bluuebunny/crossref_metadata_2025 huggingface dataset:
Resource Letter CS–1: Complex Systems
Authors: Newman M. E. J.
Published: July 2011

A complex system is a system composed of many interacting parts, often called agents, which displays collective behavior that does not follow trivially from the behaviors of the individual parts. Examples include condensed-matter systems, ecosystems, stock markets and economies, biological evolution, and indeed the whole of human society. Substantial progress has been made in the quantitative understanding of complex systems, particularly since the 1980s, using a combination of basic theory, much of it derived from physics, and computer simulation. The subject is a broad one, drawing on techniques and ideas from a wide range of areas. Here, I give a selection of introductory resources, ranging from classic papers to recent books and reviews.
Resolution of the ellipsoid paradox in thermodynamics
Authors: Yoder Theodore J. , Adkins Gregory S.
Published: July 2011

We discuss a challenge to the second law of thermodynamics in an optical setting, in which two black bodies at strategically chosen points inside a perfectly reflecting cavity of appropriate shape apparently transfer energy asymmetrically so that one body experiences a net gain of energy at the other’s expense. We show how the finite sizes of the black bodies lead to a resolution of the apparent paradox. We describe a simulation that allows us to follow the paths of individual rays and show numerically that the second law requirement of energy balance is satisfied. We also demonstrate that the energy balance condition is satisfied in the more general situation where the cavity and black bodies are of arbitrary shape.
Bats Use Echo Harmonic Structure to Distinguish Their Targets from Background Clutter
Authors: Bates Mary E. , Simmons James A. , Zorikov Tengiz V.
Published: July 2011

Bats use temporal differences in sonar echoes to suppress interference from background clutter.
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
Authors: Mukhtar M. Shahid , Carvunis Anne-Ruxandra , Dreze Matija , Epple Petra , Steinbrenner Jens , Moore Jonathan , Tasan Murat , Galli Mary , Hao Tong , Nishimura Marc T. , Pevzner Samuel J. , Donovan Susan E. , Ghamsari Lila , Santhanam Balaji , Romero Viviana , Poulin Matthew M. , Gebreab Fana , Gutierrez Bryan J. , Tam Stanley , Monachello Dario , Boxem Mike , Harbort Christopher J. , McDonald Nathan , Gai Lantian , Chen Huaming , He Yijian ,   European Union Effectoromics Consortium, Vandenhaute Jean , Roth Frederick P. , Hill David E. , Ecker Joseph R. , Vidal Marc , Beynon Jim , Braun Pascal , Dangl Jeffery L.
Published: July 2011

An analysis of protein-protein interactions in
Arabidopsis
identifies the plant interactome.
Initiation Complex Structure and Promoter Proofreading
Authors: Liu Xin , Bushnell David A. , Silva Daniel-Adriano , Huang Xuhui , Kornberg Roger D.
Published: July 2011

RNA polymerase II transcription complexes reveal the basis of abortive initiation and its role in promoter control.
Tenfold Population Increase in Western Europe at the Neandertal–to–Modern Human Transition
Authors: Mellars Paul , French Jennifer C.
Published: July 2011

The ability of modern humans to sustain larger populations contributed to the decline of Neandertals in Western Europe.
When the World’s Population Took Off: The Springboard of the Neolithic Demographic Transition
Authors: Bocquet-Appel Jean-Pierre
Published: July 2011

During the economic transition from foraging to farming, the signal of a major demographic shift can be observed in cemetery data of world archaeological sequences. This signal is characterized by an abrupt increase in the proportion of juvenile skeletons and is interpreted as the signature of a major demographic shift in human history, known as the Neolithic Demographic Transition (NDT). This expresses an increase in the input into the age pyramids of the corresponding living populations with an estimated increase in the total fertility rate of two births per woman. The unprecedented demographic masses that the NDT rapidly brought into play make this one of the fundamental structural processes of human history.
The World Through a Bat's Ear
Authors: Fenton M. Brock
Published: July 2011

Using echolocation, bats can distinguish true targets from background clutter and find insect prey or flowers with nectar.
How an Alluring Geologic Enigma Won the Mars Rover Sweepstakes
Authors: Kerr Richard A.
Published: July 2011

To up the odds of finding signs of life on Mars, NASA has chosen mineralogically diverse but mysterious Gale crater as the target for its $2.5 billion Curiosity rover.
Russia Launches a Telescope, Decades in the Making
Authors: Clery Daniel
Published: July 2011

Champagne corks were popping in Russia last week after the country's first successful launch of an orbiting observatory in the post-Soviet era.
When Is It Ramadan? An Arab Astronomer Has Answers
Authors: Cartlidge Edwin
Published: July 2011

Astrophysicist Nidhal Guessoum advocates a scientific approach to the problem of determining when months begin in the Islamic calendar, which traditionally relies on eye-witness observations of the moon.
A Battle No Soldier Wants to Fight
Authors: Miller Greg
Published: July 2011

Could brain injuries suffered in battle put troops at risk for dementia? Recent findings of pathology in athletes, among other evidence, are raising concerns.
A Pitched Battle Over Life Span
Authors: Couzin-Frankel Jennifer
Published: July 2011

Predicting whether life expectancies will keep rising is as much art as science. Two demographers disagree about what the coming years will bring.
Gray Ladies in The Spotlight
Authors: Malakoff David
Published: July 2011

