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Article ; Online: Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data.

Diemer, Geoffrey S / Stedman, Kenneth M

2016 Volume 83, Issue 1-2, Page(s) 38–49

Abstract: The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and adaptation. Here, we utilize microvirus sequences ... ...

Abstract	The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and adaptation. Here, we utilize microvirus sequences from diverse physiochemical environments, including novel sequences from a high-temperature acidic lake, to chart the outcome of natural selection in the main structural protein of the virus. Each icosahedral microvirus virion is composed of sixty identical capsid proteins that interact along twofold, threefold and fivefold symmetry axis interfaces to encapsidate a small, circular, single-stranded DNA genome. Viable assembly of the virus is guided by scaffolding proteins, which coordinate inter-subunit contacts between the capsid proteins. Structure-based analysis indicates that amino acid sequence conservation is predominantly localized to the twofold axis interface. While preservation of this quaternary interface appears to be essential, tertiary and secondary structural features of the capsid protein are permissive to considerable sequence variation.
MeSH term(s)	Amino Acid Sequence ; Capsid/physiology ; Capsid Proteins/genetics ; DNA, Single-Stranded ; Evolution, Molecular ; Genetic Variation ; Microviridae/genetics ; Microvirus/genetics ; Models, Molecular ; Sequence Analysis, DNA/methods ; Virion/genetics
Chemical Substances	Capsid Proteins ; DNA, Single-Stranded
Language	English
Publishing date	2016-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	120148-7
ISSN	1432-1432 ; 0022-2844
ISSN (online)	1432-1432
ISSN	0022-2844
DOI	10.1007/s00239-016-9751-y
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Article ; Online: A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses.

Diemer, Geoffrey S / Stedman, Kenneth M

Biology direct

2012 Volume 7, Page(s) 13

Abstract: Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to ... ...

Abstract	Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. Conclusions: This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. Reviewers: This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
MeSH term(s)	Amino Acid Sequence ; California ; DNA Viruses/genetics ; Environmental Microbiology ; Genome, Viral/genetics ; Hot Springs/virology ; Lakes/virology ; Phylogeny ; RNA Viruses/genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Viral Proteins/chemistry ; Viral Proteins/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2012-06-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1745-6150
ISSN (online)	1745-6150
DOI	10.1186/1745-6150-7-13
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Article ; Online: A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

Diemer Geoffrey S / Stedman Kenneth M

Biology Direct, Vol 7, Iss 1, p

2012 Volume 13

Abstract: Abstract Background Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to ...

Abstract	Abstract Background Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Results Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. Conclusions This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. Reviewers This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
Keywords	Non-retroviral RNA virus integration ; RNA-DNA recombination ; Viral metagenomics ; Metaviromics ; Virus ecology ; Viral diversity ; Modular theory of virus evolution ; Interviral lateral gene transfer ; RNA World ; DNA World ; Virus World ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2012-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes.

Stedman, Kenneth M / Kosmicki, Nicholas R / Diemer, Geoffrey S

Journal of virology

2013 Volume 87, Issue 3, Page(s) 1919

MeSH term(s)	Archaea/virology ; Archaeal Viruses/genetics ; Archaeal Viruses/isolation & purification ; Hot Springs/virology ; Metagenomics/methods ; RNA Viruses/genetics ; RNA Viruses/isolation & purification
Language	English
Publishing date	2013-01-10
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02610-12
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Article: Stabilization and formulation of a recombinant Human Cytomegalovirus vector for use as a candidate HIV-1 vaccine

Kumru, Ozan S / Saleh-Birdjandi, Soraia / Antunez, Lorena R / Sayeed, Eddy / Robinson, David / van den Worm, Sjoerd / Diemer, Geoffrey S / Perez, Wilma / Caposio, Patrizia / Früh, Klaus / Joshi, Sangeeta B / Volkin, David B

Vaccine. 2019 Oct. 16, v. 37, no. 44

2019

Abstract: Live attenuated viral vaccine/vector candidates are inherently unstable and infectivity titer losses can readily occur without defining appropriate formulations, storage conditions and clinical handling practices. During initial process development of a ... ...

