTO variants and obesity (odds ratio [OR] = 1.25, 95% Confidence Interval = 1.11-1.24, p = 2.10 × 10(-9)) and FTO variants and T2D (OR = 1.14, 95% CI = 1.08-1.21, p = 2.34 × 10(-6)). The meta-analysis also demonstrated that FTO variant rs8050136 was significantly associated with sleep apnea (OR = 1.14, 95% CI = 1.07-1.22, p = 3.33 × 10(-5)); however, the association was attenuated after adjustment for body mass index (BMI). Novel phenotype associations with obesity-associated FTO variants included fibrocystic breast disease (rs9941349, OR = 0.81, 95% CI = 0.74-0.91, p = 5.41 × 10(-5)) and trends toward associations with non-alcoholic liver disease and gram-positive bacterial infections. FTO variants not associated with obesity demonstrated other potential disease associations including non-inflammatory disorders of the cervix and chronic periodontitis. These results suggest that genetic variants in FTO may have pleiotropic associations, some of which are not mediated by obesity.

Relating centromeric topography in fixed human chromosomes to α-satellite DNA and CENP-B distribution

Despite extensive analyses on the centromere and its associated proteins, detailed studies of centromeric DNA structure have provided limited information about its topography in condensed chromatin. We have developed a method with correlative fluorescence light microscopy and atomic force microscopy that investigates the physical and structural organization of α-satellite DNA sequences in the context of its associated protein, CENP-B, on human metaphase chromosome topography. Comparison of centromeric DNA and protein distribution patterns in fixed homologous chromosomes indicates that CENP-B and α-satellite DNA are distributed distinctly from one another and relative to observed centromeric ridge topography. Our approach facilitates correlated studies of multiple chromatin components comprising higher-order structures of human metaphase chromosomes.

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology.

Toward a roadmap in global biobanking for health

Biobanks can have a pivotal role in elucidating disease etiology, translation, and advancing public health. However, meeting these challenges hinges on a critical shift in the way science is conducted and requires biobank harmonization. There is growing recognition that a common strategy is imperative to develop biobanking globally and effectively. To help guide this strategy, we articulate key principles, goals, and priorities underpinning a roadmap for global biobanking to accelerate health science, patient care, and public health. The need to manage and share very large amounts of data has driven innovations on many fronts. Although technological solutions are allowing biobanks to reach new levels of integration, increasingly powerful data-collection tools, analytical techniques, and the results they generate raise new ethical and legal issues and challenges, necessitating a reconsideration of previous policies, practices, and ethical norms. These manifold advances and the investments that support them are also fueling opportunities for biobanks to ultimately become integral parts of health-care systems in many countries. International harmonization to increase interoperability and sustainability are two strategic priorities for biobanking. Tackling these issues requires an environment favorably inclined toward scientific funding and equipped to address socio-ethical challenges. Cooperation and collaboration must extend beyond systems to enable the exchange of data and samples to strategic alliances between many organizations, including governmental bodies, funding agencies, public and private science enterprises, and other stakeholders, including patients. A common vision is required and we articulate the essential basis of such a vision herein.

Contributions of dysglycaemia, obesity, and insulin resistance to impaired endothelium-dependent vasodilation in humans

BACKGROUND

Individual effects of hyperglycaemia and obesity to impair vascular health are recognized. However, the relative contributions of dysglycaemia versus other obesity-related traits to vascular dysfunction have not been systematically evaluated.

METHODS

We undertook a cross-sectional evaluation of factors contributing to vascular function in 271 consecutive subjects, categorized as non-obese normal glucose tolerant (n = 115), non-obese dysglycaemic (n = 32), obese normal glucose tolerant (n = 57), obese dysglycaemic (n = 38), or type 2 diabetic (n = 29). Vascular function was measured invasively as leg blood flow responses to methacholine chloride, an endothelium-dependent vasodilator. Categorical and continuous analyses were carried out to assess the contributions of hyperglycaemia to vascular dysfunction.

