bluuebunny/crossref_metadata_2025 huggingface dataset:
Dyslexia: A New Synergy Between Education and Cognitive Neuroscience
Authors: Gabrieli John D. E.
Published: July 2009

Dissecting Dyslexia and Learning

Difficulties in learning to read, despite reasonable effort and instruction, form the basis of dyslexia.
Gabrieli
(p.
280
; see the cover) now reviews the latest research into the causes of dyslexia. Neuroimaging studies may give early notice of impending dyslexia, and it is hoped that early interventions may lessen the impact of dyslexia. Learning occurs in many settings. Humans uniquely use the formalized settings of schools and curriculum. Infants and children also do plenty of learning outside these settings, often intermingling social interactions.

Meltzoff
et al.

(p.
284
) survey the variety of learning contexts that people experience and discuss how recent advances in neuroscience and robotics are driving a new synthesis of learning.
Demographic Variability, Vaccination, and the Spatiotemporal Dynamics of Rotavirus Epidemics
Authors: Pitzer Virginia E. , Viboud Cécile , Simonsen Lone , Steiner Claudia , Panozzo Catherine A. , Alonso Wladimir J. , Miller Mark A. , Glass Roger I. , Glasser John W. , Parashar Umesh D. , Grenfell Bryan T.
Published: July 2009

Ecology of Diarrhea

Rotavirus is an important cause of morbidity and mortality globally, and, although the infection takes a terrible toll on infant lives, its epidemiology is rather poorly known. New vaccines have become available and are being introduced in the United States prior to global rollout, but they may have some unexpected effects on disease dynamics.

Pitzer
et al.

(p.
290
; see the Perspective by

Medley and Nokes

) analyzed data and developed models describing the epidemiology of rotavirus before and during adoption of the vaccine. Ecological analysis showed that the birth rate predicted the timing of epidemics much better than climatic variables and that shifts in birth rates explained changes over the years. But as increasing numbers of infants are vaccinated, the pool of susceptible individuals in the population will be reduced, which will affect the annual waves of geographic spread of rotavirus.
Undulatory Swimming in Sand: Subsurface Locomotion of the Sandfish Lizard
Authors: Maladen Ryan D. , Ding Yang , Li Chen , Goldman Daniel I.
Published: July 2009

Swimming Through Sand

Although composed of solid particles, sand can behave like a fluid. If you had to swim through sand, how would you do it? Would you use your arms and legs for propulsion or would you make your body as compact as possible and try to wiggle and slither your way through?

Maladen
et al.

(p.
314
) used x-ray imaging to study the motion of sandfish lizards as they burrowed into sand. The sandfish lizard does not use its limbs, but instead flattens them against its body and uses large-amplitude traveling wave oscillation of its body to propel itself. Modeling can explain the motion the lizard uses to propel itself through a medium that is neither liquid nor solid.
Reversal of RNA Dominance by Displacement of Protein Sequestered on Triplet Repeat RNA
Authors: Wheeler Thurman M. , Sobczak Krzysztof , Lueck John D. , Osborne Robert J. , Lin Xiaoyan , Dirksen Robert T. , Thornton Charles A.
Published: July 2009

Resisting Repeats

A set of diseases, including myotonic dystrophy, are caused by the expansion of a simple repeat in genomic DNA, which, when transcribed into RNA, can be toxic to other cellular processes. Ameliorating the effects of this toxic, repeat-laden RNA may also relieve the symptoms of the disease.

Wheeler
et al.

(p.
336
; see the Perspective by

Cooper

) developed an antisense morpholino oligonucleotide complementary to the expanded repeats found in the myotonic dystrophy protein kinase messenger RNA (mRNA). The morpholino bound the repeats in vitro and displaced the inappropriately bound and sequestered RNA splicing factor, Muscleblind-like 1. In an in vivo mouse model for myotonic dystrophy, local injection of the morpholino corrected a number of cellular defects in muscle, including the alternative mRNA splicing of several genes, among them the muscle-specific chloride channel, CIC1, leading to a marked reduction in the myotonia.
The Human SepSecS-tRNA
Sec
Complex Reveals the Mechanism of Selenocysteine Formation
Authors: Palioura Sotiria , Sherrer R. Lynn , Steitz Thomas A. , Söll Dieter , Simonović Miljan
Published: July 2009

Making Selenocysteine

In humans, selenocysteine is the only amino acid that lacks its own transfer RNA (tRNA) synthetase and is synthesized on its cognate tRNA. The process involves mischarging of tRNA
sec
with serine, phosphorylation of the serine, and then conversion of the phosphoserine into selenocysteine by the enzyme SepSecS using selenophosphate as the selenium donor.

Palioura
et al.

(p.
321
) now provide insight into the mechanism of selenocysteine formation, based on the crystal structure of human tRNA
sec
complexed with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro activity assays. Binding of tRNA
sec
to SepSecS is required to properly orient phosphoserine attached to tRNA
sec
for pyroxidal phosphate–based catalysis.
Tiger Moth Jams Bat Sonar
Authors: Corcoran Aaron J. , Barber Jesse R. , Conner William E.
Published: July 2009

Moths Battling Bats

Many night-flying insects hear the sonar sounds of attacking bats and take evasive action. Among moths, evasive flight is often accompanied by the production of ultrasonic sounds. Three functions of these sounds have been proposed: to startle the bat, to warn of distastefulness, or to “jam” the bat's sonar system.

Corcoran
et al.