Abstract	Live attenuated viral vaccine/vector candidates are inherently unstable and infectivity titer losses can readily occur without defining appropriate formulations, storage conditions and clinical handling practices. During initial process development of a candidate vaccine against HIV-1 using a recombinant Human Cytomegalovirus vector (rHCMV-1), large vector titer losses were observed after storage at 4 °C and after undergoing freeze-thaw. Thus, the goal of this work was to develop candidate frozen liquid formulations of rHCMV-1 with improved freeze-thaw and short-term liquid stability for potential use in early clinical trials. To this end, a virus stability screening protocol was developed including use of a rapid, in vitro cell-based immunofluorescence focus assay to quantitate viral titers. A library of ∼50 pharmaceutical excipients (from various known classes of additives) were evaluated for their effect on vector stability after freeze-thaw cycling or incubation at 4 °C for several days. Certain additives including sugars and polymers (e.g., trehalose, sucrose, sorbitol, hydrolyzed gelatin, dextran 40) as well as removal of NaCl (lower ionic strength) protected rHCMV-1 against freeze-thaw mediated losses in viral titers. Optimized solution conditions (e.g., solution pH, buffers and sugar type) slowed the rate of rHCMV-1 titer losses in the liquid state at 4 °C. After evaluating various excipient combinations, three new candidate formulations were designed and rHCMV-1 stability was benchmarked against both the currently-used and a previously reported formulation. The new candidate formulations were significantly more stable in terms of reducing rHCMV-1 titer losses after 5 freeze-thaw cycles or incubation at 4 °C for 30 days. This case study highlights the utility of semi-empirical design of frozen liquid formulations of a live viral vaccine candidate, where protection against infectivity titer losses due to freeze-thaw and short-term liquid storage are sufficient to enable more rapid initiation of early clinical trials.
Keywords	Human betaherpesvirus 5 ; Human immunodeficiency virus 1 ; additives ; buffers ; case studies ; clinical trials ; dextran ; fluorescent antibody technique ; freeze-thaw cycles ; gelatin ; hydrolysis ; ionic strength ; liquids ; live vaccines ; pH ; pathogenicity ; polymers ; screening ; sodium chloride ; sorbitol ; storage temperature ; sucrose ; trehalose ; viral load ; viral vaccines ; viruses
Language	English
Dates of publication	2019-1016
Size	p. 6696-6706.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2019.09.027
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Article ; Online: Stabilization and formulation of a recombinant Human Cytomegalovirus vector for use as a candidate HIV-1 vaccine.

Vaccine

2019 Volume 37, Issue 44, Page(s) 6696–6706

Abstract	Live attenuated viral vaccine/vector candidates are inherently unstable and infectivity titer losses can readily occur without defining appropriate formulations, storage conditions and clinical handling practices. During initial process development of a candidate vaccine against HIV-1 using a recombinant Human Cytomegalovirus vector (rHCMV-1), large vector titer losses were observed after storage at 4 °C and after undergoing freeze-thaw. Thus, the goal of this work was to develop candidate frozen liquid formulations of rHCMV-1 with improved freeze-thaw and short-term liquid stability for potential use in early clinical trials. To this end, a virus stability screening protocol was developed including use of a rapid, in vitro cell-based immunofluorescence focus assay to quantitate viral titers. A library of ∼50 pharmaceutical excipients (from various known classes of additives) were evaluated for their effect on vector stability after freeze-thaw cycling or incubation at 4 °C for several days. Certain additives including sugars and polymers (e.g., trehalose, sucrose, sorbitol, hydrolyzed gelatin, dextran 40) as well as removal of NaCl (lower ionic strength) protected rHCMV-1 against freeze-thaw mediated losses in viral titers. Optimized solution conditions (e.g., solution pH, buffers and sugar type) slowed the rate of rHCMV-1 titer losses in the liquid state at 4 °C. After evaluating various excipient combinations, three new candidate formulations were designed and rHCMV-1 stability was benchmarked against both the currently-used and a previously reported formulation. The new candidate formulations were significantly more stable in terms of reducing rHCMV-1 titer losses after 5 freeze-thaw cycles or incubation at 4 °C for 30 days. This case study highlights the utility of semi-empirical design of frozen liquid formulations of a live viral vaccine candidate, where protection against infectivity titer losses due to freeze-thaw and short-term liquid storage are sufficient to enable more rapid initiation of early clinical trials.
MeSH term(s)	AIDS Vaccines/chemistry ; AIDS Vaccines/genetics ; AIDS Vaccines/immunology ; Cell Line ; Chemistry, Pharmaceutical ; Cryopreservation ; Cytomegalovirus/genetics ; Drug Stability ; Freezing ; Genetic Engineering ; Genetic Vectors/genetics ; HIV Infections/immunology ; HIV Infections/prevention & control ; HIV-1/genetics ; HIV-1/immunology ; Humans ; Vaccines, Synthetic/chemistry ; Vaccines, Synthetic/genetics ; Vaccines, Synthetic/immunology
Chemical Substances	AIDS Vaccines ; Vaccines, Synthetic
Language	English
Publishing date	2019-09-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2019.09.027
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Article ; Online: Evidence for endotoxin contamination in plastic Na+-heparin blood collection tube lots.

