bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of rampant genitalic variation in the spider genus Homalonychus (Araneae, Homalonychidae)
Authors: Crews Sarah C.
Published: March 2009

Abstract. Animal genitalia are often complex and thought to vary little within species but differ between closely related species making them useful as primary characters in species diagnosis. Spiders are no exception, with nearly all of the 40,462 (at the time of this writing) described species differentiated by genitalic characteristics. However, in some cases, the genitalia of putative species are not uniform, but rather vary within species. When intraspecific variation overlaps interspecific variation, it can be difficult (if not impossible) to place a name on a specimen. The quantification of shape variation in genitalia has not often been attempted, probably because until recently it was not a methodologically and computationally simple process. In the two currently recognized species of the spider genus Homalonychus, genitalic variation is rampant in both male and female structures, with some parts of the genitalia (e.g., the retrolateral tibial apophysis) differing in each specimen examined. In this study, geometric morphometric analysis employing landmark data is used to quantify both intra‐ and interspecific variation in this genus. The large amount of variation is condensed into two or three groups depending on the structures examined, and these groups correspond to either the two species or to previously established mitochondrial DNA clades within one of the species. The results also show that analyses of female structures do not separate the groups as readily as the analyses of the male structures. The large amount of variation present in some structures is not correlated with geography or population genetic structure.
Polyfluorochrome marking slows growth only during the marking month in the green sea urchin Strongylocentrotus droebachiensis
Authors: Ellers Olaf , Johnson Amy S.
Published: March 2009

Abstract. Used singly, the fluorochrome tags tetracycline and calcein have yielded important insights into sea urchin biology, especially regarding growth. We present a new method of tagging using sequential fluorochrome markers, as well as a more precise method of quantifying growth. Such polyfluorochromes enable repeated markings that allow measurement of multiple growth points and unique identification of individuals or groups. We marked sea urchins, Strongylocentrotus droebachiensis, with four fluorochromes: alizarin complexone, calcein, calcein blue, and tetracycline. All fluorochromes marked both by injection and immersion. We examined the clarity of the mark produced with low, metabolically scaled doses, and higher doses similar to those that have been previously used. We tested the effect of fluorochromes on survival, growth, jaw size, and gonad size by marking a size range (3.9–44.3 mm in diameter) of urchins with either one or all four fluorochromes. We quantified growth using a nominal diameter, that is a fitted constant, times the cube root of weight, which increased the precision of measurements by a factor of six relative to measured diameter. Growth rate was a decreasing function of diameter except for a growth lag in the smallest urchins. Growth rate data for all sizes were fitted using: gamma distributions; Tanaka functions; and, for larger sizes, straight lines (von Bertalanffy model). All treatments produced clear marks, with higher doses producing more reliably clear marks. Tetracycline marking did not affect growth; other treatments produced only transient slowing of growth in the marking month. Growth rate, survival, gonad production, and jaw weight did not differ between control and treatments during the following 6 months. Thus, polyfluorochromes produce reliable marks that do not significantly affect growth or gonad production.
Allelic inheritance in naturally occurring parthenogenetic offspring of the gonochoric sea star Patiria miniata
Authors: Sunday Jennifer , Raeburn Lisa , Stewart Heather , Hart Michael W.
Published: March 2009

Abstract. In laboratory studies of fertilization using the gonochoric broadcast‐spawning asterinid sea star Patiria miniata, we found many cases in which some mature eggs spawned by females formed cleavage‐stage embryos and feeding bipinnaria larvae without fertilization by sperm. Segregation of maternal microsatellite alleles among the parthenogenetic offspring of known heterozygous females was consistent with several specific modes of asexual reproduction, including polar body suppression. Cryptic outcrossing by sperm contamination was ruled out by the failure to observe non‐maternal alleles. The potential for asexual reproduction by the normally outcrossing members of P. miniata may suggest a shared propensity for asexuality among asterinid species from several clades in which isolated adults can produce offspring without outcrossing.
Marketing healthy food to the least interested consumers
Authors: Lone Todd A. , Pence Dan , Levi Annette E. , Chan Kenny K. , Bianco‐Simeral Stephanie
Published: March 2009

This study discusses specific marketing strategies for two broad groups of consumers with radically different approaches to food selection. For over three decades strategies aimed at improving food choices assumed that providing nutritional information would change eating behaviors. We show that this strategy is only effective for consumers, a largely female group, already highly interested in the nutrient density and subsequent healthfulness of their food choices. In contrast, the nutritional information strategy does not change the food choices for those who have low interest in their food's nutrition, a group that is overwhelmingly male. These gender differences when making food choices are an opportunity for foodservice providers to implement a ‘dual‐track’ marketing strategy that can expand their customer base and increase their revenue while still meeting emerging nutrition mandates. In addition, this new approach will help address the nation's obesity epidemic.
The prevalence of impaired glucose metabolism in Hispanics with two or more risk factors for metabolic syndrome in the primary care setting
Authors: Neira Claudia P. , Hartig Margaret , Cowan Patricia A. , Velasquez‐Mieyer Pedro A.
Published: March 2009

Purpose: The purposes of this observational prospective study were (a) to identify the prevalence of undiagnosed impaired glucose metabolism (IGM) including impaired fasting glucose (IFG), impaired glucose tolerance (IGT), and type 2 diabetes mellitus (T2DM) in 55 Hispanic subjects with two or more risk factors for the metabolic syndrome, (b) to examine the association between glucose metabolism and cardiometabolic risk factors (CMRF), including metabolic syndrome components, and (c) to identify predictors of IGM.

