bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Pan-Genomic Analysis Approach in Target Selection for Multiplex PCR Identification and Detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia Complex Species: a Proof-of-Concept Study
Authors: Ho Chi-Chun , Lau Candy C. Y. , Martelli Paolo , Chan San-Yuen , Tse Cindy W. S. , Wu Alan K. L. , Yuen Kwok-Yung , Lau Susanna K. P. , Woo Patrick C. Y. 
Published: December 2010

ABSTRACT

Burkholderia pseudomallei
,
Burkholderia thailandensis
, and the
Burkholderia cepacia
complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23
B. pseudomallei
, four
B. thailandensis
, and 16
B. cepacia
complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for
B. pseudomallei
,
B. thailandensis
, and the
B. cepacia
complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43
B. pseudomallei
, seven
B. thailandensis
, and 20
B. cepacia
complex (
B. multivorans
,
n
= 6;
B. cenocepacia
,
n
= 3;
B. cepacia
,
n
= 4;
B. arboris
,
n
= 2;
B. contaminans
,
B. anthina
, and
B. pyrrocinia
,
n
= 1 each; other unnamed members,
n
= 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for
B. pseudomallei
and the
B. cepacia
complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of
B. pseudomallei
,
B. thailandensis
, and the
B. cepacia
complex was developed and verified.
Comparison of Salmonella enterica Serovar Heidelberg Isolates from Human Patients with Those from Animal and Food Sources
Authors: Han Jing , David Donna E. , Deck Joanna , Lynne Aaron M. , Kaldhone Pravin , Nayak Rajesh , Stefanova Rossina , Foley Steven L. 
Published: December 2010

ABSTRACT

Seventy-eight
Salmonella enterica
serovar Heidelberg isolates from humans were tested for antimicrobial susceptibility, resistance genes, and plasmids and genotyped by pulsed-field gel electrophoresis (PFGE). Most (88%) contained plasmids, and 47% were resistant to antimicrobials. The overall results were compared to those of previous
S
. Heidelberg studies of food- and animal-related sources, and multiple similarities were observed.
Rifampin Stability in 7H9 Broth and Löwenstein-Jensen Medium
Authors: Yu Xia , Jiang Guanglu , Li Huiwen , Zhao Yanlin , Zhang Hongtao , Zhao Liping , Ma Yu , Coulter Christopher , Huang Hairong 
Published: December 2010

ABSTRACT

The objectives of this study were to monitor the stability of rifampin (RIF) in Löwenstein-Jensen medium (L-J medium) and 7H9 broth, which are the media commonly used for drug susceptibility testing (DST) of
Mycobacterium tuberculosis
. Rifampin degradation in stock solution, 7H9 broth, and L-J medium and during the inspissation process for L-J medium preparation was serially monitored by high-performance liquid chromatography (HPLC). L-J medium-based DST was conducted to examine the effect of L-J medium storage on the DST outcome. The RIF stock solution was stable for at least 3 months when kept at either 4°C or −20°C; RIF in 7H9 broth and L-J medium was almost 50% decayed after 1 week of storage at 37°C, and rifampin could not be detected in 7H9 or L-J medium after 3 weeks or 6 weeks of storage at 37°C. Approximately half of the drug was decomposed after 4 months of storage at 4°C for both media, and after 6 months of storage at 4°C, RIF in L-J medium was undetectable, while 38% of RIF remained in 7H9 medium. Approximately 21, 24, 29, and 35% RIF degradations were detected when the L-J medium was coagulated at 75°C, 80°C, 85°C, and 90°C, respectively. The DST outcomes when using L-J medium stored for different periods of time were consistent with the RIF concentration monitoring data. Rifampin in stock solution is stable for at least 3 months at a reduced storage temperature. Media containing RIF should be prepared strictly according to validated standard operating procedures. RIF degradation is a possible reason for false resistance categorizations of
M. tuberculosis
isolates in the clinical laboratory.
Imipenem-Resistant Nocardia cyriacigeorgica Infection in a Child with Chronic Granulomatous Disease
Authors: Hagerman Andrés , Rodríguez-Nava Verónica , Boiron Patrick , Crisinel Pierre-Alex , Posfay-Barbe Klara M. 
Published: December 2010

