bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti
Authors: Tiricz Hilda , Szűcs Attila , Farkas Attila , Pap Bernadett , Lima Rui M. , Maróti Gergely , Kondorosi Éva , Kereszt Attila 
Published: August 2013

ABSTRACT

Leguminous plants establish symbiosis with nitrogen-fixing alpha- and betaproteobacteria, collectively called rhizobia, which provide combined nitrogen to support plant growth. Members of the inverted repeat-lacking clade of legumes impose terminal differentiation on their endosymbiotic bacterium partners with the help of the nodule-specific cysteine-rich (NCR) peptide family composed of close to 600 members. Among the few tested NCR peptides, cationic ones had antirhizobial activity measured by reduction or elimination of the CFU and uptake of the membrane-impermeable dye propidium iodide. Here, the antimicrobial spectrum of two of these peptides, NCR247 and NCR335, was investigated, and their effect on the transcriptome of the natural target
Sinorhizobium meliloti
was characterized. Both peptides were able to kill quickly a wide range of Gram-negative and Gram-positive bacteria; however, their spectra were only partially overlapping, and differences were found also in their efficacy on given strains, indicating that the actions of NCR247 and NCR335 might be similar though not identical. Treatment of
S. meliloti
cultures with either peptide resulted in a quick downregulation of genes involved in basic cellular functions, such as transcription-translation and energy production, as well as upregulation of genes involved in stress and oxidative stress responses and membrane transport. Similar changes provoked mainly in Gram-positive bacteria by antimicrobial agents were coupled with the destruction of membrane potential, indicating that it might also be a common step in the bactericidal actions of NCR247 and NCR335.
Global Study of IS
6110
in a Successful Mycobacterium tuberculosis Strain: Clues for Deciphering Its Behavior and for Its Rapid Detection
Authors: Millán-Lou Maria Isabel , López-Calleja Ana Isabel , Colmenarejo Cristina , Lezcano Maria Antonia , Vitoria Maria Asunción , del Portillo Patricia , Otal Isabel , Martín Carlos , Samper Sofía 
Published: August 2013

ABSTRACT

The
Mycobacterium tuberculosis
insertion sequence IS
6110
, besides being a very useful tool in molecular epidemiology, seems to have an impact on the biology of bacilli. In the present work, we mapped the 12 points of insertion of IS
6110
in the genome of a successful strain named
M. tuberculosis
Zaragoza (which has been referred to as the MTZ strain). This strain, belonging to principal genetic group 3, caused a large unsuspected tuberculosis outbreak involving 85 patients in Zaragoza, Spain, in 2001 to 2004. The mapping of the points of insertion of IS
6110
in the genome of the Zaragoza strain offers clues for a better understanding of the adaptability and virulence of
M. tuberculosis.
Surprisingly, the presence of one copy of IS
6110
was found in
Rv2286c
, as was recently described for a successful Beijing sublineage. As a result of this analysis, a rapid method for detecting this particular
M. tuberculosis
strain has been designed.
Classical Molecular Tests Using Urine Samples as a Potential Screening Tool for Human Papillomavirus Detection in Human Immunodeficiency Virus-Infected Women
Authors: Munoz Marina , Camargo Milena , Soto-De Leon Sara C. , Sanchez Ricardo , Pineda-Peña Andrea C. , Perez-Prados Antonio , Patarroyo Manuel E. , Patarroyo Manuel A. 
Published: August 2013