(p.
325
) studied a species of tiger moth (
Bertholdia trigona
) that emits a particularly dense series of ultrasonic clicks and the interception behavior of big brown bats (
Eptesicus fuscus
) presented with silenced or sound-producing tethered moths. If the moth sounds evoke startle, naïve bats should initially break off their attacks, but then the bats should habituate to the sounds and complete subsequent attacks. In contrast, if the moth sounds have a warning effect, naïve bats should initially complete their attacks on sound-emitting moths, discover that the moths are distasteful, and refuse to capture them in future trials. Most of the bats in the tests reliably caught the silenced moths but avoided completing attacks on sound-producing moths, with no evidence of increasing or decreasing probability of capture from the first to the last trial, which suggests that the moths effectively jammed the bats' sonar.
Toward a Smarter Web
Authors: Hornby Gregory S. , Kurtoglu Tolga
Published: July 2009

Interactive evolutionary algorithms are increasingly implemented in Web sites to respond to user preferences.
Nonlocal Transport in the Quantum Spin Hall State
Authors: Roth Andreas , Brüne Christoph , Buhmann Hartmut , Molenkamp Laurens W. , Maciejko Joseph , Qi Xiao-Liang , Zhang Shou-Cheng
Published: July 2009

Living on the Edge

Topological insulators are a recently described state of matter in which the bulk material is an insulator but with a metallic surface state that is protected by the topology of the Fermi surface.

Roth
et al.

(p.
294
; see the Perspective by

Büttiker

) now show that the current flow on the surface takes place in edge states around the boundary of the sample. These are similar to the current transport in high-quality two-dimensional electron gases in high magnetic field, which confirms theoretical work on these materials.
CH Stretching Excitation in the Early Barrier F + CHD
3
Reaction Inhibits CH Bond Cleavage
Authors: Zhang Weiqing , Kawamata Hiroshi , Liu Kopin
Published: July 2009

Shaking Prevents Breaking

Intuition suggests that vibrational excitation of a molecular bond ought to increase the likelihood of its breaking in an ensuing chemical reaction.

W. Zhang
et al.

(p.
303
) observe precisely the opposite outcome in a spectroscopic study of the F + CHD
3
reaction. Exciting the C-H stretch leads exclusively to the formation of DF and CHD
2
products, in contrast to the more abundant yields of both HF and DF observed in the absence of CH vibration. Though the mechanism underlying this effect remains unclear, the result highlights unanticipated complexity in the reaction dynamics of a relatively simple molecule.
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
Authors: Choudhary Chunaram , Kumar Chanchal , Gnad Florian , Nielsen Michael L. , Rehman Michael , Walther Tobias C. , Olsen Jesper V. , Mann Matthias
Published: July 2009

Lysine Acetylation Catalog

Covalent posttranslational modification is an essential cellular regulatory mechanism by which the activity of proteins can be controlled. Advances in mass spectrometry made it possible for

Choudhary
et al.

(p.
834
, published online 16 July) to assess the prevalence of lysine acetylation throughout the whole proteome. Acetylation is much more widespread than previously appreciated and occurs on proteins participating in all sorts of biological functions. Acetylation can influence susceptibility of proteins to phosphorylation and occurs frequently on enzymes that control the modification of other proteins by covalent ubiquitination and on proteins that form large macromolecular complexes. The findings also help to characterize the actions of lysine deacetylase inhibitors, which have shown clinical promise in treatments for cancer.
The Flexible Organism
Ecological Developmental Biology
Integrating Epigenetics, Medicine, and Evolution

by Scott F. Gilbert and David Epel

Sinauer Associates, Sunderland, MA, 2009. 496 pp. $49.95. ISBN 9780878932993.
Authors: Pfennig David W. , Ledón-Rettig Cris
Published: July 2009

Gilbert and Epel focus on embryonic and larval development of metazoans to explore where "embryology meets the real world."
Foundations for a New Science of Learning
Authors: Meltzoff Andrew N. , Kuhl Patricia K. , Movellan Javier , Sejnowski Terrence J.
Published: July 2009

Dissecting Dyslexia and Learning

Difficulties in learning to read, despite reasonable effort and instruction, form the basis of dyslexia.Gabrieli(p.280; see the cover) now reviews the latest research into the causes of dyslexia. Neuroimaging studies may give early notice of impending dyslexia, and it is hoped that early interventions may lessen the impact of dyslexia. Learning occurs in many settings. Humans uniquely use the formalized settings of schools and curriculum. Infants and children also do plenty of learning outside these settings, often intermingling social interactions.Meltzoffet al.(p.284) survey the variety of learning contexts that people experience and discuss how recent advances in neuroscience and robotics are driving a new synthesis of learning.
Entanglement with a Twist
The Age of Entanglement
When Quantum Physics Was Reborn

by Louisa Gilder

Alfred A. Knopf, New York, 2008. 462 pp. $27.50, C$32. ISBN 9781400044177.
Authors: Dowling Jonathan P.
Published: July 2009

Weaving her narrative around a series of imagined face-to-face dialogues, Gilder offers an account of the development of quantum physics that pays particular attention to developments through the second half of the 20th century.
Is Quantum Theory Exact?
Authors: Adler Stephen L. , Bassi Angelo
Published: July 2009

Future experiments may tell us if quantum mechanics is an approximation to a deeper-level theory.
Edge-State Physics Without Magnetic Fields
Authors: Büttiker Markus
Published: July 2009

A novel class of materials called topological insulators allows spin physics to be probed without the need for magnetic fields.
What Drives Climate Flip-Flops?
Authors: Timmermann Axel , Menviel Laurie
Published: July 2009

A numerical modeling study questions the validity of a key paradigm in rapid climate change studies.
Does Viral Diversity Matter?
Authors: Medley Graham F. , Nokes D. James
Published: July 2009

