bluuebunny/crossref_metadata_2025 huggingface dataset:
Simplified Analysis Strategies for Fluid-Structure Interaction in High Speed Turbomachinery
Authors: Consuegra Brittany , Flowers George T.
Published: July 2010

High pressure seals are usually mounted between the rotating and stationary components in high-pressure turbomachinery and often experience intense vibration. These vibrations can interact with the fluid to produce unsteady flows, which can in turn induce structural vibrations that result in machine failure. The reduction of the adverse effects of these vibrations is considered one of the most challenging problems for turbopump design. However, detailed analyses of such fluid-structure interaction problems can be extremely time-consuming and inefficient. The purpose of the present study is to evaluate the effectiveness of simplified, lumped-parameter techniques in analyzing and predicting such behavior, as compared to more sophisticated techniques, with the goal of defining the range of validity for such techniques. A fluid-structure driven vibration is evaluated using a lumped parameter analysis for a wide range of parametric configurations and the results are validated and compared using a bench-top laboratory test rig.
Observation of the Magnon Hall Effect
Authors: Onose Y. , Ideue T. , Katsura H. , Shiomi Y. , Nagaosa N. , Tokura Y.
Published: July 2010

Observing the Magnon Hall Effect

The anomalous thermal Hall effect occurs when transverse heat transport is generated in the absence of an external magnetic field. The transport may be mediated by free carriers, phonons, or spin waves (magnons).

Onose
et al.

(p.
297
) observed this effect in an insulating ferromagnet and were able to rule out free carriers and phonons as the mediators of the thermal transport. Instead, the observations are consistent with a theory ascribing its origin to magnon propagation. This thermal magnon Hall effect is caused by the spin-orbit interaction, which acts in a fashion similar to the magnetic field in the conventional Hall effect. Its observation in an insulator may enable the elimination of losses in spintronic applications.
Disordering of an Organic Overlayer on a Metal Surface Upon Cooling
Authors: Schöll A. , Kilian L. , Zou Y. , Ziroff J. , Hame S. , Reinert F. , Umbach E. , Fink R. H.
Published: July 2010

Coolly Disordered

Generally speaking, at higher temperature phases materials are more disordered—for example, when solids melt to form liquids. In some cases, however—for example, under high pressure—a more disordered phase can emerge upon cooling.

Schöll
et al.

(p.
303
) now show that an organic molecule, a naphthalene derivative, adsorbed on a silver surface disorders upon cooling below room temperature. This process is driven by the surface bond becoming stronger upon cooling and preventing weaker interactions that allow ordering between molecules in the plane.
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
Authors: Siegel Justin B. , Zanghellini Alexandre , Lovick Helena M. , Kiss Gert , Lambert Abigail R. , St.Clair Jennifer L. , Gallaher Jasmine L. , Hilvert Donald , Gelb Michael H. , Stoddard Barry L. , Houk Kendall N. , Michael Forrest E. , Baker David
Published: July 2010

Biocatalytic Boost

Enzymes tend to direct reactions toward specific products much more selectively than synthetic catalysts. Unfortunately, this selectivity has evolved for cellular purposes and may not promote the sorts of reactions chemists are seeking to enhance (see the Perspective by

Lutz

).

Siegel
et al.

(p.
309
) now describe the design of enzymes that catalyze the bimolecular Diels-Alder reaction, a carbon-carbon bond formation reaction that is central to organic synthesis but unknown in natural metabolism. The enzymes display high stereoselectivity and substrate specificity, and an x-ray structure of the most active enzyme confirms that the structure matches the design.

Savile
et al.

(p.
305
, published online 17 June) applied a directed evolution approach to modify an existing transaminase enzyme so that it recognized a complex ketone in place of its smaller native substrate, and could tolerate the high temperature and organic cosolvent necessary to dissolve this ketone. This biocatalytic reaction improved the production efficiency of a drug that treats diabetes.
Trophic Structure and Community Stability in an Overfished Ecosystem
Authors: Utne-Palm Anne C. , Salvanes Anne G. V. , Currie Bronwen , Kaartvedt Stein , Nilsson Göran E. , Braithwaite Victoria A. , Stecyk Jonathan A. W. , Hundt Matthias , van der Bank Megan , Flynn Bradley , Sandvik Guro K. , Klevjer Thor A. , Sweetman Andrew K. , Brüchert Volker , Pittman Karin , Peard Kathleen R. , Lunde Ida G. , Strandabø Rønnaug A. U. , Gibbons Mark J.
Published: July 2010

Gobbled by Gobies

A common feature of overfished marine ecosystems is a tendency for biomass to become dominated by jellyfish and microbes, and for the habitat to become anoxic or hypoxic as large fish species are removed. The Benguela ecosystem off the coast of Namibia is a case in point.

Utne-Palm
et al.

(p.
333
) describe how the loss of overfished sardines from the Benguela fishery has provided an opportunity for an endemic fish species, the bearded goby, to exploit jellyfish and microbial biomass and to increase in number. These small fish have in turn become the predominant prey species for the larger fish, birds, and mammals in the region. The significance of the goby lies in its ability to forage on resources traditionally regarded as “dead-ends.” The bearded goby has thus become a key stabilizing component to the turnover of energy in the Benguela ecosystem.
Imagination in Chemistry
Image and Reality
Kekulé, Kopp, and the Scientific Imagination

by Alan J. Rocke

University of Chicago Press, Chicago, 2010. 401 pp. $45, £29. ISBN 9780226723327. Synthesis.
Authors: Ramberg Peter J.
Published: July 2010

Through a consideration of the efforts of 19th-century chemists to understand the unseen world of molecules and atoms, Rocke explores the role of the visual imagination in scientific research.
Familial DNA Testing Scores a Win in Serial Killer Case
Authors: Miller Greg
Published: July 2010

