bluuebunny/crossref_metadata_2025 huggingface dataset:
The Automatic Winding Device of a Mechanical Watch Movement and Its Application in Energy Harvesting
Authors: Xie Longhan , Menet Carmen G. , Ching Ho , Du Ruxu
Published: June 2009

Invented more than 200 years ago, the automatic winding device of mechanical watch movement is one of the most successful energy harvesting devices. It harvests the kinematical energy from body movements and drives the mechanical watch movement. According to literatures, however, few have studied its kinematics in detail. In this paper, the kinematical model of automatic winding device is developed. The model is a pendulum model with a set of gears that converts the bidirectional motion to unidirectional motion. The simulation shows that the efficiency of the device is about 46.3%. Experiment validations are also conducted, which confirm the simulation results. With some modifications, it can be used to drive various mobile electronic devices.
Analysis of Laminar Falling Film Condensation Over a Vertical Plate With an Accelerating Vapor Flow
Authors: Khaled A.-R. A. , Radhwan Abdulhaiy M. , Al-Muaikel S. A.
Published: June 2009

Laminar falling film condensations over a vertical plate with an accelerating vapor flow is analyzed in this work in the presence of condensate suction or slip effects at the plate surface. The following assumptions are made: (i) laminar condensate flow having constant properties, (ii) pure vapor with a uniform saturation temperature in the vapor region, and (iii) the shear stress at the liquid/vapor interface is negligible. The appropriate fundamental governing partial differential equations for the condensate and vapor flows (continuity, momentum, and energy equations) for the above case are identified, nondimensionalized, and transformed using nonsimilarity transformation. The transformed equations were solved using numerical, iterative, and implicit finite-difference methods. It is shown that the freestream striking angle has insignificant influence on the condensation mass and heat transfer rates, except when slip condition is present and at relatively small Grl/Re2 values. Moreover, it is shown that increasing the values of the dimensionless suction parameter (VS) results to an increase in dimensionless mass of condensate (Γ(L)/(μl Re)) and Nusselt number (Nu(L)/Re1/2). Thus, it results in an increase in condensation mass and heat transfer rates. Finally, it is found that the condensation and heat transfer rates increase as Jakob number, slip parameter, and saturation temperature increase. Finally, the results of this work not only enrich the literature of condensation but also provide additional methods for saving thermal energy.
Competitive Interactions Between Cells: Death, Growth, and Geography
Authors: Johnston Laura A.
Published: June 2009

Winner Takes All?

Competition between individual cells plays a role in normal animal development and cell homeostasis.
Johnston
(p.
1679
) reviews two situations of cell competition in
Drosophila
, one involving epithelial cells in the wing and another involving germline or somatic stem cells. “Loss” in cell competition is evidenced by the “weaker” cell's death or displacement. On the other hand, winners may engulf the loser or display enhanced proliferation. Competitive interactions allow cells to sense and eliminate poor-quality cells during development.
Innovating Education in Croatia
Authors: Primorac Dragan
Published: June 2009

Reforms that are raising the quality of IT in Croatian science and education aim to create a knowledge-based society.
Elevated CO
2
Enhances Otolith Growth in Young Fish
Authors: Checkley David M. , Dickson Andrew G. , Takahashi Motomitsu , Radich J. Adam , Eisenkolb Nadine , Asch Rebecca
Published: June 2009

Acidification of the oceans may have unexpected effects on the development of bony structures in fish larvae.
Growth Factors, Matrices, and Forces Combine and Control Stem Cells
Authors: Discher Dennis E. , Mooney David J. , Zandstra Peter W.
Published: June 2009

Stem cell fate is influenced by a number of factors and interactions that require robust control for safe and effective regeneration of functional tissue. Coordinated interactions with soluble factors, other cells, and extracellular matrices define a local biochemical and mechanical niche with complex and dynamic regulation that stem cells sense. Decellularized tissue matrices and synthetic polymer niches are being used in the clinic, and they are also beginning to clarify fundamental aspects of how stem cells contribute to homeostasis and repair, for example, at sites of fibrosis. Multifaceted technologies are increasingly required to produce and interrogate cells ex vivo, to build predictive models, and, ultimately, to enhance stem cell integration in vivo for therapeutic benefit.
Mitochondrial STAT3 Supports Ras-Dependent Oncogenic Transformation
Authors: Gough Daniel J. , Corlett Alicia , Schlessinger Karni , Wegrzyn Joanna , Larner Andrew C. , Levy David E.
Published: June 2009

Ras, STAT3, and Transformation

The STAT (signal transducer and activator of transcription) proteins are activated in response to receptor stimulation and act in the nucleus to regulate gene expression.

Gough
et al.

(p.
1713
) found that STAT3 functioned in transformation of cells by the oncogene Ras. However, this activity was maintained in mutants of STAT that fail to activate transcription. Instead, the active STAT3 appeared to be associated with mitochondria. Furthermore, modified STAT3 targeted to the mitochondria promoted transformation by Ras, and mitochondrial function was disrupted in Ras-transformed cells lacking STAT3. Such transformation-specific effects of STAT3 could be a useful target in developing anticancer therapies.
The Increasing Complexity of the Cancer Stem Cell Paradigm
Authors: Rosen Jeffrey M. , Jordan Craig T.
Published: June 2009

