bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xenoepitope Substitution Avoids Deceptive Imprinting and Broadens the Immune Response to Foot-and-Mouth Disease Virus
Authors: Szczepanek Steven M. , Barrette Roger W. , Rood Debra , Alejo Diana , Silbart Lawrence K. 
Published: February 2012

ABSTRACTMany RNA viruses encode error-prone polymerases which introduce mutations into B and T cell epitopes, providing a mechanism for immunological escape. When regions of hypervariability are found within immunodominant epitopes with no known function, they are referred to as “decoy epitopes,” which often deceptively imprint the host's immune response. In this work, a decoy epitope was identified in the foot-and-mouth disease virus (FMDV) serotype O VP1 G-H loop after multiple sequence alignment of 118 isolates. A series of chimeric cyclic peptides resembling the type O G-H loop were prepared, each bearing a defined “B cell xenoepitope” from another virus in place of the native decoy epitope. These sequences were derived from porcine respiratory and reproductive syndrome virus (PRRSV), from HIV, or from a presumptively tolerogenic sequence from murine albumin and were subsequently used as immunogens in BALB/c mice. Cross-reactive antibody responses against all peptides were compared to a wild-type peptide and ovalbumin (OVA). A broadened antibody response was generated in animals inoculated with the PRRSV chimeric peptide, in which virus binding of serum antibodies was also observed. A B cell epitope mapping experiment did not reveal recognition of any contiguous linear epitopes, raising the possibility that the refocused response was directed to a conformational epitope. Taken together, these results indicate that xenoepitope substitution is a novel method for immune refocusing against decoy epitopes of RNA viruses such as FMDV as part of the rational design of next-generation vaccines.
Analysis of Multiple Leptospira interrogans Serovar Canicola Vaccine Proteomes and Identification of LipL32 as a Biomarker for Potency
Authors: Humphryes P. C. , Weeks M. E. , Gielbert A. , Thomson G. , Coldham N. G. 
Published: February 2012

ABSTRACTThe current batch potency test forLeptospira interrogansserovar Canicola vaccines requires the use of a large number of hamsters and has severe effects (i.e., hepatic and renal failure resulting in death); while this vaccine is effective, a safer, cheaper, more ethical replacement is desired. The aim of this study was to analyze vaccine proteomes and identify target molecules common to allL. interrogansserovar Canicola vaccines which could be used to design anin vitropotency test. Initial analysis ofL. interrogansserovar Canicola vaccines (A to E) from different manufacturers, using theLimulusamebocyte lysate assay and silver-stained sodium dodecyl sulfate polyacrylamide gels, indicated that lipopolysaccharide was not present in all vaccines, preventing it from being a suitable target molecule. The protein contents of vaccines A to E were therefore determined by two-dimensional liquid chromatography mass spectrometry ([2D-LC/MS] 221 ± 31, 9 ± 8, 34 ± 4, 21 ± 5, and 34 ± 17 proteins [mean ± 1 standard deviation] found, respectively). The outer membrane protein LipL32 was established to be common to all and to be present at a significantly higher (P≤ 0.05) relative spectral abundance in a batch of vaccine which passed thein vivopotency test than in one which had failed. Further analysis using multiple reaction monitoring revealed that the concentration of the N terminus of LipL32 was significantly lower (P≤ 0.01) in failed batches (n= 2) of vaccine than in passed batches (n= 2); the concentration of the C terminus between the two batches was approximately the same. Anin vitro Leptospiravaccine potency test, based on N-terminal amino acid quantification of LipL32, was subsequently developed.
Purpureocillium lilacinum as a Cause of Cavitary Pulmonary Disease: a New Clinical Presentation and Observations on Atypical Morphologic Characteristics of the Isolate
Authors: Khan Ziauddin , Ahmad Suhail , Al-Ghimlas Fahad , Al-Mutairi Sana , Joseph Leena , Chandy Rachel , Sutton Deanna A. , Guarro Josep 
Published: February 2012

ABSTRACT

The first case of cavitary pulmonary disease caused by
Purpureocillium lilacinum
is described. The isolate showed atypical microscopic characteristics similar to
Acremonium
and
Fusarium
spp., which necessitated molecular identification by sequencing of multiple conserved loci. The patient responded to voriconazole, reinforcing its therapeutic efficacy for
P. lilacinum
infections.
Production and Evaluation of Antibodies and Phage Display-Derived Peptide Ligands for Immunomagnetic Separation of Mycobacterium bovis
Authors: Stewart Linda D. , McNair James , McCallan Lyanne , Thompson Suzan , Kulakov Leonid A. , Grant Irene R. 
Published: February 2012

