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1.  Pharmacodynamic assays to facilitate preclinical and clinical development of pre-mRNA splicing modulatory drug candidates 
The spliceosome has recently emerged as a new target for cancer chemotherapy and novel antitumor spliceosome targeted agents are under development. Here, we describe two types of novel pharmacodynamic assays that facilitate drug discovery and development of this intriguing class of innovative therapeutics; the first assay is useful for preclinical optimization of small-molecule agents that target the SF3B1 spliceosomal protein in animals, the second assay is an ex vivo validated, gel-based assay for the measurement of drug exposure in human leukocytes. The first assay utilizes a highly specific bioluminescent splicing reporter, based on the skipping of exons 4–11 of a Luc-MDM2 construct, which specifically yields active luciferase when treated with small-molecule spliceosome modulators. We demonstrate that this reporter can be used to monitor alternative splicing in whole cells in vitro. We describe here that cell lines carrying the reporter can be used in vivo for the efficient pharmacodynamic analysis of agents during drug optimization and development. We also demonstrate dose- and time-dependent on-target activity of sudemycin D6 (SD6), which leads to dramatic tumor regression. The second assay relies on the treatment of freshly drawn human blood with SD6 ex vivo treatment. Changes in alternative splicing are determined by RT-PCR using genes previously identified in in vitro experiments. The Luc-MDM2 alternative splicing bioluminescent reporter and the splicing changes observed in human leukocytes should allow for the more facile translation of novel splicing modulators into clinical application.
doi:10.1002/prp2.158
PMCID: PMC4492733  PMID: 26171237
Cancer; exon-skipping reporter; in vivo imaging; pre-mRNA splicing; spliceosome modulators; sudemycin D6
2.  Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone 
Park, Daniel J. | Dudas, Gytis | Wohl, Shirlee | Goba, Augustine | Whitmer, Shannon L.M. | Andersen, Kristian G. | Sealfon, Rachel S. | Ladner, Jason T. | Kugelman, Jeffrey R. | Matranga, Christian B. | Winnicki, Sarah M. | Qu, James | Gire, Stephen K. | Gladden-Young, Adrianne | Jalloh, Simbirie | Nosamiefan, Dolo | Yozwiak, Nathan L. | Moses, Lina M. | Jiang, Pan-Pan | Lin, Aaron E. | Schaffner, Stephen F. | Bird, Brian | Towner, Jonathan | Mamoh, Mambu | Gbakie, Michael | Kanneh, Lansana | Kargbo, David | Massally, James L.B. | Kamara, Fatima K. | Konuwa, Edwin | Sellu, Josephine | Jalloh, Abdul A. | Mustapha, Ibrahim | Foday, Momoh | Yillah, Mohamed | Erickson, Bobbie R. | Sealy, Tara | Blau, Dianna | Paddock, Christopher | Brault, Aaron | Amman, Brian | Basile, Jane | Bearden, Scott | Belser, Jessica | Bergeron, Eric | Campbell, Shelley | Chakrabarti, Ayan | Dodd, Kimberly | Flint, Mike | Gibbons, Aridth | Goodman, Christin | Klena, John | McMullan, Laura | Morgan, Laura | Russell, Brandy | Salzer, Johanna | Sanchez, Angela | Wang, David | Jungreis, Irwin | Tomkins-Tinch, Christopher | Kislyuk, Andrey | Lin, Michael F. | Chapman, Sinead | MacInnis, Bronwyn | Matthews, Ashley | Bochicchio, James | Hensley, Lisa E. | Kuhn, Jens H. | Nusbaum, Chad | Schieffelin, John S. | Birren, Bruce W. | Forget, Marc | Nichol, Stuart T. | Palacios, Gustavo F. | Ndiaye, Daouda | Happi, Christian | Gevao, Sahr M. | Vandi, Mohamed A. | Kargbo, Brima | Holmes, Edward C. | Bedford, Trevor | Gnirke, Andreas | Ströher, Ute | Rambaut, Andrew | Garry, Robert F. | Sabeti, Pardis C.