ABSTRACT

Nocardia
spp. can lead to local or disseminated infections, especially in immunocompromised patients. Combination therapy of amikacin and imipenem is commonly used to treat severe nocardial infections. We describe a patient with imipenem-resistant
Nocardia cyriacigeorgica
, which, to our knowledge, has not been previously reported among isolates of this species.
Intracellular Assembly of Cyanophage Syn5 Proceeds through a Scaffold-Containing Procapsid
Authors: Raytcheva Desislava A. , Haase-Pettingell Cameron , Piret Jacqueline M. , King Jonathan A. 
Published: December 2010

ABSTRACTSyn5 is a marine cyanophage that is propagated on the marine photosynthetic cyanobacterial strainSynechococcussp. WH8109 under laboratory conditions. Cryoelectron images of this double-stranded DNA (dsDNA) phage reveal an icosahedral capsid with short tail appendages and a single novel hornlike structure at the vertex opposite the tail. Despite the major impact of cyanophages on life in the oceans, there is limited information on cyanophage intracellular assembly processes within their photosynthetic hosts. The one-step growth curve of Syn5 demonstrated a short cycle with an eclipse period of ∼45 min, a latent phase of ∼60 min, and a burst size of 20 to 30 particles per cell at 28°C. SDS-PAGE and Western blot analysis of cell lysates at different times after infection showed the synthesis of major virion proteins and their increase as the infection progressed. The scaffolding protein of Syn5, absent from virions, was identified in the lysates and expressed from the cloned gene. It migrated anomalously on SDS-PAGE, similar to the phage T7 scaffolding protein. Particles lacking DNA but containing the coat and scaffolding proteins were purified from Syn5-infected cells using CsCl centrifugation followed by sucrose gradient centrifugation. Electron microscopic images of the purified particles showed shells lacking condensed DNA but filled with protein density, presumably scaffolding protein. These findings suggest that the cyanophages form infectious virions through the initial assembly of scaffolding-containing procapsids, similar to the assembly pathways for the enteric dsDNA bacteriophages. Since cyanobacteria predate the enteric bacteria, this procapsid-mediated assembly pathway may have originated with the cyanophages.
Efficient Culture Adaptation of Hepatitis C Virus Recombinants with Genotype-Specific Core-NS2 by Using Previously Identified Mutations
Authors: Scheel Troels K. H. , Gottwein Judith M. , Carlsen Thomas H. R. , Li Yi-Ping , Jensen Tanja B. , Spengler Ulrich , Weis Nina , Bukh Jens 
Published: December 2010

ABSTRACT
Hepatitis C virus (HCV) is an important cause of chronic liver disease, and interferon-based therapy cures only 40 to 80% of patients, depending on HCV genotype. Research was accelerated by genotype 2a (strain JFH1) infectious cell culture systems. We previously developed viable JFH1-based recombinants encoding the structural proteins (core, E1, E2), p7, and NS2 of prototype isolates of the seven major HCV genotypes; most recombinants required adaptive mutations. To enable genotype-, subtype-, and isolate-specific studies, we developed efficient core-NS2 recombinants from additional genotype 1a (HC-TN and DH6), 1b (DH1 and DH5), and 3a (DBN) isolates, using previously identified adaptive mutations. Introduction of mutations from isolates of the same subtype either led to immediate efficient virus production or accelerated culture adaptation. The DH6 and DH5 recombinants without introduced mutations did not adapt to culture. Universal adaptive effects of mutations in NS3 (Q1247L, I1312V, K1398Q, R1408W, and Q1496L) and NS5A (V2418L) were investigated for JFH1-based genotype 1 to 5 core-NS2 recombinants; several mutations conferred adaptation to H77C (1a), J4 (1b), S52 (3a), and SA13 (5a) but not to ED43 (4a). The mutations permitting robust virus production in Huh7.5 cells had no apparent effect on viral replication but allowed efficient assembly of intracellular infectious HCV for adapted novel or previously developed recombinants. In conclusion, previously identified mutations permitted development of novel HCV core-NS2 genotype recombinants. Mutations adapting several recombinants to culture were identified, but no mutations were universally adaptive across genotypes. This work provides tools for analysis of HCV genotype specificity and may promote the understanding of genotype-specific patterns in HCV disease and control.
Establishment of a Chimeric, Replication-Deficient Influenza A Virus Vector by Modulation of Splicing Efficiency
Authors: Wolschek Markus , Samm Elisabeth , Seper Helena , Sturlan Sanda , Kuznetsova Irina , Schwager Cornelia , Khassidov Alexandra , Kittel Christian , Muster Thomas , Egorov Andrej , Bergmann Michael 
Published: December 2010

