bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of BD Bactec Plus Aerobic/F Medium to VersaTREK Redox 1 Blood Culture Medium for Detection of Candida spp. in Seeded Blood Culture Specimens Containing Therapeutic Levels of Antifungal Agents
Authors: Riedel Stefan , Eisinger Stephen W. , Dam Lisa , Stamper Paul D. , Carroll Karen C. 
Published: January 2011

ABSTRACT

Recovery of
Candida
spp. using the BD Bactec FX blood culture (BC) system (Bactec Plus Aerobic/F medium) and the VersaTREK system (aerobic Redox medium) was evaluated using seeded BC bottles with and without the addition of commonly used antifungal agents. BC bottles (
n
= 1,442) were each inoculated with 10 ml human whole blood and 0.1 ml of suspensions of
Candida
spp., with or without antifungal agents. BC bottles were incubated in the corresponding system for a maximum of 5 days. In the absence of antifungal agents, Bactec FX recovered 97.4% of
Candida
spp., and VersaTREK recovered 99.1% (
P
= 0.154). With regard to length of time to detection (LTD) and overall recovery, both systems had various levels of effectiveness in recovering
C. glabrata
. In bottles containing antifungal agents, Bactec FX recovered 83.1% of isolates, whereas VersaTREK recovered 50.7% of
Candida
spp. (
P
< 0.001). For BC bottles without the addition of antifungal agents, the median LTD for VersaTREK was 2.2 h faster than that of Bactec FX (
P
< 0.001). In the presence of antifungal agents, the Bactec FX recovery time was significantly faster than that of VersaTREK (median difference of 10.8 h,
P
< 0.001). We conclude that both systems have comparable abilities to recover
Candida
spp. from seeded blood cultures in the absence of antifungal agents. In the presence of therapeutic levels of commonly used antifungal agents, the Bactec FX system demonstrated a significantly greater recovery of various
Candida
spp., as well as a shorter LTD.
Development of a Selective Culture Medium for Primary Isolation of the Main Brucella Species
Authors: De Miguel M. J. , Marín C. M. , Muñoz P. M. , Dieste L. , Grilló M. J. , Blasco J. M. 
Published: January 2011

ABSTRACT

Bacteriological diagnosis of brucellosis is performed by culturing animal samples directly on both Farrell medium (FM) and modified Thayer-Martin medium (mTM). However, despite inhibiting most contaminating microorganisms, FM also inhibits the growth of
Brucella ovis
and some
B. melitensis
and
B. abortus
strains. In contrast, mTM is adequate for growth of all
Brucella
species but only partially inhibitory for contaminants. Moreover, the performance of both culture media for isolating
B. suis
has never been established properly. We first determined the performance of both media for
B. suis
isolation, proving that FM significantly inhibits
B. suis
growth. We also determined the susceptibility of
B. suis
to the antibiotics contained in both selective media, proving that nalidixic acid and bacitracin are highly inhibitory, thus explaining the reduced performance of FM for
B. suis
isolation. Based on these results, a new selective medium (CITA) containing vancomycin, colistin, nystatin, nitrofurantoin, and amphotericin B was tested for isolation of the main
Brucella
species, including
B. suis
. CITA's performance was evaluated using reference contaminant strains but also field samples taken from brucella-infected animals or animals suspected of infection. CITA inhibited most contaminant microorganisms but allowed the growth of all
Brucella
species, to levels similar to those for both the control medium without antibiotics and mTM. Moreover, CITA medium was more sensitive than both mTM and FM for isolating all
Brucella
species from field samples. Altogether, these results demonstrate the adequate performance of CITA medium for the primary isolation of the main
Brucella
species, including
B. suis
.
Emergence of Disseminated Infections Due to Geosmithia argillacea in Patients with Chronic Granulomatous Disease Receiving Long-Term Azole Antifungal Prophylaxis
Authors: Machouart Marie , Garcia-Hermoso Dea , Rivier Alexandre , Hassouni Noura , Catherinot Emilie , Salmon Alexandra , Debourgogne Anne , Coignard Hélène , Lecuit Marc , Bougnoux Marie-Elisabeth , Blanche Stéphane , Lortholary Olivier 
Published: January 2011