A growing corps of graying women are actively engaged in the civic life of their often male-dominated communities, taking on stabilizing social roles that others sometimes can't.
Regional Snapshots
Authors: Vogel Gretchen
Published: July 2011

Science
has created several "snapshots," descriptions of composite characters, to try to capture some of the demographic trends that set countries and regions apart.
Bioinformatics Is “HIP” in the Islets
Authors: Cheng Mickie H.
Published: July 2011

Combing GWAS data for disease-relevant interacting proteins predicts a role for HIP14 in diabetes.
Speaking from the Mind
Authors: Wang Wei
Published: July 2011

A new communication assist device deciphers speech directly from cortical activity.
Long-Term Immunogenicity after One and Two Doses of a Monovalent MF59-Adjuvanted A/H1N1 Influenza Virus Vaccine Coadministered with the Seasonal 2009-2010 Nonadjuvanted Influenza Virus Vaccine in HIV-Infected Children, Adolescents, and Young Adults in a Randomized Controlled Trial
Authors: Viganò Alessandra , Giacomet Vania , Pariani Elena , Giani Elisa , Manfredini Valeria , Bedogni Giorgio , Erba Paola , Amendola Antonella , Zanetti Alessandro , Zuccotti Gianvincenzo
Published: July 2011

Few data are available on the safety and long-term immunogenicity of A/H1N1 pandemic influenza vaccines for HIV-infected pediatric patients. We performed a randomized controlled trial to evaluate the safety and long-term immunogenicity of 1 versus 2 doses of the 2009 monovalent pandemic influenza A/H1N1 MF59-adjuvanted vaccine (PV) coadministered with the seasonal 2009-2010 trivalent nonadjuvanted influenza vaccine (SV) to HIV-infected children, adolescents, and young adults. A total of 66 HIV-infected patients aged 9 to 26 years were randomized to receive one (group 1) or two (group 2) doses of PV coadministered with 1 dose of SV. The main outcome was the seroconversion rate for PV at 1 month. Secondary outcomes were the geometric mean titer ratios and the seroprotection rates at 1 month for all vaccines, seroconversion rates at 1 month for SV, and longitudinal changes of antibody titers (ABTs) at 1, 2, 6, and 12 months for all vaccines. Groups 1 and 2 had similar CD4 counts and HIV RNA levels during the study. The seroconversion rate for PV was 100% at 1 month in both groups. ABTs for PV were high during the first 6 months and declined below seroprotection levels thereafter. Longitudinal changes in ABTs were similar in groups 1 and 2 for both PV and SV. The side effects of vaccination were mild and mostly local. In HIV-infected children, adolescents, and young adults, the immune response triggered by a single dose of PV was similar to that obtained with a double dose and was associated with long-term antibody response.
Clinical and Laboratory Diagnostic Characteristics and Cytotoxigenic Potential of Hafnia alvei and Hafnia paralvei Strains
Authors: Abbott Sharon L. , Moler Silvia , Green Nicole , Tran Robert K. , Wainwright Katlyn , Janda J. Michael
Published: July 2011

A collection of 68
Hafnia
strains previously identified to the species level by 16S rRNA gene sequencing were investigated for simple phenotypic properties that could aid in their recognition in the clinical laboratory. Four tests, including malonate utilization, fermentation of salicin and
d
-arabinose, and expression of β-glucosidase activity, correctly assigned each strain to either
Hafnia alvei
or
H. paralvei
. Antibiotic susceptibility profiles were generated for 35
H. alvei
and
H. paralvei
isolates using Etest strips for 24 antibiotics. All strains were susceptible to aminoglycosides, quinolones, carbapenems, and monobactams. Most of the
Hafnia
isolates had a colistin MIC of ≥2 μg/ml. Sequencing of an internal
ampC
gene fragment allowed genotypic differentiation of the two
Hafnia
species. Approximately 70% of the hafniae tested additionally produced a cytolytic toxin active on Vero cells which may play a role in gastroenteritis.
Performance Characteristics and Comparison of Abbott and artus Real-Time Systems for Hepatitis B Virus DNA Quantification
Authors: Ismail Ashrafali M. , Sivakumar Jayashree , Anantharam Raghavendran , Dayalan Sujitha , Samuel Prasanna , Fletcher Gnanadurai J. , Gnanamony Manu , Abraham Priya
Published: July 2011

Virological monitoring of hepatitis B virus (HBV) DNA is critical to the management of HBV infection. With several HBV DNA quantification assays available, it is important to use the most efficient testing system for virological monitoring. In this study, we evaluated the performance characteristics and comparability of three HBV DNA quantification systems: Abbott HBV real-time PCR (Abbott PCR), artus HBV real-time PCR with QIAamp DNA blood kit purification (artus-DB), and artus HBV real-time PCR with the QIAamp DSP virus kit purification (artus-DSP). The lower limits of detection of these systems were established against the WHO international standards for HBV DNA and were found to be 1.43, 82, and 9 IU/ml, respectively. The intra-assay and interassay coefficients of variation of plasma samples (1 to 6 log
10
IU/ml) ranged between 0.05 to 8.34% and 0.16 to 3.48% for the Abbott PCR, 1.53 to 26.85% and 0.50 to 12.89% for artus-DB, and 0.29 to 7.42% and 0.94 to 3.01% for artus-DSP, respectively. Ninety HBV clinical samples were used for comparison of assays, and paired quantitative results showed strong correlation by linear regression analysis (artus-DB with Abbott PCR,
r
= 0.95; Abbott PCR with artus-DSP,
r
= 0.97; and artus-DSP with artus-DB,
r
= 0.94). Bland-Altman analysis showed a good level of agreement for Abbott PCR and artus-DSP, with a mean difference of 0.10 log
10
IU/ml and limits of agreement of −0.91 to 1.11 log
10
IU/ml. No genotype-specific bias was seen in all three systems for HBV genotypes A, C, and D, which are predominant in this region. This finding illustrates that the Abbott real-time HBV and artus-DSP systems show more comparable performance than the artus-DB system, meeting the current guidelines for assays to be used in the management of hepatitis B.
First Report of Prosthetic Joint Infection by Gemella sanguinis and Associated “Pseudosatelliting” Phenomenon on Culture
Authors: Leung Daniel T. , Davis Eric M. , Qian Qinfang , Gold Howard S.
Published: July 2011