Cell  2015;161(7):1516-1526.
Summary
The 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission.
Graphical Abstract
Highlights
•In Sierra Leone, transmission has primarily been within-country, not between-country•Infectious doses are large enough for intrahost variants to transmit between hosts•A prolonged epidemic removes deleterious mutations from the viral population•There is preliminary evidence for human RNA editing effects on the Ebola genome
Ebola virus genomes from 232 patients sampled over 7 months in Sierra Leone were sequenced. Transmission of intrahost genetic variants suggests a sufficiently high infectious dose during transmission. The human host may have caused direct alterations to the Ebola virus genome.
doi:10.1016/j.cell.2015.06.007
PMCID: PMC4503805  PMID: 26091036
3.  Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA 
Archives of virology  2013;159(5):1229-1237.
Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOVH.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
doi:10.1007/s00705-013-1877-2
PMCID: PMC4010566  PMID: 24190508
cDNA clone; cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; reverse genetics; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
4.  Genome Sequencing of 18 Francisella Strains To Aid in Assay Development and Testing 
Genome Announcements  2015;3(2):e00147-15.
Francisella tularensis is a highly infectious bacterium with the potential to cause high fatality rates if infections are untreated. To aid in the development of rapid and accurate detection assays, we have sequenced and annotated the genomes of 18 F. tularensis and Francisella philomiragia strains.
doi:10.1128/genomeA.00147-15
PMCID: PMC4417685  PMID: 25931589
5.  Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica 
Genome Announcements  2015;3(2):e00148-15.
The genus Yersinia includes three human pathogens, of which Yersinia pestis is responsible for >2,000 illnesses each year. To aid in the development of detection assays and aid further phylogenetic elucidation, we sequenced and assembled the complete genomes of 32 strains (across 9 Yersinia species).
doi:10.1128/genomeA.00148-15
PMCID: PMC4417686  PMID: 25931590
6.  Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species 
Genome Announcements  2015;3(2):e00151-15.
In 2011, the Association of Analytical Communities (AOAC) International released a list of Bacillus strains relevant to biothreat molecular detection assays. We present the complete and annotated genome assemblies for the 15 strains listed on the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
doi:10.1128/genomeA.00151-15
PMCID: PMC4417687  PMID: 25931591
7.  Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor 
Genome Announcements  2015;3(2):e00159-15.
The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full genome sequences for a panel of 59 Burkholderia strains, selected to aid in detection assay development.
doi:10.1128/genomeA.00159-15
PMCID: PMC4417688  PMID: 25931592
8.  Complete Coding Sequences of Eastern Equine Encephalitis Virus and Venezuelan Equine Encephalitis Virus Strains Isolated from Human Cases 
Genome Announcements  2015;3(2):e00243-15.
We obtained the complete coding genome of an eastern equine encephalitis virus (EEEV) strain, EEEV V105-00210, and the complete genome of a Venezuelan equine encephalitis virus (VEEV) strain, VEEV INH-9813. They were obtained from human cases and are proposed as reference challenge strains for vaccine and therapeutic development in animal models.
doi:10.1128/genomeA.00243-15
PMCID: PMC4408325  PMID: 25908124
9.  Pre-mRNA Splicing-Modulatory Pharmacophores: The Total Synthesis of Herboxidiene, a Pladienolide-Herboxidiene Hybrid Analog and Related Derivatives 
ACS chemical biology  2013;9(3):643-648.
Herboxidiene is a natural product that has previously been shown to exhibit antitumor activity by targeting the spliceosome. This activity makes herboxidiene a valuable starting point for the development of anticancer drugs. Here, we report an improved enantioselective synthesis of herboxidiene and the first report of its biologically active totally synthetic analog: 6-norherboxidiene. The synthesis of the tetrahydropyran moiety utilizes the novel application of inverse electron-demand Diels-Alder chemistry and the Ferrier-type rearrangement as key steps. We report, for the first time, cytotoxicity IC50s for synthetic herboxidiene and analogs in human tumor cell lines. We have also demonstrated that synthetic herboxidiene and its analogs can potently modulate the alternate splicing of MDM-2 pre-mRNA.
doi:10.1021/cb400695j
PMCID: PMC3962696  PMID: 24377313
10.  Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals 
Veterinary microbiology  2008;133(0):145-153.
