bluuebunny/crossref_metadata_2025 huggingface dataset:
Resource Letter FC-1: The physics of fundamental constants
Authors: Mohr Peter J. , Newell David B.
Published: March 2010

This Resource Letter provides a guide to the literature on the physics of fundamental constants and their values as determined within the International System of Units (SI). Journal articles, books, and websites that provide relevant information are surveyed. Literature on redefining the SI in terms of exact values of fundamental constants is also included.
Studying the scattering length by varying the depth of the potential well
Authors: Ahmed Zafar
Published: March 2010

Discussions of the scattering length frequently focus on the special case of the deuteron, and sometimes statements that are not true in general are made. To obtain a deeper understanding, we study the scattering length as a function of the depth V0 of a square well and an exponential well and show how the scattering length becomes infinite at values of V0 for which new bound states appear at zero energy.
Millikan Lecture 2009: Physics for all: From special needs to Olympiads
Authors: Eisenkraft Arthur
Published: March 2010

Can “all” students learn “real” physics? Physics First and Physics for All have become a success story for thousands of students in urban, suburban, and rural districts. At the same time, the International Physics Olympiad and other competitions have raised the expectation of what the most motivated students can achieve. Many physics educators are exploring ways to set higher goals for our most gifted students while also providing physics instruction to students previously excluded from our physics classes. Great novels and symphonies are accessible to people of different backgrounds and levels of expertise. We should develop teaching strategies that enable us to share an understanding of physics with all students because everyone deserves an opportunity to reflect on the wondrous workings of our universe.
Investigating viscous damping using a webcam
Authors: Shamim Sohaib , Zia Wasif , Anwar Muhammad Sabieh
Published: March 2010

We describe an experiment involving a mass oscillating in a viscous fluid. The mechanical oscillator is tracked using a simple webcam, and an image processing algorithm records the position of the geometrical center as a function of time. Interesting information can be extracted from the displacement-time graphs, in particular, for the underdamped case. For example, we use these oscillations to determine the viscosity of the fluid. Our mean value of 1.08±0.07 mPa s for distilled water is in good agreement with the accepted value at 20 °C. The experiment has been successfully employed in an introductory laboratory setting.
Altruism, Spite, and Greenbeards
Authors: West Stuart A. , Gardner Andy
Published: March 2010

Spite and Altruism

Many social animal species can exhibit altruism—the loss of their own individual fitness to help others. One of the most extreme examples is that of the social insects (bees and ants) where, in a colony of related individuals, only a few reproduce. The nonreproductive individuals contribute to the success of the young of these individuals thereby increasing their collective fitness. Spite occurs when an individual damages its own fitness to harm another's. This negative form of altruism can arise if the victim is less related to the perpetrator than an average member of the population.
West and Gardner
(p.
1341
) review the current literature on the origins and maintenance of altruism and spite and the associated phenomenon of greenbeards. Greenbeards use a visible inherited character to signal relatedness and spur altruism. Greenbeard genes provide a mechanism to link the genes that encode cooperative behavior with those that cause cooperators to associate. These traits maybe an ornament or a type of behavior, and they may result in altruistic or spiteful behavior.
Variations in the Sun’s Meridional Flow over a Solar Cycle
Authors: Hathaway David H. , Rightmire Lisa
Published: March 2010

Solar Meridional Flow

The surface of the Sun is composed of plasma that exhibits observable flow patterns. The weakest flow pattern occurs along meridional lines from the equator toward the poles.
Hathaway and Rightmire
(p.
1350
) measured the meridional flow using observations taken with the Michelson Doppler Imager onboard the Solar and Heliospheric Observatory between 1996 and 2009 and found that meridional flow varied with the solar cycle, such that flow was faster during the 2004–2009 minimum than during the 1996–1997 minimum. This finding provides further evidence that the last solar minimum was peculiar by comparison with previous cycles.
Gravity Field, Shape, and Moment of Inertia of Titan
Authors: Iess Luciano , Rappaport Nicole J. , Jacobson Robert A. , Racioppa Paolo , Stevenson David J. , Tortora Paolo , Armstrong John W. , Asmar Sami W.
Published: March 2010

Titan Through to the Core

Gravity measurements acquired from orbiting spacecraft can provide useful information about the interior of planets and their moons.

Iess
et al.

(p.
1367
; see the Perspective by

Sohl

) used gravity data from four flybys of the Cassini spacecraft past Saturn's moon, Titan, to model the moon's gravity field and probe its deep interior structure. Their analysis implies that Titan is a partially differentiated body with a core consisting of a mix of ice and rock or hydrated silicates.
Interesting Times for Marine N
2
O
Authors: Codispoti Louis A.
Published: March 2010

Changes in ocean chemistry could exacerbate global warming by raising the atmospheric concentration of nitrous oxide, a potent greenhouse gas.
Cavity Quantum Electrodynamics with Anderson-Localized Modes
Authors: Sapienza Luca , Thyrrestrup Henri , Stobbe Søren , Garcia Pedro David , Smolka Stephan , Lodahl Peter
Published: March 2010

Scattered and Coupled

Cavity electrodynamics explores the coupling of light with matter—ideally, that of a single photon with a single atom. Typically, this requires that the photon and the atom be confined to increase the likelihood of interaction, but scattering of light is an unavoidable product of an engineered device and is usually considered to be detrimental because it leads to loss of the photons from the cavity.

Sapienza
et al.

