bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing
Authors: Oyola Samuel O. , Gu Yong , Manske Magnus , Otto Thomas D. , O'Brien John , Alcock Daniel , MacInnis Bronwyn , Berriman Matthew , Newbold Chris I. , Kwiatkowski Dominic P. , Swerdlow Harold P. , Quail Michael A. 
Published: December 2012

ABSTRACT

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches
Plasmodium falciparum
DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci.
Isolation of a Novel Strain of Mycobacterium iranicum from a Woman in the United States
Authors: Balakrishnan Nandhakumar , Tortoli Enrico , Engel Susan L. , Breitschwerdt Edward B. 
Published: December 2012

ABSTRACT

A novel strain of
Mycobacterium iranicum
, a recently described nontuberculous
Mycobacterium
species, was isolated from the sputum of a woman. The source of infection was not determined; however, fomite transmission of inhaled aerosolized secretions from her husband's sleep apnea equipment was historically possible.
Genotypic Characterization of Enterotoxigenic Escherichia coli Strains Causing Traveler's Diarrhea
Authors: Rivera Fulton P. , Medina Anicia M. , Aldasoro Edelweiss , Sangil Anna , Gascon Joaquim , Ochoa Theresa J. , Vila Jordi , Ruiz Joaquim 
Published: December 2012

ABSTRACT

This study aims to characterize the presence of virulence factors of enterotoxigenic
Escherichia coli
(ETEC) causing traveler's diarrhea. Among 52 ETEC isolates, the most common toxin type was STh, and the most frequent colonization factors (CFs) were CS21, CS6, and CS3. On the other hand, the nonclassical virulence factors EAST1 and EatA were frequently present.
Comparison of Droplet Digital PCR to Real-Time PCR for Quantitative Detection of Cytomegalovirus
Authors: Hayden R. T. , Gu Z. , Ingersoll J. , Abdul-Ali D. , Shi L. , Pounds S. , Caliendo A. M. 
Published: December 2012

ABSTRACT

Quantitative real-time PCR (QRT-PCR) has been widely implemented for clinical viral load testing, but a lack of standardization and relatively poor precision have hindered its usefulness. Digital PCR offers highly precise, direct quantification without requiring a calibration curve. Performance characteristics of real-time PCR were compared to those of droplet digital PCR (ddPCR) for cytomegalovirus (CMV) load testing. Tenfold serial dilutions of the World Health Organization (WHO) and the National Institute of Standards and Technology (NIST) CMV quantitative standards were tested, together with the AcroMetrix CMV tc panel (Life Technologies, Carlsbad, CA) and 50 human plasma specimens. Each method was evaluated using all three standards for quantitative linearity, lower limit of detection (LOD), and accuracy. Quantitative correlation, mean viral load, and variability were compared. Real-time PCR showed somewhat higher sensitivity than ddPCR (LODs, 3 log
10
versus 4 log
10
copies/ml and IU/ml for NIST and WHO standards, respectively). Both methods showed a high degree of linearity and quantitative correlation for standards (
R
2
≥ 0.98 in each of 6 regression models) and clinical samples (
R
2
= 0.93) across their detectable ranges. For higher concentrations, ddPCR showed less variability than QRT-PCR for the WHO standards and AcroMetrix standards (
P
< 0.05). QRT-PCR showed less variability and greater sensitivity than did ddPCR in clinical samples. Both digital and real-time PCR provide accurate CMV load data over a wide linear dynamic range. Digital PCR may provide an opportunity to reduce the quantitative variability currently seen using real-time PCR, but methods need to be further optimized to match the sensitivity of real-time PCR.
Enterovirus 68 in Pediatric Patients Hospitalized for Acute Airway Diseases
Authors: Renois Fanny , Bouin Alexis , Andreoletti Laurent 
Published: December 2012

ABSTRACT

Enterovirus 68 was detected in 10 respiratory specimens from pediatric patients hospitalized for acute wheezing or bronchitis during 2009 in the northeast of France. Viral loads ranged from 2 × 10
5
to 7.2 × 10
7
copies/ml. Alignment of 5′ nontranslated regions and phylogenetic analysis of partial VP1 gene sequences show that these viruses clustered and belonged to clade C.
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Rapid Identification of Tick Vectors
Authors: Yssouf Amina , Flaudrops Christophe , Drali Rezak , Kernif Tahar , Socolovschi Cristina , Berenger Jean-Michel , Raoult Didier , Parola Philippe 
Published: December 2012