RESULTS

Even among normoglycaemic subjects, obese subjects had impaired vascular function compared to non-obese subjects (p = 0.004). Vascular function was also impaired in non-obese dysglycaemic subjects (p = 0.04 versus non-obese normoglycaemic subjects), to a level comparable to normoglycaemic obese subjects. Within obese subject groups, gradations of dysglycaemia including the presence of diabetes were not associated with further worsening of these vascular responses beyond the effect of obesity alone (p = not significant comparing all obese groups, p < 0.001 versus lean normoglycaemic subjects). After univariate and multivariable modelling analyses we found that effects of glycaemia were less powerful than effects of insulin resistance and obesity on vascular dysfunction.

CONCLUSIONS

Dysglycaemia contributes to impaired vascular function in non-obese subjects, but obesity and insulin resistance are more important determinants of vascular function in obese and diabetic subjects.

Extraction of RNA from dictyostelium

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. The extraction of RNA from Dictyostelium is relatively easy because RNA levels are very high in comparison to DNA levels (i.e., ~40 times higher). Certain commercially available kits, such as Trizol (Invitrogen) and RNeasy (QIAGEN) have been used successfully, although lysis conditions need to be adjusted. RNA samples are stable for several years at -80°C in diethylpyrocarbonate (DEPC)-treated H(2)O. For longer-term storage, the RNA pellet can be stored in 100% ethanol at -80°C. Such samples are suitable for Northern blots, reverse transcriptase-polymerase chain reaction (RT-PCR), and microarray analysis of gene expression.

Making permanent stocks of dictyostelium

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrients are depleted from the immediate environment of the cells. Dictyostelium can be grown axenically or in the presence of bacteria, either on agar plates or in suspension. Because Dictyostelium growth rates are relatively slow compared to those of bacteria or yeast, laboratories commonly maintain stocks of growing cultures in order to start experiments rapidly. However, it is important to remember that the genome of Dictyostelium, like that of any living organism, is subject to genetic modification. It is well documented that cell lines that are kept in culture for an extended period of time exhibit undesirable changes that yield unreliable experimental results (Hughes et al. 2007). Dictyostelium strains from different laboratories are known to contain various large genome duplications, presumably due to clone selection. Thus, good handling of the cells is essential. To obtain consistent results, new cultures must be started every 2-4 wk, and cultures should never be allowed to grow beyond 4 × 10(6) cells/mL. If overgrowth occurs, a new culture should be started. This protocol describes two methods for preparing long-term stocks of Dictyostelium, either as frozen cells or as spores.

Transformation of dictyostelium with plasmid DNA by calcium phosphate precipitation

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. Calcium phosphate precipitation is a commonly used method for DNA-mediated transformation in Dictyostelium. Calcium phosphate precipitation produces high-copy-number transformants and is often used for overexpression experiments in conjunction with the G418 resistance gene, which needs to be present at high levels to produce efficient selection.

Growth and maintenance of dictyostelium cells

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a "social ameba" because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. Dictyostelium also provides an excellent model system for the study of phagocytosis, the molecular basis of various human diseases, and the mechanisms of drug action. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Most Dictyostelium strains used in the laboratory can be grown either with bacteria or in axenic medium. When grown in the presence of bacteria, cells double approximately every 4 h, whereas axenically grown cells double more slowly, every 8-12 h. The cells can be grown in a standard microbiology incubator or on the laboratory bench, provided the room temperature is consistently ~22°C. This protocol describes a variety of methods for growing and maintaining Dictyostelium.

Selection of dictyostelium transformants

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. Two commonly used methods for DNA-mediated transformation in Dictyostelium are calcium phosphate precipitation and electroporation. Transformants can then be selected in liquid media or on bacterial plates. The latter method reduces the chances of contamination because the cells are grown in buffered agar containing live or dead bacteria, rather than in a rich broth. This method also facilitates the isolation of clones from transformations because each transformant produces a single colony on the plate instead of the pools of transformants obtained in liquid culture. For gene ablation experiments, it is important to obtain a minimum of two independent clones with the same phenotype to exclude the possibility that the phenotype is due to a nonspecific mutation.

