Liver Phantoms Cast in 3D-Printed Mold for Image-Guided Procedures.

INTRODUCTION: Image-guided invasive procedures on the liver require a steep learning curve to acquire the necessary skills. The best and safest way to achieve these skills is through hands-on courses that include simulations and phantoms of different complications, without any risks for patients. There are many liver phantoms on the market made of various materials; however, there are few multimodal liver phantoms, and only two are cast in a 3D-printed mold. METHODS: We created a virtual liver and 3D-printed mold by segmenting a CT scan. The InVesalius and Autodesk Fusion 360 software packages were used for segmentation and 3D modeling. Using this modular mold, we cast and tested silicone- and gelatin-based liver phantoms with tumor and vascular formations inside. We tested the gelatin liver phantoms for several procedures, including ultrasound diagnosis, elastography, fibroscan, ultrasound-guided biopsy, ultrasound-guided drainage, ultrasound-guided radio-frequency ablation, CT scan diagnosis, CT-ultrasound fusion, CT-guided biopsy, and MRI diagnosis. The phantoms were also used in hands-on ultrasound courses at four international congresses. RESULTS: We evaluated the feedback of 33 doctors regarding their experiences in using and learning on liver phantoms to validate our model for training in ultrasound procedures. CONCLUSIONS: We validated our liver phantom solution, demonstrating its positive impact on the education of young doctors who can safely learn new procedures thus improving the outcomes of patients with different liver pathologies.

Texture Analysis in Uterine Cervix Carcinoma: Primary Tumour and Lymph Node Assessment.

The conventional magnetic resonance imaging (MRI) evaluation and staging of cervical cancer encounters several pitfalls, partially due to subjective evaluations of medical images. Fifty-six patients with histologically proven cervical malignancies (squamous cell carcinomas, n = 42; adenocarcinomas, n = 14) who underwent pre-treatment MRI examinations were retrospectively included. The lymph node status (non-metastatic lymph nodes, n = 39; metastatic lymph nodes, n = 17) was assessed using pathological and imaging findings. The texture analysis of primary tumours and lymph nodes was performed on T2-weighted images. Texture parameters with the highest ability to discriminate between the two histological types of primary tumours and metastatic and non-metastatic lymph nodes were selected based on Fisher coefficients (cut-off value > 3). The parameters' discriminative ability was tested using an k nearest neighbour (KNN) classifier, and by comparing their absolute values through an univariate and receiver operating characteristic analysis. Results: The KNN classified metastatic and non-metastatic lymph nodes with 93.75% accuracy. Ten entropy variations were able to identify metastatic lymph nodes (sensitivity: 79.17-88%; specificity: 93.48-97.83%). No parameters exceeded the cut-off value when differentiating between histopathological entities. In conclusion, texture analysis can offer a superior non-invasive characterization of lymph node status, which can improve the staging accuracy of cervical cancers.

Genetic influence on splenic natural killer cell frequencies and maturation among aged mice.

Natural killer (NK) cells are cytotoxic innate lymphocytes that are integral to host defenses against viruses and neoplastic cells. Aging causes phenotypic and functional impairment of NK cells, which diminishes innate immune surveillance, yet the factors that determine the aged NK cell phenotype have not been completely defined. For instance, the genetic basis of the aged NK cell phenotype has not been established, but if determined, could highlight important genetic regulators of NK cells later in life. In this study, we estimated the heritability of splenic NK cell frequencies in aged mice from 15 classical and four wild-derived inbred strains. Our data suggest that frequencies of total (NKp46+CD3-) NK and mature (NKp46+CD3-CD11b+CD27-) NK cells were highly heritable at old age, and that total NK cell frequencies were independent predictors of median strain life spans. Strains with divergent phenotypes were compared to young-adult controls, and trends of age-related NK cell phenotypic alterations were confirmed. Finally, in silico mapping techniques revealed candidate genes associated with the aged NK cell phenotype. To our knowledge, these results are the first to demonstrate the genetic basis of the aged NK cell phenotype and will inform future mechanistic studies of NK cell dysfunction during aging.

In situ measurements of the sub-surface gamma dose from Chernobyl fallout.

Methods of estimating external radiation exposure of soil-dwelling organisms are currently of much research and regulatory interest. In this paper, we report the first in situ measurements of the sub-surface gamma dose rate for 137Cs contaminated land that quantify variation in dose rate with depth. Two contrasting sites have been investigated. The first site comprised a mineral type soil with a low percentage of organic matter and the second site chosen was in a peat-bog. The different soil compositions afford different 137Cs mobility and this results in variations in the measured gamma dose-rate with soil depth. For each site the paper reports the measured dose rates, the 137Cs activity depth profile, the 137Cs inventory and a description of the soil-characteristics. It is suggested that these data can be used to produce estimates of the sub-surface gamma dose rate in other sites of 137Cs contamination.

Salmon silk genes contribute to the elucidation of the flavone pathway in maize (Zea mays L.).