The investigation and study of cancer stem cells (CSCs) have received enormous attention over the past 5 to 10 years but remain topics of considerable controversy. Opinions about the validity of the CSC hypothesis, the biological properties of CSCs, and the relevance of CSCs to cancer therapy differ widely. In the following commentary, we discuss the nature of the debate, the parameters by which CSCs can or cannot be defined, and the identification of new potential therapeutic targets elucidated by considering cancer as a problem in stem cell biology.
Synthetic Heterochromatin Bypasses RNAi and Centromeric Repeats to Establish Functional Centromeres
Authors: Kagansky Alexander , Folco Hernan Diego , Almeida Ricardo , Pidoux Alison L. , Boukaba Abdelhalim , Simmer Femke , Urano Takeshi , Hamilton Georgina L. , Allshire Robin C.
Published: June 2009

Synthetic Centromere

Every eukaryotic chromosome must have a centromere where the cell division machinery latches onto each chromosome pair to ensure an even apportioning of the genetic material between daughter cells. The characteristic (but not conserved) repeat sequences associated with most centromeres are thought to be required to induce an RNA interference (RNAi) response and thereby promote the formation of heterochromatin, needed for centromere function.

Kagansky
et al.

(p.
1716
) now show in fission yeast that these outer repeat sequences can be replaced in their entirety by very short sequences that recruit an enzyme, Clr4, which promotes the formation of heterochromatin in the absence of RNAi. Thus, flanking heterochromatin, regardless of its derivation, is all that is required for the formation of a functional centromere.
Building an Open Cloud
Authors: Nelson Michael R.
Published: June 2009

As the Internet is increasingly used not only for communication but also for computing, issues of protocol, security, and openness need to be addressed.
Dynamic Signaling Network for the Specification of Embryonic Pancreas and Liver Progenitors
Authors: Wandzioch Ewa , Zaret Kenneth S.
Published: June 2009

Integrating Organ Induction

During animal development, multiple signaling pathways specify the induction of organ progenitors such as those in the pancreas and liver.
Wandzioch and Zaret
(p.
1707
) investigated how three signaling pathways converge on the earliest genes specifying these organs. Within hours, multiple changes were observed in the inductive network with different signals operating in parallel. The findings may help to explain the incomplete programming seen in various stem cell differentiation protocols.
Rate Control and Reaction Engineering
Authors: Nørskov J. K. , Bligaard T. , Kleis J.
Published: June 2009

A concept for evaluating the relative importance of steps in complex reactions may guide the development of better catalysts.
The NIH Draft Guidelines on Human Stem Cell Research
Authors: Majumder Mary A. , Cohen Cynthia B.
Published: June 2009

New guidelines have positive aspects, but challenges remain in relation to previously approved stem cell lines, informed consent, oversight, and research embryos.
Phase Transition in a Cell
Authors: Goff Loïc Le , Lecuit Thomas
Published: June 2009

The polarized distribution of P granules in a worm embryo is achieved, not by movement of the granules, but by a condensation process.
Auxin at the Evo-Devo Intersection
Authors: Friedman William E.
Published: June 2009

The female gametophyte of flowering plants may have evolved through iteration of a modular structure and a gradient of the hormone auxin.
Out With the Old, In With the New?
Authors: Pedersen Roger
Published: June 2009

President Obama's recent announcement of a new policy for Federal Funding of stem cell research changes the landscape for this important area of biomedicine in the United States. His Executive Order and the subsequent draft guidelines of the National Institutes of Health (NIH) remove a major existing limitation on federal support for research using pluripotent human embryonic stem cells (hESCs). These stem cells can specialize into all body cell types. Thus, in principle they can be used to produce a wide range of tissues for therapeutic use. In addition, their study will very likely generate new insights into human early developmental mechanisms. The new Obama policy promises to speed research by making many new hESC lines eligible for federally funded studies. But the draft NIH guidelines accompanying the new policy need revision, because their donor consent rules for embryos used to generate hESCs would make some—and perhaps even all—of the previously approved hESCs ineligible for further federal funding. This would needlessly hinder progress in the stem cell field, and reasonable exceptions should be made to correct this unintended outcome.
ITER Gets the Nod for Slower, Step-by-Step Approach
Authors: Clery Daniel
Published: June 2009

The managers of the ITER fusion project are still scrambling to draw up a final design, schedule, and cost estimate for the massive reactor. But the international partners behind the effort agreed last week to build the project in stages so engineers can make corrections if something goes awry early on.
Biodiversity Databases Spread, Prompting Unification Call
Authors: Thomas Claire
Published: June 2009

Scientists increasingly recognize the value of collaborative, open-access data sharing for understanding the world. But there's still a wide gap between wanting to share and figuring out how to do it right, discovered those who attended an international meeting on biodiversity this month.
The Brain Collector
Authors: Miller Greg
Published: June 2009

Jacopo Annese plans to create an open-access digital brain library—starting with the most famous amnesic patient of all time.
Autoimmune Type 1 Diabetes Genetic Susceptibility Encoded by Human Leukocyte Antigen DRB1 and DQB1 Genes in Tunisia
Authors: Stayoussef Mouna , Benmansour Jihen , Al-Irhayim Abdul-Qader , Said Hichem B. , Rayana Chiheb B. , Mahjoub Touhami , Almawi Wassim Y.
Published: June 2009

