bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence and Continuous Evolution of Genotype 1E Rubella Viruses in China
Authors: Zhu Zhen , Cui Aili , Wang Huanhuan , Zhang Yan , Liu Chunyu , Wang Changyin , Zhou Shujie , Chen Xia , Zhang Zhenying , Feng Daxin , Wang Yan , Chen Haiyun , Pan Zhengfan , Zeng Xiangjie , Zhou Jianhui , Wang Shuang , Chang Xin , Lei Yue , Tian Hong , Liu Yang , Zhou Shunde , Zhan Jun , Chen Hui , Gu Suyi , Tian Xiaoling , Liu Jianfeng , Chen Ying , Fu Hong , Yang Xiuhui , Zheng Huanying , Liu Leng , Zheng Lei , Gao Hui , He Jilan , Sun Li , Xu Wenbo 
Published: December 2011

ABSTRACT

In China, rubella vaccination was introduced into the national immunization program in 2008, and a rubella epidemic occurred in the same year. In order to know whether changes in the genotypic distribution of rubella viruses have occurred in the postvaccination era, we investigate in detail the epidemiological profile of rubella in China and estimate the evolutionary rate, molecular clock phylogeny, and demographic history of the predominant rubella virus genotypes circulating in China using Bayesian Markov chain Monte Carlo phylodynamic analyses. 1E was found to be the predominant rubella virus genotype since its initial isolation in China in 2001, and no genotypic shift has occurred since then. The results suggest that the global 1E genotype may have diverged in 1995 and that it has evolved at a mutation rate of 1.65 × 10
−3
per site per year. The Chinese 1E rubella virus isolates were grouped into either cluster 1 or cluster 2, which likely originated in 1997 and 2006, respectively. Cluster 1 viruses were found in all provinces examined in this study and had a mutation rate of 1.90 × 10
−3
per site per year. The effective number of infections remained constant until 2007, and along with the introduction of rubella vaccine into the national immunization program, although the circulation of cluster 1 viruses has not been interrupted, some viral lineages have disappeared, and the epidemic started a decline that led to a decrease in the effective population size. Cluster 2 viruses were found only in Hainan Province, likely because of importation.
Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing
Authors: Pérez-Osorio Ailyn C. , Boyle David S. , Ingham Zachary K. , Ostash Alla , Gautom Romesh K. , Colombel Craig , Houze Yolanda , Leader Brandon T. 
Published: December 2011

ABSTRACTTuberculosis (TB) remains a significant global health problem for which rapid diagnosis is critical to both treatment and control. This report describes a multiplex PCR method, the Mycobacterial IDentification and Drug Resistance Screen (MID-DRS) assay, which allows identification of members of theMycobacterium tuberculosiscomplex (MTBC) and the simultaneous amplification of targets for sequencing-based drug resistance screening of rifampin-resistant (rifampinr), isoniazidr, and pyrazinamiderTB. Additionally, the same multiplex reaction amplifies a specific 16S rRNA gene target for rapid identification ofM. aviumcomplex (MAC) and a region of the heat shock protein 65 gene (hsp65) for further DNA sequencing-based confirmation or identification of other mycobacterial species. Comparison of preliminary results generated with MID-DRS versus culture-based methods for a total of 188 bacterial isolates demonstrated MID-DRS sensitivity and specificity as 100% and 96.8% for MTBC identification; 100% and 98.3% for MAC identification; 97.4% and 98.7% for rifampinrTB identification; 60.6% and 100% for isoniazidrTB identification; and 75.0% and 98.1% for pyrazinamiderTB identification. The performance of the MID-DRS was also tested on acid-fast-bacterium (AFB)-positive clinical specimens, resulting in sensitivity and specificity of 100% and 78.6% for detection of MTBC and 100% and 97.8% for detection of MAC. In conclusion, use of the MID-DRS reduces the time necessary for initial identification and drug resistance screening of TB specimens to as little as 2 days. Since all targets needed for completing the assay are included in a single PCR amplification step, assay costs, preparation time, and risks due to user errors are also reduced.
Human Leptospira Isolates Circulating in Mayotte (Indian Ocean) Have Unique Serological and Molecular Features
Authors: Bourhy P. , Collet L. , Lernout T. , Zinini F. , Hartskeerl R. A. , van der Linden Hans , Thiberge J. M. , Diancourt L. , Brisse S. , Giry C. , Pettinelli F. , Picardeau M. 
Published: December 2011

