bluuebunny/crossref_metadata_2025_split huggingface dataset:
Similarity and Divergence among Adherent-Invasive
Escherichia coli
and Extraintestinal Pathogenic
E. coli
Strains
Authors: Martinez-Medina Margarita , Mora Azucena , Blanco Miguel , López Cecilia , Alonso María Pilar , Bonacorsi Stéphane , Nicolas-Chanoine Marie-Hélène , Darfeuille-Michaud Arlette , Garcia-Gil Jesus , Blanco Jorge 
Published: October 2009

ABSTRACT

Adherent-invasive
Escherichia coli
(AIEC) pathovar strains, which are associated with Crohn's disease, share many genetic and phenotypic features with extraintestinal pathogenic
E. coli
(ExPEC) strains, but little is known about the level of genetic similarity between the two pathovars. We aimed to determine the frequency of strains with the “AIEC phenotype” among a collection of ExPEC strains and to further search for a common phylogenetic origin for the intestinal and extraintestinal AIEC strains. The adhesion, invasion, and intramacrophage replication capabilities (AIEC phenotype) of 63 ExPEC strains were determined. Correlations between virulence genotype and AIEC phenotype and between intestinal/extraintestinal origin, serotype, and phylogroup were evaluated for the 63 ExPEC and 23 intestinal AIEC strains. Phylogenetic relationships between extraintestinal and intestinal AIEC strains were determined using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. Only four (6.35%) ExPEC strains, belonging to the O6:H1, O83:H1, and O25:H4 serotypes, were classified as having an AIEC phenotype. These strains were found to be genetically related to some intestinal AIEC strains of the same serotypes as revealed by MLST. No particular virulence gene sets correlated with the intestinal/extraintestinal origin of the strains or with the AIEC phenotype, whereas the gene sets did correlate with the serogroup. We identified two intestinal AIEC strains and one extraintestinal AIEC strain belonging to the O25:H4 serotype that also belonged to the emerging and virulent clonal group ST131. In conclusion, the ExPEC and AIEC pathovars share similar virulence gene sets, and certain strains are phylogenetically related. However, the majority of ExPEC strains did not behave like AIEC strains, thus confirming that the AIEC pathovar possesses virulence-specific features that, to date, are detectable only phenotypically.
Diagnostic Bioluminescent Phage for Detection of
Yersinia pestis
Authors: Schofield David A. , Molineux Ian J. , Westwater Caroline 
Published: October 2009

ABSTRACT

Yersinia pestis
is the etiological agent of the plague. Because of the disease's inherent communicability, rapid clinical course, and high mortality, it is critical that an outbreak, whether it is natural or deliberate, be detected and diagnosed quickly. The objective of this research was to generate a recombinant
luxAB
(“light”)-tagged reporter phage that can detect
Y. pestis
by rapidly and specifically conferring a bioluminescent signal response to these cells. The bacterial
luxAB
reporter genes were integrated into a noncoding region of the CDC plague-diagnostic phage φA1122 by homologous recombination. The identity and fitness of the recombinant phage were assessed through PCR analysis and lysis assays and functionally verified by the ability to transduce a bioluminescent signal to recipient cells. The reporter phage conferred a bioluminescent phenotype to
Y. pestis
within 12 min of infection at 28°C. The signal response time and signal strength were dependent on the number of cells present. A positive signal was obtained from 10
2
cells within 60 min. A signal response was not detectable with
Escherichia coli
, although a weak signal (100-fold lower than that with
Y. pestis
) was obtained with 1 (of 10)
Yersinia enterocolitica
strains and 2 (of 10)
Yersinia
pseudotuberculosis
strains at the restrictive temperature. Importantly, serum did not prevent the ability of the reporter phage to infect
Y. pestis
, nor did it significantly quench the resulting bioluminescent signal. Collectively, the results indicate that the reporter phage displays promise for the rapid and specific diagnostic detection of cultivated
Y. pestis
isolates or infected clinical specimens.
Interactions and Oligomerization of Hantavirus Glycoproteins
Authors: Hepojoki Jussi , Strandin Tomas , Vaheri Antti , Lankinen Hilkka 
Published: October 2009