We report the first case of a prosthetic joint infection caused by
Gemella sanguinis
. This report includes a description of a “pseudosatelliting” phenomenon by
G. sanguinis
, the use of gene sequencing for pathogen identification, and successful use of debridement, retention, and chronic antibiotic suppression to preserve the prosthesis.
Variable Prevalence and Functional Diversity of the Antiretroviral Restriction Factor TRIMCyp in Macaca fascicularis
Authors: Dietrich Elizabeth A. , Brennan Greg , Ferguson Betsy , Wiseman Roger W. , O'Connor David , Hu Shiu-Lok
Published: July 2011

The retroviral restriction factor TRIMCyp, derived from the
TRIM5
gene, blocks replication at a postentry step. TRIMCyp has so far been found in four species of Asian macaques,
Macaca fascicularis
,
M. mulatta
,
M. nemestrina
, and
M. leonina
.
M. fascicularis
is commonly used as a model for AIDS research, but TRIMCyp has not been analyzed in detail in this species. We analyzed the prevalence of TRIMCyp in samples from Indonesia, Indochina, the Philippines, and Mauritius. We found that TRIMCyp is present at a higher frequency in Indonesian than in Indochinese
M. fascicularis
macaques and is also present in samples from the Philippines. TRIMCyp is absent in Mauritian
M. fascicularis
macaques. We then analyzed the restriction specificity of TRIMCyp derived from three animals of Indonesian origin. One allele, like the prototypic TRIMCyp alleles described for
M. mulatta
and
M. nemestrina
, restricts human immunodeficiency virus type 2 (HIV-2) and feline immunodeficiency virus (FIV) but not HIV-1. The others restrict HIV-1 and FIV but not HIV-2. Mutagenesis studies confirmed that polymorphisms at amino acid residues 369 and 446 in TRIMCyp (or residues 66 and 143 in the cyclophilin A [CypA] domain) confer restriction specificity. Additionally, we identified a polymorphism in the coiled-coil domain that appears to affect TRIMCyp expression or stability. Taken together, these data show that
M. fascicularis
has the most diverse array of
TRIM5
restriction factors described for any primate species to date. These findings are relevant to our understanding of the evolution of retroviral restriction factors and the use of
M. fascicularis
models in AIDS research.
Molecular Surveillance of HIV-1 in Madrid, Spain: a Phylogeographic Analysis
Authors: González-Alba José M. , Holguín África , Garcia Rosa , García-Bujalance Silvia , Alonso Roberto , Suárez Avelina , Delgado Rafael , Cardeñoso Laura , González Rosa , García-Bermejo Isabel , Portero Francisca , de Mendoza Carmen , González-Candelas Fernando , Galán Juan-Carlos
Published: July 2011

The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (
n
= 2,792) from 11 Madrid hospitals of viral
pol
sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.
Major Histocompatibility Complex-Dependent Cytotoxic T Lymphocyte Repertoire and Functional Avidity Contribute to Strain-Specific Disease Susceptibility after Murine Respiratory Syncytial Virus Infection
Authors: Jessen Birthe , Faller Simone , Krempl Christine D. , Ehl Stephan
Published: July 2011

Susceptibility to respiratory syncytial virus (RSV) infection in mice is genetically determined. While RSV causes little pathology in C57BL/6 mice, pulmonary inflammation and weight loss occur in BALB/c mice. Using major histocompatibility complex (MHC)-congenic mice, we observed that the H-2dallele can partially transfer disease susceptibility to C57BL/6 mice. This was not explained by altered viral elimination or differences in the magnitude of the overall virus-specific cytotoxic T lymphocyte (CTL) response. However, H-2dmice showed a more focused response, with 70% of virus-specific CTL representing Vβ8.2+CTL directed against the immunodominant epitope M2-1 82, while in H-2bmice only 20% of antiviral CTL were Vβ9+CTL specific for the immunodominant epitope M187. The immunodominant H-2d-restricted CTL lysed target cells less efficiently than the immunodominant H-2bCTL, probably contributing to prolonged CTL stimulation and cytokine-mediated immunopathology. Accordingly, reduction of dominance of the M2-1 82-specific CTL population by introduction of an M187 response in the F1 generation of a C57BL/6N × C57BL/6-H-2dmating (C57BL/6-H-2dxbmice) attenuated disease. Moreover, disease in H-2dmice was less pronounced after infection with an RSV mutant failing to activate M2-1 82-specific CTL or after depletion of Vβ8.2+cells. These data illustrate how the MHC-determined diversity and functional avidity of CTL responses contribute to disease susceptibility after viral infection.
Amiloride Is a Competitive Inhibitor of Coxsackievirus B3 RNA Polymerase
Authors: Gazina Elena V. , Smidansky Eric D. , Holien Jessica K. , Harrison David N. , Cromer Brett A. , Arnold Jamie J. , Parker Michael W. , Cameron Craig E. , Petrou Steven
Published: July 2011