ABSTRACT

Leptospirosis is one of the most widespread zoonoses in the world. However, there is a lack of information on circulating
Leptospira
strains in remote parts of the world. We describe the serological and molecular features of leptospires isolated from 94 leptospirosis patients in Mayotte, a French department located in the Comoros archipelago, between 2007 and 2010. Multilocus sequence typing identified these isolates as
Leptospira interrogans
,
L. kirschneri
,
L. borgpetersenii
, and members of a previously undefined phylogenetic group. This group, consisting of 15 strains, could represent a novel species. Serological typing revealed that 70% of the isolates belonged to the serogroup complex Mini/Sejroe/Hebdomadis, followed by the serogroups Pyrogenes, Grippotyphosa, and Pomona. However, unambiguous typing at the serovar level was not possible for most of the strains because the isolate could belong to more than one serovar or because serovar and species did not match the original classification. Our results indicate that the serovar and genotype distribution in Mayotte differs from what is observed in other regions, thus suggesting a high degree of diversity of circulating isolates worldwide. These results are essential for the improvement of current diagnostic tools and provide a starting point for a better understanding of the epidemiology of leptospirosis in this area of endemicity.
Epidemiology and Risk Factors of Community Onset Infections Caused by Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains
Authors: Kang Cheol-In , Wi Yu Mi , Lee Mi Young , Ko Kwan Soo , Chung Doo Ryeon , Peck Kyong Ran , Lee Nam Yong , Song Jae-Hoon 
Published: December 2011

ABSTRACT

Limited clinical information is available regarding community onset infections caused by extended-spectrum β-lactamase (ESBL)-producing
Escherichia coli
. A case-control study was performed to evaluate the epidemiology and risk factors of these types of infections. A case patient was defined as a person whose clinical sample yielded ESBL-producing
E. coli
. For each case patient, one control was randomly chosen from a group of outpatients from whom non-ESBL-producing
E. coli
had been isolated and for whom a clinical sample had been sent to the same laboratory for culturing during the following week. Of 108 cases of ESBL-producing
E. coli
, 56 (51.9%) were classified as health care associated (HCA). Univariate analysis showed male gender, HCA infection, severe underlying illness, and a prior receipt of antibiotics to be associated with ESBL-producing
E. coli
. In the multivariate analysis, HCA infection (odds ratio [OR], 3.18; 95% confidence interval [CI], 1.67 to 6.06;
P
< 0.001) and previous use of antibiotics (OR, 4.88; 95% CI, 2.08 to 11.48;
P
< 0.001) were found to be significantly associated with the ESBL group. In a multivariate analysis that included each antibiotic, previous use of fluoroquinolone (OR, 7.32; 95% CI, 1.58 to 34.01;
P
= 0.011) was significantly associated with ESBL-producing
E. coli
. Of 101 isolates in which ESBLs and their molecular relationships were studied, all isolates produced ESBLs from the CTX-M family (CTX-M-14, 40 isolates; CTX-M-15, 39 isolates; and other members of the CTX-M family, 22 isolates). In conclusion, this study confirms that ESBL-producing
E. coli
strains are a notable cause of community onset infections in predisposed patients. HCA infection and previous use of fluoroquinolone were significant factors associated with ESBL-producing
E. coli
in community onset infections.
Strong Correlation between Liver and Serum Levels of Hepatitis C Virus Core Antigen and RNA in Chronically Infected Patients
Authors: Descamps V. , Op de Beeck A. , Plassart C. , Brochot E. , François C. , Helle F. , Adler M. , Bourgeois N. , Degré D. , Duverlie G. , Castelain S. 
Published: December 2011

ABSTRACT

HCV core antigen (Ag) and HCV RNA levels were evaluated in matched liver biopsy samples and sera from 22 patients with hepatitis C infection by using the quantitative Architect HCV Ag immunoassay and a real-time RT-qPCR assay, respectively. The data showed a strong correlation between liver and serum compartments of HCV Ag levels (
r
= 0.80) and HCV RNA levels (
r
= 0.87). In summary, the serum HCV Ag and RNA levels reflect the intrahepatic values.
Viral Interferon Regulatory Factors Decrease the Induction of Type I and Type II Interferon during Rhesus Macaque Rhadinovirus Infection
Authors: Robinson Bridget A. , Estep Ryan D. , Messaoudi Ilhem , Rogers Kelsey S. , Wong Scott W. 
Published: December 2011

