bluuebunny/crossref_metadata_2025_split huggingface dataset:
Animal Models of Acute Photodamage: Comparisons of Anatomic, Cellular and Molecular Responses in C57BL/6J, SKH1 and Balb/c Mice
Authors: Sharma Meena R. , Werth Benjamin , Werth Victoria P. 
Published: February 2011

AbstractHuman cutaneous photodamage is a major medical problem that includes premature aging and fragility of the skin. Nonxenografted animal models have not been comparatively evaluated for how well they resemble the changes seen in human skin. Here, we sought to identify a suitable mouse model that recapitulates key anatomic, cellular and molecular responses observed in human skin during acute UV exposure. Adult females from three strains of mice, C57BL/6J, SKH1 and Balb/c were exposed to UVB and then evaluated 3 or 20 h after the last irradiation. Skin from UVB‐exposed C57BL/6J mice showed features resembling human photodamage, including epidermal thickening, infiltration of the dermis with inflammatory cells, induction of tumor necrosis factor‐α (TNF‐α) mRNA, accumulation of glycosaminoglycans, particularly hyaluronan in the epidermis and loss of collagen. Hairless SKH1 mouse skin responded similarly, but without any induction of TNF‐α mRNA or chondroitin sulfate. Irradiated Balb/c mice were the least similar to humans. Our results in C57BL/6J mice and to a lesser extent in SKH1 mice, show cutaneous responses to a course of UVB‐irradiation that mirror those seen in human skin. Proper choice of model is critical for investigating cellular and molecular mechanisms of photodamage and photoaging.
Genetic tool development underpins recent advances in thermophilic whole‐cell biocatalysts
Authors: Taylor M. P. , van Zyl L. , Tuffin I. M. , Leak D. J. , Cowan D. A. 
Published: February 2011

SummaryThe environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. The application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose‐derived carbohydrates. Fundamental to the success of this work has been the development of reliable genetic and molecular systems. These technical tools are now available to assist in the development of other (hyper)thermophilic strains with diverse phenotypes such as hemicellulolytic and cellulolytic properties, branched chain alcohol production and other ‘valuable bioproduct’ synthetic capabilities. Here we present an insight into the historical limitations, recent developments and current status of a number of genetic systems for thermophiles. We also highlight the value of reliable genetic methods for increasing our knowledge of thermophile physiology. We argue that the development of robust genetic systems is paramount in the evolution of future thermophilic based bioprocesses and make suggestions for future approaches and genetic targets that will facilitate this process.
Mapping evolutionary process: a multi‐taxa approach to conservation prioritization
Authors: Thomassen Henri A. , Fuller Trevon , Buermann Wolfgang , Milá Borja , Kieswetter Charles M. , Jarrín‐V. Pablo , Cameron Susan E. , Mason Eliza , Schweizer Rena , Schlunegger Jasmin , Chan Janice , Wang Ophelia , Peralvo Manuel , Schneider Christopher J. , Graham Catherine H. , Pollinger John P. , Saatchi Sassan , Wayne Robert K. , Smith Thomas B. 
Published: February 2011

AbstractHuman‐induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adaptin situto changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species‐level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization.
Conciliation biology: the eco‐evolutionary management of permanently invaded biotic systems
Authors: Carroll Scott P. 
Published: February 2011

AbstractBiotic invaders and similar anthropogenic novelties such as domesticates, transgenics, and cancers can alter ecology and evolution in environmental, agricultural, natural resource, public health, and medical systems. The resulting biological changes may either hinder or serve management objectives. For example, biological control and eradication programs are often defeated by unanticipated resistance evolution and by irreversibility of invader impacts. Moreover, eradication may be ill‐advised when nonnatives introduce beneficial functions. Thus, contexts that appear to call for eradication may instead demand managed coexistence of natives with nonnatives, and yet applied biologists have not generally considered the need to manage the eco‐evolutionary dynamics that commonly result from interactions of natives with nonnatives. Here, I advocate a conciliatory approach to managing systems where novel organisms cannot or should not be eradicated. Conciliatory strategies incorporate benefits of nonnatives to address many practical needs including slowing rates of resistance evolution, promoting evolution of indigenous biological control, cultivating replacement services and novel functions, and managing native–nonnative coevolution. Evolutionary links across disciplines foster cohesion essential for managing the broad impacts of novel biotic systems. Rather than signaling defeat, conciliation biology thus utilizes the predictive power of evolutionary theory to offer diverse and flexible pathways to more sustainable outcomes.
Involvement in extreme violence and violence‐related trauma: A review with relevance to young people in custody
Authors: Welfare Heather , Hollin Clive R. 
Published: February 2011

