bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection of Point Mutations Conferring Resistance to Fluoroquinolone in
gyrA
of
Helicobacter pylori
by Allele-Specific PCR
Authors: Nishizawa Toshihiro , Suzuki Hidekazu , Umezawa Ayako , Muraoka Hiroe , Iwasaki Eisuke , Masaoka Tatsuhiro , Kobayashi Intetsu , Hibi Toshifumi 
Published: November 2006

ABSTRACT

Helicobacter pylori
strains with reduced susceptibility to fluoroquinolones have a mutation at either codon 87 Asn or 91 Asp of the
gyrA
gene. A rapid test based on an allele-specific PCR (AS-PCR) was designed to detect the
gyrA
mutations. Clinical
H. pylori
isolates were obtained from the stomachs of 51 patients with
H. pylori
infections who showed treatment failure. The MICs of gatifloxacin (GAT) were determined by the agar dilution method. Identical genotyping results were obtained with AS-PCR and conventional PCR. The
gyrA
mutations of
H. pylori
causing reduced susceptibility to fluoroquinolones could be detected successfully by this method. A significant association was observed between the presence of mutations, as detected by AS-PCR, and the resistance of the strains to GAT. Moreover, genotyping by AS-PCR took less than 3 to 4 h. The AS-PCR method for the detection of
gyrA
mutations in
H. pylori
is useful for easy identification of fluoroquinolone-resistant strains of
H. pylori
.
Structural and Functional Characterization of Sapovirus RNA-Dependent RNA Polymerase
Authors: Fullerton Stephen W. B. , Blaschke Martina , Coutard Bruno , Gebhardt Julia , Gorbalenya Alexander , Canard Bruno , Tucker Paul A. , Rohayem Jacques 
Published: November 2006

ABSTRACT

Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the
Caliciviridae
family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D
pol
-like protein. Enzymatically active sapovirus 3D
pol
and its defective mutant were expressed in
Escherichia coli
and purified. The overall structure of the sapovirus 3D
pol
was determined by X-ray crystallography to 2.32-Å resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D
pol
prefers Mn
2+
over Mg
2+
but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D
pol
synthesizes a double-stranded RNA or labels the template 3′ terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D
pol
an attractive target for developing drugs to control calicivirus infection in humans.
Proinflammatory Cytokine Gene Induction by Human T-Cell Leukemia Virus Type 1 (HTLV-1) and HTLV-2 Tax in Primary Human Glial Cells
Authors: Banerjee Prabal , Rochford Rosemary , Antel J. , Canute G. , Wrzesinski Stephen , Sieburg Michelle , Feuer Gerold 
Published: November 2006

ABSTRACTInfection with human T-cell leukemia virus type 1 (HTLV-1) can result in the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a chronic inflammatory disease of the central nervous system (CNS). HTLV-2 is highly related to HTLV-1 at the genetic level and shares a high degree of sequence homology, but infection with HTLV-2 is relatively nonpathogenic compared to HTLV-1. Although the pathogenesis of HAM/TSP remains to be fully elucidated, previous evidence suggests that elevated levels of the proinflammatory cytokines in the CNS are associated with neuropathogenesis. We demonstrate that HTLV-1 infection in astrogliomas results in a robust induction of interleukin-1β (IL-1β), IL-1α, tumor necrosis factor alpha (TNF-α), TNF-β, and IL-6 expression. HTLV encodes for a viral transcriptional transactivator protein named Tax that also induces the transcription of cellular genes. To investigate and compare the effects of Tax1 and Tax2 expression on the dysregulation of proinflammatory cytokines, lentivirus vectors were used to transduce primary human astrocytomas and oligodendrogliomas. The expression of Tax1 in primary human astrocytomas and oligodendrogliomas resulted in significantly higher levels of proinflammatory cytokine gene expression compared to Tax2. Notably, Tax1 expression uniquely sensitized primary human astrocytomas to apoptosis. A Tax2/Tax1 chimera encoding the C-terminal 53 amino acids of the Tax1 fused to the Tax2 gene (Tax221) demonstrated a phenotype that resembled Tax1, with respect to proinflammatory cytokine gene expression and sensitization to apoptosis. The patterns of differential cytokine induction and sensitization to apoptosis displayed by Tax1 and Tax2 may reflect differences relating to the heightened neuropathogenicity associated with HTLV-1 infection and the development of HAM/TSP.
Mutually Exclusive T-Cell Receptor Induction and Differential Susceptibility to Human Immunodeficiency Virus Type 1 Mutational Escape Associated with a Two-Amino-Acid Difference between HLA Class I Subtypes
Authors: Yu Xu G. , Lichterfeld Mathias , Chetty Senica , Williams Katie L. , Mui Stanley K. , Miura Toshiyuki , Frahm Nicole , Feeney Margaret E. , Tang Yanhua , Pereyra Florencia , LaBute Montiago X. , Pfafferott Katja , Leslie Alisdair , Crawford Hayley , Allgaier Rachel , Hildebrand William , Kaslow Richard , Brander Christian , Allen Todd M. , Rosenberg Eric S. , Kiepiela Photini , Vajpayee Madhu , Goepfert Paul A. , Altfeld Marcus , Goulder Philip J. R. , Walker Bruce D. 
Published: November 2006