ABSTRACTKaposi's sarcoma-associated herpesvirus and rhesus macaque rhadinovirus (RRV), two closely related gammaherpesviruses, are unique in their expression of viral homologs of cellular interferon regulatory factors (IRFs), termed viral IRFs (vIRFs). To assess the role of vIRFs duringde novoinfection, we have utilized the bacterial artificial chromosome clone of wild-type RRV17577(WTBACRRV) to generate a recombinant virus with all 8 of the vIRFs deleted (vIRF-ko RRV). The infection of primary rhesus fibroblasts and peripheral blood mononuclear cells (PBMCs) with vIRF-ko RRV resulted in earlier and increased induction of type I interferon (IFN) (IFN-α/β) and type II IFN (IFN-γ). Additionally, plasmacytoid dendritic cells maintained higher levels of IFN-α production in PBMC cultures infected with vIRF-ko RRV than in cultures infected with WTBACRRV. Moreover, the nuclear accumulation of phosphorylated IRF-3, which is necessary for the induction of type I IFN, was also inhibited following WTBACRRV infection. These findings demonstrate that duringde novoRRV infection, vIRFs are inhibiting the induction of IFN at the transcriptional level, and one potential mechanism for this is the disruption of the activation and localization of IRF-3.
Identification of Cell Surface Molecules Involved in Dystroglycan-Independent Lassa Virus Cell Entry
Authors: Shimojima Masayuki , Ströher Ute , Ebihara Hideki , Feldmann Heinz , Kawaoka Yoshihiro 
Published: December 2011

ABSTRACT
Although O-mannosylated dystroglycan is a receptor for Lassa virus, a causative agent of Lassa fever, recent findings suggest the existence of an alternative receptor(s). Here we identified four molecules as receptors for Lassa virus: Axl and Tyro3, from the TAM family, and dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) and liver and lymph node sinusoidal endothelial calcium-dependent lectin (LSECtin), from the C-type lectin family. These molecules enhanced the binding of Lassa virus to cells and mediated infection independently of dystroglycan. Axl- or Tyro3-mediated infection required intracellular signaling via the tyrosine kinase activity of Axl or Tyro3, whereas DC-SIGN- or LSECtin-mediated infection and binding were dependent on a specific carbohydrate and on ions. The identification of these four molecules as Lassa virus receptors advances our understanding of Lassa virus cell entry.
Selection and Accumulation of an HIV-1 Escape Mutant by Three Types of HIV-1-Specific Cytotoxic T Lymphocytes Recognizing Wild-Type and/or Escape Mutant Epitopes
Authors: Akahoshi Tomohiro , Chikata Takayuki , Tamura Yoshiko , Gatanaga Hiroyuki , Oka Shinichi , Takiguchi Masafumi 
Published: December 2011

ABSTRACT

It is known that cytotoxic T lymphocytes (CTLs) recognizing HIV-1 escape mutants are elicited in HIV-1-infected individuals, but their role in the control of HIV-1 replication remains unclear. We investigated the antiviral ability of CTLs recognizing the HLA-A*24:02-restricted Gag28 -36 (KYKLKHIVW) epitope and/or its escape mutant (KYRLKHIVW) elicited in the early and chronic phases of the infection. Wild-type (WT)-epitope-specific CTLs, as well as cross-reactive CTLs recognizing both WT and K30R (3R) epitopes, which were predominantly elicited at early and/or chronic phases in HLA-A*24:02
+
individuals infected with the WT virus, suppressed the replication of the WT virus but failed to suppress that of the 3R virus, indicating that the 3R virus was selected by these 2 types of CTLs. On the other hand, cross-reactive and 3R-specific CTLs, which were elicited in those infected with the 3R virus, did not suppress the replication of either WT or 3R virus, indicating that these CTLs did not contribute to the control of 3R virus replication. High accumulation of the 3R mutation was found in a Japanese population recently recruited. The selection and accumulation of this 3R mutation resulted from the antiviral ability of these Gag28-specific CTLs and high prevalence of HLA-A*24:02 in a Japanese population. The present study highlighted the mechanisms for the roles of cross-reactive and mutant-epitope-specific CTLs, as well as high accumulation of escape mutants, in an HIV-1-infected population.
Intraspecific and interspecific interactions among proteins regulating exopolysaccharide synthesis in Streptococcus thermophilus, Streptococcus iniae, and Lactococcus lactis subsp. cremoris and the assessment of potential lateral gene transfer
Authors: Cefalo Angela D. , Broadbent Jeffery R. , Welker Dennis L. 
Published: December 2011