ABSTRACT

A method for rapid species identification of ticks may help clinicians predict the disease outcomes of patients with tick bites and may inform the decision as to whether to administer postexposure prophylactic antibiotic treatment. We aimed to establish a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) spectrum database based on the analysis of the legs of six tick vectors:
Amblyomma variegatum
,
Rhipicephalus sanguineus
,
Hyalomma marginatum rufipes
,
Ixodes ricinus
,
Dermacentor marginatus
, and
Dermacentor reticulatus
. A blind test was performed on a trial set of ticks to identify specimens of each species. Subsequently, we used MALDI-TOF MS to identify ticks obtained from the wild or removed from patients. The latter tick samples were also identified by 12S ribosomal DNA (rDNA) sequencing and were tested for bacterial infections. Ticks obtained from the wild or removed from patients (
R. sanguineus
,
I. ricinus
, and
D. marginatus
) were accurately identified using MALDI-TOF MS, with the exception of those ticks for which no spectra were available in the database. Furthermore, one damaged specimen was correctly identified as
I. ricinus
, a vector of Lyme disease, using MALDI-TOF MS only. Six of the 14 ticks removed from patients were found to be infected by pathogens that included
Rickettsia
,
Anaplasma
, and
Borrelia
spp. MALDI-TOF MS appears to be an effective tool for the rapid identification of tick vectors that requires no previous expertise in tick identification. The benefits for clinicians include the more targeted surveillance of patients for symptoms of potentially transmitted diseases and the ability to make more informed decisions as to whether to administer postexposure prophylactic treatment.
Molecular Characterization of Mycoplasma agalactiae Reveals the Presence of an Endemic Clone in Spain
Authors: Ariza-Miguel Jaime , Rodríguez-Lázaro David , Hernández Marta 
Published: December 2012

ABSTRACT

Mycoplasma agalactiae
isolates from Spain were genetically characterized to investigate their genomic diversity and to better understand their relationship to isolates from other countries. Molecular typing revealed a high genomic homogeneity in Spanish
M. agalactiae
isolates, which clearly shows the circulation of one endemic clonal population.
Urease Operon and Urease Activity in Commensal and Disease-Causing Nontypeable Haemophilus influenzae
Authors: Zhang Lixin , Patel Mayuri , Xie Jingping , Davis Gregg S. , Marrs Carl F. , Gilsdorf Janet R. 
Published: December 2012

ABSTRACT

The
ure
operon was significantly more prevalent in
Haemophilus influenzae
isolates causing otitis media and chronic obstructive pulmonary disease (COPD)-associated bronchitis than in those from throats of healthy individuals (97% versus 78.1%,
P
< 0.001). Strains lacking the
ure
operon are over 8 times more likely to be from the throat than either otitis media or COPD isolates.
Myeloid-Derived Suppressor Cells in Murine Retrovirus-Induced AIDS Inhibit T- and B-Cell ResponsesIn VitroThat Are Used To Define the Immunodeficiency
Authors: Green Kathy A. , Cook W. James , Green William R. 
Published: December 2012

ABSTRACTMyeloid-derived suppressor cells (MDSCs) have been characterized in several disease settings, especially in many tumor systems. Compared to their involvement in tumor microenvironments, however, MDSCs have been less well studied in their responses to infectious disease processes, in particular to retroviruses that induce immunodeficiency. Here, we demonstrate for the first time the development of a highly immunosuppressive MDSC population that is dependent on infection by the LP-BM5 retrovirus, which causes murine acquired immunodeficiency. These MDSCs express a cell surface marker signature (CD11b+Gr-1+Ly6C+) characteristic of monocyte-type MDSCs. Such MDSCs profoundly inhibit immune responsiveness by a cell dose- and substantially inducible nitric oxide synthase (iNOS)-dependent mechanism that is independent of arginase activity, PD-1–PD-L1 expression, and interleukin 10 (IL-10) production. These MDSCs display levels of immunosuppressive function in parallel with the extent of disease in LP-BM5-infected wild-type (w.t.) versus knockout mouse strains that are differentially susceptible to pathogenesis. These MDSCs suppressed not only T-cell but also B-cell responses, which are an understudied target for MDSC inhibition. The MDSC immunosuppression of B-cell responses was confirmed by the use of purified B responder cells, multiple B-cell stimuli, and independent assays measuring B-cell expansion. Retroviral load measurements indicated that the suppressive Ly6Glow/±Ly6C+CD11b+-enriched MDSC subset was positive for LP-BM5, albeit at a significantly lower level than that of nonfractionated splenocytes from LP-BM5-infected mice. These results, including the strong direct MDSC inhibition of B-cell responsiveness, are novel for murine retrovirus-induced immunosuppression and, as this broadly suppressive function mirrors that of the LP-BM5-induced disease syndrome, support a possible pathogenic effector role for these retrovirus-induced MDSCs.
ATF6 Signaling Is Required for Efficient West Nile Virus Replication by Promoting Cell Survival and Inhibition of Innate Immune Responses
Authors: Ambrose Rebecca L. , Mackenzie Jason M. 
Published: December 2012