Detailed analyses of population demographics and viral diversity should help predict the impact of childhood vaccination for endemic viruses such as rotavirus.
Beneficial Biofuels—The Food, Energy, and Environment Trilemma
Authors: Tilman David , Socolow Robert , Foley Jonathan A. , Hill Jason , Larson Eric , Lynd Lee , Pacala Stephen , Reilly John , Searchinger Tim , Somerville Chris , Williams Robert
Published: July 2009

Exploiting multiple feedstocks, under new policies and accounting rules, to balance biofuel production, food security, and greenhouse-gas reduction.
Earth System Research Priorities
Authors: Reid Walter V. , Bréchignac Catherine , Tseh Lee Yuan
Published: July 2009

Human-induced climate change was unknown outside of limited scientific circles just 25 years ago, but it has now become the focus of intense national discussions and international negotiations. One chapter in the story of how this issue moved from lab benches to national capitals was recognized by the 2007 Nobel Peace Prize, which was co-awarded to the Intergovernmental Panel on Climate Change (IPCC) for its influential assessments of the state of scientific knowledge. But the story also involves the research itself; in particular, that catalyzed by the Global Environmental Change Research Programmes
*
and the Earth System Science Partnership. These programs, sponsored by the International Council for Science (ICSU) in partnerships with other international science organizations (
www.icsu.org
), have helped to catalyze and guide global environmental research for several decades. But it's time to propose new research priorities, and ICSU seeks input through a Web consultation process now under way.
Questions About the Language of God
Authors: Kaiser Jocelyn
Published: July 2009

Although many scientists say geneticist Francis Collins will make a superb director of the National Institutes of Health, a discussion about whether Collins's very public religious views will influence his leadership of NIH has been playing out on blogs.
Geophysicist McNutt Named to Lead U.S. Geological Survey
Authors: Kerr Richard A.
Published: July 2009

Marcia McNutt, president and CEO of the Monterey Bay Aquarium Research Institute, was nominated last week to be the next director of the U.S. Geological Survey.
Sequencing Neandertal Mitochondrial Genomes by the Half-Dozen
Authors: Pennisi Elizabeth
Published: July 2009

On page 318 of this week's issue of
Science
, researchers describe a new technique to decipher the entire mitochondrial genomes from five Neandertals. These genomes show relatively little genetic diversity among Neandertals scattered across Europe and Russia.
Lunar Survey Spacecraft Develops an Attitude Problem
Authors: Bagla Pallava
Published: July 2009

India's first moon probe, Chandrayaan-1, has suffered a critical malfunction that jeopardizes the remainder of the mission. The spacecraft, which entered lunar orbit last November, can no longer orient itself with high precision.
Roundup of Utah Collectors Stirs a Debate on Enforcement
Authors: Kloor Keith
Published: July 2009

Last month, 16 residents of Blanding, Utah, were arrested and accused of stealing prehistoric Indian artifacts from public and tribal lands, the culmination of a 2.5-year-old undercover investigation by the Federal Bureau of Investigation and the Department of the Interior that netted 24 alleged looters in the archaeology-rich Four Corners region.
Prosperity's Plague
Authors: Taubes Gary
Published: July 2009

Researchers have linked a growing number of chronic diseases to the metabolic disorder known as insulin resistance; two general theories have emerged about its mechanism.
Shifting Orbits Gave Solar System A Big Shakeup, Model Suggests
Authors: Kerr Richard A.
Published: July 2009

Dynamicists simulating the solar system's early days are finding that a violent reshuffling of bodies large and small may explain many of today's planetary mysteries.
Single-Antigen Serological Testing for Bovine Tuberculosis
Authors: Green Lawrence R. , Jones Cynthia C. , Sherwood Anne L. , Garkavi Inna V. , Cangelosi Gerard A. , Thacker Tyler C. , Palmer Mitchell V. , Waters W. Ray , Rathe Chris V.
Published: July 2009

Antibody responses are useful indicators of
Mycobacterium bovis
infection of cattle. Tests for such responses often use multiple
M. bovis
antigens as detection probes. This is recommended because responses to single antigens may be too variable for consistent diagnosis. However, the use of multiple antigens increases costs and the risk of false-positive results. As an alternative, the SeraLyte-
Mbv
system detects responses to a single
M. bovis
antigen, MPB83, by using a chemiluminescent testing platform with a high degree of analytical sensitivity. Testing with the SeraLyte-
Mbv
system was conducted in a blinded fashion with sera from experimentally infected and control cattle. To assess the species specificity of the single-antigen test, the sample included sera from animals infected with
M. bovis
(
n
= 27),
M. kansasii
(
n
= 4),
M. avium
subsp.
paratuberculosis
(
n
= 11),
M. avium
subsp.
avium
(
n
= 12), and uninfected animals (
n
= 15). Upon unblinding of the results, the sensitivity of the SeraLyte-
Mbv
system relative to the results for animals with known
M. bovis
infection was 89%. Consistent with the conservation of MPB83 sequences within the genus
Mycobacterium
, all 4
M. kansasii
-infected animals tested positive with the SeraLyte-
Mbv
system and all 23
M. avium
-infected animals tested negative. Blinded analysis of 30 serum samples collected from nine animals at various time points postinfection indicated 100% sensitivity after ≥3 months postinfection. All 15 uninfected samples in the blinded sample set tested negative with the SeraLyte-
Mbv
system. Unblinded analysis of sera from an additional 895 animals in 10 accredited bovine tuberculosis-free states revealed 98% specificity overall. The results support the feasibility of single-antigen testing for bovine tuberculosis with the SeraLyte-
Mbv
system.
Comparative Evaluation of the Immune Responses and Protection Engendered by LC16m8 and Dryvax Smallpox Vaccines in a Mouse Model
Authors: Meseda Clement A. , Mayer Anne E. , Kumar Arunima , Garcia Alonzo D. , Campbell Joseph , Listrani Paul , Manischewitz Jody , King Lisa R. , Golding Hana , Merchlinsky Michael , Weir Jerry P.
Published: July 2009

