bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular biological study on speciation and phylogeny of the order Entomobryomorpha (Collembola: Hexapoda)
Authors: PARK Kyung‐Hwa 
Published: September 2009

AbstractIn order to elucidate the phylogenetic relationship among groups of the order Entomobryomorpha (Collembola), the sequences on theITS 1toITS 2fragments of the rRNA gene were analyzed in 11 species of three families. In order to avoid the potential risks and inconsistencies of a single method or data set, the phylogenetic reconstructions were based on three different approaches: methods of maximum parsimony, maximum likelihood and neighbor joining. The inferred phylogenies supported monophyly of the order Entomobryomorpha. The relationships between families were different, but the orders of branching within each family were the same. Entomobryidae and Isotomidae were paraphyletic, whereas Tomoceridae was monophyletic. Tomoceridae was subdivided into two branches; the molecular analysis provided results distinctive enough to separate the two genera by the high bootstrap value. On the other hand, two different populations of putativeHomidia koreanaappeared to be different species, although their chaetotaxy is identical. A wide coverage of characters, including not only morphological characters but also genetic data such as allozymes and DNA sequences, will give a more accurate picture of the classification and phylogeny of the studied group.
An evaluation of the SPIFE® 3000 semi‐automated gel electrophoresis system for the identification of hemoglobin variants and comparison of relative electrophoretic mobilities with manual gel electrophoresis methods
Authors: HOYER J. D. , MARKLEY K. M. , SAVEDRA M. E. , KUBIK K. S. , SCHEIDT R. M. 
Published: September 2009

SummaryLaboratory identification of hemoglobin (Hb) variants can involve multiple techniques. The use of semi‐automated instruments that perform gel electrophoresis and staining, such as the SPIFE® 3000 electrophoresis system, can greatly reduce the labor required for these commonly used techniques. We performed a comparison of the method involved in SPIFE® 3000 system with those of manual gel electrophoresis. A total of 22 540 samples were analyzed using the SPIFE® 3000, and compared with mobilities on cellulose acetate and citrate agar gels using standard manual methods. The results were compared using relative electrophoretic mobilities (REM). Of the 191 Hb variants identified, only 13 had REM that differed from manual electrophoresis when analyzed using the SPIFE® 3000 system. One variant (Hb O‐Indonesia) showed different mobility on both acid and alkaline gels, two (Hb E, Hb Sunshine Seth) on alkaline gel only, and 10 (Hbs N‐Baltimore, N‐Seattle, O‐Arab, Shelby, Summer Hill, Tak, Hasharon, M‐Iwate, Q‐Iran, and Setif) on acid gels only. The SPIFE® 3000 semi‐automated electrophoresis system produces similar results when compared with those of standard manual electrophoresis methods.
Human Immune Proteome in Experimental Colonization with
Staphylococcus aureus
Authors: Holtfreter Silva , Nguyen Thi Thu Hoai , Wertheim Heiman , Steil Leif , Kusch Harald , Truong Quoc Phong , Engelmann Susanne , Hecker Michael , Völker Uwe , van Belkum Alex , Bröker Barbara M. 
Published: September 2009

ABSTRACT

More than 20% of adults are persistently colonized with
Staphylococcus aureus.
When hospitalized, these carriers have increased risks of infection with their own strains. However, a recent study demonstrated a lower incidence of bacteremia-related death among carriers than among noncarriers, raising the question whether the adaptive immune system plays a protective role. In fact,
S. aureus
carriers mount a highly specific neutralizing antibody response against superantigens of their colonizing strains. We now used 2-dimensional immunoblotting to investigate the profiles of antibodies from healthy individuals against
S. aureus
extracellular proteins. Moreover, we tested whether symptom-free experimental colonization of these individuals with an
S. aureus
strain of low virulence, 8325-4, is sufficient to induce an antibody response. Sera obtained before and 4 weeks after colonization were screened for immunoglobulin G (IgG) antibody binding to extracellular staphylococcal proteins. At baseline, most volunteers harbored IgG directed against conserved virulence factors, including alpha-hemolysin (Hla), beta-hemolysin (Hlb), phospholipase C (Plc), staphylococcal serine protease (SspA), and cysteine protease (SspB). However, the variability of spot patterns and intensities was striking and could be important in case of infection. Experimental nasal colonization with
S. aureus
8325-4 did not elicit new antibodies or boost the humoral response. Thus, the high antibody prevalence in humans is likely not induced by short-term nasal colonization, and presumably minor infections are required to trigger anti-
S. aureus
antibody responses.
Epidemiology and Clinical Presentations of Human Coronavirus NL63 Infections in Hong Kong Children
Authors: Leung Ting Fan , Li Chung Yi , Lam Wai Yip , Wong Gary W. K. , Cheuk Edmund , Ip Margaret , Ng Pak Cheung , Chan Paul K. S. 
Published: September 2009

