bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quorum sensing negatively regulates chitinase in Vibrio harveyi
Authors: Defoirdt Tom , Darshanee Ruwandeepika H.A. , Karunasagar Indrani , Boon Nico , Bossier Peter 
Published: July 2009

SummaryQuorum sensing, bacterial cell‐to‐cell communication, regulates the virulence of Vibrio harveyi towards different hosts. Chitinase can be considered as a virulence factor because it helps pathogenic bacteria to attach to the host and to penetrate its tissues (e.g. in case of shrimp). Here, we show that quorum sensing negatively regulates chitinase in V. harveyi. Chitinolytic activity towards natural chitin from crab shells, the synthetic chitin derivative chitin azure, and fluorogenic chitin oligomers was significantly higher in a mutant in which the quorum‐sensing system is completely inactivated when compared with a mutant in which the system is maximally active. Furthermore, the addition of signal molecule containing cell‐free culture fluids decreased chitinase activity in a Harveyi Autoinducer 1 and Autoinducer 2‐deficient double mutant. Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum‐sensing system is maximally active when compared with the mutant in which the system is completely inactivated. [Correction added on 25 September 2009, after first online publication: the preceding sentence was corrected from ‘Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum‐sensing system is completely inactivated when compared with the mutant in which the system is maximally active.’] We argue that this regulation might help the vibrios to switch between host‐associated and free‐living life styles.
Optimization of a Whole-Blood Gamma Interferon Assay for Detection of
Mycobacterium bovis
-Infected Cattle
Authors: Schiller Irene , Waters W. Ray , Vordermeier H. Martin , Nonnecke Brian , Welsh Michael , Keck Nicolas , Whelan Adam , Sigafoose Teresa , Stamm Christoph , Palmer Mitchell , Thacker Tyler , Hardegger Roland , Marg-Haufe Beatrice , Raeber Alex , Oesch Bruno 
Published: July 2009

ABSTRACT

Antigens of
Mycobacterium bovis
elicit a cell-mediated immune response upon intradermal injection in cattle. In vitro, such antigens stimulate the production of gamma interferon (IFN-γ) by bovine T cells in whole-blood culture (IFN-γ assay). We have analyzed various parameters of the in vitro IFN-γ assay, ranging from blood sampling to execution of the IFN-γ test, in view of potential simplifications of the assay. Here, we show that IFN-γ responses may be reduced under certain animal handling/holding conditions and that a delayed time from blood collection to culture may lead to a reduced in vitro IFN-γ response. Delayed initiation of culture in a purified-protein-derivative-based assay (24 h compared to 8 h after blood collection), however, resulted in a significant improvement of specificity (97% compared to 85%), whereas there was only a modest reduction of sensitivity (from 96% to 90%), which was statistically not significant. Furthermore, we show that the stimulation temperature needs to be 33°C or higher; that carbon dioxide is not required for stimulation; and that various plate formats, ranging from 24 to 96 wells per plate, can be utilized. The produced IFN-γ is stable at 4°C for 28 days as well as after repeated freeze-thaw cycles. Thus, stimulation of samples may be initiated in the field without the need for a carbon dioxide source, and bovine IFN-γ is stable under various routine laboratory temperature scenarios. These findings demonstrate opportunities for improvements in the bovine IFN-γ test platform and flexibilities in test application.
Transcriptional Errors in Human Immunodeficiency Virus Type 1 Generate Targets for T-Cell Responses
Authors: Garrison Keith E. , Champiat Stephane , York Vanessa A. , Agrawal Ashish T. , Kallas Esper G. , Martin Jeffrey N. , Hecht Frederick M. , Deeks Steven G. , Nixon Douglas F. 
Published: July 2009

ABSTRACT
We measured T-cell responses to human immunodeficiency virus type 1 (HIV-1) cryptic epitopes encoded by regions of the viral genome not normally translated into viral proteins. T-cell responses to cryptic epitopes and to regions normally spliced out of the HIV-1 viral proteins Rev and Tat were detected in HIV-1-infected subjects.
Genotypic Comparison of Invasive
Neisseria meningitidis
Serogroup Y Isolates from the United States, South Africa, and Israel, Isolated from 1999 through 2002
Authors: Whitney Anne M. , Coulson Garry B. , von Gottberg Anne , Block Colin , Keller Nathan , Mayer Leonard W. , Messonnier Nancy E. , Klugman Keith P. 
Published: July 2009

