bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Grazing Intensity during Drought in an Arizona Grassland
Authors: LOESER MATTHEW R. R. , SISK THOMAS D. , CREWS TIMOTHY E.
Published: November 2006

Abstract:  The ecological benefits of changing cattle grazing practices in the western United States remain controversial, due in part to a lack of experimentation. In 1997 we initiated an experimental study of two rangeland alternatives, cattle removal and high‐impact grazing, and compared grassland community responses with those with more conventional, moderate grazing practices. The study was conducted in a high‐elevation, semiarid grassland near Flagstaff, Arizona (U.S.A.). We conducted annual plant surveys of modified Whittaker plots for 8 years and examined plant composition shifts among treatments and years. High‐impact grazing had strong directional effects that led to a decline in perennial forb cover and an increase in annual plants, particularly the exotic cheatgrass (Bromus tectorum L.). A twofold increase in plant cover by exotic species followed a severe drought in the sixth year of the study, and this increase was greatest in the high‐impact grazing plots, where native cover declined by one‐half. Cattle removal resulted in little increase in native plant cover and reduced plant species richness relative to the moderate grazing control. Our results suggest that some intermediate level of cattle grazing may maintain greater levels of native plant diversity than the alternatives of cattle removal or high‐density, short‐duration grazing practices. Furthermore, episodic drought interacts with cattle grazing, leading to infrequent, but biologically important shifts in plant communities. Our results demonstrate the importance of climatic variation in determining ecological effects of grazing practices, and we recommend improving conservation efforts in arid rangelands by developing management plans that anticipate this variation.
Area‐Based Refinement for Selection of Reserve Sites with the Benefit‐Function Approach
Authors: ARPONEN ANNI , KONDELIN HANNA , MOILANEN ATTE
Published: November 2006

Abstract:  Optimization of resource use is necessary for efficient conservation planning. Many reserve‐selection algorithms aim to identify representative but inexpensive networks, which may lead to selecting small sites due to their lower costs and collectively higher species richness. Nevertheless, larger sites would be preferable regarding species' long‐term persistence. An area‐based refinement can be used to overcome this problem. We used a reserve‐planning framework in which continuous benefit functions valued representation (numbers of populations), and differential species weights were based on a species' local rarity and threatened status. We introduced a refinement based on the species‐area relationship that provides relatively higher values for larger sites. We applied the proposed method to rich fen vegetation in southern Finland. The species‐area refinement resulted in a network of significantly larger sites with minor trade‐offs with representation (numbers of populations). Giving endangered species higher weights ensured that the trade‐off occurred mostly between site size and representation of low‐priority species. We recommend using a species‐area refinement for practical, maximum‐coverage conservation planning.
Coding Issues for the Interventionalist: A Consensus Statement by the ASDIN
Authors: Schon Donald , LeBlanc Lori M. ,   the ASDIN‐RPA Coding Committee
Published: December 2006

The field of Interventional Nephrology has matured and expanded over the last decade. The American Society of Diagnostic and Interventional Nephrology (ASDIN) has recognized the need for standardization and uniformity in coding of interventional procedures on dialysis access. After extensive study, an ASDIN committee developed a coding manual in 2004 with revisions in 2005 and 2006, which is available to ASDIN members through the ASDIN web site. This article comprises a brief overview of appropriate coding for access related procedures and contrasts the ASDIN recommendations with a recent interventional radiology generated approch.
Utility of Static Pressure Ratio Recording during Angioplasty of Arteriovenous Graft Stenosis
Authors: Asif Arif , Besarab Anatole , Gadalean Florin , Merrill Donna , Rismeyer Anne E. , Contreras Gabriel , Leclercq Baudouin , Lenz Oliver , Wallach Jeffery , Wallach Joshua , Levine Michael I.
Published: December 2006

Intra‐access static pressure ratio (SPR) (intra‐access pressure/mean arterial pressure) can be measured during angioplasty (PTA) to assess the functional importance of an arteriovenous graft (AVG) stenosis. We used SPR in 70 patients with AVGs who underwent 98 angioplasty procedures. SPR was measured during angioplasty by placing a catheter tip at mid‐access. Inflow stenosis (IF) = stenosis proximal to the tip of the catheter. Outflow stenosis (OF) = stenosis distal to the tip of the catheter up to the superior vena cava‐atrial junction. Post PTA, access flow (Qa) was assessed within 2 weeks. Complete data sets for both SPR and Qa were available in 83 procedures. Using a normal SPR ratio of 0.3–0.4 at mid‐graft, three patterns of SPR were noted. In 63 of 83 (76%) cases SPR was elevated prior to PTA (0.71 ± 0.13 SD). PTA reduced SPR toward normal range (0.44 ± 0.12) in 53 cases (84%). In the remaining 10 (16%), SPR decreased to a low value (0.22 ± 0.03) and normalized (0.40 ± .0.11) only after PTA of a coexisting inflow stenosis. In 12 of 83 (14%) procedures, the initial SPR was low (0.18 ± 0.04) and increased toward normal (0.3 ± 0.08) following IF stenosis PTA in seven (58%) cases. For the remaining five (42%) cases SPR increased to a high value (0.70 ± 0.21) and decreased toward normal range (0.33 ± 0.07) only after OF stenosis angioplasty. In 8 of 83 (10%) procedures, initial SPR was normal (0.33 ± 0.02). Angiography revealed coexisting IF and OF stenoses. SPR remained within the normal range after PTA of these lesions (0.33 ± 0.02). Qa increased significantly in 74 of 83 (89%) procedures (before = 572 ± 201, after = 1109 ± 368 ml/min; p < 0.001). SPR measurements can assist in hemodynamic assessment of an AVG during angioplasty procedure.
Linking Work Design to Mass Customization: A Sociotechnical Systems Perspective*
Authors: Liu Gensheng (Jason) , Shah Rachna , Schroeder Roger G.
Published: November 2006