ABSTRACT

Human coronavirus NL63 (HCoV-NL63) has been found in children presenting with respiratory tract infections (RTIs). However, the epidemiology and clinical course of this newly identified virus have not been fully elucidated. This study investigated the epidemiology, seasonality, and clinical features of HCoV-NL63 in Hong Kong children. This study consisted of two cohorts of children hospitalized in a university-affiliated teaching hospital. In the 12-month retrospective part of the study, reverse transcription-PCR was used to detect HCoVs in nasopharyngeal aspirates (NPAs). Positive samples were sequenced to confirm the identity of the virus and to determine its phylogenetic relationship with the HCoV-NL63 strains found elsewhere. The second part covered a subsequent 12-month period in which patients were prospectively recruited. Altogether, 1,981 and 1,001 NPA specimens were studied in 2005-2006 and 2006-2007, respectively. Seventy-four (2.5%) HCoV isolates were identified and consisted of 17 (0.6%) HCoV-NL63 isolates, 37 (1.2%) HCoV-OC43 isolates, 14 (0.5%) HCoV-HKU1 isolates, and 6 (0.2%) HCoV-229E isolates. HCoV-NL63 infection was more common in 2006-2007 than 2005-2006 (1.2% and 0.3%, respectively;
P
= 0.006). From 2005 to 2007, the peak season for HCoV-NL63 infection was in September-October, which was earlier than the peak for HCoV-OC43 infections (December-January). HCoV-NL63-infected patients were younger and more likely to have croup, febrile convulsions, and acute gastroenteritis. The majority of local HCoV-NL63 isolates were phylogenetically closely related to those found in Belgium and The Netherlands. In conclusion, HCoV-NL63 is an important yet uncommon virus among our hospitalized children with acute RTIs.
Chronic Hepatitis, Hepatic Dysplasia, Fibrosis, and Biliary Hyperplasia in Hamsters Naturally Infected with a Novel Helicobacter Classified in the
H. bilis
Cluster
Authors: Fox J. G. , Shen Z. , Muthupalani S. , Rogers A. R. , Kirchain S. M. , Dewhirst F. E. 
Published: September 2009

ABSTRACT

We recently described helicobacter-associated progressive, proliferative, and dysplastic typhlocolitis in aging (18- to 24-month-old) Syrian hamsters. Other pathogens associated with typhlocolitis in hamsters,
Clostridium difficile
,
Lawsonia intracellularis
, and
Giardia
spp., were not indentified. The presence of
Helicobacter
genus-specific DNA was noted by PCR in cecal and paraffin-embedded liver samples from aged hamsters by the use of
Helicobacter
-specific PCR primers. By 16S rRNA analysis, the
Helicobacter
sp. isolated from the liver tissue was identical to the cecal isolates from hamsters. The six hamster 16S rRNA sequences form a genotypic cluster most closely related to
Helicobacter
sp.
Flexispira
taxon 8, part of the
Helicobacter bilis
/
H. cinaedi
group. Livers from aged helicobacter-infected hamsters showed various stages of predominantly portocentric and, to a lesser extent, perivenular fibrosis. Within nodules, there was cellular atypia consistent with nodular dysplasia. The livers also exhibited a range of chronic active portal/interface and lobular inflammation, with significant portal hepatitis being present. The inflammation was composed of a mixture of lymphocytes, neutrophils, and macrophages, indicative of its chronic-active nature in these aged hamsters infected with
Helicobacter
spp. The isolation of novel
Helicobacter
spp., their identification by PCR from the diseased livers of aged hamsters, and their taxonomic classification as belonging to the
Helicobacter bilis
cluster strengthen the argument that
H. bilis
and closely related
Helicobacter
spp. play an etiological role in hepatobiliary disease in both animals and humans.
Mycobacterium tuberculosis
Strains with Highly Discordant Rifampin Susceptibility Test Results
Authors: Van Deun A. , Barrera L. , Bastian I. , Fattorini L. , Hoffmann H. , Kam K. M. , Rigouts L. , Rüsch-Gerdes S. , Wright A. 
Published: September 2009