ABSTRACT
Segment 8 of the influenza A virus codes for two proteins (NS1 and NS2/NEP) via splicing. Here, we developed a viral vector expressing a cytokine or chemokine instead of the interferon antagonist NS1. To achieve both the desired genetic stability and high transgene expression levels, NS2/NEP mRNA splicing efficacy had to be fine-tuned by modification of splicing elements. Expression levels of secreted foreign proteins could be further enhanced by fusing the N-terminal 13 amino acids of NS1 with an IgK-derived secretion signal peptide. Thus, the first start codon was used for translation initiation of both NS2/NEP and the foreign protein.
JNK1 Is Required for Lentivirus Entry and Gene Transfer
Authors: Lee Meng-Horng , Padmashali Roshan , Andreadis Stelios T. 
Published: December 2010

ABSTRACTAlthough a lot of progress has been made in development of lentiviral vectors for gene therapy, the interactions of these vectors with cellular factors have not been explored adequately. Here we show that lentivirus infection phosphorylates JNK and that blocking the kinase activity of JNK decreases gene transfer in a dose-dependent manner, regardless of the viral envelope glycoprotein. Knockdown by small interfering RNA (siRNA) revealed that JNK1 but not JNK2 was required for productive gene transfer. The effect of JNK on gene transfer was not due to changes in the cell cycle, as JNK knockdown did not affect the cell cycle profile of target cells and even increased cell proliferation. In addition, confluent cell monolayers also exhibited JNK phosphorylation upon lentivirus infection and a dose-dependent decrease in gene transfer efficiency upon JNK inhibition. On the other hand, JNK activation was necessary for lentivirus internalization into the cell cytoplasm, while inhibition of JNK activity decreased virus entry without affecting binding to the cell surface. These experiments suggest that JNK is required for lentivirus entry into target cells and may have implications for gene transfer or for development of antiviral agents.
Rhesus Rotavirus Entry into a Polarized Epithelium Is Endocytosis Dependent and Involves Sequential VP4 Conformational Changes
Authors: Wolf Marie , Vo Phuoc T. , Greenberg Harry B. 
Published: December 2010

ABSTRACT

Rotavirus (RV) cell entry is an incompletely understood process, involving VP4 and VP7, the viral proteins composing the outermost layer of the nonenveloped RV triple-layered icosahedral particle (TLP), encasing VP6. VP4 can exist in three conformational states: soluble, cleaved spike, and folded back. In order to better understand the events leading to RV entry, we established a detection system to image input virus by monitoring the rhesus RV (RRV) antigens VP4, VP6, and VP7 at very early times postinfection. We provide evidence that decapsidation occurs directly after cell membrane penetration. We also demonstrate that several VP4 and VP7 conformational changes take place during entry. In particular, we detected, for the first time, the generation of folded-back VP5 in the context of the initiation of infection. Folded-back VP5 appears to be limited to the entry step. We furthermore demonstrate that RRV enters the cell cytoplasm through an endocytosis pathway. The endocytosis hypothesis is supported by the colocalization of RRV antigens with the early endosome markers Rab4 and Rab5. Finally, we provide evidence that the entry process is likely dependent on the endocytic Ca
2+
concentration, as bafilomycin A1 treatment as well as an augmentation of the extracellular calcium reservoir using CaEGTA, which both lead to an elevated intraendosomal calcium concentration, resulted in the accumulation of intact virions in the actin network. Together, these findings suggest that internalization, decapsidation, and cell membrane penetration involve endocytosis, calcium-dependent uncoating, and VP4 conformational changes, including a fold-back.
Foot-and-Mouth Disease Virus Exhibits an Altered Tropism in the Presence of Specific Immunoglobulins, Enabling Productive Infection and Killing of Dendritic Cells
Authors: Robinson L. , Windsor M. , McLaughlin K. , Hope J. , Jackson T. , Charleston B. 
Published: December 2010