Mass customization has gained increasing importance in recent years due to its ability to provide customized products efficiently and effectively, and manufacturing companies are continuously searching for ways to develop their mass‐customization ability. Despite extensive literature focusing on mass customization, few studies have systematically examined the impact of work‐design practices on a company's mass‐customization ability. Using the Sociotechnical Systems theory as a foundation, we link work‐design practices with mass‐customization ability, specifically identifying ten work‐design practices and examining their impact on mass‐customization ability using survey data and empirical research methods. The results support our hypothesized links and suggest that work‐design practices that manage both the technical and the social dimensions for achieving organization success have significant impact on a company's ability to achieve mass customization.
Supplier‐Switching Inertia and Competitive Asymmetry: A Demand‐Side Perspective*
Authors: Li Sali , Madhok Anoop , Plaschka Gerhard , Verma Rohit
Published: November 2006

Building on strategic management, operations strategy, and supplier management literatures, this article presents a framework for supplier selection from the demand‐side perspective. We highlight the role of a purchasing firm's switching inertia in the supplier‐selection process and demonstrate the usefulness of our framework for the industrial automation industry. Empirical data for this study was collected from 171 corporate and plant‐level executives in pharmaceutical, chemical, and paper‐and‐pulp manufacturing industries in the United States. A series of Web‐based individually customized discrete choice experiments asked the respondents to either switch to the new supplier or stay with the existing supplier. Based on the results of these experiments, we demonstrate the existence of switching inertia in the supplier‐selection process and discuss the managerial implications for incumbent and challenger supplier firms.
A Wavelet‐Based Approach to Preserve Privacy for Classification Mining*
Authors: Bapna Sanjay , Gangopadhyay Aryya
Published: November 2006

Despite the commercial success of data mining, a major drawback has been acknowledged across academic, industry, and government sectors, namely, the issue of violating the privacy of individuals. We propose a data transformation method based on wavelets to disguise private data while preserving the original classification patterns. Wavelet transformations have been used extensively in signal processing for data reduction, multiresolution analysis, and removing noise from data. In our implementation, two commonly used wavelet transforms, the Haar and the Daub‐4 transforms, are tested for pattern and privacy preservation in classification mining tasks. Empirical results confirm that the Haar and the Daub‐4 transforms preserve the classification patterns and preserve the privacy for real valued data.
Direct Ink Writing of Three‐Dimensional Ceramic Structures
Authors: Lewis Jennifer A. , Smay James E. , Stuecker John , Cesarano Joseph
Published: November 2006

The ability to pattern ceramic materials in three dimensions (3D) is critical for structural, functional, and biomedical applications. One facile approach is direct ink writing (DIW), in which 3D structures are built layer‐by‐layer through the deposition of colloidal‐ or polymer‐based inks. This approach allows one to design and rapidly fabricate ceramic materials in complex 3D shapes without the need for expensive tooling, dies, or lithographic masks. In this feature article, we present both droplet‐ and filament‐based DIW techniques. We focus on the various ink designs and their corresponding rheological behavior, ink deposition mechanics, potential shapes and the toolpaths required, and representative examples of 3D ceramic structures assembled by each technique. The opportunities and challenges associated with DIW are also highlighted.
THE PRACTICE OF HIGHER EDUCATION: IN PURSUIT OF EXCELLENCE AND OF EQUITY
Authors: Bridges David
Published: November 2006

Abstract In this essay, David Bridges explores the notion of practice with particular application to the practice of higher education. He considers whether some of the changes in practices linked to the massification of higher education have in fact resulted in the breakdown of higher education as a practice, at least on Alasdair MacIntyre’s definition of the term. Specifically, Bridges examines whether higher education has lost its sense of the forms of human excellence around which its life is constructed. Finally, he points to issues of equity raised by the huge variety of forms that higher education now takes and asks whether this variety might mean that students are winning entry to some very different qualities of experience when judged against the requirement that they should contribute to the development of human excellence.
Autonomic regulation during orthostatic stress in highlanders: comparison with sea‐level residents
Authors: Gulli Giosué , Claydon Victoria E. , Slessarev Marat , Zenebe Guta , Gebremedhin Amha , Rivera‐Ch Maria , Appenzeller Otto , Hainsworth Roger
Published: December 2006

This report is a comparison of orthostatic tolerance and autonomic function in three groups of high‐altitude dwellers: Andeans with and without chronic mountain sickness (CMS) and healthy Ethiopians. Results are compared with those from healthy sea‐level residents. The aim was to determine whether different high‐altitude populations adapted differently to the prevailing hypobaric hypoxia. Orthostatic tolerance was assessed using a test involving head‐up tilt (HUT) and graded lower body suction. This was performed at the subjects' resident altitude. Blood pressure (Portapres) and R–R interval (ECG) were recorded during the test, and spectral and cross‐spectral analyses of heart period and systolic blood pressure time series were performed using data obtained both while supine and during HUT. The transfer function gain in the low‐frequency range (LF, ∼0.1 Hz) at the point of maximal coherence was used as a measure of cardiac baroreflex sensitivity (BRS). As previously reported, Peruvians displayed an unusually good orthostatic tolerance, while Ethiopians showed an orthostatic tolerance comparable to that of healthy sea‐level residents. There were no significant differences between groups in the supine values of the spectral analysis results. Head‐up tilt induced the expected changes in Ethiopians (an increase in the LF components and a decrease in the respiratory components) but not in Andeans. Cross‐spectral analysis showed abnormal results from all groups of high‐altitude dwellers. These results indicate that Ethiopians, but not Peruvians, behave similarly to sea‐level residents in terms of orthostatic tolerance and autonomic responses to orthostatic stress, as assessed from spectral analyses, and this indicates good adaptation to their environment. However, in all the high‐altitude groups the results of cross‐spectral analysis were atypical, suggesting some degree of impairment in baroreflex function.
Electromechanical and pharmacomechanical signalling pathways for conducted vasodilatation along endothelium of hamster feed arteries
Authors: Domeier Timothy L. , Segal Steven S.
Published: December 2006