(p.
1352
; see the Perspective by

Wiersma

) saw extreme light scattering as an opportunity for the spontaneous generation of localized modes of light that can be exploited to induce light-matter coupling. Thus, working with a process where scattering is considered a resource rather than a nuisance, as in this case, may prove useful for realizing robust quantum information devices.
Parent-Offspring Conflict and Coadaptation
Authors: Hinde Camilla A. , Johnstone Rufus A. , Kilner Rebecca M.
Published: March 2010

Speak to Me, Mama

Maternal effects are effects of the mother (for example, hormones) on her offspring that are independent of genetic inheritance, but related to the mother's phenotype and her environment. Despite their universal occurrence, little is known about the evolutionary influence of maternal effects.

Hinde
et al.

(p.
1373
; see the cover) modeled maternal effects in birds and showed that nestling begging, as well as provoking feeding, also provides parents with information about offspring vigor. Conversely, maternal effects provide information to the unborn offspring about parental quality. Experimental studies with canaries provided support for the theoretical predictions, and together these studies show that parent-offspring conflict (that is, the conflict between the offspring for its immediate needs and the need of the parent to conserve resources for any future offspring) is resolved by the reciprocal exchange of information before and after birth. Hormonal signaling ensures a match between parental capacity for resource provisioning and offspring behavior and development after hatching that meet the mother's capacity to provide resources.
Revealing Titan's Interior
Authors: Sohl Frank
Published: March 2010

Gravity field measurements by the Cassini spacecraft suggest that Titan's interior was too cold for the primordial mixture of ice and rock to melt and fully separate.
Random Quantum Networks
Authors: Wiersma Diederik S.
Published: March 2010

The optical modes of disordered materials can couple with atomic emission and could create states that would be useful in quantum information processing.
Trees, Fast and Accurate
Authors: Allman Elizabeth S. , Rhodes John A.
Published: March 2010

A scalable and fast method for building very large evolutionary trees achieves greater accuracy than previously thought.
Elephants, Ivory, and Trade
Authors: Wasser Samuel , Poole Joyce , Lee Phyllis , Lindsay Keith , Dobson Andrew , Hart John , Douglas-Hamilton Iain , Wittemyer George , Granli Petter , Morgan Bethan , Gunn Jody , Alberts Susan , Beyers Rene , Chiyo Patrick , Croze Harvey , Estes Richard , Gobush Kathleen , Joram Ponjoli , Kikoti Alfred , Kingdon Jonathan , King Lucy , Macdonald David , Moss Cynthia , Mutayoba Benezeth , Njumbi Steve , Omondi Patrick , Nowak Katarzyna
Published: March 2010

Trade decisions made by the Convention on International Trade in Endangered Species must place science over politics.
Peace Through Vaccine Diplomacy
Authors: Hotez Peter J.
Published: March 2010

Can vaccinations help to resolve conflicts and nurture diplomacy? Later this month, Indonesia, the world's most populous Islamic country, will host U.S. President Obama, a visit that could establish important scientific ties between the United States and Indonesia and implement a potentially powerful piece of vaccine diplomacy.
Chile's Earthquake May Set Back Research for Years
Authors: Kaiser Jocelyn , Regalado Antonio
Published: March 2010

Scientists in Chile have lost years of research from last month's massive earthquake, which overturned microscopes, destroyed research labs, and took the life of a young marine biologist.
Severe Drought Puts Spotlight on Chinese Dams
Authors: Stone Richard
Published: March 2010

Environmental groups in Thailand and elsewhere are laying at least part of the blame for low levels of the Lancang-Mekong River on China's doorstep. They claim that China's management of a series of dams on the Lancang River has aggravated the unfolding crisis.
New Tuberculosis Lab Hailed as Breakthrough in Health Diplomacy
Authors: Stone Richard
Published: March 2010

Researchers from Stanford University and a consortium of nonprofit organizations have been working side by side with colleagues from the North Korean Ministry of Public Health to help set up the isolated nation's first laboratory capable of growing the mycobacterium that causes tuberculosis and detecting drug-resistant strains.
APA Seeks to Overhaul Personality Disorder Diagnoses
Authors: Holden Constance
Published: March 2010

A work group of the American Psychiatric Association is proposing revisions for personality disorders in the forthcoming fifth version of the
Diagnostic and Statistical Manual of Mental Disorders
, often referred to as psychiatry's bible.
Elsevier to Editor: Change Controversial Journal or Resign
Authors: Enserink Martin
Published: March 2010

The editor of the journal
Medical Hypotheses
—an oddity in the world of scientific publishing because it does not practice peer review—will apparently lose his job over the publication last summer of a paper that says HIV does not cause AIDS.
Ironing Out Consensus on the Iron-Based Superconductors
Authors: Cho Adrian
Published: March 2010

The emerging understanding of the 2-year-old materials could change physicists' views on the decades-old mystery of high-temperature superconductivity.
NASA Dives Into Its Past to Retrieve Vintage Satellite Data
Authors: Pringle Heather
Published: March 2010

Once forgotten or erased, 1960s-era satellite images are being salvaged from old equipment and proving valuable in climate and space science.
Enzyme-Linked Immunosorbent Assay for Measurement of Cytomegalovirus Glycoprotein B Antibody in Serum
Authors: Hackett Daniel J. , Zhang Changpin , Stefanescu Carla , Pass Robert F.
Published: March 2010