Data sources: Subjects underwent a physical examination and a 2‐h 75‐g oral glucose tolerance test. Data were analyzed using SAS v9.1 with p ≤ .05 considered significant. Nonparametric tests were applied including Mann–Whitney–Wilcoxon test and Spearman correlation coefficient. Stepwise logistic multiple regression was used to predict IGM.

Conclusions: Twenty‐five patients (46%) had IGM (18% IFG, 15% IGT, and 13%T2DM). Normal fasting glucose was found in 48% of subjects who had IGM. Lipid abnormalities were present in 98% including elevated triglycerides (TG 66%), total cholesterol (48%), low‐density lipoprotein (68.8%), and low high‐density lipoprotein (67.9%). Twenty‐nine percent had body mass index (BMI) >25 kg/m2 and 62% had BMI >30 kg/m, hypertension (24%), and elevated high‐sensitivity C‐reactive protein (63%), and mean number of cardiometabolic risk factors (#CMRF) was 4.5. Mean values for each risk factor were no different between groups except for #CMRF (p = .0001) and TG (p = .0001). Total #CMRF was the best predictor of IGM.

Implications for Practice: The prevalence of IGM is extremely high in Hispanics with metabolic syndrome. Screening for IGM with fasting blood glucose alone underestimates the prevalence of IGM in this population. In subjects with multiple CMRF, screening at lower levels of BMI is warranted.
Mind, Brain, and Education: Building a Scientific Groundwork for Learning and Teaching1
Authors: Fischer Kurt W.
Published: March 2009

ABSTRACT— The primary goal of the emerging field of Mind, Brain, and Education is to join biology, cognitive science, development, and education in order to create a sound grounding of education in research. The growing, worldwide movement needs to avoid the myths and distortions of popular conceptions of brain and genetics and build on the best integration of research with practice, creating a strong infrastructure that joins scientists with educators to study effective learning and teaching in educational settings. Science and practice together provide many potentially powerful tools to improve education. Neuroscience and genetics make possible analysis of the “black box” of biological processes that underpin learning. Understanding the biology of abilities and disabilities helps educators and parents to facilitate individual students’ learning and development. Cognitive science provides analyses of the mental models/metaphors that pervade meaning making in human cultures, creating tools for avoiding unconscious distortions and crafting effective educational tools. Developmental and learning science produce tools to analyze learning pathways, including both shared patterns and learning differences. To reach the potential of grounding education effectively in research requires improving the infrastructure by creating (a) research schools where practice and science jointly shape educational research, (b) shared databases on learning and development, and (c) a new profession of educational engineers or translators to facilitate connecting research with practice and policy.
How Many Brains Does It Take to Build a New Light: Knowledge Management Challenges of a Transdisciplinary Project
Authors: Della Chiesa Bruno , Christoph Vanessa , Hinton Christina
Published: March 2009

ABSTRACT— The Organization for Economic Cooperation and Development’s (OECD) Center for Educational Research and Innovation (CERI) carried out the Learning Sciences and Brain Research project (1999–2007) to investigate how neuroscience research can inform education policy and practice. This transdisciplinary project brought many challenges. Within the political community, participation in the project varied, with some countries resisting approval of the project altogether, in the beginning. In the neuroscientific community, participants struggled to represent their knowledge in a way that would be meaningful and relevant to educators. Within the educational community, response to the project varied, with many educational researchers resisting it for fear that neuroscience research might make their work obsolete. Achieving dialogue among these communities was even more challenging. One clear obstacle was that participants had difficulty recognizing tacit knowledge in their own field and making this knowledge explicit for partners in other fields. This article analyzes these challenges through a knowledge management framework.
Can the Differences Between Education and Neuroscience be Overcome by Mind, Brain, and Education?
Authors: Samuels Boba M.
Published: March 2009

ABSTRACT—The new field of Mind, Brain, and Education (MBE)—sometimes called educational neuroscience—is posited as a mediator between neuroscience and education. Several foundational concerns, however, can be raised about this emerging field. The differences between neuroscience and education are many, including differences in their histories, philosophies, and epistemologies. Historically, science and education have demonstrated separate, but interwoven, influences on society; philosophically, the values by which they operate are often in opposition; and epistemologically, the fields have relied on different conceptualizations of knowledge. Discussion about these differences has been largely absent in attempts to promote MBE. Two steps are proposed to respond to this omission. First, encouraging discussion about disciplinary differences and assumptions may enable better understanding between disciplines and facilitate the establishment of a more collaborative research community. Second, atransdisciplinaryframework that focuses on salient issues of interest across disciplines should be considered. Transdisciplinarity aims for the creation of an inclusive research environment that transcends traditional disciplinary approaches to complex problems. This article initiates an exploration of disciplinary differences and proposes commitment to transdisciplinarity as a guiding principle that may increase the viability of MBE as a mediating field between neuroscience and education.
Middle lobe syndrome: a nationwide study on clinicopathological features and surgical treatment
Authors: Einarsson Jon Thorkell , Einarsson Jonas Geir , Isaksson Helgi , Gudbjartsson Tomas , Gudmundsson Gunnar
Published: March 2009

Introduction:  Middle lobe syndrome (MLS) is a relatively uncommon lung disease that is characterized by damage to the middle lobe and often needs surgical intervention.

Objective:  To study clinical, radiological and histological features of all patients who underwent surgical resection for MLS in Iceland over a 13‐year period, including evaluation of surgical outcome.