Conducted vasodilatation (CVD) reflects the initiation and rapid (>mm s−1) spread of hyperpolarization along the endothelium and into smooth muscle. The ion channels that initiate CVD remain unclear as do signalling pathways that may complement electromechanical relaxation. Using isolated pressurized (75 mmHg; 37°C) feed arteries (n= 63; diameter: rest: 53 ± 2 μm, maximal: 98 ± 2 μm) from hamster retractor skeletal muscle, we investigated the contribution of calcium‐activated potassium channels (KCa) and endothelium‐derived autacoids to CVD. Local delivery (1 μm micropipette tip; 500–2000 ms pulse) of acetylcholine (ACh) at the downstream end initiated a local increase in endothelial cell [Ca2+]i (Fura‐PE3; Δratio 340/380 nm = 0.215 ± 0.032) that preceded CVD along the entire vessel. During local perifusion with KCa antagonists, iberiotoxin (5 μm) had no effect, but charybdotoxin (CTX, 5 μm) + apamin (APA, 10 μm) abolished CVD reversibly. Remarkably, this local inhibition of KCa unmasked a ‘slow‐conducted vasodilatation’ (SCVD) that spread >1200 μm at ∼21 μm s−1 (n= 27). Recorded 500 μm upstream from the ACh stimulus, a rise in endothelial cell [Ca2+]i (Δratio 340/380 nm) = 0.146 ± 0.017; P < 0.05) preceded SCVD (Δdiameter = 14 ± 3 μm) by ∼10 s. Before KCa inhibition, antagonism of nitric oxide synthase (Nω‐nitro‐l‐arginine, 250 μm; l‐NNA) and cyclooxygenase (indomethacin, 5 μm; INDO) had no effect on the amplitude of CVD yet response duration decreased by one‐third (P < 0.05). During local CTX + APA perifusion, l‐NNA + INDO abolished SCVD while conducted [Ca2+]i responses remained intact. Thus, ACh triggers electromechanical relaxation of smooth muscle cells along the vessel initiated by local KCa, and the ensuing ‘wave’ of Ca2+ along the endothelium releases autacoids to promote pharmacomechanical relaxation.
Stability and plasticity of intrinsic membrane properties in hippocampal CA1 pyramidal neurons: effects of internal anions
Authors: Kaczorowski Catherine Cook , Disterhoft John , Spruston Nelson
Published: December 2006

CA1 pyramidal neurons from animals that have acquired hippocampal tasks show increased neuronal excitability, as evidenced by a reduction in the postburst afterhyperpolarization (AHP). Studies of AHP plasticity require stable long‐term recordings, which are affected by the intracellular solutions potassium methylsulphate (KMeth) or potassium gluconate (KGluc). Here we show immediate and gradual effects of these intracellular solutions on measurement of the AHP and basic membrane properties, and on the induction of AHP plasticity in CA1 pyramidal neurons from rat hippocampal slices. The AHP measured immediately after establishing whole‐cell recordings was larger with KMeth than with KGluc. In general, the AHP in KMeth was comparable to the AHP measured in the perforated‐patch configuration. However, KMeth induced time‐dependent changes in the intrinsic membrane properties of CA1 pyramidal neurons. Specifically, input resistance progressively increased by 70% after 50 min; correspondingly, the current required to trigger an action potential and the fast afterdepolarization following action potentials gradually decreased by about 50%. Conversely, these measures were stable in KGluc. We also demonstrate that activity‐dependent plasticity of the AHP occurs with physiologically relevant stimuli in KGluc. AHPs triggered with theta‐burst firing every 30 s were progressively reduced, whereas AHPs elicited every 150 s were stable. Blockade of the apamin‐sensitive AHP current (IAHP) was insufficient to block AHP plasticity, suggesting that plasticity is manifested through changes in the apamin‐insensitive slow AHP current (sIAHP). These changes were observed in the presence of synaptic blockers, and therefore reflect changes in the intrinsic properties of the neurons. However, no AHP plasticity was observed using KMeth. In summary, these data show that KMeth produces time‐dependent changes in basic membrane properties and prevents or obscures activity‐dependent reduction of the AHP. In whole‐cell recordings using KGluc, repetitive theta‐burst firing induced AHP plasticity that mimics learning‐related reduction in the AHP.
Old-Growth Forests Can Accumulate Carbon in Soils
Authors: Zhou Guoyi , Liu Shuguang , Li Zhian , Zhang Deqiang , Tang Xuli , Zhou Chuanyan , Yan Junhua , Mo Jiangming
Published: November 2006