ABSTRACT

The objectives of this study were to investigate the origin of highly discordant rifampin (rifampicin) (RMP) drug susceptibility test results obtained for
Mycobacterium tuberculosis
strains during proficiency testing. Nine Supra-National Tuberculosis Reference Laboratories tested the RMP susceptibilities of 19 selected
M. tuberculosis
strains, using standard culture-based methods. The strains were classified as definitely resistant (R) (
n
= 6) or susceptible (S) (
n
= 2) or probably resistant (PR) (
n
= 8) or susceptible (PS) (
n
= 3) based on
rpoB
mutations and treatment outcome. All methods yielded a susceptible result for the two S and three PS strains lacking an
rpoB
mutation and a resistant result for one R strain with a Ser531Leu mutation and one PR strain with a double mutation. Although the remaining 12 R and PR strains had
rpoB
mutations (four Asp516Tyr, three Leu511Pro, two Leu533Pro, one each His526Leu/Ser, and one Ile572Phe), they were all susceptible by the radiometric Bactec 460TB or Bactec 960 MGIT methods. In contrast, only one was susceptible by the proportion method on Löwenstein-Jensen medium and two on Middlebrook 7H10 agar. Low-level but probably clinically relevant RMP resistance linked to specific
rpoB
mutations is easily missed by standard growth-based methods, particularly the automated broth-based systems. Further studies are required to confirm these findings, to determine the frequency of these low-level-resistant isolates, and to identify technical improvements that may identify such strains.
Molecular and Phenotypic Evaluation of
Lichtheimia corymbifera
(Formerly
Absidia corymbifera
) Complex Isolates Associated with Human Mucormycosis: Rehabilitation of
L. ramosa
Authors: Garcia-Hermoso Dea , Hoinard Damien , Gantier Jean-Charles , Grenouillet Frédéric , Dromer Françoise , Dannaoui Eric 
Published: September 2009

ABSTRACT

Thirty-eight isolates (including 28 isolates from patients) morphologically identified as
Lichtheimia corymbifera
(formerly
Absidia corymbifera
) were studied by sequence analysis (analysis of the internal transcribed spacer [ITS] region of the ribosomal DNA, the D1-D2 region of 28S, and a portion of the elongation factor 1α [EF-1α] gene). Phenotypic characteristics, including morphology, antifungal susceptibility, and carbohydrate assimilation, were also determined. Analysis of the three loci uncovered two well-delimited clades. The maximum sequence similarity values between isolates from both clades were 66, 95, and 93% for the ITS, 28S, and EF-1α loci, respectively, with differences in the lengths of the ITS sequences being detected (763 to 770 bp for isolates of clade 1 versus 841 to 865 bp for isolates of clade 2). Morphologically, the shapes and the sizes of the sporangiospores were significantly different among the isolates from both clades. On the basis of the molecular and morphological data, we considered isolates of clade 2 to belong to a different species named
Lichtheimia ramosa
because reference strains CBS 269.65 and CBS 270.65 (which initially belonged to
Absidia ramosa
) clustered within this clade. As neotype
A. corymbifera
strain CBS 429.75 belongs to clade 1, the name
L. corymbifera
was conserved for clade 1 isolates. Of note, the amphotericin B MICs were significantly lower for
L. ramosa
than for
L. corymbifera
(
P
< 0.005) but were always ≤0.5 μg/ml for both species. Among the isolates tested, the assimilation of melezitose was positive for 67% of the
L. ramosa
isolates and negative for all
L. corymbifera
isolates. In conclusion, this study reveals that two
Lichtheimia
species are commonly associated with mucormycosis in humans.
Persistence of Transgene Expression Influences CD8+T-Cell Expansion and Maintenance following Immunization with Recombinant Adenovirus
Authors: Finn Jonathan D. , Bassett Jennifer , Millar James B. , Grinshtein Natalie , Yang Teng Chih , Parsons Robin , Evelegh Carole , Wan Yonghong , Parks Robin J. , Bramson Jonathan L. 
Published: September 2009