ABSTRACTHuman papillomavirus (HPV) is the main risk factor associated with the development of cervical cancer (CC); however, there are other factors, such as immunosuppression caused by the human immunodeficiency virus (HIV), that favor progression of the illness. This study was thus aimed at evaluating the functionality of classical PCR-based molecular tests for the generic identification of HPV DNA (GP5+/GP6+, MY09/MY11, and pU1M/2R primers, individually or in combination) using cervical and urine samples from 194 HIV-positive women. Infected samples were tested with type-specific primers for six high-risk types (HPV-16, -18, -31, -33, -45, and -58) and two low-risk types (HPV-6 and -11). HPV infection prevalence rates were 70.1% for the cervical samples and 63.9% for the urine samples. HPV-16 was the most prevalent viral type in the cervical and urine samples, with higher rates of multiple infections than single infections detected in such samples. HPV DNA detection by PCR (mainly with the pU1M/2R primer set) in urine samples was positively associated with abnormal cytological findings (atypical squamous cells of undetermined significance/squamous intraepithelial lesions [ASCUS/SIL]). It was determined that the operative characteristics for detection of cytological abnormalities were similar for cervical and urine samples. This suggested using PCR for the detection of HPV DNA in urine samples as a potential screening strategy for CC prevention in future prevention and control programs along with currently implemented strategies for reducing the impact of the disease, i.e., urine samples are economical, are easy to collect, have wide acceptability among women, and have operative characteristics similar to those of cervical samples.
National Surveillance of Methicillin-Resistant Staphylococcus aureus in China Highlights a Still-Evolving Epidemiology with 15 Novel Emerging Multilocus Sequence Types
Authors: Xiao Meng , Wang He , Zhao Ying , Mao Lei-Li , Brown Mitchell , Yu Yun-Song , O'Sullivan Matthew V. N. , Kong Fanrong , Xu Ying-Chun 
Published: August 2013

ABSTRACT

The global spread of methicillin-resistant
Staphylococcus aureus
(MRSA) is a serious problem, particularly in mainland China. In order to better understand the national molecular epidemiology and resistance profiles of hospital-associated MRSA (HA-MRSA) in China, a laboratory-based multicenter surveillance study was conducted. Sixty-nine hospitals in 45 large cities in 27 provinces were involved, and a total of 1,141 HA-MRSA isolates were collected during the 6-month study period in 2011. All MRSA isolates were characterized by multilocus sequence typing (MLST), staphylococcal cassette chromosome
mec
(SCC
mec
) typing,
spa
typing, detection of the Panton-Valentine leukocidin (PVL) locus (
lukS-PV
and
lukF-PV
), and antibiogram analysis. ST239-III-t030, ST239-III-t037, and ST5-II-t002 were the predominant HA-MRSA clones (overall prevalence rates, 57.1%, 12.9%, and 8.1%, respectively), although the prevalence rates of these major clones varied markedly in different administrative regions. Of note, 6.6% of the HA-MRSA isolates were found to belong to ST59, which had typical community-associated MRSA (CA-MRSA) features, including carriage of SCC
mec
type IV or V and PVL and less antimicrobial resistance than other major HA-MRSA clones. Moreover, among 36 MLST sequence types (STs) identified, 15 STs, accounting for 3.5% of total isolates, were novel. A novel ST designated ST2590, which is a single-locus variant of ST5-II-t002, was identified in three hospitals in two large cities, with a total of 17 isolates. To further monitor trends in HA-MRSA prevalence, epidemic clonal shifts, clone emergence, and transmission between community and health care settings, longitudinal national MRSA surveillance is required.
Outbreak of Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strains
Authors: Vilacoba Elisabet , Almuzara Marisa , Gulone Lucia , Rodriguez Rocio , Pallone Elida , Bakai Romina , Centrón Daniela , Ramírez María Soledad 
Published: August 2013

ABSTRACT

Acinetobacter baumannii
pigmented strains are not common in clinical settings. Here, we report an outbreak caused by indigo-pigmented
A. baumannii
strains isolated in an acute care hospital in Argentina from March to September 2012. Pan-PCR assays exposed a unique pattern belonging to the recently described regional CC113
B
/CC79
P
clonal complex that confirms the relevant relationships among the indigo-pigmented
A. baumannii
strains. All of them were extensively drug resistant and harbored different genetic elements associated with horizontal genetic transfer, such as the transposon Tn
2006
, class 2 integrons, AbaR-type islands, IS
125
, IS
26
,
strA
,
strB
,
florR
, and the small recombinase IS
CR2
associated with the
sul2
gene preceded by IS
Aba1
.
Detection of Cytomegalovirus Drug Resistance Mutations by Next-Generation Sequencing
Authors: Sahoo Malaya K. , Lefterova Martina I. , Yamamoto Fumiko , Waggoner Jesse J. , Chou Sunwen , Holmes Susan P. , Anderson Matthew W. , Pinsky Benjamin A. 
Published: August 2013