Amiloride and its derivative 5-(
N
-ethyl-
N
-isopropyl)amiloride (EIPA) were previously shown to inhibit coxsackievirus B3 (CVB3) RNA replication in cell culture, with two amino acid substitutions in the viral RNA-dependent RNA polymerase 3D
pol
conferring partial resistance of CVB3 to these compounds (D. N. Harrison, E. V. Gazina, D. F. Purcell, D. A. Anderson, and S. Petrou, J. Virol.
82:
1465–1473, 2008). Here we demonstrate that amiloride and EIPA inhibit the enzymatic activity of CVB3 3D
pol
in vitro
, affecting both VPg uridylylation and RNA elongation. Examination of the mechanism of inhibition of 3D
pol
by amiloride showed that the compound acts as a competitive inhibitor, competing with incoming nucleoside triphosphates (NTPs) and Mg
2+
. Docking analysis suggested a binding site for amiloride and EIPA in 3D
pol
, located in close proximity to one of the Mg
2+
ions and overlapping the nucleotide binding site, thus explaining the observed competition. This is the first report of a molecular mechanism of action of nonnucleoside inhibitors against a picornaviral RNA-dependent RNA polymerase.
Analysis of a Clonal Lineage of HIV-1 Envelope V2/V3 Conformational Epitope-Specific Broadly Neutralizing Antibodies and Their Inferred Unmutated Common Ancestors
Authors: Bonsignori Mattia , Hwang Kwan-Ki , Chen Xi , Tsao Chun-Yen , Morris Lynn , Gray Elin , Marshall Dawn J. , Crump John A. , Kapiga Saidi H. , Sam Noel E. , Sinangil Faruk , Pancera Marie , Yongping Yang , Zhang Baoshan , Zhu Jiang , Kwong Peter D. , O'Dell Sijy , Mascola John R. , Wu Lan , Nabel Gary J. , Phogat Sanjay , Seaman Michael S. , Whitesides John F. , Moody M. Anthony , Kelsoe Garnett , Yang Xinzhen , Sodroski Joseph , Shaw George M. , Montefiori David C. , Kepler Thomas B. , Tomaras Georgia D. , Alam S. Munir , Liao Hua-Xin , Haynes Barton F.
Published: July 2011

V2/V3 conformational epitope antibodies that broadly neutralize HIV-1 (PG9 and PG16) have been recently described. Since an elicitation of previously known broadly neutralizing antibodies has proven elusive, the induction of antibodies with such specificity is an important goal for HIV-1 vaccine development. A critical question is which immunogens and vaccine formulations might be used to trigger and drive the development of memory B cell precursors with V2/V3 conformational epitope specificity. In this paper we identified a clonal lineage of four V2/V3 conformational epitope broadly neutralizing antibodies (CH01 to CH04) from an African HIV-1-infected broad neutralizer and inferred their common reverted unmutated ancestor (RUA) antibodies. While conformational epitope antibodies rarely bind recombinant Env monomers, a screen of 32 recombinant envelopes for binding to the CH01 to CH04 antibodies showed monoclonal antibody (MAb) binding to the E.A244 gp120 Env and to chronic Env AE.CM243; MAbs CH01 and CH02 also bound to transmitted/founder Env B.9021. CH01 to CH04 neutralized 38% to 49% of a panel of 91 HIV-1 tier 2 pseudoviruses, while the RUAs neutralized only 16% of HIV-1 isolates. Although the reverted unmutated ancestors showed restricted neutralizing activity, they retained the ability to bind to the E.A244 gp120 HIV-1 envelope with an affinity predicted to trigger B cell development. Thus, E.A244, B.9021, and AE.CM243 Envs are three potential immunogen candidates for studies aimed at defining strategies to induce V2/V3 conformational epitope-specific antibodies.
Construction of a Lytically Replicating Kaposi's Sarcoma-Associated Herpesvirus
Authors: Budt Matthias , Hristozova Tsvetana , Hille Georg , Berger Katrin , Brune Wolfram
Published: July 2011

Karposi's sarcoma-associated herpesvirus (KSHV) is found predominantly in a latent state in most cell types, impeding investigations of the lytic replication cycle. Here, we engineered the cloned KSHV genome, bacterial artificial chromosome 36 (BAC36), to enforce constitutive expression of the main lytic switch regulator, the replication and transcription activator (RTA) (open reading frame 50 [ORF50]). The resulting virus, KSHV-lyt, activated by default the lytic cycle and replicated to high titers in various cells. Using KSHV-lyt, we showed that ORF33 (encoding a tegument protein) is essential for lytic KSHV replication in cell culture, but ORF73 (encoding the latent nuclear antigen [LANA]) is not. Thus, KSHV-lyt should be highly useful to study viral gene function during lytic replication.
Infection of Lymphoblastoid Cell Lines by Kaposi's Sarcoma-Associated Herpesvirus: Critical Role of Cell-Associated Virus
Authors: Myoung Jinjong , Ganem Don
Published: July 2011

