Joseph W. Carlson

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that >80% drive expression patterns in the brain; the observed patterns were, on average, comprised of <100 cells. Our results suggest that the D. melanogaster genome contains >50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.

The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ‘fossil’ transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17–18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression. Xenopus laevis, also known as the African clawed frog or platanna, is an important model organism that is used in the study of vertebrate cell and developmental biology. It is a palaeotetraploid—the product of genome duplications that occurred many millions of years ago. This makes X. laevis ideal for the study of polyploidy, but has greatly complicated genome sequencing. Here an international research collaboration reports the X. laevis genome sequence and compares it to that of the related X. tropicalis. Their analyses confirm that X. laevis is an allotetraploid and distinguishes two subgenomes that evolved asymmetrically—one often retained the ancestral state and the other was subject to gene loss, deletion, rearrangement and reduced expression. The two diploid progenitor species diverged about 34 million years ago, combining to form an allotetraploid about 18 million years ago.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites.

We demonstrate the versatility of a collection of insertions of the transposon Minos-mediated integration cassette (MiMIC), in Drosophila melanogaster. MiMIC contains a gene-trap cassette and the yellow+ marker flanked by two inverted bacteriophage ΦC31 integrase attP sites. MiMIC integrates almost at random in the genome to create sites for DNAmanipulation. The attP sites allow the replacement of the intervening sequence of the transposon with any other sequence through recombinase-mediated cassette exchange (RMCE). We can revert insertions that function as gene traps and cause mutant phenotypes to revert to wild type by RMCE and modify insertions to control GAL4 or QF overexpression systems or perform lineage analysis using the Flp recombinase system. Insertions in coding introns can be exchanged with protein-tag cassettes to create fusion proteins to follow protein expression and perform biochemical experiments. The applications of MiMIC vastly extend the D. melanogaster toolkit.

Determining the composition of protein complexes is an essential step toward understanding the cell as an integrated system. Using coaffinity purification coupled to mass spectrometry analysis, we examined protein associations involving nearly 5,000 individual, FLAG-HA epitope-tagged Drosophila proteins. Stringent analysis of these data, based on a statistical framework designed to define individual protein-protein interactions, led to the generation of a Drosophila protein interaction map (DPiM) encompassing 556 protein complexes. The high quality of the DPiM and its usefulness as a paradigm for metazoan proteomes are apparent from the recovery of many known complexes, significant enrichment for shared functional attributes, and validation in human cells. The DPiM defines potential novel members for several important protein complexes and assigns functional links to 586 protein-coding genes lacking previous experimental annotation. The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution.

Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.

Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species.We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes.This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

Two bacterial artificial chromosome (BAC) libraries, spanning almost the entire D. melanogaster genome in insert sizes of 20 and 80 kb, that allow easy integration into the fruit fly genome at defined docking sites provide a rich resource to study gene expression and function. We constructed Drosophila melanogaster bacterial artificial chromosome libraries with 21-kilobase and 83-kilobase inserts in the P[acman] system. We mapped clones representing 12-fold coverage and encompassing more than 95% of annotated genes onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using ΦC31 integrase to rescue mutations. They can be modified through recombineering, for example, to incorporate protein tags and assess expression patterns.

The Drosophila Gene Disruption Project (GDP) has created a public collection of mutant strains containing single transposon insertions associated with different genes. These strains often disrupt gene function directly, allow production of new alleles, and have many other applications for analyzing gene function. Here we describe the addition of ∼7600 new strains, which were selected from >140,000 additional P or piggyBac element integrations and 12,500 newly generated insertions of the Minos transposon. These additions nearly double the size of the collection and increase the number of tagged genes to at least 9440, approximately two-thirds of all annotated protein-coding genes. We also compare the site specificity of the three major transposons used in the project. All three elements insert only rarely within many Polycomb-regulated regions, a property that may contribute to the origin of "transposon-free regions" (TFRs) in metazoan genomes. Within other genomic regions, Minos transposes essentially at random, whereas P or piggyBac elements display distinctive hotspots and coldspots. P elements, as previously shown, have a strong preference for promoters. In contrast, piggyBac site selectivity suggests that it has evolved to reduce deleterious and increase adaptive changes in host gene expression. The propensity of Minos to integrate broadly makes possible a hybrid finishing strategy for the project that will bring >95% of Drosophila genes under experimental control within their native genomic contexts.

Abstract Purpose: This study was designed to elucidate the role of amplification at 8q24 in the pathophysiology of ovarian and breast cancer because increased copy number at this locus is one of the most frequent genomic abnormalities in these cancers. Experimental Design: To accomplish this, we assessed the association of amplification at 8q24 with outcome in ovarian cancers using fluorescence in situ hybridization to tissue microarrays and measured responses of ovarian and breast cancer cell lines to specific small interfering RNAs against the oncogene MYC and a putative noncoding RNA, PVT1, both of which map to 8q24. Results: Amplification of 8q24 was associated with significantly reduced survival duration. In addition, small interfering RNA–mediated reduction in either PVT1 or MYC expression inhibited proliferation in breast and ovarian cancer cell lines in which they were both amplified and overexpressed but not in lines in which they were not amplified/overexpressed. Inhibition of PVT1 expression also induced a strong apoptotic response in cell lines in which it was overexpressed but not in lines in which it was not amplified/overexpressed. Inhibition of MYC, on the other hand, did not induce an apoptotic response in cell lines in which MYC was amplified and overexpressed. Conclusions: These results suggest that MYC and PVT1 contribute independently to ovarian and breast pathogenesis when overexpressed because of genomic abnormalities. They also suggest that PVT1-mediated inhibition of apoptosis may explain why amplification of 8q24 is associated with reduced survival duration in patients treated with agents that act through apoptotic mechanisms.

Genome sequences for most metazoans and plants are incomplete because of the presence of repeated DNA in the heterochromatin. The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. We describe the generation of 15 Mb of finished or improved heterochromatic sequence with the use of available clone resources and assembly methods. We also constructed a bacterial artificial chromosome-based physical map that spans 13 Mb of the pericentromeric heterochromatin and a cytogenetic map that positions 11 Mb in specific chromosomal locations. We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans.

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are "off" and survival/growth pathways "on." Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common "cell line" gene expression pattern.

Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysis indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence-absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.The genome is the complete DNA sequence of an individual. It is a crucial foundation for many studies in medicine, agriculture, and conservation biology. Advances in genetics have made it possible to rapidly sequence, or read out, the genome of many organisms. For closely related species, scientists can then do detailed comparisons, revealing similar genes with a shared past or a common role, but comparing more distantly related organisms remains difficult. One major challenge is that genes are often lost or duplicated over evolutionary time. One way to be more confident is to look at ‘synteny’, or how genes are organized or ordered within the genome. In some groups of species, synteny persists across millions of years of evolution. Combining sequence similarity with gene order could make comparisons between distantly related species more robust. To do this, Lovell et al. developed GENESPACE, a software that links similarities between DNA sequences to the order of genes in a genome. This allows researchers to visualize and explore related DNA sequences and determine whether genes have been lost or duplicated. To demonstrate the value of GENESPACE, Lovell et al. explored evolution in vertebrates and flowering plants. The software was able to highlight the shared sequences between unique sex chromosomes in birds and mammals, and it was able to track the positions of genes important in the evolution of grass crops including maize, wheat, and rice. Exploring the genetic code in this way could lead to a better understanding of the evolution of important sections of the genome. It might also allow scientists to find target genes for applications like crop improvement. Lovell et al. have designed the GENESPACE software to be easy for other scientists to use, allowing them to make graphics and perform analyses with few programming skills.

The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.

Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm. Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.

The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster.

We demonstrate the hohlraum radiation temperature and symmetry required for ignition-scale inertial confinement fusion capsule implosions. Cryogenic gas-filled hohlraums with 2.2 mm-diameter capsules are heated with unprecedented laser energies of 1.2 MJ delivered by 192 ultraviolet laser beams on the National Ignition Facility. Laser backscatter measurements show that these hohlraums absorb 87% to 91% of the incident laser power resulting in peak radiation temperatures of T(RAD)=300 eV and a symmetric implosion to a 100 μm diameter hot core.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence-absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the 'Pawnee' cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence-absence and functional annotation database among genomes and within the two outbred haplotypes of the 'Lakota' genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.

Abstract A high frequency solution of the electromagnetic field produced by a circular surface coil adjacend to a homogenous conducting, dielectric sphere is used to predict the attainable signal to noise ratio ( S/N ) and specific absorption rate (SAR) for in vivo 1 H NMR spec troscopy experiments from 200 to 430 MHz (4.7–10T). Above 200 MHz the S/N increases more rapidly with frequency and the SAR increases less rapidly compared with the respective S/N and SAR frequency dependence below 200 MHz. The difference in frequency dependence is due to dielectric resonances of the magnetic field inside the sphere at frequencies above 200 MHz. It is predicted that surface coil 1 H NMR experiments may be performed on a head‐sized sphere, having conductivity and relative dielectric constant of brain, at frequencies up to 430 MHz without exceeding 8 W/kg local SAR and 3.2 W/kg SAR. The calculations of the S/N and SAR are used to determine optimum surface coil geometries for NMR experments. The power radited by the surface coil in the absence of shielding and asymmetries in the received signal with respect to the plane defined by the surface coil axix and the direction of the static magnetic field are significant at high frequency. Experimental measurements of the magnetic field inside a head‐sized sphere verfy the presence of dielectric resonances at frequencies above 200 MHz. © 1991 Academic Press, Inc.

A technique is described for the simultaneous acquisition of MRI data using two independent receiver coils surrounding the same region of tissue, which enables the collection of data necessary for image reconstruction in a reduced number of phase-encoded acquisitions. This results in a 50% reduction in minimum scan time and may be useful in time-critical procedures. The algorithm and imaging procedures are described, and example images are shown that illustrate the reconstruction. Signal to noise is decreased by the square root of the time savings, making this technique applicable to cases in which the need to decrease minimum scan time outweighs the signal to noise penalty.

Abstract We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using ΦC31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.

Theoretical analysis predicts that performing magnetic resonance (MR) imaging with partial (less than 90 degrees) flip angles can reduce imaging times two- to fourfold when lesions with elevated T1 values are being examined. This time savings occurs because repetition time (TR) is reduced when imaging is performed with partial flips. Partial flip MR imaging can also improve signal-to-noise ratio (S/N) in fast body imaging. For this study, analytical tools were used to predict image contrast and S/N for short TR, partial flip sequences. Experimental implementation of the short TR, partial flip sequences that analytical work had predicted would be optimal supported the analytical predictions and demonstrated their validity. Partial flip MR imaging is applicable to reducing imaging time only when the ratio of signal differences to noise exceeds threshold values in conventional MR images. Partial flip sequences can be used to advantage in MR imaging of both the head and the body, and the observed effects are predictable through theoretical analysis.

ObjectiveDespite its generally favorable prognosis at primary diagnosis, recurrence of endometrial cancer remains an important clinical challenge. The aim of this study was to analyze the value of molecular classification in recurrent endometrial cancer.MethodsThis study included patients with recurrent endometrial cancer who underwent primary surgical treatment between 2004 and 2015 at the Karolinska University Hospital, Sweden and the Bern University Hospital, Switzerland (KImBer cohort) with molecular classification of the primary tumor.ResultsOut of 594 molecularly classified endometrial cancer patients, 101 patients experienced recurrence, consisting of 2 POLEmut, 33 MMRd, 30 p53abn, and 36 NSMP tumors. Mean age at recurrence was 71 years and mean follow-up was 54 months. Overall, median time to first recurrence was 16 months (95% CI 12–20); with the shortest median time in MMRd patients, with 13 months (95% CI 5–21). The pattern of recurrence was distinct among molecular subgroups: MMRd tumors experienced more locoregional, while p53abn cases showed more abdominal recurrences (P = .042). Median survival after recurrence was best for MMRd cases (43 months, 95% CI 11–76), compared to 39 months (95% CI 21–57) and 10 months (95% CI 7–13) for the NSMP and p53abn cases respectively (log-rank, P = .001).ConclusionMolecular classification is a significant indicator of survival after recurrence in endometrial cancer patients, and patterns of recurrence differ by molecular subgroups. While MMRd endometrial cancer show more locoregional recurrence and the best survival rates after recurrence, p53abn patients experience abdominal recurrence more often and had the worst prognosis of all recurrent patients.

Abstract Techniques are described for the design of shielded gradient coils for superconducting MRI systems. These design methods are suited for constructing the most efficient gradient coil that meets a specified homogeneity requirement. Tradeoffs in coil design of efficiency with coil size and gap size are discussed. Residual eddy currents from coils constructed with a finite number of wires are calculated and give guidelines for the construction of efficient, whole‐body gradient coils.

Abstract Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide 1 . While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued 2 . The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species ( Saccharum officinarum ) and the wild species ( Saccharum spontaneum ). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Lasing in the ultraviolet has been observed in neodymium-doped fluorozirconate glass (ZBLAN) fibres at room temperature. For a cavity output coupling of &lt; 0.1%, 74 µW of power was obtained at 381 nm (4D3/2 → 4I11/2 transition of Nd3+) when a 45 cm long fibre was pumped with 275 mW at a wavelength of nominally 590 nm.

