bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequent mutations in the MITF pathway in melanoma
Authors: Cronin Julia C. , Wunderlich John , Loftus Stacie K. , Prickett Todd D. , Wei Xiaomu , Ridd Katie , Vemula Swapna , Burrell Allison S. , Agrawal Neena S. , Lin Jimmy C. , Banister Carolyn E. , Buckhaults Phillip , Rosenberg Steven A. , Bastian Boris C. , Pavan William J. , Samuels Yardena 
Published: April 2009

SummaryMicrophthalmia‐associated transcription factor (MITF) is involved in melanocyte cell development, pigmentation and neoplasia. To determine whether MITF is somatically mutated in melanoma, we compared the sequence of MITF from primary and metastatic lesions to patient‐matched normal DNA. In the 50 metastatic melanoma tumor lines analysed, we discovered four samples that had genomic amplifications of MITF and four that had MITF mutations in the regions encoding the transactivation, DNA binding or basic, helix‐loop‐helix domains. Sequence analysis for SOX10, a transcription factor, which both acts upstream of MITF and synergizes with MITF, identified an additional three samples with frameshift or nonsense mutations. Microphthalmia‐associated transcription factor and SOX10 were found to be mutated in a mutually exclusive fashion, possibly suggesting disruption in a common genetic pathway. Taken together we found that over 20% of the metastatic melanoma cases had alterations in the MITF pathway. We show that the MITF pathway is also altered in primary melanomas: 2/26 demonstrated mutations in MITF and 6/55 demonstrated mutations in SOX10. Our findings suggest that altered MITF function during melanomagenesis can be achieved by MITF amplification, MITF single base substitutions or by mutation of its regulator SOX10.
Antibodies to Pneumococcal Proteins PhtD, CbpA, and LytC in Filipino Pregnant Women and Their Infants in Relation to Pneumococcal Carriage
Authors: Holmlund Emma , Quiambao Beatriz , Ollgren Jukka , Jaakkola Teija , Neyt Cécile , Poolman Jan , Nohynek Hanna , Käyhty Helena 
Published: April 2009

ABSTRACT

This study focuses on the immunogenicity of the following three pneumococcal vaccine candidate proteins in Filipino infants, all inducing protection in animal models: pneumococcal histidine triad protein D (PhtD), choline binding protein A (CbpA), and the lysozyme LytC. The immunoglobulin G antibody concentrations to PhtD, its putative, protective, and exposed C-terminal fragment (PhtD C), CbpA, and LytC were measured by enzyme immunoassay in 52 serum samples from pregnant women, 39 cord blood samples, and consecutive serum samples (
n
= 263) from 52 newborns between 6 weeks and 10 months of age scheduled to be taken at six time points. A nasopharyngeal swab to detect pneumococcal carriage was taken parallel to the serum samples. The antibody concentrations in the cord blood samples were similar to those in the samples from the mothers. In infant sera, the geometric mean antibody concentrations (GMCs) for all three proteins decreased until the age of 18 weeks and started to increase after that age, suggesting that the infants' own antibody production started close to the age of 4 to 5 months. The increase in GMCs by age, most clear-cut for CbpA, was associated with pneumococcal carriage. Anti-PhtD concentrations were higher than anti-PhtD C concentrations but correlated well (
r
of 0.89 at 10.5 months), suggesting that antibodies are directed to the supposedly exposed and protective C-terminal part of PhtD. Our results show that young children are able to develop an antibody response to PhtD, CbpA, and LytC and encourage the development of pneumococcal protein vaccines for this age group.
Evaluation of an Immunofiltration Assay That Detects Immunoglobulin M Antibodies against the ZEBRA Protein for the Diagnosis of Epstein-Barr Virus Infectious Mononucleosis in Immunocompetent Patients
Authors: Bravo Dayana , Muñoz-Cobo Beatriz , Costa Elisa , Clari M. Angeles , Tormo Nuria , Navarro David 
Published: April 2009

