Epstein-Barr Virus in Burkitt Lymphoma in Africa Reveals a Limited Set of Whole Genome and Sequence Patterns: Analysis of Archival Datasets and Field Samples From Uganda, Tanzania, and Kenya.

Unlabelled: Epstein-Barr virus (EBV) is associated with endemic Burkitt lymphoma (eBL), but the contribution of EBV variants is ill-defined. Studies of EBV whole genome sequences (WGS) have identified phylogroups that appear to be distinct for Asian versus non-Asian EBV, but samples from BL or Africa, where EBV was first discovered, are under-represented. We conducted a phylogenetic analysis of EBV WGS and sequences obtained primarily from BL patients in Africa and representative non-African EBV from other conditions or regions using data from GenBank, Sequence Read Archive, or Genomic Data Commons for the Burkitt Lymphoma Genome Sequencing Project (BLGSP) to generate data to support the use of a simpler biomarker of geographic or phenotypic associations.

Draft Genome Sequences of sp. Clones TML/M2B and TML/C7B, with Different Motilities, Isolated in a Laboratory.

Two novel sp. clones, TML/M2B and TML/C7B, with 2 different stable growth phenotypes, were isolated from a laboratory tissue culture. The draft genome sequences generated through genomic sequencing of clones TML/M2B and TML/C7B contain 4 and 2 contigs, respectively.

Comparative Genomics, Infectivity and Cytopathogenicity of American Isolates of Zika Virus that Developed Persistent Infections in Human Embryonic Kidney (HEK293) Cells.

Zika virus (ZIKV) transmission can cause serious fetal neurological abnormalities. ZIKV persistence in various human cells and tissues can serve as infectious reservoirs and post serious threats to public health. The human embryonic kidney (HEK293) cell line with known neuronal developmental properties was readily infected by ZIKV in a strain-dependent fashion.

Genomic Alterations of Staphylococcus aureus ATCC 25923 after Prolonged Passage in the Laboratory.

Staphylococcus aureus reference strain ATCC 25923 has been maintained for more than a decade in our laboratory. Genomic study revealed that the resulting strain AFIPCBER_B_8.4 has lost a 37-kb genomic fragment of the ATCC 25923 parental strain.

Comparative genomics, infectivity and cytopathogenicity of Zika viruses produced by acutely and persistently infected human hematopoietic cell lines.

Zika virus (ZIKV), an arthropod-borne virus, has emerged as a major human pathogen. Prolonged or persistent ZIKV infection of human cells and tissues may serve as a reservoir for the virus and present serious challenges to the safety of public health. Human hematopoietic cell lines with different developmental properties revealed differences in susceptibility and outcomes to ZIKV infection.

Frequency of EBV LMP-1 Promoter and Coding Variations in Burkitt Lymphoma Samples in Africa and South America and Peripheral Blood in Uganda.

Epstein-Barr virus (EBV) is linked to several cancers, including endemic Burkitt lymphoma (eBL), but causal variants are unknown. We recently reported novel sequence variants in the LMP-1 gene and promoter in EBV genomes sequenced from 13 of 14 BL biopsies. Alignments of the novel sequence variants for 114 published EBV genomes, including 27 from BL cases, revealed four LMP-1 variant patterns, designated A to D.

Intraspecies comparative genomics of three strains of with different antibiotic sensitivity.

We recently reported the genome of (OT) strain Karp (GenBank Accession #: NZ_LYMA00000000.2, https://www.ncbi.

Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable to the Genome Size of the Strain Ikeda.

Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae This study presents the draft genome sequence of strain Karp, with 2.0 Mb as the size of the completed genome. This nearly finished draft genome sequence was annotated with the RAST server and the contents compared to those of the other strains.

Developing Peptide Mimotopes of Capsular Polysaccharides and Lipopolysaccharides Protective Antigens of Pathogenic Burkholderia Bacteria.

Burkholderia pseudomallei (BP) and Burkholderia mallei (BM) are two species of pathogenic Burkholderia bacteria. Our laboratory previously identified four monoclonal antibodies (MAbs) that reacted against Burkholderia capsular polysaccharides (PS) and lipopolysaccharides (LPS) and effectively protected against a lethal dose of BP/BM infections in mice. In this study, we used phage display panning against three different phage peptide libraries to select phage clones specifically recognized by each of the four protective MAbs.

Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species.

Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes.

Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness.

We examined the microbial composition in the diseased lung and early-phase microbial cultures from the blood of a patient with a rapidly progressing fatal pulmonary illness. Although no microbes could be isolated from such cultures during the initial study, the HTS-microbiome study revealed the presence of a unique mixture of alphaproteobacteria, composed mainly of different families of Rhizobiales microbes. Microbial 16S rDNA sequences matching closely to Afipia cberi were identified mainly in the patient's diseased lung tissue, but only rarely in the early-phase blood cultures.

Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations.