Human leukocyte antigen (HLA) class II genes contribute to the genetic susceptibility to type 1 diabetes (T1D), and susceptible alleles and haplotypes were implicated in the pathogenesis of T1D. This study investigated the heterogeneity in HLA class II haplotype distribution among Tunisian patients with T1D. This was a retrospective case control study done in Monastir in central Tunisia. The subjects comprised 88 T1D patients and 112 healthy controls. HLA-DRB1 and -DQB1 genotyping was done by PCR-sequence-specific priming. Significant DRB1 and DQB1 allelic differences were seen between T1D patients and controls; these differences comprised
DRB1*030101
and
DQB1*0302
, which were higher in T1D patients than in control subjects, and
DRB1*070101
,
DRB1*110101
,
DQB1*030101
, and
DQB1*060101
, which were lower in T1D patients than in control subjects. In addition, the frequencies of
DRB1*030101-DQB1*0201
and
DRB1*040101-DQB1*0302
were higher in T1D patients than in control subjects, and the frequencies of
DRB1*070101-DQB1*0201
and
DRB1*110101-DQB1*030101
haplotypes were lower in T1D patients than in control subjects. Multiple logistic regression analysis revealed the positive association of
DRB1*030101-DQB1*0201
and
DRB1*040101-DQB1*0302
and the negative association of only
DRB1*070101-DQB1*0201
haplotypes with T1D. Furthermore, a significantly increased prevalence of
DRB1*030101-DQB1*0201
homozygotes was seen for T1D subjects than for control subjects. Our results confirm the association of specific HLA-DR and -DQ alleles and haplotypes with T1D in Tunisians. The identification of similar and unique haplotypes in Tunisians compared to other Caucasians highlights the need for evaluating the contribution of HLA class II to the genetic susceptibility to T1D with regard to haplotype usage and also to ethnic origin and racial background.
Immunogenicity of Novel DosR Regulon-Encoded Candidate Antigens of
Mycobacterium tuberculosis
in Three High-Burden Populations in Africa
Authors: Black Gillian F. , Thiel Bonnie A. , Ota Martin O. , Parida Shreemanta K. , Adegbola Richard , Boom W. Henry , Dockrell Hazel M. , Franken Kees L. M. C. , Friggen Annemiek H. , Hill Philip C. , Klein Michel R. , Lalor Maeve K. , Mayanja Harriet , Schoolnik Gary , Stanley Kim , Weldingh Karin , Kaufmann Stefan H. E. , Walzl Gerhard , Ottenhoff Tom H. M.
Published: June 2009

Increasing knowledge about DosR regulon-encoded proteins has led us to produce novel
Mycobacterium tuberculosis
antigens for immunogenicity testing in human populations in three countries in Africa to which tuberculosis (TB) is endemic. A total of 131 tuberculin skin test-positive and/or ESAT-6/CFP10-positive, human immunodeficiency virus-negative adult household contacts of active pulmonary TB cases from South Africa (
n
= 56), The Gambia (
n
= 26), and Uganda (
n
= 49) were tested for gamma interferon responses to 7 classical and 51 DosR regulon-encoded
M. tuberculosis
recombinant protein antigens. ESAT-6/CFP10 fusion protein evoked responses in >75% of study participants in all three countries. Of the DosR regulon-encoded antigens tested, Rv1733c was the most commonly recognized by participants from both South Africa and Uganda and the third most commonly recognized antigen in The Gambia. The four most frequently recognized DosR regulon-encoded antigens in Uganda (Rv1733c, Rv0081, Rv1735c, and Rv1737c) included the three most immunogenic antigens in South Africa. In contrast, Rv3131 induced the highest percentage of responders in Gambian contacts (38%), compared to only 3.4% of Ugandan contacts and no South African contacts. Appreciable percentages of TB contacts with a high likelihood of latent
M. tuberculosis
infection responded to several novel DosR regulon-encoded
M. tuberculosis
proteins. In addition to significant similarities in antigen recognition profiles between the three African population groups, there were also disparities, which may stem from genetic differences between both pathogen and host populations. Our findings have implications for the selection of potential TB vaccine candidates and for determining biosignatures of latent
M. tuberculosis
infection, active TB disease, and protective immunity.
Phase I Safety and Immunogenicity Study of a Candidate Meningococcal Disease Vaccine Based on
Neisseria lactamica
Outer Membrane Vesicles
Authors: Gorringe Andrew R. , Taylor Stephen , Brookes Charlotte , Matheson Mary , Finney Michelle , Kerr Moyra , Hudson Michael , Findlow Jamie , Borrow Ray , Andrews Nick , Kafatos George , Evans Cariad M. , Read Robert C.
Published: June 2009

Natural immunity to meningococcal disease in young children is associated epidemiologically with carriage of commensal
Neisseria
species, including
Neisseria lactamica
. We have previously demonstrated that outer membrane vesicles (OMVs) from
N. lactamica
provide protection against lethal challenge in a mouse model of meningococcal septicemia. We evaluated the safety and immunogenicity of an
N. lactamica
OMV vaccine in a phase I placebo-controlled, double-blinded clinical trial. Ninety-seven healthy young adult male volunteers were randomized to receive three doses of either an OMV vaccine or an Alhydrogel control. Subsequently, some subjects who had received the OMV vaccine also received a fourth dose of OMV vaccine, 6 months after the third dose. Injection site reactions were more frequent in the OMV-receiving group, but all reactions were mild or moderate in intensity. The OMV vaccine was immunogenic, eliciting rises in titers of immunoglobulin G (IgG) against the vaccine OMVs, together with a significant booster response, as determined by an enzyme-linked immunosorbent assay. Additionally, the vaccine induced modest cross-reactive immunity to six diverse strains of serogroup B
Neisseria meningitidis
, including IgG against meningococcal OMVs, serum bactericidal antibodies, and opsonophagocytic activity. The percentages of subjects showing ≥4-fold rises in bactericidal antibody titer obtained were similar to those previously reported for the Norwegian meningococcal OMV vaccine against the same heterologous meningococcal strain panel. In conclusion, this
N. lactamica
OMV vaccine is safe and induces a weak but broad humoral immune response to
N. meningitidis
.
Discriminating Foot-and-Mouth Disease Virus-Infected and Vaccinated Animals by Use of β-Galactosidase Allosteric Biosensors
Authors: Sánchez-Aparicio M. Teresa , Rosas María Flora , Ferraz Rosa Maria , Delgui Laura , Veloso Juan J. , Blanco Esther , Villaverde Antonio , Sobrino Francisco
Published: June 2009