Multicellular development of dictyostelium

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a "social ameba" because it can form a multicellular structure when nutrients are depleted from the immediate environment of the cells. In the laboratory, this is accomplished simply by replacing the growth medium with a buffer solution. For best results, it is important to harvest the cells while they are still in exponential growth (1-4 × 10(6) cells/mL). At high cell density, many of the cells in a culture will have initiated development, thus yielding asynchronous development. Dictyostelium cells can be developed on solid media, either on filter paper or on KK2 plates. If only the early stages of development are important (e.g., to study chemotaxis), cells can be developed in suspension. Under these conditions, cells will only progress through the first 6-8 h of development. Addition of cAMP pulses to the starved suspension culture will allow development to progress up to the 12-h stage, corresponding to the beginning of culmination.

Transformation of dictyostelium with plasmid DNA by electroporation

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. This protocol describes the use of electroporation for DNA-mediated transformation in Dictyostelium.

Dictyostelium discoideum: The Social Ameba

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a "social ameba" because it can form a multicellular structure when nutrient conditions are limiting. D. discoideum and related organisms, known as the Dictyostelia, have been studied for almost 150 years. The cellular and molecular aspects of their multicellular lifestyle have been studied in detail, and general principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from this work and have been found to be conserved across all eukaryotes. The bacteriovore nature of the unicellular stage provides an excellent model in which to study phagocytosis and the mechanisms of bacterial virulence. D. discoideum has also been used successfully to explore the molecular basis of various human diseases, as well as the mechanisms of drug action and the pathways that lead to resistance to certain therapeutic agents. The availability of a complete genome sequence has further widened the scope of studies using D. discoideum. A large potential for secondary metabolism has become apparent, which opens the door to discovering new compounds with potential medical applications. Numerous putative orthologs of genes responsible for diseases in humans, but whose molecular functions are still uncharacterized, are present in the D. discoideum genome. Finally, the availability of community resources, including the genome database dictyBase and the Dicty Stock Center, makes D. discoideum an easily accessible and powerful model organism to study.

Extraction of DNA from dictyostelium

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. Extraction of genomic DNA is used to clone gene fragments and for analysis of mutants to determine the site of vector integration. Because Dictyostelium cells contain relatively high levels of carbohydrate and nucleases, commercially available DNA preparation kits are not very successful. The DNA isolated according to the following protocol is suitable for digestion by restriction enzymes, amplification by polymerase chain reaction (PCR), and Southern blotting.

Simvastatin Modulates Angiotensin II Signaling Pathway by Preventing Rac1-Mediated Upregulation of p27

Recent experimental observations have suggested that statins may exert modulatory effects on a number of pathobiological processes beyond their cholesterol-lowering properties. Some of the pleiotropic effects of statins seem to be mediated by their ability to block the synthesis of isoprenoid intermediates, which serve as important lipid attachments required for the proper function and activation of the small GTP-binding proteins. The current study explored the modulatory effects of simvastatin (SMV) on the angiotensin II (Ang II)-induced Rac1-mediated, upregulation of cyclin-dependent kinase inhibitor p27. Ang II (100 nM) stimulation of rat mesangial cells induced a significant increase in p27 protein expression. Co-treatment of cells with SMV (1 microM) inhibited Ang II-induced upregulation of p27 protein. Addition of mevalonate (200 microM) or geranylgeranyl pyrophosphate (5 microM) reversed the inhibitory effect of SMV on p27 protein expression, suggesting that the effect of SMV is geranylgeranyl dependent. This study also provides evidence for a sequential link between Ang II stimulation and downstream activation of Rac1, intracellular H2O2 production, and Akt kinase leading to upregulation of p27 protein in mesangial cells. It was also shown that SMV, by inhibiting Rac1 activity, reversed Ang II-induced increase in intracellular H2O2 production, Akt activation, and p27 protein expression. The data presented in this study not only elucidate Ang II-mediated signaling cascade in mesangial cells but also demonstrate for the first time the modulatory effects of SMV on Ang II-induced signaling pathway at the cell cycle level.