ABSTRACT

West Nile virus strain Kunjin (WNV
KUN
) is an enveloped, positive-sense RNA virus within the virus family
Flaviviridae
. Many flaviviruses have been shown to manipulate multiple signaling pathways, including autophagic, innate immune, and stress responses, in order to benefit replication. In particular, we have demonstrated that WNV
KUN
regulates the unfolded protein response (UPR), skewing the downstream effectors toward chaperone expression and Xbp-1 activation while preventing PERK-mediated translation attenuation and C/EBP homologous protein (CHOP) upregulation. WNV
KUN
-regulated UPR signaling can then be hijacked in order to affect type I interferon (IFN) responses, preventing IFN-mediated STAT1 phosphorylation and nuclear translocation. To extend our previous observations, we aimed to investigate the contribution of ATF6- and IRE1-mediated signaling during WNV
KUN
replication and how the two sensors contribute to the inhibition of IFN signaling. ATF6-deficient cells infected with WNV
KUN
showed decreased protein and virion production. These cells also demonstrated increased eIF2α phosphorylation and CHOP transcription, absent in infected matched control cells. Thus, we propose that in the absence of ATF6, WNV
KUN
is incapable of manipulating the PERK-mediated response to infection. In contrast, infection of IRE1
−/−
knockout cells showed no discernible differences compared to IRE1
+/+
cells. However, both ATF6 and IRE1 were required for WNV
KUN
-induced inhibition of STAT1 phosphorylation. We suggest that the combination of abhorrent UPR signaling, promotion of cell death, and increased innate immune responses contributes to the replication defects in ATF6-deficient cells, thus demonstrating the dual importance of ATF6 in maintaining cell viability and modulating immune responses during WNV
KUN
infection.
Poly(C)-Binding Protein 1, a Novel N
pro
-Interacting Protein Involved in Classical Swine Fever Virus Growth
Authors: Li Dan , Li Su , Sun Yuan , Dong Hong , Li Yongfeng , Zhao Bibo , Guo Dongwei , Weng Changjiang , Qiu Hua-Ji 
Published: December 2012

ABSTRACT

N
pro
is a multifunctional autoprotease unique to pestiviruses. The interacting partners of the N
pro
protein of classical swine fever virus (CSFV), a swine pestivirus, have been insufficiently defined. Using a yeast two-hybrid screen, we identified poly(C)-binding protein 1 (PCBP1) as a novel interacting partner of the CSFV N
pro
protein and confirmed this by coimmunoprecipitation, glutathione
S
-transferase (GST) pulldown, and confocal assays. Knockdown of PCBP1 by small interfering RNA suppressed CSFV growth, while overexpression of PCBP1 promoted CSFV growth. Furthermore, we showed that type I interferon was downregulated by PCBP1, as well as N
pro
. Our results suggest that cellular PCBP1 positively modulates CSFV growth.
2G12-Expressing B Cell Lines May Aid in HIV Carbohydrate Vaccine Design Strategies
Authors: Doores Katie J. , Huber Michael , Le Khoa M. , Wang Sheng-Kai , Doyle-Cooper Colleen , Cooper Anthony , Pantophlet Ralph , Wong Chi-Huey , Nemazee David , Burton Dennis R. 
Published: December 2012