ABSTRACTPrevious studies determined that the CD8+T-cell response elicited by recombinant adenovirus exhibited a protracted contraction phase that was associated with long-term presentation of antigen. To gain further insight into this process, a doxycycline-regulated adenovirus was constructed to enable controlled extinction of transgene expression in vivo. We investigated the impact of premature termination of transgene expression at various time points (day 3 to day 60) following immunization. When transgene expression was terminated before the maximum response had been attained, overall expansion was attenuated, yielding a small memory population. When transgene expression was terminated between day 13 and day 30, the memory population was not sustained, demonstrating that the early memory population was antigen dependent. Extinction of transgene expression at day 60 had no obvious impact on memory maintenance, indicating that maintenance of the memory population may ultimately become independent of transgene expression. Premature termination of antigen expression had significant but modest effects on the phenotype and cytokine profile of the memory population. These results offer new insights into the mechanisms of memory CD8+T-cell maintenance following immunization with a recombinant adenovirus.
The Nedd4-Type Rsp5p Ubiquitin Ligase Inhibits Tombusvirus Replication by Regulating Degradation of the p92 Replication Protein and Decreasing the Activity of the Tombusvirus Replicase
Authors: Barajas Daniel , Li Zhenghe , Nagy Peter D. 
Published: September 2009

ABSTRACT

Recent in vitro proteomics screens revealed that many host proteins could interact with the replication proteins of
Tomato bushy stunt virus
(TBSV), which is a small, plus-stranded RNA virus (Z. Li, D. Barajas, T. Panavas, D. A. Herbst, and P. D. Nagy, J. Virol. 82:6911-6926, 2008). To further our understanding of the roles of host factors in TBSV replication, we have tested the effect of Rsp5p, which is a member of the Nedd4 family of E3 ubiquitin ligases. The full-length Rsp5p, via its WW domain, is shown to interact with p33 and the central portion of p92
pol
replication proteins. We find that overexpression of Rsp5p inhibits TBSV replication in
Saccharomyces cerevisiae
yeast, while downregulation of Rsp5p leads to increased TBSV accumulation. The inhibition is caused by Rsp5p-guided degradation of p92
pol
, while the negative effect on the p33 level is less pronounced. Interestingly, recombinant Rsp5p also inhibits TBSV RNA replication in a cell-free replication assay, likely due to its ability to bind to p33 and p92
pol
. We show that the WW domain of Rsp5p, which is involved in protein interactions, is responsible for inhibition of TBSV replication, whereas the HECT domain, involved in protein ubiquitination, is not necessary for Rsp5p-mediated inhibition of viral replication. Overall, our data suggest that direct binding between Rsp5p and p92
pol
reduces the stability of p92
pol
, with consequent inhibition of TBSV replicase activity.
The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus
Authors: Baltz Jennifer L. , Filman David J. , Ciustea Mihai , Silverman Janice Elaine Y. , Lautenschlager Catherine L. , Coen Donald M. , Ricciardi Robert P. , Hogle James M. 
Published: September 2009

ABSTRACTKaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 Å. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.
A Proteomic Approach To Identify Candidate Substrates of Human Adenovirus E4orf6-E1B55K and Other Viral Cullin-Based E3 Ubiquitin Ligases
Authors: Dallaire Frédéric , Blanchette Paola , Branton Philip E. 
Published: September 2009

ABSTRACT

It has been known for some time that the human adenovirus serotype 5 (Ad5) E4orf6 and E1B55K proteins work in concert to degrade p53 and to regulate selective export of late viral mRNAs during productive infection. Both of these functions rely on the formation by the Ad5 E4orf6 protein of a cullin 5-based E3 ubiquitin ligase complex containing elongins B and C. E1B55K is believed to function as the substrate recognition module for the complex and, in addition to p53, Mre11 and DNA ligase IV have also been identified as substrates. To discover additional substrates we have taken a proteomic approach by using two-dimensional difference gel electrophoresis to detect cellular proteins that decrease significantly in amount in p53-null H1299 human lung carcinoma cells after expression of E1B55K and E4orf6 using adenovirus vectors. Several species were detected and identified by mass spectroscopy, and for one of these, integrin α3, we went on in a parallel study to confirm it as a
bone fide
substrate of the complex (F. Dallaire et al., J. Virol. 83:5329-5338, 2009). Although the system has some limitations, it may still be of some general use in identifying candidate substrates of any viral cullin-based E3 ubiquitin ligase complex, and we suggest a series of criteria for substrate validation.
Ty3 Nuclear Entry Is Initiated by Viruslike Particle Docking on GLFG Nucleoporins
Authors: Beliakova-Bethell Nadejda , Terry Laura J. , Bilanchone Virginia , DaSilva Rhonda , Nagashima Kunio , Wente Susan R. , Sandmeyer Suzanne 
Published: September 2009