ABSTRACT

The relative contributions of HLA alleles and T-cell receptors (TCRs) to the prevention of mutational viral escape are unclear. Here, we examined human immunodeficiency virus type 1 (HIV-1)-specific CD8
+
T-cell responses restricted by two closely related HLA class I alleles, B*5701 and B*5703, that differ by two amino acids but are both associated with a dominant response to the same HIV-1 Gag epitope KF11 (KAFSPEVIPMF). When this epitope is presented by HLA-B*5701, it induces a TCR repertoire that is highly conserved among individuals, cross-recognizes viral epitope variants, and is rarely associated with mutational escape. In contrast, KF11 presented by HLA-B*5703 induces an entirely different, more heterogeneous TCR β-chain repertoire that fails to recognize specific KF11 escape variants which frequently arise in clade C-infected HLA-B*5703
+
individuals. These data show the influence of HLA allele subtypes on TCR selection and indicate that extensive TCR diversity is not a prerequisite to prevention of allowable viral mutations.
Comparative Analysis of Twelve Genomes of Three Novel Group 2c and Group 2d Coronaviruses Reveals Unique Group and Subgroup Features
Authors: Woo Patrick C. Y. , Wang Ming , Lau Susanna K. P. , Xu Huifang , Poon Rosana W. S. , Guo Rongtong , Wong Beatrice H. L. , Gao Kai , Tsoi Hoi-wah , Huang Yi , Li Kenneth S. M. , Lam Carol S. F. , Chan Kwok-hung , Zheng Bo-jian , Yuen Kwok-yung 
Published: November 2006

ABSTRACT
Twelve complete genomes of three novel coronaviruses—bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d)—were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories.
The Trabecula cranii: development and homology of an enigmatic vertebrate head structure
Authors: Cerny Robert , Horáček Ivan , Olsson Lennart 
Published: November 2006

Abstract
The vertebrate cranium consists of three parts: neuro-, viscero- and dermatocranium, which differ in both developmental and phylogenetic origin. Traditionally, developmental origin has been used as a criterion for homology, but this becomes problematic when skull elements such as the parietal bone are now shown, by modern fate-mapping studies, to have different developmental origins in different groups of tetrapods. This indicates a flexibility of developmental programmes and regulatory pathways which has probably been very important in cranial evolution. The trabecula cranii is an intriguing cranial element in the anterior cranial base in vertebrates. It forms a viscerocranial part of the neurocranium and is believed to be neural crest-derived in gnathostomes, but a similarly named structure in lampreys has been shown to have a mesodermal origin. Topographically, this trabecula seems to be homologous to the gnathostome trabecula cranii, and might also have the same function: to form a border between adjacent morphogenetic domains, to constrain and redirect growth of both brain and stomodeum and thus to refine developmental schedules of both. We suggest that such a border zone can recruit cells from either the mesoderm (as in the lamprey) or from the neural crest (as in the gnathostomes investigated), and still retain its homology. In our view, the trabecula is an interface element that integrates the respective divergent morphogenetics programs of the preotic head into a balanced unit; we suggest that such a definition can be used to define "the sameness" of this element throughout vertebrates.
Out of place and out of time – towards a more integrated approach to heterochrony
Authors: Spicer John , Rundle Simon 
Published: November 2006

Abstract
Heterochrony (changes in the relative timing of development between species) has been studied almost exclusively using morphological characters, with a focus on changes in size and shape (as a surrogate for time) between ancestral species and their descendents. Such an approach is restrictive in that it precludes the investigation of heterochronies in other, non-morphological traits and, therefore, hampers a more integrated approach to heterochrony. Such an integrated approach, where cellular, molecular and genetic approaches are used within a comparative phylogenetic framework to investigate developmental sequences, has been advocated by workers such as Smith and Raff. Here we suggest that equal emphasis should be given to the importance of physiological and ecological mechanisms that relate to changes in developmental sequence. Reviews of the history and status of physiological and ecological heterochrony reveal several examples for each, although progress has been hampered to some degree by a lack of recognition of physiological heterochrony and a lack of mechanistic understanding (heterochronies in evolutionary ecology). What emerges is that each discipline potentially brings something quite different, and complementary, to the study of heterochrony. The emergence of physiological heterochrony has arguably put the emphasis back on the object of selection and how the developing organism works: studies relating ecology and heterochrony have sought to establish whether or not there is an adaptive basis to altered sequences. We propose that any future studies of heterochrony should seek to exploit these different strengths rather than see them as merely complementary approaches.
Peptides and proteins regulating food intake: a comparative view
Authors: Gorissen Marnix , Flik Gert , Huising Mark 
Published: November 2006