ABSTRACTThe highly conserved cluster of high-mannose glycans on the HIV-1 envelope glycoprotein, gp120, has been highlighted as a target for neutralizing antibodies. 2G12, the first HIV-1 antiglycan neutralizing antibody described, binds with an unusual domain-exchanged structure that creates a high-affinity multivalent binding surface. It is an interesting challenge for rational vaccine design to generate immunogens capable of eliciting domain-exchanged 2G12-like responses. We recently showed that di-mannose recognition by the variable domains of 2G12 is independent of domain exchange but that exchange is critical for virus neutralization. Carbohydrate-based immunogens aimed at inducing 2G12-like antibodies may need to drive both di-mannose recognition and domain exchange through interactions with B cell receptors. Here we assessed the ability of such immunogens to activate mouse B cell lines displaying domain-exchanged wild-type 2G12 (2G12 WT), a non-domain-exchanged Y-shaped variant (2G12 I19R), and germ line 2G12 (2G12 gl). We show that several immunogens, including heat-killed yeast and bacteria, can activate both 2G12 WT and 2G12 I19R B cells. However, only discrete clusters of high-mannose glycans, as on recombinant forms of the HIV-1 envelope trimer and oligodendrons, activate 2G12 WT B cells. Furthermore, no immunogen tested activated 2G12 gl cells. Our results support the hypothesis that in order to drive domain exchange of an antimannose antibody response, a boost with an immunogen displaying discrete clusters of high-mannose glycans not recognized by conventional Y-shaped antibodies will be required. Additionally, a molecule capable of activating 2G12 gl cells might also be required. The results highlight broadly neutralizing antibody-expressing mouse B cells as potentially useful tools for carbohydrate immunogen screening.
Hepatitis B Virus mRNA-Mediated miR-122 Inhibition Upregulates PTTG1-Binding Protein, Which Promotes Hepatocellular Carcinoma Tumor Growth and Cell Invasion
Authors: Li Changfei , Wang Yanzhong , Wang Saifeng , Wu Bo , Hao Junli , Fan Hongxia , Ju Ying , Ding Yuping , Chen Lizhao , Chu Xiaoyu , Liu Wenjun , Ye Xin , Meng Songdong 
Published: December 2012

ABSTRACT

As the most abundant liver-specific microRNA, miR-122 is involved in diverse aspects of hepatic function and neoplastic transformation. Our previous study showed that miR-122 levels are significantly decreased in hepatitis B virus (HBV)-infected patients, which may facilitate viral replication and persistence (S. Wang, L. Qiu, X. Yan, W. Jin, Y. Wang, L. Chen, E. Wu, X. Ye, G. F. Gao, F. Wang, Y. Chen, Z. Duan, and S. Meng, Hepatology
55:
730–741, 2012). Loss of miR-122 expression in patients with hepatitis B enhances hepatitis B virus replication through cyclin G1-modulated P53 activity.). In this study, we provide evidence that all HBV mRNAs harboring an miR-122 complementary site act as sponges to bind and sequester endogenous miR-122, indicating that the highly redundant HBV transcripts are involved in HBV-mediated miR-122 suppression. We next identified pituitary tumor-transforming gene 1 (PTTG1) binding factor (PBF) as a target of miR-122 and demonstrated that HBV replication causes an obvious increase in PBF levels. Furthermore, we observed that the miR-122 levels were decreased and PBF was upregulated in chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC). Overexpression and knockdown studies both revealed that PBF enhances proliferation and invasion of HCC cells, and silencing PBF resulted in a dramatic reduction of HCC tumor growth
in vivo
. Mechanistic analysis demonstrated that PBF interacts with PTTG1 and facilitates PTTG1 nuclear translocation, subsequently increasing its transcriptional activities. Therefore, we identified a novel HBV mRNA-miR-122-PBF regulatory pathway that facilitates malignant hepatocyte growth and invasion in CHB which may contribute to CHB-induced HCC development and progression. Our work underscores the reciprocal interplay of host miRNA sequestration and depletion by viral mRNAs, which may contribute to chronic-infection-related cancer.
Pseudoinfectious Venezuelan Equine Encephalitis Virus: a New Means of Alphavirus Attenuation
Authors: Atasheva Svetlana , Kim Dal Young , Akhrymuk Maryna , Morgan David G. , Frolova Elena I. , Frolov Ilya 
Published: December 2012