Methods:  Information on patients who underwent surgery of the right middle lobe in Iceland from 1984 to 2006 was obtained from a centralized diagnosis and pathology registry. Clinical data were collected retrospectively from clinical records from hospitals and from private offices. All pathology specimens were reviewed.

Results:  We studied 18 patients, 3 males and 15 females between the ages 2 and 86 years (mean 55). The most common clinical features were recurrent infection (n = 15), chronic cough with productive sputum (n = 9), chest pain (n = 8) or dyspnea (n = 7). The most common findings on chest radiographs and on computerized tomography of the chest were atelectasis, consolidation and bronchiectasis. One patient had a foreign body. The most common major histological finding was bronchiectasis in nine patients, and two had foreign body reaction. Minor findings included bronchiolitis, organizing pneumonia and peribronchial inflammation. All patients survived surgery with minor peri‐ and postoperative complications.

Conclusion:  MLS is more common in females, and recurrent infections, chronic productive cough and dyspnea were the most common symptoms. Bronchiectasis is the most common histological finding. MLS can be treated effectively with lobectomy with low mortality and rate of complications.

Please cite this paper as: Einarsson JT, Einarsson JG, Isaksson H, Gudbjartsson T and Gudmundsson G. Middle lobe syndrome: a nationwide study on clinicopathological features and surgical treatment. The Clinical Respiratory Journal 2009; 3: 77–81.
Work Motivation: Advancing Theory and Impact
Authors: Kanfer Ruth
Published: March 2009

It is not often that one gets the opportunity to engage other scholars in lively written dialogue on a topic close to his/her professional heart. So I felt honored to provide the target article on work motivation (Kanfer, 2009), and I looked forward to reading my colleagues’ commentaries. As I had hoped, each commentary was quite stimulating. Some commentaries were also provocative, whereas others were more instructive. Regardless of orientation and issue, however, each commentary reflected a positive, forward-looking tone. That is, from a Reichenbach (1951) perspective, the commentaries seem to emphasize discovery (e.g., building new perspectives and approaches) over justification (e.g., extending, refining, and reconciling extant theories that dominated much of the late 20th century). Although paradigmatic work remains important, its role is cast more in the service of new advances rather than the other way around. As the commentaries also demonstrate, many new ideas and research directions are emerging. Their traction and utility for work motivation scientists and organizational personnel raise exciting, empirical questions.
Aniridia among children and teenagers in Sweden and Norway
Authors: Edén Ulla , Beijar Caroline , Riise Ruth , Tornqvist Kristina
Published: March 2009

In the November 2008 issue (AOS 86:7), the article by Ulla Edén et al. was not published correctly in the printed issue. Unfortunately, part of the section ‘Visual acuity’ in the Results was repeated on page 732, and the start of the Discussion was omitted on page 732.

The full and correct version of this article is printed hereunder.

The Publisher apologises for this error.

Reference

Edén U,
Beijar C,
Riise R &
Tornqvist K (2008): .
Acta Ophthalmol
86: 730–734.

Purpose:  To investigate patients under the age of 20 with aniridia in Sweden and Norway in order to estimate the prevalence of aniridia, to describe clinical signs and identify complications in the young, which will help improve diagnostic tools and treatment.

Methods:  A thorough search for patients with aniridia (of all ages) was performed. Sixty‐two of the 181 patients were under the age of 20. Fifty‐two of them were examined and they constituted the study population. Patient history was obtained and all participants underwent clinical ophthalmologic examination, including photography. Blood samples were taken for mutation analysis.

Results:  Epidemiological data are only based on the results in Sweden. The age‐specific prevalence in Sweden was 1:47 000, male/female ratio was 0.57, mean age 12 years and median age 14 years. The proportion of sporadic cases including WAGR (Wilms tumour, Aniridia, Genitourinary abnormalities, Mental Retardation) and Gillespie syndrome (aniridia, cerebellar ataxia and mental retardation) was 48%. In the entire study population (Sweden and Norway), the mean visual acuity (VA) was 0.2 (range 0.04–0.9). We found VA < 0.3 in 80% and <0.1 in 18% of the patients. Twenty‐two patients (42%) had one or more of the sight threatening complications such as cataract/lens luxation, corneal clouding or glaucoma.

Conclusion:  Descriptions of aniridia in the younger are rare. This study shows that aniridia seems to be more common than previously estimated and that some complications appear early in life. Watchfulness as regards these complications and regular examinations are essential even in the youngest.
Choking Phenomena in a Vortex Flow Passing a Laval Tube: An Analytical Treatment
Authors: Van Holten Theo , Heiligers Monique , Jaeken Annemie
Published: March 2009

The behavior of a vortex flow through a Laval nozzle was studied in connection with the purification of natural gas. By creating a vortex and passing it through a Laval nozzle, the gas will be cooled, and water droplets will form and will be centrifuged out of the gas. This system is named the Condi-Cyclone. An analytical theory is developed to reveal the most important phenomena of the flow, to first order accuracy. Experiments have been performed with a prototype of the Condi-Cyclone. A Euler numerical simulation was performed, using the geometry of the test channel. This paper presents an analytical theory for a vortex flow through a Laval nozzle. It will demonstrate that when a vortex is present the total velocity reaches sonic conditions upstream of the nozzle throat, that the axial component of the velocity in the nozzle throat is equal to the local speed of sound and that the mass flow through the Laval nozzle decreases with increasing vortex strength. The predictions of the analytical theory have been compared with the results of the experiments and the Euler numerical simulation, and it can be concluded that the analytical theory describes the main characteristics of the flow very well.
A Principle to Generate Flow for Thermal Convective Base Sensors
Authors: Dinh Thien X. , Ogami Yoshifumi
Published: March 2009