Old-growth forests have traditionally been considered negligible as carbon sinks because carbon uptake has been thought to be balanced by respiration. We show that the top 20-centimeter soil layer in preserved old-growth forests in southern China accumulated atmospheric carbon at an unexpectedly high average rate of 0.61 megagrams of carbon hectare-1 year-1 from 1979 to 2003. This study suggests that the carbon cycle processes in the belowground system of these forests are changing in response to the changing environment. The result directly challenges the prevailing belief in ecosystem ecology regarding carbon budget in old-growth forests and supports the establishment of a new, nonequilibrium conceptual framework to study soil carbon dynamics
Prevention of
Brca1
-Mediated Mammary Tumorigenesis in Mice by a Progesterone Antagonist
Authors: Poole Aleksandra Jovanovic , Li Ying , Kim Yoon , Lin Suh-Chin J. , Lee Wen-Hwa , Lee Eva Y.-H. P.
Published: November 2006

Women with mutations in the breast cancer susceptibility gene
BRCA1
are predisposed to breast and ovarian cancers. Why the BRCA1 protein suppresses tumor development specifically in ovarian hormone–sensitive tissues remains unclear. We demonstrate that mammary glands of nulliparous
Brca1
/
p53
-deficient mice accumulate lateral branches and undergo extensive alveologenesis, a phenotype that occurs only during pregnancy in wild-type mice. Progesterone receptors, but not estrogen receptors, are overexpressed in the mutant mammary epithelial cells because of a defect in their degradation by the proteasome pathway. Treatment of
Brca1
/
p53
-deficient mice with the progesterone antagonist mifepristone (RU 486) prevented mammary tumorigenesis. These findings reveal a tissue-specific function for the BRCA1 protein and raise the possibility that antiprogesterone treatment may be useful for breast cancerpreventioninindividuals with
BRCA1
mutations.
Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria
Authors: Ottesen Elizabeth A. , Hong Jong Wook , Quake Stephen R. , Leadbetter Jared R.
Published: November 2006

Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA–based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment.
Increasing Trend of Extreme Rain Events Over India in a Warming Environment
Authors: Goswami B. N. , Venugopal V. , Sengupta D. , Madhusoodanan M. S. , Xavier Prince K.
Published: November 2006

Against a backdrop of rising global surface temperature, the stability of the Indian monsoon rainfall over the past century has been a puzzle. By using a daily rainfall data set, we show (i) significant rising trends in the frequency and the magnitude of extreme rain events and (ii) a significant decreasing trend in the frequency of moderate events over central India during the monsoon seasons from 1951 to 2000. The seasonal mean rainfall does not show a significant trend, because the contribution from increasing heavy events is offset by decreasing moderate events. A substantial increase in hazards related to heavy rain is expected over central India in the future.
Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"
Authors: Mulligan Connie J. , Kitchen Andrew , Miyamoto Michael M.
Published: November 2006

Bazin
et al
. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.
Optical Atomic Coherence at the 1-Second Time Scale
Authors: Boyd Martin M. , Zelevinsky Tanya , Ludlow Andrew D. , Foreman Seth M. , Blatt Sebastian , Ido Tetsuya , Ye Jun
Published: November 2006

Highest-resolution laser spectroscopy has generally been limited to single trapped ion systems because of the rapid decoherence that plagues neutral atom ensembles. Precision spectroscopy of ultracold neutral atoms confined in a trapping potential now shows superior optical coherence without any deleterious effects from motional degrees of freedom, revealing optical resonance linewidths at the hertz level with a good signal-to-noise ratio. The resonance quality factor of 2.4 × 10
14
is the highest ever recovered in any form of coherent spectroscopy. The spectral resolution permits direct observation of the breaking of nuclear spin degeneracy for the
1
S
0
and
3
P
0
optical clock states of
87
Sr under a small magnetic bias field. This optical approach for excitation of nuclear spin states allows an accurate measurement of the differential Landé
g
factor between
1
S
0
and
3
P
0
. The optical atomic coherence demonstrated for collective excitation of a large number of atoms will have a strong impact on quantum measurement and precision frequency metrology.
G Protein Signaling in Yeast: New Components, New Connections, New Compartments
Authors: Slessareva Janna E. , Dohlman Henrik G.
Published: November 2006

Signaling by cell surface receptors and heterotrimeric guanine nucleotide–binding proteins (G proteins) is one of the most exhaustively studied processes in the cell but remains a major focus of molecular pharmacology research. The pheromone-response system in yeast (see the Connections Map at
Science
's Signal Transduction Knowledge Environment) has provided numerous major advances in our understanding of G protein signaling and regulation. However, the basic features of this prototypical pathway have remained largely unchanged since the mid-1990s. New tools available in yeast are beginning to uncover new pathway components and interactions and have revealed signaling in unexpected locations within the cell.
The Sensitivity of the OptiMAL Rapid Diagnostic Test to the Presence of
Plasmodium falciparum
Gametocytes Compromises Its Ability To Monitor Treatment Outcomes in an Area of Papua New Guinea in which Malaria Is Endemic
Authors: Mueller Ivo , Betuela Inoni , Ginny Meza , Reeder John C. , Genton Blaise
Published: November 2006

Using in vivo samples from treatment failure malaria cases, we demonstrate the high sensitivity of the parasite lactase dehydrogenase (pLDH)-based OptiMAL rapid diagnostic test in the detection of
P. falciparum
gametocytes. This high sensitivity limits the use of pLDH-based tests in the monitoring of treatment outcomes in circumstances where gametocytemia is common.
Molecular Confirmation that
Fasciola gigantica
Can Undertake Aberrant Migrations in Human Hosts
Authors: Le Thanh Hoa , De Nguyen Van , Agatsuma Takeshi , Blair David , Vercruysse Jozef , Dorny Pierre , Nguyen Thanh Giang Thi , McManus Donald P.
Published: November 2006