ABSTRACT

In this report the basis for the structural architecture of the envelope of hantaviruses, family
Bunyaviridae
, is systematically studied by the interactions of two glycoproteins N and C (Gn and Gc, respectively) and their respective disulfide bridge-mediated homo- and heteromeric oligomerizations. In virion extracts Gn and Gc associated in both homo- and hetero-oligomers which were, at least partially, thiol bridge mediated. Due to strong homo-oligomerization, the hetero-oligomers of Gn and Gc are likely to be mediated by homo-oligomeric subunits. A reversible pH-induced disappearance of a neutralizing epitope in Gc and dissociation of the Gn-Gc complex at pH values below 6.2 provide proteochemical evidence for the fusogenicity of Gc. Incomplete inactivation of virions at acidic pH indicates that additional factors are required for hantavirus fusion, as in the case of pestiviruses of the
Flaviviridae
. Based on similarities to class II fusion proteins, a structure model was created of hantavirus Gc using the Semliki Forest virus E1 protein as a template. In total, 10 binding regions for Gn were found by peptide scanning, of which five represent homotypic (Gn
I
to Gn
V
) and five represent heterotypic (Gc
I
to Gc
V
) interaction sites that we assign as intra- and interspike connections, respectively. In conclusion, the glycoprotein associations were compiled to a model wherein the surface of hantaviruses is formed of homotetrameric Gn complexes interconnected with Gc homodimers. This organization would create the grid-like surface pattern described earlier for hantaviruses in negatively stained electron microscopy specimens.
The Human Papillomavirus Type 18 E2 Protein Is a Cell Cycle-Dependent Target of the SCF
Skp2
Ubiquitin Ligase
Authors: Bellanger Sophie , Tan Chye Ling , Nei Wenlong , He Ping Ping , Thierry Françoise 
Published: October 2009

ABSTRACT

The human papillomavirus type 18 (HPV-18) E2 gene is inactivated in cervical carcinoma after integration of the viral DNA into the host cellular genome. Since E2 represses the transcription of the two viral oncogenes E6 and E7, integration which allows their strong expression is considered a major step in transformation by HPV. We show here that E2 is specifically degraded at the end of the G
1
phase in a Brd4-independent manner, implying that its regulatory functions are cell cycle dependent. Degradation of E2 occurs via the Skp1/Cullin1/F-box Skp2 (SCF
Skp2
) ubiquitin ligase, since silencing of Skp2 induces stabilization of E2. In addition, the amino-terminal domain of E2 can interact with Skp2 as shown by coimmunoprecipitation experiments. We previously showed that E2 inhibits the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase, leading to accumulation of several of its substrates. We demonstrate here that Skp2, which is a known APC/C substrate in G
1
, is also stabilized by E2. Therefore, by negative feedback, SCF
Skp2
activation could lead to E2 degradation and E6/E7 expression specifically in the late G
1
phase. Moreover, since the SCF
Skp2
can trigger S-phase entry and Skp2 itself is a known oncogene, we believe that E2-mediated accumulation of Skp2, together with E2 degradation leading to putative release of E6 and E7 inhibition, could induce premature S-phase entry in HPV-infected cells, pointing to a direct role of E2 in the early steps of HPV-mediated transformation.
The Range of Human APOBEC3H Sensitivity to Lentiviral Vif Proteins
Authors: Li Melody M. H. , Wu Lily I. , Emerman Michael 
Published: October 2009