The immune response elicited by LC16m8, a candidate smallpox vaccine that was developed in Japan by cold selection during serial passage of the Lister vaccine virus in primary rabbit kidney cells, was compared to Dryvax in a mouse model. LC16m8 carries a mutation resulting in the truncation of the B5 protein, an important neutralizing target of the extracellular envelope form of vaccinia virus (EV). LC16m8 elicited a broad-spectrum immunoglobulin G (IgG) response that neutralized both EV and the intracellular mature form of vaccinia virus and provoked cell-mediated immune responses, including the activation of CD4
+
and CD8
+
cells, similarly to Dryvax. Mice inoculated with LC16m8 had detectable but low levels of anti-B5 IgG compared to Dryvax, but both Dryvax and LC16m8 sera neutralized vaccinia virus EV in vitro. A truncated B5 protein (∼8 kDa) was expressed abundantly in LC16m8-infected cells, and both murine immune sera and human vaccinia virus immunoglobulin recognized the truncated recombinant B5 protein in antigen-specific enzyme-linked immunosorbent assays. At a high-dose intranasal challenge (100 or 250 50% lethal doses), LC16m8 and Dryvax conferred similar levels of protection against vaccinia virus strain WR postvaccination. Taken together, the results extend our current understanding of the protective immune responses elicited by LC16m8 and indicate that the relative efficacy in a mouse model rivals that of previously licensed smallpox vaccines.
Oral Immunization with AttenuatedSalmonella entericaSerovar Typhimurium EncodingCryptosporidium parvumCp23 and Cp40 Antigens Induces a Specific Immune Response in Mice
Authors: Benitez Alvaro J. , McNair Nina , Mead Jan R.
Published: July 2009

AttenuatedSalmonella entericaserovar Typhimurium vaccine strain SL3261 was used as an antigen delivery system for the oral immunization of mice against twoCryptosporidium parvumantigens, Cp23 and Cp40. Each antigen was subcloned into the pTECH1 vector system, which allows them to be expressed as fusion proteins with highly immunogenic fragment C of tetanus toxin under the control of the anaerobically induciblenirBpromoter. The recombinant vector was introduced intoSalmonellaTyphimurium vaccine strain SL3261, and the stable soluble expression of the chimeric protein was evaluated and confirmed by Western blotting with polyclonalC. parvumantisera. Mice were inoculated orally with a single dose of SL3261/pTECH-Cp23 or Cp40, respectively, and plasmid stability was demonstrated both in vitro and in vivo. Specific serum immunoglobulin G (IgG) antibodies against the Cp23 or Cp40 antigen were detected by enzyme-linked immunosorbent assay 35 days after immunization. Also, serum IgA and mucosal (feces) IgA antibodies were detected in 30% of the mice immunized with Cp23. In addition, prime-boosting with Cp23 and Cp40 DNA vaccine vectors followed bySalmonellaimmunization significantly increased antibody responses to both antigens. Our data show that a single oral inoculation with recombinantS. Typhimurium SL3261 can induce specific antibody responses to the Cp23 or Cp40 antigen fromC. parvumin mice, suggesting that recombinantSalmonellais a feasible delivery system for a vaccine againstC. parvuminfection.
Towards Identification of the Mechanisms of Action of Parasite-Derived Peptide GK1 on the Immunogenicity of an Influenza Vaccine
Authors: Segura-Velázquez René , Fragoso Gladis , Sciutto Edda , Sarukhan Adelaida
Published: July 2009

Previous studies have shown that the synthetic peptide GK1, derived from
Taenia crassiceps
cysticerci, enhances the immunogenicity of the commercial inactivated influenza vaccine Fluzone in both young and aged mice. In particular, antibody responses were much improved. Since GK1 is a peptide and is rapidly cleared from the body, it offers the possibility to improve vaccine performance without undesirable effects. This study was therefore designed to understand the mechanisms of action involved in the adjuvant properties of GK1. For this, transgenic mice expressing a T-cell receptor specific for an epitope from the influenza virus hemagglutinin (HA) protein were employed. The GK1 peptide significantly increased the in vivo proliferative response of HA-specific CD4
+
T cells when it was coimmunized with the HA epitope. Dendritic cells treated in vitro with GK1 were capable of enhancing T-cell activation. Furthermore, in synergy with lipopolysaccharide, GK1 enhanced the expression of major histocompatibility complex class II and costimulatory molecules of dendritic cells and promoted the secretion of proinflammatory cytokines and chemokines upon antigen-driven T-cell interaction. These data provide important insights into the mechanism that underlies the GK1 adjuvant capacity observed previously and underline the feasibility of using the transgenic mouse model described herein as a tool for investigation of the modes of action of different influenza vaccine adjuvants.
Safety and Immunogenicity of the Merck Adenovirus Serotype 5 (MRKAd5) and MRKAd6 Human Immunodeficiency Virus Type 1 Trigene Vaccines Alone and in Combination in Healthy Adults
Authors: Harro Clayton , Sun Xiao , Stek Jon E. , Leavitt Randi Y. , Mehrotra Devan V. , Wang Fubao , Bett Andrew J. , Casimiro Danilo R. , Shiver John W. , DiNubile Mark J. , Quirk Erin
Published: July 2009