The Gene Ontology (GO) database and informatics resource

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Percutaneous mitral valve dilatation with the Multi-Track System

We developed the Multi-Track System for percutaneous mitral valvotomy and described the preliminary results in 1995. Here we report the first 100 consecutive cases after the original publication. Two separate balloon catheters are positioned on a single guidewire. The first catheter, with only a distal guidewire lumen, is introduced into the vein and then advanced into the mitral orifice. Subsequently, a rapid exchange balloon catheter running on the same guidewire is inserted and lined up with the first catheter so the two are positioned side by side. Both balloons are then inflated simultaneously. Age of the patients was 31 +/- 12.8 years and weight 50 +/- 14 kg. Valve area increased 0.75 +/- 0.22 cm(2) to 2.00 +/- 0.32 cm(2)and mean left atrial pressure dropped from 27 +/- 8 to 11 +/- 5 mm Hg. One patient had significant mitral insufficiency after dilatation, which did not require surgery. The Multi-Track System is a valid alternative to the existing procedures for the treatment of mitral stenosis and uses simpler and less costly catheters. Cathet. Cardiovasc. Intervent. 48:178-183, 1999.

Cancer incidence rate and mortality rate in sickle cell disease patients at Howard University Hospital: 1986-1995

The incidence of cancer in patients with sickle cell disease (SCD) is not known. The 10-year follow-up data on 696 patients with SCD was analyzed at our institution in order to determine the cancer incidence and cancer mortality rates. The age range was 18 to 79 years, with a mean age of 28.8 years. There were 377 females and 319 males. The median follow-up was 3 years. Five patients developed cancer during this period. The cancer incidence rate was 5/2,864 or 1.74 per 1,000 patient years. The 95% CI was 0.64 to 4.32 per 1,000 patient years. There were 68 deaths with 3 being due to cancer. The cancer mortality rate was 3/2,873 or 1.04 cases per 1,000 patient years. Our data represent the first published paper that the authors are aware of, where the cancer incidence and mortality rates have been calculated for any group of patients with SCD.

Effect of intracoronary saline infusion on dissection during excimer laser coronary angioplasty: a randomized trial. The Percutaneous Excimer Laser Coronary Angioplasty (PELCA) Investigators

OBJECTIVES

We sought to evaluate whether intracoronary saline infusion during excimer laser coronary angioplasty decreases the incidence of significant laser-induced coronary artery dissections.

BACKGROUND

Despite procedural success rates > 90%, coronary artery dissections occur in 17% to 27% of excimer laser coronary angioplasty procedures. Excimer laser irradiation of blood results in vapor bubble formation and acoustomechanical trauma to the vessel wall. Saline infusion into a coronary artery may minimize blood irradiation and consequent arterial wall damage.

METHODS

In this prospective, randomized, controlled study, consecutive patients undergoing excimer laser coronary angioplasty were randomly assigned to conventional laser irradiation in a blood medium or to laser irradiation with blood displacement by intracoronary saline infusion. In the patients randomized to intracoronary saline infusion, prewarmed normal saline was injected through the coronary artery guide catheter at a rate of 1 to 2 ml/s using a power injector. The incidence and severity of dissection after excimer laser ablation were evaluated in a core laboratory by angiographers with no knowledge of treatment assignment. The severity of coronary artery dissection was rated on an ordinal scale of 1 to 5. Dissections of grade 2 or higher were considered significant.

RESULTS

The mean (+/- SE) dissection grade after laser angioplasty in patients treated with intracoronary saline infusion was 0.43 +/- 0.13 compared with 0.91 +/- 0.26 in patients undergoing laser angioplasty in a blood medium. The incidence of significant dissection was 7% in saline-treated patients compared with 24% in conventionally treated patients (p < 0.05). No significant complications were associated with saline infusion.