ABSTRACTAntiviral therapy for cytomegalovirus (CMV) plays an important role in the clinical management of solid organ and hematopoietic stem cell transplant recipients. However, CMV antiviral therapy can be complicated by drug resistance associated with mutations in the phosphotransferase UL97 and the DNA polymerase UL54. We have developed an amplicon-based high-throughput sequencing strategy for detecting CMV drug resistance mutations in clinical plasma specimens using a microfluidics PCR platform for multiplexed library preparation and a benchtop next-generation sequencing instrument. Plasmid clones of the UL97 and UL54 genes were used to demonstrate the low overall empirical error rate of the assay (0.189%) and to develop a statistical algorithm for identifying authentic low-abundance variants. The ability of the assay to detect resistance mutations was tested with mixes of wild-type and mutant plasmids, as well as clinical CMV isolates and plasma samples that were known to contain mutations that confer resistance. Finally, 48 clinical plasma specimens with a range of viral loads (394 to 2,191,011 copies/ml plasma) were sequenced using multiplexing of up to 24 specimens per run. This led to the identification of seven resistance mutations, three of which were present in <20% of the sequenced population. Thus, this assay offers more sensitive detection of minor variants and a higher multiplexing capacity than current methods for the genotypic detection of CMV drug resistance mutations.
Rapid Identification of Microbes in Positive Blood Cultures by Use of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System
Authors: Foster Arnold G. W. 
Published: August 2013

ABSTRACT
Sepsis is a major cause of death worldwide among nonhospitalized people and hospitalized patients. A wide range of pathogens are involved, and the correct identification and correct antimicrobial therapy are critical to ensure optimal clinical outcomes. With the recent introduction of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), rapid identification of bacteria and fungi is now possible. The purpose of this study was to develop a rapid technique for identifying organisms in positive blood cultures using the Vitek MS system (bioMérieux). This technique is a lysis centrifugation method which involves a four-step washing and centrifugation procedure. A total of 253 positive monomicrobial blood cultures (Bactec Plus aerobic, anaerobic, and pediatric bottles) were tested using the Vitek MS system (KnowledgeBase version 2.0), with 92.1% and 88.1% of organisms overall being identified to the genus level and the species level, respectively. Of 161 Gram-positive bacterial isolates, 95.7% and 90.1% were identified to the genus level and the species level, respectively; of 92 Gram-negative bacterial isolates, 84.7% and 83.7% were identified to the genus level and the species level, respectively. The results obtained using this method demonstrate that the Vitek MS system can be used for rapid and effective identification of bacteria from positive blood cultures within 30 to 45 min after the positive signal has been provided by the Bactec FX blood culture system (Becton, Dickinson). This will lead to faster administration of the appropriate antimicrobial therapy and increase the chances for optimal clinical outcomes for patients.
Detection and Identification of Yeasts from Formalin-Fixed, Paraffin-Embedded Tissue by Use of PCR-Electrospray Ionization Mass Spectrometry
Authors: Simner Patricia J. , Buckwalter Seanne P. , Uhl James R. , Wengenack Nancy L. , Pritt Bobbi S. 
Published: August 2013