Kaposi's sarcoma-associated herpesvirus (KSHV) displays strong lymphotropism
in vivo
, but paradoxically, established B cell lines have largely been refractory to infection by soluble KSHV virions. Here we show that this block can be overcome by exposure to cell-associated virus. Doxycycline-inducible recombinant KSHV.219 (rKSHV.219)-harboring SLK (iSLK.219) cells were employed as KSHV donors. Cocultivation of lymphoid cell lines with reactivated iSLK.219 cells resulted in readily demonstrable viral entry into each cell line; similar observations were made in primary tonsillar B cell cultures. Moreover, infected lymphoid cells were able to outgrow upon puromycin selection, indicating development of persistent infection. Infected BJAB cells display signatures of latent infection, including classical latency-associated transcripts, a punctate pattern of LANA expression, and episomal maintenance of the KSHV genome. However, when lytically activated by various chemical stimuli, infected BJAB cells were able to produce only low levels of infectious virions. These data demonstrate that (i) cell-associated viruses can bypass viral entry blocks in most lymphoid cell lines, (ii) the determinants of cell-associated virus entry differ from those of soluble virion infection, and (iii) immortalized lymphoblastoid lines have partial postentry blocks to efficient lytic reactivation.
The Alpha Subunit of Eukaryotic Initiation Factor 2B (eIF2B) Is Required for eIF2-Mediated Translational Suppression of Vesicular Stomatitis Virus
Authors: Elsby Rachel , Heiber Joshua F. , Reid Peter , Kimball Scot R. , Pavitt Graham D. , Barber Glen N.
Published: July 2011

Eukaryotic translation initiation factor 2B (eIF2B) is a heteropentameric guanine nucleotide exchange factor that converts protein synthesis initiation factor 2 (eIF2) from a GDP-bound form to the active eIF2-GTP complex. Cellular stress can repress translation initiation by activating kinases capable of phosphorylating the alpha subunit of eIF2 (eIF2α), which sequesters eIF2B to prevent exchange activity. Previously, we demonstrated that tumor cells are sensitive to viral replication, possibly due to the occurrence of defects in eIF2B that overcome the inhibitory effects of eIF2α phosphorylation. To extend this analysis, we have investigated the importance of eIF2Bα function and report that this subunit can functionally substitute for its counterpart, GCN3, in yeast. In addition, a variant of mammalian eIF2Bα harboring a point mutation (T41A) was able overcome translational inhibition invoked by amino acid depravation, which activates
Saccharomyces cerevisiae
GCN2 to phosphorylate the yeast eIF2α homolog SUI2. Significantly, we also demonstrate that the loss of eIF2Bα, or the expression of the T41A variant in mammalian cells, is sufficient to neutralize the consequences of eIF2α phosphorylation and render normal cells susceptible to virus infection. Our data emphasize the importance of eIF2Bα in mediating the eIF2 kinase translation-inhibitory activity and may provide insight into the complex nature of viral oncolysis.
Spinoculation Triggers Dynamic Actin and Cofilin Activity That Facilitates HIV-1 Infection of Transformed and Resting CD4 T Cells
Authors: Guo Jia , Wang Weifeng , Yu Dongyang , Wu Yuntao
Published: July 2011

Centrifugal inoculation, or spinoculation, is widely used in virology research to enhance viral infection. However, the mechanism remained obscure. Using HIV-1 infection of human T cells as a model, we demonstrate that spinoculation triggers dynamic actin and cofilin activity, probably resulting from cellular responses to centrifugal stress. This actin activity also leads to the upregulation of the HIV-1 receptor and coreceptor, CD4 and CXCR4, enhancing viral binding and entry. We also demonstrate that an actin inhibitor, jasplakinolide, diminishes spin-mediated enhancement. In addition, small interfering RNA (siRNA) knockdown of LIMK1, a cofilin kinase, decreases the enhancement. These results suggest that spin-mediated enhancement cannot be explained simply by a virus-concentrating effect; rather, it is coupled with spin-induced cytoskeletal dynamics that promote receptor mobilization, viral entry, and postentry processes. Our results highlight the importance of cofilin and a dynamic cytoskeleton for the initiation of viral infection. Our results also indicate that caution needs to be taken in data interpretation when cells are spinoculated; some of the spin-induced cellular permissiveness may be beyond the natural capacity of an infecting virus.
Molecular Evolution Analysis of the Human Immunodeficiency Virus Type 1 Envelope in Simian/Human Immunodeficiency Virus-Infected Macaques: Implications for Challenge Dose Selection
Authors: Varela Mariana , Landskron Lisa , Lai Rachel P. J. , McKinley Trevelyan J. , Bogers Willy M. , Verschoor Ernst J. , Dubbes Rob , Barnett Susan W. , Frost Simon D. W. , Heeney Jonathan L.
Published: July 2011

Since the demonstration that almost 80% of human immunodeficiency virus type 1 (HIV-1) infections result from the transmission of a single variant from the donor, biological features similar to those of HIV mucosal transmission have been reported for macaques inoculated with simian immunodeficiency virus (SIV). Here we describe the early diversification events and the impact of challenge doses on viral kinetics and on the number of variants transmitted in macaques infected with the chimeric simian/human immunodeficiency virus SHIV
sf162p4
. We show that there is a correlation between the dose administered and the number of variants transmitted and that certain inoculum variants are preferentially transmitted. This could provide insight into the viral determinants of transmission and could aid in vaccine development. Challenge through the mucosal route with high doses results in the transmission of multiple variants in all the animals. Such an unrealistic scenario could underestimate potential intervention measures. We thus propose the use of molecular evolution analysis to aid in the determination of challenge doses that better mimic the transmission dynamics seen in natural HIV-1 infection.
Inhibition of Dengue Virus Infections in Cell Cultures and in AG129 Mice by a Small Interfering RNA Targeting a Highly Conserved Sequence
Authors: Stein David A. , Perry Stuart T. , Buck Michael D. , Oehmen Christopher S. , Fischer Matthew A. , Poore Elizabeth , Smith Jessica L. , Lancaster Alissa M. , Hirsch Alec J. , Slifka Mark K. , Nelson Jay A. , Shresta Sujan , Früh Klaus
Published: July 2011