CONCLUSIONS

Intracoronary saline infusion should be incorporated into all excimer laser coronary angioplasty procedures.

Dysphagia due to secondary achalasia as an early manifestation of squamous cell carcinoma

A 59-year-old man, a smoker, presented with features of airflow obstruction due to squamous cell carcinoma of central airways mimicking chronic obstructive airways disease. He also had pronounced dysphagia. Computed tomographic and magnetic resonance imaging scans showed mediastinal tumour invasion but no direct oesophageal involvement. Oesophageal manometry studies revealed that dysphagia was due to the oesophageal motility disorder, secondary achalasia.

Mechanisms and outcome of severe mitral regurgitation after Inoue balloon valvuloplasty. North American Inoue Balloon Investigators

OBJECTIVES

The purpose of this study was to assess the incidence, mechanism and outcome of severe mitral regurgitation after treatment of mitral stenosis with percutaneous mitral valvuloplasty using the Inoue balloon.

BACKGROUND

Severe mitral regurgitation occurs in up to 15% of percutaneous balloon valvuloplasty procedures for acquired mitral stenosis. The incidence and mechanism of production of mitral regurgitation with the recently introduced single-balloon Inoue technique have not been characterized.

METHODS

We examined the incidence, mechanism, predictors and outcome of severe mitral regurgitation after Inoue balloon valvuloplasty in 280 patients in the North American multicenter registry. Twenty-one patients who developed either clinically significant or angiographically severe regurgitation were identified, and their echocardiograms were reviewed to determine the mechanism of regurgitation. These patients were then compared with the remaining patients without severe regurgitation to identify predictors of this outcome.

RESULTS

The incidence of severe regurgitation in this study was 7.5%, and the mean grade of angiographic regurgitation in these patients increased from 0.9 +/- 1.0 to 2.8 +/- 0.7 (p < 0.05). The most common cause of regurgitation (43%) was rupture of chordae tendineae to the anterior or posterior mitral leaflet. Tearing of a leaflet (usually the posterior one) occurred in 30% of patients; and no recognizable structural abnormality, with wide splitting of the commissures and a central regurgitant jet, was present in five patients (26%). All patients with definite posterior leaflet tears had heavily calcified leaflets. Patients who developed severe regurgitation had fewer balloon inflations and a higher grade of preexisting mitral regurgitation but were otherwise similar to the remaining patients without severe regurgitation. During 6-month follow-up, 71% of the patients with severe regurgitation were treated surgically; the grade of regurgitation decreased in four patients (19%), and five patients (24%) have not required mitral valve replacement during 18 +/- 5 months of follow-up.

CONCLUSIONS

Severe mitral regurgitation is a relatively infrequent complication of Inoue balloon valvuloplasty and results from disruption of the valve integrity, including chordal rupture and leaflet tearing. Careful balloon positioning may help avoid chordal rupture, and heavily calcified posterior leaflets may be at greater risk of tearing. Most patients who develop severe regurgitation will require nonemergency mitral valve replacement.

Ultrasound features of low power interstitial laser hyperthermia

Low power interstitial laser hyperthermia (ILH) is a reliable means of producing in situ thermal necrosis. Ultrasonic studies have been carried out of the changes that occur in canine liver during ILH performed at laparotomy. With a single fibre delivering Nd-YAG laser at 1-1.5 W for 670 s an hyperechoic region developed at the fibre tip measuring 5-6 mm in diameter; around this developed an area of hypoechoic change (up to 500s) giving a total area of changed echogenicity of 14-16 mm. With a multiple fibre system using 4 laser fibres simultaneously the sonographic changes were a summation of the changes seen with a single fibre, the hypoechoic areas overlapping. With this four fibre system the creation of large (3.5 x 2.8 cm) areas of thermal necrosis was possible. There was good correlation between the sonographic and pathological measurements of the region of thermal change. The sonographic studies showed the extension and overlap of regions of thermal necrosis and allowed visualization and accurate measurement of the area undergoing change. The same combined technique has been successfully applied in a small number of clinical cases and may be of use in the treatment of tumours in solid organs.