ABSTRACT

Diagnosis of yeast infection is typically accomplished by fungal smear and culture, histopathologic examination, and/or serologic studies. Newer assays based on mass spectrometry may be useful for yeast identification when histologic examination is inconclusive, fungal cultures are not ordered, or cultures fail to yield a causative agent. The purpose of this study was to evaluate the ability of the PLEX-ID broad fungal assay to accurately detect and identify yeasts in formalin-fixed paraffin-embedded (FFPE) tissues. Tissue samples from 78 FFPE specimens with both histopathology and corresponding culture results for a variety of yeasts were tested using the PLEX-ID broad fungal assay. A 40-μm FFPE tissue section from each specimen was digested with proteinase K followed by nucleic acid extraction and PCR using broad-range fungal primers. Yeast DNA in amplified products was identified using electrospray ionization mass spectrometry. Discordant results were resolved by D2 rRNA gene sequencing. PLEX-ID analysis detected yeast DNA in 78.2% (61/78) of the cases, of which 91.8% (56/61) were concordant with culture results. Of the 5 discordant positive results, 4 PLEX-ID results were considered to result from environmental contaminants, while 1 clinically important discrepancy was observed (
Blastomyces dermatitidis
by culture and
Cryptococcus neoformans
by PLEX-ID). Sequencing of the discordant sample was unsuccessful. The majority of histopathology results (89.7% [70/78]) correlated with culture results. The PLEX-ID broad fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional culture and histopathology tests.
Molecular Detection of Culture-Confirmed Bacterial Bloodstream Infections with Limited Enrichment Time
Authors: Moore Miranda S. , McCann Chase D. , Jordan Jeanne A. 
Published: August 2013

ABSTRACT
Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and pyrosequencing protocols, the molecular approach yielded results in 11.8 ± 2.9 h compared to means of 27.9 ± 13.6 h to obtain the Gram stain results and 81.6 ± 24.0 h to generate the final culture-based identification. The molecular approach enabled accurate detection of most bacteria present in incubating blood culture bottles on average about 16 h sooner than Gram stain results became available and approximately 3 days sooner than the phenotypic identification was entered in the Laboratory Information System. If implemented, this more rapid molecular approach could minimize the number of doses of unnecessary or ineffective antibiotics administered to patients.
Herpes Simplex Virus 1 Ubiquitin-Specific Protease UL36 Inhibits Beta Interferon Production by Deubiquitinating TRAF3
Authors: Wang Shuai , Wang Kezhen , Li Jie , Zheng Chunfu 
Published: August 2013

ABSTRACT
Interferon (IFN)-mediated innate immune defense is a potent antiviral mechanism. Viruses evade innate immunity and limit secretion of beta interferon (IFN-β) to replicate and survive in the host. The largest tegument protein of herpes simplex virus 1 (HSV-1), UL36, contains a novel deubiquitinase (DUB) motif embedded in its N terminus, denoted UL36 ubiquitin-specific protease (UL36USP). In the present study, we demonstrate that HSV-1 UL36USP inhibits Sendai virus (SeV)-induced interferon regulatory factor 3 (IRF3) dimerization, promoter activation, and transcription of IFN-β. The DUB activity of UL36USP is essential to block IFN-β production. UL36USP also inhibited IFN-β promoter activity induced by overexpression of the N terminus of RIG-I (RIG-IN) and MAVS, but not TBK-1, IκB kinase ε (IKKε), and IRF3/5D. UL36USP was subsequently shown to deubiquitinate TRAF3 and prevent the recruitment of the downstream adaptor TBK1. The recombinant HSV-1 lacking UL36USP DUB activity was generated. Cells infected with the mutant virus produced more IFN-β than wild-type (WT) HSV-1-infected cells. These findings demonstrate HSV-1 UL36USP removes polyubiquitin chains on TRAF3 and counteracts the IFN-β pathway.
Cytokine-Dependent Induction of CD4+T cells with Cytotoxic Potential during Influenza Virus Infection
Authors: Hua Laiqing , Yao Shuyu , Pham Duy , Jiang Li , Wright Jeffrey , Sawant Deepali , Dent Alexander L. , Braciale Thomas J. , Kaplan Mark H. , Sun Jie 
Published: August 2013