Preexisting immunity to adenovirus serotype 5 (Ad5) diminishes immune responses to vaccines using Ad5 as a vector. Alternate Ad serotypes as vaccine vectors might overcome Ad5-specific neutralizing antibodies and enhance immune responses in populations with a high prevalence of Ad5 immunity. To test this hypothesis, healthy human immunodeficiency virus (HIV)-seronegative adults were enrolled in a blinded, randomized, dose-escalating, placebo-controlled study. In part A, subjects with baseline Ad6 titers of ≤18 received the Merck Ad6 (MRKAd6) HIV type 1 (HIV-1) trigene vaccine at weeks 0, 4, and 26. In part B, subjects stratified by Ad5 titers (≤200 or >200) and Ad6 titers (≤18 or >18) received the MRKAd5-plus-MRKAd6 (MRKAd5+6) HIV-1 trigene vaccine at weeks 0, 4, and 26. Immunogenicity was assessed by an enzyme-linked immunospot (ELISPOT) assay at week 30. No serious adverse events occurred. MRKAd6 trigene vaccine recipients responded more often to Nef than to Gag or Pol. In part A, ELISPOT response rates to ≥2 vaccine antigens were 14%, 63%, and 71% at 10
9
, 10
10
, and 10
11
viral genomes (vg)/dose, respectively. All responders had positive Nef-specific ELISPOT results. In part B, Nef-ELISPOT response rates at 10
10
vg/dose of the MRKAd5+6 trigene vaccine were 50% in the low-Ad5/low-Ad6 stratum (
n
= 8), 78% in the low-Ad5/high-Ad6 stratum (
n
= 9), 75% in the high-Ad5/low-Ad6 stratum (
n
= 8), and 44% in the high-Ad5/high-Ad6 stratum (
n
= 9). The MRKAd6 and MRKAd5+6 trigene vaccines elicited dose-dependent responses predominantly to Nef and were generally well tolerated, indicating that Ad6 should be considered a candidate vector for future vaccines. Although small sample sizes limit the conclusions that can be drawn from this exploratory study, combining two Ad vectors may be a useful vaccine strategy for circumventing isolated immunity to a single Ad serotype.
Characterization of
Listeria monocytogenes
Isolates from Human Listeriosis Cases in Italy
Authors: Mammina Caterina , Aleo Aurora , Romani Cristina , Pellissier Nathalie , Nicoletti Pierluigi , Pecile Patrizia , Nastasi Antonino , Pontello Mirella M.
Published: July 2009

The objective of this study was to characterize by serotyping, pulsed-field gel electrophoresis (PFGE), and PCR amplification of virulence genes and markers of epidemic clones I, II, and III (ECI, ECII, and ECIII) 54 human isolates from apparently sporadic cases of infection occurring in the Lombardy region and in the province of Florence, Tuscany, Italy, in the years 1996 to 2007.
Listeria monocytogenes
isolates were provided by the clinical microbiology laboratories of the Lombardy region and the “Careggi” Hospital of Florence, Tuscany, Italy. Serotyping, PFGE after digestion with the AscI and ApaI enzymes, and PCR amplification for the
inlA
,
inlC
, and
inlJ
genes and ECI, ECII, and ECIII markers were performed according to procedures described previously. Twenty-five (46.3%)
L. monocytogenes
isolates were assigned to serotype 1/2a, 23 (42.6%) to serotype 4b, and 6 (11.1%) to serotype 1/2b. Thirty-one AscI pulsotypes were recognized among the 54 human isolates. Eleven molecular subtype clusters, of which eight included indistinguishable pulsotypes and three included closely related pulsotypes, were shared by two to seven isolates. Fifteen isolates exhibited unique AscI pulsotypes. Three groups of clustered isolates and two apparently sporadic isolates generated EC amplicons. All strains tested positive for the
inlA
,
inlC
, and
inlJ
genes. Based on the results of serotyping and molecular typing, there were 11 occasions when
L. monocytogenes
strains with the same subtype were isolated from more than one listeriosis case. A total of 39 out of 54 isolates (72.2%) were attributed to molecular subtype clusters. The results of the study suggest that routine subtyping of
L. monocytogenes
strains from human listeriosis cases could allow more-timely detection of outbreaks possibly caused by food-borne isolates from a common source and could lead to control of ongoing food exposure, thus preventing the occurrence of more cases.
Characterization of Clinical
Enterococcus faecalis
Small-Colony Variants
Authors: Wellinghausen Nele , Chatterjee Indranil , Berger Anja , Niederfuehr Andrea , Proctor Richard A. , Kahl Barbara C.
Published: July 2009

In this report, we present a clinical case of chronic aortic valve endocarditis caused by
Enterococcus faecalis
small-colony variants (SCVs), with ensuing characterization of the SCV phenotype in comparison to the clonally related normal phenotype with respect to alterations in microscopic and ultrastructural morphology, growth behavior, and metabolic pathways. In contrast to the normal phenotype, light and electron microscopy of the
Enterococcus
SCVs demonstrated the presence of heterogeneous cells of different sizes with aberrant shapes. Furthermore, SCVs showed excessive production of an intercellular substance and alterations in cell division displayed by a thick, coarse cell wall and incomplete, branched, and multiple cross walls without obvious cell separation. In addition, empty “ghost” cells were visible. In growth experiments, SCVs displayed an extended lag phase with delayed entrance into the stationary phase. Interestingly, SCV cells growing under aerobic conditions did not attain the growth and viability of the normal phenotype or those of SCVs growing under microaerobic conditions, suggesting impaired growth behavior and enhanced vulnerability in the presence of oxygen. By metabolite analysis, SCVs failed to produce significant amounts of acetate or lactate under aerobic growth conditions but were able to produce lactate under microaerobic growth conditions, implicating the induction of a fermentative metabolism. In conclusion, the observed structural alterations and changes in the cellular growth and metabolic pathways facilitated the survival of
Enterococcus
SCVs under microaerobic conditions in vitro and thus presumably in vivo during endocarditis.
Quantification of Hepatitis C Virus (HCV) RNA in a Multicenter Study: Implications for Management of HCV Genotype 1-Infected Patients
Authors: Pisani Giulio , Cristiano Karen , Marino Francesco , Luciani Francesca , Bisso Guillermo M. , Mele Claudio , Adriani Daniela , Gentili Giuliano , Wirz Maria
Published: July 2009

