bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Nucleoside Reverse Transcriptase Inhibitors on Mitochondrial DNA and RNA in Human Skeletal Muscle Cells
Authors: Saitoh Akihiko , Haas Richard H. , Naviaux Robert K. , Salva Neurita G. , Wong Justine K. , Spector Stephen A. 
Published: June 2008

ABSTRACTWe previously reported that 2′,3′-dideoxyinosine (didanosine, or ddI) significantly altered mitochondrial DNA (mtDNA) in peripheral blood mononuclear cells in human immunodeficiency virus type 1 (HIV-1)-infected children who had undetectable plasma HIV-1 RNA for more than 2 years while receiving highly active antiretroviral therapy. This research examines the in vitro effects of nucleoside reverse transcriptase inhibitors (NRTIs) on mitochondria of human skeletal muscle cells (HSMCs), including myoblasts and differentiated myotubes. mtDNA, mitochondrial RNA (mtRNA), and mRNA levels for nuclear mitochondrial regulatory factors were quantified in vitro using HSMCs, including myoblasts and differentiated myotubes, treated with NRTIs singly and in combination. After 5 days of treatment, mtDNA was significantly decreased in myoblasts and myotubes treated with ddI (P< 0.001 andP= 0.01, respectively) and ddI-containing regimens (P< 0.001 andP< 0.001, respectively) compared to levels in untreated cells. mtRNA (MTCYB) was also significantly decreased in the myoblasts and myotubes treated with ddI (P= 0.004) and ddI-containing regimens (P< 0.001). Regardless of the NRTI regimens examined, NRTI combinations significantly decreased mtRNA (MTCO3) in myoblasts and myotubes (P= 0.02 andP= 0.01, respectively). No significant differences were observed for nuclear mitochondrial regulatory factor mRNA in myoblasts or myotubes when treated with NRTIs (P> 0.07). ddI and ddI-containing regimens significantly decrease mtDNA and mtRNA in HSMCs, most notably in myoblasts. These findings may be of particular importance in developing countries, where ddI is widely used for first-line treatment of HIV-infected children.
Phenotypic and Genotypic Analyses of
Neisseria gonorrhoeae
Isolates That Express Frequently Recovered PorB PIA Variable Region Types Suggest that Certain P1a Porin Sequences Confer a Selective Advantage for Urogenital Tract Infection
Authors: Garvin Lotisha E. , Bash Margaret C. , Keys Christine , Warner Douglas M. , Ram Sanjay , Shafer William M. , Jerse Ann E. 
Published: June 2008

ABSTRACT

Typing of the
porB
variable region (VR) is an epidemiological tool that classifies gonococcal strains based on sequence differences in regions of the
porB
gene that encode surface-exposed loops. The frequent isolation of certain
porB
VR types suggests that some porin sequences confer a selective advantage during infection and/or transmission. Alternatively, certain porin types may be markers of strains that are successful due to factors unrelated to porin. In support of the first hypothesis, here we show urogenital tract isolates representing the most common PIA VR types identified in an urban clinic in Baltimore, MD, over a 10-year period belonged to several different clonal types, as determined by pulsed-field gel electrophoresis (PFGE). Serum resistance, which was confirmed by factor H and C4b-binding protein binding studies, was more often associated with gonococcal the most common VR types. In contrast, three porin-independent phenotypes, namely, lactoferrin utilization, β-lactamase production, and multiple transferable resistance (Mtr), were segregated with the PFGE cluster and not with the VR type. Data combined with another PIA strain collection showed a strong correlation between serum resistance and the most common VR types. A comparison of VR typing hybridization patterns and nucleotide sequences of 12
porB1a
genes suggests that certain porin loop 1, 3, 6, and/or 7 sequences may play a role in the serum resistance phenotype. We conclude that some PorB PIA sequences confer a survival or transmission advantage in the urogenital tract, perhaps via increased resistance to complement-mediated killing. The capacity of some porin types to evade a porin-specific adaptive immune response must also be considered.
Rat Pneumonia and Soft-Tissue Infection Models for the Study of
Acinetobacter baumannii
Biology
Authors: Russo Thomas A. , Beanan Janet M. , Olson Ruth , MacDonald Ulrike , Luke Nicole R. , Gill Steven R. , Campagnari Anthony A. 
Published: June 2008