Definitive diagnosis of vesicular or vesicular-like lesions in livestock animals presents challenges both for veterinary clinicians and diagnostic laboratories. It is often impossible to diagnose the causative disease agent on a clinical basis alone and difficult to collect ample vesicular epithelium samples. Due to restrictions of time and sample size, once laboratory tests have ruled out foot-and-mouth disease, vesicular stomatitis and swine vesicular disease a definitive diagnosis may remain elusive. With the ability to test a small quantity of sample for a large number of pathogens simultaneously, DNA microarrays represent a potential solution to this problem. This study describes the application of a long oligonucleotide microarray assay to the identification of viruses known to cause vesicular or vesicular-like lesions in livestock animals. Eighteen virus isolates from cell culture were successfully identified to genus level, including representatives of each foot-and-mouth disease virus serotype, two species of vesicular stomatitis virus, swine vesicular disease virus, vesicular exanthema of swine virus, bovine herpesvirus 1, orf virus, pseudocowpox virus, bluetongue virus serotype 1 and bovine viral diarrhoea virus 1. Vesicular stomatitis virus and vesicular exanthema of swine virus were also identified in vesicular epithelium samples, with varying levels of sensitivity. The results indicate that with further development this microarray assay could be a valuable tool for the diagnosis of vesicular and vesicular-like diseases.
doi:10.1016/j.vetmic.2008.05.030
PMCID: PMC4310687  PMID: 18621489
11.  Short Communication: New Recognition Of Enterovirus Infections In Bottlenose Dolphins (Tursiops Truncatus) 
Veterinary microbiology  2009;139(0):170-175.
An enterovirus was cultured from an erosive tongue lesion of a bottlenose dolphin (Tursiops truncatus). The morphology of virions on negative staining electron microscopy was consistent with those of enteroviruses. Analysis of 2613 bp of the polyprotein gene identified the isolate as a novel enterovirus strain, tentatively named bottlenose dolphin enterovirus (BDEV), that nests within the species Bovine enterovirus. Serologic evidence of exposure to enteroviruses was common in both free ranging and managed collection dolphins. Managed collection dolphins were more likely to have high antibody levels, although the highest levels were reported in free ranging populations. Associations between enterovirus antibody levels, and age, sex, complete blood counts, and clinical serum biochemistries were explored. Dolphins with higher antibody levels were more likely to be hyperproteinemic and hyperglobulinemic.
doi:10.1016/j.vetmic.2009.05.010
PMCID: PMC4310689  PMID: 19581059
12.  MOLECULAR CHARACTERIZATION OF SEVERE AND MILD CASES OF INFLUENZA A (H1N1) 2009 STRAIN FROM ARGENTINA 
Medicina  2010;70(6):518-523.
While worldwide pandemic influenza A(H1N1) pdm case fatality rate (CFR) was 0.4%, Argentina’s was 4.5%. A total of 34 strains from mild and severe cases were analyzed. A full genome sequencing was carried out on 26 of these, and a partial sequencing on the remaining eight. We observed no evidence that the high CFR can be attributed to direct virus changes. No evidence of re-assortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence was observed. Although the mutation D225G associated with severity in the latest reports from the Ukraine and Norway is not observed among the Argentine strains, an amino acid change in the area (S206T) surrounding the HA receptor binding domain was observed, the same previously established worldwide.
PMCID: PMC4310694  PMID: 21163739
H1N1 pdm; influenza; Argentina
13.  Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics 
mBio  2015;6(1):e02227-14.