ABSTRACTThe performance of an immunofiltration assay (IMFA) that detects immunoglobulin M (IgM) antibodies to the Epstein-Barr virus (EBV) ZEBRA (BamHI Z EBV replication activator) protein was evaluated for the diagnosis of EBV infectious mononucleosis (IM) in immunocompetent patients. The test panel consisted of 47 sera displaying an EBV-specific antibody profile compatible with an acute primary EBV infection from patients with clinical and biological features of EBV IM, 20 sera from healthy individuals either with a past EBV infection or who were EBV seronegative, 20 sera displaying an equivocal EBV antibody pattern (viral capsid antigen IgG positive [VCA IgG+], VCA IgM+, and EBV nuclear antigen-1 IgG+), and 15 sera obtained from patients with a mononucleosis-like syndrome owing to cytomegalovirus, human herpesvirus 6, or parvovirus B19. Overall, the sensitivity and the specificity of the assay were found to be 92.5%, and 97.3%, respectively. The sensitivity of the assay for the diagnosis of heterophile antibody-negative EBV IM was 86.2%. The IMFA is rapid, easy to perform, and, thus, suitable for point-of-care testing, and it may be used as a first-line test for the diagnosis of acute EBV IM in immunocompetent patients.
9-O-Acetylated Sialoglycoproteins Are Important Immunomodulators in Indian Visceral Leishmaniasis
Authors: Ghoshal Angana , Mukhopadhyay Sumi , Saha Bibhuti , Mandal Chitra 
Published: April 2009

ABSTRACTOverexpression of disease-associated 9-O-acetylated sialoglycoproteins (9-O-AcSGPs) on peripheral blood mononuclear cells (PBMC) of visceral leishmaniasis (VL) patients (PBMCVL) compared to their levels of expression in healthy individuals has been demonstrated using a lectin, achatinin-H, with specificity toward 9-O-acetylated sialic acid derivatives α2-6 linkage with subterminalN-acetylgalactosamine (9-O-AcSAα2-6GalNAc). The decreased presence of disease-associated 9-O-AcSGPs on different immune cells of parasitologically cured individuals after successful treatment relative to the levels in patients with active VL prior to treatment was demonstrated. However, their contributory role as immunomodulatory determinants on PBMCVLremained unexplored. Accordingly, 9-O-AcSGPs on PBMCVLwere sensitized with achatinin-H, leading to their enhanced proliferation compared to that observed with different known mitogens or parasite antigen. This lymphoproliferative response was characterized by evaluation of the TH1/TH2 response by intracellular staining and enzyme-linked immunosorbent assay for secreted cytokines, and the results were corroborated by their genetic expression. Sensitized PBMCVLevidenced a mixed TH1/TH2 cellular response with a predominance of the TH1 response, indicating the ability of 9-O-AcSGPs to modulate the host cell toward a favorable response. Interestingly, the humoral and cellular responses showed a good correlation. Further, high levels of anti-9-O-AcSGP antibodies with an order of distribution of immunoglobulin M (IgM) > IgG1 = IgG3 > IgG4 > IgG2 > IgE could be explained by a mixed TH1/TH2 response. A good correlation of enhanced 9-O-AcSGPs with both the cell-mediated (r= 0.98) and humoral (r= 0.99) response was observed. In summary, it may be concluded that sensitization of 9-O-AcSGPs on PBMCVLmay provide a basis for the modulation of the host's immune response by their controlled expression, leading to a beneficial immune response and influencing the disease pathology.
Identification of
Streptococcus agalactiae
Isolates from Various Phylogenetic Lineages by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Lartigue Marie-Frédérique , Héry-Arnaud Geneviève , Haguenoer Eve , Domelier Anne-Sophie , Schmit Pierre-Olivier , van der Mee-Marquet Nathalie , Lanotte Philippe , Mereghetti Laurent , Kostrzewa Markus , Quentin Roland 
Published: April 2009