ABSTRACT

Acinetobacter baumannii
is a bacterial pathogen of increasing medical importance. Little is known about its mechanisms of pathogenesis, and safe reliable agents with predictable activity against
A. baumannii
are presently nonexistent. The availability of relevant animal infection models will facilitate the study of
Acinetobacter
biology. In this report we tested the hypothesis that the rat pneumonia and soft-tissue infection models that our laboratory had previously used for studies of extraintestinal pathogenic
Escherichia coli
were clinically relevant for
A. baumannii
. Advantages of these models over previously described models were that the animals were not rendered neutropenic and they did not receive porcine mucin with bacterial challenge. Using the
A. baumannii
model pathogen 307-0294 as the challenge pathogen, the pneumonia model demonstrated all of the features of infection that are critical for a clinically relevant model: namely, bacterial growth/clearance, an ensuing host inflammatory response, acute lung injury, and, following progressive bacterial proliferation, death due to respiratory failure. We were also able to demonstrate growth of 307-0294 in the soft-tissue infection model. Next we tested the hypothesis that the soft-tissue infection model could be used to discriminate between the inherent differences in virulence of various
A. baumannii
clinical isolates. The ability of
A. baumannii
to grow and/or be cleared in this model was dependent on the challenge strain. We also hypothesized that complement is an important host factor in protecting against
A. baumannii
infection in vivo. In support of this hypothesis was the observation that the serum sensitivity of various
A. baumannii
clinical isolates in vitro roughly paralleled their growth/clearance in the soft-tissue infection model in vivo. Lastly we hypothesized that the soft-tissue infection model would serve as an efficient screening mechanism for identifying gene essentiality for drug discovery. Random mutants of 307-0294 were initially screened for lack of growth in human ascites in vitro. Selected mutants were subsequently used for challenge in the soft-tissue infection model to determine if the disrupted gene was essential for growth in vivo. Using this approach, we have been able to successfully identify a number of genes essential for the growth of 307-0294 in vivo. In summary, these models are clinically relevant and can be used to study the innate virulence of various
Acinetobacter
clinical isolates and to assess potential virulence factors, vaccine candidates, and drug targets in vivo and can be used for pharmacokinetic and chemotherapeutic investigations.
Impaired Opsonization with C3b and Phagocytosis ofStreptococcus pneumoniaein Sera from Subjects with Defects in the Classical Complement Pathway
Authors: Yuste Jose , Sen Ashwin , Truedsson Lennart , Jönsson Göran , Tay Liang-Seah , Hyams Catherine , Baxendale Helen E. , Goldblatt Fiona , Botto Marina , Brown Jeremy S. 
Published: June 2008

ABSTRACTResults from studies using mice deficient in specific complement factors and clinical data on patients with an inherited deficiency of the classical complement pathway component C2 suggest that the classical pathway is vital for immunity toStreptococcus pneumoniae. However, the consequences of defects in classical pathway activity for opsonization with C3b and the phagocytosis of differentS. pneumoniaeserotypes in human serum are not known, and there has not been a systematic analysis of the abilities of sera from subjects with a C2 deficiency to opsonizeS. pneumoniae. Hence, to investigate the role of the classical pathway in immunity toS. pneumoniaein more detail, flow cytometry assays of opsonization with C3b and the phagocytosis of three capsular serotypes ofS. pneumoniaewere performed using human sera depleted of the complement factor C1q or B or sera obtained from C2-deficient subjects. The results demonstrate that, in human serum, the classical pathway is vital for C3b-iC3b deposition onto cells of all three serotypes ofS. pneumoniaeand seems to be more important than the alternative pathway for phagocytosis. Compared to the results for sera from normal subjects, C3b-iC3b deposition and total anti-S. pneumoniaeantibody activity levels in sera obtained from C2−/−subjects were reduced and the efficiency of phagocytosis of all threeS. pneumoniaestrains was impaired. Anticapsular antibody levels did not correlate with phagocytosis or C3b-iC3b deposition. These data confirm that the classical pathway is vital for complement-mediated phagocytosis ofS. pneumoniaeand demonstrate why subjects with a C2 deficiency have a marked increase in susceptibility toS. pneumoniaeinfections.
The Fibrinogen- and Fibronectin-Binding Domains of
Staphylococcus aureus
Fibronectin-Binding Protein A Synergistically Promote Endothelial Invasion and Experimental Endocarditis
Authors: Piroth Lionel , Que Yok-Ai , Widmer Eleonora , Panchaud Alexandre , Piu Stéphane , Entenza José M. , Moreillon Philippe 
Published: June 2008