Assessment of the viral load in hepatitis C virus (HCV) genotype 1-infected patients is critical before, during, and after antiviral therapy. In patients achieving a rapid virological response at week 4 of treatment, the viral load at the baseline is considered a predictive criterion of a sustained virological response 24 weeks after the discontinuation of treatment. A ≥2-log10drop in the viral load at week 12 of treatment (early virological response) triggers the continuation of therapy. We organized a multicenter study (MS) for diagnostic laboratories involved in the quantification of HCV RNA. Commercial assays, including two based on real-time reverse transcription-PCR (TaqMan system), and in-house methods, were used by the 61 participants. The overall reproducibility of the commercial quantitative nucleic acid amplification techniques (qNAT) was acceptable. As the intermethod variability among commercial qNAT for HCV RNA was still present, the manufacturers of these test kits should join efforts to harmonize the means of quantification of HCV RNA. This study also shows that caution should be exercised when the baseline viral load is evaluated and when the 2-log10reduction after 12 weeks of therapy is interpreted. Finally, this MS confirms the higher sensitivity of the commercial qNAT based on the TaqMan system, making them the elective assays for the monitoring of therapy.
Real-Time Quantitative Reverse Transcription-PCR Assays Specifically Detecting Bluetongue Virus Serotypes 1, 6, and 8
Authors: Hoffmann Bernd , Eschbaumer Michael , Beer Martin
Published: July 2009

Bluetongue virus (BTV) is a major pathogen of ruminants. Especially serotypes 1, 6, and 8 are of concern to veterinary authorities in central Europe. This article describes highly sensitive real-time reverse transcription-PCR assays directed to BTV genome segment 2 for specific detection of BTV-1, -6, or -8 in animal samples.
Efficacy of Bilateral Bronchoalveolar Lavage for Diagnosis of Ventilator-Associated Pneumonia
Authors: Zaccard Colleen R. , Schell Ronald F. , Spiegel Carol A.
Published: July 2009

Ventilator-associated pneumonia (VAP) is a common nosocomial infection causing significant morbidity and mortality. The goal of this study was to determine the efficacy of bilateral versus unilateral bronchoalveolar lavage (BAL) for the detection of the causative bacterial agents of VAP. We retrospectively studied the quantitative bacterial cultures of 399 BAL sample pairs collected from 287 mechanically ventilated patients over a 5-year period at a U.S. tertiary-care teaching hospital. Trauma was the underlying illness in 69% of patients. No evidence of bacterial infection was found in 226 BAL pairs (56.6%). Among 173 positive BAL sample pairs, significant bacterial counts were detected exclusively in 6.4% of left-lung and 12.1% of right-lung samples. In contrast, 81.5% of positive sample pairs had significant bacterial counts in both lungs. All bacteria recovered at significant concentrations from bilateral samples would have been detected in a unilateral right-lung sample in 89% of positive sample pairs. Unilateral sampling would have failed to recover one or more significant isolates in 11% of positive pairs had only the right lung been sampled and in 16.7% had only the left lung been sampled. Our study shows that preferential sampling of the right lung improves the diagnostic efficacy of unilateral BAL for the detection of the etiologic agents of VAP. If bilateral sampling is performed, our results also indicate that pooling left- and right-lung samples for a single quantitative culture is comparable to processing samples individually.
Evaluation of the Cavidi ExaVir Load Assay (Version 3) for Plasma Human Immunodeficiency Virus Type 1 Load Monitoring
Authors: Greengrass Vicki L. , Plate Megan M. , Steele Pauline M. , Denholm Justin T. , Cherry Catherine L. , Morris Lisa M. , Hearps Anna , Crowe Suzanne M.
Published: July 2009

We evaluated the new low-cost ExaVir Load (version 3) reverse transcriptase viral load assay against the Roche Cobas Amplicor assay. Results for samples tested using the reverse transcriptase assay correlated well with those obtained with the Roche assay (
r
= 0.85;
n
= 202). The version 3 reverse transcriptase assay shows improved sensitivity compared to the previous version.
Airway Infection with a Novel
Cupriavidus
Species in Persons with Cystic Fibrosis
Authors: Kalka-Moll Wiltrud Maria , LiPuma John J. , Accurso Frank J. , Plum Georg , van Koningsbruggen Silke , Vandamme Peter
Published: July 2009

We describe the recovery and identification of a bacterium that represents a new species of the genus
Cupriavidus
from cultures of respiratory tract specimens from two patients with cystic fibrosis (CF). The elucidation of the role of this species in CF lung disease will require an evaluation of a greater number of cases.
Report of Neonatal Meningitis Due to
Salmonella enterica
Serotype Agona and Review of Breast Milk-Associated Neonatal
Salmonella
Infections
Authors: Cooke Fiona J. , Ginwalla Sara , Hampton Michael D. , Wain John , Ross-Russell Robert , Lever Andrew , Farrington Mark
Published: July 2009

We present the first documented case of
Salmonella enterica
serotype Agona meningitis in a 6-day-old baby.
S. enterica
serotype Agona was isolated concurrently from infant cerebrospinal fluid and parental fecal samples, and
Salmonella
was isolated from breast milk. The role of breast milk in transmission of
Salmonella enterica
is discussed.
Assessment of Flocked Swabs for Use in Identification of Streptococcal Pharyngitis
Authors: Goldfarb David M. , Slinger Robert , Tam Ron K. , Barrowman Nicholas , Chan Francis
Published: July 2009