The dengue viruses (DENVs) exist as numerous genetic strains that are grouped into four antigenically distinct serotypes. DENV strains from each serotype can cause severe disease and threaten public health in tropical and subtropical regions worldwide. No licensed antiviral agent to treat DENV infections is currently available, and there is an acute need for the development of novel therapeutics. We found that a synthetic small interfering RNA (siRNA) (DC-3) targeting the highly conserved 5′ cyclization sequence (5′CS) region of the DENV genome reduced, by more than 100-fold, the titers of representative strains from each DENV serotype
in vitro
. To determine if DC-3 siRNA could inhibit DENV
in vivo
, an “
in vivo
-ready” version of DC-3 was synthesized and tested against DENV-2 by using a mouse model of antibody-dependent enhancement of infection (ADE)-induced disease. Compared with the rapid weight loss and 5-day average survival time of the control groups, mice receiving the DC-3 siRNA had an average survival time of 15 days and showed little weight loss for approximately 12 days. DC-3-treated mice also contained significantly less virus than control groups in several tissues at various time points postinfection. These results suggest that exogenously introduced siRNA combined with the endogenous RNA interference processing machinery has the capacity to prevent severe dengue disease. Overall, the data indicate that DC-3 siRNA represents a useful research reagent and has potential as a novel approach to therapeutic intervention against the genetically diverse dengue viruses.
Generation of Replication-Defective Virus-Based Vaccines That Confer Full Protection in Sheep against Virulent Bluetongue Virus Challenge
Authors: Matsuo Eiko , Celma Cristina C. P. , Boyce Mark , Viarouge Cyril , Sailleau Corinne , Dubois Eric , Bréard Emmanuel , Thiéry Richard , Zientara Stéphan , Roy Polly
Published: July 2011

The reverse genetics technology for bluetongue virus (BTV) has been used in combination with complementing cell lines to recover defective BTV-1 mutants. To generate a potential disabled infectious single cycle (DISC) vaccine strain, we used a reverse genetics system to rescue defective virus strains with large deletions in an essential BTV gene that encodes the VP6 protein (segment S9) of the internal core. Four VP6-deficient BTV-1 mutants were generated by using a complementing cell line that provided the VP6 protein
in trans
. Characterization of the growth properties of mutant viruses showed that each mutant has the necessary characteristics for a potential vaccine strain: (i) viral protein expression in noncomplementing mammalian cells, (ii) no infectious virus generated in noncomplementing cells, and (iii) efficient replication in the complementing VP6 cell line. Further, a defective BTV-8 strain was made by reassorting the two RNA segments that encode the two outer capsid proteins (VP2 and VP5) of a highly pathogenic BTV-8 with the remaining eight RNA segments of one of the BTV-1 DISC viruses. The protective capabilities of BTV-1 and BTV-8 DISC viruses were assessed in sheep by challenge with specific virulent strains using several assay systems. The data obtained from these studies demonstrated that the DISC viruses are highly protective and could offer a promising alternative to the currently available attenuated and killed virus vaccines and are also compliant as DIVA (differentiating infected from vaccinated animals) vaccines.
Expression Profiling of the Intermediate and Late Stages of Poxvirus Replication
Authors: Yang Zhilong , Reynolds Sara E. , Martens Craig A. , Bruno Daniel P. , Porcella Stephen F. , Moss Bernard
Published: July 2011

The double-stranded DNA genome of vaccinia virus (VACV), the prototype poxvirus, contains approximately 200 open reading frames (ORFs) that are transcribed at early, intermediate, and late stages of infection. Previous high-throughput deep RNA sequencing allowed us to map 118 VACV early genes that are expressed before viral DNA replication and 93 postreplicative genes. However, the intermediate- and late-stage postreplicative genes could not be differentiated. Here, we synchronized infections with a reversible inhibitor of DNA replication and used a VACV mutant that conditionally transcribes late genes to sequence the two classes of mRNAs. In addition, each postreplicative ORF was individually expressed under conditions that distinguished intermediate and late classes. We identified 38 VACV genes that belong to the late class and 53 that belong to the intermediate class, with some of the latter continuing to be expressed late. These data allowed us to prepare a genome-wide early, intermediate, and late transcription map. Inspection of sequences upstream of these ORFs revealed distinctive characteristics of intermediate and late promoters and suggested that some promoters have intermediate and late elements. The intermediate genes encoded many DNA binding/packaging and core-associated proteins in addition to late transcription factors; the late genes encoded many morphogenesis and mature virion membrane proteins, including those involved in entry, in addition to early transcription factors. The top-ranked antigens for CD4
+
T cells and B cells were mainly intermediate rather than late gene products. The differentiation of intermediate and late genes may enhance understanding of poxvirus replication and lead to improvements in expression vectors and recombinant vaccines.
ChePep Controls Helicobacter pylori Infection of the Gastric Glands and Chemotaxis in the
Epsilonproteobacteria
Authors: Howitt Michael R. , Lee Josephine Y. , Lertsethtakarn Paphavee , Vogelmann Roger , Joubert Lydia-Marie , Ottemann Karen M. , Amieva Manuel R.
Published: July 2011

