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Search Results: 1 - 10 of 5098 matches for " Karen Mungall "
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The Sequence Ontology: a tool for the unification of genome annotations
Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner
Genome Biology , 2005, DOI: 10.1186/gb-2005-6-5-r44
Abstract: Genomic annotations are the focal point of sequencing, bioinformatics analysis, and molecular biology. They are the means by which we attach what we know about a genome to its sequence. Unfortunately, biological terminology is notoriously ambiguous; the same word is often used to describe more than one thing and there are many dialects. For example, does a coding sequence (CDS) contain the stop codon or is the stop codon part of the 3'-untranslated region (3' UTR)? There really is no right or wrong answer to such questions, but consistency is crucial when attempting to compare annotations from different sources, or even when comparing annotations performed by the same group over an extended period of time.At present, GenBank [1] houses 220 viral genomes, 152 bacterial genomes, 20 eukaryotic genomes and 18 archeal genomes. Other centers such as The Institute for Genomic Research (TIGR) [2] and the Joint Genome Institute (JGI) [3] also maintain and distribute annotations, as do many model organism databases such as FlyBase [4], WormBase [5], The Arabidopsis Information Resource (TAIR) [6] and the Saccharomyces Genome Database (SGD) [7]. Each of these groups has their own databases and many use their own data model to describe their annotations. There is no single place at which all sets of genome annotations can be found, and several sets are informally mirrored in multiple locations, leading to location-specific version differences. This can make it hazardous to exchange, combine and compare annotation data. Clearly, if genomic annotations were always described using the same language, then comparative analysis of the wealth of information distributed by these institutions would be enormously simplified: Hence the Sequence Ontology (SO) project. SO began 2 years ago, when a group of scientists and developers from the model organism databases - FlyBase, WormBase, Ensembl, SGD and MGI - came together to collect and unify the terms they used in their sequence annotation
Annotation of Two Large Contiguous Regions from the Haemonchus contortus Genome Using RNA-seq and Comparative Analysis with Caenorhabditis elegans
Roz Laing, Martin Hunt, Anna V. Protasio, Gary Saunders, Karen Mungall, Steven Laing, Frank Jackson, Michael Quail, Robin Beech, Matthew Berriman, John S. Gilleard
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023216
Abstract: The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.
Obol: Integrating Language and Meaning in Bio-Ontologies
Christopher J. Mungall
Comparative and Functional Genomics , 2004, DOI: 10.1002/cfg.435
Abstract: Ontologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language.With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non-trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.
Meeting Review: Epigenetics in Development and Disease
Andrew J. Mungall
Comparative and Functional Genomics , 2002, DOI: 10.1002/cfg.176
Abstract: The 2002 Keystone symposia held in Taos, New Mexico (21–26 February) saw the convergence of two related fields; Epigenetics in Development and Disease, and RNA Interference, Cosuppression and Related Phenomena. The meeting highlights presented here concentrate upon the sessions within the Epigenetics in Development and Disease meeting, although there were joint sessions which will also be discussed. Of course epigenetic regulation is not restricted to the vertebrates but I have chosen, rightly or wrongly, to limit the highlights to those concerning vertebrates.
Importance of Video-EEG Monitoring in the Diagnosis of Refractory Panic Attacks
Batool F. Kirmani,Diana Mungall
Case Reports in Psychiatry , 2013, DOI: 10.1155/2013/340792
Abstract: Partial seizures can be misdiagnosed as panic attacks. There is considerable overlap of symptoms between temporal lobe seizures and panic attacks making the diagnosis extremely challenging. Temporal lobe seizures can present with intense fear and autonomic symptoms which are also seen in panic disorders. This results in delay in diagnosis and management. We report an interesting case of a young woman who was diagnosed with right temporal lobe seizures with symptoms suggestive of a panic attack. We report an interesting case of a 24-year-old woman who sustained a motor vehicle accident at the age of sixteen resulting in significant head trauma. She was an unrestrained passenger and suffered major injuries, including an epidural hematoma. She was hospitalized and was in a coma for 3.5 months. She underwent extensive speech and physical therapy after the incident. She had residual mild cognitive decline and developed episodes characterized by anxiety, fear, whole body tingling, and associated autonomic symptoms lasting between one and two minutes. Interestingly, there was preservation of consciousness and speech during these episodes. She is able to carry on a normal conversation during and after the event. She does have a psychiatric history which includes depression and prolonged periods of irritability resulting in verbal outbursts even before the accident. She was admitted to the psychiatry facility a few years ago as a result of a hypomanic episode. Given her history, panic attacks were still high on the differential diagnosis. She was referred to an outside neurologist based on her history of head trauma and refractory nature of the episodes; seizures were considered in the differential diagnosis because of head trauma and abnormal imaging. Her electroencephalogram (EEG) was negative but magnetic resonance imaging did show encephalomalacia in the right temporal lobe. She was given a trial of valproic acid which did not affect the frequency of spells. She was eventually switched to a low dose of Lamotrigine XR 100?mg daily for mood stabilization and 4 possible seizures. She continues to have these episodes with a frequency of one to two per week. She was referred to our epilepsy center eight years after head trauma because of refractory panic attacks and suspicion of seizures due to head trauma. She was admitted to the inpatient unit for intensive video-EEG monitoring to capture these spells for definitive diagnosis. We were able to capture a few of her stereotypical episodes and they did correlate with abnormal brain waves. EEG revealed seizure
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
Kathryn E Holt, Nicholas R Thomson, John Wain, Gemma C Langridge, Rumina Hasan, Zulfiqar A Bhutta, Michael A Quail, Halina Norbertczak, Danielle Walker, Mark Simmonds, Brian White, Nathalie Bason, Karen Mungall, Gordon Dougan, Julian Parkhill
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-36
Abstract: We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2) identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes.Recombination and pseudogene-formation have been important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in Salmonella.Salmonella enterica serovars Typhi and Paratyphi A (Typhi, Paratyphi A) are human-restricted bacterial pathogens that cause related systemic diseases, known as typhoid, paratyphoid or enteric fever [1]. Together, these pathogens infect more than 25 million people annually worl
The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081
Nicholas R Thomson ,Sarah Howard,Brendan W Wren,Matthew T. G Holden,Lisa Crossman,Gregory L Challis,Carol Churcher,Karen Mungall,Karen Brooks,Tracey Chillingworth,Theresa Feltwell,Zahra Abdellah,Heidi Hauser,Kay Jagels,Mark Maddison,Sharon Moule,Mandy Sanders,Sally Whitehead,Michael A Quail,Gordon Dougan,Julian Parkhill,Michael B Prentice
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020206
Abstract: The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.