Abstract Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about datasets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.

Utilisation de bobines multiples pour acquerir les signaux, puis utilisation de l'information supplementaire comme une partie de la reconstruction

Adenosine deaminases that act on RNA [adenosine deaminase, RNA specific (ADAR)] catalyze the site-specific conversion of adenosine to inosine in primary mRNA transcripts. These re-coding events affect coding potential, splice sites, and stability of mature mRNAs. ADAR is an essential gene, and studies in mouse, Caenorhabditis elegans, and Drosophila suggest that its primary function is to modify adult behavior by altering signaling components in the nervous system. By comparing the sequence of isogenic cDNAs to genomic DNA, we have identified and experimentally verified 27 new targets of Drosophila ADAR. Our analyses led us to identify new classes of genes whose transcripts are targets of ADAR, including components of the actin cytoskeleton and genes involved in ion homeostasis and signal transduction. Our results indicate that editing in Drosophila increases the diversity of the proteome, and does so in a manner that has direct functional consequences on protein function.

In recent years, evidence is accumulating that cancer cells develop strategies to escape immune recognition. HLA class I HC down-regulation is one of the most investigated. In addition, different HLA haplotypes are known to correlate to both risk of acquiring diseases and also prognosis in survival of disease or cancer. We have previously shown that patients with serous adenocarcinoma of the ovary in advanced surgical stage disease have a particularly poor prognosis if they carry the HLA-A02* genotype. We aimed to study the relationship between HLA-A02* genotype in these patients and the subsequent HLA class I HC protein product defects in the tumour tissue. One hundred and sixty-two paraffin-embedded tumour lesions obtained from Swedish women with epithelial ovarian cancer were stained with HLA class I heavy chain (HC) and β2-microglobulin (β2-m)-specific monoclonal antibodies (mAb). Healthy ovary and tonsil tissue served as a control. The HLA genotype of these patients was determined by PCR/sequence-specific primer method. The probability of survival was calculated using the Kaplan–Meier method, and the hazard ratio (HR) was estimated using proportional hazard regression. Immunohistochemical staining of ovarian cancer lesions with mAb showed a significantly higher frequency of HLA class I HC and β2-m down-regulation in patients with worse prognosis (WP) than in those with better prognosis. In univariate analysis, both HLA class I HC down-regulation in ovarian cancer lesions and WP were associated with poor survival. In multivariate Cox-analysis, the WP group (all with an HLA-A02* genotype) had a significant higher HR to HLA class I HC down-regulation. HLA-A02* is a valuable prognostic biomarker in epithelial ovarian cancer. HLA class I HC loss and/or down-regulation was significantly more frequent in tumour tissues from HLA-A02* positive patients with serous adenocarcinoma surgical stage III–IV. In multivariate analysis, we show that the prognostic impact is reasonably correlated to the HLA genetic rather than to the expression of its protein products.

The atomic force microscope (AFM) has been used to image a variety of biological systems, but has rarely been applied to soluble protein-lipid complexes.One of the primary physiological protein-lipid complexes is the high-density lipoproteins (HDL), responsible for the transport of cholesterol from the peripheral tissues and other lipoproteins to the liver.We have used the AFM to directly image discoidal reconstituted HDL (rHDL) particles for the first time.The height of these particles is consistent with a phospholipid bilayer structure, but careful high resolution measurements of particle diameters has indicated that they fuse when adsorbed to mica.Furthermore, it has been demonstrated that the AFM can be used to initiate this bilayer fusion in a controlled manner, allowing the fabrication of stabilized, nanometer scale, phospholipid bilayer "domains."

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.

We describe a method for high-throughput production of protein expression-ready clones. Open-reading frames (ORFs) are amplified by PCR from sequence-verified cDNA clones and subcloned into an appropriate loxP-containing donor vector. Each ORF is represented by two types of clones, one containing the native stop codon for expression of the native protein or amino-terminal fusion constructs and the other made without the stop codon to allow for carboxy-terminal fusion constructs. The expression-ready clone is sequenced to verify that no PCR errors have been introduced. We have made over 11,000 clones ranging in size from 78–6,699 bp with a median of 1,056 bp. This is the largest set of fully sequence-verified ­“movable ORFs” of any model organism genome project. The donor clone facilitates rapid and simple transfer of the ORF into any expression vector of choice. Vectors are available for expressing these ORFs in bacteria, cell lines, or transgenic animals. The flexibility of this ORF clone collection makes possible a variety of proteomic applications, including protein interaction mapping, high-throughput cell-based expression screens, and functional studies. We have transferred 5,800 ORFs to a vector that allows production of a FLAG-HA tagged protein in Drosophila tissue culture cells with a metallothionein-inducible promoter. These clones are being used to produce a protein complex map of Drosophila from Schneider cells.

Fibrillar collagens promote cell proliferation, migration, and survival in various epithelial cancers and are generally associated with tumor aggressiveness. However, the impact of fibrillar collagens on soft tissue sarcoma behavior remains poorly understood. Unexpectedly, this study finds that fibrillar collagen-related gene expression is associated with favorable patient prognosis in rhabdomyosarcoma. By developing and using collagen matrices with distinct stiffness and in vivo-like microarchitectures, this study uncovers that the activation of DDR1 has pro-apoptotic and of integrin β1 pro-survival function, specifically in 3D rhabdomyosarcoma cell cultures. It demonstrates that rhabdomyosarcoma cell-intrinsic or extrinsic matrix remodeling promotes cell survival. Mechanistically, the 3D-specific collagen-induced apoptosis results from a dual DDR1-independent and a synergistic DDR1-dependent TRPV4-mediated response to mechanical confinement. Altogether, these results indicate that dense microfibrillar collagen-rich microenvironments are detrimental to rhabdomyosarcoma cells through an apoptotic response orchestrated by the induction of DDR1 signaling and mechanical confinement. This mechanism helps to explain the preference of rhabdomyosarcoma cells to grow in and metastasize to low fibrillar collagen microenvironments such as the lung.

Abstract The current distribution on thin conductors and rf field homogeneity for rf coils is described theoretically. After a pedagogical introduction to the techniques and an exact solution for the current or an isolated strip conductor, this article describes current distribution and field uniformity for a variety of conventional and quadrature rf coil designs. © 1986 Academic Press, Inc.