ABSTRACT

We report two cases of invasive infections due to
Geosmithia argillacea
, an emerging mold, in patients with chronic granulomatous disease receiving prolonged azole antifungal prophylaxis. One patient died despite receiving a combination of four antifungals, and the other developed cerebral and medullary lesions under a combination of caspofungin, posaconazole, terbinafine, and gamma interferon.
The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating
Authors: Clemens Kristina , Larsen Liza , Zhang Min , Kuznetsov Yurii , Bilanchone Virginia , Randall Arlo , Harned Adam , DaSilva Rhonda , Nagashima Kunio , McPherson Alexander , Baldi Pierre , Sandmeyer Suzanne 
Published: January 2011

ABSTRACT
Cells expressing the yeast retrotransposon Ty3 form concentrated foci of Ty3 proteins and RNA within which virus-like particle (VLP) assembly occurs. Gag3, the major structural protein of the Ty3 retrotransposon, is composed of capsid (CA), spacer (SP), and nucleocapsid (NC) domains analogous to retroviral domains. Unlike the known SP domains of retroviruses, Ty3 SP is highly acidic. The current studies investigated the role of this domain. Although deletion of Ty3 SP dramatically reduced retrotransposition, significant Gag3 processing and cDNA synthesis occurred. Mutations that interfered with cleavage at the SP-NC junction disrupted CA-SP processing, cDNA synthesis, and electron-dense core formation. Mutations that interfered with cleavage of CA-SP allowed cleavage of the SP-NC junction, production of electron-dense cores, and cDNA synthesis but blocked retrotransposition. A mutant in which acidic residues of SP were replaced with alanine failed to form both Gag3 foci and VLPs. We propose a speculative “spring” model for Gag3 during assembly. In the first phase during concentration of Gag3 into foci, intramolecular interactions between negatively charged SP and positively charged NC domains of Gag3 limit multimerization. In the second phase, the NC domain binds RNA, and the bound form is stabilized by intermolecular interactions with the SP domain. These interactions promote CA domain multimerization. In the third phase, a negatively charged SP domain destabilizes the remaining CA-SP shell for cDNA release.
Identification of a Small-Molecule Entry Inhibitor for Filoviruses
Authors: Basu Arnab , Li Bing , Mills Debra M. , Panchal Rekha G. , Cardinale Steven C. , Butler Michelle M. , Peet Norton P. , Majgier-Baranowska Helena , Williams John D. , Patel Ishan , Moir Donald T. , Bavari Sina , Ray Ranjit , Farzan Michael R. , Rong Lijun , Bowlin Terry L. 
Published: January 2011

ABSTRACTEbola virus (EBOV) causes severe hemorrhagic fever, for which therapeutic options are not available. Preventing the entry of EBOV into host cells is an attractive antiviral strategy, which has been validated for HIV by the FDA approval of the anti-HIV drug enfuvirtide. To identify inhibitors of EBOV entry, the EBOV envelope glycoprotein (EBOV-GP) gene was used to generate pseudotype viruses for screening of chemical libraries. A benzodiazepine derivative (compound 7) was identified from a high-throughput screen (HTS) of small-molecule compound libraries utilizing the pseudotype virus. Compound 7 was validated as an inhibitor of infectious EBOV and Marburg virus (MARV) in cell-based assays, with 50% inhibitory concentrations (IC50s) of 10 μM and 12 μM, respectively. Time-of-addition and binding studies suggested that compound 7 binds to EBOV-GP at an early stage during EBOV infection. Preliminary Schrödinger SiteMap calculations, using a published EBOV-GP crystal structure in its prefusion conformation, suggested a hydrophobic pocket at or near the GP1 and GP2 interface as a suitable site for compound 7 binding. This prediction was supported by mutational analysis implying that residues Asn69, Leu70, Leu184, Ile185, Leu186, Lys190, and Lys191 are critical for the binding of compound 7 and its analogs with EBOV-GP. We hypothesize that compound 7 binds to this hydrophobic pocket and as a consequence inhibits EBOV infection of cells, but the details of the mechanism remain to be determined. In summary, we have identified a novel series of benzodiazepine compounds that are suitable for optimization as potential inhibitors of filoviral infection.
T Cell-, Interleukin-12-, and Gamma Interferon-Driven Viral Clearance in Measles Virus-Infected Brain Tissue
Authors: Stubblefield Park Samantha R. , Widness Mi , Levine Alan D. , Patterson Catherine E. 
Published: January 2011