Two cases of aberrant migration by the liver fluke
Fasciola gigantica
in humans are reported. In both cases, subadult worms emerged through the skin. The identity of the worms was confirmed from their DNA sequences. This uncommon human pathogen might be more likely than
F. hepatica
to undertake aberrant migrations in humans.
Characterization of Small-Colony-Variant
Stenotrophomonas maltophilia
Isolated from the Sputum Specimens of Five Patients with Cystic Fibrosis
Authors: Anderson Scott W. , Stapp Jennifer R. , Burns Jane L. , Qin Xuan
Published: November 2006

Cystic fibrosis (CF) patients are predisposed to chronic respiratory infection by nonfermentative gram-negative bacilli, including
Stenotrophomonas maltophilia. S. maltophilia
is highly resistant to most antibiotics, with the exception of sulfamethoxazole-trimethoprim (SXT). SXT-resistant
S. maltophilia
has been reported, but the mechanism of resistance is not well defined. Repeated findings of suspected small-colony-variant (SCV)
S. maltophilia
isolates from the sputa of five CF patients were confirmed by partial 16S rRNA gene sequencing. The SCV
S. maltophilia
isolates were the only
S. maltophilia
isolates in these cultures, and none were clonally related. DNA fingerprint analysis confirmed that once established, the SCV
S. maltophilia
strains persisted. Nutritional studies of SCV
S. maltophilia
have suggested auxotrophy in hemin, methionine, and thymidine associated with resistance to multiple antibiotics, including SXT. The phenotypic switch from wild-type to SCV
S. maltophilia
was reproducible in vitro by exposure to SXT, suggesting that prolonged exposure to antibiotics may select for both the SCV
S. maltophilia
phenotype and SXT resistance by interference with the dihydrofolate reductase pathway. Recovery of SCV
S. maltophilia
from the sputum of CF patients has implications for both laboratory testing and patient management.
Temperate Bacteriophages Affect Pulsed-Field Gel Electrophoresis Patterns of
Campylobacter jejuni
Authors: Barton Connie , Ng Lai-King , Tyler Shaun D. , Clark Clifford G.
Published: November 2006

The recently sequenced genome of
Campylobacter jejuni
RM1221 revealed the presence of three integrated bacteriophage-like elements. In this study, genes from the first element, a Mu-like bacteriophage, were amplified by PCR and used to probe pulsed-field gels of clinical
C. jejuni
strains obtained from a waterborne outbreak (Ontario, Canada, 2000). These highly similar strains differed only by their pulsed-field gel electrophoresis (PFGE) patterns due to an apparent insertion or deletion of a 40-kb fragment. Bacteriophage probes hybridized to these different bands in Southern blot analysis, indicating that homologues of bacteriophage genes were present in the outbreak strains. Investigation of the bacteriophage insertion sites in these isolates suggested that bacteriophage acquisition, loss, or transposition was responsible for the PFGE pattern variation. The bacteriophage gene sequences were similar, but not identical, in the outbreak strains and RM1221, indicating that differences may exist between the bacteriophages.
Geographic Information Systems and Genotyping in Identification of Rotavirus G12 Infections in Residents of an Urban Slum with Subsequent Detection in Hospitalized Children: Emergence of G12 Genotype in South India
Authors: Ramani Sasirekha , Banerjee Indrani , Primrose Gladstone Beryl , Sarkar Rajiv , Selvapandian David , Le Fevre Andrea M. , Jaffar Shabbar , Iturriza-Gomara Miren , Gray James J. , Estes Mary K. , Brown David W. , Kang Gagandeep
Published: November 2006

Rotavirus infections by G12 strains in several countries have recently been described. In this study, we report the emergence of G12 strains in south India. Fourteen cases of G12 infection were identified between June and September 2005. G12 was seen in combination with P[6], P[8], or nontypeable P type. Nine cases, including five symptomatic infections and four asymptomatic infections, were identified as part of routine surveillance for rotavirus infections in a birth cohort in the community between June and July 2005. Significant temporal and time-space clustering of eight of these cases represents a possible recent introduction of a new rotavirus VP7 genotype. Previous rotavirus infections had been documented for six of the nine children in the community. In the following 2 months, five cases of G12 infection were identified among children presenting to a referral hospital with diarrhea. This is the first description of symptomatic and asymptomatic G12 infections in children in the community. The detection of G12 strains from different parts of the world in recent years suggests the possibility of its emergence as an important global genotype. Monitoring of cocirculating rotavirus strains and detection of emerging strains is important in the context of the availability of rotavirus vaccines.
Toward Universal Varicella-Zoster Virus (VZV) Genotyping: Diversity of VZV Strains from France and Spain
Authors: Loparev Vladimir , Martro Elisa , Rubtcova Elena , Rodrigo Carlos , Piette Jean-Charles , Caumes Eric , Vernant Jean-Paul , Schmid D. Scott , Fillet Anne-Marie
Published: November 2006