The development of multiple high-quality reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple reference haplotypes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation in nature. Here, we address these challenges through the concept of a pan-genome annotation, where conserved gene order is used to restrict gene families and define the expected physical position of all genes that share a common ancestor among multiple genome annotations. By leveraging pan-genome annotations and exploring the underlying syntenic relationships among genomes, we dissect presence-absence and structural variation at four levels of biological organization: among three tetraploid cotton species, across 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic pan-genome annotations in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred and other complex genomes.

Abstract Uterine leiomyosarcoma (uLMS) is a rare and aggressive cancer representing approximately 2-5% of all uterine malignancies. The molecular heterogeneity and pathogenesis of uLMS are notwell understood. To unravel the intricate molecular landscape of uLMS, we conducted a multi-omics workflow consisting of 4 high-throughput sequencing technologies; short- and long-readwhole genome sequencing (WGS), RNA-Seq, and Tandem mass tag (TMT) labeling enablingmassively parallel proteome proteomic analyses. Our study cohort consisted of 97 fresh frozentissue samples collected from 68 female patients, with 19 uLMS, 37 leiomyoma (LM), and 41normal myometrium (MM). A deep analysis of somatic variants with clinical impact revealed 46variants present in 90% of samples and two actionable therapeutic targets: IDH1_p.Arg132Cysand KRAS_p.Gly12Val. Also, 80% of the samples presented a chromothripsis signature and 60%presented the SBS3 COSMIC signature related to homologous recombination deficiency (HRD).Analysis of the proliferation score in RNA-Seq data revealed a notable difference among thetumor groups, signifying a higher proliferation index in the uLMS group, suggesting a moreaggressive growth pattern with implications for clinical behavior and disease progression. Afterapplying a customized workflow to identify balanced chromosomal abnormalities of genefusions with clinical impact, the proto-oncogene eukaryotic elongation factor 1 alpha (EEF1A1)emerged as a prominent fusion partner. Eight fusions in 7 samples were identified withtranscriptional overexpression in positive cases. At the proteomic level the enrichment analysisunveiled activated pathways associated with the innate immune system, while suppressedpathways pertained to extracellular matrix (ECM) organization and smooth muscle contraction.With an integrated bioinformatics pipeline, we identified copy number amplification of theCTHRC1 gene in 80% of the samples, accompanied by increased gene expression and proteinlevels. This gene is related to collagen remodeling and degradation and has been demonstratedto be upregulated in some solid tumors and is closely associated with malignancy. Survivalcurve analysis highlighted a significantly poorer prognosis in uLMS exhibiting CTHRC1 geneamplification with potential clinical relevance of CTHRC1 amplification as a prognostic indicatorin uLMS. Taken together these results show the overall suppression of ECM and collagenremodeling in uLMS associated with poor prognosis. Additionally, these data provide the firstevidence that the EEF1A1 gene has a strong selective pressure in uLMS underscoring theindispensable role of precision genomics in advancing precision medicine. Citation Format: Raul Maia Falcao, Jorge Estefano de Souza, William Mathieson, Joseph Woodward Carlson, Tirzah Braz Petta. Deep multi-omics analysis of uterine leiomyosarcoma reveals defective HRD signature, a novel gene fusion and the amplification of the poor-prognosis CTHRC1 gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1751.

<title>Abstract</title> Uterine leiomyosarcoma (uLMS) is a rare and aggressive cancer representing approximately 2-5% of all uterine malignancies. The molecular heterogeneity and pathogenesis of uLMS are not well understood and translational studies with the aim of discovering the vulnerabilities of this tumor type are of high priority. We conducted an innovative comprehensive multi-omics integration study from DNA to protein using fresh frozen tumors to unravel unprecedented molecular features of uLMS. Here we present that two tumors harbor actionable therapeutic targets,<italic> IDH1</italic>_p.Arg132Cys and <italic>KRAS</italic>_p.Gly12Cys and homologous recombination deficiency (HRD) was the most predominant genomic signature, suggesting that uLMS patients could benefit from individualised precision medicine. Additionally, 80% of the samples presented a chromothripsis signature reinforcing the aneuploidy phenotype of these tumors. Moreover, uLMS with high proliferation score and high Ki67 expression presented a worse overall survival. By applying an innovative pipeline to explore structural variants, we observed a high frequency of balanced translocation involving the gene <italic>EEF1A1</italic> with enrichment of EGFR pathway. For the first time, uLMS proteomics analysis shows the enrichment of pathways associated with the suppression of innate immune system and extracellular matrix (ECM) organization. Finally, our comprehensive multi-omics integration analysis identified amplification of the gene <italic>CTHRC1 </italic>a gene from the matrisome with negative impact on the overall survival. Taken together, the deep functional multi-omics approach contributes to the detection of new molecular features of uLMS and suggests that patients would benefit from precision oncology in clinical practice.

Abstract A collection of modified procedures for setting rf transmitter levels using a three‐pulse sequence is described. Based on a geometrically weighted ratio of four signals, an estimate of the flip angle is calculated and used for an updating prescription. These techniques are designed to perform rapidly yet eschew systematic errors due to relaxation during the pulse sequence. © 1990 Academic Press, Inc.

In principle, tomographic imaging of breast implants provides the information needed to compute implant volume. We have investigated the reliability of this measurement as a means of diagnosing the loss of gel from the implant. We find that measurement errors, postimplantation changes of the implant, uncertainties in the patients' records, and lack of knowledge of the implant temperature in the body can lead to significant discrepancies, making this measurement unreliable as a diagnostic tool.

Abstract Solutions for the magnetic fields in and around spherical conductive NMR samples are presented. These results affect the expressions for the signal-to-noise of NMR on conductive samples when the skin depth of RF penetration is not large compared to the sample size. The exact solution presented here of a circular surface coil adjacent to a spherical conductive sample demonstrates the effect of eddy current shielding of RF fields produced by non-homogeneous coils. Specific results are presented for various surface coils adjacent to a spherical sample at 10 and 150 MHz. Beyond a frequency-dependent depth, the signal-to-noise of different surface coils is shown to be nearly identical.