Epstein Barr virus (EBV) sequence variation is thought to contribute to Burkitt lymphoma (BL), but lack of data from primary BL tumors hampers efforts to test this hypothesis. We directly sequenced EBV from 12 BL biopsies from Ghana, Brazil, and Argentina, aligned the obtained reads to the wild-type (WT) EBV reference sequence, and compared them with 100 published EBV genomes from normal and diseased people from around the world. The 12 BL EBVs were Type 1.

Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study.

This report describes the draft genome sequence of a newly isolated strain, Pantoea sp. MBLJ3. The genome is 4.

Genome sequencing and annotation of strain OHSU_II.

We report the 5.1 Mb noncontiguous draft genome of strain OHSU_II, isolated from blood of a female patient. The genome consists of 5,087,893 bp circular chromosome with no identifiable autonomous plasmid with a G + C content of 61.

Isolation and characterization of two novel bacteria Afipia cberi and Mesorhizobium hominis from blood of a patient afflicted with fatal pulmonary illness.

We recently isolated and discovered new Bradyrhizobiaceae microbes from the cryopreserved culture broth of blood samples from 3 patients with poorly defined illnesses using modified SP4 media and culture conditions coupled with genomic sequencing. Using a similar protocol, we studied a previously cryopreserved culture broth of blood sample from a patient who had succumbed to an acute onset of fulminant pulmonary illness. We report that two phases of microbial growth were observed in the re-initiated culture.

Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology.

Background: We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform. The purpose of this study was to examine if rapid detection and characterization of a viral agent could be effectively achieved by HTS using a platform that has become readily available in general biology laboratories.

Results: Raw read sequences, averaging 175 bps in length, were mapped with DNA databases of human, bacteria, fungi and virus genomes using the CLC Genomics Workbench bioinformatics tool.

Isolation of novel Afipia septicemium and identification of previously unknown bacteria Bradyrhizobium sp. OHSU_III from blood of patients with poorly defined illnesses.

Cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. We re-initiated a set of 3 cultures for analysis of the "uncultivable" or poorly-grown microbes using NGS technology. Broth of cultures from 3 blood samples, submitted from OHSU between 2000 and 2004, were inoculated into culture flasks containing fresh modified SP4 medium and kept at room temperature (RT), 30°C and 35°C.

Differentially expressed genes and pathways induced by organophosphates in human neuroblastoma cells.

Organophosphates (OPs) are toxic chemicals commonly used as pesticides and herbicides. Some OPs are highly toxic to humans and have been used in warfare and terrorist attacks. In order to elucidate the molecular mechanisms of injury caused by OPs, the differentially expressed genes were analyzed in human SK-N-SH neuroblastoma cells induced by three OPs.

Development of real-time PCR array for simultaneous detection of eight human blood-borne viral pathogens.

Background: Real-time PCR array for rapid detection of multiple viral pathogens should be highly useful in cases where the sample volume and the time of testing are limited, i.e. in the eligibility testing of tissue and organ donors.

Production and characterization of chimeric monoclonal antibodies against Burkholderia pseudomallei and B. mallei using the DHFR expression system.

Burkholderia pseudomallei (BP) and B. mallei (BM) are closely related gram-negative, facultative anaerobic bacteria which cause life-threatening melioidosis in human and glanders in horse, respectively. Our laboratory has previously generated and characterized more than 100 mouse monoclonal antibodies (MAbs) against BP and BM, according to in vitro and in vivo assay.

In Vitro and In Vivo studies of monoclonal antibodies with prominent bactericidal activity against Burkholderia pseudomallei and Burkholderia mallei.

Our laboratory has developed more than a hundred mouse monoclonal antibodies (MAbs) against Burkholderia pseudomallei and Burkholderia mallei. These antibodies have been categorized into different groups based on their specificities and the biochemical natures of their target antigens. The current study first examined the bactericidal activities of a number of these MAbs by an in vitro opsonic assay.

Construction and molecular characterization of mouse single-chain variable fragment antibodies against Burkholderia mallei and Burkholderia pseudomallei.

We have selected two lipopolysaccharide (LPS) specific Burkholderia mallei mouse monoclonal antibodies (mAbs) and four anti-capsular B. pseudomallei-specific mAbs to generate mouse single-chain variable fragment (scFv) antibodies. This selection was made through extensive in vitro and in vivo assay from our library of mAbs against B.

Relationship between antigenicity and pathogenicity for Burkholderia pseudomallei and Burkholderia mallei revealed by a large panel of mouse MAbs.

Burkholderia pseudomallei and Burkholderia mallei are two closely related gram-negative bacterial species classified by the CDC as category B biowarfare agents. To develop monoclonal antibodies (MAbs) that can recognize as many different strains and/or clinical isolates of these two pathogens as possible, we immunized mice with heat-killed bacterial whole cells and membrane preparations from multiple strains and/or clinical isolates of B. pseudomallei and B.

Human single-chain Fv antibodies against Burkholderia mallei and Burkholderia pseudomallei.

Much effort has been devoted to the development of mouse monoclonal antibodies that react specifically with Burkholderia mallei and Burkholderia pseudomallei for diagnostic and/or therapeutic purposes. Our present study focused on the screening of a phage-displayed nonimmune human single-chain Fv (scFv) antibody library against heat-killed B. mallei and B.