ABSTRACT 
Until recently, Ebola virus (EBOV) was a rarely encountered human pathogen that caused disease among small populations with extraordinarily high lethality. At the end of 2013, EBOV initiated an unprecedented disease outbreak in West Africa that is still ongoing and has already caused thousands of deaths. Recent studies revealed the genomic changes this particular EBOV variant undergoes over time during human-to-human transmission. Here we highlight the genomic changes that might negatively impact the efficacy of currently available EBOV sequence-based candidate therapeutics, such as small interfering RNAs (siRNAs), phosphorodiamidate morpholino oligomers (PMOs), and antibodies. Ten of the observed mutations modify the sequence of the binding sites of monoclonal antibody (MAb) 13F6, MAb 1H3, MAb 6D8, MAb 13C6, and siRNA EK-1, VP24, and VP35 targets and might influence the binding efficacy of the sequence-based therapeutics, suggesting that their efficacy should be reevaluated against the currently circulating strain.
doi:10.1128/mBio.02227-14
PMCID: PMC4313914  PMID: 25604787
14.  Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses 
Virology  2013;448:10.1016/j.virol.2013.10.024.
Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito-bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1, U2, and U3 that apparently arose by gene duplication. To further investigate the U1-U2-U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically.
doi:10.1016/j.virol.2013.10.024
PMCID: PMC3873333  PMID: 24314659
Flanders virus; Hart Park virus; Hart Park serogroup; rhabdovirus; gene duplication; U1, U2, and U3 proteins; SH protein; coupled translation; bird-associated arbovirus
15.  Optimization of Antitumor Modulators of Pre-mRNA Splicing 
Journal of medicinal chemistry  2013;56(24):10033-10044.
The spliceosome regulates pre-mRNA splicing, which is a critical process in normal mammalian cells. Recently recurrent mutations in numerous spliceosomal proteins have been associated with a number of cancers. Previously natural product antitumor agents have been shown to interact with one of the proteins that is subject to recurrent mutations (SF3B1). We report the optimization of a class of tumor-selective spliceosome modulators, which demonstrate significant in vivo antitumor activity. This optimization culminated in the discovery of sudemycin D6, which shows potent cytotoxic activity in the melanoma line SK-MEL-2 (IC50= 39 nM) and other tumor lines, including: JeKo-1 (IC50= 26 nM), HeLa (IC50= 50 nM), and SK-N-AS (IC50= 81 nM). We also report improved processes for the synthesis of these compounds. Our work supports the idea that sudemycin D6 is worthy of further investigation as a novel preclinical anticancer agent with application in the treatment of numerous human cancers.
doi:10.1021/jm401370h
PMCID: PMC3932738  PMID: 24325474
16.  Reidentification of Ebola Virus E718 and ME as Ebola Virus/H.sapiens-tc/COD/1976/Yambuku-Ecran 
Genome Announcements  2014;2(6):e01178-14.
Ebola virus (EBOV) was discovered in 1976 around Yambuku, Zaire. A lack of nomenclature standards resulted in a variety of designations for each isolate, leading to confusion in the literature and databases. We sequenced the genome of isolate E718/ME/Ecran and unified the various designations under Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Ecran.
doi:10.1128/genomeA.01178-14
PMCID: PMC4239354  PMID: 25414499
17.  Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014 
Viruses  2014;6(11):4760-4799.
In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.
doi:10.3390/v6114760
PMCID: PMC4246247  PMID: 25421896
Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; Lomela; Lokolia; Makona; mononegavirad; Mononegavirales; mononegavirus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
19.  Viral diversity and clonal evolution from unphased genomic data 
BMC Genomics  2014;15(Suppl 6):S17.
Background
Clonal expansion is a process in which a single organism reproduces asexually, giving rise to a diversifying population. It is pervasive in nature, from within-host pathogen evolution to emergent infectious disease outbreaks. Standard phylogenetic tools rely on full-length genomes of individual pathogens or population consensus sequences (phased genotypes).
Although high-throughput sequencing technologies are able to sample population diversity, the short sequence reads inherent to them preclude assessing whether two reads originate from the same clone (unphased genotypes). This obstacle severely limits the application of phylogenetic methods and investigation of within-host dynamics of acute infections using this rich data source.