Newhall, Kathryn J / Diemer, Geoffrey S / Leshinsky, Natalia / Kerkof, Keith / Chute, Hilary T / Russell, Chris B / Rees, William / Welcher, Andrew A / Patterson, Scott D / Means, Gary D

Clinical chemistry

2010 Volume 56, Issue 9, Page(s) 1483–1491

Abstract: Background: Biomarker assays are often conducted on whole blood samples in the course of drug development studies. Because bacterial lipopolysaccharide (LPS) (endotoxin) contamination is known to cause spontaneous cytokine production by monocytes, ... ...

Abstract	Background: Biomarker assays are often conducted on whole blood samples in the course of drug development studies. Because bacterial lipopolysaccharide (LPS) (endotoxin) contamination is known to cause spontaneous cytokine production by monocytes, contamination of blood collection tubes may interfere with biomarker assay results. Methods: Whole blood from healthy donors was collected into plastic or glass sodium (Na(+))-heparin Vacutainer() blood collection tubes and heparinized syringes. Samples were analyzed for phosphoprotein response, cytokine production, and RNA expression. Tubes were tested for endotoxin contamination by use of the limulus amoebocyte lysate assay. Results: Results of phospho-flow cytometry, branched DNA (bDNA), and ELISA assays indicated that a specific lot (#5339582) of plastic Na(+)-heparin Vacutainer tubes was highly contaminated with an endotoxinlike substance, and contamination was confirmed by the limulus amoebocyte lysate assay. Analysis of multiple-analyte panels revealed that analytes whose changed expression was predictive of LPS stimulation were increased when whole blood was incubated in contaminated tubes for 6 or 18 h. Two additional lots of plastic tubes tested had detectable amounts of endotoxin sufficient to strongly alter phospho-flow cytometry analyses, as determined by the fold change in phosphorylation of p38 mitogen-activated protein kinase in response to tumor necrosis factor alpha and LPS. In contrast, 3 lots of glass tubes had substantially lower levels of spontaneous blood activation. Conclusions: Endotoxin contamination associated with tubes from 3 lots of a particular type of plastic Na(+)-heparin Vacutainer tube dramatically affected biomarker assay measurements. Prescreening these tubes is suggested before their use in clinical sample analysis.
MeSH term(s)	Anticoagulants ; Biomarkers/blood ; Blood Specimen Collection/instrumentation ; C-Reactive Protein/biosynthesis ; C-Reactive Protein/genetics ; Chemokine CCL2/blood ; Chemokine CCL2/genetics ; Chemokine CCL7/blood ; Chemokine CCL7/genetics ; Endotoxins/analysis ; Enzyme-Linked Immunosorbent Assay ; Equipment Contamination ; Flow Cytometry ; Heparin ; Humans ; Interleukin-1beta/blood ; Interleukin-6/blood ; Interleukin-6/genetics ; Lipopolysaccharides/pharmacology ; Phosphorylation ; Plastics ; RNA, Messenger/blood ; Serum Amyloid P-Component/biosynthesis ; Serum Amyloid P-Component/genetics ; Time Factors ; Tumor Necrosis Factor-alpha/biosynthesis ; Tumor Necrosis Factor-alpha/pharmacology ; p38 Mitogen-Activated Protein Kinases/blood
Chemical Substances	Anticoagulants ; Biomarkers ; Chemokine CCL2 ; Chemokine CCL7 ; Endotoxins ; Interleukin-1beta ; Interleukin-6 ; Lipopolysaccharides ; Plastics ; RNA, Messenger ; Serum Amyloid P-Component ; Tumor Necrosis Factor-alpha ; PTX3 protein (148591-49-5) ; Heparin (9005-49-6) ; C-Reactive Protein (9007-41-4) ; p38 Mitogen-Activated Protein Kinases (EC 2.7.11.24)
Keywords	covid19
Language	English
Publishing date	2010-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2006.144618
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Article: Nectin-like protein 2 defines a subset of T-cell zone dendritic cells and is a ligand for class-I-restricted T-cell-associated molecule.