Recombinant β-galactosidases accommodating one or two different peptides from the foot-and-mouth disease virus (FMDV) nonstructural protein 3B per enzyme monomer showed a drastic enzymatic activity reduction, which mainly affected proteins with double insertions. Recombinant β-galactosidases were enzymatically reactivated by 3B-specific murine monoclonal and rabbit polyclonal antibodies. Interestingly, these recombinant β-galactosidases, particularly those including one copy of each of the two 3B sequences, were efficiently reactivated by sera from infected pigs. We found reaction conditions that allowed differentiation between sera of FMDV-infected pigs, cattle, and sheep and those of naïve and conventionally vaccinated animals. These FMDV infection-specific biosensors can provide an effective and versatile alternative for the serological distinction of FMDV-infected animals.
Characterization of Monoclonal Antibodies to Junin Virus Nucleocapsid Protein and Application to the Diagnosis of Hemorrhagic Fever Caused by South American Arenaviruses
Authors: Nakauchi Mina , Fukushi Shuetsu , Saijo Masayuki , Mizutani Tetsuya , Ure Agustín E. , Romanowski Victor , Kurane Ichiro , Morikawa Shigeru
Published: June 2009

Junin virus (JUNV), Machupo virus, Guanarito virus, Sabia virus, and Chapare virus are members of New World arenavirus clade B and are the etiological agents of viral hemorrhagic fevers that occur in South America. In this study, we produced three monoclonal antibodies (MAbs) to the recombinant nucleocapsid protein of JUNV, designated C6-9, C11-12, and E4-2. The specificity of these MAbs was examined by enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay, and an epitope-mapping method. Using these MAbs, we developed antigen (Ag) capture ELISA systems. We showed that by using MAb C6-9, JUNV Ag was specifically detected. On the other hand, by using MAb C11-12 or E-4-2, the Ags of all human pathogenic South American arenaviruses were detected. The combined use of these Ag capture ELISA systems in the present study may be useful for the diagnosis of acute-phase viral hemorrhagic fever due to infection by a South American arenavirus.
Age-Dependent Seroprevalence of Toscana Virus in Central Italy and Correlation with the Clinical Profile
Authors: Terrosi C. , Olivieri R. , Bianco C. , Cellesi C. , Cusi M. G.
Published: June 2009

In order to estimate the antibody prevalence rates for Toscana virus (TOSV) among children and adults, we evaluated the seroprevalence of TOSV in a population (
n
= 2,737) living in Tuscany during the period of 1999 to 2006. The seroprevalence rate was 19.8% in adults and 5.8% in children, showing an age-dependent increase in TOSV-specific immunity. Meningitis due to TOSV infection was more frequent in adults than in children.
Leishmania
OligoC-TesT as a Simple, Rapid, and Standardized Tool for Molecular Diagnosis of Cutaneous Leishmaniasis in Peru
Authors: Espinosa Diego , Boggild Andrea K. , Deborggraeve Stijn , Laurent Thierry , Valencia Cristian , Pacheco Rosa , Miranda-Verástegui César , Llanos-Cuentas Alejandro , Leclipteux Thierry , Dujardin Jean-Claude , Büscher Philippe , Arévalo Jorge
Published: June 2009

Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of
Leishmania
was developed. The
Leishmania
OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified
Leishmania
DNA. In this study, we estimated the diagnostic accuracy of the
Leishmania
OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the
Leishmania
OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (
P
= 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (
P
= 0.317). In addition, the
Leishmania
OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the
Leishmania
OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru.
Emergence of European Avian Influenza Virus-Like H1N1 Swine Influenza A Viruses in China
Authors: Liu Jinhua , Bi Yuhai , Qin Kun , Fu Guanghua , Yang Jun , Peng Jinshan , Ma Guangpeng , Liu Qinfang , Pu Juan , Tian Fulin
Published: June 2009

During swine influenza surveillance from 2007 to 2008, 10 H1N1 viruses were isolated and analyzed for their antigenic and phylogenetic properties. Our study revealed the emergence of avian-origin European H1N1 swine influenza virus in China, which highlights the necessity of swine influenza surveillance for potential pandemic preparedness.
Epidemiology and Phylogenetic Analysis of Crimean-Congo Hemorrhagic Fever Viruses in Xinjiang, China
Authors: Sun Surong , Dai Xiang , Aishan Muhetaer , Wang Xinhui , Meng Weiwei , Feng Conghui , Zhang Fuchun , Hang Changshou , Hu Zhihong , Zhang Yujiang
Published: June 2009