Measurement of antibody to cytomegalovirus (CMV) glycoprotein B (gB) is valuable in the assessment of the antibody response to infection and to gB-containing vaccines. For this purpose, an enzyme-linked immunosorbent assay (ELISA) with a recombinant CMV gB molecule as the antigen was evaluated. Sera from 168 anti-CMV IgG-positive and 100 seronegative subjects were used to evaluate the anti-gB antibody assay. A cutoff optical density (OD) that would distinguish gB antibody-positive from -negative sera was established. Titers of antibody to gB determined by endpoint dilution were compared with those calculated using regression analysis. The run-to-run and interoperator reproducibilities of results were measured. The mean OD + 5 standard deviations from 50 anti-CMV IgG antibody-negative sera (0.2472) was used as the cutoff between anti-gB antibody-positive and -negative results. All sera from 100 anti-CMV IgG-seronegative subjects were negative for antibody to gB. All but 1 of 168 sera from seropositive subjects were positive for antibody to gB. Observed antibody levels based on titration to the endpoint were very similar to results calculated using linear regression. The run-to-run consistency of endpoints was excellent, with 38 runs from one operator and 48 runs from another all giving results within 1 dilution of the mean value for each of three anti-CMV IgG antibody-positive serum pools. The geometric mean titer of antibody to gB for 99 sera from seropositive blood donors was 1/10,937. This ELISA gives accurate and reproducible results for the relative quantity of anti-CMV gB IgG in serum over a wide range of antibody levels.
Humoral Immune Response in Dogs Naturally Infected withBorrelia burgdorferiSensu Lato and in Dogs after Immunization with aBorreliaVaccine
Authors: Leschnik Michael W. , Kirtz Georges , Khanakah Gelas , Duscher Georg , Leidinger Ernst , Thalhammer Johann G. , Joachim Anja , Stanek Gerold
Published: March 2010

Lyme arthritis in dogs can be induced under experimental and natural conditions. However, the veterinary relevance of canine borreliosis is still under extensive investigation. The prevalence of symptoms is clearly low, although the risk of tick exposure is high. Current research focuses on case definitions, methods for diagnosing clinical disease in dogs, and discrimination between an immune response to a natural infection and an immune response to vaccination. In this experimental study, 23 dogs raised under tick-free conditions were allocated to two groups. The 11 dogs in the first group were vaccinated with a commercial borrelia vaccine and subsequently developed detectable antibody titers. The 12 dogs in the second group were walked on two consecutive days in an area where ticks were endemic. On day 5 after exposure, engorged ticks were removed from the 12 dogs and were analyzed forBorreliaDNA by a real-time PCR assay. Blood samples were taken before exposure/vaccination and at defined time points thereafter. Antibody responses were evaluated using an immunofluorescence antibody test (IFAT) and Western blotting. Seven dogs from whichBorrelia-positive ticks were removed seroconverted and developed individual immune responses. Blood and urine samples taken from the tick-exposed group at weeks 1 and 3 for real-time PCR analysis and culture were always negative for bacterial DNA. In conclusion, despite serological evidence of infection/immunization, no clinical signs of disease were observed. The antibody patterns in a single Western blot did not permit differentiation between the different antigen sources (vaccine versus natural infection). However, repeated Western blot analyses may be useful for the confirmation of infection or vaccination status, since the time courses of the levels of specific antibodies seem to be different.
Cytokine Protein Expression Levels in Tracheobronchial Lymph Node Homogenates of Pigs Infected with Pseudorabies Virus
Authors: Miller Laura C. , Zanella Eraldo L. , Waters W. Ray , Lager Kelly M.
Published: March 2010

Pseudorabies virus (PRV) is a neurotropic alphaherpesvirus that produces fatal encephalitis in newborn pigs, respiratory disorders in fattening pigs, and reproductive failure in sows. Following primary infection of the respiratory tract, PRV can develop into a systemic infection with dispersion of the virus via the lymphatic system that involves mononuclear cells in tracheobronchial lymph nodes (TBLNs). The objectives of the present study were to evaluate the pathogenesis and to determine the early immune cytokine profiles in TBLNs following experimental infection with a feral swine PRV isolate at 1, 3, 6, and 14 days postinfection (dpi). Forty healthy pigs were purchased from a PRV-negative herd. Twenty pigs received the Florida strain isolate (FS268) of feral swine PRV intranasally, and 20 uninfected controls received a sham inoculum. Compared to the levels in the controls, the levels of alpha interferon (IFN-α), interleukin-1β (IL-1β), IL-12, and IFN-γ were increased in TBLN homogenates from PRV-infected pigs at 1 dpi, whereas the IL-18 levels were decreased from 3 to 6 dpi. The protein levels of IL-4 and IL-10 did not differ between the controls and the PRV-infected pigs at any time point. Flow cytometric analysis of TBLN homogenates of PRV-infected pigs and the controls revealed increases in the percentages of B cells at 6 dpi, CD4+cells at 14 dpi, and CD25 expression in TBLN homogenates (in the total mononuclear fraction and on B cells) in the PRV-infected pigs. Collectively, these findings demonstrate that a feral PRV in commercial swine can modulate the host's early immune response to allow the virus to establish an infection.
Pilot Study of Whole-Blood Gamma Interferon Response to the
Vibrio cholerae
Toxin B Subunit and Resistance to Enterotoxigenic
Escherichia coli
-Associated Diarrhea
Authors: Flores Jose , DuPont Herbert L. , Paredes-Paredes Mercedes , Aguirre-Garcia M. Magdalena , Rojas Araceli , Gonzalez Alexei , Okhuysen Pablo C.
Published: March 2010

