Identification of an Emergent Pathogen, Bartonella vinsonii, Using Next-Generation Sequencing in a Patient With Culture-Negative Endocarditis.

Diagnosis and treatment of culture negative endocarditis remains a challenge. This report describes a rare cause of endocarditis in humans, Bartonella vinsonii, identified through next generation sequencing of plasma microbial cell-free DNA with confirmation of cardiac valve tissue infection through immunohistochemical staining and polymerase chain reaction.

Meaningful Use of Electronic Health Records for Quality Assessment and Review of Clinical Ethics Consultation.

Evolving practice requires peer review of clinical ethics (CE) consultation for quality assessment and improvement. Many institutions have identified the chart note as the basis for this process, but to our knowledge, electronic health record (EHR) systems are not necessarily designed to easily include CE consultation notes. This article provides a framework for the inclusion of CE consultation notes into the formal EHR, describing a developed system in the Epic EHR that allows for the elaborated electronic notation of the CE chart note. The implementation of the "meaningful use" criteria for EHR, mandated by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009, requires that health professionals meet certain standards for quality, efficiency, and safety, all of which overlap with the goals of standardization, peer review, and quality improvement within CE consultation.

A Case of Systemic Lupus Erythematosus Presenting as Guillain-Barré Syndrome.

Systemic lupus erythematosus (SLE) is an autoimmune systemic disease with multiple organ involvement with high morbidity and mortality rate. Among the severe potential fatal complications are those of the central and peripheral nervous system which usually develop during the course of the disease and very rarely from the outset of the disease. We are reporting a rare case of Miller-Fisher (MFS) variant of Guillain-Barré syndrome (GBS) as the first manifestation of SLE in a 41-year-old female who progressed to flaccid paralysis with no neurological improvement with initial immunosuppressive therapy, plasmapheresis, and first cycle of intravenous immunoglobulin (IVIG) but with remarkable and complete recovery after the second 5-day course of IVIG.

Non-Systemic Vasculitic Neuropathy: An Enigmatic Clinical Entity.

BACKGROUND: Non-systemic vasculitic peripheral neuropathy is a rare condition characterized by necrotizing inflammation resulting in luminal narrowing of the vasa nervorum, leading to ischemic injury to peripheral nerves. Here, we present the case of 63-year-old woman with subacute onset of severe hyperesthesia of the lower extremities accompanied by foot drop. CASE REPORT: A 63-year-old woman with prolonged history of uncontrolled diabetes mellitus presented with subacute onset of severe bilateral lower extremity hyperesthesia and motor weakness along with left-sided foot drop. She had multiple emergency room visits with no relief of her symptoms. High doses of analgesics were insufficient to control pain. Laboratory tests were positive only for high erythrocyte sedimentation rate and C-reactive protein. A skin biopsy obtained 5 cm above the left lateral malleolus revealed medium-sized dermal vasculitis with dense mononuclear infiltrate. Electromyography showed peripheral neuropathy. A nerve biopsy was needed to reveal the exact diagnosis. CONCLUSIONS: Diagnosis of non-systemic vasculitic peripheral neuropathy can be delayed or missed in patients with uncontrolled diabetes mellitus, leading to significant morbidity. Elevated markers of inflammation in the absence of a possible explanation should prompt the clinician to perform a nerve biopsy; however, it is an invasive procedure and is associated with complications of post-neuropathic pain and delayed wound healing. Magnetic resonance angiography of the lower limbs, if combined with skin biopsy, can save the patient from undergoing nerve biopsy.

Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.

Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15-18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.

Finding the missing link in neuromyelitis optica presenting with recurrent transverse myelitis flares.

Neuromyelitis optica (NMO) is a distinct clinical entity from multiple sclerosis with its own clinical, laboratory and pathological characteristics. Definitive diagnosis of NMO is challenging at times as there can be a long interval between the occurrence of the index event and other neurological deficits which would fulfill the diagnostic criteria. Detection of NMO antibody could serve as an early marker in the disease progression. We present a young woman previously identified to have NMO antibody with recurring episodes of transverse myelitis for 3 years before manifesting with optic neuritis.

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related species. This article reports on the comparison of gene order between these 12 species and on the fixed rearrangement events that disrupt gene order. Three major themes are addressed: the conservation of syntenic blocks across species, the disruption of syntenic blocks (via chromosomal inversion events) and its relationship to the phylogenetic distribution of these species, and the rate of rearrangement events over evolutionary time. Comparison of syntenic blocks across this large genomic data set confirms that genetic elements are largely (95%) localized to the same Muller element across genus Drosophila species and paracentric inversions serve as the dominant mechanism for shuffling the order of genes along a chromosome. Gene-order scrambling between species is in accordance with the estimated evolutionary distances between them and we find it to approximate a linear process over time (linear to exponential with alternate divergence time estimates). We find the distribution of synteny segment sizes to be biased by a large number of small segments with comparatively fewer large segments. Our results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported. Identification of conserved syntenic blocks across these genomes suggests a large number of conserved blocks with varying levels of embryonic expression correlation in Drosophila melanogaster. On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation.

Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps.

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.

Genome-scale analysis of positionally relocated genes.

During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the relocation of individual genes. This latter category, which we will refer to as positionally relocated genes (PRGs), is the subject of this report. Assessment of the magnitude of such PRGs and of possible contributing mechanisms is aided by a comparative analysis of related genomes, where conserved chromosomal organization can aid in identifying genes that have acquired a new location in a lineage of these genomes. Here we utilize two methods to comprehensively identify relocated protein-coding genes in the recently sequenced genomes of 12 species of genus Drosophila. We use exceptions to the general rule of maintenance of chromosome arm (Muller element) association for most Drosophila genes to identify one major class of PRGs. We also identify a partially overlapping set of PRGs among "embedded genes," located within the extents of other surrounding genes. We provide evidence that PRG movements have at least two different origins: Some events occur via retrotransposition of processed RNAs and others via a DNA-based transposition mechanism. Overall, we identify several hundred PRGs that arose within a lineage of the genus Drosophila phylogeny and provide suggestive evidence that a few thousand such events have occurred within the radiation of the insect order Diptera, thereby illustrating the magnitude of the contribution of PRG movement to chromosomal reorganization during evolution.

VectorBase: a home for invertebrate vectors of human pathogens.

VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.

Techniques for multi-genome synteny analysis to overcome assembly limitations.

Genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species, and speciation analysis. With the rapid availability of multiple genomes, there is a need for efficient solutions to aid in comparative syntenic analysis. Current methods rely on homology assessment and multiple alignment based solutions to determine homologs of genetic markers between species and to infer syntenic relationships. One of the primary challenges facing multi-genome syntenic analysis is the uncertainty posed by genome assembly data with un-sequenced gaps and possible assembly errors. Currently, manual intervention is necessary to tune and correct the results of homology assessment and synteny inference. This paper presents a novel automated approach to overcome some of these limitations. It uses a graph based algorithm to infer sub-graphs denoting synteny chains with the objective of choosing the best locations for homologous elements, in the presence of paralogs, in order to maximize synteny. These synteny chains are expanded by merging sub-graphs based on various user defined thresholds for micro-syntenic scrambling. This approach comprehends and accommodates for contig and scaffold gaps in the assembly to determine homologous genetic elements that might either fall in unsequenced assembly gaps or lie on the edges of sequenced segments or on small fragments. Furthermore, it provides an automated solution for breakpoint analysis and a comparative study of chromosomal rearrangements between species. This approach was applied to a comparative study involving Drosophila.melanogaster and Drosophila.pseudoobscura genomes, as an example, and has been useful in analyzing inter-species syntenic relationships.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.