Microbes use directed motility to colonize harsh and dynamic environments. We discovered that
Helicobacter pylori
strains establish bacterial colonies deep in the gastric glands and identified a novel protein, ChePep, necessary to colonize this niche. ChePep is preferentially localized to the flagellar pole. Although mutants lacking ChePep have normal flagellar ultrastructure and are motile, they have a slight defect in swarming ability. By tracking the movement of single bacteria, we found that ∆ChePep mutants cannot control the rotation of their flagella and swim with abnormally frequent reversals. These mutants even sustain bursts of movement backwards with the flagella pulling the bacteria. Genetic analysis of the chemotaxis signaling pathway shows that ChePep regulates flagellar rotation through the chemotaxis system. By examining
H. pylori
within a microscopic pH gradient, we determined that ChePep is critical for regulating chemotactic behavior. The
chePep
gene is unique to the
Epsilonproteobacteria
but is found throughout this diverse group. We expressed ChePep from other members of the
Epsilonproteobacteria
, including the zoonotic pathogen
Campylobacter jejuni
and the deep sea hydrothermal vent inhabitant
Caminibacter mediatlanticus
, in
H. pylori
and found that ChePep is functionally conserved across this class. ChePep represents a new family of chemotaxis regulators unique to the
Epsilonproteobacteria
and illustrates the different strategies that microbes have evolved to control motility.

IMPORTANCE
Helicobacter pylori
strains infect half of all humans worldwide and contribute to the development of peptic ulcers and gastric cancer.
H. pylori
cannot survive within the acidic lumen of the stomach and uses flagella to actively swim to and colonize the protective mucus and epithelium. The chemotaxis system allows
H. pylori
to navigate by regulating the rotation of its flagella. We identified a new protein, ChePep, which controls chemotaxis in
H. pylori
. ChePep mutants fail to colonize the gastric glands of mice and are completely outcompeted by normal
H. pylori
. Genes encoding ChePep are found only in the class
Epsilonproteobacteria
, which includes the human pathogen
Campylobacter jejuni
and environmental microbes like the deep-sea hydrothermal vent colonizer
Caminibacter mediatlanticus
, and we show that ChePep function is conserved in this class. Our study identifies a new colonization factor in
H. pylori
and also provides insight into the control and evolution of bacterial chemotaxis.
Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans
Authors: Forche A. , Abbey D. , Pisithkul T. , Weinzierl M. A. , Ringstrom T. , Bruck D. , Petersen K. , Berman J.
Published: July 2011

Genetic diversity is often generated during adaptation to stress, and in eukaryotes some of this diversity is thought to arise via recombination and reassortment of alleles during meiosis.
Candida albicans
, the most prevalent pathogen of humans, has no known meiotic cycle, and yet it is a heterozygous diploid that undergoes mitotic recombination during somatic growth. It has been shown that clinical isolates as well as strains passaged once through a mammalian host undergo increased levels of recombination. Here, we tested the hypothesis that stress conditions increase rates of mitotic recombination in
C. albicans
, which is measured as loss of heterozygosity (LOH) at specific loci. We show that LOH rates are elevated during
in vitro
exposure to oxidative stress, heat stress, and antifungal drugs. In addition, an increase in stress severity correlated well with increased LOH rates. LOH events can arise through local recombination, through homozygosis of longer tracts of chromosome arms, or by whole-chromosome homozygosis. Chromosome arm homozygosis was most prevalent in cultures grown under conventional lab conditions. Importantly, exposure to different stress conditions affected the levels of different types of LOH events, with oxidative stress causing increased recombination, while fluconazole and high temperature caused increases in events involving whole chromosomes. Thus,
C. albicans
generates increased amounts and different types of genetic diversity in response to a range of stress conditions, a process that we term “stress-induced LOH” that arises either by elevating rates of recombination and/or by increasing rates of chromosome missegregation.

IMPORTANCE
Stress-induced mutagenesis fuels the evolution of bacterial pathogens and is mainly driven by genetic changes via mitotic recombination. Little is known about this process in other organisms.
Candida albicans
, an opportunistic fungal pathogen, causes infections that require adaptation to different host environmental niches. We measured the rates of LOH and the types of LOH events that appeared in the absence and in the presence of physiologically relevant stresses and found that stress causes a significant increase in the rates of LOH and that this increase is proportional to the degree of stress. Furthermore, the types of LOH events that arose differed in a stress-dependent manner, indicating that eukaryotic cells generate increased genetic diversity in response to a range of stress conditions. We propose that this “stress-induced LOH” facilitates the rapid adaptation of
C. albicans
, which does not undergo meiosis, to changing environments within the host.
A multinational randomised study comparing didactic lectures with case scenario in a severe sepsis medical simulation course
Authors: Li Chih-Huang , Kuan Win-Sen , Mahadevan Malcolm , Daniel-Underwood Lynda , Chiu Te-Fa , Nguyen H Bryant
Published: July 2011

Background

Medical simulation has been used to teach critical illness in a variety of settings. This study examined the effect of didactic lectures compared with simulated case scenario in a medical simulation course on the early management of severe sepsis.