Enterotoxigenic
Escherichia coli
(ETEC), which produces heat-labile toxin (LT), is a common cause of travelers' diarrhea (TD). The B subunit of ETEC LT is immunologically related to the B subunit of
Vibrio cholerae
toxin (CT). In this pilot study we evaluated the whole-blood gamma interferon response to CT B in 17 U.S. adults traveling to Mexico. Only one of nine subjects who demonstrated a cellular immune response as determined by whole-blood gamma interferon production to CT B on arrival to Mexico developed diarrhea, whereas five of eight without a cellular response developed diarrhea. Markers of the cellular immune response to ETEC LT could help in identifying individuals immune to ETEC LT, and these markers deserve additional study.
Beneficial Dysregulation of the Time Course of Inflammatory Mediators in Lipopolysaccharide-Induced Tumor Necrosis Factor Alpha Factor-Deficient Mice
Authors: Srinivasan Sreedevi , Leeman Susan E. , Amar Salomon
Published: March 2010

To begin to understand the surprising survival of macrophage-specific lipopolysaccharide-induced tumor necrosis factor alpha factor-deficient (macLITAF−/−) animals after a lethal dose of lipopolysaccharide (LPS), as reported earlier, the present follow-up study focuses on the role of LITAF in the regulation of inflammatory cytokines secreted in response to lethal or sublethal doses of LPS administered to wild-type (WT) and macLITAF−/−mice. A time course study of kinase expression in peritoneal macrophages revealed increased phosphorylation of prosurvival kinases Akt, Erk1/2, and ribosomal S6 kinase (RSK) in macLITAF−/−mice compared to that in WT mice (n= 8), confirming their role in LPS-mediated diseases. macLITAF−/−mice (n= 8) survived a lethal dose of LPS plusd-galactosamine (d-GalN), expressing lower serum levels of pro- and anti-inflammatory cytokines than the WT levels. To extend our knowledge on LPS-induced inflammatory events, an effective sublethal dose of LPS was administered to the animals (n= 14). WT animals exhibited an acute inflammatory response that decreased after 4 h. Interestingly, macLITAF−/−mice exhibited an initial delay in the secretion of proinflammatory cytokines that peaked after 8 h and reached WT levels after 18 h. Anti-inflammatory cytokine secretions were initially delayed but increased after 4 h and remained elevated compared to WT levels, even after 18 h. Our results demonstrate that LITAF deficiencyin vivoaffects cytokines other than TNF-α and influences the balance between the pro- and anti-inflammatory cytokines, which protects the animals from the deleterious effects of an LPS-induced inflammatory response, resulting in a beneficial host regulation of inflammatory cytokines and in enhanced survival. Therapeutic intervention aimed at reducing LITAF via kinase modulators may prove useful in preventing LPS-induced mortality.
Simultaneous Cocirculation of Both European Varicella-Zoster Virus Genotypes (E1 and E2) in Mexico City
Authors: Rodríguez-Castillo Araceli , Vaughan Gilberto , Ramírez-González José Ernesto , Escobar-Gutiérrez Alejandro
Published: March 2010

Full-length genome analysis of varicella-zoster virus (VZV) has shown that viral strains can be classified into seven different genotypes: European (E), Mosaic (M), and Japanese (J), and the E and M genotypes can be further subclassified into E1, E2, and M1 through 4, respectively. The distribution of the main VZV genotypes in Mexico was described earlier, demonstrating the predominance of E genotype, although other genotypes (M1 and M4) were also identified. However, no information regarding the circulation of either E genotype in the country is available. In the present study, we confirm the presence of both E1 and E2 genotypes in the country and explore the possibility of coinfection as the triggering factor for increased virulence among severe cases. A total of 61 different European VZV isolates collected in the Mexico City metropolitan area from 2005 to 2006 were typed by using a PCR method based on genotype-specific primer amplification. Fifty isolates belonged to the E1 genotype, and the eleven remaining samples were classified as E2 genotypes. No coinfection with both E genotypes was identified among these specimens. We provide here new information on the distribution of VZV genotypes circulating in Mexico City.
Multicenter Comparison of the ISO Standard 20776-1 and the Serial 2-Fold Dilution Procedures To Dilute Hydrophilic and Hydrophobic Antifungal Agents for Susceptibility Testing
Authors: Gomez-Lopez Alicia , Arendrup Maiken Cavling , Lass-Floerl Cornelia , Rodriguez-Tudela Juan-Luis , Cuenca-Estrella Manuel
Published: March 2010

A multicenter study was conducted to assess the accuracy of the ISO standard 20776-1 and the serial 2-fold dilution procedures for antifungal susceptibility testing. Fluconazole trays can be accurately prepared by following ISO and serial dilution schemes. However, itraconazole trays showed a significant lack of reproducibility that was independent of which method was followed.
Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Bacterial Strains Routinely Isolated in a Clinical Microbiology Laboratory
Authors: Bizzini A. , Durussel C. , Bille J. , Greub G. , Prod'hom G.
Published: March 2010