ABSTRACT

The
APOBEC3H
gene is polymorphic in humans, with four major population-dependent haplotypes that encode proteins with different levels of antiviral activity. Haplotype II, present most frequently in African populations, encodes the most stable protein and is most active against human immunodeficiency virus type 1 (HIV-1). In contrast to human APOBEC3G, which can be completely counteracted by HIV-1 Vif, the protein encoded by
APOBEC3H
haplotype II is only partially sensitive to Vif, while the protein encoded by
APOBEC3H
haplotype I is completely resistant to HIV-1 Vif. We mapped a residue on APOBEC3H that determines this partial Vif sensitivity. However, it is unclear how HIV-1 can replicate in vivo without the ability to neutralize APOBEC3H antiviral activity. In order to directly address this question, we cloned
vif
genes from HIV-1-infected individuals with different
APOBEC3H
genotypes and tested them for their ability to inhibit human APOBEC3H. We found that while the
APOBEC3H
genotype of infected individuals significantly influences the activity of Vif encoded by their virus, none of the Vif variants tested can completely neutralize APOBEC3H as well as they neutralize APOBEC3G. Consistent with this genetic result, APOBEC3H protein expression in human peripheral blood mononuclear cells was below our limit of detection using newly developed antibodies against the endogenous protein. These results demonstrate that human APOBEC3H is not as strong of a selective force for current HIV-1 infections as human APOBEC3G.
Role of Nuclear Factor Y in Stress-Induced Activation of the Herpes Simplex Virus Type 1 ICP0 Promoter
Authors: Kushnir Anna S. , Davido David J. , Schaffer Priscilla A. 
Published: October 2009

ABSTRACT
Herpesviruses are characterized by the ability to establish lifelong latent infections and to reactivate periodically, leading to recurrent disease. The herpes simplex virus type 1 (HSV-1) genome is maintained in a quiescent state in sensory neurons during latency, which is characterized by the absence of detectable viral protein synthesis. Cellular factors induced by stress may act directly on promoters within the latent viral genome to induce the transcription of viral genes and trigger reactivation. In order to identify which viral promoters are induced by stress and elucidate the cellular mechanism responsible for the induction, we generated a panel of HSV-1 promoter-luciferase constructs and measured their response to heat shock. Of the promoters tested, those of ICP0 and ICP22 were the most strongly upregulated after heat shock. Microarray analysis of lytically infected cells supported the upregulation of ICP0 and ICP22 promoters by heat shock. Mutagenic analysis of the ICP0 promoter identified two regions necessary for efficient heat-induced promoter activity, both containing predicted nuclear factor Y (NF-Y) sites, at bases −708 and −75 upstream of the transcriptional start site. While gel shift analysis confirmed NF-Y binding to both sites, only the site at −708 was important for efficient heat-induced activity. Reverse transcription-PCR analysis of selected viral transcripts in the presence of dominant-negative NF-Y confirmed the requirement for NF-Y in the induction of the ICP0 but not the ICP22 promoter by heat shock in lytically infected cells. These findings suggest that the immediate-early ICP0 gene may be among the first genes to be induced during the early events in HSV-1 reactivation, that NF-Y is important for this induction, and that other factors induce the ICP22 promoter.
Transcriptional Downregulation of
p27KIP1
through Regulation of E2F Function during LMP1-Mediated Transformation
Authors: Everly David N. , Mainou Bernardo A. , Raab-Traub Nancy 
Published: October 2009

ABSTRACT

LMP1 induces the phenotypic transformation of fibroblasts and affects regulators of the cell cycle during this process. LMP1 decreases expression of the cyclin-dependent kinase inhibitor p27 and increases the levels and phosphorylation of cyclin-dependent kinase 2 and the retinoblastoma protein. In the present study, the effects of LMP1 on cell cycle progression and the mechanism of p27 downregulation by LMP1 were determined. Although p27 is frequently regulated at the posttranscriptional level during cell cycle progression and in cancer, LMP1 did not decrease ectopically expressed p27. However, LMP1 did decrease p27 RNA levels and inhibited the activity of p27 promoter reporters. The LMP1-regulated promoter element was mapped to a region containing two E2F sites. Electrophoretic mobility shift assays determined that the regulated
cis
element bound an inhibitory E2F complex containing E2F4 and p130. These findings indicate that LMP1 decreases p27 transcription through effects on E2F family transcription factors. This property likely contributes to the ability of LMP1 to stimulate cell cycle progression.
Replicative Capacity of Human Immunodeficiency Virus Type 1 Transmitted from Mother to Child Is Associated with Pediatric Disease Progression Rate
Authors: Prado Julia G. , Prendergast Andrew , Thobakgale Christina , Molina Claudia , Tudor-Williams Gareth , Ndung'u Thumbi , Walker Bruce D. , Goulder Philip 
Published: October 2009