We utilized maize (Zea mays L.) lines expressing the salmon silk (sm) phenotype, quantitative trait locus analysis, and analytical chemistry of flavone compounds to establish the order of undefined steps in the synthesis of the flavone maysin in maize silks. In addition to the previously described sm1 gene, we identified a second sm locus, which we designate sm2, located on the long arm of maize chromosome 2. Our data indicate that the sm1 gene encodes or controls a glucose modification enzyme and sm2 encodes or controls a rhamnosyl transferase. The order of intermediates in the late steps of maysin synthesis was established as luteolin --> isoorientin --> rhamnosylisoorientin --> maysin.

Development of an integrated laboratory information management system for the maize mapping project.

MOTIVATION: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons. RESULTS: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available. AVAILABILITY: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.

iMap: a database-driven utility to integrate and access the genetic and physical maps of maize.

MOTIVATION: Because of the unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize is required for storing, integrating, accessing and visualizing the underlying data. RESULTS: The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig can be viewed via pop-up windows that feature links to external data resources. Searches can be conducted for genetic locus, probe or sequence accession number; search results include relevant map positions, anchored BAC contigs and links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org AVAILABILITY: The iMap utility package is available for non-commercial use upon request from the authors.

cMap: the comparative genetic map viewer.

UNLABELLED: cMap, a www comparative genetic map graphical utility, has a search capability and provides comparison of two genetic maps within or between species with dynamic links to data resources and text lists of the shared loci, running in a relational database environment. Currently, maps from three species (maize 'Zea mays L.', rice 'Oryza sativa L.', and sorghum 'Sorghum bicolor L.'), representing over 13,800 distinct loci, are available for comparison at http://www.agron.missouri.edu/cMapDB/cMap.html. AVAILABILITY: cMap source code is available without cost on request for non-commercial use.

The origins of maize genetics.

Early geneticists, and generations since, have been drawn to maize to study basic questions, its curious phenomena and its practical applications. Part of the allure of this unique crop plant lies in the collegiality of the Maize Genetics Cooperation, extending all the way from the 'roaring twenties' of genetics to today.

The biological basis of epistasis between quantitative trait loci for flavone and 3-deoxyanthocyanin synthesis in maize (Zea mays L.).

A major weakness in our understanding of the genetic basis of complex traits has been that of defining the extent and biological basis of epistasis. Our research group has been studying the genetic control of the accumulation of maysin, a C-glycosyl flavone, in maize, Zea mays (L.), silks. Previously, we demonstrated the importance of the p1 locus as a QTL for maysin synthesis. The p1 locus often exhibits significant epistatic interactions with other loci. We developed a mapping population, (W23al x GT119)F2, specifically designed to test whether genes in an intersecting pathway might be detected as QTLs for maysin synthesis and result in epistatic interaction effects. The a1 gene is not required for the synthesis of flavones but is required for the synthesis of 3-deoxyanthocyanins, an intersecting pathway, in maize silks. The p1 locus (P < 0.0001) was a QTL for both flavones and 3-deoxyanthocyanins. The a1 locus was also highly significant (P < 0.0001) for both traits, as was the p1 x a1 epistatic interaction (P < 0.0001). Our results demonstrate that altering the flux of biochemical intermediates between pathways may be the biological basis of major QTL effects and epistatic interactions.

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits.

Genetic mechanisms underlying apimaysin and maysin synthesis and corn earworm antibiosis in maize (Zea mays L.).

C-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14. 1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.

Quantitative trait loci and metabolic pathways.

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for "channeling" of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits.

Potentials of the National Corn Genome Initiative.

The present paper summarizes future needs in information and tools, technology, infrastructure, training, funding, and bioinformatics, to provide the genomic knowledge and tools for breeding and biotechnological goals in maize. The National Corn Genome Initiative (NCGA) has developed through actions taken by the National Corn Growers Association (NCGA) and participation in a planning process by institutions, companies, and organizations. At the web address for the NCGI, http://www.inverizon.com/ncgi, are detailed analyses of goals and costs, impact and value, and strategy and approaches. The NCGI has also produced an informative and perceptive video suitable for public groups or schools, about agricultural contributions to life and the place of maize in these contributions. High potential can be expected, from cross-application of knowledge obtained in maize and other cereals. Development of information and tools for all crops, whether monocots or dicots, will be gained through an initiative, and each crop will be positioned to advance with cost-effective parallels, especially for expressed sequences, markers, and physical mapping.

Dosage effects on morphological and quantitative traits in maize aneuploids.

Dosage effects generated by either loss or gain of a chromosome segment were used to identify chromosome regions associated with morphological and quantitative characters in maize (Zea mays L.). Using B-A translocation stocks introgressed into a B73Ht background, a chromosome arm dosage series in a Mo17Ht x B73Ht F1 hybrid background was created for 18 of the 20 chromosome arms. The dosage series was then evaluated for 12 quantitatively inherited characters to associate specific phenotypic changes in a trait with a specific chromosome arm. Not only did our results show the familiar aneuploid syndrome phenomenon, but differential dosage effects among particular chromosome arms were demonstrated. All the quantitative traits measured and all the chromosome arms examined in this study were responsive to changes in chromosome arm dosage. The possible bases behind those differences and their utility in identifying quantitative trait loci, as well as the genetic relationships among the group of quantitatively inherited characters studied, are considered. Key words : corn, chromosome arm, B-A translocations, dosage analysis.