A discarded piece of pizza and a relatively new method of DNA testing have helped police catch the man they suspect is the serial killer nicknamed the "Grim Sleeper," the Los Angeles police announced last week.
The Dilemma of Pernkopf's Atlas
Authors: Pringle Heather
Published: July 2010

A University of Vienna investigation determined in 1998 that Eduard Pernkopf's anatomy department used bodies of executed prisoners from the Gestapo and from Vienna's assize court to produce the illustrations in his
Topographical Anatomy of Man
. What should anatomists in 2010 do with an atlas that is both scientifically valuable and morally tainted? Researchers remain deeply divided.
Poly(Anhydride) Nanoparticles Act as Active Th1 Adjuvants through Toll-Like Receptor Exploitation
Authors: Tamayo I. , Irache J. M. , Mansilla C. , Ochoa-Repáraz J. , Lasarte J. J. , Gamazo C.
Published: July 2010

The mechanisms that underlie the potent Th1-adjuvant capacity of poly(methyl vinyl ether-co-maleic anhydride) nanoparticles (NPs) were investigated. Traditionally, polymer NPs have been considered delivery systems that promote a closer interaction between antigen and antigen-presenting cells (APCs). Our results revealed that poly(anhydride) NPs also act as agonists of various Toll-like receptors (TLRs) (TLR2, -4, and -5), triggering a Th1-profile cytokine release (gamma interferon [IFN-γ], 478 pg/ml versus 39.6 pg/ml from negative control; interleukin-12 [IL-12], 40 pg/ml versus 7.2 pg/ml from negative control) and, after incubation with dendritic cells, inducing a 2.5- to 3.5-fold increase of CD54 and CD86 costimulatory molecule expression. Furthermore,in vivostudies suggest that NPs actively elicit a CD8+T-cell response. Immunization with empty NPs resulted in a significant delay in the mean survival date (from day 7 until day 23 postchallenge) and a protection level of 30% after challenge against a lethal dose ofSalmonellaentericaserovar Enteritidis. Taken together, our results provide a better understanding of how NPs act as active Th1 adjuvants in immunoprophylaxis and immunotherapy through TLR exploitation.
Recombinant Allergens Combined with Biological Markers in the Diagnosis of Allergic Bronchopulmonary Aspergillosis in Cystic Fibrosis Patients
Authors: Fricker-Hidalgo Hélène , Coltey Bérangère , Llerena Catherine , Renversez Jean-Charles , Grillot Renée , Pin Isabelle , Pelloux Hervé , Pinel Claudine
Published: July 2010

Allergic bronchopulmonary aspergillosis (ABPA) is a frequent complication in cystic fibrosis patients. The diagnosis remains difficult and requires a combination of clinical, radiological, biological, and mycological criteria. The aim of this study was to analyze the added value of two recombinant antigens, rAspf4 and rAspf6, associated with the detection of specific IgG; precipitins; total IgE; and
Aspergillus fumigatus
in sputum for the diagnosis of ABPA. In a retrospective study, we determined the specific IgE responses to these recombinants in 133 sera of 65 cystic fibrosis patients. We selected an average of five serum samples from each of the 17 patients with ABPA (13 proven and 4 probable ABPA) and from 3 patients with
Aspergillus
bronchitis and rhinosinusitis. One serum sample for the 45 patients without ABPA was tested. The sensitivity of specific IgE detection against rAspf4 calculated per patient (92.3%) was significantly higher (
P
< 0.05) than that of rAspf6 (53.8%). When rAspf4 IgE detection was associated with anti-
Aspergillus
IgG enzyme-linked immunosorbent assay (ELISA) and precipitin detection, the sensitivity rose to 100%. The specificities of rAspf4 and rAspf6 IgE detection were 93.7% and 91.6%, respectively. Other diagnostic criteria had slightly lower specificities (87.5% for anti-
Aspergillus
IgG ELISA, 89.6% for precipitins, 84.4% for total IgE, and 85.0% for positive
A. fumigatus
culture in sputum). In conclusion, this retrospective study showed the relevance of rAspf4 IgE detection, in combination with other biological markers (
Aspergillus
IgG ELISA, precipitins, and total IgE), for improving the biological diagnosis of ABPA.
Utility of Pandemic H1N1 2009 Influenza Virus Recombinant Hemagglutinin Protein-Based Enzyme-Linked Immunosorbent Assay for Serosurveillance
Authors: Arankalle V. A. , Virkar R. G. , Tandale B. V. , Ingle N. B.
Published: July 2010

An enzyme-linked immunosorbent assay (ELISA) for the detection of IgG antibodies against the pandemic H1N1 2009 influenza A virus, employing a recombinant hemagglutinin protein of the virus, was compared to the hemagglutination inhibition (HI) test using 783 serum samples. The results showed a concordance of 98.4%, suggesting the utility of the ELISA in serosurveillance. Two hundred sixty-nine (100%) serum samples with an HI titer of ≥20 were ELISA reactive.
Dynamic Changes in Inflammatory Cytokines in Pigs Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus
Authors: Liu Yonggang , Shi Wenda , Zhou Enmin , Wang Shujie , Hu Shouping , Cai Xuehui , Rong Fulong , Wu Jiabin , Xu Min , Xu Mingming , Li Liqin
Published: July 2010