We compared the performance of flocked swabs to that of traditional swabs for culture of beta-hemolytic streptococci in children with pharyngitis. Sensitivity was higher for flocked swabs, but this did not reach statistical significance. We conclude that flocked swabs can be used in place of traditional swabs for diagnosis of streptococcal pharyngitis.
Prevalence and Management of Invalid GeneXpert Enterovirus Results Obtained with Cerebrospinal Fluid Samples: a 2-Year Study
Authors: Sefers Susan E. , Raymer Anna K. , Kilby Jessica T. , Persing David H. , Tang Yi-Wei
Published: July 2009

A total of 525 cerebrospinal fluid (CSF) samples submitted during the 2007 and 2008 enteroviral seasons were included in a study to determine the prevalence of and potential risk factors for invalid Cepheid GeneXpert enterovirus assay (GXEA) results, as well as possible solutions for the problem. The invalid GXEA results were reported for 43 (8.2%) specimens and correlated with increased visibility of red blood cells (P< 0.0001) but not with CSF xanthochromia and clotting. Invalid GXEA result rates were markedly diminished by 82.1% and 96.0% and test sensitivities were minimally decreased by 1.7% and 3.6% when these specimens were tested at a 1:5 dilution and after a freeze-thaw cycle, respectively.
Selective Expression of Human Immunodeficiency Virus Nef in Specific Immune Cell Populations of Transgenic Mice Is Associated with Distinct AIDS-Like Phenotypes
Authors: Hanna Zaher , Priceputu Elena , Chrobak Pavel , Hu Chunyan , Dugas Véronique , Goupil Mathieu , Marquis Miriam , de Repentigny Louis , Jolicoeur Paul
Published: July 2009

We previously reported that CD4C/human immunodeficiency virus (HIV)Neftransgenic (Tg) mice, expressing Nef in CD4+T cells and cells of the macrophage/dendritic cell (DC) lineage, develop a severe AIDS-like disease, characterized by depletion of CD4+T cells, as well as lung, heart, and kidney diseases. In order to determine the contribution of distinct populations of hematopoietic cells to the development of this AIDS-like disease, five additional Tg strains expressing Nef through restricted cell-specific regulatory elements were generated. These Tg strains express Nef in CD4+T cells, DCs, and macrophages (CD4E/HIVNef); in CD4+T cells and DCs (mCD4/HIVNefand CD4F/HIVNef); in macrophages and DCs (CD68/HIVNef); or mainly in DCs (CD11c/HIVNef). None of these Tg strains developed significant lung and kidney diseases, suggesting the existence of as-yet-unidentified Nef-expressing cell subset(s) that are responsible for inducing organ disease in CD4C/HIVNefTg mice. Mice from all five strains developed persistent oral carriage ofCandida albicans, suggesting an impaired immune function. Only strains expressing Nef in CD4+T cells showed CD4+T-cell depletion, activation, and apoptosis. These results demonstrate that expression of Nef in CD4+T cells is the primary determinant of their depletion. Therefore, the pattern of Nef expression in specific cell population(s) largely determines the nature of the resulting pathological changes.
Novel Translation Products from Simian Immunodeficiency Virus SIVmac239 Env-Encoding mRNA Contain both Rev and Cryptic T-Cell Epitopes
Authors: Maness Nicholas J. , Sacha Jonah B. , Piaskowski Shari M. , Weisgrau Kimberly L. , Rakasz Eva G. , May Gemma E. , Buechler Matthew B. , Walsh Andrew D. , Wilson Nancy A. , Watkins David I.
Published: July 2009

Understanding the correlates of immune protection against human immunodeficiency virus and simian immunodeficiency virus (SIV) will require defining the entire cellular immune response against the viruses. Here, we define two novel translation products from the SIVenvmRNA that are targeted by the T-cell response in SIV-infected rhesus macaques. The shorter product is a subset of the larger product, which contains both the first exon of the Rev protein and a translated portion of therevintron. Our data suggest that the translation of viral alternate reading frames may be an important source of T-cell epitopes, including epitopes normally derived from functional proteins.
Upregulation of Interleukin 7 Receptor Alpha and Programmed Death 1 Marks an Epitope-Specific CD8+T-Cell Response That Disappears following Primary Epstein-Barr Virus Infection
Authors: Sauce Delphine , Larsen Martin , Abbott Rachel J. M. , Hislop Andrew D. , Leese Alison M. , Khan Naeem , Papagno Laura , Freeman Gordon J. , Rickinson Alan B.
Published: July 2009

In immunocompetent individuals, the stability of the herpesvirus-host balance limits opportunities to study the disappearance of a virus-specific CD8+T-cell response. However, we noticed that in HLA-A*0201-positive infectious mononucleosis (IM) patients undergoing primary Epstein-Barr virus (EBV) infection, the initial CD8 response targets three EBV lytic antigen-derived epitopes, YVLDHLIVV (YVL), GLCTLVAML (GLC), and TLDYKPLSV (TLD), but only the YVL and GLC reactivities persist long-term; the TLD response disappears within 10 to 27 months. While present, TLD-specific cells remained largely indistinguishable from YVL and GLC reactivities in many phenotypic and functional respects but showed unique temporal changes in two markers of T-cell fate, interleukin 7 receptor alpha (IL-7Rα; CD127) and programmed death 1 (PD-1). Thus, following the antigen-driven downregulation of IL-7Rα seen on all populations in acute IM, in every case, the TLD-specific population recovered expression unusually quickly post-IM. As well, in four of six patients studied, TLD-specific cells showed very strong PD-1 upregulation in the last blood sample obtained before the cells’ disappearance. Our data suggest that the disappearance of this individual epitope reactivity from an otherwise stable EBV-specific response (i) reflects a selective loss of cognate antigen restimulation (rather than of IL-7-dependent signals) and (ii) is immediately preceded, and perhaps mediated, by PD-1 upregulation to unprecedented levels.
RNA-Based Regulation of Transcription and Translation of Aureusvirus Subgenomic mRNA1
Authors: Xu Wei , White K. Andrew
Published: July 2009