In 2004 and 2005, an epidemiological survey of Crimean-Congo hemorrhagic fever virus (CCHFV) was conducted in Xinjiang, China. A total of 5,629 serum samples of human and livestock were collected and tested for the CCHFV antibody, and 17,319 ticks were collected for viral identification. Reverse passive hemagglutination inhibition assays showed that the average prevalence of CCHFV antibody was 1.7% for the humans and 12.7% for the livestock. A relatively high antibody prevalence, ranging from 19.1% to 23.4%, was found in the livestock of the northwest, southwest, and northeast parts of the Tarim Basin. When the ticks were pooled to inoculate suckling mice, followed by reverse transcription-PCR (RT-PCR) to detect CCHFV RNA, the average RT-PCR-positive rates for
Hyalomma asiaticum kozlovi
and
H. asiaticum asiaticum
were 12.9% and 2.6%, respectively. A significant correlation was found between the antibody prevalence in the livestock and the CCHFV prevalence in
H. asiaticum
of the same geographic region. No CCHFV RNA was detected in
Dermacentor nivenus
,
Rhipicephalus turanius
, or
Rhipicephalus sanguineus.
A total of 27 partial S segments of CCHFVs were sequenced and used for phylogeny analysis. All but one Chinese isolate grouped into the Asia 1 clade, which contains the strains from Xinjiang and Uzbekistan, while the other strain, Fub90009, grouped with strains from the Middle East.
Unexpectedly High Proportion of Ancestral Manu Genotype
Mycobacterium tuberculosis
Strains Cultured from Tuberculosis Patients in Egypt
Authors: Helal Zeinab H. , El-Din Ashour Mohamed Seif , Eissa Somaia A. , Abd-Elatef Ghanem , Zozio Thierry , Babapoor Sankhiros , Rastogi Nalin , Khan Mazhar I.
Published: June 2009

Tuberculosis is one of the important public health problems in Egypt. However, limited information on the
Mycobacterium tuberculosis
genotypes circulating in Egypt is available. A total of 151
M. tuberculosis
strains were characterized by spoligotyping. The results revealed that 74.8% of
M. tuberculosis
isolates grouped into 13 different clusters, while 25.2% had unique spoligotype patterns. Comparison with an international spoligotyping database (the SITVIT2 database) showed that types SIT53 (T1 variant) and SIT54 (Manu2 variant) were the most common types between cluster groups. In addition, new shared types SIT2977, SIT2978, and SIT2979 were observed. The results identified for the first time an unusually high proportion of ancestral Manu strains of
M. tuberculosis
from patients in Egypt. The percentage of the Manu clade in this study (27.15%) was significantly higher than its overall representation of 0.4% in the SITVIT2 database. We show that in Egypt tuberculosis is caused by a predominant
M. tuberculosis
genotype belonging to the ancestral Manu lineage which could be a missing link in the split between ancestral and modern tubercle bacilli during the evolution of
M. tuberculosis
.
Comparison of Typing Results Obtained for Methicillin-Resistant
Staphylococcus aureus
Isolates with the DiversiLab System and Pulsed-Field Gel Electrophoresis
Authors: Tenover Fred C. , Gay Emily A. , Frye Stacie , Eells Samantha J. , Healy Mimi , McGowan John E.
Published: June 2009

We compared the results of typing methicillin-resistant
Staphylococcus aureus
(MRSA) isolates using the DiversiLab system (DL) to the results obtained using pulsed-field gel electrophoresis (PFGE). One hundred five MRSA isolates of PFGE types USA100 to USA1100 and the Brazilian clone, from the Centers for Disease Control and Prevention (CDC) and Project ICARE strain collections, were typed using DL. In addition, four unique sets of MRSA isolates from purported MRSA outbreaks that had been previously typed by DL, each consisting of six isolates (where five isolates were classified as indistinguishable by DL and one was an unrelated DL type) were typed by PFGE. DL separated the 105 MRSA isolates of known USA types into 11 clusters and six unique banding patterns. DL grouped most of the USA100, USA200, and USA1100 isolates into unique clusters. Multilocus sequence type 8 isolates (i.e., USA300 and USA500) often clustered together at >95% similarity in DL dendrograms. Nevertheless, USA300 and USA500 DL patterns could be distinguished using the pattern overlay function of the DL software. Among the hospital outbreak clusters, PFGE and DL identified the same “unrelated” organism in three of four sets. However, PFGE showed more pattern diversity than did DL, suggesting that two of the sets were less likely to represent true outbreaks. In summary, DL is useful for screening MRSA isolates to rule out potential outbreaks of MRSA in hospitals, but PFGE provides better discrimination of potential outbreak strains and is more useful for confirming strain relatedness and specific USA types.
Proteomic Identification of OprL as a Seromarker for Initial Diagnosis ofPseudomonas aeruginosaInfection of Patients with Cystic Fibrosis
Authors: Rao Aparna R. , Laxova Anita , Farrell Philip M. , Barbieri Joseph T.
Published: June 2009

Identification of new immunogenic antigens that diagnose initialPseudomonas aeruginosainfections in patients with cystic fibrosis (CF) alone or as an adjunct to microbiology is needed. In the present study, a proteomic analysis was performed to obtain a global assessment of the host immune response during the initialP. aeruginosainfection of patients with CF. Matrix-assisted laser desorption ionization-time of flight mass spectrometry was used to identify outer membrane protein L (OprL), a non-type III secretion system (TTSS) protein, as an early immunogenic protein during the initialP. aeruginosainfection of patients with CF. Longitudinal Western blot analysis of sera from 12 of 14 patients with CF detected antibodies to OprL during the initialP. aeruginosainfection. In addition, also detected were antibodies to ExoS, ExoU, or ExoS and ExoU, the latter indicating sequentialP. aeruginosainfections during initial infections. Detection of serum reactivity to OprL, along with proteins of the TTSS, and in conjunction with microbiology may diagnose initialP. aeruginosainfections in patients with CF.
Distribution of
lag-1
Alleles and Sequence-Based Types among
Legionella pneumophila
Serogroup 1 Clinical and Environmental Isolates in the United States
Authors: Kozak Natalia A. , Benson Robert F. , Brown Ellen , Alexander Nicole T. , Taylor Thomas H. , Shelton Brian G. , Fields Barry S.
Published: June 2009