Thirty-one isolates from France and Spain were genotyped using a published method analyzing DNA sequence variation in open reading frame (ORF) 22, together with an evaluation of three well-characterized single nucleotide polymorphisms (SNP) in ORF 38, 54, and 62. Nineteen were allocated to the European (E) genotype, six were mosaic-1 (M1), and two were mosaic-2 (M2). Four strains were assigned to a new genotype, mosaic-4 (M4). All isolates were wild type, with no Oka vaccine-associated markers. No isolates of the mosaic-3 (M3) or Japanese (J) genotype were observed. We also evaluated 13 selected isolates of E, J, M1, and M2 strains (9 of the 31 described above) using an alternative genotyping method based on the assessment of multiple SNP located in ORF 1, 9, 10, 21, 31, 50, 54, 62, and 68. This method assigns wild-type varicella-zoster virus (VZV) strains to seven genotypes: A1, A2, J1, B1, B2, C, and C1. VZV isolates identified as E (ORF22 method) had the genetic signature of genotype C VZV strains, M1 strains were A1, and M2 were A2. No J strains were detected, but parental Oka and vaccine Oka (genotype J) corresponded to genotype J1. M4 isolates (B) share the SNP array observed for M1 and E viruses, and probably represent recombinants between African-Asian (M1) and European (E) viruses. The two genotyping methods, using entirely different genomic targets, produced identical clusters for the strains examined, suggesting robust phylogenetic linkages among VZV strains circulating in Europe.
Development of a Flow Chart for Identification of Gram-Positive Anaerobic Cocci in the Clinical Laboratory
Authors: Song Yuli , Liu Chengxu , Finegold Sydney M.
Published: November 2006

Gram-positive anaerobic cocci (GPAC) are a heterogeneous group of organisms that are isolated from clinical specimens more often than any group of anaerobic bacteria except
Bacteroides
species, yet many strains are still difficult or impossible to identify in the diagnostic laboratory. In this study, a total of 124 strains, including 13 reference strains of GPAC species and 111 isolates that had been recovered from clinical specimens previously and identified by 16S rRNA gene sequencing, were subjected to biochemical characterization. Based on the results, a short biochemical scheme that involves the minimum essential biochemical tests for accurate identification of clinically important GPAC was developed.
Burkholderia glumae
Infection in an Infant with Chronic Granulomatous Disease
Authors: Weinberg Jason B. , Alexander Barbara D. , Majure Joseph M. , Williams Larry W. , Kim Jason Y. , Vandamme Peter , LiPuma John J.
Published: November 2006

An 8-month-old boy developed a necrotic lung mass from which
Burkholderia glumae
was recovered, leading to the diagnosis of chronic granulomatous disease (CGD). While other
Burkholderia
species have been identified as important pathogens in persons with CGD,
B. glumae
has not been previously reported to cause human infection.
Tomato Chlorotic Mottle Virus Is a Target of RNA Silencing but the Presence of Specific Short Interfering RNAs Does Not Guarantee Resistance in Transgenic Plants
Authors: Ribeiro Simone G. , Lohuis Hendrikus , Goldbach Rob , Prins Marcel
Published: November 2006

Tomato chlorotic mottle virus (ToCMoV) is a begomovirus found widespread in tomato fields in Brazil. ToCMoV isolate BA-Se1 (ToCMoV-[BA-Se1]) was shown to trigger the plant RNA silencing surveillance in different host plants and, coinciding with a decrease in viral DNA levels, small interfering RNAs (siRNAs) specific to ToCMoV-[BA-Se1] accumulated in infected plants. Although not homogeneously distributed, the siRNA population in both infected
Nicotiana benthamiana
and tomato plants represented the entire DNA-A and DNA-B genomes. We determined that in
N. benthamiana
, the primary targets corresponded to the 5′ end of AC1 and the embedded AC4, the intergenic region and 5′ end of AV1 and overlapping central part of AC5. Subsequently, transgenic
N. benthamiana
plants were generated that were preprogrammed to express double-stranded RNA corresponding to this most targeted portion of the virus genome by using an intron-hairpin construct. These plants were shown to indeed produce ToCMoV-specific siRNAs. When challenge inoculated, most transgenic lines showed significant delays in symptom development, and two lines had immune plants. Interestingly, the levels of transgene-produced siRNAs were similar in resistant and susceptible siblings of the same line. This indicates that, in contrast to RNA viruses, the mere presence of transgene siRNAs corresponding to DNA virus sequences does not guarantee virus resistance and that other factors may play a role in determining RNA-mediated resistance to DNA viruses.
Mitotic Kinesin-Like Protein 2 Binds and Colocalizes with Papillomavirus E2 during Mitosis
Authors: Yu Ting , Peng Yu-Cai , Androphy Elliot J.
Published: November 2006

MKlp2 is a kinesin-like motor protein of the central mitotic spindle required for completion of cytokinesis. Papillomavirus E2 is a sequence specific DNA binding protein that regulates viral transcription and replication and is responsible for partitioning viral episomes into daughter cells during cell division. We demonstrate that MKlp2 specifically associates with the E2 protein during mitosis. Using chromatin immunoprecipitation, we show viral genomes are in complex with MKlp2 only within this stage of cell cycle. By immunofluorescence, a subpopulation of papillomavirus E2 colocalizes with MKlp2 in the midbody/midplate during late mitosis. We conclude that during specific stages of mitosis, the papillomavirus E2 protein binds to MKlp2, and infer that association with this motor protein ensures viral genome partitioning during cytokinesis.
Regulation of Hepadnavirus Reverse Transcription by Dynamic Nucleocapsid Phosphorylation
Authors: Basagoudanavar Suresh H. , Perlman David H. , Hu Jianming
Published: November 2006

