Molecular characterization of encephalomyocarditis virus strains isolated from an African elephant and rats in a French zoo

In November 2013, a fatal encephalomyocarditis virus (EMCV) case in a captive African elephant ( Loxodonta africana) occurred at the Réserve Africaine de Sigean, a zoo in the south of France. Here we report the molecular characterization of the EMCV strains isolated from samples collected from the dead elephant and from 3 rats ( Rattus rattus) captured in the zoo at the same time. The EMCV infection was confirmed by reverse-transcription real-time PCR (RT-rtPCR) and genome sequencing. Complete genome sequencing and sequence alignment indicated that the elephant’s EMCV strain was 98.1–99.9% identical to the rat EMCV isolates at the nucleotide sequence level. Phylogenetic analysis of the ORF, P1, VP1, and 3D sequences revealed that the elephant and rat strains clustered into lineage A of the EMCV 1 group. To our knowledge, molecular characterization of EMCV in France and Europe has not been reported previously in a captive elephant. The full genome analyses of EMCV isolated from an elephant and rats in the same outbreak emphasizes the role of rodents in EMCV introduction and circulation in zoos.

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SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Scientific Reports ◽

10.1038/s41598-019-55144-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Weili Cai ◽

Schyler Nunziata ◽

John Rascoe ◽

Michael J. Stulberg

Keyword(s):

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Coverage ◽

Metagenomic Sample ◽

Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

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PHYSIOLOGIC AND MOLECULAR CHARACTERIZATION OF THE ROLE OF NITRIC OXIDE IN HEMORRHAGIC SHOCK

Shock ◽

10.1097/00024382-199703000-00001 ◽

1997 ◽

Vol 7 (3) ◽

pp. 157-163 ◽

Cited By ~ 41

Author(s):

Edward Kelly ◽

Nishit S. Shah ◽

Nathan N. Morgan ◽

Simon C. Watkins ◽

Andrew B. Peitzman ◽

...

Keyword(s):

Nitric Oxide ◽

Hemorrhagic Shock ◽

Molecular Characterization

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Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran

Heliyon ◽

10.1016/j.heliyon.2021.e08027 ◽

2021 ◽

Vol 7 (9) ◽

pp. e08027

Author(s):

Amir Kaffashi ◽

Jiabin Huang ◽

Amir Bairami ◽

Mohammad Hossein Fallah Mehrabadi ◽

Somayeh Yaslianifard ◽

...

Keyword(s):

Molecular Characterization ◽

Genome Sequencing ◽

Complete Genome ◽

Complete Genome Sequencing

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Molecular insights into regulation of JAK2 in myeloproliferative neoplasms

Blood ◽

10.1182/blood-2015-01-621110 ◽

2015 ◽

Vol 125 (22) ◽

pp. 3388-3392 ◽

Cited By ~ 39

Author(s):

Olli Silvennoinen ◽

Stevan R. Hubbard

Keyword(s):

Molecular Characterization ◽

Human Disease ◽

Molecular Mechanisms ◽

Myeloproliferative Neoplasms ◽

Critical Role ◽

Hematologic Malignancies ◽

Janus Kinase ◽

Constitutive Activation

Abstract The critical role of Janus kinase-2 (JAK2) in regulation of myelopoiesis was established 2 decades ago, but identification of mutations in the pseudokinase domain of JAK2 in myeloproliferative neoplasms (MPNs) and in other hematologic malignancies highlighted the role of JAK2 in human disease. These findings have revolutionized the diagnostics of MPNs and led to development of novel JAK2 therapeutics. However, the molecular mechanisms by which mutations in the pseudokinase domain lead to hyperactivation of JAK2 and clinical disease have been unclear. Here, we describe recent advances in the molecular characterization of the JAK2 pseudokinase domain and how pathogenic mutations lead to constitutive activation of JAK2.

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