ABSTRACT
Venezuelan equine encephalitis virus (VEEV) is a reemerging virus that causes a severe and often fatal disease in equids and humans. In spite of a continuous public health threat, to date, no vaccines or antiviral drugs have been developed for human use. Experimental vaccines demonstrate either poor efficiency or severe adverse effects. In this study, we developed a new strategy of alphavirus modification aimed at making these viruses capable of replication and efficient induction of the immune response without causing a progressive infection, which might lead to disease development. To achieve this, we developed a pseudoinfectious virus (PIV) version of VEEV. VEE PIV mimics natural viral infection in that it efficiently replicates its genome, expresses all of the viral structural proteins, and releases viral particles at levels similar to those found in wild-type VEEV-infected cells. However, the mutations introduced into the capsid protein make this protein almost incapable of packaging the PIV genome, and most of the released virions lack genetic material and do not produce a spreading infection. Thus, VEE PIV mimics viral infection in terms of antigen production but is safer due to its inability to incorporate the viral genome into released virions. These genome-free virions are referred to as virus-like particles (VLPs). Importantly, the capsid-specific mutations introduced make the PIV a very strong inducer of the innate immune response and add self-adjuvant characteristics to the designed virus. This unique strategy of virus modification can be applied for vaccine development against other alphaviruses.
Components of Promyelocytic Leukemia Nuclear Bodies (ND10) Act Cooperatively To Repress Herpesvirus Infection
Authors: Glass Mandy , Everett Roger D. 
Published: December 2012

ABSTRACT
Upon the entry of the viral genome into the nucleus, herpes simplex virus type 1 (HSV-1) gene expression is rapidly repressed by constitutively expressed cellular proteins. This intrinsic antiviral defense is normally counteracted by ICP0, which allows virus infection to proceed efficiently. Replication of ICP0-null mutant HSV-1, however, is severely repressed by mechanisms that are conferred, at least in part, by nuclear domain 10 (ND10) components, including hDaxx, the promyelocytic leukemia (PML) protein, and Sp100. To investigate if these ND10 components repress viral gene expression in a cooperative manner, we simultaneously depleted host cells for hDaxx, PML, and Sp100 by multiple short hairpin RNA (shRNA) knockdown from a single lentivirus vector. We found that replication and gene expression of ICP0-null mutant HSV-1 were cooperatively repressed by hDaxx, PML, and Sp100 immediately upon infection, and all stages of virus replication were inhibited. Plaque-forming efficiency was enhanced at least 50-fold in the triple-depleted cells, a much larger increase than achieved by depletion of any single ND10 protein. Similar effects were also observed during infection of triple-depleted cells with human cytomegalovirus (HCMV). Moreover, using a cell culture model of quiescent infection, we found that triple depletion resulted in a much larger number of viral genomes escaping repression. However, triple depletion was unable to fully overcome the ICP0-null phenotype, implying the presence of additional repressive host factors, possibly components of the SUMO modification or DNA repair pathways. We conclude that several ND10 components cooperate in an additive manner to regulate HSV-1 and HCMV infection.
Insights into a Viral Lytic Pathway from an Archaeal Virus-Host System
Authors: Snyder Jamie C. , Brumfield Susan K. , Kerchner Keshia M. , Quax Tessa E. F. , Prangishvili David , Young Mark J. 
Published: December 2012

ABSTRACT

Archaeal host cells infected by
Sulfolobus
turreted icosahedral virus (STIV) and
Sulfolobus islandicus
rod-shaped virus 2 (SIRV2) produce unusual pyramid-like structures on the cell surface prior to virus-induced cell lysis. This viral lysis process is distinct from known viral lysis processes associated with bacterial or eukaryal viruses. The STIV protein C92 and the SIRV2 protein 98 are the only viral proteins required for the formation of the pyramid lysis structures of STIV and SIRV2, respectively. Since SIRV2 and STIV have fundamentally different morphotypes and genome sequences, it is surprising that they share this lysis system. In this study, we have constructed a collection of C92/P98 chimeric proteins and tested their abilities, both in the context of virus replication and alone, to form pyramid lysis structures in
S. solfataricus
. The results of this study illustrate that these proteins are functionally homologous when expressed as individual chimeric proteins but not when expressed in the context of complete STIV infection.