ABSTRACTRecent evidence has identified the role of granzyme B- and perforin-expressing CD4+T cells with cytotoxic potential in antiviral immunity. However, thein vivocytokine cues and downstream pathways governing the differentiation of these cells are unclear. Here, we have identified that CD4+T cells with cytotoxic potential are specifically induced at the site of infection during influenza virus infection. The development of CD4+T cells with cytotoxic potentialin vivowas dependent on the cooperation of the STAT2-dependent type I interferon signaling and the interleukin-2/interleukin-2 receptor alpha pathway for the induction of the transcription factors T-bet and Blimp-1. We showed that Blimp-1 promoted the binding of T-bet to the promoters of cytolytic genes in CD4+T cells and was required for the cytolytic function of thein vitro- andin vivo-generated CD4+T cells with cytotoxic potential. Thus, our data define the molecular basis of regulation of thein vivodevelopment of this functionally cytotoxic Th subset during acute respiratory virus infection. The potential implications for the functions of these cells are discussed.
A Host YB-1 Ribonucleoprotein Complex Is Hijacked by Hepatitis C Virus for the Control of NS3-Dependent Particle Production
Authors: Chatel-Chaix Laurent , Germain Marie-Anne , Motorina Alena , Bonneil Éric , Thibault Pierre , Baril Martin , Lamarre Daniel 
Published: August 2013

ABSTRACT
Hepatitis C virus (HCV) orchestrates the different stages of its life cycle in time and space through the sequential participation of HCV proteins and cellular machineries; hence, these represent tractable molecular host targets for HCV elimination by combination therapies. We recently identified multifunctional Y-box-binding protein 1 (YB-1 or YBX1) as an interacting partner of NS3/4A protein and HCV genomic RNA that negatively regulates the equilibrium between viral translation/replication and particle production. To identify novel host factors that regulate the production of infectious particles, we elucidated the YB-1 interactome in human hepatoma cells by a quantitative mass spectrometry approach. We identified 71 YB-1-associated proteins that included previously reported HCV regulators DDX3, heterogeneous nuclear RNP A1, and ILF2. Of the potential YB-1 interactors, 26 proteins significantly modulated HCV replication in a gene-silencing screening. Following extensive interaction and functional validation, we identified three YB-1 partners, C1QBP, LARP-1, and IGF2BP2, that redistribute to the surface of core-containing lipid droplets in HCV JFH-1-expressing cells, similarly to YB-1 and DDX6. Importantly, knockdown of these proteins stimulated the release and/or egress of HCV particles without affecting virus assembly, suggesting a functional YB-1 protein complex that negatively regulates virus production. Furthermore, a JFH-1 strain with the NS3 Q221L mutation, which promotes virus production, was less sensitive to this negative regulation, suggesting that this HCV-specific YB-1 protein complex modulates an NS3-dependent step in virus production. Overall, our data support a model in which HCV hijacks host cell machinery containing numerous RNA-binding proteins to control the equilibrium between viral RNA replication and NS3-dependent late steps in particle production.
Quantifying Selection against Synonymous Mutations in HIV-1
env
Evolution
Authors: Zanini Fabio , Neher Richard A. 
Published: August 2013

ABSTRACT

Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8
+
T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the
env
gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not.
Middle East Respiratory Syndrome Coronavirus Spike Protein Delivered by Modified Vaccinia Virus Ankara Efficiently Induces Virus-Neutralizing Antibodies
Authors: Song Fei , Fux Robert , Provacia Lisette B. , Volz Asisa , Eickmann Markus , Becker Stephan , Osterhaus Albert D. M. E. , Haagmans Bart L. , Sutter Gerd 
Published: August 2013

ABSTRACT
Middle East respiratory syndrome coronavirus (MERS-CoV) has recently emerged as a causative agent of severe respiratory disease in humans. Here, we constructed recombinant modified vaccinia virus Ankara (MVA) expressing full-length MERS-CoV spike (S) protein (MVA-MERS-S). The genetic stability and growth characteristics of MVA-MERS-S make it a suitable candidate vaccine for clinical testing. Vaccinated mice produced high levels of serum antibodies neutralizing MERS-CoV. Thus, MVA-MERS-S may serve for further development of an emergency vaccine against MERS-CoV.