ABSTRACTGenetic studies with immunocompetent mice show the importance of both T cells and gamma interferon (IFN-γ) for survival of a measles virus (MV) challenge; however, the direct role of T cells and IFN-γ within the MV-infected brain has not been addressed. Organotypic brain explants represent a successfulex vivosystem to define central nervous system (CNS)-specific mechanisms of leukocyte migration, activation, and MV clearance. Within the heterogeneous, brain-derived, primed leukocyte population which reduced MV RNA levels in brain explants by 60%, CD3 T cells are the active antiviral cells, as purified CD3-positive cells are highly antiviral and CD3-negative leukocytes are unable to reduce the viral load. Neutralization of CCL5 and CXCL10 decreases leukocyte migration to areas of infection by 70%. However, despite chemokines directing the migration of T cells to infected neurons, chemokine neutralization revealed that migration is not required for viral clearance, suggesting a cytokine-mediated antiviral mechanism. In accordance with our hypothesis, the ability of leukocytes to clear the virus is abrogated when explants are treated with anti-IFN-γ neutralizing antibodies. IFN-γ applied to infected slices in the absence of primed leukocytes reduces the viral load by more than 80%; therefore, in brain tissue, IFN-γ is both necessary and sufficient to clear MV. Secretion of IFN-γ is stimulated by interleukin-12 (IL-12) in the brain, as neutralization of IL-12 results in loss of antiviral activity and stimulation of leukocytes with IL-12/IL-18 enhances their immune effector function of viral clearance. MV-primed leukocytes can reduce both West Nile and mouse hepatitis viral RNAs, indicating that cytokine-mediated viral clearance occurs in an antigen-independent manner. The IFN-γ signal is transduced within the brain explant by the Jak/STAT signaling pathway, as inhibition of Jak kinases results in a loss of antiviral activity driven by either brain-derived leukocytes or recombinant IFN-γ. These results reveal that primed T cells directly act to clear MV infection of the brain by using a noncytolytic IL-12- and IFN-γ-dependent mechanism in the CNS and that this mechanism relies upon Jak/STAT signaling.
Regulation of Nm23-H1 and Cell Invasiveness by Kaposi's Sarcoma-Associated Herpesvirus
Authors: Qin Zhiqiang , Dai Lu , Toole Bryan , Robertson Erle , Parsons Chris 
Published: January 2011

ABSTRACT

The Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS), and the induction of an invasive cellular phenotype by KSHV following
de novo
infection is an important pathogenic component mediating tumor progression. The metastasis suppressor gene known as Nm23-H1 regulates tumor cell invasiveness, but whether KSHV itself regulates Nm23-H1 expression or subcellular localization, and whether this impacts cell invasiveness, has not been established. We found that KSHV increases expression and nuclear translocation of Nm23-H1 and that nuclear translocation of Nm23-H1 is regulated by the KSHV-encoded latency-associated nuclear antigen (LANA). Moreover, activation of the Ras-BRaf-MAPK (mitogen-activated protein kinase) signal transduction pathway, secretion of promigratory factors associated with this pathway, and cell invasiveness are dependent on KSHV regulation of Nm23-H1. Finally, induction of cytoplasmic overexpression of Nm23-H1 using a pharmacologic inhibitor of DNA methylation reduced KSHV-associated Ras-BRaf-MAPK pathway activation and suppressed KSHV-induced invasiveness. These data provide the first evidence for KSHV regulation of Nm23-H1 as a mechanism for KSHV induction of an invasive cellular phenotype and support the potential utility of targeting Nm23-H1 as a therapeutic approach for the treatment of KS.
Identification of Domains on the Fusion (F) Protein Trimer That Influence the Hemagglutinin-Neuraminidase Specificity of the F Protein in Mediating Cell-Cell Fusion
Authors: Tsurudome Masato , Ito Morihiro , Nishio Machiko , Nakahashi Mito , Kawano Mitsuo , Komada Hiroshi , Nosaka Tetsuya , Ito Yasuhiko 
Published: January 2011