Reverse transcription, an essential step in the life cycle of all retroelements, is a complex, multistep process whose regulation is not yet clearly understood. We have recently shown that reverse transcription in the pararetrovirus duck hepatitis B virus is associated with complete dephosphorylation of the viral core protein, which forms the nucleocapsid wherein reverse transcription takes place. Here we present a genetic study of the role of this dynamic nucleocapsid phosphorylation in regulating viral reverse transcription. Detailed analyses of the reverse transcription products synthesized within nucleocapsids composed of core phosphorylation site mutants revealed that alanine substitutions, mimicking the nonphosphorylated state, completely blocked reverse transcription at a very early stage. In contrast, aspartate substitutions, mimicking the phosphorylated state, allowed complete first-strand DNA synthesis but were severely defective in accumulating mature double-stranded DNA. The latter defect was due to a combination of mutant nucleocapsid instability during maturation and a block in mature second-strand DNA synthesis. Thus, the reversible phosphorylation of the nucleocapsids regulates the ordered progression of reverse transcription.
Involvement of the PA28γ-Dependent Pathway in Insulin Resistance Induced by Hepatitis C Virus Core Protein
Authors: Miyamoto Hironobu , Moriishi Kohji , Moriya Kyoji , Murata Shigeo , Tanaka Keiji , Suzuki Tetsuro , Miyamura Tatsuo , Koike Kazuhiko , Matsuura Yoshiharu
Published: November 2006

The hepatitis C virus (HCV) core protein is a component of nucleocapsids and a pathogenic factor for hepatitis C. Several epidemiological and experimental studies have suggested that HCV infection is associated with insulin resistance, leading to type 2 diabetes. We have previously reported that HCV core gene-transgenic (PA28γ+/+CoreTg) mice develop marked insulin resistance and that the HCV core protein is degraded in the nucleus through a PA28γ-dependent pathway. In this study, we examined whether PA28γ is required for HCV core-induced insulin resistance in vivo. HCV core gene-transgenic mice lacking the PA28γ gene (PA28γ−/−CoreTg) were prepared by mating of PA28γ+/+CoreTg with PA28γ-knockout mice. Although there was no significant difference in the glucose tolerance test results among the mice, the insulin sensitivity in PA28γ−/−CoreTg mice was recovered to a normal level in the insulin tolerance test. Tyrosine phosphorylation of insulin receptor substrate 1 (IRS1), production of IRS2, and phosphorylation of Akt were suppressed in the livers of PA28γ+/+CoreTg mice in response to insulin stimulation, whereas they were restored in the livers of PA28γ−/−CoreTg mice. Furthermore, activation of the tumor necrosis factor alpha promoter in human liver cell lines or mice by the HCV core protein was suppressed by the knockdown or knockout of the PA28γ gene. These results suggest that the HCV core protein suppresses insulin signaling through a PA28γ-dependent pathway.
Not All Cytokine-Producing CD8
+
T Cells Suppress Simian Immunodeficiency Virus Replication
Authors: Chung Chungwon , Lee Wonhee , Loffredo John T. , Burwitz Benjamin , Friedrich Thomas C. , Giraldo Vela Juan Pablo , Napoe Gnankang , Rakasz Eva G. , Wilson Nancy A. , Allison David B. , Watkins David I.
Published: November 2006

Current assays of CD8
+
T-lymphocyte function measure cytokine production rather than the ability of these lymphocytes to suppress viral replication. Here we show that CD8
+
T-cell clones recognizing the same epitope vary enormously in the ability to suppress simian immunodeficiency virus SIVmac239 replication in an in vitro suppression assay. However, all Nef
165-173
IW9- and Vif
66-73
HW8-specific clones from elite controllers effectively suppressed SIV replication. Interestingly, in vitro suppression efficacy was not always associated with the ability to produce gamma interferon, tumor necrosis factor alpha, or interleukin-2.
The Transdominant Endogenous Retrovirus enJS56A1 Associates with and Blocks Intracellular Trafficking of Jaagsiekte Sheep Retrovirus Gag
Authors: Murcia Pablo R. , Arnaud Frederick , Palmarini Massimo
Published: November 2006

The sheep genome harbors approximately 20 endogenous retroviruses (enJSRVs) highly related to the exogenous Jaagsiekte sheep retrovirus (JSRV). One of the enJSRV loci, enJS56A1, acts as a unique restriction factor by blocking JSRV in a transdominant fashion at a late stage of the retroviral cycle. To better understand the molecular basis of this restriction (termed JLR, for
J
SRV
l
ate
r
estriction), we functionally characterized JSRV and enJS56A1 Gag proteins. We identified the putative JSRV Gag membrane binding and late domains and determined their lack of involvement in JLR. In addition, by using enJS56A1 truncation mutants, we established that the entire Gag protein is necessary to restrict JSRV exit. By using differentially tagged viruses, we observed, by confocal microscopy, colocalization between JSRV and enJS56A1 Gag proteins. By coimmunoprecipitation and molecular complementation analyses, we also revealed intracellular association and likely coassembly between JSRV and enJS56A1 Gag proteins. Interestingly, JSRV and enJS56A1 Gag proteins showed distinct intracellular targeting: JSRV exhibited pericentrosomal accumulation of Gag staining, while enJS56A1 Gag did not accumulate in this region. Furthermore, the number of cells displaying pericentrosomal JSRV Gag was drastically reduced in the presence of enJS56A1. We identified amino acid residue R21 in JSRV Gag as the primary determinant of centrosome targeting. We concluded that JLR is dependent on a Gag-Gag interaction between enJS56A1 and JSRV leading to altered cellular localization of the latter.
A Novel Repeat-Associated Small Interfering RNA-Mediated Silencing Pathway Downregulates Complementary Sense
gypsy
Transcripts in Somatic Cells of the
Drosophila
Ovary
Authors: Pélisson Alain , Sarot Emeline , Payen-Groschêne Geneviève , Bucheton Alain
Published: November 2006