This paper presents a thin millimeter-scaled device that can generate a closed flow within itself with a velocity of the order of a few m/s. The device comprises a piezoelectric pump with a PZT membrane, housing chamber, and a closed network channel connected to the housing chamber through a specific throat. We investigate the device by computational fluid dynamics. This device is used to produce several free jet flows depending on the structure of the network channel. In this study, four jet flows comprising two perpendicular pairs of flows are demonstrated. If the PZT membrane vibrates within a suitable range, the self-similarity of the axial velocity (along the jet direction) to the cross distances scaled by the half-widths of the jet is observed for a certain range of axial distance. Each jet flow can bend almost freely in three dimensions. The two remaining flow components are small as compared to the axial component. The device potentially has wide applications in flow-based sensors.
Free Surface Model Derived From the Analytical Solution of Stokes Flow in a Wedge
Authors: Hewson R. W.
Published: March 2009

The formation of a thin liquid film onto a moving substrate is a commonly encountered industrial process, and one that is encountered in lubrication, oil extraction processes, and coating flows. The formation of such a film is analyzed via the analytical Stokes flow solution for the flow in a wedge bounded on one side by a free surface and on the other by a moving surface. The full solution is obtained by numerically integrating a set of ordinary differential equations from far downstream, in the region of the final film thickness. The results show excellent agreement with the results obtained by the Bretherton equation, the Ruschak equation, the Coyne and Elrod model, and a two-dimensional free surface finite element simulation of the problem.
Numerical Modeling of Laminar Pulsating Flow in Porous Media
Authors: Kim S.-M. , Ghiaasiaan S. M.
Published: March 2009

The laminar pulsating flow through porous media was numerically studied. Two-dimensional flows in systems composed of a number of unit cells of generic porous structures were simulated using a computational fluid mechanics tool, with sinusoidal variations in flow with time as the boundary condition. The porous media were periodic arrays of square cylinders. Detailed numerical data for the porosity ranging from 0.64 to 0.84, with flow pulsation frequencies of 20–64 Hz were obtained. Based on these numerical data, the instantaneous as well as the cycle-average permeability and Forchheimer coefficients, to be used in the standard unsteady volume-averaged momentum conservation equation for flow in porous media, were derived. It was found that the cycle-average permeability coefficients were nearly the same as those for steady flow, but the cycle-average Forchheimer coefficients were significantly larger than those for steady flow and were sensitive to the flow oscillation frequency. Significant phase lags were observed between the volume-averaged velocity and the pressure waves. The phase difference between pressure and velocity waves, which is important for pulse tube cryocooling, depended strongly on porosity and the mean-flow Reynolds number.
Wind-Driven Upwelling in the Southern Ocean and the Deglacial Rise in Atmospheric CO
2
Authors: Anderson R. F. , Ali S. , Bradtmiller L. I. , Nielsen S. H. H. , Fleisher M. Q. , Anderson B. E. , Burckle L. H.
Published: March 2009

Wind-driven upwelling in the ocean around Antarctica helps regulate the exchange of carbon dioxide (CO
2
) between the deep sea and the atmosphere, as well as the supply of dissolved silicon to the euphotic zone of the Southern Ocean. Diatom productivity south of the Antarctic Polar Front and the subsequent burial of biogenic opal in underlying sediments are limited by this silicon supply. We show that opal burial rates, and thus upwelling, were enhanced during the termination of the last ice age in each sector of the Southern Ocean. In the record with the greatest temporal resolution, we find evidence for two intervals of enhanced upwelling concurrent with the two intervals of rising atmospheric CO
2
during deglaciation. These results directly link increased ventilation of deep water to the deglacial rise in atmospheric CO
2
.
Clear Sky Visibility Has Decreased over Land Globally from 1973 to 2007
Authors: Wang Kaicun , Dickinson Robert E. , Liang Shunlin
Published: March 2009

Visibility in the clear sky is reduced by the presence of aerosols, whose types and concentrations have a large impact on the amount of solar radiation that reaches Earth's surface. Here we establish a global climatology of inverse visibilities over land from 1973 to 2007 and interpret it in terms of changes in aerosol optical depth and the consequent impacts on incident solar radiation. The aerosol contribution to “global dimming,” first reported in terms of strong decreases in measured incident solar radiation up to the mid-1980s, has monotonically increased over the period analyzed. Since that time, visibility has increased over Europe, consistent with reported European “brightening,” but has decreased substantially over south and east Asia, South America, Australia, and Africa, resulting in net global dimming over land.
Paternal Control of Embryonic Patterning in
Arabidopsis thaliana
Authors: Bayer Martin , Nawy Tal , Giglione Carmela , Galli Mary , Meinnel Thierry , Lukowitz Wolfgang
Published: March 2009

The
YODA
(
YDA
) mitogen-activated protein kinase pathway promotes elongation of the
Arabidopsis
zygote and development of its basal daughter cell into the extra-embryonic suspensor. Here, we show that the interleukin-1 receptor–associated kinase (IRAK)/Pelle-like kinase gene
SHORT SUSPENSOR
(
SSP
) regulates this pathway through a previously unknown parent-of-origin effect.
SSP
transcripts are produced in mature pollen but do not appear to be translated. Instead, they are delivered via the sperm cells to the zygote and the endosperm, where SSP protein transiently accumulates. Ectopic expression of SSP protein in the leaf epidermis is sufficient to activate
YDA
-dependent signaling. We propose that SSP protein produced from paternal transcripts upon fertilization triggers zygotic
YDA
activity, providing an essential temporal cue for the regulation of the asymmetric first division.
Time-Variable Deformation in the New Madrid Seismic Zone
Authors: Calais Eric , Stein Seth
Published: March 2009