ABSTRACTFoot-and-mouth disease virus (FMDV) causes an acute vesicular disease of farm animals. The development of successful control strategies is limited by an incomplete understanding of the immune response to FMDV. Dendritic cells (DC) mediate the induction of immunity to pathogens, but their role in FMDV infection of cattle is uncharacterized. Bovine monocyte-derived DC (moDC) were exposed to integrin-binding and cell culture-adapted strains of FMDVin vitro. MoDC were not largely susceptible to infection by integrin-binding FMDV but were susceptible to culture-adapted virus. Binding specific antibodies to integrin-binding FMDV at neutralizing or subneutralizing IgG concentrations significantly enhanced infection via CD32 (FcγR). Monocytes also expressed CD32 but were nonsusceptible to FMDV immune complex (IC) infection, indicating a requirement for additional factors involved in cellular susceptibility. Infection of moDC by the FMDV IC was productive and associated with high levels of cell death. Infected moDC were unable to efficiently stimulate FMDV-specific CD4+memory T cells, but exposing moDC to IC containing inactivated FMDV resulted in significantly increased T cell stimulation. Thus, neutralized FMDV concurrently loses its ability to infect susceptible cells while gaining the capacity to infect immune cells. This represents a change in the tropism of FMDV that could occur after the onset of the antibody response. We propose that IC could dynamically influence the anti-FMDV immune response and that this may explain why the early immune response to FMDV has evolved toward T cell independencein vivo. Moreover, we propose that DC targeting could prove useful in the development of effective vaccines against FMDV.
A Single Amino Acid Substitution in the Capsid of Foot-and-Mouth Disease Virus Can Increase Acid Resistance
Authors: Martín-Acebes Miguel A. , Vázquez-Calvo Ángela , Rincón Verónica , Mateu Mauricio G. , Sobrino Francisco 
Published: December 2010

ABSTRACT

Foot-and-mouth disease virus (FMDV) particles lose infectivity due to their disassembly at pH values slightly below neutrality. This acid-dependent disassembly process is required for viral RNA release inside endosomes. To study the molecular determinants of viral resistance to acid-induced disassembly, six FMDV variants with increased resistance to acid inactivation were isolated. Infection by these mutants was more sensitive to drugs that raise the endosomal pH (NH
4
Cl and concanamycin A) than was infection by the parental C-S8c1 virus, confirming that the increase in acid resistance is related to a lower pH requirement for productive uncoating. Amino acid replacement N17D at the N terminus of VP1 capsid protein was found in all six mutants. This single substitution was shown to be responsible for increased acid resistance when introduced into an infectious FMDV clone. The increased resistance of this mutant against acid-induced inactivation was shown to be due to its increased resistance against capsid dissociation into pentameric subunits. Interestingly, the N17D mutation was located close to but not at the interpentamer interfaces. The mutants described here extend the panel of FMDV variants exhibiting different pH sensitivities and illustrate the adaptive flexibility of viral quasispecies to pH variations.
Factors Supporting Intrathecal Humoral Responses following Viral Encephalomyelitis
Authors: Phares Timothy W. , Marques Cristina P. , Stohlman Stephen A. , Hinton David R. , Bergmann Cornelia C. 
Published: December 2010