Galibert, Laurent / Diemer, Geoffrey S / Liu, Zhi / Johnson, Richard S / Smith, Jeffrey L / Walzer, Thierry / Comeau, Michael R / Rauch, Charles T / Wolfson, Martin F / Sorensen, Rick A / Van der Vuurst de Vries, Anne-Renée / Branstetter, Daniel G / Koelling, Raymond M / Scholler, John / Fanslow, William C / Baum, Peter R / Derry, Jonathan M / Yan, Wei

The Journal of biological chemistry

2005 Volume 280, Issue 23, Page(s) 21955–21964

Abstract: Dendritic cells (DCs) are a phenotypically and functionally heterogenous population of leukocytes with distinct subsets serving a different set of specialized immune functions. Here we applied an in vitro whole cell panning approach using antibody phage ... ...

Abstract	Dendritic cells (DCs) are a phenotypically and functionally heterogenous population of leukocytes with distinct subsets serving a different set of specialized immune functions. Here we applied an in vitro whole cell panning approach using antibody phage display technology to identify cell-surface epitopes specifically expressed on human blood BDCA3(+) DCs. A single-chain antibody fragment (anti-1F12 scFv) was isolated that recognizes a conserved surface antigen expressed on both human BDCA3(+) DCs and mouse CD8alpha(+) DCs. We demonstrate that anti-1F12 scFv binds Nectin-like protein 2 (Necl2, Tslc1, SynCaM, SgIGSF, or Igsf4), an adhesion molecule involved in tumor suppression, synapse formation, and spermatogenesis. Thus, Necl2 defines a specialized subset of DCs in both mouse and human. We further show that Necl2 binds Class-I-restricted T-cell-associated molecule (CRTAM), a receptor primarily expressed on activated cytotoxic lymphocytes. When present on antigen presenting cells, Necl2 regulates IL-22 expression by activated CD8(+) T-cells. We propose that Necl2/CRTAM molecular pair could regulate a large panel of cell/cell interactions both within and outside of the immune system.
MeSH term(s)	Animals ; Blotting, Western ; CD8-Positive T-Lymphocytes/immunology ; Cell Adhesion ; Cell Adhesion Molecule-1 ; Cell Adhesion Molecules ; Cell Aggregation ; Cell Line, Tumor ; Cell Membrane/metabolism ; Cell Separation ; Coculture Techniques ; Dendritic Cells/cytology ; Electrophoresis, Polyacrylamide Gel ; Female ; Flow Cytometry ; Humans ; Immune System/physiology ; Immunoblotting ; Immunoglobulins/metabolism ; Immunoglobulins/physiology ; Immunoprecipitation ; Interleukins/biosynthesis ; Lentivirus/genetics ; Leukocytes/metabolism ; Ligands ; Lymphocytes/cytology ; Mass Spectrometry ; Membrane Proteins/metabolism ; Membrane Proteins/physiology ; Mice ; Mice, Inbred C57BL ; Octoxynol/pharmacology ; Peptide Library ; Phenotype ; Polymerase Chain Reaction ; Protein Binding ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/metabolism ; Spleen/metabolism ; T-Lymphocytes/metabolism ; Interleukin-22
Chemical Substances	Cadm1 protein, mouse ; Cell Adhesion Molecule-1 ; Cell Adhesion Molecules ; Immunoglobulins ; Interleukins ; Ligands ; Membrane Proteins ; Peptide Library ; RNA, Messenger ; Recombinant Fusion Proteins ; class-I restricted T cell-associated molecule ; Octoxynol (9002-93-1)
Language	English
Publishing date	2005-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M502095200
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