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced in diagnostic microbiology laboratories for the identification of bacterial and yeast strains isolated from clinical samples. In the present study, we prospectively compared MALDI-TOF MS to the conventional phenotypic method for the identification of routine isolates. Colonies were analyzed by MALDI-TOF MS either by direct deposition on the target plate or after a formic acid-acetonitrile extraction step if no valid result was initially obtained. Among 1,371 isolates identified by conventional methods, 1,278 (93.2%) were putatively identified to the species level by MALDI-TOF MS and 73 (5.3%) were identified to the genus level, but no reliable identification was obtained for 20 (1.5%). Among the 1,278 isolates identified to the species level by MALDI-TOF MS, 63 (4.9%) discordant results were initially identified. Most discordant results (42/63) were due to systematic database-related taxonomical differences, 14 were explained by poor discrimination of the MALDI-TOF MS spectra obtained, and 7 were due to errors in the initial conventional identification. An extraction step was required to obtain a valid MALDI-TOF MS identification for 25.6% of the 1,278 valid isolates. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional phenotypic identification for most bacterial strains routinely isolated in clinical microbiology laboratories.
Disseminated
Scedosporium
/
Pseudallescheria
Infection after Double-Lung Transplantation in Patients with Cystic Fibrosis
Authors: Morio Florent , Horeau-Langlard Delphine , Gay-Andrieu Françoise , Talarmin Jean-Philippe , Haloun Alain , Treilhaud Michelle , Despins Philippe , Jossic Frédérique , Nourry Laurence , Danner-Boucher Isabelle , Pattier Sabine , Bouchara Jean-Philippe , Le Pape Patrice , Miegeville Michel
Published: March 2010

We report a case of disseminated
Scedosporium
/
Pseudallescheria
infection due to
P
seudallescheria boydii
sensu stricto after lung transplantation in a patient with cystic fibrosis. Dissemination occurred under voriconazole. Despite surgery and combination therapy with voriconazole, caspofungin, and terbinafine, the patient died 8 months after transplantation. Previously reported cases are reviewed.
New Polymorphic Microsatellite Markers Able To Distinguish among
Candida parapsilosis
Sensu Stricto Isolates
Authors: Sabino Raquel , Sampaio Paula , Rosado Laura , Stevens David A. , Clemons Karl V. , Pais Célia
Published: March 2010

Among the
Candida
species causing bloodstream infections,
Candida parapsilosis
is one of the most frequently isolated. The objective of the present work was the identification of new microsatellite loci able to distinguish among
C. parapsilosis
isolates. DNA sequences with trinucleotide repeats were selected from the
C. parapsilosis
genome database. PCR primer sets flanking the microsatellite repeats were designed and tested with 20 independent isolates. On the basis of the amplification efficiency, specificity, and observed polymorphism, four of the sequences were selected for strain typing. Two hundred thirty-three independent
C. parapsilosis
sensu stricto isolates were genotyped by using these markers. The polymorphic loci exhibited from 20 to 42 alleles and 39 to 92 genotypes. In a multiplex analysis, 192 genotypes were obtained and the combined discriminatory power of the four microsatellites was 0.99. Reproducibility was demonstrated by submission of subcultures of 4 isolates each, in triplicate, interspersed with unique numbers among a group of 30 isolates for blind testing. Comparison of the genotypes obtained by microsatellite analysis and those obtained by randomly amplified polymorphic DNA analysis, restriction fragment length polymorphism analysis, and internal transcribed sequence grouping was performed and showed that the microsatellite method could distinguish individual isolates; none of the other methods could do that. Related species,
C. orthopsilosis
and
C. metapsilosis
, were not confused with
C. parapsilosis
sensu stricto. These new microsatellites are a valuable tool for use for the differentiation of
C. parapsilosis
sensu stricto strains, vital in epidemiology to answer questions of strain relatedness and determine pathways of transmission.
Identification and Genotyping of
Mycobacterium tuberculosis
Complex Species by Use of a SNaPshot Minisequencing-Based Assay
Authors: Bouakaze C. , Keyser C. , de Martino S. J. , Sougakoff W. , Veziris N. , Dabernat H. , Ludes B.
Published: March 2010

The aim of the present study was to investigate the use of the SNaPshot minisequencing method for the identification of
Mycobacterium tuberculosis
complex (MTBC) isolates to the species level and for further genotyping of
M. tuberculosis
isolates. We developed an innovative strategy based on two multiplex allele-specific minisequencing assays that allowed detection of eight species-specific and eight lineage-specific single nucleotide polymorphisms (SNPs). Each assay consisted of an eightplex PCR amplification, followed by an eightplex minisequencing reaction with the SNaPshot multiplex kit (Applied Biosystems) and, finally, analysis of the extension products by capillary electrophoresis. The whole strategy was developed with a panel of 56 MTBC strains and 15 negative controls. All MTBC strains tested except one
M. africanum
clinical isolate were accurately identified to the species level, and all
M. tuberculosis
isolates were successfully further genotyped. This two-step strategy based on SNaPshot minisequencing allows the simultaneous differentiation of closely related members of the MTBC, the distinction between principal genetic groups, and the characterization of
M. tuberculosis
isolates into one of the seven prominent SNP cluster groups (SCGs) and could be a useful tool for diagnostic and epidemiological purposes.
Genetic and Antigenic Characterization of Newly Isolated Bovine Toroviruses from Japanese Cattle
Authors: Ito Toshihiro , Katayama Shigeji , Okada Nobutaka , Masubuchi Katsuo , Fukuyama Shin-ichi , Shimizu Mitsugu
Published: March 2010