Methods
We introduce two measures of diversity to study the evolution of clonal populations using unphased genomic data, which eliminate the need to construct full-length genomes. Our method follows a maximum likelihood approach to estimate evolutionary rates and times to the most recent common ancestor, based on a relaxed molecular clock model; independent of a growth model. Deviations from neutral evolution indicate the presence of selection and bottleneck events.
Results
We evaluated our methods in silico and then compared it against existing approaches with the well-characterized 2009 H1N1 influenza pandemic. We then applied our method to high-throughput genomic data from marburgvirus-infected non-human primates and inferred the time of infection and the intra-host evolutionary rate, and identified purifying selection in viral populations.
Conclusions
Our method has the power to make use of minor variants present in less than 1% of the population and capture genomic diversification within days of infection, making it an ideal tool for the study of acute RNA viral infection dynamics.
doi:10.1186/1471-2164-15-S6-S17
PMCID: PMC4240099  PMID: 25573168
Clonal evolution; Evolutionary dynamics; Viral genomic diversity; Marburgvirus
20.  Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (Arteriviridae: Arterivirus) 
Genome Announcements  2014;2(5):e00978-14.
Simian hemorrhagic fever virus (SHFV) variant NIH LVR42-0/M6941 is the only remaining SHFV in culture, and only a single genome sequence record exists in GenBank/RefSeq. We compared the genomic sequence of NIH LVR42-0/M6941 acquired from the ATCC in 2011 to NIH LVR42-0/M6941 genomes sequenced directly from nonhuman primates experimentally infected in 1989.
doi:10.1128/genomeA.00978-14
PMCID: PMC4192379  PMID: 25301647
21.  Transcriptome reconstruction and annotation of cynomolgus and African green monkey 
BMC Genomics  2014;15(1):846.
Background
Non-human primates (NHPs) and humans share major biological mechanisms, functions, and responses due to their close evolutionary relationship and, as such, provide ideal animal models to study human diseases. RNA expression in NHPs provides specific signatures that are informative of disease mechanisms and therapeutic modes of action. Unlike the human transcriptome, the transcriptomes of major NHP animal models are yet to be comprehensively annotated.
Results
In this manuscript, employing deep RNA sequencing of seven tissue samples, we characterize the transcriptomes of two commonly used NHP animal models: Cynomolgus macaque (Macaca fascicularis) and African green monkey (Chlorocebus aethiops). We present the Multi-Species Annotation (MSA) pipeline that leverages well-annotated primate species and annotates 99.8% of reconstructed transcripts. We elucidate tissue-specific expression profiles and report 13 experimentally validated novel transcripts in these NHP animal models.
Conclusion
We report comprehensively annotated transcriptomes of two non-human primates, which we have made publically available on a customized UCSC Genome Browser interface. The MSA pipeline is also freely available.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-846) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-846
PMCID: PMC4194418  PMID: 25277458
Cynomolgus macaque; Macaca fascicularis; African green monkey; Chlorocebus aethiops; RNA-seq; Transcriptome; Genomics; Annotation; Database
22.  Development and Evaluation of a Panel of Filovirus Sequence Capture Probes for Pathogen Detection by Next-Generation Sequencing 
PLoS ONE  2014;9(9):e107007.
A detailed understanding of the circulating pathogens in a particular geographic location aids in effectively utilizing targeted, rapid diagnostic assays, thus allowing for appropriate therapeutic and containment procedures. This is especially important in regions prevalent for highly pathogenic viruses co-circulating with other endemic pathogens such as the malaria parasite. The importance of biosurveillance is highlighted by the ongoing Ebola virus disease outbreak in West Africa. For example, a more comprehensive assessment of the regional pathogens could have identified the risk of a filovirus disease outbreak earlier and led to an improved diagnostic and response capacity in the region. In this context, being able to rapidly screen a single sample for multiple pathogens in a single tube reaction could improve both diagnostics as well as pathogen surveillance. Here, probes were designed to capture identifying filovirus sequence for the ebolaviruses Sudan, Ebola, Reston, Taï Forest, and Bundibugyo and the Marburg virus variants Musoke, Ci67, and Angola. These probes were combined into a single probe panel, and the captured filovirus sequence was successfully identified using the MiSeq next-generation sequencing platform. This panel was then used to identify the specific filovirus from nonhuman primates experimentally infected with Ebola virus as well as Bundibugyo virus in human sera samples from the Democratic Republic of the Congo, thus demonstrating the utility for pathogen detection using clinical samples. While not as sensitive and rapid as real-time PCR, this panel, along with incorporating additional sequence capture probe panels, could be used for broad pathogen screening and biosurveillance.