Approximately 84% of legionellosis cases are due to
Legionella pneumophila
serogroup 1. Moreover, a majority of
L. pneumophila
serogroup 1 clinical isolates react positively with monoclonal antibody 2 (MAb2) of the international standard panel. Over 94% of the legionellosis outbreaks investigated by the Centers for Disease Control and Prevention are due to this subset of
L. pneumophila
serogroup 1. To date, there is no complete explanation for the enhanced ability of these strains to cause disease. To better characterize these organisms, we subtyped 100 clinical
L. pneumophila
serogroup 1 isolates and 50 environmental
L. pneumophila
serogroup 1 isolates from the United States by (i) reactivity with MAb2, (ii) presence of a
lag-1
gene required for the MAb2 epitope, and (iii) sequence-based typing analysis. Our results showed that the MAb2 epitope and
lag-1
gene are overrepresented in clinical
L. pneumophila
serogroup 1 isolates. MAb2 recognized 75% of clinical isolates but only 6% of environmental isolates. Similarly, 75% of clinical isolates but only 8% of environmental isolates harbored
lag-1
. We identified three distinct
lag-1
alleles, referred to as Philadelphia, Arizona, and Lens alleles, among 79 isolates carrying this gene. The Arizona allele is described for the first time in this study. We identified 59 different sequence types (STs), and 34 STs (58%) were unique to the United States. Our results support the hypothesis that a select group of STs may have an enhanced ability to cause legionellosis. Combining sequence typing and
lag-1
analysis shows that STs tend to associate with a single
lag-1
allele type, suggesting a hierarchy of virulence genotypes. Further analysis of ST and
lag-1
profiles may identify genotypes of
L. pneumophila
serogroup 1 that warrant immediate intervention.
A New World Primate Deficient in Tetherin-Mediated Restriction of Human Immunodeficiency Virus Type 1
Authors: Wong Swee Kee , Connole Michelle , Sullivan JoAnne S. , Choe Hyeryun , Carville Angela , Farzan Michael
Published: June 2009

Human immunodeficiency virus type 1 (HIV-1) does not replicate in primary cells of New World primates. To better understand this restriction, we expressed owl monkey (
Aotus nancymaae
) CD4 and CXCR4 in the owl monkey kidney cell line, OMK. An HIV-1 variant modified to evade the owl monkey restriction factor TRIM-cyp replicated efficiently in these cells but could not replicate in primary
A. nancymaae
CD4-positive T cells. To understand this difference, we examined APOBEC3G and tetherin orthologs from OMK cells and primary
A. nancymaae
cells. We observed that OMK cells expressed substantially lower levels of APOBEC3G than did
A. nancymaae
cells.
A. nancymaae
, but not marmoset (
Callithrix jacchus
), APOBEC3G was partially downregulated by HIV-1 vif and reduced but did not abolish HIV-1 replication when stably expressed in OMK cells. The functional difference between
A. nancymaae
and marmoset APOBEC3Gs mapped to residue 128, previously shown to distinguish African green monkey from human APOBEC3G. We also characterized tetherin orthologs from OMK and
A. nancymaae
cells. The
A. nancymaae
tetherin ortholog, but not OMK tetherin, prevented HIV-1 release. Alteration of threonine 181 of OMK tetherin rescued its function and its efficient N glycosylation. All alleles of
A
otus lemurinus griseimembra
examined, but none of
A. nancymaae
or
A
otus vociferans
, encoded this nonfunctional tetherin ortholog. Our data indicate that HIV-1 replication in owl monkeys is not restricted at entry but can be limited by APOBEC3G and tetherin. Further,
A. lemurinus griseimembra
does not restrict HIV-1 replication via tetherin, a property likely useful for the study of tetherin-restricted viruses.
Human Immunodeficiency Virus Type 1 Escapes from Interleukin-2-Producing CD4
+
T-Cell Responses without High-Frequency Fixation of Mutations
Authors: Jones R. Brad , Yue Feng-Yun , Gu Xiao Xiao Jenny , Hunter Diana V. , Mujib Shariq , Gyenes Gabor , Mason Rosemarie D. , Mohamed Ruqaya , MacDonald Kelly S. , Kovacs Colin , Ostrowski Mario A.
Published: June 2009

The presence of interleukin-2 (IL-2)-producing human immunodeficiency virus type 1 (HIV-1)-specific CD4
+
T-cell responses has been associated with the immunological control of HIV-1 replication; however, the causal relationship between these factors remains unclear. Here we show that IL-2-producing HIV-1-specific CD4
+
T cells can be cloned from acutely HIV-1-infected individuals. Despite the early presence of these cells, each of the individuals in the present study exhibited progressive disease, with one individual showing rapid progression. In this rapid progressor, three IL-2-producing HIV-1 Gag-specific CD4
+
T-cell responses were identified and mapped to the following optimal epitopes: HIVWASRELER, REPRGSDIAGT, and FRDYVDRFYKT. Responses to these epitopes in peripheral blood mononuclear cells were monitored longitudinally to >1 year postinfection, and contemporaneous circulating plasma viruses were sequenced. A variant of the FRDYVDRFYKT epitope sequence, FRDYVDQFYKT, was observed in 1/21 plasma viruses sequenced at 5 months postinfection and 1/10 viruses at 7 months postinfection. This variant failed to stimulate the corresponding CD4
+
T-cell clone and thus constitutes an escape mutant. Responses to each of the three Gag epitopes were rapidly lost, and this loss was accompanied by a loss of antigen-specific cells in the periphery as measured by using an FRDYVDRFYKT-presenting major histocompatibility complex class II tetramer. Highly active antiretroviral therapy was associated with the reemergence of FRDYVDRFYKT-specific cells by tetramer. Thus, our data support that IL-2-producing HIV-1-specific CD4
+
T-cell responses can exert immune pressure during early HIV-1 infection but that the inability of these responses to enforce enduring control of viral replication is related to the deletion and/or dysfunction of HIV-1-specific CD4
+
T cells rather than to the fixation of escape mutations at high frequencies.
Bluetongue Virus VP6 Acts Early in the Replication Cycle and Can Form the Basis of Chimeric Virus Formation
Authors: Matsuo Eiko , Roy Polly
Published: June 2009