ABSTRACT Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas ( https://plantgeneatlas.jgi.doe.gov ) and Phytozome ( https://phytozome-next.jgi.doe.gov ), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Background: Uterine leiomyosarcoma (uLMS) are rare and malignant tumors that arise in the myometrium cells and whose diagnosis is based on histopathological features. Identifying diagnostic biomarkers for uLMS is a challenge due to molecular heterogeneity and the scarcity of samples. In vivo and in vitro models for uLMS are urgently needed. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 (MIM:177045) develop spontaneous uLMS. This study aimed to analyze the role of PSMB9 in uLMS tumorigenesis and patient outcome. Methods: Molecular data from 3 non-related uLMS cohorts were integrated and analyzed by proteotranscriptomic using gene expression and protein abundance levels in 68 normal adjacent myometrium (MM), 66 uterine leiomyoma (LM), and 67 uLMS. Results: the immunoproteasome pathway is upregulated and the gene PMSB9 shows heterogeneous expression values in uLMS. Quartile group analysis showed no significant difference between groups high and low PSMB9 expression groups at 3-years overall survival (OS). Using CYBERSORTx analysis we observed 9 out of 17 samples in the high group clustering together due to high M2 macrophages and CD4 memory resting, and high CD8+/PSMB9 ratio was associated with better OS. The main pathway regulated in the high group is IFNγ and in the low is the ECM pathway dependent on the proto-oncogene SRC. Conclusion: these findings suggest 2 subtypes of uLMS (immune-related and ECM-related) with different candidate mechanisms of malignancy.

Continuous oscillation on the (2)P(3/2) ? (4)I(11/2) transition of Nd(3+) in a f luorozirconate glass (ZBLAN) fiber at room temperature has been observed. When pumped at ~590 nm, a Nd:ZBLAN f iber 39 cm in length lases in the violet at 412 nm and produces ~0.5 mW of power for 320 mW of pump power and a cavity output coupling of 0.4%. The breadth of the laser's excitation spectrum is ~12 nm (581-593 nm).

Acquisition of relaxation rate dispersion curves from magnetic resonance images was demonstrated on a clinical, whole-body imaging system. Study of the behavior of relaxation rates over a range of field strengths probes the structural environment of imaged hydrogen protons and reveals information about the composition of tissue. The authors determined relaxation rates in extremities and heads of healthy volunteers. The sensitivity of the measurement is sufficient to obtain a distinctive relaxation rate dispersion behavior for different tissues.

A general solution for the power deposited in an NMR sample by an rf coil is presented. The result is simplified in the long wavelength, long skin depth approximation. This formalism is used to derive an expression for noise correlation in two independent receiver coils.

Abstract Cowpea, Vigna unguiculata L . Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six sub-populations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4,963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO-terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million SNPs relative to each assembly and over 40 structural variants &gt;1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea. Article Summary This study reports annotated genome assemblies of six cowpea accessions. Together with the previously reported annotated genome of IT97K-499-35, these constitute a pan-genome resource representing six subpopulations of domesticated cowpea. Annotations include genes, variant calls for SNPs and short indels, larger presence or absence variants, and inversions. Noncore genes are enriched for loci involved in stress response and harbor many genic variants with potential effects on coding sequence.

Over the years, the molecular classification of endometrial carcinoma has evolved significantly. Both POLEmut and MMRdef cases share tumor biological similarities like high tumor mutational burden and induce strong lymphatic reactions. While therefore use case scenarios for pretesting with tumor-infiltrating lymphocytes to replace molecular analysis did not show promising results, such testing may be warranted in cases where an inverse prediction, such as that of POLEwt, is being considered. For that reason we used a spatial digital pathology method to quantitatively examine CD3+ and CD8+ immune infiltrates in comparison to conventional histopathological parameters, prognostics and as potential pretest before molecular analysis.We applied a four-color multiplex immunofluorescence assay for pan-cytokeratin, CD3, CD8, and DAPI on 252 endometrial carcinomas as testing and compared it to further 213 cases as validation cohort from a similar multiplexing assay. We quantitatively assessed immune infiltrates in microscopic distances within the carcinoma, in a close distance of 50 microns, and in more distant areas.Regarding prognostics, high CD3+ and CD8+ densities in intra-tumoral and close subregions pointed toward a favorable outcome. However, TCGA subtyping outperforms prognostication of CD3 and CD8 based parameters. Different CD3+ and CD8+ densities were significantly associated with the TCGA subgroups, but not consistently for histopathological parameter. In the testing cohort, intra-tumoral densities of less than 50 intra-tumoral CD8+ cells/mm2 were the most suitable parameter to assume a POLEwt, irrespective of an MMRdef, NSMP or p53abn background. An application to the validation cohort corroborates these findings with an overall sensitivity of 95.5%.Molecular confirmation of POLEmut cases remains the gold standard. Even if CD3+ and CD8+ cell densities appeared less prognostic than TCGA, low intra-tumoral CD8+ values predict a POLE wild-type at substantial percentage rates, but not vice versa. This inverse correlation might be useful to increase pretest probabilities in consecutive POLE testing. Molecular subtyping is currently not conducted in one-third of cases deemed low-risk based on conventional clinical and histopathological parameters. However, this percentage could potentially be increased to two-thirds by excluding sequencing of predicted POLE wild-type cases, which could be determined through precise quantification of intra-tumoral CD8+ cells.

To develop and validate pre- and postoperative mathematical models to predict recurrence/progression of endometrial cancer, and to evaluate if these models outperform the ESMO/ESGO/ESTRO prognostic risk groups. All 1538 women in the prospective IETA4 cohort who underwent preoperative structured ultrasound examination followed by hysterectomy from 2011 to 2015, were followed up until 2019-2020 or to time of death. The ESMO/ESGO/ESTRO pre- and postoperative risk groups (based on myometrial invasion, grade, stage, LVSI) were forced into the respective model. Based on scientific knowledge we also included age, BMI, extrauterine tumour spread on ultrasound, colour score, multiple-multifocal vascular pattern, endometrial-myometrial border, endometrial echogenicity and tumour AP diameter as candidate variables. A multivariable fractional polynomial algorithm was run to fit a Fine-and-Gray competing risk model, with death from other causes as a competing event. Calibration plots were generated, and Harrell's C discrimination index was calculated. Follow-up data was complete in 1429/1538 (92.9%) patients. Recurrence/progression occurred in 228 (15.9%) and death from other causes in 121 (8.5%), 659 (46%) were low-risk. A preoperative model including the ESMO/ESGO/ESTRO preoperative risk group and the retained variables extrauterine spread on ultrasound, non-uniform echogenicity, age ≥65 years, and tumour AP diameter > 2 cm was superior to ESMO/ESGO/ESTRO preoperative risk group alone, Harrell's C 0.761 (95% CI 0.727-0.795) vs. 0.706 (95% CI 0.674-0.739). The postoperative model including the retained variables age > 65 years and tumour AP diameter > 2 cm, improved Harrell's C from 0.758 (0.723-0.792) to 0.785 (0.754-0.816) compared to including only the 2020 postoperative ESMO/ESGO/ESTRO risks group. Adding sonographic and demographic variables to the ESMO/ESGO/ESTRO prognostic groups improved risk prediction and may be valuable to further individualise patient management.