Torovirus, a member of theCoronaviridaefamily, is a gastrointestinal infectious agent that has been identified in humans, cattle, pigs, and equines. Toroviruses, except equine torovirus, are difficult to propagate in cell culture; indeed, to date, only the Aichi/2004 strain of bovine torovirus (BToV) has been isolated among the human, bovine, and porcine toroviruses. In the present study, four cytopathogenic BToVs were isolated from diarrheal feces of the cattle using the HRT-18 cell line, and their genetic and antigenic properties were compared. The cytopathogenic features of BToV isolates in HRT-18 cells were similar to those of the Aichi/2004 strain. However, none of the isolates showed cytopathogenic effects in the HRT-18 cells of different origin, suggesting that one significant factor contributing to the cytopathogenicity of BToV depends on properties of the HRT-18 cells themselves. All BToVs isolated were able to agglutinate mouse, but not chicken, erythrocytes, while they lacked receptor-destroying enzyme activity. Analysis of the N terminus of the spike gene showed that three isolates, but not the Gifu-2007TI/E strain, were phylogenetically located in cluster 1 and its analogs and revealed high cross-reactivity with each other, as demonstrated by neutralization (NT) and hemagglutination inhibition (HI) assays. The Gifu-2007TI/E strain was classified close to cluster 2 and exhibited relatively low cross-reactivity with these viruses; however, the difference was not sufficient to classify BToVs into serotypes, suggesting that at least two subtypes distinguishable by the structure of the N terminus of the spike gene and that both NT and HI tests may be exist.
Molecular Epidemiology of Vancomycin-Resistant
Enterococcus faecium
: a Prospective, Multicenter Study in South American Hospitals
Authors: Panesso Diana , Reyes Jinnethe , Rincón Sandra , Díaz Lorena , Galloway-Peña Jessica , Zurita Jeannete , Carrillo Carlos , Merentes Altagracia , Guzmán Manuel , Adachi Javier A. , Murray Barbara E. , Arias Cesar A.
Published: March 2010

Enterococcus faecium
has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant
E. faecium
(VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14
fms
genes, the
esp
gene of
E. faecium
[

esp
Efm

], and the
hyl
gene of
E. faecium
[

hyl
Efm

]) and plasmids carrying the
fms20-fms21
(
pilA
),

hyl
Efm

, and
vanA
genes. Of 723 enterococcal isolates recovered,
E. faecalis
was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were
E. faecium
). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The

ebpA
Efm
-ebpB
Efm
-ebpC
Efm

(
pilB
) and
fms11
-
fms19
-
fms16
clusters were detected in all VREfm isolates from the region, whereas

esp
Efm

and

hyl
Efm

were detected in 69% and 23% of the isolates, respectively. The
fms20
-
fms21
(
pilA
) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with

hyl
Efm

and the
vanA
gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and
vanA
genes suggests that
E. faecium
from the CC17 genogroup may disseminate in the region in the coming years.
Helicobacter pullorum
Outbreak in C57BL/6NTac and C3H/HeNTac Barrier-Maintained Mice
Authors: Boutin S. R. , Shen Z. , Roesch P. L. , Stiefel S. M. , Sanderson A. E. , Multari H. M. , Pridhoko E. A. , Smith J. C. , Taylor N. S. , Lohmiller J. J. , Dewhirst F. E. , Klein H. J. , Fox J. G.
Published: March 2010

Helicobacter pullorum
is a bacterial pathogen in humans. By using microaerobic culture techniques,
H. pullorum
was isolated from the feces of barrier-maintained mice and identified, on the basis of biochemical, restriction fragment length polymorphism, and 16S rRNA gene sequence analyses. This finding presents an opportunity to study
H. pullorum
pathogenesis in mice.
Electron Cryotomography of Tula Hantavirus Suggests a Unique Assembly Paradigm for Enveloped Viruses
Authors: Huiskonen Juha T. , Hepojoki Jussi , Laurinmäki Pasi , Vaheri Antti , Lankinen Hilkka , Butcher Sarah J. , Grünewald Kay
Published: March 2010

Hantaviruses (family
Bunyaviridae
) are rodent-borne emerging viruses that cause a serious, worldwide threat to human health. Hantavirus diseases include hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. Virions are enveloped and contain a tripartite single-stranded negative-sense RNA genome. Two types of glycoproteins, G
N
and G
C
, are embedded in the viral membrane and form protrusions, or “spikes.” The membrane encloses a ribonucleoprotein core, which consists of the RNA segments, the nucleocapsid protein, and the RNA-dependent RNA polymerase. Detailed information on hantavirus virion structure and glycoprotein spike composition is scarce. Here, we have studied the structures of Tula hantavirus virions using electron cryomicroscopy and tomography. Three-dimensional density maps show how the hantavirus surface glycoproteins, membrane, and ribonucleoprotein are organized. The structure of the G
N
-G
C
spike complex was solved to 3.6-nm resolution by averaging tomographic subvolumes. Each spike complex is a square-shaped assembly with 4-fold symmetry. Spike complexes formed ordered patches on the viral membrane by means of specific lateral interactions. These interactions may be sufficient for creating membrane curvature during virus budding. In conclusion, the structure and assembly principles of Tula hantavirus exemplify a unique assembly paradigm for enveloped viruses.
Comprehensive Analysis of Rhesus Lymphocryptovirus MicroRNA Expression
Authors: Riley Kasandra J.-L. , Rabinowitz Gabrielle S. , Steitz Joan A.
Published: March 2010