ABSTRACT

Variations in proteins related to bacterial diversity may affect species identification performed using matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry. Using this method, we identified 110
Streptococcus agalactiae
isolates characterized by serotyping and multilocus sequence typing. Serotype III and sequence type 23 strains expressed the widest variation in molecular weight of putative “species-identifying” biomarker ions. Recognition of the diversity of MALDI patterns observed in strains that represent all major intraspecies lineages assists in the constitution of an optimal reference database.
First Insight into
Mycobacterium tuberculosis
Epidemiology and Genetic Diversity in Trinidad and Tobago
Authors: Baboolal Shirematee , Millet Julie , Akpaka Patrick Eberechi , Ramoutar Dottin , Rastogi Nalin 
Published: April 2009

ABSTRACT

This report is based on a 1-year recruitment of all of the culture-positive
Mycobacterium tuberculosis
cases in Trinidad and Tobago (
n
= 132). The study population was characterized by a high male-to-female sex ratio of 4 and a human immunodeficiency virus-tuberculosis (TB) coinfection rate of 30%. It mainly occurred among African descendants, who represent 37.5% of the total population but 69.7% of all TB cases (
P
< 0.001). Spoligotyping resulted in 25 different patterns and 12 clusters (2 to 74 strains per cluster), with the predominance of a highly conserved spoligotype international type clone, SIT566.
Aspergillus
Section
Fumigati
Typing by PCR-Restriction Fragment Polymorphism
Authors: Staab Janet F. , Balajee S. Arunmozhi , Marr Kieren A. 
Published: April 2009

ABSTRACT

Recent studies have shown that there are multiple clinically important members of the
Aspergillus
section
Fumigati
that are difficult to distinguish on the basis of morphological features (e.g.,
Aspergillus fumigatus
,
A. lentulus
, and
Neosartorya udagawae
). Identification of these organisms may be clinically important, as some species vary in their susceptibilities to antifungal agents. In a prior study, we utilized multilocus sequence typing to describe
A. lentulus
as a species distinct from
A. fumigatus
. The sequence data show that the gene encoding β-tubulin,
benA
, has high interspecies variability at intronic regions but is conserved among isolates of the same species. These data were used to develop a PCR-restriction fragment length polymorphism (PCR-RFLP) method that rapidly and accurately distinguishes
A. fumigatus
,
A. lentulus
, and
N. udagawae
, three major species within the section
Fumigati
that have previously been implicated in disease. Digestion of the
benA
amplicon with BccI generated unique banding patterns; the results were validated by screening a collection of clinical strains and by in silico analysis of the
benA
sequences of
Aspergillus
spp. deposited in the GenBank database. PCR-RFLP of
benA
is a simple method for the identification of clinically important, similar morphotypes of
Aspergillus
spp. within the section
Fumigati
.
Resistance of
Acanthamoeba
Cysts to Disinfection in Multiple Contact Lens Solutions
Authors: Johnston Stephanie P. , Sriram Rama , Qvarnstrom Yvonne , Roy Sharon , Verani Jennifer , Yoder Jonathan , Lorick Suchita , Roberts Jacquelin , Beach Michael J. , Visvesvara Govinda 
Published: April 2009