Abstract
Energy homeostasis is under multiple endocrine and neural controls that involve both central and peripheral hormones and neuropeptides. Disorders of energy balance (e.g., obesitas and anorexia nervosa) are caused by subtle dysregulation of these regulatory mechanisms. The hypothalamic arcuate nucleus is a main site of central regulation where two distinct subpopulations of neurons co-express either neuropeptide Y (NPY) and agouti-related protein (AgRP), or proopiomelanocortin (POMC) and cocaine and amphetamine-regulated transcript (CART): the former set of peptides increases food intake; the latter decreases food intake and affect energy metabolism. Key peripheral hormones affecting energy metabolism include cholecystokinin (CCK), leptin and insulin, which decrease food intake, and ghrelin, which increases food intake. CCK and ghrelin regulate food intake in the short term (by affecting meal size), whereas leptin and insulin regulate food intake over longer periods spanning several meals. These signals and their physiology are reasonably well understood in mammals. On the other hand, knowledge on energy metabolism in earlier vertebrates is scant. Recently characterised central food intake regulatory mechanisms in fish suggest that they operate in a manner similar to their mammalian counterparts. Peripheral mechanisms have been poorly studied outside mammals. The recent identification of leptin in several fish species provides new insights and opportunities to enhance our understanding of the regulation of food intake. Comparative analysis of these peripheral mechanisms may shed new light on the function and evolution of the mechanisms controlling energy homeostasis. In this review, we summarise recent developments in understanding of mechanisms and signals that regulate energy balance in mammals, and compare these to what we now know about their orthologues in earlier vertebrates, with a particular focus on bony fishes.
Does Negotiation Have a Future in Controlling Weapons of Mass Destruction?
Authors: Jensen Lloyd 
Published: November 2006

AbstractDespite the heightened level of concern about weapons of mass destruction since 9/11, negotiations for strengthening the WMD nonproliferation regime have been somewhat less than productive. The fact that the material and technology for producing such weapons is also used for peaceful purposes helps explain the limited progress. Lack of trust, concern about equality and fairness as well as the tendency to use negotiations for ulterior purposes also make progress difficult. After considering these points, the article discusses some of the incentives and disincentives that have been used to influence positions on the nonproliferation issue and how paying attention to the needs and interests of the would-be proliferators might increase the chances of reaching mutually beneficial agreements.
The Logic of a Soft Intervention Strategy: The United States and Conflict Conciliation in Africa
Authors: Rothchild Donald 
Published: November 2006

AbstractWhat forms of U.S. intervention are likely to prove realizable and to be appropriate for facilitating the implementation of peace agreements and protecting human rights in Africa? The choices for action are certainly wider than the polar opposites of disengagement and large-scale military intervention. Because the United States can afford neither prolonged military hegemony nor the indulgence of neo-isolationism, it must find some form of creative engagement that fulfills its obligations to facilitate and protect in ways that are acceptable to both American and overseas opinion. Limited interests in Africa and the nature of public pressures leave little alternative to utilizing soft intervention approaches in most cases. Within the category of soft intervention, there appears to be a continuum of means leading to possible movement into muscular intervention. At one end, there is coercive diplomacy, which is associated with threats of military and economic sanctions; if these sanctions are actually used, the intervening state becomes involved in muscular intervention. At the other end is diplomacy associated not with threats, but with the promise of rewards. Between the two poles lies diplomacy that involves neither threats nor rewards (i.e., conciliation and mediation without the use of pressures and incentives). In real world contexts, third parties tend to apply mixed packages of non-coercive and coercive incentives, with coercive incentives becoming increasingly dominant as the costs of altering preferences and the intensity of conflict rise.
Group Attachments in Negotiation and Collective Action
Authors: Druckman Daniel 
Published: November 2006

AbstractThe impact of group attachments on negotiating behavior is a theme (or variable) that runs through many articles published in International Negotiation. It is also a popular topic for research on groups reported in other outlets. This literature set in motion the analytical probe discussed in this article. Focusing attention primarily on ingroup-favoring biases, four questions are asked: What is the phenomenon? Why does it occur? How can it be reduced? Where is it manifest in a larger policy context within which negotiations take place? Highlighted in this essay are the prevalence of the bias, the variety of plausible explanations for its occurrence, the distinction between patriotic and nationalistic group attachments, and the connections between group loyalty, policy making, and collective action. The insights achieved also reveal a number of areas for further research. This topic is one example of the many research accomplishments that herald the birth and maturity of a field of study and practice. In this special issue, we take pause to document these accomplishments as we look forward to another decade of progress.
Swelling behaviour of montmorillonite by poly-6-amide
Authors: Fukushima Y. , Okada A. , Kawasumi M. , Kurauchi T. , Kamigaito O. 
Published: November 2006