New geodetic measurements show that the New Madrid is currently deforming too slowly, if at all, to account for large earthquakes in the region over the past 5000 years. This result, together with increasing evidence for temporal clustering and spatial migration of earthquake sequences in continental interiors, indicates that either tectonic loading rates or fault properties vary over a few thousand years.
Preferential Generation of Follicular B Helper T Cells from Foxp3
+
T Cells in Gut Peyer's Patches
Authors: Tsuji Masayuki , Komatsu Noriko , Kawamoto Shimpei , Suzuki Keiichiro , Kanagawa Osami , Honjo Tasuku , Hori Shohei , Fagarasan Sidonia
Published: March 2009

Most of the immunoglobulin A (IgA) in the gut is generated by B cells in the germinal centers of Peyer's patches through a process that requires the presence of CD4
+
follicular B helper T(T
FH
) cells. The nature of these T
FH
cells in Peyer's patches has been elusive. Here, we demonstrate that suppressive Foxp3
+
CD4
+
T cells can differentiate into T
FH
cells in mouse Peyer's patches. The conversion of Foxp3
+
T cells into T
FH
cells requires the loss of Foxp3 expression and subsequent interaction with B cells. Thus, environmental cues present in gut Peyer's patches promote the selective differentiation of distinct helper T cell subsets, such as T
FH
cells.
Through a Glass of Darkness
Authors: Ferreira Pedro
Published: March 2009

Einstein's Telescope
. The Hunt for Dark Matter and Dark Energy in the Universe.
By Evalyn Gates
. Norton, New York, 2009. 328 pp. $25.95, C$28.50. ISBN 9780393062380.

Writing for a broad, nonspecialist audience, Gates discusses black holes, dark energy, dark matter, and similar topics
Evaluation of Antibodies against Different Epstein-Barr Virus Nuclear Antigen 1 Peptides in Diagnosis of Nasopharyngeal Carcinoma
Authors: Gu Ai-Di , Mo Hao-Yuan , Bei Jin-Xin , Xie Yan-Bo , Chen Li-Zhen , Feng Qi-Sheng , Kang Tiebang , Zeng Yi-Xin
Published: March 2009

Epstein-Barr virus nuclear antigen 1 (EBNA1) is a protein expressed consistently in nasopharyngeal carcinoma (NPC). Although antibody levels against three different EBNA1 peptides were all high in NPC patients, the correlation between any two biomarkers was low. Therefore, the selection of distinct EBNA1 peptides could render different results in serological detection for individuals with NPC.
Distribution of Phage-Associated Virulence Genes in Pharyngeal Group A Streptococcal Strains Isolated in Italy
Authors: Vitali Luca Agostino , D'Ercole Stefania , Petrelli Dezemona , Di Luca Maria Chiara , Rombini Silvia , Prenna Manuela , Ripa Sandro
Published: March 2009

The presence and assortment of 16 known virulence/resistance genetic determinants carried by prophages or prophage-like elements were tested in 212 clinical group AStreptococcus(GAS) strains and related to available data from SmaI macrorestriction/pulsed-field gel electrophoresis analysis andemmtyping. A strong correlation existed among the three analyses. This finding supports the substantial contribution to the evolution and diversification of the GAS genome attributed to phages.
High Levels of
mecA
DNA Detected by a Quantitative Real-Time PCR Assay Are Associated with Mortality in Patients with Methicillin-Resistant
Staphylococcus aureus
Bacteremia
Authors: Ho Ya-Chi , Chang Shan-Chwen , Lin Su-Ru , Wang Wei-Kung
Published: March 2009

Persistent methicillin-resistant
Staphylococcus aureus
(MRSA) bacteremia is known to be a poor prognostic factor. While several PCR assays for the detection of MRSA in various clinical samples were recently reported, the possibility that a quantitative PCR assay could be used to quantify and monitor MRSA bacteremia has not been explored. In this study, we established a quantitative real-time PCR assay for the
mecA
gene using known copy numbers of a plasmid containing
mecA
DNA as a standard and the previously described
mecA
-specific primers and probe (P. Francois et al., J. Clin. Microbiol. 41:254-260, 2003). We employed this assay to examine 250 sequential whole-blood samples from 20 adult patients, including 13 survivors and 7 nonsurvivors, with culture-proven MRSA bacteremia at the intensive care units of National Taiwan University Hospital between 1 July 2006 and 31 January 2007. The levels of
mecA
DNA in the nonsurvivors were significantly higher than those in the survivors during the three periods of bacteremia examined (days 0 to 2, 3 to 5, and 6 to 8) (
P
= 0.003 by two-tailed Mann-Whitney U test). Moreover, the nonsurvivors had higher
mecA
DNA levels than the survivors after 3 days and 7 days of anti-MRSA therapy (medians for nonsurvivors and survivors at 3 days, 5.86 and 4.30 log copies/ml, respectively; medians for nonsurvivors and survivors at 7 days, 5.21 and 4.36 log copies/ml, respectively;
P
= 0.02 and
P
= 0.04, respectively, by two-tailed Mann-Whitney U test). Together, these findings suggest that the level of
mecA
DNA in blood could potentially be used to monitor MRSA bacteremia and evaluate responses to therapy.
First Insight into Genetic Diversity of the
Mycobacterium tuberculosis
Complex in Albania Obtained by Multilocus Variable-Number Tandem-Repeat Analysis and Spoligotyping Reveals the Presence of Beijing Multidrug-Resistant Isolates
Authors: Tafaj Silva , Zhang Jian , Hauck Yolande , Pourcel Christine , Hafizi Hasan , Zoraqi Grigor , Sola Christophe
Published: March 2009