ABSTRACT

Acanthamoebae are free-living amoebae found in the environment, including soil, freshwater, brackish water, seawater, hot tubs, and Jacuzzis.
Acanthamoeba
species can cause keratitis, a painful vision-threatening infection of the cornea, and fatal granulomatous encephalitis in humans. More than 20 species of
Acanthamoeba
belonging to morphological groups I, II, and III distributed in 15 genotypes have been described. Among these,
Acanthamoeba castellanii
,
A
.
polyphaga
, and
A. hatchetti
are frequently identified as causing
Acanthamoeba
keratitis (AK). Improper contact lens care and contact with nonsterile water while wearing contact lenses are known risk factors for AK. During a recent multistate outbreak, AK was found to be associated with the use of Advanced Medical Optics Complete MoisturePlus multipurpose contact lens solution, which was hypothesized to have had insufficient anti-
Acanthamoeba
activity. As part of the investigation of that outbreak, we compared the efficacies of 11 different contact lens solutions against cysts of
A. castellanii
,
A. polyphaga
, and
A. hatchetti
(the isolates of all species were genotype T4), which were isolated in 2007 from specimens obtained during the outbreak investigation. The data, generated with
A. castellanii
,
A. polyphaga
, and
A. hatchetti
cysts, suggest that the two contact lens solutions containing hydrogen peroxide were the only solutions that showed any disinfection ability, with 0% and 66% growth, respectively, being detected with
A. castellanii
and 0% and 33% growth, respectively, being detected with
A. polyphaga
. There was no statistically significant difference in disinfection efficacy between the 11 solutions for
A. hatchetti
.
Adenovirus Microsatellite Reveals Dynamics of Transmission during a Recent Epidemic of Human Adenovirus Serotype 14 Infection
Authors: Houng Huo-Shu H. , Lott Lisa , Gong Heping , Kuschner Robert A. , Lynch Julia A. , Metzgar David 
Published: April 2009

ABSTRACT
This study reveals diverse-length polymorphisms in long mononucleotide repeats (microsatellites) in several serotypes of epidemic human respiratory adenovirus. The length of one of these microsatellites, a homopolymeric thymidine [poly(T)] repeat, is measured in 68 isolates of adenovirus serotype 14. These isolates were collected during a series of sudden and sometimes fatal outbreaks among both military recruits and civilians as the virus emerged for the first time in the United States in 2006 and 2007. The results demonstrate the usefulness of adenoviral microsatellites as high-resolution molecular strain markers. The described homopolymer is hypervariable in length, varying from 12 to 17 bp in the analyzed sample set. All intermediate lengths were identified in at least one isolate. Furthermore, the specific length of the marker is stable for significant periods of time (up to 7 months) at individual sites where the virus is in consistent circulation. The microsatellite also can maintain specific length identity through site-to-site transmission events, as determined by the analysis of isolates from three advanced training sites that appeared to be subject to pathogen transfer from one of the affected recruit training installations. Public database searches revealed that the polymorphic nature of the microsatellite extends to other species B serotypes, and that other polymorphic microsatellites can be identified readily in a variety of epidemic respiratory adenovirus clades. This study shows that microsatellites are a ubiquitous source of polymorphic markers for human adenoviruses and demonstrates their use through an epidemiological analysis of isolates from a recent North American epidemic.
RNA (E6 and E7) Assays versus DNA (E6 and E7) Assays for Risk Evaluation for Women Infected with Human Papillomavirus
Authors: Cattani Paola , Siddu Alessia , D'Onghia Sara , Marchetti Simona , Santangelo Rosaria , Vellone Valerio G. , Zannoni Gian Franco , Fadda Giovanni 
Published: April 2009