Porcine reproductive and respiratory syndrome virus (PRRSV) infection induces both humoral and cellular immune responses. In this study, we investigated the changes in cytokine levels in peripheral blood between the highly pathogenic PRRSV HuN4 strain and its derivative strain HuN4-F112 obtained by serial propagation in MARC145 cells to 112 passages. The results demonstrated that pigs infected with HuN4 showed a loss of appetite, decrease in body weight, raised body temperature, and respiratory symptoms, along with interstitial pneumonia lesions. The PRRSV amounts in the pigs infected with HuN4 were 10
5
to 10
9
copies/ml in the blood and 10
10
to 10
11
copies/g in the lung tissues, whereas the virus amounts with HuN4-F112 were 10
2.15
to 10
3.13
copies/ml in the blood and 10
3.0
to 10
3.6
copies/g in the lungs. Moreover, the levels of interleukin 1 (IL-1), IL-6, tumor necrosis factor alpha (TNF-α), and alpha interferon (IFN-α) in peripheral blood were upregulated 7 days postinoculation with HuN4, which was earlier than in the HuN4-F112 group. Furthermore, cytokine levels in the pigs infected with HuN4 returned to normal on the 21st day postinoculation, while the levels in those infected with HuN4-F112 continued to increase. These results demonstrated that the pigs infected with the highly pathogenic PRRSV HuN4 strain generated earlier and higher levels of inflammatory cytokines, and the results also indicated that HuN4 may aggravate inflammation and damage tissues and organs. The low-pathogenic PRRSV HuN4-F112 strain induced lower levels of inflammatory cytokines, which may enhance the immune responses against the infection.
Impact of Free-Living Amoebae on Presence of
Parachlamydia acanthamoebae
in the Hospital Environment and Its Survival
In Vitro
without Requirement for Amoebae
Authors: Fukumoto Tatsuya , Matsuo Junji , Hayashi Masahiro , Oguri Satoshi , Nakamura Shinji , Mizutani Yoshihiko , Yao Takashi , Akizawa Kouzi , Suzuki Haruki , Shimizu Chikara , Matsuno Kazuhiko , Yamaguchi Hiroyuki
Published: July 2010

Parachlamydia acanthamoebae
is an obligately intracellular bacterium that infects free-living amoebae and is a potential human pathogen in hospital-acquired pneumonia. We examined whether the presence of
P. acanthamoebae
is related to the presence of
Acanthamoeba
in an actual hospital environment and assessed the
in vitro
survival of
P. acanthamoebae
. Ninety smear samples were collected between November 2007 and March 2008 (trial 1,
n
= 52) and between October 2008 and February 2009 (trial 2,
n
= 38) from the floor (dry conditions,
n
= 56) and sink outlets (moist conditions,
n
= 34) of a hospital. The prevalences of
P. acanthamoebae
DNA in the first and second trials were 64.3% and 76%, respectively. The prevalences of
Acanthamoeba
DNA in the first and second trials were 48% and 63.1%, respectively. A statistical correlation between the prevalence of
P. acanthamoebae
and that of
Acanthamoeba
was found (trial 1,
P
= 0.011; trial 2,
P
= 0.022), and that correlation increased when samples from just the dry area (floor smear samples,
P
= 0.002) were analyzed but decreased when samples from a moist area were analyzed (
P
= 0.273). The
in vitro
experiment showed that, without
Acanthamoeba
,
P. acanthamoebae
could not survive in dry conditions for 3 days at 30°C or 15 days at 15°C. Thus, both organisms were coincidentally found in an actual hospital environment, with the presence of
Acanthamoeba
having a significant effect on the long-term survival of
P. acanthamoebae
, suggesting that this potential human pathogen could spread through a hospital environment via
Acanthamoeba
.
Genotypic and Phenotypic Characterization of Enterotoxigenic
Escherichia coli
Strains Isolated from Peruvian Children
Authors: Rivera F. P. , Ochoa T. J. , Maves R. C. , Bernal M. , Medina A. M. , Meza R. , Barletta F. , Mercado E. , Ecker L. , Gil A. I. , Hall E. R. , Huicho L. , Lanata C. F.
Published: July 2010

Enterotoxigenic
Escherichia coli
(ETEC) is a major cause of childhood diarrhea. The present study sought to determine the prevalence and distribution of toxin types, colonization factors (CFs), and antimicrobial susceptibility of ETEC strains isolated from Peruvian children. We analyzed ETEC strains isolated from Peruvian children between 2 and 24 months of age in a passive surveillance study. Five
E. coli
colonies per patient were studied by multiplex real-time PCR to identify ETEC virulence factors. ETEC-associated toxins were confirmed using a GM1-based enzyme-linked immunosorbent assay. Confirmed strains were tested for CFs by dot blot assay using 21 monoclonal antibodies. We analyzed 1,129 samples from children with diarrhea and 744 control children and found ETEC in 5.3% and 4.3%, respectively. ETEC was more frequently isolated from children >12 months of age than from children <12 months of age (
P
< 0.001). Fifty-two percent of ETEC isolates from children with diarrhea and 72% of isolates from controls were heat-labile enterotoxin (LT) positive and heat-stable enterotoxin (ST) negative; 25% and 19%, respectively, were LT negative and ST positive; and 23% and 9%, respectively, were LT positive and ST positive. CFs were identified in 64% of diarrheal samples and 37% of control samples (
P
< 0.05). The most common CFs were CS6 (14% and 7%, respectively), CS12 (12% and 4%, respectively), and CS1 (9% and 4%, respectively). ST-producing ETEC strains caused more severe diarrhea than non-ST-producing ETEC strains. The strains were most frequently resistant to ampicillin (71%) and co-trimoxazole (61%). ETEC was thus found to be more prevalent in older infants. LT was the most common toxin type; 64% of strains had an identified CF. These data are relevant in estimating the burden of disease due to ETEC and the potential coverage of children in Peru by investigational vaccines.
Evaluation of a Loop-Mediated Isothermal Amplification Method Using Fecal Specimens for Differential Detection of
Taenia
Species from Humans
Authors: Nkouawa Agathe , Sako Yasuhito , Li Tiaoying , Chen Xingwang , Wandra Toni , Swastika I. Kadek , Nakao Minoru , Yanagida Tetsuya , Nakaya Kazuhiro , Qiu Dongchuan , Ito Akira
Published: July 2010