ABSTRACT

This study describes the development and optimization of an immunomagnetic separation (IMS) method to isolate
Mycobacterium bovis
cells from lymph node tissues. Gamma-irradiated whole
M. bovis
AF2122/97 cells and ethanol-extracted surface antigens of such cells were used to produce
M. bovis
-specific polyclonal and monoclonal antibodies in rabbits and mice. They were also used to generate
M. bovis
-specific peptide ligands by phage display biopanning. The various antibodies and peptide ligands obtained were used to coat MyOne tosyl-activated Dynabeads (Life Technologies), singly or in combination, and evaluated for IMS. Initially,
M. bovis
capture from Middlebrook 7H9 broth suspensions (concentration range, 10 to 10
5
CFU/ml) was evaluated by IMS combined with an
M. bovis
-specific touchdown PCR. IMS-PCR results and, subsequently, IMS-culture results indicated that the beads with greatest immunocapture capability for
M. bovis
in broth were those coated simultaneously with a monoclonal antibody and a biotinylated 12-mer peptide. These dually coated beads exhibited minimal capture (mean of 0.36% recovery) of 12 other
Mycobacterium
spp. occasionally encountered in veterinary tuberculosis (TB) diagnostic laboratories. When the optimized IMS method was applied to various
M. bovis-
spiked lymph node matrices, it demonstrated excellent detection sensitivities (50% limits of detection of 3.16 and 57.7 CFU/ml of lymph node tissue homogenate for IMS-PCR and IMS-culture, respectively). The optimized IMS method therefore has the potential to improve isolation of
M. bovis
from lymph nodes and hence the diagnosis of bovine tuberculosis.
Comparison of the Microflex LT and Vitek MS Systems for Routine Identification of Bacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Martiny Delphine , Busson Laurent , Wybo Ingrid , El Haj Rachid Ait , Dediste Anne , Vandenberg Olivier 
Published: February 2012

ABSTRACT

This study compared the performance of three matrix-assisted laser desorption ionization–time of flight mass spectrometry systems: Microflex LT (Bruker Daltonics, Bremen, Germany), Vitek MS RUO (Axima Assurance-Saramis database; bioMérieux, Marcy l'Etoile, France), and Vitek MS IVD (bioMérieux). A total of 1,129 isolates, including 1,003 routine isolates, 73 anaerobes, and 53 bacterial enteropathogens, were tested on the Microflex LT and Axima Assurance devices. The spectra were analyzed using three databases: Biotyper (Bruker Daltonics), Saramis, and Vitek MS (bioMérieux). Among the routine isolates requiring identification to the species level (
n
= 986), 92.7% and 93.2% were correctly identified by the Biotyper and Vitek MS databases, respectively. The Vitek MS database is more specific for the identification of
Streptococcus viridans
. For the anaerobes, the Biotyper database often identified
Fusobacterium
isolates to only the genus level, which is of low clinical significance, whereas 20% of the
Bacteroides
species were not identified or were misidentified by the Vitek MS database. For the enteropathogens, the poor discrimination between
Escherichia coli
and
Shigella
explains the high proportion of unidentified organisms. In contrast to the Biotyper database, the Vitek MS database properly discriminated all of the
Salmonella entrica
serovar Typhi isolates (
n
= 5). The performance of the Saramis database was globally poorer. In conclusion, for routine procedures, the Microflex LT and Vitek-MS systems are equally good choices in terms of analytical efficiency. Other factors, including price, work flow, and lab activity, will affect the choice of a system.
Development of Mitochondrial Loop-Mediated Isothermal Amplification for Detection of the Small Liver Fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda; Platyhelminthes)
Authors: Le Thanh Hoa , Nguyen Nga Thi Bich , Truong Nam Hai , De Nguyen Van 
Published: February 2012