Purpose.  This review is concerned with the points of contact between two diverse literatures: first, the association between childhood abuse and the development of violent conduct; second, the effects of involvement in the perpetration of acts of violence.Method.  The empirical literature in the two areas of concern is considered along with complementary explanations for the extant evidence.Results.  There is a weight of evidence indicating that childhood abuse is associated with later violence alongside a literature that considers this association in terms of the traumatic effects of abuse. The perpetration of violent acts can have debilitating effects on the individual offender: these effects have also been considered in terms of trauma.Conclusion.  It is suggested that there are potential advantages to adopting a trauma‐based framework to inform practice with violent young people. This suggestion raises several areas for research to inform the development of evidence‐based practice that are presented in outline form.
Torque Teno Virus Viremia Load Size in Patients with Selected Congenital Defects of Innate Immunity
Authors: Maggi Fabrizio , Pifferi Massimo , Michelucci Angela , Albani Melania , Sbranti Selenia , Lanini Letizia , Simi Paolo , Macchia Pierantonio , Pistello Mauro , Bendinelli Mauro 
Published: February 2011

ABSTRACTPlasma loads of torque teno virus (TTV) among individuals differ extensively beginning early in life, suggesting a role for innate immunity. Here, congenital mannose-binding lectin deficiencies, but not deficiencies in respiratory ciliary function, correlated with increased TTV loads. Notably, however, the presence of either disorder was associated with particularly high TTV loads.
New Delhi Metallo-β-Lactamase (NDM-1)-Producing Klebsiella pneumoniae: Case Report and Laboratory Detection Strategies
Authors: Mochon A. Brian , Garner Omai B. , Hindler Janet A. , Krogstad Paul , Ward Kevin W. , Lewinski Michael A. , Rasheed James K. , Anderson Karen F. , Limbago Brandi M. , Humphries Romney M. 
Published: February 2011

ABSTRACT

The spread of antimicrobial resistance among
Enterobacteriaceae
is a significant clinical threat. We report the first case of an
Enterobacteriaceae
strain harboring the NDM-1 metallo-β-lactamase in a pediatric patient in the United States. We describe strategies for the detection of this novel resistance mechanism encountered in an isolate of
Klebsiella pneumoniae
.
Complete Genome Sequence of a Yersinia enterocolitica “Old World” (3/O:9) Strain and Comparison with the “New World” (1B/O:8) Strain
Authors: Wang Xin , Li Yang , Jing Huaiqi , Ren Yan , Zhou Zhemin , Wang Shaojing , Kan Biao , Xu Jianguo , Wang Lei 
Published: February 2011

ABSTRACT

Yersinia enterocolitica
is a heterogeneous bacterial species with a wide range of animal reservoirs through which human intestinal illness can be facilitated. In contrast to the epidemiological pattern observed in the United States, infections in China present a pattern similar to those in European countries and Japan, wherein “Old World” strains (biotypes 2 to 5) are prevalent. To gain insights into the evolution of
Y. enterocolitica
and pathogenic properties toward human hosts, we sequenced the genome of a biotype 3 strain, 105.5R(r) (O:9), obtained from a Chinese patient. Comparative genome sequence analysis with strain 8081 (1B/O:8) revealed new insights into
Y. enterocolitica
. Both strains have more than 14% specific genes. In strain 105.5R(r), putative virulence factors were found in strain-specific genomic pathogenicity islands that comprised a novel type III secretion system and
rtx
-like genes. Many of the loci representing ancestral clusters, which are believed to contribute to enteric survival and pathogenesis, are present in strain 105.5R(r) but lost in strain 8081. Insertion elements in 105.5R(r) have a pattern distinct from those in strain 8081 and were exclusively located in a strain-specific region. In summary, our comparative genome analysis indicates that these two strains may have attained their pathogenicity by completely separate evolutionary events, and the 105.5R(r) strain, a representative of the Old World biogroup, lies in a branch of
Y. enterocolitica
that is distinct from the “New World” 8081 strain.
Simultaneous Detection and Identification of Aspergillus and Mucorales Species in Tissues Collected from Patients with Fungal Rhinosinusitis
Authors: Zhao Zuotao , Li Lili , Wan Zhe , Chen Wei , Liu Honggang , Li Ruoyu 
Published: February 2011