ABSTRACTHuman immunodeficiency virus (HIV)-infected infants in the developing world typically progress to AIDS or death within the first 2 years of life. However, a minority progress relatively slowly. This study addresses the potential contribution of viral factors to HIV disease progression in eight infants selected from a well-characterized cohort of C clade HIV-infected infants, monitored prospectively from birth in Durban, South Africa. Three infants were defined as “progressors,” and five were defined as “slow progressors.” We observed that slow-progressor infants carry HIV isolates with significantly lower replicative capacity compared to virus from progressors. Furthermore, our data suggest a link between the attenuated viral phenotype and HLA-B* 57/5801 epitope-specific Gag mutational patterns of the transmitted virus and not to coreceptor usage or to the presence of Nef deletions or insertions. These data underline the importance of virus-host interactions and highlight the contribution of viral attenuation through Gag-specific CD8+T-cell escape mutations, among other factors, in the control of pediatric HIV infection.
The Poxvirus A35 Protein Is an Immunoregulator
Authors: Rehm Kristina E. , Jones Gwendolyn J. B. , Tripp Alice A. , Metcalf Mark W. , Roper Rachel L. 
Published: October 2009

ABSTRACT
It was shown previously that the highly conserved vaccinia virus A35 gene is an important virulence factor in respiratory infection of mice. We show here that A35 is also required for full virulence by the intraperitoneal route of infection. A virus mutant in which the A35 gene has been removed replicated normally and elicited improved antibody, gamma interferon-secreting cell, and cytotoxic T-lymphocyte responses compared to wild-type virus, suggesting that A35 increases poxvirus virulence by immunomodulation. The enhanced immune response correlated with an improved control of viral titers in target organs after the development of the specific immune response. Finally, the A35 deletion mutant virus also provided protection from lethal challenge (1,000 50% lethal doses) equal to that of the wild-type virus. Together, these data suggest that A35 deletion viruses will make safer and more efficacious vaccines for poxviruses. In addition, the A35 deletion viruses will serve as improved platform vectors for other infectious diseases and cancer and will be superior vaccine choices for postexposure poxvirus vaccination, as they also provide improved kinetics of the immune response.
On the relationship between matric potential and dielectric properties of organic free soils: a sensitivity study
Authors: Wagner Norman , Scheuermann Alexander 
Published: October 2009

High-frequency electromagnetic determination of moisture in porous media, (e.g., soil) is based on the strong relationship between volumetric water content and relative dielectric permittivity. In particular, in fine-grained soils the movement of water is influenced by different surface-bonding forces due to interface processes. The interface effects lead to a number of dielectric relaxation processes (free- and bound-water phase, Maxwell–Wagner effect, counterion relaxation effects). These relaxation processes are the reason for the strong frequency dependence of the electromagnetic material properties below 1 GHz. The matric potential is a measure of the bonding forces on water in the soil. Based on a thermodynamic relationship between soil matric potential and dielectric relaxation behaviour of water in different binding states, a broadband dielectric relaxation model was developed that considers low-frequency dispersion up to 1 MHz as well as losses due to direct-current conductivity. The sensitivity of the model on soil suction was systematically analyzed based on a pedotransfer function (PTF) for soil textures ranging from pure sand up to pure clay. The results are compared with known empirical and semiempirical calibration functions, as well as theoretical mixing models.
Adsorption characteristics of coal in constant-pressure tests
Authors: Sabir Ali , Chalaturnyk R. J. 
Published: October 2009

Adsorption characteristics of coal have traditionally been studied using crushed coal specimens. When adsorption tests are run on a crushed coal specimen, adsorption kinematics are not involved and therefore the equilibrium of gases is attained rapidly. In this study, the kinematics of CO2 adsorption have been examined on intact coal and crushed coal specimens using experimental methods where pressure rather than volume of the adsorbing gas was kept constant. To understand the adsorption characteristics of the intact specimen, adsorption isotherms for the crushed coal specimen are required from similar test conditions. The crushed coal adsorption isotherms measured in this study are very similar in shape. However, they indicate a slightly larger capacity than those measured in other studies even for coals of similar rank. The average difference between the total adsorption capacity of crushed coal and the intact coal is about 7 mL of adsorbed CO2 per gram of coal at 4000 kPa. Although the difference in adsorption capacities of intact and crushed coal is small, it is important to understand the impact of adsorption kinematics to reach the final adsorption on the intact coal specimen.
GENERATIONAL SUCCESSION: EXAMPLES FROM TUNISIAN FAMILY FIRMS
Authors: FATTOUM SALMA , FAYOLLE ALAIN 
Published: October 2009