ABSTRACT

Staphylococcus aureus
experimental endocarditis relies on sequential fibrinogen binding (for valve colonization) and fibronectin binding (for endothelial invasion) conferred by peptidoglycan-attached adhesins. Fibronectin-binding protein A (FnBPA) reconciles these two properties—as well as elastin binding—and promotes experimental endocarditis by itself. Here we attempted to delineate the minimal subdomain of FnBPA responsible for fibrinogen and fibronectin binding, cell invasion, and in vivo endocarditis. A large library of truncated constructs of FnBPA was expressed in
Lactococcus lactis
and tested in vitro and in animals. A 127-amino-acid subdomain spanning the hinge of the FnBPA fibrinogen-binding and fibronectin-binding regions appeared necessary and sufficient to confer the sum of these properties. Competition with synthetic peptides could not delineate specific fibrinogen- and fibronectin-binding sites, suggesting that dual binding arose from protein folding, irrespective of clearly defined binding domains. Moreover, coexpressing the 127-amino-acid subdomain with remote domains of FnBPA further increased fibrinogen binding by ≥10 times, confirming the importance of domain interactions for binding efficacy. In animals, fibrinogen binding (but not fibronectin binding) was significantly associated with endocarditis induction, whereas both fibrinogen binding and fibronectin binding were associated with disease severity. Moreover, fibrinogen binding also combined with fibronectin binding to synergize the invasion of cultured cell lines significantly, a feature correlating with endocarditis severity. Thus, while fibrinogen binding and fibronectin binding were believed to act sequentially in colonization and invasion, they appeared unexpectedly intertwined in terms of both functional anatomy and pathogenicity (in endocarditis). This unforeseen FnBPA subtlety might bear importance for the development of antiadhesin strategies.
A Novel Immunoprecipitation Strategy Identifies a Unique Functional Mimic of the Glial Cell Line-Derived Neurotrophic Factor Family Ligands in the PathogenTrypanosoma cruzi
Authors: Lu Bo , PereiraPerrin Mercio 
Published: June 2008

ABSTRACTThe journey of the Chagas' disease parasiteTrypanosoma cruziin the human body usually starts in the skin after an insect bite, when trypomastigotes get through the extracellular matrix to bind specific surface receptors in the epidermis and dermis to enter cells, where they differentiate and replicate. As the infection spreads to the heart, nervous system, and other parts of the body via the circulatory system, the parasite must also cope with additional receptors in the immune system and vascular endothelium. The molecular underpinnings that govern host cell receptor recognition byT. cruzicounterreceptors remain largely unknown. Here, we describe an immunoprecipitation strategy designed to concurrently identify host receptors and complementing parasite counterreceptors. Extracellular domains of growth factor receptors fused to human immunoglobulin G (IgG) Fc were incubated with parasite lysates, immunoprecipitated on protein G-Sepharose, and eluted with Laemmli sample buffer. PossibleT. cruzicounterreceptors pulled down by the receptor-Fc bait were visualized on immunoblots probed with multispecific high-affinity IgG from chronic chagasic sera and on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels stained with silver or Coomassie blue. In screening receptors important for nervous system repair, this parasite counterreceptor immunoprecipitation (PcIP) assay identified 7 to 11 polypeptides (molecular masses, 14 kDa to 55 kDa) that bound to the coreceptors of glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) GFRα-1, -2, and -3. Binding was specific because theT. cruzimimic of host GFLs, named TGFL, did not react with GFL coreceptor tyrosine kinase RET and with other neurotrophic receptors. The polypeptides were located on the parasite outer membrane and bound noncovalently to each other. TGFL eluted from the GFL receptor/protein G affinity column with 0.5 M NaCl, pH 7.5, and potently promoted neurite outgrowth and cell survival in a GFL-sensitive mouse pheochromocytoma cell line. Given that GFLs are neuron survival factors crucial for development and maintenance of central and peripheral nervous systems, it may be thatT. cruzimimicry of host GFLs helps in mutually beneficial host repair of infected and damaged nervous tissue. As there are >30 growth factor receptor-Fc chimeras commercially available, this PcIP assay can be readily adapted to identify receptors/counterreceptors in otherT. cruziinvasion sites and in other infections such as Lyme disease, amebiasis, and schistosomiasis.
Screen for Leukotoxin Mutants in
Aggregatibacter actinomycetemcomitans
: Genes of the Phosphotransferase System Are Required for Leukotoxin Biosynthesis
Authors: Isaza Maria P. , Duncan Matthew S. , Kaplan Jeffrey B. , Kachlany Scott C. 
Published: June 2008