ABSTRACT
In the majority of cases, high-risk human papillomavirus (HR HPV) infections regress spontaneously, with only a small percentage progressing to high-grade lesions. Current screening methods are based on DNA detection. An alternative would be to monitor expression of the E6 and E7 viral oncogenes continuously expressed by malignant phenotypes. In the work reported in this paper, we compared the two methods for a group of women with high-risk HPV infections. Cervical specimens from 400 women, previously found to be HPV DNA positive, were analyzed for HPV DNA by a liquid hybridization assay and typed by multiplex PCR (for types 16, 18, 31, and 33). Identification of HR HPV E6 and E7 RNA transcripts was performed using real-time reverse transcription-PCR and nucleic acid sequence-based amplification assays. Results were compared with concurrent cytological data. HR HPVs were found in 61.2% of patients. The most common genotype was HPV type 16 (HPV-16) (47.1%), followed by HPV-18, HPV-31, and HPV-33. Nine percent of cases involved other genotypes. Among 223 HPV DNA-positive samples, only 118 were positive in the RNA test. Among HPV DNA-positive patients with normal cytology, we detected E6 and E7 RNA transcripts in two cases (18.2%). The rate of detection increased gradually with the grade of the observed lesions, rising from 20% for patients with atypical squamous cells of undetermined significance to 48.1% for women with low-grade squamous intraepithelial lesions and 86.3% for those with high-grade squamous intraepithelial lesions. These results suggest that testing for HPV E6 and E7 transcripts could be a useful tool for screening and patient management, providing more accurate predictions of risk than those obtained by DNA testing.
Novel Recombinant Virus Assay for Measuring Susceptibility of Human Immunodeficiency Virus Type 1 Group M Subtypes To Clinically Approved Drugs
Authors: Covens Kris , Dekeersmaeker Nathalie , Schrooten Yoeri , Weber Jan , Schols Dominique , Quiñones-Mateu Miguel E. , Vandamme Anne-Mieke , Van Laethem Kristel 
Published: April 2009

ABSTRACTCombination therapy can successfully suppress human immunodeficiency virus (HIV) replication in patients but selects for drug resistance, requiring subsequent resistance-guided therapeutic changes. This report describes the development and validation of a novel assay that offers a uniform method to measure susceptibility to all clinically approved HIV type 1 (HIV-1) drugs targeting reverse transcriptase (RT), protease (PR), integrase (IN), and viral entry. It is an assay in which the antiviral effect on infection within a single replication cycle is measured in triply transfected U87.CD4.CXCR4.CCR5 cells, based on homologous recombination between patient-derived amplicons and molecular proviral clones tagged with the enhanced green fluorescent protein (EGFP) reporter gene and from which certain viral genomic regions are removed. The deletions stretch from p17 codon 7 to PR codon 98 in pNL4.3-ΔgagPR-EGFP, from PR codons 1 to 99 in pNL4.3-ΔPR-EGFP, from RT codons 1 to 560 in pNL4.3-ΔRT-EGFP, from IN codons 1 to 288 in pNL4.3-ΔIN-EGFP, and from gp120 codon 34 to gp41 codon 237 in pNL4.3-Δenv-EGFP. The optimized experimental conditions enable the investigation of patient samples regardless of viral subtype or coreceptor use. The extraction and amplification success rate for a set of clinical samples belonging to a broad range of HIV-1 group M genetic forms (A-J, CRF01-03, CRF05, and CRF12-13) and displaying a viral load range of 200 to >500,000 RNA copies/ml was 97%. The drug susceptibility measurements, based on discrimination between infected and noninfected cells on a single-cell level by flow cytometry, were reproducible, with coefficients of variation for resistance ranging from 7% to 31%, and were consistent with scientific literature in terms of magnitude and specificity.
Reliability of the Vitek 2 Yeast Susceptibility Test for Detection of In Vitro Resistance to Fluconazole and Voriconazole in Clinical Isolates of
Candida albicans
and
Candida glabrata
Authors: Posteraro Brunella , Martucci Rosa , La Sorda Marilena , Fiori Barbara , Sanglard Dominique , De Carolis Elena , Florio Ada Rita , Fadda Giovanni , Sanguinetti Maurizio 
Published: April 2009

ABSTRACT

The Vitek 2 yeast susceptibility test was evaluated by testing 122
Candida
isolates against fluconazole and voriconazole. Excellent categorical agreement with the CLSI broth microdilution method was observed (97.5% for both the azoles). Moreover, the Vitek 2 system was able to identify all but 2 of 59 investigated fluconazole-resistant organisms.
Rapid Molecular Characterization of
Clostridium difficile
and Assessment of Populations of
C. difficile
in Stool Specimens
Authors: Wroblewski Danielle , Hannett George E. , Bopp Dianna J. , Dumyati Ghinwa K. , Halse Tanya A. , Dumas Nellie B. , Musser Kimberlee A. 
Published: April 2009