We characterized a set of 100
Mycobacterium tuberculosis
complex clinical isolates from tuberculosis (TB) patients in Albania, typing them with a 24-locus variable-number tandem-repeat-spoligotyping scheme. Depending on the cluster definition, 43 to 49 patients were distributed into 15 to 16 clusters which were likely to be epidemiologically linked, indicative of a recent transmission rate of 28 to 34%. This result suggests that TB is under control in Albania. However, two multidrug-resistant (MDR) Beijing genotypes harboring the same S531A mutation on the
rpoB
gene were also found, suggesting a potential recent transmission of MDR TB. Three brand new genotypes, Albania-1 to Albania-3, are also described.
Mutations in gp120 Contribute to the Resistance of Human Immunodeficiency Virus Type 1 to Membrane-Anchored C-Peptide maC46
Authors: Hermann Felix G. , Egerer Lisa , Brauer Frances , Gerum Christian , Schwalbe Harald , Dietrich Ursula , von Laer Dorothee
Published: March 2009

Binding of the human immunodeficiency virus (HIV) envelope glycoprotein (Env) to the cellular CD4 receptor and a chemokine coreceptor initiates a series of conformational changes in the Env subunits gp120 and gp41. Eventually, the trimeric gp41 folds into a six-helix bundle, thereby inducing fusion of the viral and cellular membranes. C peptides derived from the C-terminal heptad repeat (CHR) of gp41 are efficient entry inhibitors as they block the six-helix bundle formation. Previously, we developed a membrane-anchored C peptide (maC46) expressed from a retroviral vector that also shows high activity against virus strains resistant to enfuvirtide (T-20), an antiviral C peptide approved for clinical use. Here, we present a systematic analysis of mutations in Env that confer resistance of HIV type 1 (HIV-1) to maC46. We selected an HIV-1 BaL strain with 10-fold reduced sensitivity to maC46 (BaL_C46) by passaging virus for nearly 200 days in the presence of gradually increasing concentrations of maC46. In comparison to wild-type BaL, BaL_C46 had five mutations at highly conserved positions in Env, three in gp120, one in the N-terminal heptad-repeat (NHR), and one in the CHR of gp41. No mutations were found in the NHR domain around the GIV motif that are known to cause resistance to enfuvirtide. Instead, maC46 resistance was found to depend on complementary mutations in the NHR and CHR that considerably favor binding of the mutated NHR to the mutated CHR over binding to maC46. In addition, resistance was highly dependent on mutations in gp120 that accelerated entry. Taken together, resistance to maC46 did not develop readily and required multiple cooperating mutations at conserved positions of the viral envelope glycoproteins gp120 and gp41.
Isolation and Preliminary Characterization of Herpes Simplex Virus 1 Primary Enveloped Virions from the Perinuclear Space
Authors: Padula Maryn E. , Sydnor Mariam L. , Wilson Duncan W.
Published: March 2009

Herpes simplex virus 1 (HSV-1) nucleocapsids exit the nucleus by budding into the inner nuclear membrane, where they exist briefly as primary enveloped virions. These virus particles subsequently fuse their envelopes with the outer nuclear membrane, permitting nucleocapsids to then enter the cytoplasm and complete assembly. We have developed a method to isolate primary enveloped virions from HSV-1-infected cells and subjected the primary enveloped virion preparation to MALDI-MS/MS (matrix-assisted laser desorption ionization-tandem mass spectrometry) analyses. We identified most capsid proteins, a tegument protein (VP22), a glycoprotein (gD), and a cellular protein (annexin A2) in the primary enveloped virion preparation. We determined that annexin A2 does not play an essential role in infection under our experimental conditions. Elucidating the structure and biochemical properties of this unique virus assembly intermediate will provide new insights into HSV-1 biology.
CD4+T Cells Are Required for the Priming of CD8+T Cells following Infection with Herpes Simplex Virus Type 1
Authors: Rajasagi Naveen K. , Kassim Sadik H. , Kollias Christina M. , Zhao Xiangyi , Chervenak Robert , Jennings Stephen R.
Published: March 2009

The role of CD4+helper T cells in modulating the acquired immune response to herpes simplex virus type 1 (HSV-1) remains ill defined; in particular, it is unclear whether CD4+T cells are needed for the generation of the protective HSV-1-specific CD8+-T-cell response. This study examined the contribution of CD4+T cells in the generation of the primary CD8+-T-cell responses following acute infection with HSV-1. The results demonstrate that the CD8+-T-cell response generated in the draining lymph nodes of CD4+-T-cell-depleted C57BL/6 mice and B6-MHC-II−/−mice is quantitatively and qualitatively distinct from the CD8+T cells generated in normal C57BL/6 mice. Phenotypic analyses show that virus-specific CD8+T cells express comparable levels of the activation marker CD44 in mice lacking CD4+T cells and normal mice. In contrast, CD8+T cells generated in the absence of CD4+T cells express the interleukin 2 receptor α-chain (CD25) at lower levels. Importantly, the CD8+T cells in the CD4+-T-cell-deficient environment are functionally active with respect to the expression of cytolytic activity in vivo but exhibit a diminished capacity to produce gamma interferon and tumor necrosis factor alpha. Furthermore, the primary expansion of HSV-1-specific CD8+T cells is diminished in the absence of CD4+-T-cell help. These results suggest that CD4+-T-cell help is essential for the generation of fully functional CD8+T cells during the primary response to HSV-1 infection.
Adenovirus Transforming Protein E1A Induces c-Myc in Quiescent Cells by a Novel Mechanism
Authors: Kadeppagari Ravi-Kumar , Sankar Natesan , Thimmapaya Bayar
Published: March 2009