ABSTRACT

Aggregatibacter
(formerly
Actinobacillus
)
actinomycetemcomitans
is a pathogen that causes localized aggressive periodontitis and extraoral infections including infective endocarditis. Recently, we reported that
A. actinomycetemcomitans
is beta-hemolytic on certain growth media due to the production of leukotoxin (LtxA). Based on this observation and our ability to generate random transposon insertions in
A. actinomycetemcomitans
, we developed and carried out a rapid screen for LtxA mutants. Using PCR, we mapped several of the mutations to genes that are known or predicted to be required for LtxA production, including
ltxA, ltxB, ltxD
, and
tdeA
. In addition, we identified an insertion in a gene previously not recognized to be involved in LtxA biosynthesis,
ptsH. ptsH
encodes the protein HPr, a phosphocarrier protein that is part of the sugar phosphotransferase system. HPr results in the phosphorylation of other proteins and ultimately in the activation of adenylate cyclase and cyclic AMP (cAMP) production. The
ptsH
mutant showed only partial hemolysis on blood agar and did not produce LtxA. The phenotype was complemented by supplying wild-type
ptsH
in
trans
, and real-time PCR analysis showed that the
ptsH
mutant produced approximately 10-fold less
ltxA
mRNA than the wild-type strain. The levels of cAMP in the
ptsH
mutant were significantly lower than in the wild-type strain, and LtxA production could be restored by adding exogenous cAMP to the culture.
Identification of Two Translocon Proteins of
Vibrio parahaemolyticus
Type III Secretion System 2
Authors: Kodama Toshio , Hiyoshi Hirotaka , Gotoh Kazuyoshi , Akeda Yukihiro , Matsuda Shigeaki , Park Kwon-Sam , Cantarelli Vlademir V. , Iida Tetsuya , Honda Takeshi 
Published: June 2008

ABSTRACT

The type III secretion system (T3SS) translocon complex is composed of several associated proteins, which form a translocation channel through the host cell plasma membrane. These proteins are key molecules that are involved in the pathogenicity of many T3SS-positive bacteria, because they are necessary to deliver effector proteins into host cells. A T3SS designated T3SS2 of
Vibrio parahaemolyticus
is thought to be related to the enterotoxicity of this bacterium in humans, but the effector translocation mechanism of T3SS2 is unclear because there is only one gene (the VPA1362 gene) in the T3SS2 region that is homologous to other translocon protein genes. It is also not known whether the VPA1362 protein is functional in the translocon of T3SS2 or whether it is sufficient to form the translocation channel of T3SS2. In this study, we identified both VPA1362 (designated VopB2) and VPA1361 (designated VopD2) as T3SS2-dependent secretion proteins. Functional analysis of these proteins showed that they are essential for T3SS2-dependent cytotoxicity, for the translocation of one of the T3SS2 effector proteins (VopT), and for the contact-dependent activity of pore formation in infected cells in vitro. Their targeting to the host cell membrane depends on T3SS2, and furthermore, they are necessary for T3SS2-dependent enterotoxicity in vivo. These results indicate that VopB2 and VopD2 act as translocon proteins of
V. parahaemolyticus
T3SS2 and hence have a critical role in the T3SS2-dependent enterotoxicity of this bacterium.
Genetic diversity and relationships among Dutch elm disease tolerantUlmus pumilaL. accessions from China
Authors: Zalapa Juan E. , Brunet Johanne , Guries Raymond P. 
Published: June 2008