doi:10.1371/journal.pone.0107007
PMCID: PMC4160210  PMID: 25207553
23.  Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase 
Journal of proteome research  2011;10(4):2104-2112.
In this study a UPLC-tandem (Waters Xevo TQ) MRM based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice; including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a “fingerprint” characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples.
doi:10.1021/pr1011119
PMCID: PMC4158837  PMID: 21322650
metabolomics; metabolic networks; metabolic complexity; hydrophilic metabolites; LC/MS; MRM; reversed-phase HPLC; C57BL/6 mice
24.  Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names 
Kuhn, Jens H. | Andersen, Kristian G. | Bào, Yīmíng | Bavari, Sina | Becker, Stephan | Bennett, Richard S. | Bergman, Nicholas H. | Blinkova, Olga | Bradfute, Steven | Brister, J. Rodney | Bukreyev, Alexander | Chandran, Kartik | Chepurnov, Alexander A. | Davey, Robert A. | Dietzgen, Ralf G. | Doggett, Norman A. | Dolnik, Olga | Dye, John M. | Enterlein, Sven | Fenimore, Paul W. | Formenty, Pierre | Freiberg, Alexander N. | Garry, Robert F. | Garza, Nicole L. | Gire, Stephen K. | Gonzalez, Jean-Paul | Griffiths, Anthony | Happi, Christian T. | Hensley, Lisa E. | Herbert, Andrew S. | Hevey, Michael C. | Hoenen, Thomas | Honko, Anna N. | Ignatyev, Georgy M. | Jahrling, Peter B. | Johnson, Joshua C. | Johnson, Karl M. | Kindrachuk, Jason | Klenk, Hans-Dieter | Kobinger, Gary | Kochel, Tadeusz J. | Lackemeyer, Matthew G. | Lackner, Daniel F. | Leroy, Eric M. | Lever, Mark S. | Mühlberger, Elke | Netesov, Sergey V. | Olinger, Gene G. | Omilabu, Sunday A. | Palacios, Gustavo | Panchal, Rekha G. | Park, Daniel J. | Patterson, Jean L. | Paweska, Janusz T. | Peters, Clarence J. | Pettitt, James | Pitt, Louise | Radoshitzky, Sheli R. | Ryabchikova, Elena I. | Saphire, Erica Ollmann | Sabeti, Pardis C. | Sealfon, Rachel | Shestopalov, Aleksandr M. | Smither, Sophie J. | Sullivan, Nancy J. | Swanepoel, Robert | Takada, Ayato | Towner, Jonathan S. | van der Groen, Guido | Volchkov, Viktor E. | Volchkova, Valentina A. | Wahl-Jensen, Victoria | Warren, Travis K. | Warfield, Kelly L. | Weidmann, Manfred | Nichol, Stuart T.
Viruses  2014;6(9):3663-3682.
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
doi:10.3390/v6093663
PMCID: PMC4189044  PMID: 25256396
Bundibugyo virus; cDNA clone; cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; Ravn virus; RefSeq; Reston virus; reverse genetics; Sudan virus; Taï Forest virus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
25.  Draft Genome Assembly of Acinetobacter baumannii ATCC 19606 
Genome Announcements  2014;2(4):e00832-14.
Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, and treatment technologies. Here we present the improved draft assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome contains 3,750 coding regions and has a 39.1% G+C content.
doi:10.1128/genomeA.00832-14
PMCID: PMC4153487  PMID: 25146140

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