Previously we showed that the E1A binding proteins p300 and CBP negatively regulate c-Myc in quiescent cells and that binding of E1A to p300 results in the induction of c-Myc and thereby induction of S phase. We demonstrated that p300 and HDAC3 cooperate with the transcription factor YY1 at an upstream YY1 binding site and repress the
Myc
promoter. Here we show that the small E1A protein induces c-Myc by interfering with the protein-protein interaction between p300, YY1, and HDAC3. Wild-type E1A but not the E1A mutants that do not bind to p300 interfered in recruitment of YY1, p300, and HDAC3 to the YY1 binding site. As E1A started to accumulate after infection, it transiently associated with promoter-bound p300. Subsequently, YY1, p300, and HDAC3 began to dissociate from the promoter. Later in infection, E1A dissociated from the promoter as well as p300, YY1, and HDAC3. Removal of HDAC3 from the promoter correlated with increased acetylation of Myc chromatin and induction. In vivo E1A stably associated with p300 and dissociated YY1 and HDAC3 from the trimolecular complex. In vitro protein-protein interaction studies indicated that E1A initially binds to the p300-YY1-HDAC3 complex, briefly associates with it, and then dissociates the complex, recapitulating somewhat the in vivo situation. Thus, E1A binding to the C-terminal region of p300 disrupts the important corepressor function provided by p300 in repressing c-Myc. Our results reveal a novel mechanism by which a viral oncoprotein activates c-Myc in quiescent cells and raise the possibility that the oncoproteins encoded by the small-DNA tumor viruses may use this mechanism to induce c-Myc, which may be critical for cell transformation.
Cell-Specific Transduction of
Prdm1
-Expressing Lineages Mediated by a Receptor for Avian Leukosis Virus Subgroup B
Authors: Asimakopoulos Fotis , Varmus Harold E.
Published: March 2009

The transcription factor Blimp-1 has emerged as a regulator of cell fate in embryonic (germ cell) and adult (B- and T-cell immune effector and epithelial) lineages. It has also been proposed to act as a tumor suppressor in B-cell malignancy. Here, we present a novel in vivo system enabling the targeted genetic manipulation of cells expressing
Prdm1
, the gene encoding Blimp-1. We created bacterial artificial chromosome-transgenic mice expressing the avian leukosis virus (ALV) receptor TVB, fused to monomeric red fluorescent protein, under regulation by
Prdm1
transcriptional elements, and we achieved transduction of TVB-expressing lymphocytes by ALV vectors bearing a subgroup B envelope. The system presented here incorporates a number of innovations. First, it is the first mammalian transgenic system that employs the ALV receptor TVB, thus expanding the flexibility and scope of ALV-mediated gene delivery. Second, it represents the first ALV-based system that allows gene transfer and expression into in vivo-activated mature lymphocytes, a cell type that has traditionally presented formidable challenges to efficient retroviral transduction. Third,
Prdm1
:TVB-mRFP transgenic animals could provide an invaluable tool for exploring the diverse roles of Blimp-1 in lineage commitment, immune regulation, and tumorigenesis.
The U
L
31 and U
L
34 Gene Products of Herpes Simplex Virus 1 Are Required for Optimal Localization of Viral Glycoproteins D and M to the Inner Nuclear Membranes of Infected Cells
Authors: Wills Elizabeth , Mou Fan , Baines Joel D.
Published: March 2009

U
L
31 and U
L
34 of herpes simplex virus type 1 form a complex necessary for nucleocapsid budding at the inner nuclear membrane (INM). Previous examination by immunogold electron microscopy and electron tomography showed that pU
L
31, pU
L
34, and glycoproteins D and M are recruited to perinuclear virions and densely staining regions of the INM where nucleocapsids bud into the perinuclear space. We now show by quantitative immunogold electron microscopy coupled with analysis of variance that gD-specific immunoreactivity is significantly reduced at both the INM and outer nuclear membrane (ONM) of cells infected with a U
L
34 null virus. While the amount of gM associated with the nuclear membrane (NM) was only slightly (
P
= 0.027) reduced in cells infected with the U
L
34 null virus, enrichment of gM in the INM at the expense of that in the ONM was greatly dependent on U
L
34 (
P
< 0.0001). pU
L
34 also interacted directly or indirectly with immature forms of gD (species expected to reside in the endoplasmic reticulum or nuclear membrane) in lysates of infected cells and with the cytosolic tail of gD fused to glutathione
S
-transferase in rabbit reticulocyte lysates, suggesting a role for the pU
L
34/gD interaction in recruiting gD to the NM. The effects of U
L
34 on gD and gM localization were not a consequence of decreased total expression of gD and gM, as determined by flow cytometry. Separately, pU
L
31 was dispensable for targeting gD and gM to the two leaflets of the NM but was required for (i) the proper INM-versus-ONM ratio of gD and gM in infected cells and (ii) the presence of electron-dense regions in the INM, representing nucleocapsid budding sites. We conclude that in addition to their roles in nucleocapsid envelopment and lamina alteration, U
L
31 and U
L
34 play separate but related roles in recruiting appropriate components to nucleocapsid budding sites at the INM.
A Kaposi's Sarcoma-Associated Herpesvirus Protein That Forms Inhibitory Complexes with Type I Interferon Receptor Subunits, Jak and STAT Proteins, and Blocks Interferon-Mediated Signal Transduction
Authors: Bisson Sabine A. , Page Anne-Laure , Ganem Don
Published: March 2009