ABSTRACT
For most paramyxoviruses, virus type-specific interaction between fusion (F) protein and attachment protein (hemagglutinin-neuraminidase [HN], hemagglutinin [H], or glycoprotein [G]) is a prerequisite for mediating virus-cell fusion and cell-cell fusion. Our previous cell-cell fusion assay using the chimeric F proteins of human parainfluenza virus 2 (HPIV2) and simian virus 41 (SV41) suggested that the middle region of the HPIV2 F protein contains the site(s) that determines its specificity for the HPIV2 HN protein. In the present study, we further investigated the sites of the F protein that could be critical for determining the HN protein specificity. By analyzing the reported structure of the F protein of parainfluenza virus 5 (PIV5), we found that four major domains (M1, M2, M3, and M4) and five minor domains (A to E) in the middle region of the PIV5 F protein were exposed on the trimer surface. We then replaced these domains with the SV41 F counterparts individually or in combination and examined whether the resulting chimeras could mediate cell-cell fusion when coexpressed with the SV41 HN protein. The results showed that a chimera designated M(1+2), which harbored SV41 F-derived domains M1 and M2, mediated cell-cell fusion with the coexpressed SV41 HN protein, suggesting that these domains are involved in determining the HN protein specificity. Intriguingly, another chimera which harbored the SV41 F-derived domain B in addition to domains M1 and M2 showed increased specificity for the SV41 HN protein compared to that of M(1+2), although it was capable of mediating cell-cell fusion by itself.
Chromatin Reassembly Factors Are Involved in Transcriptional Interference Promoting HIV Latency
Authors: Gallastegui Edurne , Millán-Zambrano Gonzalo , Terme Jean-Michel , Chávez Sebastián , Jordan Albert 
Published: January 2011

ABSTRACT
The establishment of a stable reservoir of latently infected cells allows HIV to persist in the host. Usually, HIV infection of T cells results in integration of the viral genome, with a preference for regions in the human genome containing active genes, viral expression, and production of new viruses. However, in rare cases T cells become latently infected, and this is presumed to be due to a combination of two factors: integrated viruses are not efficiently transcribed and infected T cells revert to a resting memory state. HIV latency has been associated with provirus integration in regions of constitutive heterochromatin, gene deserts, or very highly expressed genes. We have investigated the transcriptional consequences of latent HIV integration into cellular genes and the involvement of chromatin reassembly factors (CRFs) in the transcriptional interference that a host gene exerts on the integrated cryptic HIV promoter. Chimeric transcripts containing sequences from the host gene and HIV can be detected, having been initiated at promoters of either the cell or the virus. Reactivation of HIV downregulates host gene expression. Cryptic promoters might remain inactive due to the repressive chromatin configuration established by CRFs during transcription elongation. Depletion of CRFs such as Spt6, Chd1, and FACT, or the histone chaperones ASF1a and HIRA, promoted HIV reactivation, concomitantly with chromatin relaxation and a decrease in general RNA polymerase activity. Overall, our results indicate that CRFs play a role in maintaining HIV latency by transcriptional interference when the provirus is integrated into an intron of a highly active gene.
Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type 1 Activity
Authors: Wang Xiaojun , Abudu Aierken , Son SungMo , Dang Ying , Venta Patrick J. , Zheng Yong-Hui 
Published: January 2011

ABSTRACT

Human APOBEC3H (A3H) has one cytidine deaminase domain (CDD) and inhibits the replication of retrotransposons and human immunodeficiency virus type 1 (HIV-1) in a Vif-resistant manner. Human
A3H
has five single amino acid polymorphisms (N15Δ, R18L, G105R, K121D, and E178D), and four haplotypes (I to IV) have previously been identified in various human populations. Haplotype II was primarily found in African-derived populations, and it was the only one that could be stably expressed. Here, we identified three new haplotypes from six human population samples, which we have named V, VI, and VII. Haplotypes V and VII are stably expressed and inhibit HIV-1 replication. Notably, haplotype V was identified in samples from all African-, Asian-, and Caucasian-derived populations studied. Using haplotype VII, we investigated the A3H anti-HIV-1 mechanism. We found that A3H virion packaging is independent of its CDD but dependent on a
112
YYXW
115
motif. This motif binds HIV-1 nucleocapsid in an RNA-dependent manner, and a single Y112A mutation completely disrupts A3H virion incorporation. We further studied the mechanism of A3H resistance to Vif. Although the previously identified APOBEC3G Vif-responsive motif
128
DPDY
131
is not conserved in A3H, placement of this motif into A3H does not make it become less resistant to HIV-1 Vif. We conclude that stably expressed A3H haplotypes may be more broadly distributed in humans than previously realized, and A3H protein is resistant to Vif. These results have important implications for the role of A3H in retrotransposon and HIV-1 inhibition.
Simian Immunodeficiency Virus SIVmac239Δnef Vaccination Elicits Different Tat
28-35
SL8-Specific CD8
+
T-Cell Clonotypes Compared to a DNA Prime/Adenovirus Type 5 Boost Regimen in Rhesus Macaques
Authors: Burwitz Benjamin J. , Ende Zachary , Sudolcan Benjamin , Reynolds Matthew R. , Greene Justin M. , Bimber Benjamin N. , Almeida Jorge R. , Kurniawan Monica , Venturi Vanessa , Gostick Emma , Wiseman Roger W. , Douek Daniel C. , Price David A. , O'Connor David H. 
Published: January 2011