Quantitative trait loci and metabolic pathways: genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks.

Interpretation of quantitative trait locus (QTL) studies of agronomic traits is limited by lack of knowledge of biochemical pathways leading to trait expression. To more fully elucidate the biological significance of detected QTL, we chose a trait that is the product of a well-characterized pathway, namely the concentration of maysin, a C-glycosyl flavone, in silks of maize, Zea mays L. Maysin is a host-plant resistance factor against the corn earworm, Helicoverpa zea (Boddie). We determined silk maysin concentrations and restriction fragment length polymorphism genotypes at flavonoid pathway loci or linked markers for 285 F2 plants derived from the cross of lines GT114 and GT119. Single-factor analysis of variance indicated that the p1 region on chromosome 1 accounted for 58.0% of the phenotypic variance and showed additive gene action. The p1 locus is a transcription activator for portions of the flavonoid pathway. A second QTL, represented by marker umc 105a near the brown pericarp1 locus on chromosome 9, accounted for 10.8% of the variance. Gene action of this region was dominant for low maysin, but was only expressed in the presence of a functional p1 allele. The model explaining the greatest proportion of phenotypic variance (75.9%) included p1, umc105a, umc166b (chromosome 1), r1 (chromosome 10), and two epistatic interaction terms, p1 x umc105a and p1 x r1. Our results provide evidence that regulatory loci have a central role and that there is a complex interplay among different branches of the flavonoid pathway in the expression of this trait.

Genetic variation in dosage effects in maize aneuploids.

In maize (Zea mays L.), the consequences of aneuploidy have been well documented, however, genetic variation in the responses to aneuploidy has not been examined. Using simple B-A translocation stocks to generate a dosage series involving segments from 14 chromosome arms, we tested for the presence of genetic variation for dosage responses in maize by examining reciprocal and maternal genotype effects on the dosage responses. Reciprocal effects examined whether there were differences between two distinctly different inbred backgrounds, Mo17Ht and B73Ht, in how they responded to loss or gain of a B73Ht segment in the Mo17Ht x B73Ht (TB) F1 cross versus a Mo17Ht segment in the B73Ht x Mo17Ht (TB) F1 cross. Maternal genotype effects questioned whether different inbred backgrounds, Sc41R, T8, and either Mo17Ht or B73Ht (depending on the male), when used as females responded differently to the loss or gain of a chromosome arm segment from the same male (either B73Ht TB or Mo17Ht TB) in an F1 cross. Numerous examples of reciprocal and maternal genetic effects were identified in this study. Most of the genetic effects were due to differences in magnitude of response rather than direction; however, tassel-branch number involving the 5S chromosome segment in the B73Ht male background and the 7L chromosome segment in the Mo17Ht male background showed a trend toward the maternal genotype effects being due to differences in the direction of the response. Key words : quantitative traits, corn, B-A translocations, dosage analysis.

Cloning maize telomeres by complementation in Saccharomyces cerevisiae.

Maize telomeric restriction fragments were cloned by virtue of their ability to function as telomeres on a linear plasmid in Saccharomyces cerevisiae. Nine maize telomeric YAC transformants (MTYs) were selected by hybridization to the Arabidopsis telomere repeat (CCCTAAA) from a pool of 1537 primary transformants. Bal31 digestion of MTY3 and MTY9 DNA indicated that the telomere hybridizing tracts are located at the terminus of the linear chromosome and therefore function as telomeres in yeast. Subclones generated for pMTY7 (pMTY7SC1) and pMTY9 (pMTY9ER) hybridized to Bal31 sensitive restriction fragments in maize DNA, indicating that maize telomeric restriction fragments had been cloned. Both pMTY7SC and pMTY9ER detected telomeric RFLPs, allowing the endpoints of seven chromosome arms to be determined. Additionally, pMTY7ER mapped to the centromeric regions of chromosomes 2 and 3, suggesting a relationship between centromeric and telomeric sequences. DNA sequencing of pMTY7SC and pMTY9ER revealed that both subclones contained CA-rich regions with sporadic occurrences of the telomere repeat and its degenerate repeats.

Physical and genetic mapping of chromosome 9S in maize using mutations with terminal deficiencies.

Deletion mapping was employed to determine the physical order of five morphological variants, pyd1, yg2, wd1, v28 and u31, with respect to restriction fragment length polymorphism (RFLP) markers located at the distal end of chromosome 9S in maize. The genetic materials used were a series of terminal-deficiency mutants, newly derived with McCLintock's original stocks developed in the 1940s, via breakage-fusion-bridge cycles. A combined physical map and genetic map has been constructed based on data gathered from both genetic complementation tests and RFLP analysis. The location of v31 in relation to RFLP markers was further determined by interval mapping. The physical distance between the healed telomeric end and the most distal RFLP marker in two terminal-deficiency lines was established by using pulsed field gel electrophoresis and verified by Bal31 digestion. The results from this study set a foundation for studies on the mechanism of healing of broken chromosome ends in higher plants.