Methods

A prospective multicentre randomised study was performed enrolling resident physicians in emergency medicine from four hospitals in Asia. Participants were randomly assigned to a course that included didactic lectures followed by a skills workshop and simulated case scenario (lecture-first) or to a course that included a skills workshop and simulated case scenario followed by didactic lectures (simulation-first). A pre-test was given to the participants at the beginning of the course, post-test 1 was given after the didactic lectures or simulated case scenario depending on the study group assignment, then a final post-test 2 was given at the end of the course. Performance on the simulated case scenario was evaluated with a performance task checklist.

Results

98 participants were enrolled in the study. Post-test 2 scores were significantly higher than pre-test scores in all participants (80.8±12.0% vs 65.4±12.2%, p<0.01). There was no difference in pre-test scores between the two study groups. The lecture-first group had significantly higher post-test 1 scores than the simulation-first group (78.8±10.6% vs 71.6±12.6%, p<0.01). There was no difference in post-test 2 scores between the two groups. The simulated case scenario task performance completion was 90.8% (95% CI 86.6% to 95.0%) in the lecture-first group compared with 83.8% (95% CI 79.5% to 88.1%) in the simulation-first group (p=0.02).

Conclusions

A medical simulation course can improve resident physician knowledge in the early management of severe sepsis. Such a course should include a comprehensive curriculum that includes didactic lectures followed by simulation experience.
Two for the price of one: a dual treatment benefit of long-acting octreotide in occult bleeding and diuretic intractable ascites
Authors: Lee Bee Leng , Turner Jeff , Hurley Joanna , Green John , Hawkes Neil , Alcolado Ruth
Published: July 2011

Transfusion-dependent anaemia and portal hypertension are recognised complications of hereditary haemorrhagic telangiectasia (HHT). The anaemia is a result of chronic bleeding from gastrointestinal telangiectasias, which are usually multiple and located throughout the gastrointestinal tract. As a result, treatment with argon plasma coagulation via gastroscopy and or colonoscopy is often insufficient to prevent ongoing blood loss. Portal hypertension in HHT occurs as a result of blood shunting between the hepatic artery and the portal vein within the liver. The somatostatin analogue octreotide has been used as a treatment for bleeding angiodysplasia; however, its possible role as a treatment for diuretic intractable ascites secondary to portal hypertension has not been previously established. The authors report a case that apparently illustrates a dual benefit of long-acting octreotide in the management of both occult bleeding and refractory ascites in a patient with HHT.
Practice ownership – past, present and future
Authors: Wright Malcolm
Published: July 2011

If you were reading the Veterinary Record in 1980, you would have found, on average, at least two adverts for practices for sale and three adverts offering jobs with partnership prospects or partnerships wanted in each issue. Read it today and you may find a practice for sale once a month and a partnership advert hardly ever. What has been behind this change? Almost certainly it relates to the changes in attitude and demands of graduates over the past 30 years. In this article, Malcolm Wright looks at the past, present and future of practice ownership to gain an insight into how these changes have evolved and their effects on the future.
Comments on the dilemma in the June issue: ‘Financially strapped owner with a suffering cat’
Authors: Fountain Kay
Published: July 2011

The dilemma in the June issue concerned a client presenting a cat at a private clinic out of hours for depression and straining to urinate (In Practice, June 2011, volume 33, pages 297–298). Evaluation of the cat revealed a blocked bladder and the signalment, history and clinical presentation together suggested urolithiasis. Unfortunately, the owner did not have the funds required to stabilise, catheterise and hospitalise her pet. It was also a difficult situation for the vet who might have had to consider euthanasia as a possible way forward. Steven McCulloch commented that suffering could be defined as a profoundly negative mental state, the cause of which had overridden the individual's ordinary physiological and behavioural coping mechanism; therefore, if that suffering could not be alleviated, it was morally justified to perform euthanasia. Hence, an animal should be euthanased first because it was suffering and secondly because the suffering could not be resolved. The animal was assumed to be in pain and suffering so the criterion for morally justified euthanasia was satisfied. However, in a medical sense, the second criterion was not satisfied because the cat could be stabilised and unblocked without significant irreversible complications, but it was satisfied in a financial sense because the owner did not have enough money for therapy. Referral to a charity clinic with no prior treatment, referral to a charity clinic with conservative treatment or treatment at reduced cost at the clinic were all options that the vet could consider as possible ways forward. The last two were preferable from the cat's point of view. However, supererogatory acts such as the last option could be criticised for encouraging irresponsible behaviour (eg, unable to afford veterinary fees, no insurance) and might also be construed as unfair to those who paid the normal fee.
Responsible use of anthelmintics for nematode control in sheep and cattle
Authors: Sargison Neil
Published: July 2011

Globally, nematode parasites are arguably the most important causes of suboptimal productivity in sheep and cattle, albeit that they often occur concurrently with other problems. The control of nematode parasites is therefore a prerequisite for economically efficient meat production. For many years, in the UK, this involved the frequent routine use of broad‐spectrum anthelmintics to suppress contamination of pasture, but the consequent emergence of anthelmintic resistance has meant that the livestock industry has had to re‐evaluate its approach to the management of these parasites. This article discusses how the use of certain nematode parasite control regimens has led to the evolution of species resistant to licensed anthelmintic drugs, and suggests some strategies for reducing the further development of anthelmintic resistance.