We compared the performance of loop-mediated isothermal amplification (LAMP) with that of a multiplex PCR method for differential detection of human
Taenia
parasites in fecal specimens from taeniasis patients. The LAMP method, with no false positives, showed a higher sensitivity (88.4%) than the multiplex PCR (37.2%). Thus, it is expected that the LAMP method has a high value for molecular diagnosis of taeniasis.
Emergence and Localized Circulation of a Vaccine-Derived Poliovirus in an Isolated Mountain Community in Guangxi, China
Authors: Yan Dongmei , Li Li , Zhu Shuangli , Zhang Yong , An Junjing , Wang Dongyan , Wen Ning , Jorba Jaume , Liu Wei , Zhong Ge , Huang Lin , Kew Olen , Liang Xiaofeng , Xu Wenbo
Published: July 2010

From March to May 2006, type 1 circulating vaccine-derived poliovirus (cVDPV) was isolated from one case patient with acute flaccid paralysis (AFP) and six unimmunized healthy contacts in isolated mountain villages in Guangxi, China. We conducted epidemiological investigations in the affected communities and nucleotide sequence analyses of the cVDPV isolates. The results of the investigations showed that the AFP patient, an unimmunized 10-year-old boy, and five laboratory-confirmed contacts lived in the same village; one contact lived in a neighboring village. Only ∼27% of children 5 to 10 years of age in the affected villages had received three or more doses of the trivalent oral poliovirus vaccine (OPV). Nucleotide sequence analyses revealed that the cVDPV isolates differed from the Sabin 1 (S1) isolate at 1.4 to 2.2% of VP1 nucleotide positions and shared 12 nucleotide substitutions within VP1. All isolates were S1/S2/S1/S3 recombinants sharing common recombination junctions. Key determinants of attenuation were replaced. Phylogenetic analysis suggested that the cVDPV circulated locally for ∼12 months following the initiating OPV dose. No VDPVs were found after mass OPV immunizations, conducted from May to June 2006, that targeted all children <12 years of age. Our findings reinforce the point that VDPVs can emerge and spread in isolated communities with immunity gaps. Maintenance of sensitive AFP and poliovirus surveillance is essential to permit early detection and a rapid response to VDPV circulation.
Clinical Utility of Genotypic Resistance Tests for HIV-1-Infected Patients with Low-Level Virological Failure
Authors: Elgalib A. , Perry M. , Aboud M. , Mullen J. , O'Shea S. , Chrystie I. L. , Kulasegaram R. , Tong C. Y. W.
Published: July 2010

The usefulness of genotypic resistance tests (GRT) among HIV-1 patients with low-level virological failure (LLVF) was evaluated. Up to 78% of samples with <1,000 copies/ml were sequenced successfully. For samples with 50 to 200 copies/ml, the success rate was as high as 69%. LLVF should not deter clinicians from requesting GRT.
Detection of Highly Prevalent Hepatitis B Virus Coinfection among HIV-Seropositive Persons in Ghana
Authors: Geretti Anna Maria , Patel Mauli , Sarfo Fred Stephen , Chadwick David , Verheyen Jens , Fraune Maria , Garcia Ana , Phillips Richard Odame
Published: July 2010

Simple hepatitis B surface antigen (HBsAg) tests may facilitate ascertainment of hepatitis B virus (HBV) infection in settings with high endemicity but limited infrastructure. We evaluated two rapid HBsAg tests and characterized HBV coinfection in a Ghanaian HIV-positive cohort. Samples from 838 patients were tested by the rapid assays Determine and Vikia and the reference assays Architect, Murex version 3, and Liaison Ultra. The assays were also evaluated using the 2nd International Standard, a seroconversion panel, and two mutant panels. HBsAg-positive samples underwent HBV DNA quantification by real-time PCR and surface and polymerase gene population sequencing. Overall, 140/838 patients (16.7%; 95% confidence interval, 14.2 to 19.2%) were HBsAg positive, and of these, 103/140 (73.6%) were e-antigen negative and 118/140 (84.3%) showed an HBV DNA level of >14 IU/ml (median, 8,279 IU/ml). Assay sensitivities and specificities were as follows: Architect, 97.9 and 99.6%; Liaison, 97.1 and 99.4%; Murex, 98.6 and 99.3%; Determine, 69.3 and 100%; and Vikia, 70.7 and 100%. With Determine, the limit of detection was >1.5 to 3.4 HBsAg IU/ml, and the median HBV DNA loads were 598 and 10,905 IU/ml in Determine-negative and -positive samples, respectively (P= 0.0005). Results were similar with the Vikia assay. HBV DNA sequencing indicated infection with genotype E in 82/86 (95.3%) patients. HBsAg mutations affected assay performance, including a T123A mutant that escaped detection by Architect. Major drug resistance mutations were observed in 4/86 patients (4.6%). The prevalence of HBV coinfection was high in this HIV-positive Ghanaian cohort. The two rapid assays identified HBsAg-positive patients at risk for liver disease with high specificity, albeit with only moderate sensitivity.
Clinical and Economic Outcomes for Patients with Health Care-Associated
Staphylococcus aureus
Pneumonia
Authors: Shorr Andrew F. , Haque Nadia , Taneja Charu , Zervos Marcus , Lamerato Lois , Kothari Smita , Zilber Sophia , Donabedian Susan , Perri Mary Beth , Spalding James , Oster Gerry
Published: July 2010