Replication of the
gypsy
endogenous retrovirus involves contamination of the female germ line by adjacent somatic tissues. This is prevented by
flam
, an as-yet-uncloned heterochromatic pericentromeric locus, at the level of transcript accumulation in these somatic ovarian tissues. We tested the effect of a presumptive RNA silencing mechanism on the accumulation of RNAs produced by constructs containing various
gypsy
sequences and report that the efficiency of silencing is indeed correlated with the amount of complementary RNAs, 25 to 30 nucleotides in length, in the ovary. For instance, while these RNAs were found to display a three- to fivefold excess of the antisense strands, only the transcripts that contain the complementary sense
gypsy
sequences could be repressed, indicating that they are targeted at the RNA, not DNA, level. Their size and asymmetry in strand polarity are typical of the novel repeat-associated small interfering RNA (rasiRNA)-mediated pathway, recently suspected to prevent the deleterious expression of selfish DNA specifically in the germ line. Unlike microRNAs (but like rasiRNAs and, surprisingly, siRNAs as well),
gypsy
rasiRNAs are modified at the 3′ end. The rasiRNA-associated protein Piwi (but not Aub) is required for
gypsy
silencing, whereas Dicer-2 (which makes siRNAs) is not. In contrast,
piwi
,
aub
, and
flam
do not appear to affect somatic siRNA-mediated silencing. The amount of
gypsy
rasiRNAs is genetically determined by the
flam
locus in a provirus copy number-independent manner and is triggered in the somatic tissues by some pericentromeric provirus(es), which are thereby able to protect the germ line from retroviral invasion.
Long-Lasting Decrease in Viremia in Macaques Chronically Infected with Simian Immunodeficiency Virus SIVmac251 after Therapeutic DNA Immunization
Authors: von Gegerfelt Agneta S. , Rosati Margherita , Alicea Candido , Valentin Antonio , Roth Patricia , Bear Jenifer , Franchini Genoveffa , Albert Paul S. , Bischofberger Norbert , Boyer Jean D. , Weiner David B. , Markham Phillip , Israel Zimra R. , Eldridge John H. , Pavlakis George N. , Felber Barbara K.
Published: November 2006

Rhesus macaques chronically infected with highly pathogenic simian immunodeficiency virus (SIV) SIVmac251 were treated with antiretroviral drugs and vaccinated with combinations of DNA vectors expressing SIV antigens. Vaccination during therapy increased cellular immune responses. After the animals were released from therapy, the virus levels of 12 immunized animals were significantly lower (
P
= 0.001) compared to those of 11 animals treated with only antiretroviral drugs. Vaccinated animals showed a persistent increase in immune responses, thus indicating both a virological and an immunological benefit following DNA therapeutic vaccination. Several animals show a long-lasting decrease in viremia, suggesting that therapeutic vaccination may provide an additional benefit to antiretroviral therapy.
The Human TRIM5α Restriction Factor Mediates Accelerated Uncoating of the N-Tropic Murine Leukemia Virus Capsid
Authors: Perron Michel J. , Stremlau Matthew , Lee Mark , Javanbakht Hassan , Song Byeongwoon , Sodroski Joseph
Published: November 2006

The host cell factors TRIM5α
hu
and Fv-1 restrict N-tropic murine leukemia virus (N-MLV) infection at an early postentry step before or after reverse transcription, respectively. Interestingly, the identity of residue 110 of the MLV capsid determines susceptibility to both TRIM5α
hu
and Fv-1. In this study, we investigate the fate of the MLV capsid in cells expressing either the TRIM5α
hu
or Fv-1 restriction factor. The expression of TRIM5α
hu
, but not Fv-1, specifically promoted the premature conversion of particulate N-MLV capsids within infected cells to soluble capsid proteins. The TRIM5α
hu
-mediated disassembly of particulate N-MLV capsids was dependent upon residue 110 of the viral capsid. Furthermore, the deletion or disruption of TRIM5α
hu
domains necessary for potent N-MLV restriction completely abrogated the disappearance of particulate N-MLV capsids observed with wild-type TRIM5α
hu
. These results suggest that premature disassembly of the viral capsid contributes to the restriction of N-MLV infection by TRIM5α
hu
, but not by Fv-1.
My approach to pathology of the pituitary gland
Authors: Al-Brahim N Y Y , Asa S L
Published: December 2006

The sellar region is the site of a large number of pathological entities arising from the pituitary and adjacent anatomical structures, including brain, blood vessels, nerves and meninges. The surgical pathology of this area requires the accurate identification of neoplastic lesions, including pituitary adenoma and carcinoma, craniopharyngioma, neurological neoplasms, germ cell tumours, haematological malignancies and metastases, as well as non-neoplastic lesions such as cysts, hyperplasias and inflammatory disorders. This review provides a practical approach to the diagnosis of pituitary specimens that are sent to the pathologist at the time of surgery. The initial examination requires routine haematoxylin and eosin staining to establish whether the lesion is a primary adenohypophysial proliferation or one of the many other pathologies that occurs in this area. The most common lesions resected surgically are pituitary adenomas. These are evaluated with several special stains and immunohistochemical markers that are now available to accurately classify these pathologies. The complex subclassification of pituitary adenomas is now recognised to reflect specific clinical features and genetic changes that predict targeted treatments for patients with pituitary disorders.