ABSTRACT

Rapid detection and differentiation of
Aspergillus
and Mucorales species in fungal rhinosinusitis diagnosis are desirable, since the clinical management and prognosis associated with the two taxa are fundamentally different. We describe an assay based on a combination of broad-range PCR amplification and reverse line blot hybridization (PCR/RLB) to detect and differentiate the pathogens causing fungal rhinosinusitis, which include five
Aspergillus
species (
A. fumigatus
,
A. flavus
,
A. niger
,
A. terreus
, and
A. nidulans
) and seven Mucorales species (
Mucor heimalis
,
Mucor racemosus
,
Mucor cercinelloidea
,
Rhizopus arrhizus
,
Rhizopus microsporus
,
Rhizomucor pusillus
, and
Absidia corymbifera
). The assay was validated with 98 well-characterized clinical isolates and 41 clinical tissue specimens. PCR/RLB showed high sensitivity and specificity, with 100% correct identifications of 98 clinical isolates and no cross-hybridization between the species-specific probes. Results for five control isolates,
Candida albicans
,
Fusarium solani
,
Scedosporium apiospermum
,
Penicillium marneffei
, and
Exophiala verrucosa
, were negative as judged by PCR/RLB. The analytical sensitivity of PCR/RLB was found to be 1.8 × 10
−3
ng/μl by 10-fold serial dilution of
Aspergillus
genomic DNA. The assay identified 35 of 41 (85.4%) clinical specimens, exhibiting a higher sensitivity than fungal culture (22 of 41; 53.7%) and direct sequencing (18 of 41; 43.9%). PCR/RLB similarly showed high specificity, with correct identification 16 of 18 specimens detected by internal transcribed spacer (ITS) sequencing and 16 of 22 detected by fungal culture, but it also has the additional advantage of being able to detect mixed infection in a single clinical specimen. The PCR/RLB assay thus provides a rapid and reliable option for laboratory diagnosis of fungal rhinosinusitis.
International External Quality Assurance for Laboratory Identification and Typing of Streptococcus agalactiae (Group B Streptococci)
Authors: Afshar Baharak , Broughton Karen , Creti Roberta , Decheva Antoaneta , Hufnagel Markus , Kriz Paula , Lambertsen Lotte , Lovgren Marguerite , Melin Pierrette , Orefici Graziella , Poyart Claire , Radtke Andreas , Rodriguez-Granger Javier , Sørensen Uffe B. Skov , Telford John , Valinsky Lea , Zachariadou Levantia ,   members of the DEVANI Study Group, Efstratiou Androulla 
Published: February 2011

ABSTRACT

We report the results from the first international multicenter external quality assessment (EQA) studies for molecular and serological typing of group B streptococcus (GBS) strains as part of DEVANI (
De
sign of a
V
accine
a
gainst
N
eonatal
I
nfections), a pan-European program. A questionnaire-based surveillance was undertaken among eight laboratories participating in DEVANI and six laboratories not participating in DEVANI from 13 countries in order to assess their current microbiological procedures for GBS screening, diagnosis, and typing. GBS strains from three EQA distributions were characterized using molecular and serological methods based on GBS capsular polysaccharide typing. Participants were asked to test the first distribution using their current serotyping and genotyping methods. The Strep-B-Latex agglutination method was the most widely used method, with a typeability value of >90%. A multiplex PCR assay for GBS capsular gene typing was also used by 2 of 14 centers, which achieved a typeability value of 93%; this assay detected only 9 of 10 GBS capsular polysaccharide genes. From the second and third EQA studies, standardized protocols were prepared for serological and molecular typing of GBS strains based on the Strep-B-Latex agglutination method and a novel multiplex PCR assay that detected all 10 GBS capsular types (Ia to IX). These standardized protocols are being used by many European laboratories, and as the use of these methods increases, it is imperative to continuously improve and assess laboratory performance and offer training to any laboratories that have technical difficulties.
Transmission of Methicillin-Resistant Staphylococcus aureus between Human and Hamster
Authors: Ferreira Jorge Pinto , Fowler Vance G. , Correa Maria T. , Lyman Roberta , Ruffin Felicia , Anderson Kevin L. 
Published: February 2011