AbstractIntercalated compounds of montmorillonite and poly-6-amide were prepared by heating mixtures of ɛ-caprolactam and 5, 10, 15 and 30 wt% of montmorillonite, cation-exchanged with NH3+(CH2)11COOH, at 250°C in a nitrogen atmosphere, and examined by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), gel permeation chromatography (GPC) and elemental analysis. ɛ-caprolactam was polymerized to poly-6-amide by the heat treatment. The mean number-average molecular weight decreased from 3·6 × 104 to 0·8 × 104 with increasing montmorillonite content. TEM showed that considerable swelling had taken place subsequent to polymerization and that the clay layers were uniformly distributed in the final clay/poly-6-amide products. Both XRD and TEM showed that the basal spacing of the compound increased from 51 Å to 210 Å with increasing polyamide content. The driving force for the swelling was considered to be a combination of the polymerization energy of ɛ-caprolactam and the attractive interaction between the interlayer cation and ɛ-caprolactam.
Conductimetric investigations on the dissolution of metakaolinite in dilute hydrofluoric acid. Structural implications
Authors: Murat M. , Driouche M. 
Published: November 2006

AbstarctConductimetric curves based on dissolution in dilute HF of a series of metakaolinite samples prepared by thermal dehydroxylation of kaolinite in air from 500°C to 987°C, have been interpreted in terms of (i) short-time conductivity variation, and (ii) specific initial dissolution rate (rsi). The first parameter has been correlated with a disorganization factor (Fd, equal to unity for an entirely amorphous silica-alumina mix) which does not exceed 0·52 for metakaolinite and, like rsi, reaches a maximum for samples prepared at about 720–750°C. These results, which agree with other data obtained by calorimetry and infrared spectroscopy, show that metakaolinite is never entirely amorphous and has a degree of disorder which varies with the conditions of preparation, and increases for samples which have been mechanically treated by grinding.
Formation of illitic minerals at surface temperatures in Purbeckian sediments (Lower Berriasian, Swiss and French Jura)
Authors: Deconinck J. F. , Strasser A. , Debrabant P. 
Published: November 2006

AbstractThe clay-mineralogical assemblages of Purbeckian carbonate sediments of the Swiss and French Jura Mountains are often composed of illite and interstratified illite-smectite. These illitic minerals occur mainly in thin layers of green marls which show evidence of subaerial exposure and mark the top of shallowing-upward sequences. X-ray diffraction, chemical and thermal analyses coupled with transmission electron microscopy suggest that the Purbeckian illitic minerals replaced smectite in intermediate continental-marine environments. The transition from smectite to illite and interstratified illite-smectite probably resulted from repeated cycles of wetting by marine waters and subsequent drying in hypersaline environments, under a hot Purbeckian climate.
Evidence for the multiphase nature of bentonites from Mössbauer and EPR spectroscopy
Authors: Goodman B. A. , Nadeau P. H. , Chadwick J. 
Published: November 2006

AbstractMössbauer spectra of several smectites demonstrate the existence of at least three phases with distinct Fe populations: (i) a component with very low Fe content (< 1%), which shows slowly-relaxing paramagnetic hyperfine structure at both 4·2 K and 77 K; (ii) a component with intermediate Fe content (∼ 1–10%) which is seen as doublets in the spectra at 4·2 K, 77 K and ambient temperature; (iii) an Fe-rich phase (> 30% Fe), which shows magnetic ordering at 4·2 K and 77 K. These data are consistent with components (i) and (ii) corresponding to Fe incorporated in aluminosilicate structures from distinct phases, whereas (iii) is characteristic of an iron oxide phase, probably goethite in most cases. These conclusions are supported by EPR measurements which show magnetically-dilute Fe in more than one type of structural environment plus an additional component with magnetically-interacting ions.
Identification of oxide impurity phases and distribution of structural iron in some diagenetic illitic clays as determined by Mössbauer spectroscopy
Authors: Goodman B. A. , Nadeau P. H. 
Published: November 2006

AbstractSeven diagenetic illitie clays have been investigated by Mössbauer spectroscopy to characterize the forms of iron. Four specimens had measurable amounts of iron oxide impurity phases, accounting for up to ∼95% of the total Fe. Goethite, microcrystalline and probably aluminous, was identified as the oxide phase in three of these samples, the other containing hematite. This latter sample was also the only one which had tetrahedral Fe(III). Five of the samples contained measurable amounts of Fe(II), but the aluminosilicate Fe was present largely as 6-coordinated Fe(III) which had two distinctly different sets of parameters. These results are discussed in terms of the structural properties of illites.