ABSTRACT

Yeast retrotransposons form intracellular particles within which replication occurs. Because fungal nuclear membranes do not break down during mitosis, similar to retroviruses infecting nondividing cells, the cDNA produced must be translocated through nuclear pore complexes. The
Saccharomyces cerevisiae
long terminal repeat retrotransposon Ty3 assembles its Gag3 and Gag3-Pol3 precursor polyproteins into viruslike particles in association with perinuclear P-body foci. These perinuclear clusters of Ty3 viruslike particles localized to sites of clustered nuclear pore complexes (NPCs) in a
nup120
Δ mutant, indicating that Ty3 particles and NPCs interact physically. The NPC channels are lined with nucleoporins (Nups) with extended FG (Phe-Gly) motif repeat domains, further classified as FG, FxFG, or GLFG repeat types. These domains mediate partitioning of proteins between the cytoplasm and the nucleus. Here we have systematically examined the requirements for FG repeat domains in Ty3 nuclear transport. The GLFG domains interacted in vitro with virus-like particle Gag3, and this interaction was disrupted by mutations in the amino-terminal domain of Gag3, which is predicted to lie on the external surface of the particles. Accordingly, Ty3 transposition was decreased in strains with the GLFG repeats deleted. The spacer-nucleocapsid domain of Gag3, which is predicted to be internal to the particle, interacted with GLFG repeats and nucleocapsid localized to the nucleus. We conclude that Ty3 particle docking on nuclear pores is facilitated by interactions between Gag3 and GLFG Nups and that nuclear entry of the preintegration complex is further promoted by nuclear localization signals within the nucleocapsid and integrase.
A Novel Picornavirus Associated with Gastroenteritis
Authors: Li Linlin , Victoria Joseph , Kapoor Amit , Blinkova Olga , Wang Chunlin , Babrzadeh Farbod , Mason Carl J. , Pandey Prativa , Triki Hinda , Bahri Olfa , Oderinde Bamidele Soji , Baba Marycelin Mandu , Bukbuk David Nadeba , Besser John M. , Bartkus Joanne M. , Delwart Eric L. 
Published: September 2009

ABSTRACT

A novel picornavirus genome was sequenced, showing 42.6%, 35.2%, and 44.6% of deduced amino acid identities corresponding to the P1, P2, and P3 regions, respectively, of the Aichi virus. Divergent strains of this new virus, which we named salivirus, were detected in 18 stool samples from Nigeria, Tunisia, Nepal, and the United States. A statistical association was seen between virus shedding and unexplained cases of gastroenteritis in Nepal (
P
= 0.0056). Viruses with approximately 90% nucleotide similarity, named klassevirus, were also recently reported in three cases of unexplained diarrhea from the United States and Australia and in sewage from Spain, reflecting a global distribution and supporting a pathogenic role for this new group of picornaviruses.
The Minimum Replication Origin of Merkel Cell Polyomavirus Has a Unique Large T-Antigen Loading Architecture and Requires Small T-Antigen Expression for Optimal Replication
Authors: Kwun Hyun Jin , Guastafierro Anna , Shuda Masahiro , Meinke Gretchen , Bohm Andrew , Moore Patrick S. , Chang Yuan 
Published: September 2009

ABSTRACT
Merkel cell polyomavirus (MCV) is a recently discovered human polyomavirus causing the majority of human Merkel cell carcinomas. We mapped a 71-bp minimal MCV replication core origin sufficient for initiating eukaryotic DNA replication in the presence of wild-type MCV large T protein (LT). The origin includes a poly(T)-rich tract and eight variably oriented, GAGGC-like pentanucleotide sequences (PS) that serve as LT recognition sites. Mutation analysis shows that only four of the eight PS are required for origin replication. A single point mutation in one origin PS from a naturally occurring, tumor-derived virus reduces LT assembly on the origin and eliminates viral DNA replication. Tumor-derived LT having mutations truncating either the origin-binding domain or the helicase domain also prevent LT-origin assembly. Optimal MCV replication requires coexpression of MCV small T protein (sT), together with LT. An intact DnaJ domain on the LT is required for replication but is dispensable on the sT. In contrast, PP2A targeting by sT is required for enhanced replication. The MCV origin provides a novel model for eukaryotic replication from a defined DNA element and illustrates the selective pressure within tumors to abrogate independent MCV replication.