ABSTRACT

The proportion of meningococcal disease in the United States, South Africa, and Israel caused by
Neisseria meningitidis
serogroup Y (NmY) was greater than the worldwide average during the period 1999-2002. Genotypic characterization of 300 NmY isolates by multilocus sequence typing, 16S rRNA gene sequencing, and PorA variable region typing was conducted to determine the relationships of the isolates from these three countries. Seventy different genotypes were found. Two groups of ST-23 clonal complex isolates accounted for 88% of the U.S. isolates, 12% of the South African isolates, and 96% of the isolates from Israel. The single common clone (ST-23/16S-19/P1.5-2,10-1) represented 57, 5, and 35% of the NmY isolates from the United States, South Africa, and Israel. The predominant clone in South Africa (ST-175/16S-21/P1.5-1,2-2), and 11 other closely related clones made up 77% of the South African study isolates and were not found among the isolates from the United States or Israel. ST-175 was the predicted founder of the ST-175 clonal complex, and isolates of ST-175 and related sequence types have been described previously in other African countries. Continued active surveillance and genetic characterization of NmY isolates causing disease in the United States, South Africa, and Israel will provide valuable data for local and global epidemiology and allow monitoring for any expansion of existing clonal complexes and detection of the emergence of new virulent clones in the population.
Severe Cytomegalovirus-Associated Esophagitis in an Immunocompetent Patient after Short-Term Steroid Therapy
Authors: Weile Jan , Streeck Benjamin , Muck Johannes , Krebs Gerd , Jakobus Karl-Heinz , Knabbe Cornelius , Weber Friedhelm 
Published: July 2009

ABSTRACT
A case of severe human cytomegalovirus esophagitis after short-term corticosteroid therapy in a patient with no other apparent cause of immunodeficiency, such as human immunodeficiency virus infection, neoplasia, or previous organ transplantation, is described herein. The cytomegalovirus esophagus infection was successfully treated with ganciclovir.
Cost Analysis of Multiplex PCR Testing for Diagnosing Respiratory Virus Infections
Authors: Mahony James B. , Blackhouse Gord , Babwah Jesse , Smieja Marek , Buracond Sonya , Chong Sylvia , Ciccotelli William , O'Shea Tim , Alnakhli Daifallah , Griffiths-Turner May , Goeree Ron 
Published: July 2009

ABSTRACT
We performed a cost analysis study using decision tree modeling to determine whether the use of multiplex PCR testing for respiratory viruses (xTAG RVP test) is a more or less costly strategy than the status quo testing methods used for the diagnosis of respiratory virus infections in pediatric patients. The decision tree model was constructed by using four testing strategies for respiratory virus detection, viz., direct fluorescent-antibody staining (DFA) alone, DFA plus shell vial culture (SVC), the xTAG RVP test alone, or DFA plus the xTAG RVP test. A review of the charts of 661 pediatric patients was used to determine the length of hospital stay, the number of days in isolation, antibiotic usage, and all other medical procedures performed. The cost of hospitalization by diagnostic status was determined on the basis of the average cost per patient and the number of patients in each arm of the decision tree. The cost per case was the highest for DFA plus SVC at $3,914 (in Canadian dollars), and the lowest was for the xTAG RVP test alone at $3,623, while the costs of DFA alone ($3,911) and DFA plus RVP ($3,849) were intermediate. When all four diagnostic strategies were compared, the least costly strategy was the xTAG RVP test alone when the prevalence of infection was 11% or higher and DFA alone when the prevalence was under 11%. These data indicate a savings of $291 per case investigated if the strategy of using the xTAG RVP test alone was used to replace the status quo test of DFA plus SVC, resulting in a savings of $529,620 per year in direct costs for the four Hamilton, Ontario, Canada, hospitals on the basis of the testing of specimens from 1,820 pediatric inpatients. We conclude that the use of the xTAG RVP test is the least costly strategy for the diagnosis of respiratory virus infections in children and would generate a significant savings for hospitals.
Diagnosis of Bacteremia in Whole-Blood Samples by Use of a Commercial Universal 16S rRNA Gene-Based PCR and Sequence Analysis
Authors: Wellinghausen Nele , Kochem Anna-Julia , Disqué Claudia , Mühl Helge , Gebert Susanne , Winter Juliane , Matten Jens , Sakka Samir G. 
Published: July 2009