A minor core protein, VP6, of bluetongue virus (BTV) possesses nucleoside triphosphatase, RNA binding, and helicase activities. Although the enzymatic functions of VP6 have been documented in vitro using purified protein, its definitive role in BTV replication remains unclear. In this study, using a recently developed T7 transcript-based reverse genetics system for BTV, we examined the importance of VP6 in virus replication. We show that VP6 is active early in replication, consistent with a role as part of the transcriptase or packaging complex, and that its action can be provided intransby a newly developed complementary cell line. Furthermore, the genomic segment encoding VP6 was mutated to reveal thecis-acting sequences required for replication or packaging, which subsequently enabled the construction of a chimeric BTV expressing enhanced green fluorescent protein. These data confirm that one of the 10 genome segments of BTV can be replaced with a chimeric RNA containing the essential packaging and replication signals of BTV and the coding sequence of a foreign gene.
A Novel Genotype H9N2 Influenza Virus Possessing Human H5N1 Internal Genomes Has Been Circulating in Poultry in Eastern China since 1998
Authors: Zhang Pinghu , Tang Yinghua , Liu Xiaowen , Liu Wenbo , Zhang Xiaorong , Liu Hongqi , Peng Daxin , Gao Song , Wu Yantao , Zhang Luyong , Lu Shan , Liu Xiufan
Published: June 2009

Many novel reassortant influenza viruses of the H9N2 genotype have emerged in aquatic birds in southern China since their initial isolation in this region in 1994. However, the genesis and evolution of H9N2 viruses in poultry in eastern China have not been investigated systematically. In the current study, H9N2 influenza viruses isolated from poultry in eastern China during the past 10 years were characterized genetically and antigenically. Phylogenetic analysis revealed that these H9N2 viruses have undergone extensive reassortment to generate multiple novel genotypes, including four genotypes (J, F, K, and L) that have never been recognized before. The major H9N2 influenza viruses represented by A/Chicken/Beijing/1/1994 (Ck/BJ/1/94)-like viruses circulating in poultry in eastern China before 1998 have been gradually replaced by A/Chicken/Shanghai/F/1998 (Ck/SH/F/98)-like viruses, which have a genotype different from that of viruses isolated in southern China. The similarity of the internal genes of these H9N2 viruses to those of the H5N1 influenza viruses isolated from 2001 onwards suggests that the Ck/SH/F/98-like virus may have been the donor of internal genes of human and poultry H5N1 influenza viruses circulating in Eurasia. Experimental studies showed that some of these H9N2 viruses could be efficiently transmitted by the respiratory tract in chicken flocks. Our study provides new insight into the genesis and evolution of H9N2 influenza viruses and supports the notion that some of these viruses may have been the donors of internal genes found in H5N1 viruses.
Previously Unrecognized Amino Acid Substitutions in the Hemagglutinin and Fusion Proteins of Measles Virus Modulate Cell-Cell Fusion, Hemadsorption, Virus Growth, and Penetration Rate
Authors: Okada Hiromi , Itoh Masae , Nagata Kyosuke , Takeuchi Kaoru
Published: June 2009

Wild-type measles virus (MV) isolated in B95a cells could be adapted to Vero cells after several blind passages. In this study, we have determined the complete nucleotide sequences of the genomes of the wild type (T11wild) and its Vero cell-adapted (T11Ve-23) MV strain and identified amino acid substitutions R516G, E271K, D439E and G464W (D439E/G464W), N481Y/H495R, and Y187H/L204F in the nucleocapsid, V, fusion (F), hemagglutinin (H), and large proteins, respectively. Expression of mutated H and F proteins from cDNA revealed that the H495R substitution, in addition to N481Y, in the H protein was necessary for the wild-type H protein to use CD46 efficiently as a receptor and that the G464W substitution in the F protein was important for enhanced cell-cell fusion. Recombinant wild-type MV strains harboring the F protein with the mutations D439E/G464W [F(D439E/G464W)] and/or H(N481Y/H495R) protein revealed that both mutated F and H proteins were required for efficient syncytium formation and virus growth in Vero cells. Interestingly, a recombinant wild-type MV strain harboring the H(N481Y/H495R) protein penetrated slowly into Vero cells, while a recombinant wild-type MV strain harboring both the F(D439E/G464W) and H(N481Y/H495R) proteins penetrated efficiently into Vero cells, indicating that the F(D439E/G464W) protein compensates for the inefficient penetration of a wild-type MV strain harboring the H(N481Y/H495R) protein. Thus, the F and H proteins synergistically function to ensure efficient wild-type MV growth in Vero cells.
Inhibition of Intrahepatic Gamma Interferon Production by Hepatitis C Virus Nonstructural Protein 5A in Transgenic Mice
Authors: Kanda Tatsuo , Steele Robert , Ray Ranjit , Ray Ratna B.
Published: June 2009