ABSTRACT

Mitochondrial DNA sequences offer major advantages over the more usual nuclear targets for loop-mediated isothermal amplification approaches (mito-LAMP) because multiple copies occur in every cell. Four LAMP primers [F3, FIP(F1c+F2), BIP(B1c+B2), and B3] were designed based on the mitochondrial
nad1
sequence of
Opisthorchis viverrini
and used for a highly specific assay (mito-OvLAMP) to distinguish DNA of
O. viverrini
from that of another opisthorchiid (
Clonorchis sinensis
) and other trematodes (
Haplorchis pumilio
,
Haplorchis taichui
,
Fasciola hepatica
, and
Fasciola gigantica
). Conventional PCR was applied using F3/B3 primer pairs to verify the specificity of the primers for
O. viverrini
DNA templates. All LAMP-positive samples could be detected with the naked eye in sunlight, by gel electrophoresis (stained with ethidium bromide), and by addition of SYBR green I to the product in sunlight or under UV light. Only DNA from
O. viverrini
yielded amplification products by LAMP (and by PCR verification), and the LAMP limit of detection was as little as 100 fg (10
−4
ng DNA), indicating that this assay is 10 to 100 times more sensitive than PCR. Field testing was done using representative egg and metacercarial samples collected from localities where the fluke is endemic. With the advantages of simplicity, rapidity, sensitivity, and cost effectiveness, mito-OvLAMP is a good tool for molecular detection and epidemiology studies in regions or countries where
O. viverrini
is endemic, which can lead to more effective control of opisthorchiasis and trematodiasis.
Contribution of Amoebic Coculture to Recovery of Legionella Isolates from Respiratory Samples: Prospective Analysis over a Period of 32 Months
Authors: Descours G. , Suet A. , Ginevra C. , Campese C. , Slimani S. , Ader F. , Che D. , Lina G. , Jarraud S. 
Published: February 2012

ABSTRACT

We evaluated the contribution of amoebic coculture to the recovery of
Legionella
spp. from 379 respiratory samples. The sensitivity of axenic culture was 42.1%. The combination of axenic culture with amoebic coculture increased the
Legionella
isolation rate to 47.1%. Amoebic coculture was particularly efficient in isolating
Legionella
spp. from respiratory samples contaminated with oropharyngeal flora.
Discovery of Potential Diagnostic and Vaccine Antigens in Herpes Simplex Virus 1 and 2 by Proteome-Wide Antibody Profiling
Authors: Kalantari-Dehaghi Mina , Chun Sookhee , Chentoufi Aziz Alami , Pablo Jozelyn , Liang Li , Dasgupta Gargi , Molina Douglas M. , Jasinskas Algis , Nakajima-Sasaki Rie , Felgner Jiin , Hermanson Gary , BenMohamed Lbachir , Felgner Philip L. , Davies D. Huw 
Published: February 2012

ABSTRACTRoutine serodiagnosis of herpes simplex virus (HSV) infections is currently performed using recombinant glycoprotein G (gG) antigens from herpes simplex virus 1 (HSV-1) and HSV-2. This is a single-antigen test and has only one diagnostic application. Relatively little is known about HSV antigenicity at the proteome-wide level, and the full potential of mining the antibody repertoire to identify antigens with other useful diagnostic properties and candidate vaccine antigens is yet to be realized. To this end we produced HSV-1 and -2 proteome microarrays inEscherichia coliand probed them against a panel of sera from patients serotyped using commercial gG-1 and gG-2 (gGs for HSV-1 and -2, respectively) enzyme-linked immunosorbent assays. We identified many reactive antigens in both HSV-1 and -2, some of which were type specific (i.e., recognized by HSV-1- or HSV-2-positive donors only) and others of which were nonspecific or cross-reactive (i.e., recognized by both HSV-1- and HSV-2-positive donors). Both membrane and nonmembrane virion proteins were antigenic, although type-specific antigens were enriched for membrane proteins, despite being expressed inE. coli.
Tiled Microarray Identification of Novel Viral Transcript Structures and Distinct Transcriptional Profiles during Two Modes of Productive Murine Gammaherpesvirus 68 Infection
Authors: Cheng Benson Yee Hin , Zhi Jizu , Santana Alexis , Khan Sohail , Salinas Eduardo , Forrest J. Craig , Zheng Yueting , Jaggi Shirin , Leatherwood Janet , Krug Laurie T. 
Published: February 2012