ABSTRACT
In a prospective, multicenter study of 342 blood samples from 187 patients with systemic inflammatory response syndrome, sepsis, or neutropenic fever, a new commercial PCR test (SepsiTest; Molzym) was evaluated for rapid diagnosis of bacteremia. The test comprises a universal PCR from the 16S rRNA gene, with subsequent identification of bacteria from positive samples by sequence analysis of amplicons. Compared to blood culture (BC), the diagnostic sensitivity and specificity of the PCR were 87.0 and 85.8%, respectively. Considering the 34 BC-positive patients, 28 were also PCR positive in at least one of the samples, resulting in a patient-related sensitivity of 82.4%. The concordance of PCR and BC for both positive and negative samples was (47 + 247)/342, i.e., 86.0%. In total, 31 patients were PCR/sequencing positive and BC negative, in whom the PCR result was judged as possible or probable to true bacteremia in 25. In conclusion, the PCR approach facilitates the detection of bacteremia in blood samples within a few hours. Despite the indispensability of BC diagnostics, the rapid detection of bacteria by SepsiTest appears to be a valuable tool, allowing earlier pathogen-adapted antimicrobial therapy in critically ill patients.
Comparison of 24-Hour and 48-Hour Voriconazole MICs as Determined by the Clinical and Laboratory Standards Institute Broth Microdilution Method (M27-A3 Document) in Three Laboratories: Results Obtained with 2,162 Clinical Isolates of
Candida
spp. and Other Yeasts
Authors: Espinel-Ingroff Ana , Canton E. , Peman J. , Rinaldi M. G. , Fothergill A. W. 
Published: July 2009

ABSTRACT

We evaluated the performance of the 24-h broth microdilution voriconazole MIC by obtaining MICs for 2,162 clinical isolates of
Candida
spp. and other yeasts; the 24-h results were compared to 48-h reference MICs to assess essential, as well as categorical, agreement. Although the overall essential agreement was 88.6%, it ranged from 96.4 to 100% for 6 of the 11 species or groups of yeasts tested. The overall categorical agreement was 93.2%, and it was above 90% for eight species. However, unacceptable percentages of very major errors (false susceptibility) were observed for
Candida albicans
(2.7%),
C. glabrata
(4.1%),
C. tropicalis
(9.7%), and other less common yeast species (9.8%). Since it is essential to identify potentially resistant isolates and breakpoints are based on 48-h MICs, it appears that the 24-h MIC is not as clinically useful as the 48-h reference MIC. However, further characterization of these falsely susceptible MICs for three of the four common
Candida
spp. is needed to understand whether these errors are due to trailing misinterpretation or if the 48-h incubation is required to detect voriconazole resistance. Either in vivo versus in vitro correlations or the determination of resistance mechanisms should be investigated.
Thumb Infection Caused by
Streptococcus pseudoporcinus
Authors: Mahlen Steven D. , Clarridge Jill E. 
Published: July 2009

ABSTRACT

Streptococcus pseudoporcinus
, a recently described organism found in the genitourinary tract of women, was isolated from a thumb wound in a male patient subsequent to trauma. This case describes a rarely reported non-genitourinary tract clinical isolate of
S. pseudoporcinus
.
Clostridium difficile
Strains from Community-Associated Infections
Authors: Limbago Brandi M. , Long Cherie M. , Thompson Angela D. , Killgore George E. , Hannett George E. , Havill Nancy L. , Mickelson Stephanie , Lathrop Sarah , Jones Timothy F. , Park Mahin M. , Harriman Kathleen H. , Gould L. Hannah , McDonald L. Clifford , Angulo Frederick J. 
Published: July 2009

ABSTRACT

Clostridium difficile
isolates from presumed community-associated infections (
n
= 92) were characterized by toxinotyping, pulsed-field gel electrophoresis,
tcdC
and
cdtB
PCR, and antimicrobial susceptibility. Nine toxinotypes (TOX) and 31 PFGE patterns were identified. TOX 0 (48, 52%), TOX III (18, 20%), and TOX V (9, 10%) were the most common; three isolates were nontoxigenic.
Population-Based Molecular Epidemiology of Leprosy in Cebu, Philippines
Authors: Sakamuri Rama Murthy , Kimura Miyako , Li Wei , Kim Hyun-Chul , Lee Hyeyoung , Kiran Madanahally D. , Black William C. , Balagon Marivic , Gelber Robert , Cho Sang-Nae , Brennan Patrick J. , Vissa Varalakshmi 
Published: July 2009