Using the yeast two-hybrid system, intraspecific protein interactions were detected in Streptococcus iniae and Lactococcus lactis subsp. cremoris between the transmembrane activation protein (CpsC and EpsA, respectively) and the protein tyrosine kinase (CpsD and EpsB, respectively), between two protein tyrosine kinases, and between the protein tyrosine kinase and the phosphotyrosine phosphatase (CpsB and EpsC, respectively). For each of these intraspecific interactions, interspecific interactions were also detected when one protein was from S. iniae and the other was from Streptococcus thermophilus . Interactions were also observed between two protein tyrosine kinases when one protein was from either of the Streptococcus species and the other from L. lactis subsp. cremoris. The results and sequence comparisons performed in this study support the conclusion that interactions among the components of the tyrosine kinase – phosphatase regulatory system are conserved in the order Lactobacillales and that interspecific genetic exchanges of the genes that encode these proteins have the potential to form functional recombinants. A better understanding of intraspecific and interspecific protein interactions involved in regulating exopolysaccharide biosynthesis may facilitate construction of improved strains for industrial uses as well as identification of factors needed to form functional regulatory complexes in naturally occurring recombinants.
Purification and characterization of enterocin MC13 produced by a potential aquaculture probiontEnterococcus faeciumMC13 isolated from the gut ofMugil cephalus
Authors: Satish Kumar R. , Kanmani P. , Yuvaraj N. , Paari K.A. , Pattukumar V. , Arul V. 
Published: December 2011

A bacteriocin producer strain MC13 was isolated from the gut of Mugil cephalus (grey mullet) and identified as Enterococcus faecium . The bacteriocin of E. faecium MC13 was purified to homogeneity, as confirmed by Tricine sodium dodecyl sulphate – polyacrylamide gel electrophoresis (SDS–PAGE). Reverse-phase high-performance liquid chromatography (HPLC) analysis showed a single active fraction eluted at 26 min, and matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry analysis showed the molecular mass to be 2.148 kDa. The clear zone in native PAGE corresponding to enterocin MC13 band further substantiated its molecular mass. A dialyzed sample (semicrude preparation) of enterocin MC13 was broad spectrum in its action and inhibited important seafood-borne pathogens: Listeria monocytogenes , Vibrio parahaemolyticus , and Vibrio vulnificus . This antibacterial substance was sensitive to proteolytic enzymes: trypsin, protease, and chymotrypsin but insensitive to catalase and lipase, confirming that inhibition was due to the proteinaceous molecule, i.e., bacteriocin, and not due to hydrogen peroxide. Enterocin MC13 tolerated heat treatment (up to 90 °C for 20 min). Enterococcus faecium MC13 was effective in bile salt tolerance, acid tolerance, and adhesion to the HT-29 cell line. These properties reveal the potential of E. faecium MC13 to be a probiotic bacterium. Enterococcus faecium MC13 could be used as potential fish probiotic against pathogens such as V. parahaemolyticus, Vibrio harveyi , and Aeromonas hydrophila in fisheries. Also, this could be a valuable seafood biopreservative against L. monocytogenes.
Molecular identification of a polyM-specific alginate lyase from Pseudomonas sp. strain KS-408 for degradation of glycosidic linkages between two mannuronates or mannuronate and guluronate in alginate
Authors: Kam Natania , Park Yoo Jung , Lee Eun Yeol , Kim Hee Sook 
Published: December 2011