ABSTRACTCentral nervous system (CNS) infections and autoimmune inflammatory disorders are often associated with retention of antibody-secreting cells (ASC). Although beneficial or detrimental contributions of ASC to CNS diseases remain to be defined, virus-specific ASC are crucial in controlling persistent CNS infection following coronavirus-induced encephalomyelitis. This report characterizes expression kinetics of factors associated with ASC homing, differentiation, and survival in the spinal cord, the prominent site of coronavirus persistence. Infection induced a vast, gamma interferon (IFN-γ)-dependent, prolonged increase in chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, and CXCL11 mRNA, supporting a role for chemokine (C-X-C motif) receptor 3 (CXCR3)-mediated ASC recruitment. Similarly, CD4 T cell-secreted interleukin-21, a critical regulator of both peripheral activated B cells and CD8 T cells, was sustained during viral persistence. The ASC survival factors B cell-activating factor of the tumor necrosis factor (TNF) family (BAFF) and a proliferating-inducing ligand (APRIL) were also significantly elevated in the infected CNS, albeit delayed relative to the chemokines. Unlike IFN-γ-dependent BAFF upregulation, APRIL induction was IFN-γ independent. Moreover, both APRIL and BAFF were predominantly localized to astrocytes. Last, the expression kinetics of the APRIL and BAFF receptors coincided with CNS accumulation of ASC. Therefore, the factors associated with ASC migration, differentiation, and survival are all induced during acute viral encephalomyelitis, prior to ASC accumulation in the CNS. Importantly, the CNS expression kinetics implicate rapid establishment, and subsequent maintenance, of an environment capable of supporting differentiation and survival of protective antiviral ASC, recruited as plasmablasts from lymphoid organs.
Effectiveness and cost-effectiveness of an injury prevention programme for adult male amateur soccer players: design of a cluster-randomised controlled trial: Table 1
Authors: van Beijsterveldt Anna M C , Krist Mark R , Schmikli Sandor L , Stubbe Janine H , de Wit G Ardine , Inklaar Han , van de Port Ingrid G L , Backx Frank J G 
Published: December 2010

Background and aimsApproximately 16% of all sports injuries in the Netherlands are caused by outdoor soccer. A cluster-randomised controlled trial has been designed to investigate the effectiveness and cost-effectiveness of an injury prevention programme (‘The11’) for male amateur soccer players. The injury prevention programme The11, developed with the support of the World Football Association FIFA, aims to reduce the impact of intrinsic injury risk factors in soccer.MethodsTeams playing at first-class amateur level in two districts in the Netherlands are participating in the study. Teams in the intervention group were instructed to apply The11 during each practice session throughout the 2009–10 season. All participants of the control group continued their practice sessions as usual. All soccer-related injuries and related costs for each team were systematically reported online by a member of the medical staff. Player exposure to practice sessions and matches was reported weekly by the coaches. Also the use of The11 during the season after the intervention season will be monitored.DiscussionOur hypothesis is that integrating the The11 exercises in the warm-up for each practice session is effective in terms of injury incidence, injury severity, healthcare use, and its associated costs and/or absenteeism. Prevention of soccer injuries is expected to be beneficial to adult soccer players, soccer clubs, the Royal Dutch Football Association (KNVB), health insurance companies and society.
Factors influencing investigator-caused nest abandonment by North American dabbling ducks
Authors: Garrettson P. R. , Richkus K. D. , Rohwer F. C. , Johnson W. P. 
Published: December 2010

We examined factors (species, nest age, nest initiation date, clutch size, predator activity) that may affect the probability of investigator-caused nest abandonment in North American dabbling ducks and made predictions based on parental investment theory. For all nests, the best model contained species, nest stage, nest initiation date, and the interaction of species with nest initiation date. The probability of abandonment by Mallards ( Anas platyrhynchos L., 1758) was consistently higher than that of Blue-winged Teal ( Anas discors L., 1766). In these species, abandonment probability increased with later date, whereas Gadwall ( Anas strepera L., 1758), Northern Pintails ( Anas acuta L., 1758), and Northern Shovelers ( Anas clypeata L., 1758) showed the opposite pattern. Abandonment by all species declined as nest stage increased. Early-laying (≤5 eggs) females were 7 times more likely, and late-laying females were twice as likely, to abandon nests as incubating females. During incubation, abandonment probability was 38% higher during early (≤8 days) incubation than late incubation, and for each additional egg in a completed clutch, it was 19% lower. We propose a novel, two-stage model in which dabbling duck nest abandonment is influenced predominantly by opportunities for future reproduction during laying, and expected benefits from the current reproductive event during incubation.
Iterative Methods for Variational Inequalities over the Intersection of the Fixed Points Set of a Nonexpansive Semigroup in Banach Spaces
Authors: Mohamadi Issa 
Published: December 2010

AbstractThis paper presents a framework of iterative methods for finding specific common fixed points of a nonexpansive self-mappings semigroup in a Banach space. We prove, with appropriate conditions, the strong convergence to the solution of some variational inequalities.