ABSTRACT

To address the persisting problem of leprosy in Cebu, Philippines, we compiled a database of more than 200 patients who attend an established referral skin clinic. We described the patient characteristics in conventional demographic parameters and also applied multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) and single nucleotide polymorphism (SNP) typing for
Mycobacterium leprae
in biopsied skin lesion samples. These combined approaches revealed that transmission is ongoing, with the affected including the young Cebuano population under 40 years of age in both crowded cities and rural areas of the island. The emergence of multicase families (MCF) is indicative of infection unconstrained by standard care measures. For the SNPs, we designed a low-cost PCR-restriction fragment length polymorphism typing method. MLVA in
M. leprae
was highly discriminatory in this population yet could retain broad groups, as defined by the more stable SNPs, implying temporal marker stability suitable for interpreting population structures and evolution. The majority of isolates belong to an Asian lineage (SNP type 1), and the rest belong to a putative postcolonial lineage (SNP type 3). Specific alleles at two VNTR loci, (GGT)5 and 21-3, were highly associated with SNP type 3 in this population. MLVA identified
M. leprae
genotype associations for patients with known epidemiological links such as in MCFs and in some villages. These methods provide a molecular database and a rational framework for targeted approaches to search and confirm leprosy transmission in various scenarios.
Functional Analysis of N-Terminal Residues of Ty1 Integrase
Authors: Moore Sharon P. , Garfinkel David J. 
Published: July 2009

ABSTRACT

The Ty1 retrotransposon of
Saccharomyces cerevisiae
is comprised of structural and enzymatic proteins that are functionally similar to those of retroviruses. Despite overall sequence divergence, certain motifs are highly conserved. We have examined the Ty1 integrase (IN) zinc binding domain by mutating the definitive histidine and cysteine residues and thirteen residues in the intervening (X
32
) sequence between IN-H22 and IN-C55. Mutation of the zinc-coordinating histidine or cysteine residues reduced transposition by more than 4,000-fold and led to IN and reverse transcriptase (RT) instability as well as inefficient proteolytic processing. Alanine substitution of the hydrophobic residues I28, L32, I37 and V45 in the X
32
region reduced transposition 85- to 688-fold. Three of these residues, L32, I37, and V45, are highly conserved among retroviruses, although their effects on integration or viral infectivity have not been characterized. In contrast to the HHCC mutants, all the X
32
mutants exhibited stable IN and RT, and protein processing and cDNA production were unaffected. However, glutathione
S
-transferase pulldowns and intragenic complementation analysis of selected transposition-defective X
32
mutants revealed decreased IN-IN interactions. Furthermore, virus-like particles with
in-L32A
and
in-V45A
mutations did not exhibit substantial levels of concerted integration products in vitro. Our results suggest that the histidine/cysteine residues are important for steps in transposition prior to integration, while the hydrophobic residues function in IN multimerization.
Protective and Pathologic Roles of the Immune Response to Mouse Hepatitis Virus Type 1: Implications for Severe Acute Respiratory Syndrome
Authors: Khanolkar Aaruni , Hartwig Stacey M. , Haag Brayton A. , Meyerholz David K. , Epping Lecia L. , Haring Jodie S. , Varga Steven M. , Harty John T. 
Published: July 2009

ABSTRACTIntranasal mouse hepatitis virus type 1 (MHV-1) infection of mice induces lung pathology similar to that observed in severe acute respiratory syndrome (SARS) patients. However, the severity of MHV-1-induced pulmonary disease varies among mouse strains, and it has been suggested that differences in the host immune response might account for this variation. It has also been suggested that immunopathology may represent an important clinical feature of SARS. Little is known about the host immune response to MHV-1 and how it might contribute to some of the pathological changes detected in infected mice. In this study we show that an intact type I interferon system and the adaptive immune responses are required for controlling MHV-1 replication and preventing morbidity and mortality in resistant C57BL/6J mice after infection. The NK cell response also helps minimize the severity of illness following MHV-1 infection of C57BL/6J mice. In A/J and C3H/HeJ mice, which are highly susceptible to MHV-1-induced disease, we demonstrate that both CD4 and CD8 T cells contribute to morbidity during primary infection, and memory responses can enhance morbidity and mortality during subsequent reexposure to MHV-1. However, morbidity in A/J and C3H/HeJ mice can be minimized by treating them with immune serum prior to MHV-1 infection. Overall, our findings highlight the role of the host immune response in contributing to the pathogenesis of coronavirus-induced respiratory disease.
Characterization of a Novel Flavivirus from Mosquitoes in Northern Europe That Is Related to Mosquito-Borne Flaviviruses of the Tropics
Authors: Huhtamo Eili , Putkuri Niina , Kurkela Satu , Manni Tytti , Vaheri Antti , Vapalahti Olli , Uzcátegui Nathalie Y. 
Published: July 2009