While the increasing importance of methicillin-resistant
Staphylococcus aureus
(MRSA) as a pathogen in health care-associated
S. aureus
pneumonia has been documented widely, information on the clinical and economic consequences of such infections is limited. We retrospectively identified all patients admitted to a large U.S. urban teaching hospital between January 2005 and May 2008 with pneumonia and positive blood or respiratory cultures for
S. aureus
within 48 h of admission. Among these patients, those with suspected health care-associated pneumonia (HCAP) were identified using established criteria (e.g., recent hospitalization, admission from nursing home, or hemodialysis). Subjects were designated as having methicillin-resistant (MRSA) or methicillin-susceptible (MSSA) HCAP, based on initial
S. aureus
isolates. Initial therapy was designated “appropriate” versus “inappropriate” based on the expected susceptibility of the organism to the regimen received. We identified 142 patients with evidence of
S. aureus
HCAP. Their mean (standard deviation [SD]) age was 64.5 (17) years. Eighty-seven patients (61%) had initial cultures that were positive for MRSA. Most (∼90%) patients received appropriate initial antibiotic therapy (86% for MRSA versus 91% for MSSA;
P
= 0.783). There were no significant differences between MRSA and MSSA HCAP patients in mortality (29% versus 20%, respectively), surgery for pneumonia (22% versus 20%), receipt of mechanical ventilation (60% versus 58%), or admission to the intensive care unit (79% versus 76%). Mean (SD) total charges per admission were universally high ($98,170 [$94,707] for MRSA versus $104,121 [$91,314]) for MSSA [
P
= 0.712]). Almost two-thirds of patients admitted to hospital with
S. aureus
HCAP have evidence of MRSA infection.
S. aureus
HCAP, irrespective of MRSA versus MSSA status, is associated with significant mortality and high health care costs, despite appropriate initial antibiotic therapy.
The Genome Segments of a Group D Rotavirus Possess Group A-Like Conserved Termini but Encode Group-Specific Proteins
Authors: Trojnar Eva , Otto Peter , Roth Bernhard , Reetz Jochen , Johne Reimar
Published: July 2010

Rotaviruses are a leading cause of viral acute gastroenteritis in humans and animals. They are grouped according to gene composition and antigenicity of VP6. Whereas group A, B, and C rotaviruses are found in humans and animals, group D rotaviruses have been exclusively detected in birds. Despite their broad distribution among chickens, no nucleotide sequence data exist so far. Here, the first complete genome sequence of a group D rotavirus (strain 05V0049) is presented, which was amplified using sequence-independent amplification strategies and degenerate primers. Open reading frames encoding homologues of rotavirus proteins VP1 to VP4, VP6, VP7, and NSP1 to NSP5 were identified. Amino acid sequence identities between the group D rotavirus and the group A, B, and C rotaviruses varied between 12.3% and 51.7%, 11.0% and 23.1%, and 9.5% and 46.9%, respectively. Segment 10 of the group D rotavirus has an additional open reading frame. Generally, phylogenetic analysis indicated a common evolution of group A, C, and D rotaviruses, separate from that of group B. However, the NSP4 sequence of group C has only very low identities in comparison with cogent sequences of all other groups. The avian group A NSP1 sequences are more closely related to those of group D than those of mammalian group A rotaviruses. Most interestingly, the nucleotide sequences at the termini of the 11 genome segments are identical between group D and group A rotaviruses. Further investigations should clarify whether these conserved structures allow an exchange of genome segments between group A and group D rotaviruses.
Protein Kinase R Is Responsible for the Phosphorylation of eIF2α in Rotavirus Infection
Authors: Rojas Margarito , Arias Carlos F. , López Susana
Published: July 2010

The eukaryotic initiation translation factor 2 (eIF2) represents a key point in the regulation of protein synthesis. This factor delivers the initiator Met-tRNA to the ribosome, a process that is conserved in all eukaryotic cells. Many types of stress reduce global translation by triggering the phosphorylation of the α subunit of eIF2, which reduces the formation of the preinitiation translation complexes. Early during rotavirus infection, eIF2α becomes phosphorylated, and even under these conditions viral protein synthesis is not affected, while most of the cell protein synthesis is blocked. Here, we found that the kinase responsible for the phosphorylation of eIF2α in rotavirus-infected cells is PKR, since in mouse embryonic fibroblasts deficient in the kinase domain of PKR, or in MA104 cells where the expression of PKR was knocked down by RNA interference, eIF2α was not phosphorylated upon rotavirus infection. The viral component responsible for the activation of PKR seems to be viral double-stranded RNA, which is found in the cytoplasm of infected cells, outside viroplasms. Taken together, these results suggest that rotaviruses induce the PKR branch of the interferon system and have evolved a mechanism to translate its proteins, surpassing the block imposed by eIF2α phosphorylation.
Myosin Va Enhances Secretion of Herpes Simplex Virus 1 Virions and Cell Surface Expression of Viral Glycoproteins
Authors: Roberts Kari L. , Baines Joel D.
Published: July 2010