Sporadic Hemiplegic Migraine with ATP1A2 and Prothrombin Gene Mutations
Jose Aceves,Diana Mungall,Batool F. Kirmani
Case Reports in Neurological Medicine , 2013, DOI: 10.1155/2013/895057
Abstract: Background. Hemiplegic migraine is a rare type of migraine that may present in children and adolescents. Both familial and sporadic hemiplegic migraines have similar prevalence and clinical characteristics. Patient. We report an adolescent with sporadic hemiplegic migraine who previously had a similar attack in the past and who was initially evaluated for a possible acute ischemic event. Results. Magnetic resonance angiography showed dilatation of the left middle cerebral artery that resolved in a follow-up study. She was also found to have a ATP1A2 (c.2273 G>C) mutation and a heterozygous prothrombin mutation. Conclusions. We suggest that patients with sporadic hemiplegic migraine be tested for both ATP1A2 mutations which in some cases may be pathogenic, and prothrombin mutations which increase the stroke risk for this patient population. 1. Introduction Hemiplegic migraine is a rare subtype of migraine associated with transient hemiplegia [1] that occurs with equal prevalence in either sporadic or familial forms [1]. A motor aura is required for its diagnosis but it should be kept in mind that it is not the only type of aura occurring in the patient [2]. Sporadic hemiplegic migraine shares a similar clinical profile as familial hemiplegic migraine [3]. It is the only migraine disorder where pathogenetic mutations are known, since it is associated with mutations in the CANA1A, ATP1A2, and SCN1A genes [1]. Mutations in these genes have also been reported in some cases of sporadic hemiplegic migraine [4, 5]. Migraine has been reported to be a risk factor for ischemic stroke with possible mechanisms involving neuronal, vascular and coagulation abnormalities [6]. The case report presented in this paper describes a mutation in the ATP1A2 and prothrombin genes in a young adolescent with sporadic hemiplegic migraine. Mutations in the prothrombin gene may further increase the risk for stroke occurrence. 2. Case Report A previously healthy 15-year-old girl was playing tennis when suddenly her speech became slurry and the right lower face and arm became numb. The family noticed a right facial droop and the patient realized that she could not grip the racquet with her right hand. The episode lasted 30 minutes. Subsequently, she developed a severe throbbing headache localized to the right frontal-temporal area accompanied by photophobia. In the local emergency room she underwent a computed tomography of the brain which was within normal limits. She was treated with aspirin and morphine and was transferred to our institution for further evaluation. Upon arrival,
Role of Anticonvulsants in the Management of AIDS Related Seizures
Batool F. Kirmani,Diana Mungall-Robinson
Frontiers in Neurology , 2014, DOI: 10.3389/fneur.2014.00010
Abstract: Seventy percent of the AIDS patients have neurological complications. Seizures are one of the complications and can occur at any stage. Seizures can be life-threatening and treatment with anticonvulsants is warranted. The therapeutic dilemma occurs in this case because of the interactions between the anticonvulsants, especially the first generation anticonvulsants, with antiretroviral agents resulting in significant side-effects including toxicity. The non-availability of second-generation anticonvulsants and cost constraints further limit the choices for the physicians. In this mini-review, we discuss the management of AIDS related seizures with emphasis on the drug–drug interactions between anticonvulsants and antiretroviral agents. We will also address the future directions and the need for prospective studies with second-generation anticonvulsants.
中国科学 地球科学 中国科学 地球科学 , 2004,
Abstract: ?通过座着液滴技术,研究锍成分变化对锍在似诺里尔斯克玄武岩岩浆中界面张力大小变化的规律.锍的成分有两个系列:FeS-Cu2S-Ni3S2和FeO-FeS.由实验得出如下结果:1)在FeS-Cu2S-Ni3S2系列中,随着锍中Cu和Ni含量的增加,其界面张力逐渐变小;2)在FeO-FeS系列中,随着锍中氧含量增高,其界面张力逐渐变大.实验结果表明,形成大规模岩浆Cu-Ni硫化物矿床有两个重要条件,一是基性及超基性母岩浆中必须富含Cu和Ni,这样在岩浆演化早期阶段,由于硫化物熔体的界面张力相对较小,不易形成硫化物液滴,或形成的硫化物液滴不易聚集;二是岩浆定位深度较小或岩浆定位环境构造较发育,有利于大规模岩浆硫化物矿床的形成,因为在这种情况下,系统中氧逸度较高,硫化物熔体界面张力较大,有利于硫化物熔体的分离和聚集.
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