Rhesus lymphocryptovirus (rLCV) and Epstein-Barr virus (EBV) are closely related gammaherpesviruses that infect and cause disease in rhesus monkeys and humans, respectively. Thus, rLCV is an important model system for EBV pathogenesis. Both rLCV and EBV express microRNAs (miRNAs), several conserved in sequence and genomic location. We have applied deep sequencing technology to obtain an inventory of rLCV miRNA expression in latently rLCV-infected monkey B cells. Our data confirm the presence of all previously identified mature rLCV miRNAs and have resulted in the discovery of 21 new mature miRNAs arising from previously identified precursor miRNAs (pre-miRNAs), as well as two novel pre-miRNAs (rL1-34 and rL1-35) that together generate four new mature miRNAs. Thus, the total number of rLCV-encoded pre-miRNAs is 35 and the total number of rLCV mature miRNAs is 68, the most of any virus examined. The exact 5′ and 3′ ends of all mature rLCV miRNAs were pinpointed, many showing marked sequence and length heterogeneity that could modulate function. We further demonstrate that rLCV mature miRNAs associate with Argonaute proteins in rLCV-infected B cells.
Early Spatial and Temporal Events of Human T-Lymphotropic Virus Type 1 Spread following Blood-Borne Transmission in a Rabbit Model of Infection
Authors: Haynes Rashade A. H. , Zimmerman Bevin , Millward Laurie , Ware Evan , Premanandan Christopher , Yu Lianbo , Phipps Andrew J. , Lairmore Michael D.
Published: March 2010

Human T-lymphotropic virus type 1 (HTLV-1) infection causes adult T-cell leukemia/lymphoma (ATL) and is associated with a variety of lymphocyte-mediated disorders. HTLV-1 transmission occurs by transmission of infected cells via breast-feeding by infected mothers, sexual intercourse, and contaminated blood products. The route of exposure and early virus replication events are believed to be key determinants of virus-associated spread, antiviral immune responses, and ultimately disease outcomes. The lack of knowledge of early events of HTLV-1 spread following blood-borne transmission of the virus
in vivo
hinders a more complete understanding of the immunopathogenesis of HTLV-1 infections. Herein, we have used an established animal model of HTLV-1 infection to study early spatial and temporal events of the viral infection. Twelve-week-old rabbits were injected intravenously with cell-associated HTLV-1 (ACH-transformed R49). Blood and tissues were collected at defined intervals throughout the study to test the early spread of the infection. Antibody and hematologic responses were monitored throughout the infection. HTLV-1 intracellular Tax and soluble p19 matrix were tested from
ex vivo
cultured lymphocytes. Proviral copy numbers were measured by real-time PCR from blood and tissue mononuclear leukocytes. Our data indicate that intravenous infection with cell-associated HTLV-1 targets lymphocytes located in both primary lymphoid and gut-associated lymphoid compartments. A transient lymphocytosis that correlated with peak virus detection parameters was observed by 1 week postinfection before returning to baseline levels. Our data support emerging evidence that HTLV-1 promotes lymphocyte proliferation preceding early viral spread in lymphoid compartments to establish and maintain persistent infection.
A Novel Molecular Mechanism of Dual Resistance to Nucleoside and Nonnucleoside Reverse Transcriptase Inhibitors
Authors: Nikolenko Galina N. , Delviks-Frankenberry Krista A. , Pathak Vinay K.
Published: March 2010

Recently, mutations in the connection subdomain (CN) and RNase H domain of HIV-1 reverse transcriptase (RT) were observed to exhibit dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs). To elucidate the mechanism by which CN and RH mutations confer resistance to NNRTIs, we hypothesized that these mutations reduce RNase H cleavage and provide more time for the NNRTI to dissociate from the RT, resulting in the resumption of DNA synthesis and enhanced NNRTI resistance. We observed that the effect of the reduction in RNase H cleavage on NNRTI resistance is dependent upon the affinity of each NNRTI to the RT and further influenced by the presence of NNRTI-binding pocket (BP) mutants. D549N, Q475A, and Y501A mutants, which reduce RNase H cleavage, enhance resistance to nevirapine (NVP) and delavirdine (DLV), but not to efavirenz (EFV) and etravirine (ETR), consistent with their increase in affinity for RT. Combining the D549N mutant with NNRTI BP mutants further increases NNRTI resistance from 3- to 30-fold, supporting the role of NNRTI-RT affinity in our NNRTI resistance model. We also demonstrated that CNs from treatment-experienced patients, previously reported to enhance NRTI resistance, also reduce RNase H cleavage and enhance NNRTI resistance in the context of the patient RT pol domain or a wild-type pol domain. Together, these results confirm key predictions of our NNRTI resistance model and provide support for a unifying mechanism by which CN and RH mutations can exhibit dual NRTI and NNRTI resistance.
Identification of Dominant Negative Human Immunodeficiency Virus Type 1 Vif Mutants That Interfere with the Functional Inactivation of APOBEC3G by Virus-Encoded Vif
Authors: Walker Robert C. , Khan Mohammad A. , Kao Sandra , Goila-Gaur Ritu , Miyagi Eri , Strebel Klaus
Published: March 2010

APOBEC3G (A3G) is a host cytidine deaminase that serves as a potent intrinsic inhibitor of retroviral replication. A3G is packaged into human immunodeficiency virus type 1 virions and deaminates deoxycytidine to deoxyuridine on nascent minus-strand retroviral cDNA, leading to hyper-deoxyguanine-to-deoxyadenine mutations on positive-strand cDNA and inhibition of viral replication. The antiviral activity of A3G is suppressed by Vif, a lentiviral accessory protein that prevents encapsidation of A3G. In this study, we identified dominant negative mutants of Vif that interfered with the ability of wild-type Vif to inhibit the encapsidation and antiviral activity of A3G. These mutants were nonfunctional due to mutations in the highly conserved HCCH and/or SOCS box motifs, which are required for assembly of a functional Cul5-E3 ubiquitin ligase complex. Similarly, mutation or deletion of a PPLP motif, which was previously reported to be important for Vif dimerization, induced a dominant negative phenotype. Expression of dominant negative Vif counteracted the Vif-induced reduction of intracellular A3G levels, presumably by preventing Vif-induced A3G degradation. Consequently, dominant negative Vif interfered with wild-type Vif's ability to exclude A3G from viral particles and reduced viral infectivity despite the presence of wild-type Vif. The identification of dominant negative mutants of Vif presents exciting possibilities for the design of novel antiviral strategies.
Jaagsiekte Sheep Retrovirus Transformation in Madin-Darby Canine Kidney Epithelial Cell Three-Dimensional Culture
Authors: Johnson Chassidy , Sanders Kiah , Fan Hung
Published: March 2010