The final step in the egress of herpes simplex virus (HSV) virions requires virion-laden vesicles to bypass cortical actin and fuse with the plasma membrane, releasing virions into the extracellular space. Little is known about the host or viral proteins involved. In the current study, we noted that the conformation of myosin Va (myoVa), a protein known to be involved in melanosome and secretory granule trafficking to the plasma membrane in melanocytes and neuroendocrine cells, respectively, was altered by 4 h after infection with HSV-1 such that an N-terminal epitope expected to be masked in its inactive state was rendered immunoreactive. Wild-type myoVa localized throughout the cytoplasm and to a limited extent in the nuclei of HSV-infected cells. Two different dominant negative myoVa molecules containing cargo-binding domains but lacking the lever arms and actin-binding domains colocalized with markers of the trans-Golgi network (TGN). Expression of dominant negative myoVa isoforms reduced secretion of HSV-1 infectivity into the medium by 50 to 75%, reduced surface expression of glycoproteins B, M, and D, and increased intracellular virus infectivity to levels consistent with increased retention of virions in the cytoplasm. These data suggest that myoVa is activated during HSV-1 infection to help transport virion- and glycoprotein-laden vesicles from the TGN, through the cortical actin, to the plasma membrane. We cannot exclude a role for myoVa in promoting fusion of these vesicles with the inner surface of the plasma membrane. These data also indicate that myoVa is involved in exocytosis in human epithelial cells as well as other cell types.
The 7a Accessory Protein of Severe Acute Respiratory Syndrome Coronavirus Acts as an RNA Silencing Suppressor
Authors: Karjee Sumona , Minhas Ankita , Sood Vikas , Ponia Sanket S. , Banerjea Akhil C. , Chow Vincent T. K. , Mukherjee Sunil K. , Lal Sunil K.
Published: July 2010

RNA silencing suppressors (RSSs) are well studied for plant viruses but are not well defined to date for animal viruses. Here, we have identified an RSS from a medically important positive-sense mammalian virus,
Severe acute respiratory syndrome coronavirus
. The viral 7a accessory protein suppressed both transgene and virus-induced gene silencing by reducing the levels of small interfering RNA (siRNA). The suppression of silencing was analyzed by two independent assays, and the middle region (amino acids [aa] 32 to 89) of 7a was responsible for suppression. Finally, the RNA suppression property and the enhancement of heterologous replicon activity by the 7a protein were confirmed for animal cell lines.
Two Overlapping Domains of a Lyssavirus Matrix Protein That Acts on Different Cell Death Pathways
Authors: Larrous Florence , Gholami Alireza , Mouhamad Shahul , Estaquier Jérôme , Bourhy Hervé
Published: July 2010

The lyssavirus matrix (M) protein induces apoptosis. The regions of the M protein that are essential for triggering cell death pathways are not yet clearly defined. We therefore compared the M proteins from two viruses that have contrasting characteristics in terms of cellular apoptosis: a genotype 3 lyssavirus, Mokola virus (MOK), and a genotype 1 rabies virus isolated from a dog from Thailand (THA). We identified a 20-amino-acid fragment (corresponding to positions 67 to 86) that retained the cell death activities of the full-length M protein from MOK via both the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and inhibition of cytochromecoxidase (CcO) activity. We found that the amino acids at positions 77 and 81 have an essential role in triggering these two cell death pathways. Directed mutagenesis demonstrated that the amino acid at position 77 affects CcO activity, whereas the amino acid at position 81 affects TRAIL-dependent apoptosis. Mutations in the full-length M protein that compromised induction of either of these two pathways resulted in delayed apoptosis compared with the time to apoptosis for the nonmutated control.
Structure of the Recombinant Alphavirus Western Equine Encephalitis Virus Revealed by Cryoelectron Microscopy
Authors: Sherman Michael B. , Weaver Scott C.
Published: July 2010

Western equine encephalitis virus (WEEV;
Togaviridae
,
Alphavirus
) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of viral encephalitis in humans and horses in the Americas, and infection results in a range of disease, from mild flu-like illnesses to encephalitis, coma, and death. In addition to spreading via mosquito vectors, human WEEV infections can potentially occur directly via aerosol transmission. Due to its aerosol infectivity and virulence, WEEV is thus classified as a biological safety level 3 (BSL-3) agent. Because of its highly infectious nature and containment requirements, it has not been possible to investigate WEEV's structure or assembly mechanism using standard structural biology techniques. Thus, to image WEEV and other BSL-3 agents, we have constructed a first-of-its-kind BSL-3 cryoelectron microscopy (cryoEM) containment facility. cryoEM images of WEEV were used to determine the first three-dimensional structure of this important human pathogen. The overall organization of WEEV is similar to those of other alphaviruses, consistent with the high sequence similarity among alphavirus structural proteins. Surprisingly, the nucleocapsid of WEEV, a New World virus, is more similar to the Old World alphavirus Sindbis virus than to other New World alphaviruses.
Divergent Evolution in Reverse Transcriptase (RT) of HIV-1 Group O and M Lineages: Impact on Structure, Fitness, and Sensitivity to Nonnucleoside RT Inhibitors
Authors: Tebit Denis M. , Lobritz Michael , Lalonde Matthew , Immonen Taina , Singh Kamlendra , Sarafianos Stefanos , Herchenröder Ottmar , Kräusslich Hans-Georg , Arts Eric J.
Published: July 2010

Natural evolution in primate lentiviral reverse transcriptase (RT) appears to have been constrained by the necessity to maintain function within an asymmetric protein composed of two identical primary amino acid sequences (66 kDa), of which one is cleaved (51 kDa). In this study, a detailed phylogenetic analysis now segregates groups O and M into clusters based on a cysteine or tyrosine residue located at position 181 of RT and linked to other signature residues. Divergent evolution of two group O (C181 or Y181) and the main (Y181 only) HIV-1 lineages did not appreciably impact RT activity or function. Group O RT structural models, based on group M subtype B RT crystal structures, revealed that most evolutionarily linked amino acids appear on a surface-exposed region of one subunit while in a noncatalytic RT pocket of the other subunit. This pocket binds nonnucleoside RT inhibitors (NNRTI); therefore, NNRTI sensitivity was used to probe enzyme differences in these group O and M lineages. In contrast to observations showing acquired drug resistance associated with fitness loss, the C181Y mutation in the C181 group O lineage resulted in a loss of intrinsic NNRTI resistance and was accompanied by fitness loss. Other mutations linked to the NNRTI-resistant C181 lineage also resulted in altered NNRTI sensitivity and a net fitness cost. Based on RT asymmetry and conservation of the intricate reverse transcription process, millions of years of divergent primate lentivirus evolution may be constrained to discrete mutations that appear primarily in the nonfunctional, solvent-accessible NNRTI binding pocket.
Inhibition of the Ubiquitin-Proteasome System Affects Influenza A Virus Infection at a Postfusion Step
Authors: Widjaja Ivy , de Vries Erik , Tscherne Donna M. , García-Sastre Adolfo , Rottier Peter J. M. , de Haan Cornelis A. M.
Published: July 2010