ABSTRACT

Our laboratory has developed testing methods that use real-time PCR and pyrosequencing analysis to enable the rapid identification of potential hypervirulent
Clostridium difficile
strains. We describe a real-time PCR assay that detects four
C. difficile
genes encoding toxins A (
tcdA
) and B (
tcdB
) and the binary toxin genes (
cdtA
and
cdtB
), as well as a pyrosequencing assay that detects common deletions in the
tcdC
gene in less than 4 h. A subset of historical and recent
C. difficile
isolates (
n
= 31) was also analyzed by pulsed-field gel electrophoresis to determine the circulating North American pulsed-field (NAP) types that have been isolated in New York State. Thirteen different NAP types were found among the 31 isolates tested, 13 of which were NAP type 1 strains. To further assess the best approach to utilizing our conventional and molecular methods, we studied the populations of
C. difficile
in patient stool specimens (
n
= 23). Our results indicated that 13% of individual stool specimens had heterogeneous populations of
C. difficile
when we compared the molecular characterization results for multiple bacterial isolates (
n
= 10). Direct molecular analysis of stool specimens gave results that correlated well with the results obtained with cultured stool specimens; the direct molecular analysis was rapid, informative, and less costly than the testing of multiple patient stool isolates.
X-Box Binding Protein 1 Contributes to Induction of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle under Hypoxic Conditions
Authors: Dalton-Griffin Lucy , Wilson Sam J. , Kellam Paul 
Published: April 2009

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV), like other herpesviruses, has two stages to its life cycle: latency and lytic replication. KSHV is required for development of Kaposi's sarcoma, a tumor of endothelial origin, and is associated with the B-cell tumor primary effusion lymphoma (PEL) and the plasmablastic variant of multicentric Castleman's disease, all of which are characterized by predominantly latent KSHV infection. Recently, we and others have shown that the activated form of transcription factor X-box binding protein 1 (XBP-1) is a physiological trigger of KSHV lytic reactivation in PEL. Here, we show that XBP-1s transactivates the ORF50/RTA promoter though an ACGT core containing the XBP-1 response element, an element previously identified as a weakly active hypoxia response element (HRE). Hypoxia induces the KSHV lytic cycle, and active HREs that respond to hypoxia-inducible factor 1α are present in the ORF50/RTA promoter. Hypoxia also induces active XBP-1s, and here, we show that both transcription factors contribute to the induction of RTA expression, leading to the production of infectious KSHV under hypoxic conditions.
A Shared Interface Mediates Paramyxovirus Interference with Antiviral RNA Helicases MDA5 and LGP2
Authors: Parisien Jean-Patrick , Bamming Darja , Komuro Akihiko , Ramachandran Aparna , Rodriguez Jason J. , Barber Glen , Wojahn Robert D. , Horvath Curt M. 
Published: April 2009

ABSTRACT

Diverse members of the
Paramyxovirus
family of negative-strand RNA viruses effectively suppress host innate immune responses through the actions of their V proteins. The V protein mediates interference with the interferon regulatory RNA helicase MDA5 to avoid cellular antiviral responses. Analysis of the interaction interface revealed the MDA5 helicase C domain as necessary and sufficient for association with V proteins from human parainfluenza virus type 2, parainfluenza virus type 5, measles virus, mumps virus, Hendra virus, and Nipah virus. The identified ∼130-residue region is highly homologous between MDA5 and the related antiviral helicase LGP2, but not RIG-I. Results indicate that the paramyxovirus V proteins can also associate with LGP2. The V protein interaction was found to disrupt ATP hydrolysis mediated by both MDA5 and LGP2. These findings provide a potential mechanistic basis for V protein-mediated helicase interference and identify LGP2 as a second cellular RNA helicase targeted by paramyxovirus V proteins.