The family character gathers firms whose weight in the economic activity of countries is considerable for developed countries as well as for the others. However, this type of firm is exposed to not only the threats that challenge all types of firms but they must also face dangers related to their family nature. Several American and European studies were interested in the succession issues associated with family businesses. However, this topic received very little theoretical and empirical investigation in developing countries. In Tunisia, the push in favor of private firms was given in the 60s. Nearly 50 years later, those entrepreneurs who had received state aid to start their businesses are about to retire. How is this dealt with? How is succession "guaranteed"? Hard as it may be to speculate on the outcome of this succession, can we at least describe its phases first and then consider the factors that could have an impact on it? These central questions to Tunisia's economy have yet to be answered academically. Our aim, in this paper, is to improve our understanding of the nature of the relation between the founder and his successor during the process of succession in the Tunisian family business while proposing reflections to be carried out to make a success of this generational change. Our paper is organized as follows. The first part will be an analysis of the literature on family firms and the succession process. In the second part, we will introduce the methodological aspects of our study, which was conducted on six Tunisian family firms at different stages of the succession process. In the third part, we will present and discuss the results.
RADICAL STRATEGIC CHANGE IN ISRAELI HIGH TECHNOLOGY NEW VENTURES
Authors: GIMMON ELI , BENJAMIN EYAL , KATZENSTEIN LIORA 
Published: October 2009

This study note explores the major causes that stimulate Radical Strategic Change (RSC) in Israeli high technology new ventures. It explores the factors that make RSC successful in these ventures, based on the Resource-Based-View (RBV). A multiple case study methodology was applied on four Israeli-based start-up companies that experienced both an un-favorable and a favorable RSC, sequentially. Our findings suggest that the level of resources was the major impetus for these RSCs, and that the alignment of resources to the environment yielded the desired performance goals for these venture. Further research is needed to validate the findings of this study.
On some Fossiliferous Beds overlying the Red Crag at Chillesford, near Orford, Suffolk
Authors: Prestwich Joseph 
Published: October 2009

Conclusions
From the few facts above detailed it would at all events appear that the coralline and red crags are on the hills north of Orford overlaid unconformably by a deposit ten to twenty feet thick of a distinct mineral and palæontological character. In Iken parish this deposit clearly reposes upon the coralline crag, and at Chillesford the red crag is at one point shown to occur below it, and at another to outcrop at a short distance from it on a lower level. The red crag is also frequently found between these two places on the slopes of the hills, the summits of which are capped by the clays and sands. The following section would therefore, I infer, represent the structure of this part of the country.
On the Position in which Shells are found in the Red Crag
Authors: Ringler-Thomson T. G. 
Published: October 2009

Abstract

T
he
unvarying position of the bivalve and univalve shells in the red crag formation of Suffolk and Essex, in many localities, has not, that I am aware of, been ever publicly discussed. The inexhaustible stores of Pectunculi in this formation, as well as the other less numerous bivalves, are deposited in layers of various thickness, from six inches to as many or more feet, each shell having its inside or concavity downwards, and the umbones of the shells having in general an easterly direction.
Notes on Remains of Fossil Reptiles discovered by Prof. Henry Rogers of Pennsylvania, U.S., in Greensand Formations of New Jersey
Authors: Owen  
Published: October 2009

Abstract

T
he
paper descriptive of the series of fossils submitted to me in November 1848 by Prof. Rogers, and read at the meeting of the Society on the 31st of January 1849, has been unfortunately lost; the rough notes taken on the inspection of the fossils have likewise been mislaid, and I am compelled, therefore, in order that the benefit designed by Prof. Rogers to English palæontologists, by bringing over the above collection of rare and valuable instructive fossils, should not be wholly lost, to give now such notes as my restricted leisure will permit of the specimens which have been selected for the subjects of Plates X. & XI.