ABSTRACT

We applied a custom tiled microarray to examine murine gammaherpesvirus 68 (MHV68) polyadenylated transcript expression in a time course of
de novo
infection of fibroblast cells and following phorbol ester-mediated reactivation from a latently infected B cell line. During
de novo
infection, all open reading frames (ORFs) were transcribed and clustered into four major temporal groups that were overlapping yet distinct from clusters based on the phorbol ester-stimulated B cell reactivation time course. High-density transcript analysis at 2-h intervals during
de novo
infection mapped gene boundaries with a 20-nucleotide resolution, including a previously undefined ORF73 transcript and the MHV68 ORF63 homolog of Kaposi's sarcoma-associated herpesvirus vNLRP1. ORF6 transcript initiation was mapped by tiled array and confirmed by 5′ rapid amplification of cDNA ends. The ∼1.3-kb region upstream of ORF6 was responsive to lytic infection and MHV68 RTA, identifying a novel RTA-responsive promoter. Transcription in intergenic regions consistent with the previously defined expressed genomic regions was detected during both types of productive infection. We conclude that the MHV68 transcriptome is dynamic and distinct during
de novo
fibroblast infection and upon phorbol ester-stimulated B cell reactivation, highlighting the need to evaluate further transcript structure and the context-dependent molecular events that govern viral gene expression during chronic infection.
The Majority of Freshly Sorted Simian Immunodeficiency Virus (SIV)-Specific CD8+T Cells Cannot Suppress Viral Replication in SIV-Infected Macrophages
Authors: Vojnov Lara , Martins Mauricio A. , Bean Alexander T. , Veloso de Santana Marlon G. , Sacha Jonah B. , Wilson Nancy A. , Bonaldo Myrna C. , Galler Ricardo , Stevenson Mario , Watkins David I. 
Published: February 2012

ABSTRACTHuman immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) primarily infect activated CD4+T cells but can infect macrophages. Surprisingly,ex vivotetramer-sorted SIV-specific CD8+T cells that eliminated and suppressed viral replication in SIV-infected CD4+T cells failed to do so in SIV-infected macrophages. It is possible, therefore, that while AIDS virus-infected macrophages constitute only a small percentage of all virus-infected cells, they may be relatively resistant to CD8+T cell-mediated lysis and continue to produce virus over long periods of time.
Discovery of Retroviral Homologs in Bats: Implications for the Origin of Mammalian Gammaretroviruses
Authors: Cui Jie , Tachedjian Mary , Wang Lina , Tachedjian Gilda , Wang Lin-Fa , Zhang Shuyi 
Published: February 2012

ABSTRACT

Gammaretroviruses infect a wide range of vertebrate species where they are associated with leukemias, neurological diseases and immunodeficiencies. However, the origin of these infectious agents is unknown. Through a phylogenetic analysis of viral gene sequences, we show that bats harbor an especially diverse set of gammaretroviruses. In particular, phylogenetic analysis places
Rhinolophus ferrumequinum
retrovirus (RfRV), a new gammaretrovirus identified by
de novo
analysis of the
Rhinolophus ferrumequinum
transcriptome, and six other gammaretroviruses from different bat species, as basal to other mammalian gammaretroviruses. An analysis of the similarity in the phylogenetic history between the gammaretroviruses and their bat hosts provided evidence for both host-virus codivergence and cross-species transmission. Taken together, these data provide new insights into the origin of the mammalian gammaretroviruses.
Functional Hierarchy of Herpes Simplex Virus 1 Viral Glycoproteins in Cytoplasmic Virion Envelopment and Egress
Authors: Chouljenko Dmitry V. , Kim In-Joong , Chouljenko Vladimir N. , Subramanian Ramesh , Walker Jason D. , Kousoulas Konstantin G. 
Published: February 2012