We have demonstrated that influenza A virus (IAV) RNA synthesis depends on the ubiquitin-proteasome system. IAV replication was reduced both by proteasome inhibitors and in E36ts20 cells, which contain the thermolabile ubiquitin-activating enzyme E1. While virus entry was not affected in E36ts20 cells, the proteasome inhibitor MG132 retained viral particles in the cytoplasm. Addition-removal experiments of MG132 in combination with bafilomycin A1, a well-established inhibitor of IAV entry and fusion, showed that MG132 affected IAV infection at a postfusion step. This was confirmed by the lack of inhibition of IAV entry by proteasome inhibitors in a virus-like particle fusion assay.
Inhibition of Encephalomyocarditis Virus and Poliovirus Replication by Quinacrine: Implications for the Design and Discovery of Novel Antiviral Drugs
Authors: Gasparian Alexander V. , Neznanov Nickolay , Jha Sujata , Galkin Oleksandr , Moran John J. , Gudkov Andrei V. , Gurova Katerina V. , Komar Anton A.
Published: July 2010

The 9-aminoacridine (9AA) derivative quinacrine (QC) has a long history of safe human use as an antiprotozoal and antirheumatic agent. QC intercalates into DNA and RNA and can inhibit DNA replication, RNA transcription, and protein synthesis. The extent of QC intercalation into RNA depends on the complexity of its secondary and tertiary structure. Internal ribosome entry sites (IRESs) that are required for initiation of translation of some viral and cellular mRNAs typically have complex structures. Recent work has shown that some intercalating drugs, including QC, are capable of inhibiting hepatitis C virus IRES-mediated translation in a cell-free system. Here, we show that QC suppresses translation directed by the encephalomyocarditis virus (EMCV) and poliovirus IRESs in a cell-free system and in virus-infected HeLa cells. In contrast, IRESs present in the mammalian p53 transcript that are predicted to have less-complex structures were not sensitive to QC. Inhibition of IRES-mediated translation by QC correlated with the affinity of binding between QC and the particular IRES. Expression of viral capsid proteins, replication of viral RNAs, and production of virus were all strongly inhibited by QC (and 9AA). These results suggest that QC and similar intercalating drugs could potentially be used for treatment of viral infections.
Retargeting of Adenovirus Vectors through Genetic Fusion of a Single-Chain or Single-Domain Antibody to Capsid Protein IX
Authors: Poulin Kathy L. , Lanthier Robert M. , Smith Adam C. , Christou Carin , Risco Quiroz Milagros , Powell Karen L. , O'Meara Ryan W. , Kothary Rashmi , Lorimer Ian A. , Parks Robin J.
Published: July 2010

Adenovirus (Ad) vectors are the most commonly used system for gene therapy applications, due in part to their ability to infect a wide array of cell types and tissues. However, many therapies would benefit from the ability to target the Ad vector only to specific cells, such as tumor cells for cancer gene therapy. In this study, we investigated the utility of capsid protein IX (pIX) as a platform for the presentation of single-chain variable-fragment antibodies (scFv) and single-domain antibodies (sdAb) for virus retargeting. We show that scFv can be displayed on the capsid through genetic fusion to native pIX but that these molecules fail to retarget the virus, due to improper folding of the scFv. Redirecting expression of the fusion protein to the endoplasmic reticulum (ER) results in correct folding of the scFv and allows it to recognize its epitope; however, ER-targeted pIX-scFv was incorporated into the Ad capsid at a very low level which was not sufficient to retarget virus infection. In contrast, a pIX-sdAb construct was efficiently incorporated into the Ad capsid and enhanced virus infection of cells expressing the targeted receptor. Taken together, our data indicate that pIX is an effective platform for presentation of large targeting polypeptides on the surface of the virus capsid, but the nature of the ligand can significantly affect its association with virions.
Infection by Discordant Strains of HIV-1 Markedly Enhances the Neutralizing Antibody Response against Heterologous Virus
Authors: Powell Rebecca L. R. , Kinge Thompson , Nyambi Phillipe N.
Published: July 2010

High-risk cohorts in East Africa and the United States show rates of dual HIV-1 infection—the concomitant or sequential infection by two HIV-1 strains—of 50% to 100% of those of primary infection, and our normal-risk HIV-positive cohort in Cameroon exhibits a rate of dual infection of 11% per year, signifying that these infections are not exceptional. Little is known regarding the effect of dual infections on host immunity, despite the fact that they provide unique opportunities to investigate how the immune response is affected when challenged with diverse HIV-1 antigens. Using heterologous primary isolates, we have shown here that dual HIV-1 infection by genetically distant strains correlates with significantly increased potency and breadth of the anti-HIV-1 neutralizing antibody response. When the neutralization capacities of sequential plasma obtained before and after the dual infection of 4 subjects were compared to those of matched plasma obtained from 23 singly infected control subjects, a significant increase in the neutralization capacity of the sequential sample was found for 16/28 dually infected plasma/virus pairs, while only 4/159 such combinations for the control subjects exhibited a significant increase (
P
< 0.0001). Similarly, there was a significant increase in the plasma dilution capable of neutralizing 50% of virus (IC
50
) for 18/24 dually infected plasma/virus pairs, while 0/36 controls exhibited such an increase (
P
< 0.0001). These results demonstrate that dual HIV-1 infection broadens and strengthens the anti-HIV-1 immune response, suggesting that vaccination schemes that include polyvalent, genetically divergent immunogens may generate highly protective immunity against any HIV-1 challenge strain.
A New Approach to Length–Frequency Analysis: Growth Structure
Authors: Schnute Jon , Fournier David
Published: July 2010