Libraries of cDNA clones are valuable resources for analyzing the expression, structure and regulation of genes, and for studying protein functions and interactions. Full-length cDNA clones provide information about intron and exon structures, splice junctions, and 5′ and 3′ untranslated regions (UTRs). Open reading frames (ORFs) derived from cDNA clones can be used to generate constructs allowing the expression of both wild-type proteins and proteins tagged at their amino or carboxy terminus. Thus, obtaining full-length cDNA clones and sequences for most or all genes in an organism is essential for understanding genome functions. EST sequencing samples cDNA libraries at random, an approach that is most useful at the beginning of large-scale screening projects. As projects progress towards completion, however, the probability of identifying unique cDNAs by EST sequencing diminishes, resulting in poor recovery of rare transcripts. Here we describe an adapted, high-throughput protocol intended for the recovery of specific, full-length clones from plasmid cDNA libraries in 5 d.

Thin-section magnetic resonance imaging at low field strengths requires analysis of the relative merits of data collection techniques for direct three-dimensional versus multisection two-dimensional imaging. This analysis was done with specific emphasis on shortened relaxation times and the use of reduced magnetic field gradients. Three-dimensional Fourier transform techniques can provide thin-section images of good diagnostic quality when combined with partial flip-angle gradient-reversal techniques.

Abstract The nutrient-rich tubers of the greater yam Dioscorea alata L. provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an “orphan crop.” Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Abstract A gene located within the intron of a larger gene is an uncommon arrangement in any species. Few of these nested gene arrangements have been explored from an evolutionary perspective. Here we report a phylogenetic analysis of kayak (kay) and fos intron gene (fig), a divergently transcribed gene located in a kay intron, utilizing 12 Drosophila species. The evolutionary relationship between these genes is of interest because kay is the homolog of the proto-oncogene c-fos whose function is modulated by serine/threonine phosphorylation and fig is a predicted PP2C phosphatase specific for serine/threonine residues. We found that, despite an extraordinary level of diversification in the intron–exon structure of kay (11 inversions and six independent exon losses), the nested arrangement of kay and fig is conserved in all species. A genomewide analysis of protein-coding nested gene pairs revealed that ∼20% of nested pairs in D. melanogaster are also nested in D. pseudoobscura and D. virilis. A phylogenetic examination of fig revealed that there are three subfamilies of PP2C phosphatases in all 12 species of Drosophila. Overall, our phylogenetic and genomewide analyses suggest that the nested arrangement of kay and fig may be due to a functional relationship between them.

The cost of magnetic resonance imaging (MRI) is driven by magnetic field strength. Misperceptions as to the impact of field strength on performance have led to systems that are more expensive than they need to be. Careful analysis of all the factors that affect diagnostic quality lead to the conclusion that field strength per se is not a strong determinant of system performance. Freed from the constraints imposed by high-field operation, it is possible to exploit a varied set of opportunities afforded by low-field operation. In addition to lower costs and easier siting, we can take advantage of shortened T1 times, higher contrast, reduced sensitivity to motion, and reduced radiofrequency power deposition. These conceptual advantages can be made to coalesce onto practical imaging systems. We describe a low-cost MRI system that utilizes a permanent magnet of open design. Careful optimization of receiving antennas and acquisition sequences permit performance levels consistent with those needed for an effective diagnostic unit. Ancillary advantages include easy access to the patient, reduced claustrophobia, quiet and comfortable operation, and absence of a missile effect. The system can be sited in 350 sq ft and consumes a modest amount of electricity. MRI equipment of this kind can widen the population base than can access this powerful and beneficial diagnostic modality.

The purpose of this study was to evaluate the impact of spatial resolution on coronary calcium scoring by x-ray CT, to assess the scoring performance of different CT scanners as they are operated in the field and to correct for the effects of CT scanner spatial resolution on coronary calcium scoring.

One-hundred and nineteen implants were imaged in an open-sided low-field magnetic resonance imaging system. Thirty-four of these implants were removed, and postoperative reports were made available. We found a variety of signs associated with the implants, including internal structures, loss of saline in double-lumen implants, intracapsular and extracapsular fluid accumulations, signal dropout regions most likely associated with calcifications, and debris and fluid in the silicone, as well as degradation of the silicone, disruptions of the capsule and bulging, and extracapsular silicone. Conclusions of intact versus ruptured were made on the basis of these findings and found to be confirmed in 32 of 34 cases, with 1 false-positive and 1 false-negative result. Based on MRI criteria for a broad sample of the population, 27 percent of the implants were considered ruptured. (Plast. Reconstr. Surg. 96: 852, 1995.)

On the basis of shotgun subclone libraries used in the sequencing of the Drosophila melanogaster genome, a minimal tiling path of subclones across much of the genome was determined. About 320,000 shotgun clones for chromosomes X(12–20), 2R, 2L, 3R, and 4 were available from the Berkeley Drosophila Genome Project. The clone inserts have an average length of 3.4 kb and are amenable to standard PCR amplification. The resulting tiling path covers 86.2% of chromosome X(12–20), 86.2% of chromosomal arm 2R, 79.0% of 2L, 89.6% of 3R, and 80.5% of chromosome 4. In total, the 25,135 clones represent 76.7 Mb—equivalent to about 67% of the genome —and would be suitable for producing a microarray on a single slide.

Immune perception in flowering plants is mediated by a repertoire of cytoplasmic and cell-surface receptors that detect invading microbes and their effects on cells. Here, we show that several large families of immune receptors exhibit size variations related to a plant's competence to host symbiotic root fungi (mycorrhiza). Plants that do not participate in mycorrhizal associations have significantly smaller immune repertoires, while the most promiscuous symbiotic hosts (ectomycorrhizal plant species) have significantly larger immune repertoires. By contrast, we find no significant increase in immune repertoire size among legumes competent to form a symbiosis with nitrogen-fixing bacteria (rhizobia). To explain these observations, we hypothesize that plant immune repertoire size expands with symbiote species diversity.

A formalism for the calculation of fields generated by current distributions on hyperbolic surfaces of revolution is presented and used to generate designs for shielded gradient coils. One application is the development of small, insertable coils suitable for head imaging while allowing clearance for shoulders. This technique demonstrates that efficient designs that offer substantial advantages over conventional cylindrical designs are possible.

Ovarian cancer develops due to a complex interplay between hereditary and environmental factors. Although often described as one disease, ovarian cancer is actually a group of distinct tumor types. Recent research has indicated that a large percentage of ovarian cancers may originate from the fallopian tube epithelium. Although most cancers develop in patients without a known hereditary syndrome, it is clear that the number of familial cancers is larger than previously supposed. The two most common hereditary syndromes where ovarian cancer can develop are hereditary breast ovarian cancer syndrome (HBOC) and Lynch syndrome.