ABSTRACT

Transmission of methicillin-resistant
Staphylococcus aureus
(MRSA) between humans and animals is increasingly recognized. We newly document that the transmission of MRSA between human and hamster is possible.
On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?
Authors: Datta Siddhartha A. K. , Temeselew Lakew G. , Crist Rachael M. , Soheilian Ferri , Kamata Anne , Mirro Jane , Harvin Demetria , Nagashima Kunio , Cachau Raul E. , Rein Alan 
Published: February 2011

ABSTRACT
Expression of a retroviral protein, Gag, in mammalian cells is sufficient for assembly of immature virus-like particles (VLPs). VLP assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We have investigated the role of SP1, a spacer between CA and NC in HIV-1 Gag, in VLP assembly. Mutational analysis showed that even subtle changes in the first 4 residues of SP1 destroy the ability of Gag to assemble correctly, frequently leading to formation of tubes or other misassembled structures rather than proper VLPs. We also studied the conformation of the CA-SP1 junction region in solution, using both molecular dynamics simulations and circular dichroism. Consonant with nuclear magnetic resonance (NMR) studies from other laboratories, we found that SP1 is nearly unstructured in aqueous solution but undergoes a concerted change to an α-helical conformation when the polarity of the environment is reduced by addition of dimethyl sulfoxide (DMSO), trifluoroethanol, or ethanol. Remarkably, such a coil-to-helix transition is also recapitulated in an aqueous medium at high peptide concentrations. The exquisite sensitivity of SP1 to mutational changes and its ability to undergo a concentration-dependent structural transition raise the possibility that SP1 could act as a molecular switch to prime HIV-1 Gag for VLP assembly. We suggest that changes in the local environment of SP1 when Gag oligomerizes on nucleic acid might trigger this switch.
Hepatitis C Patient-Derived Glycoproteins Exhibit Marked Differences in Susceptibility to Serum Neutralizing Antibodies: Genetic Subtype Defines Antigenic but Not Neutralization Serotype
Authors: Tarr Alexander W. , Urbanowicz Richard A. , Hamed Mohamed R. , Albecka Anna , McClure C. Patrick , Brown Richard J. P. , Irving William L. , Dubuisson Jean , Ball Jonathan K. 
Published: February 2011

ABSTRACT
Neutralizing antibodies have a role in controlling hepatitis C virus (HCV) infection. A successful vaccine will need to elicit potently neutralizing antibodies that are capable of preventing the infection of genetically diverse viral isolates. However, the specificity of the neutralizing antibody response in natural HCV infection still is poorly understood. To address this, we examined the reactivity of polyclonal antibodies isolated from chronic HCV infection to the diverse patient-isolated HCV envelope glycoproteins E1 and E2 (E1E2), and we also examined the potential to neutralize the entry of pseudoparticles bearing these diverse E1E2 proteins. The genetic type of the infection was found to determine the pattern of the antibody recognition of these E1E2 proteins, with the greatest reactivity to homologous E1E2 proteins. This relationship was strongest when the component of the antibody response directed only to linear epitopes was analyzed. In contrast, the neutralization serotype did not correlate with genotype. Instead, serum-derived antibodies displayed a range of neutralization breadth and potency, while different E1E2 glycoproteins displayed different sensitivities to neutralization, such that these could be divided broadly into neutralization-sensitive and -resistant phenotypes. An important additional observation was that entry mediated by some E1E2 proteins was enhanced in the presence of some of the polyclonal antibody fractions isolated during chronic infection. These data highlight the need to use diverse E1E2 isolates, which represent extremes of neutralization sensitivity, when screening antibodies for therapeutic potential and for testing antibodies generated following immunization as part of vaccine development.
The Epstein-Barr Virus BRRF1 Protein, Na, Induces Lytic Infection in a TRAF2- and p53-Dependent Manner
Authors: Hagemeier Stacy R. , Barlow Elizabeth A. , Kleman Ariel A. , Kenney Shannon C. 
Published: February 2011