Hepatitis C virus (HCV) utilizes strategies to suppress or evade the host immune response for establishment of persistent infection. We have shown previously that HCV nonstructural protein 5A (NS5A) impairs tumor necrosis factor alpha (TNF-α)-mediated apoptosis. In this study, we have examined the immunomodulatory role of HCV NS5A protein in transgenic mouse (NS5A-Tg) liver when mice were challenged with an unrelated hepatotropic adenovirus as a nonspecific stimulus. Hepatotropic adenovirus was introduced intravenously into NS5A-Tg mice and control mice, and virus clearance from liver was compared over a time course of 3 weeks. The differential mRNA expression levels of 84 cytokine-related genes, signal pathway molecules, transcription factors, and cell surface molecules were determined using real-time reverse transcription-PCR array. NS5A-Tg mice failed to clear adenovirus from liver up to 3 weeks postinfection while control mice cleared virus within 1 to 2 weeks. Subsequent study revealed that gamma interferon (IFN-γ) expression is inhibited at both the mRNA and protein levels in NS5A-Tg mice, and an inverse expression of transcription factors Gata-3 and Tbx21 is observed. However, TNF-α mRNA and protein expression were elevated in both NS5A-Tg and control mice. Together, our results suggested that HCV NS5A acts as an immunomodulator by inhibiting IFN-γ production and may play an important role toward establishment of chronic HCV infection.
Antibody Specificities Associated with Neutralization Breadth in Plasma from Human Immunodeficiency Virus Type 1 Subtype C-Infected Blood Donors
Authors: Gray Elin S. , Taylor Natasha , Wycuff Diane , Moore Penny L. , Tomaras Georgia D. , Wibmer Constantinos Kurt , Puren Adrian , DeCamp Allan , Gilbert Peter B. , Wood Blake , Montefiori David C. , Binley James M. , Shaw George M. , Haynes Barton F. , Mascola John R. , Morris Lynn
Published: June 2009

Defining the specificities of the anti-human immunodeficiency virus type 1 (HIV-1) envelope antibodies able to mediate broad heterologous neutralization will assist in identifying targets for an HIV-1 vaccine. We screened 70 plasmas from chronically HIV-1-infected individuals for neutralization breadth. Of these, 16 (23%) were found to neutralize 80% or more of the viruses tested. Anti-CD4 binding site (CD4bs) antibodies were found in almost all plasmas independent of their neutralization breadth, but they mainly mediated neutralization of the laboratory strain HxB2 with little effect on the primary virus, Du151. Adsorption with Du151 monomeric gp120 reduced neutralizing activity to some extent in most plasma samples when tested against the matched virus, although these antibodies did not always confer cross-neutralization. For one plasma, this activity was mapped to a site overlapping the CD4-induced (CD4i) epitope and CD4bs. Anti-membrane-proximal external region (MPER) (
r
= 0.69;
P
< 0.001) and anti-CD4i (
r
= 0.49;
P
< 0.001) antibody titers were found to be correlated with the neutralization breadth. These anti-MPER antibodies were not 4E10- or 2F5-like but spanned the 4E10 epitope. Furthermore, we found that anti-cardiolipin antibodies were correlated with the neutralization breadth (
r
= 0.67;
P
< 0.001) and anti-MPER antibodies (
r
= 0.6;
P
< 0.001). Our study suggests that more than one epitope on the envelope glycoprotein is involved in the cross-reactive neutralization elicited during natural HIV-1 infection, many of which are yet to be determined, and that polyreactive antibodies are possibly involved in this phenomenon.
Mixed Infection and the Genesis of Influenza Virus Diversity
Authors: Ghedin Elodie , Fitch Adam , Boyne Alex , Griesemer Sara , DePasse Jay , Bera Jayati , Zhang Xu , Halpin Rebecca A. , Smit Marita , Jennings Lance , St. George Kirsten , Holmes Edward C. , Spiro David J.
Published: June 2009

The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.
Protective Efficacy of a Single Immunization of a Chimeric Adenovirus Vector-Based Vaccine against Simian Immunodeficiency Virus Challenge in Rhesus Monkeys
Authors: Barouch Dan H. , Liu Jinyan , Lynch Diana M. , O'Brien Kara L. , La Porte Annalena , Simmons Nathaniel L. , Riggs Ambryice M. , Clark Sarah , Abbink Peter , Montefiori David C. , Landucci Gary , Forthal Donald N. , Self Steven G. , Carville Angela , Mansfield Keith , Goudsmit Jaap
Published: June 2009

Rare serotype and chimeric recombinant adenovirus (rAd) vectors that evade anti-Ad5 immunity are currently being evaluated as potential vaccine vectors for human immunodeficiency virus type 1 and other pathogens. We have recently reported that a heterologous rAd prime-boost regimen expressing simian immunodeficiency virus (SIV) Gag afforded durable partial immune control of an SIV challenge in rhesus monkeys. However, single-shot immunization may ultimately be preferable for global vaccine delivery. We therefore evaluated the immunogenicity and protective efficacy of a single immunization of chimeric rAd5 hexon hypervariable region 48 (rAd5HVR48) vectors expressing SIV Gag, Pol, Nef, and Env against a homologous SIV challenge in rhesus monkeys. Inclusion of Env resulted in improved control of peak and set point SIV RNA levels following challenge. In contrast, DNA vaccine priming did not further improve the protective efficacy of rAd5HVR48 vectors in this system.