&lt;p&gt;This file contains Figures S1-S6. Figure S1 shows proliferation of neural stem cells after in utero electroporation of Sox5, Sox6 or Sox21, and the successful activation of viral vector expression by CRE enzyme. Figure S2 shows reduction of SOX5/6/21 levels after intracranial ARC injection. H&lt;/p&gt;

&lt;p&gt;This file contains additional description of western blot analysis, immunohistochemistry, antibodies, Sox21 targeting in mouse, bioinformatics, in utero electroporation, proliferation, senescence and cell death assays, NPC cultures and assays, and qRT-PCR.&lt;/p&gt;

&lt;p&gt;This file contains Tables S1-S3. Table S1 shows number of injected mice and tumor incidence. Table S2 shows genes and fold changes of commonly up and down regulated genes in mouse Sox5/6/21fl/fl tumors and human GBM. Table S3 shows Sox21 ChIPseq peaks association to nearest gene.&lt;/p&gt;

&lt;div&gt;Abstract&lt;p&gt;Molecular mechanisms preventing self-renewing brain stem cells from oncogenic transformation are poorly defined. We show that the expression levels of SOX5, SOX6, and SOX21 (SOX5/6/21) transcription factors increase in stem cells of the subventricular zone (SVZ) upon oncogenic stress, whereas their expression in human glioma decreases during malignant progression. Elevated levels of SOX5/6/21 promoted SVZ cells to exit the cell cycle, whereas genetic ablation of SOX5/6/21 dramatically increased the capacity of these cells to form glioma-like tumors in an oncogene-driven mouse brain tumor model. Loss-of-function experiments revealed that SOX5/6/21 prevent detrimental hyperproliferation of oncogene expressing SVZ cells by facilitating an antiproliferative expression profile. Consistently, restoring high levels of SOX5/6/21 in human primary glioblastoma cells enabled expression of CDK inhibitors and decreased p53 protein turnover, which blocked their tumorigenic capacity through cellular senescence and apoptosis. Altogether, these results provide evidence that SOX5/6/21 play a central role in driving a tumor suppressor response in brain stem cells upon oncogenic insult. &lt;i&gt;Cancer Res; 77(18); 4985–97. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;p&gt;This file contains Figures S1-S6. Figure S1 shows proliferation of neural stem cells after in utero electroporation of Sox5, Sox6 or Sox21, and the successful activation of viral vector expression by CRE enzyme. Figure S2 shows reduction of SOX5/6/21 levels after intracranial ARC injection. H&lt;/p&gt;

&lt;p&gt;This file contains Tables S1-S3. Table S1 shows number of injected mice and tumor incidence. Table S2 shows genes and fold changes of commonly up and down regulated genes in mouse Sox5/6/21fl/fl tumors and human GBM. Table S3 shows Sox21 ChIPseq peaks association to nearest gene.&lt;/p&gt;

&lt;p&gt;This file contains additional description of western blot analysis, immunohistochemistry, antibodies, Sox21 targeting in mouse, bioinformatics, in utero electroporation, proliferation, senescence and cell death assays, NPC cultures and assays, and qRT-PCR.&lt;/p&gt;

Supplementary Figures S1-S2 from Amplification of &lt;i&gt;PVT1&lt;/i&gt; Contributes to the Pathophysiology of Ovarian and Breast Cancer

Supplementary Tables S1-S4 from Amplification of &lt;i&gt;PVT1&lt;/i&gt; Contributes to the Pathophysiology of Ovarian and Breast Cancer

&lt;p&gt;Supplementary figure S1: Survival analysis (Kaplan-Meier estimates) with Breast cancer specific survival (BCSS) as end point for All patients of Cohort 1. Supplementary figure S2: Flowchart showing simplified results from Cohort 1. Supplementary figure S3: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 1. Supplementary figure S4: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 1. Supplementary figure S5: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 2. Supplementary figure S6: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 2.&lt;/p&gt;

&lt;p&gt;All supplementary materials and methods&lt;/p&gt;

&lt;p&gt;Supplementary table S1. Cell cycle genes Supplementary table S2. Cross-table of concordance between Ki67 immunohistochemical staining and gene expression signature classifications in Cohorts 1 and 2 Supplementary table S3. Clinico-pathological characteristics of patient subgroups in cohort 1 Supplementary table S4. Change in C-index when adding gene expression signatures to Ki67/IHC for All, ER+/LN-, ER+/LN-, ER- patients in Cohorts 1 and 2. Supplementary Table S5. Clinico-pathological characteristics of patient subgroups in cohort 2&lt;/p&gt;

&lt;p&gt;Supplementary table S1. Cell cycle genes Supplementary table S2. Cross-table of concordance between Ki67 immunohistochemical staining and gene expression signature classifications in Cohorts 1 and 2 Supplementary table S3. Clinico-pathological characteristics of patient subgroups in cohort 1 Supplementary table S4. Change in C-index when adding gene expression signatures to Ki67/IHC for All, ER+/LN-, ER+/LN-, ER- patients in Cohorts 1 and 2. Supplementary Table S5. Clinico-pathological characteristics of patient subgroups in cohort 2&lt;/p&gt;

&lt;p&gt;All supplementary materials and methods&lt;/p&gt;