ABSTRACT

A novel flavivirus was isolated from mosquitoes in Finland, representing the first mosquito-borne flavivirus from Northern Europe. The isolate, designated Lammi virus (LAMV), was antigenically cross-reactive with other flaviviruses and exhibited typical flavivirus morphology as determined by electron microscopy. The genomic sequence of LAMV was highly divergent from the recognized flaviviruses, and yet the polyprotein properties resembled those of mosquito-borne flaviviruses. Phylogenetic analysis of the complete coding sequence showed that LAMV represented a distinct lineage related to the
Aedes
sp.-transmitted human pathogenic flaviviruses, similarly to the newly described Nounané virus (NOUV), a flavivirus from Africa (S. Junglen et al., J. Virol. 83:4462-4468, 2009). Despite the low sequence homology, LAMV and NOUV were phylogenetically grouped closely, likely representing separate species of a novel group of flaviviruses. Despite the biological properties preferring replication in mosquito cells, the genetic relatedness of LAMV to viruses associated with vertebrate hosts warrants a search for disease associations.
Anterograde Spread of Herpes Simplex Virus Type 1 Requires Glycoprotein E and Glycoprotein I but Not Us9
Authors: McGraw Helen M. , Awasthi Sita , Wojcechowskyj Jason A. , Friedman Harvey M. 
Published: July 2009

ABSTRACT
Anterograde neuronal spread (i.e., spread from the neuron cell body toward the axon terminus) is a critical component of the alphaherpesvirus life cycle. Three viral proteins, gE, gI, and Us9, have been implicated in alphaherpesvirus anterograde spread in several animal models and neuron culture systems. We sought to better define the roles of gE, gI, and Us9 in herpes simplex virus type 1 (HSV-1) anterograde spread using a compartmentalized primary neuron culture system. We found that no anterograde spread occurred in the absence of gE or gI, indicating that these proteins are essential for HSV-1 anterograde spread. However, we did detect anterograde spread in the absence of Us9 using two independent Us9-deleted viruses. We confirmed the Us9 finding in different murine models of neuronal spread. We examined viral transport into the optic nerve and spread to the brain after retinal infection; the production of zosteriform disease after flank inoculation; and viral spread to the spinal cord after flank inoculation. In all models, anterograde spread occurred in the absence of Us9, although in some cases at reduced levels. This finding contrasts with gE- and gI-deleted viruses, which displayed no anterograde spread in any animal model. Thus, gE and gI are essential for HSV-1 anterograde spread, while Us9 is dispensable.
A Simian Immunodeficiency Virus-Infected Macaque Model To Study Viral Reservoirs That Persist during Highly Active Antiretroviral Therapy
Authors: Dinoso Jason B. , Rabi S. Alireza , Blankson Joel N. , Gama Lucio , Mankowski Joseph L. , Siliciano Robert F. , Zink M. Christine , Clements Janice E. 
Published: July 2009

ABSTRACT

The treatment of human immunodeficiency virus type 1 (HIV-1) infection with highly active antiretroviral therapy (HAART), a combination of three or more antiretroviral drugs, suppresses viremia below the clinical limit of detection (50 HIV-1 RNA copies/ml), but latently infected resting CD4
+
T cells serve as lifelong reservoirs, and low-level viremia can be detected with special assays. Recent studies have provided evidence for additional reservoirs that contribute to residual viremia but are not present in circulating cells. Identification of all the sources of residual viremia in humans may be difficult. These discoveries highlight the need for a tractable model system to identify additional viral reservoirs that could represent barriers to eradication. In this study, simian immunodeficiency virus (SIV)-infected pig-tailed macaques (
Macaca nemestrina
) were treated with four antiretroviral drugs to develop an animal model for viral suppression during effective HAART. Treatment led to a biphasic decay in viremia and a significant rise in levels of circulating CD4
+
T cells. At terminal infection time points, the frequency of circulating resting CD4
+
T cells harboring replication-competent virus was reduced to a low steady-state level similar to that observed for HIV-infected patients on HAART. The frequencies of resting CD4
+
T cells harboring replication-competent virus in the pooled head lymph nodes, gut lymph nodes, spleen, and peripheral blood were reduced relative to those for untreated SIV-infected animals. These observations closely parallel findings for HIV-infected humans on suppressive HAART and demonstrate the value of this animal model to identify and characterize viral reservoirs persisting in the setting of suppressive antiretroviral drugs.