Aneurysm or occlusive disease--factors determining the clinical course of atherosclerosis of the infrarenal aorta

Atherosclerosis of the infrarenal aorta results in distinct clinical entities--aortoiliac occlusive disease (AOD) and abdominal aortic aneurysm (AAA). Although loss of collagen has been implicated in AAA, collagen accumulation plays a role in AOD. In vivo collagen-gene expression can be assessed using complementary DNA for collagen types I and III alpha-chains. The purpose of this study is to compare total collagen (type I + III) and collagen types I and III messenger RNA in AAA, AOD and normal aorta. Specimens were collected from the infrarenal aorta during operation for AOD (n = 7), AAA (n = 7), autopsy, or organ procurement (normal; n = 7). Northern transfer analysis of total RNA was used to compare mRNA levels for type I and III collagen. After preliminary extraction, specimens were hydrolyzed for hydroxyproline analysis used to calculate total collagen (type I + III). Relative levels of type I (pro-a1[1]) mRNA were greater in both AOD (0.77 +/- 0.35) and AAA tissue (0.94 +/- 0.24; p = 0.6) than in normal aorta (0.02 +/- 0.03). Type III (pro-a1[III]) mRNA levels were also greater in AOD (2.52 +/- 0.19; p = 0.09) and AAA tissue (3.15 +/- 1.3) than in normals (0.97 +/- 0.47). Total collagen concentration was increased in AOD (45.6% +/- 3.1% dry weight; p less than 0.05) but not AAA tissue (27.8% +/- 4%) when compared to normal aorta (34.7% +/- 2.3%). Collagen type I and III gene expression is greater in older, diseased aorta, yet collagen accumulated only in AOD. This implies a similar synthetic response in both AOD and AAA. Thus, proteolytic degradation in AAA appears to determine collagen content and possibly the clinical course of the atherosclerotic process.

Assessment of a single lumbar spine radiograph in low back pain

The lumbosacral spine radiographs of 200 patients with unexplained low back pain and without neurological signs were reviewed. The purpose of the study was to determine whether significant diagnostic information would be lost by replacing the standard three film series with a single radiograph, either in the lateral or antero-posterior projection. The contribution of the coned lumbosacral junction view was also assessed. The results show that a single lateral radiograph is diagnostically satisfactory and would have the added advantages of reducing patient radiation dose and radiographic workload.

A clinical comparison of atracurium and vecuronium in women undergoing laparoscopy

In a double-blind, prospective, randomised trial in 30 women undergoing laparoscopy, atracurium and vecuronium were compared in equipotent (2 X ED95) doses. In the atracurium group, first twitch depression was significantly greater at one minute, and degree of fade significantly greater at one and two minutes, but thereafter neuromuscular monitoring showed no significant difference between the groups. Clinically there was no significant difference between the drugs. Mild intraoperative hypotension was equally common in both groups as was sinus bradycardia. Reversal and recovery were comparable in the two groups. Neostigmine was required in all patients and in three (one atracurium, two vecuronium) a second dose was required in all patients and in three (one atracurium, two vecuronium) a second dose was administered on clinical grounds. Antagonism of the neuromuscular block is required with surgery of this duration despite the intermediate duration of action of the relaxant drugs.

Intrahepatic bile duct dilatation shown by computed tomography--predilection for the left lobe?

Dilated biliary duct radicles were most obvious within the left lobe of the liver in 30 out of 42 patients with obstructive jaundice in whom intrahepatic duct dilatation was satisfactorily demonstrated by computed tomography. In 19 of these 30 patients the level of obstruction was at the lower end of the common bile duct. Recognition of this finding may prevent the erroneous diagnosis of intrahepatic or multiple obstructing lesions.