ABSTRACT
Herpes simplex virus 1 (HSV-1) viral glycoproteins gD (carboxyl terminus), gE, gK, and gM, the membrane protein UL20, and membrane-associated protein UL11 play important roles in cytoplasmic virion envelopment and egress from infected cells. We showed previously that a recombinant virus carrying a deletion of the carboxyl-terminal 29 amino acids of gD (gDΔct) and the entire gE gene (ΔgE) did not exhibit substantial defects in cytoplasmic virion envelopment and egress (H. C. Lee et al., J. Virol. 83:6115–6124, 2009). The recombinant virus ΔgM2, engineered not to express gM, produced a 3- to 4-fold decrease in viral titers and a 50% reduction in average plaque sizes in comparison to the HSV-1(F) parental virus. The recombinant virus containing all three mutations, gDΔct-ΔgM2-ΔgE, replicated approximately 1 log unit less efficiently than the HSV-1(F) parental virus and produced viral plaques which were on average one-third the size of those of HSV-1(F). The recombinant virus ΔUL11-ΔgM2, engineered not to express either UL11 or gM, replicated more than 1 log unit less efficiently and produced significantly smaller plaques than UL11-null or gM-null viruses alone, in agreement with the results of Leege et al. (T. Leege et al., J. Virol. 83:896-907, 2009). Analyses of particle-to-PFU ratios, relative plaque size, and kinetics of virus growth and ultrastructural visualization of glycoprotein-deficient mutant and wild-type virions indicate that gDΔct, gE, and gM function in a cooperative but not redundant manner in infectious virion morphogenesis. Overall, comparisons of single, double, and triple mutant viruses generated in the same HSV-1(F) genetic background indicated that lack of either UL20 or gK expression caused the most severe defects in cytoplasmic envelopment, egress, and infectious virus production, followed by the double deletion of UL11 and gM.
Mucosal Simian Immunodeficiency Virus Transmission in African Green Monkeys: Susceptibility to Infection Is Proportional to Target Cell Availability at Mucosal Sites
Authors: Pandrea Ivona , Parrish Nicholas F. , Raehtz Kevin , Gaufin Thaidra , Barbian Hannah J. , Ma Dongzhu , Kristoff Jan , Gautam Rajeev , Zhong Fang , Haret-Richter George S. , Trichel Anita , Shaw George M. , Hahn Beatrice H. , Apetrei Cristian 
Published: February 2012

ABSTRACT

African green monkeys (AGMs) are naturally infected with a simian immunodeficiency virus (SIVagm) that is nonpathogenic in its host. Although SIVagm is common and widespread, little is known about the mechanisms that govern its transmission. Since the earliest virus-host interactions may provide key insights into the nonpathogenic phenotype of SIVagm, we developed a mucosal transmission model for this virus. Using plasma from an acutely infected AGM as the virus inoculum, we exposed adult and juvenile AGMs, as well as pigtailed macaques (PTMs) as a nonnatural host control, by mucosal routes to increasing titers of virus and compared the doses needed to establish a productive infection. Four juvenile and four adult AGMs as well as two PTMs were intrarectally (IR) exposed, while two additional adult female AGMs were intravaginally (IVAG) exposed. No animal became infected following exposure to 10
5
RNA copies. Both PTMs but none of the AGMs became infected following exposure to 10
6
RNA copies. Finally, all adult AGMs and two of the four juvenile AGMs became infected following exposure to 10
7
RNA copies, acquiring either one (2 IR infected juveniles, 1 IR infected adult, 2 IVAG infected adults) or two (3 IR infected adults) transmitted founder viruses. These results were consistent with immunophenotypic data, which revealed a significant correlation between the percentage of CD4
+
T cells expressing CCR5 in the mucosa and the susceptibility to infection, in terms of both the viral dose and the numbers of transmitted founder viruses. Moreover, studies of uninfected AGMs showed that the fraction of CCR5-expressing CD4
+
T cells increased significantly with age. These results indicate that (i) AGMs are readily infected with SIVagm by both intrarectal and intravaginal routes, (ii) susceptibility to infection is proportional to the number of available CCR5
+
CD4
+
target cells in the mucosa, and (iii) the paucity of CCR5
+
CD4
+
target cells in infant and juvenile AGMs may explain the near absence of vertical transmission.
Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific
Authors: Clerissi Camille , Desdevises Yves , Grimsley Nigel 
Published: February 2012

ABSTRACT

Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40
Ostreococcus tauri
viruses on 13 independently isolated wild-type
O. tauri
strains, 4 wild-type
O. lucimarinus
strains, 1
Ostreococcus
sp. (“
Ostreococcus mediterraneus
”) clade D strain, and 1 representative species of each of two other related species of Mamiellales,
Bathycoccus prasinos
and
Micromonas pusilla
. Thirty-four out of 40 viruses infected only
O. tauri
, 5 could infect one other species of the
Ostreococcus
genus, and 1 infected two other
Ostreococcus
spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of
Ostreococcus
strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete
O. tauri
virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.