ABSTRACT
The Epstein-Barr virus (EBV) BRRF1 lytic gene product (Na) is encoded within the same immediate-early region as the BZLF1 (Z) and BRLF1(R) gene products, but its role during EBV infection has not been well defined. We previously showed that Na cooperates with the R protein to induce lytic gene expression in latently infected EBV-positive 293 cells, and in some EBV-negative cell lines it can activate the Z promoter in reporter gene assays. Here we show that overexpression of Na alone is sufficient to induce lytic gene expression in several different latently infected epithelial cell lines (Hone-Akata, CNE2-Akata, and AGS-Akata), while knockdown of endogenous Na expression reduces lytic gene expression. Consistent with its ability to interact with tumor necrosis factor receptor-associated factor 2 (TRAF2) in a yeast two-hybrid assay, we demonstrate that Na interacts with TRAF2 in cells. Furthermore, we show that TRAF2 is required for Na induction of lytic gene expression, that Na induces Jun N-terminal protein kinase (JNK) activation in a TRAF2-dependent manner, and that a JNK inhibitor abolishes the ability of Na to disrupt viral latency. Additionally, we show that Na and the tumor suppressor protein p53 cooperate to induce lytic gene expression in epithelial cells (including the C666-1 nasopharyngeal carcinoma cell line), although Na does not appear to affect p53 function. Together these data suggest that Na plays an important role in regulating the switch between latent and lytic infection in epithelial cells and that this effect requires both the TRAF2 and p53 cellular proteins.
Unmasking the Active Helicase Conformation of Nonstructural Protein 3 from Hepatitis C Virus
Authors: Ding Steve C. , Kohlway Andrew S. , Pyle Anna M. 
Published: February 2011

ABSTRACT

The nonstructural protein 3 (NS3) helicase/protease is an important component of the hepatitis C virus (HCV) replication complex. We hypothesized that a specific β-strand tethers the C terminus of the helicase domain to the protease domain, thereby maintaining HCV NS3 in a compact conformation that differs from the extended conformations observed for other
Flaviviridae
NS3 enzymes. To test this hypothesis, we removed the β-strand and explored the structural and functional attributes of the truncated NS3 protein (NS3ΔC7). Limited proteolysis, hydrodynamic, and kinetic measurements indicate that NS3ΔC7 adopts an extended conformation that contrasts with the compact form of the wild-type (WT) protein. The extended conformation of NS3ΔC7 allows the protein to quickly form functional complexes with RNA unwinding substrates. We also show that the unwinding activity of NS3ΔC7 is independent of the substrate 3′-overhang length, implying that a monomeric form of the protein promotes efficient unwinding. Our findings indicate that an open, extended conformation of NS3 is required for helicase activity and represents the biologically relevant conformation of the protein during viral replication.
Genome Structure of Caulobacter Phage phiCb5
Authors: Kazaks Andris , Voronkova Tatyana , Rumnieks Janis , Dishlers Andris , Tars Kaspars 
Published: February 2011

ABSTRACT

The complete genome sequence of caulobacter phage phiCb5 has been determined, and four open reading frames (ORFs) have been identified and characterized. As for related phages, the ORFs code for maturation, coat, replicase, and lysis proteins, but unlike other
Leviviridae
members, the lysis protein gene of phiCb5 entirely overlaps with the replicase in a different reading frame. The lysis protein of phiCb5 is about two times longer than that of the distantly related MS2 phage and presumably contains two transmembrane helices. Analysis of the proposed genome secondary structure revealed a stable 5′ stem-loop, similar to other phages, and a substantially shorter 3′ untranslated region (UTR) structure with only three stem-loops.