This paper presents a new approach to length–frequency analysis which takes account of biological structure in the mean lengths and standard deviations in length for various age-classes of fish. The new methods help determine biologically meaningful solutions, even when earlier methods lead to an ambiguous set of competing solutions. The structure of the standard deviations turns out to be especially important. For describing the means, new parameters are defined for von Bertalanffy growth which prove to have greater biological meaning and numerical stability than L∞, K, and t0. These new parameters can often be estimated easily from the raw data in cases where the species experiences a slowing of growth with age. This paper also presents χ2 methods which can be used to rank competing solutions, although the results are not definitive. All methods are illustrated using data previously published for pike and abalone. An appendix describes in detail the computer programs required for the analysis.Key words: length–frequency analysis, aging of samples, von Bertalanffy growth, growth, maximum likelihood estimation, nonlinear estimation
Reciprocal Averaging and Polar Ordination as Techniques for Analyzing Lotic Macroinvertebrate Communities
Authors: Culp Joseph M. , Davies Ronald W.
Published: July 2010

Reciprocal averaging and polar ordination techniques were applied to lotic macroinvertebrate field data to determine the relative performance of these techniques in lotic benthic community analyses. It was found that, because of inherent problems with endpoint determinations, polar ordination should only be used where a well-defined environmental gradient exists. Reciprocal averaging ordination produced interpretable axes and was preferred over polar ordination because endpoint determination was objective and simultaneous species–site ordinations were produced. Reciprocal averaging ordination allowed groupings of sites similar to those determined through cluster analysis to be recognized, while providing a visual representation of between-group relationships superior to that of cluster dendrograms. Combined with subsequent analyses of environmental data, reciprocal averaging ordination can be an excellent technique for summarizing spatial and temporal patterns of lotic macroinvertebrate communities.Key words: ordination, reciprocal averaging, benthic, lotic, communities, clustering
Factors Affecting Puget Sound Coho Salmon (Oncorhynchus kisutch) Runs
Authors: Mathews S. B. , Olson F. W.
Published: July 2010

Summer streamflow, apparently affecting survival of zero-age coho salmon (Oncorhynchus kisutch), is shown to be an important determinant of Puget Sound run strength since 1952. Recently, hatchery production has also been a significant factor. Earlier studies indicated a relationship between rearing flows and coho run strength beginning in 1935. The persistence of the correlation between streamflow and run strength for more than 40 yr is noteworthy. Although the mechanism is unclear, survival of hatchery coho may also be positively dependent upon the same environmental conditions that affect stream-reared coho; a depensatory mortality relationship between abundance of hatchery coho and abundance of stream-reared coho is postulated.Key words: coho salmon, survival, run prediction, hatchery contribution
Influence of Parental Smolt Age and Sea Age on Growth and Smolting of Hatchery-Reared Atlantic Salmon (Salmo salar)
Authors: Bailey J. K. , Saunders R. L. , Buzeta M. I.
Published: July 2010

Hatchery-reared Atlantic salmon, Salmo salar, consistently developed bimodal length–frequency distributions by the first November following hatch. In a study of 32 hatchery populations involving two year-classes, mean length in the lower mode showed little variation among populations and was not correlated with either the smolt age or sea age at first maturity of their parents. Mean length and the proportion of individuals in the upper mode were both variable among populations and correlated with parental age variables. Large mean length in the upper mode was strongly associated with early smolting male parents and late maturing female parents. The proportion of individuals in the upper mode was more strongly correlated with the age variables of the female parent. Late smolting and early maturing female parents tended to produce relatively greater proportions of fish in the upper mode. The optimum growth rate which produced the greatest proportion of individuals in the upper mode occurred when 8–15% of the total population matured precociously as parr. A threshold size hypothesis for precocious maturation is discussed.Key words: Atlantic salmon, genetics, growth, bimodality, precocious sexual maturation, smoltification
Circulation and Energetics of a Deep, Strongly Stratified Inlet
Authors: Freeland Howard J. , Farmer David M.
Published: July 2010

The paper compares a theoretical model of steady flow in a strongly stratified inlet with the observed behavior of Knight Inlet, British Columbia. Some aspects of the behavior compare favorably with the theory and some aspects do not. Specifically, the model does well in the limit of small interfacial friction coefficient, which is surprising as the evidence presented by Long (1975) suggests that interfacial friction should dominate the flow. Long demonstrates that the circulation in inlets of this type should adjust to maintain the interfacial Froude number at unity near the mouth. In the paper we demonstrate that Knight Inlet is not apparently being controlled in this way.Computations of the amount of energy required to drive the circulation, the amount that can be extracted from the wind, and the amount that is being lost by the barotropic tides indicate that tidal interactions with the sill in Knight Inlet drive the mean circulation. The wind contributes little to the overall energy budget of Knight Inlet.Key words: Knight Inlet, circulation, dynamics, energetics, internal waves, turbulence, mixing processes, entrainment