Jaagsiekte sheep retrovirus (JSRV) is the causative agent of a contagious lung cancer in sheep that shares similarities with human bronchioloalveolar carcinoma (BAC). JSRV is unique because the envelope gene (
env
) is the oncogene, as it can transform cells in culture and induce tumors in animals. The phosphatidylinositol 3-kinase (PI3K)-Akt-mTOR and H/N-Ras-MEK-mitogen-activated protein kinase (MAPK) pathways have been shown to be critical for Env transformation. However, the question still remains of how disruption of these pathways relates to tumor formation. To address this, JSRV Env transformation was studied in the context of epithelial structure, using the polarized Madin-Darby canine kidney (MDCK) epithelial cell three-dimensional (3-D) culture system. The results indicated that JSRV Env-transformed MDCK cells were larger and had full or multiple lumens, in contrast to the single lumens observed in controls. The altered phenotype was largely mediated by an increase in proliferation, in addition to overcoming the proliferative suppression signal. JSRV Env was not found to disrupt polarity or tight junctions or to inhibit lumen apoptosis. The PI3K-Akt-mTOR pathway was important for Env transformation in MDCK cells, although the mechanisms of action differed in 3-D and monolayer cultures. PI3K-dependent signaling to mTOR occurred in monolayers, while PI3K-independent signaling to mTOR occurred in 3-D culture. In contrast, the H/N-Ras-MEK-MAPK pathway was found to be inhibitory to transformation in both normal and transformed MDCK cells in 3-D culture. However, in monolayer culture, inhibition of MEK reverted the transformed phenotype, suggesting a different mechanism(s) of action in monolayer versus 3-D culture.
Role of Human Immunodeficiency Virus Type 1 Integrase in Uncoating of the Viral Core
Authors: Briones Marisa S. , Dobard Charles W. , Chow Samson A.
Published: March 2010

After membrane fusion with a target cell, the core of human immunodeficiency virus type 1 (HIV-1) enters into the cytoplasm, where uncoating occurs. The cone-shaped core is composed of the viral capsid protein (CA), which disassembles during uncoating. The underlying factors and mechanisms governing uncoating are poorly understood. Several CA mutations can cause changes in core stability and a block at reverse transcription, demonstrating the requirement for optimal core stability during viral replication. HIV-1 integrase (IN) catalyzes the insertion of the viral cDNA into the host genome, and certain IN mutations are pleiotropic. Similar to some CA mutants, two IN mutants, one with a complete deletion of IN (NL-ΔIN) and the other with a Cys-to-Ser substitution (NL-C130S), were noninfectious, with a replication block at reverse transcription. Compared to the wild type (WT), the cytoplasmic CA levels of the IN mutants in infected cells were reduced, suggesting accelerated uncoating. The role of IN during uncoating was examined by isolating and characterizing cores from NL-ΔIN and NL-C130S. Both IN mutants could form functional cores, but the core yield and stability were decreased. Also, virion incorporation of cyclophilin A (CypA), a cellular peptidyl-prolyl isomerase that binds specifically to CA, was decreased in the IN mutants. Cores isolated from WT virus depleted of CypA had an unstable-core phenotype, confirming a role of CypA in promoting optimal core stability. Taken together, our results indicate that IN is required during uncoating for maintaining CypA-CA interaction, which promotes optimal stability of the viral core.
Autographa californica
Multiple Nucleopolyhedrovirus LEF-2 Is a Capsid Protein Required for Amplification but Not Initiation of Viral DNA Replication
Authors: Wu Carol P. , Huang Yi-Ju , Wang Jen-Yeu , Wu Yueh-Lung , Lo Huei-Ru , Wang Jui-Ching , Chao Yu-Chan
Published: March 2010

The late expression factor 2 gene (
lef-2
) of baculovirus
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) has been identified as one of the factors essential for origin-dependent DNA replication in transient expression assays and has been shown to be involved in late/very late gene expression. To study the function of
lef-2
in the life cycle of AcMNPV,
lef-2
knockout and repair bacmids were generated by homologous recombination in
Escherichia coli
. Growth curve analysis showed that
lef-2
was essential for virus production. Interestingly, a DNA replication assay indicated that
lef-2
is not required for the initiation of viral DNA replication and that, rather, it is required for the amplification of DNA replication.
lef-2
is also required for the expression of late and very late genes, as the expression of these genes was abolished by
lef-2
deletion. Temporal and spatial distributions of LEF-2 protein in infected cells were also analyzed, and the data showed that LEF-2 protein was localized to the virogenic stroma in the nuclei of the infected cells. Analysis of purified virus particles revealed that LEF-2 is a viral protein component of both budded and occlusion-derived virions, predominantly in the nucleocapsids of the virus particles. This observation suggests that LEF-2 may be required immediately after virus entry into host cells for efficient viral DNA replication.