An alginate lyase gene of a newly isolated Pseudomonas sp. strain KS-408 was cloned by using PCR with the specific primers designed from homologous nucleotide sequences. A partial protein sequence of KS-408 alginate lyase was homology-modeled on the basis of the crystal structure of A1-III alginate lyase from Sphingomonas sp. strain A1. The proposed 3-D structure of KS-408 alginate lyase shows that Asn-198, His-199, Arg-246, and Tyr-253 residues are conserved for the catalytic active site. The recombinant KS-408-1F (with signal peptide) and KS-408-2F (without signal peptide) alginate lyases with the (His)6 tag consist of 393 (44.5 kDa) and 372 (42.4 kDa) amino acids with isoelectric points of 8.64 and 8.46, respectively. The purified recombinant KS-408 alginate lyase was very stable when it was incubated at 40 °C for 30 min. Alginate oligosaccharides produced by the KS-408-2F alginate lyase were purified on a Bio-Gel P2 column and analyzed by thin-layer chromatography, fast-protein liquid chromatography, and electrospray ionization mass spectrometry. 1H NMR data showed that the KS-408-2F alginate lyase cleaved the glycosidic linkages between two mannuronates (mannuronate-β(1–4)-mannuronate) or mannuronate and guluronate (mannuronate-β(1–4)-guluronate), indicating that the KS-408 alginate lyase is a polyM-specific lyase.
Cardiac Myosin Binding Protein C Insufficiency Leads to Early Onset of Mechanical Dysfunction
Authors: Desjardins Candida L. , Chen Yong , Coulton Arthur T. , Hoit Brian D. , Yu Xin , Stelzer Julian E. 
Published: December 2011

Background—
Decreased expression of cardiac myosin binding protein C (cMyBPC) as a result of genetic mutations may contribute to the development of hypertrophic cardiomyopathy (HCM); however, the mechanisms that link cMyBPC expression and HCM development, especially contractile dysfunction, remain unclear.

Methods and Results—

We evaluated cardiac mechanical function in vitro and in vivo in young mice (8–10 weeks of age) carrying no functional cMyBPC alleles (cMyBPC
−/−
) or 1 functional cMyBPC allele (cMyBPC
±
). Skinned myocardium isolated from cMyBPC
−/−
hearts displayed significant accelerations in stretch activation cross-bridge kinetics. Cardiac MRI studies revealed severely depressed in vivo left ventricular (LV) magnitude and rates of LV wall strain and torsion compared with wild-type (WT) mice. Heterozygous cMyBPC
±
hearts expressed 23±5% less cMyBPC than WT hearts but did not display overt hypertrophy. Skinned myocardium isolated from cMyBPC
±
hearts displayed small accelerations in the rate of stretch induced cross-bridge recruitment. MRI measurements revealed reductions in LV torsion and circumferential strain, as well reduced circumferential strain rates in early systole and diastole.

Conclusions—
Modest decreases in cMyBPC expression in the mouse heart result in early-onset subtle changes in cross-bridge kinetics and in vivo LV mechanical function, which could contribute to the development of HCM later in life.
Implementing Room for the River: narratives of success and failure in Kampen, the Netherlands
Authors: Warner Jeroen , van Buuren Arwin 
Published: December 2011

This article analyzes the discursive strategies surrounding the implementation of the Dutch water safety program ‘Room for the River’. When this program was announced, it was heralded as a paradigm shift fitting in with the ongoing transition to ‘living with water’. Yet announcing a paradigm shift is not the real thing. When a policy is made, it is still a dead letter. For it to become implemented, people have to act on it as if it is a reality. It needs to be socially produced – and reproduced. The present article looks at how the new river policy initiative is ‘translated’ to the local level, how discourse coalitions ‘pro’ and ‘contra’ develop and how they discursively defend their claims. In this ‘translation process’ elements of the original policy narrative are selected and reinterpreted to fit into the specific purposes of local stakeholders. While its protagonists have been active in promoting the program as a successful ‘paradigm shift’, others have questioned this claim. This contribution inventories the different narratives of success and failure on Room for the River, by homing in on an indicative case study. We show how elements of the official policy narrative are used, broadened, questioned or reinterpreted by local actors to defend their specific point of view. Their narratives try to weld discursive alliances between catchy rhetorical devices, normative values and sources of expertise. They make selective use of the dominant narrative of current river management speak, and ‘shop’ between scientific and policy venues to support these claims. Points for practitioners Policy ideas and labels are inevitably translated and modified as they ‘land’ in the local arena. A ‘success’ label may influence but cannot determine local acceptance and implementation of a policy. Locally, labels are likely to become tangled with other labels and interpretations. Multi-objective policies prove particularly vulnerable to criticism from ‘purist’ and one-issue opponents. Project managers should anticipate the dynamics of reframing and be able to adjust that discourse and labeling where necessary lest they become burdens.