Type I interferons (IFNs) are important mediators of innate antiviral defense and function by activating a signaling pathway through their cognate type I receptor (IFNAR). Here we report that lytic replication of Kaposi's sarcoma-associated herpesvirus (KSHV) efficiently blocks type I IFN signaling and that an important effector of this blockade is the viral protein RIF, the product of open reading frame 10. RIF blocks IFN signaling by formation of inhibitory complexes that contain IFNAR subunits, the Janus kinases Jak1 and Tyk2, and the STAT2 transcription factor. Activation of both Tyk2 and Jak1 is inhibited, and abnormal recruitment of STAT2 to IFNAR1 occurs despite the decrement in Tyk2 activity. As a result of these actions, phosphorylation of both STAT2 and STAT1 is impaired, with subsequent failure of ISGF3 accumulation in the nucleus. The presence in the viral genome of potent inhibitors of type I IFN signaling, along with several viral genes that block IFN induction, highlights the importance of the IFN pathway in the control of this human tumor virus infection.
A Limited Group of Class I Histone Deacetylases Acts To Repress Human Immunodeficiency Virus Type 1 Expression
Authors: Keedy Kara S. , Archin Nancie M. , Gates Adam T. , Espeseth Amy , Hazuda Daria J. , Margolis David M.
Published: March 2009

Silencing of the integrated human immunodeficiency virus type 1 (HIV-1) genome in resting CD4
+
T cells is a significant contributor to the persistence of infection, allowing the virus to evade both immune detection and pharmaceutical attack. Nonselective histone deacetylase (HDAC) inhibitors are capable of inducing expression of quiescent HIV-1 in latently infected cells. However, potent global HDAC inhibition can induce host toxicity. To determine the specific HDACs that regulate HIV-1 transcription, we evaluated HDAC1 to HDAC11 RNA expression and protein expression and compartmentalization in the resting CD4
+
T cells of HIV-1-positive, aviremic patients. HDAC1, -3, and -7 had the highest mRNA expression levels in these cells. Although all HDACs were detected in resting CD4
+
T cells by Western blot analysis, HDAC5, -8, and -11 were primarily sequestered in the cytoplasm. Using chromatin immunoprecipitation assays, we detected HDAC1, -2, and -3 at the HIV-1 promoter in Jurkat J89GFP cells. Targeted inhibition of HDACs by small interfering RNA demonstrated that HDAC2 and HDAC3 contribute to repression of HIV-1 long terminal repeat expression in the HeLa P4/R5 cell line model of latency. Together, these results suggest that HDAC inhibitors specific for a limited number of class I HDACs may offer a targeted approach to the disruption of persistent HIV-1 infection.
Impact of Human Immunodeficiency Virus Type 1 Resistance to Protease Inhibitors on Evolution of Resistance to the Maturation Inhibitor Bevirimat (PA-457)
Authors: Adamson Catherine S. , Waki Kayoko , Ablan Sherimay D. , Salzwedel Karl , Freed Eric O.
Published: March 2009

The maturation inhibitor bevirimat [3-O-(3′,3′dimethysuccinyl)betulinic acid; BVM; also known as PA-457 or DSB] potently inhibits human immunodeficiency virus type 1 (HIV-1) replication by blocking protease (PR)-mediated cleavage at the junction between capsid (CA) and spacer peptide 1 (SP1) in Gag. We previously isolated a panel of single-amino-acid substitutions that confer resistance to BVM in vitro (C. S. Adamson, S. D. Ablan, I. Boeras, R. Goila-Gaur, F. Soheilian, K. Nagashima, F. Li, K. Salzwedel, M. Sakalian, C. T. Wild, and E. O. Freed, J. Virol. 80:10957-10971, 2006). The BVM resistance mutations cluster at or near the CA-SP1 cleavage site. Because BVM likely will be used clinically in patients harboring viruses resistant to PR inhibitors (PIs), in this study we evaluated the interplay between a PI-resistant (PIR) PR and the BVM resistance mutations in Gag. As expected, the PIR mutations had no effect on inhibition by BVM; however, we observed general processing defects and a slight delay in viral replication in Jurkat T cells associated with the PIR mutations, even in the absence of compound. When combined, most BVM resistance and PIR mutations acted additively to impair viral replication, particularly in the presence of BVM. The BVM-resistant mutant SP1-A1V was an exception, as it supported robust replication in the context of either wild-type (WT) or PIR PR, even at high BVM concentrations. Significantly, the emergence of BVM resistance was delayed in the context of the PIR PR, and the SP1-A1V mutation was acquired most frequently with either WT or PIR PR. These results suggest that resistance to BVM is less likely to emerge in patients who have failed PIs than in patients who are PI naïve. We predict that the SP1-A1V substitution is the most likely to emerge in vivo, as this mutant replicates robustly independently of PR mutations or BVM. These findings offer insights into the effect of PIR mutations on the evolution of BVM resistance in PI-experienced patients.