ABSTRACT

Different human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) vaccine vectors expressing the same viral antigens can elicit disparate T-cell responses. Within this spectrum, replicating variable vaccines, like SIVmac239Δnef, appear to generate particularly efficacious CD8
+
T-cell responses. Here, we sequenced T-cell receptor β-chain (
TRB
) gene rearrangements from immunodominant Mamu-A*01-restricted Tat
28-35
SL8-specific CD8
+
T-cell populations together with the corresponding viral epitope in four rhesus macaques during acute SIVmac239Δnef infection. Ultradeep pyrosequencing showed that viral variants arose with identical kinetics in SIVmac239Δnef and pathogenic SIVmac239 infection. Furthermore, distinct Tat
28-35
SL8-specific T-cell receptor (TCR) repertoires were elicited by SIVmac239Δnef compared to those observed following a DNA/Ad5 prime-boost regimen, likely reflecting differences in antigen sequence stability.
Assembly and Replication of HIV-1 in T Cells with Low Levels of Phosphatidylinositol-(4,5)-Bisphosphate
Authors: Monde Kazuaki , Chukkapalli Vineela , Ono Akira 
Published: January 2011

ABSTRACT

HIV-1 Gag assembles into virus particles predominantly at the plasma membrane (PM). Previously, we observed that phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P
2
] is essential for Gag binding to the plasma membrane and virus release in HeLa cells. In the current study, we found that PI(4,5)P
2
also facilitates Gag binding to the PM and efficient virus release in T cells. Notably, serial passage of HIV-1 in an A3.01 clone that expresses polyphosphoinositide 5-phosphatase IV (5ptaseIV), which depletes cellular PI(4,5)P
2
, yielded an adapted mutant with a Leu-to-Arg change at matrix residue 74 (74LR). Virus replication in T cells expressing 5ptaseIV was accelerated by the 74LR mutation relative to replication of wild type HIV-1 (WT). This accelerated replication of the 74LR mutant was not due to improved virus release. In control T cells, the 74LR mutant releases virus less efficiently than does the WT, whereas in cells expressing 5ptaseIV, the WT and the 74LR mutant are similarly inefficient in virus release. Unexpectedly, we found that the 74LR mutation increased virus infectivity and compensated for the inefficient virus release. Altogether, these results indicate that PI(4,5)P
2
is essential for Gag-membrane binding, targeting of Gag to the PM, and efficient virus release in T cells, which in turn likely promotes efficient virus spread in T cell cultures. In T cells with low PI(4,5)P
2
levels, however, the reduced virus particle production can be compensated for by a mutation that enhances virus infectivity.
The Transmembrane Domain Sequence Affects the Structure and Function of the Newcastle Disease Virus Fusion Protein
Authors: Gravel Kathryn A. , McGinnes Lori W. , Reitter Julie , Morrison Trudy G. 
Published: January 2011

ABSTRACT
The role of specific sequences in the transmembrane (TM) domain of Newcastle disease virus (NDV) fusion (F) protein in the structure and function of this protein was assessed by replacing this domain with the F protein TM domains from two other paramyxoviruses, Sendai virus (SV) and measles virus (MV), or the TM domain of the unrelated glycoprotein (G) of vesicular stomatitis virus (VSV). Mutant proteins with the SV or MV F protein TM domains were expressed, transported to cell surfaces, and proteolytically cleaved at levels comparable to that of the wild-type protein, while mutant proteins with the VSV G protein TM domain were less efficiently expressed on cell surfaces and proteolytically cleaved. All mutant proteins were defective in all steps of membrane fusion, including hemifusion. In contrast to the wild-type protein, the mutant proteins did not form detectable complexes with the NDV hemagglutinin-neuraminidase (HN) protein. As determined by binding of conformation-sensitive antibodies, the conformations of the ectodomains of the mutant proteins were altered. These results show that the specific sequence of the TM domain of the NDV F protein is important for the conformation of the preactivation form of the ectodomain, the interactions of the protein with HN protein, and fusion activity.