Elm breeding programs worldwide have relied heavily on Asian elm germplasm, particularly Ulmus pumila , for the breeding of Dutch elm disease tolerant cultivars. However, the extent and patterning of genetic variation in Asian elm species is unknown. Therefore, the objective of this research was to determine the extent of genetic diversity among 53 U. pumila accessions collected throughout the People’s Republic of China. Using 23 microsatellite loci recently developed in the genus Ulmus , a total of 94 alleles were identified in 15 polymorphic and 4 monomorphic loci. The average number of alleles per locus was 4.9, with a range of 1–11 alleles. Gene diversity estimates per locus ranged from 0.08 to 0.87, and the non-exclusion probability for the 15 polymorphic loci combined was 0.7 × 10−9. Nineteen region-specific alleles were identified, and regional gene diversity estimates were moderately high (0.48–0.57). The genetic relationships among accessions and regions were estimated by UPGMA and principal coordinate analysis. Both techniques discriminated all accessions and regions. Two microsatellite markers (UR175 + UR123 or Ulm-3) were sufficient to discriminate up to 99.7% of the accessions studied. This research provides useful information for DNA-based fingerprinting, breeding, ecological studies, and diversity assessment of elm germplasm.
Conjunctive query containment and answering under description logic constraints
Authors: Calvanese Diego , Giacomo Giuseppe De , Lenzerini Maurizio 
Published: June 2008

Query containment and query answering are two important computational tasks in databases. While query answering amounts to computing the result of a query over a database, query containment is the problem of checking whether, for every database, the result of one query is a subset of the result of another query.
In this article, we deal with unions of conjunctive queries, and we address query containment and query answering under description logic constraints. Every such constraint is essentially an inclusion dependency between concepts and relations, and their expressive power is due to the possibility of using complex expressions in the specification of the dependencies, for example, intersection and difference of relations, special forms of quantification, regular expressions over binary relations. These types of constraints capture a great variety of data models, including the relational, the entity-relationship, and the object-oriented model, all extended with various forms of constraints. They also capture the basic features of the ontology languages used in the context of the Semantic Web.
We present the following results on both query containment and query answering. We provide a method for query containment under description logic constraints, thus showing that the problem is decidable, and analyze its computational complexity. We prove that query containment is undecidable in the case where we allow inequalities in the right-hand-side query, even for very simple constraints and queries. We show that query answering under description logic constraints can be reduced to query containment, and illustrate how such a reduction provides upper-bound results with respect to both combined and data complexity.
A Comparative Study of Religiocentrism among Christian, Muslim and Hindu Students in Tamil Nadu, India
Authors: Sterkens Carl , Anthony Francis-Vincent 
Published: June 2008

AbstractThis article presents a theoretical framework for religiocentrism that is suited to cross-religious comparisons between Christians, Muslims and Hindus. Religiocentrism is defined as the combination of positive attitudes toward the religious ingroup and negative attitudes toward religious outgroup(s). Empirical research proves the relevance of the construct 'religiocentrism' among Christian, Muslim and Hindu college students in Tamil Nadu. Full score comparability is possible for positive ingroup attitudes but is hampered in the case of negative outgroup attitudes because of the specificity of outgroup prejudice to each religious group. Cross-religious differences between levels of positive ingroup attitudes can be explained in terms of the differential effects of socio-cultural, socio-economic and socio-religious characteristics. This topic calls for further reflection, taking into account contextual factors such as majority versus minority position and specific religious convictions for each religious tradition, more particularly within the context of Tamil Nadu. The article ends with a discussion of the findings.
Married in the Water: Spirit Kin and Other Afflictions of Modernity in Southeastern Nigeria
Authors: Bastian Misty L. 
Published: June 2008

AbstractAs we approached another incarnation we made pacts that we would return to the spirit world at the first opportunity... Those of us who made such vows were known among the Living as abiku, spirit-children. Not all people recognised us. We were the ones who kept coming and going, unwilling to come to terms with life. We had the ability to will our deaths. Our pacts were binding. Those who broke their pacts were assailed by hallucinations and haunted by their companions. They would only find consolation when they returned to the world of the Unborn, the place of fountains, where their loved ones would be waiting for them silently. Those of us who lingered in the world, seduced by the annunciation of wonderful events, went through life with beautiful and fated eyes, carrying within us the music of a lovely and tragic mythology. Our mouths utter obscure prophesies. Our minds are invaded by images of the future. We are the strange ones, with half of our beings always in the spirit world. We were often recognised and our flesh marked with razor incisions. When we were born again to the same parents the marks, lingering on our new flesh, branded our souls in advance. Then the world would spin a web of fate around our lives. Those of us who died while still children tried to erase these marks, by making beautiful spots or interesting discolorations of them. If we didn't succeed, and were recognised, we were greeted with howls of dread, and the weeping of mothers.