Cucumber leaf spot virus
(CLSV) is an aureusvirus (family
Tombusviridae
) that has a positive-sense RNA genome encoding five proteins. During infections, CLSV transcribes two subgenomic (sg) mRNAs and the larger of the two, sg mRNA1, encodes coat protein. Here, the viral RNA sequences and structures that regulate transcription and translation of CLSV sg mRNA1 were investigated. A medium-range RNA-RNA interaction in the CLSV genome, spanning 148 nucleotides, was found to be required for the efficient transcription of sg mRNA1. Further analysis indicated that the structure formed by this interaction acted as an attenuation signal required for transcription of sg mRNA1 via a premature termination mechanism. Translation of coat protein from sg mRNA1 was determined to be facilitated by a 5′-terminal stem-loop structure in the message that resembled a tRNA anticodon stem-loop. The results from mutational analysis indicated that the 5′-terminal stem-loop mediated efficient base pairing with a 3′-cap-independent translational enhancer at the 3′ end of the message, leading to efficient translation of coat protein from sg mRNA1. Comparison of the regulatory RNA structures for sg mRNA1 of CLSV to those used by the closely related tombusviruses and certain cellular RNAs revealed interesting differences and similarities that provide evolutionary and mechanistic insights into RNA-based regulatory strategies.
Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons
Authors: Burns Cara C. , Campagnoli Ray , Shaw Jing , Vincent Annelet , Jorba Jaume , Kew Olen
Published: July 2009

Replicative fitness of poliovirus can be modulated systematically by replacement of preferred capsid region codons with synonymous unpreferred codons. To determine the key genetic contributors to fitness reduction, we introduced different sets of synonymous codons into the capsid coding region of an infectious clone derived from the type 2 prototype strain MEF-1. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased sharply with increased frequencies of the dinucleotides CpG (suppressed in higher eukaryotes and most RNA viruses) and UpA (suppressed nearly universally). Replacement of MEF-1 capsid codons with the corresponding codons from another type 2 prototype strain (Lansing), a randomization of MEF-1 synonymous codons, increased the %G+C without increasing CpG, and reductions in the effective number of codons used had much smaller individual effects on fitness. Poliovirus fitness was reduced to the threshold of viability when CpG and UpA dinucleotides were saturated within and across synonymous codons of a capsid region interval representing only ∼9% of the total genome. Codon replacements were associated with moderate decreases in total virion production but large decreases in the specific infectivities of intact poliovirions and viral RNAs. Replication of codon replacement viruses, but not MEF-1, was temperature sensitive at 39.5°C. Synthesis and processing of viral intracellular proteins were largely unaltered in most codon replacement constructs. Replacement of natural codons with synonymous codons with increased frequencies of CpG and UpA dinucleotides may offer a general approach to the development of attenuated vaccines with well-defined antigenicities and very high genetic stabilities.
Derivation and Characterization of a Simian Immunodeficiency Virus SIVmac239 Variant with Tropism for CXCR4
Authors: Del Prete Gregory Q. , Haggarty Beth , Leslie George J. , Jordan Andrea P. O. , Romano Josephine , Wang Nathaniel , Wang Jianbin , Holmes Michael C. , Montefiori David C. , Hoxie James A.
Published: July 2009

Like human immunodeficiency virus type 1 (HIV-1), most simian immunodeficiency virus (SIV) strains use CCR5 to establish infection. However, while HIV-1 can acquire the ability to use CXCR4, SIVs that utilize CXCR4 have rarely been reported. To explore possible barriers against SIV coreceptor switching, we derived an R5X4 variant, termed 239-ST1, from the R5 clone SIVmac239 by serially passaging virus in CD4
+
CXCR4
+
CCR5
−
SupT1 cells. A 239-ST1
env
clone, designated 239-ST1.2-32, used CXCR4 and CCR5 in cell-cell fusion and reporter virus infection assays and conferred the ability for rapid, cytopathic infection of SupT1 cells to SIVmac239. Viral replication was inhibitable by the CXCR4-specific antagonist AMD3100, and replication was abrogated in a novel CXCR4
−
SupT1 line. Surprisingly, parental SIVmac239 exhibited low-level replication in SupT1 cells that was not observed in CXCR4
−
SupT1 cells. Only two mutations in the 239-ST1.2-32 Env, K47E in the C1 domain and L328W in the V3 loop, were required for CXCR4 use in cell-cell fusion assays, although two other V3 changes, N316K and I324M, improved CXCR4 use in infection assays. An Env cytoplasmic tail truncation, acquired during propagation of 239-ST1 in SupT1 cells, was not required. Compared with SIVmac239, 239-ST1.2-32 was more sensitive to neutralization by five of seven serum and plasma samples from SIVmac239-infected rhesus macaques and was approximately 50-fold more sensitive to soluble CD4. Thus, SIVmac239 can acquire the ability to use CXCR4 with high efficiency, but the changes required for this phenotype may be distinct from those for HIV-1 CXCR4 use. This finding, along with the increased neutralization sensitivity of this CXCR4-using SIV, suggests a mechanism that could select strongly against this phenotype in vivo.