&lt;p&gt;Supplementary figure S1: Survival analysis (Kaplan-Meier estimates) with Breast cancer specific survival (BCSS) as end point for All patients of Cohort 1. Supplementary figure S2: Flowchart showing simplified results from Cohort 1. Supplementary figure S3: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 1. Supplementary figure S4: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 1. Supplementary figure S5: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 2. Supplementary figure S6: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 2.&lt;/p&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; This study was designed to elucidate the role of amplification at 8q24 in the pathophysiology of ovarian and breast cancer because increased copy number at this locus is one of the most frequent genomic abnormalities in these cancers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; To accomplish this, we assessed the association of amplification at 8q24 with outcome in ovarian cancers using fluorescence &lt;i&gt;in situ&lt;/i&gt; hybridization to tissue microarrays and measured responses of ovarian and breast cancer cell lines to specific small interfering RNAs against the oncogene &lt;i&gt;MYC&lt;/i&gt; and a putative noncoding RNA, &lt;i&gt;PVT1&lt;/i&gt;, both of which map to 8q24.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Amplification of 8q24 was associated with significantly reduced survival duration. In addition, small interfering RNA–mediated reduction in either &lt;i&gt;PVT1&lt;/i&gt; or &lt;i&gt;MYC&lt;/i&gt; expression inhibited proliferation in breast and ovarian cancer cell lines in which they were both amplified and overexpressed but not in lines in which they were not amplified/overexpressed. Inhibition of &lt;i&gt;PVT1&lt;/i&gt; expression also induced a strong apoptotic response in cell lines in which it was overexpressed but not in lines in which it was not amplified/overexpressed. Inhibition of &lt;i&gt;MYC&lt;/i&gt;, on the other hand, did not induce an apoptotic response in cell lines in which &lt;i&gt;MYC&lt;/i&gt; was amplified and overexpressed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These results suggest that &lt;i&gt;MYC&lt;/i&gt; and &lt;i&gt;PVT1&lt;/i&gt; contribute independently to ovarian and breast pathogenesis when overexpressed because of genomic abnormalities. They also suggest that &lt;i&gt;PVT1&lt;/i&gt;-mediated inhibition of apoptosis may explain why amplification of 8q24 is associated with reduced survival duration in patients treated with agents that act through apoptotic mechanisms.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (Δ LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (Δ LR-χ&lt;sup&gt;2&lt;/sup&gt; Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. &lt;i&gt;Clin Cancer Res; 23(24); 7512–20. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; This study was designed to elucidate the role of amplification at 8q24 in the pathophysiology of ovarian and breast cancer because increased copy number at this locus is one of the most frequent genomic abnormalities in these cancers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; To accomplish this, we assessed the association of amplification at 8q24 with outcome in ovarian cancers using fluorescence &lt;i&gt;in situ&lt;/i&gt; hybridization to tissue microarrays and measured responses of ovarian and breast cancer cell lines to specific small interfering RNAs against the oncogene &lt;i&gt;MYC&lt;/i&gt; and a putative noncoding RNA, &lt;i&gt;PVT1&lt;/i&gt;, both of which map to 8q24.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Amplification of 8q24 was associated with significantly reduced survival duration. In addition, small interfering RNA–mediated reduction in either &lt;i&gt;PVT1&lt;/i&gt; or &lt;i&gt;MYC&lt;/i&gt; expression inhibited proliferation in breast and ovarian cancer cell lines in which they were both amplified and overexpressed but not in lines in which they were not amplified/overexpressed. Inhibition of &lt;i&gt;PVT1&lt;/i&gt; expression also induced a strong apoptotic response in cell lines in which it was overexpressed but not in lines in which it was not amplified/overexpressed. Inhibition of &lt;i&gt;MYC&lt;/i&gt;, on the other hand, did not induce an apoptotic response in cell lines in which &lt;i&gt;MYC&lt;/i&gt; was amplified and overexpressed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These results suggest that &lt;i&gt;MYC&lt;/i&gt; and &lt;i&gt;PVT1&lt;/i&gt; contribute independently to ovarian and breast pathogenesis when overexpressed because of genomic abnormalities. They also suggest that &lt;i&gt;PVT1&lt;/i&gt;-mediated inhibition of apoptosis may explain why amplification of 8q24 is associated with reduced survival duration in patients treated with agents that act through apoptotic mechanisms.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (Δ LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (Δ LR-χ&lt;sup&gt;2&lt;/sup&gt; Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. &lt;i&gt;Clin Cancer Res; 23(24); 7512–20. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Supplementary Figures S1-S2 from Amplification of &lt;i&gt;PVT1&lt;/i&gt; Contributes to the Pathophysiology of Ovarian and Breast Cancer

Supplementary Tables S1-S4 from Amplification of &lt;i&gt;PVT1&lt;/i&gt; Contributes to the Pathophysiology of Ovarian and Breast Cancer

A previously published acquisition and reconstruction method for magnetic resonance imaging (MRI) which allows for a reduction in the number of phase encoding acquisitions in an imaging sequence without reducing either resolution or field of view is described. Two (or more) noninteracting receiver coils simultaneously detect signals from the same tissue, and data from each of the receiver channels are separately recorded. An imaging sequence uses phase encoded echoes in the usual sense, but the reconstruction effectively calculates multiple Fourier projections of the tissue from one echo. An implementation with two receiver coils can reduce the number of needed phase encoded acquisitions by 50%. The reconstruction algorithm is analyzed, the signal-to-noise ratio is calculated, and artifacts are discussed. The technique has not yet been implementated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

To describe the sonographic features of endometrial cancer in relation to stage, grade, and histological type using the International Endometrial Tumor Analysis (IETA) terminology. Prospective multicentre study on 1714 women with endometrial cancer undergoing a standardised transvaginal gray-scale and Doppler ultrasound examination by an experienced ultrasound examiner using a high-end ultrasound system. Clinical and sonographic data were entered into a web-based protocol. Sonographic characteristics according to IETA were compared with outcome of hysterectomy, i.e. tumour stage, grade, and histological type. After excluding 175 women (no or delayed hysterectomy, final diagnosis other than endometrial cancer, or incomplete data), 1539 women were included in our statistical analysis. Mean age was 65 years (SD, 10.5), and mean BMI 30 (SD 7.1), 1378 (89.7%) women were postmenopausal, and 1296 (84.2%) reported abnormal vaginal bleeding. Gray-scale and colour Doppler features changed with increasing grade and stage. High-risk tumours (stage 1A, grade 3 or non-endometrioid or ≥ stage 1B) were less likely to have regular endometrial myometrial border (difference of -23%, 95% CI -27 to -18%), whilst they were larger (mean endometrial thickness; difference of +9mm, 95% CI +8 to +11mm), more frequently had non-uniform echogenicity (difference of -10%, 95% CI -15 to -5%), the multiple, multifocal vessel pattern (difference of +21%, 95% CI +16 to +26%), and a moderate or high colour score (difference of +22%, 95% CI +18 to +27%), than low-risk tumours. Gray-scale and colour Doppler ultrasound features of endometrial tumours vary by grade and stage. This knowledge may improve preoperative ultrasound discrimination between low and high-risk cancer.

Magnetic forces and torques were measured in a 640‐G permanent magnet The forces on external objects were directed in such a way and of such a strength that the likelihood of injury from unsupported ferromagnetic objects was very small. The forces and torques on ferromagnetic objects within the subject were comparable to those produced by gravitational and inertial efforts in daily living.

We describe the implementation of a field-cycling electromagnet in a whole-body clinical MRI system. A pulsed magnet is driven on during dead times of the NMR sequence and serves to increase the equilibrium magnetization induced in the patient. Signal transmission and reception occurs only during the period when the electromagnet is turned off and does not otherwise influence the data collection. Applications of the technology include image quality enhancement for low field MRI and for in vivo localized relaxation rate measurements.