bluuebunny/crossref_metadata_2025 huggingface dataset:
Overall pitch height as a cue for lexical tone perception
Authors: Shen Jing , Deutsch Diana , Le Jinghong
Published: October 2011

Absolute pitch has been hypothesized to be involved in processing lexical tones in tone languages, which associate pitch information with verbal labels. Since possessors of absolute pitch in music utilize the overall pitch of a tone in making identification judgments, the hypothesis was tested that native speakers of Mandarin utilize the overall pitch of a lexical tone as a cue to retrieve its tone label. In a reaction time task, Mandarin syllables in all four tones were presented both in their original forms and also transposed to four different levels of pitch height; subjects listened to each token and judged whether or not its meaning corresponded to the original. It was found that although Mandarin syllables with transposed overall pitch heights were judged to be the same tones as the original tokens, subjects were significantly slower in making judgments for those syllables that were transposed to different levels of pitch height, compared to those that were presented at their original pitch heights. This effect was most extreme for tones 1 and 3. These findings suggest that overall pitch height serves as a cue for identifying lexical tones and further strengthens the link between absolute pitch and lexical tone perception.
Timing of perceptual cues in Scots Gaelic
Authors: Warner Natasha , Carnie Andrew , Fisher Muriel , Schertz Jessamyn , Mathieu Lionel , Gorrie Colin , Hammond Michael , Archangeli Diana
Published: October 2011

Scots Gaelic, an endangered language, has several typologically unusual sound distinctions. Work on English or other languages cannot predict what perceptual cues Gaelic listeners might use to perceive these distinctions. The current work uses gating experiments, run in Scotland with 16 native listeners (monolingual in Gaelic until at least school age), to investigate timing of perceptual cues to the palatalization, preaspiration, and nasal frication contrasts. Results show that perceptual information about consonant palatalization is located primarily in the consonant itself, with weaker cues in the preceding vowel. For preaspiration, there is no perceptual information in the preceding vowel, but even half of the preaspiration provides a sufficient cue. The claimed nasal fricatives are particularly interesting, as true nasalized fricatives may be aerodynamically impossible, but nasalization could be realized on the preceding vowel, or without frication. The results show that listeners are only marginally able to hear this distinction, and that information does not increase through the signal: The little perceptual information present is already available during the preceding vowel. This confirms aerodynamic results showing some neutralization of this distinction and some nasalization during the preceding vowel. Overall, the results help us determine how information is conveyed using typologically unusual distinctions.
Examining the role of variability in emotional tone of voice during online spoken word recognition
Authors: Wilson Maura L. , McLennan Conor T.
Published: October 2011

Previous studies demonstrate that listeners are faster to recognize words recently spoken by the same talker, relative to a different talker, when processing is relatively slow. The purpose of the present study was to examine intra-talker variability in emotional tone of voice on listeners' online perception of spoken words. Based on previous work, we predicted reduced priming in the mismatch condition, when words are repeated in a different emotional tone of voice (e.g., sad and frightened), relative to the match condition, when words are repeated in the same emotional tone of voice (e.g., frightened)—when processing is relatively slow (experiment 2, hard lexical decision) and equivalent priming in the match and mismatch conditions when processing is relatively fast (experiment 1, easy lexical decision). The present study should provide a greater understanding of the role that variability in emotional tone of voice plays in listeners' online perception of spoken words.
Acoustical Society of America Silver Medal in Signal Processing in Acoustics
Authors: Birdsall Theodore G.
Published: October 2011

The Silver Medal is presented to individuals, without age limitation, for contributions to the advancement of science, engineering, or human welfare through the application of acoustic principles, or through research accomplishment in acoustics.
Response to Comments on “Changes in Climatic Water Balance Drive Downhill Shifts in Plant Species’ Optimum Elevations”
Authors: Dobrowski Solomon Z. , Crimmins Shawn M. , Greenberg Jonathan A. , Abatzoglou John T. , Mynsberge Alison R.
Published: October 2011

Wolf and Anderegg, Hijmans, and Stephenson and Das suggest that our findings of changes in climatic water balance driving downhill shifts in plant species distributions are flawed. We demonstrate that the conclusions these authors make are subject to the selection of methods they apply and do not provide sufficient evidence to reject our original findings.
The Dynamic Architecture of
Hox
Gene Clusters
Authors: Noordermeer Daan , Leleu Marion , Splinter Erik , Rougemont Jacques , De Laat Wouter , Duboule Denis
Published: October 2011

Sequential activation of
Hox
genes correlates with a transition of negative to positive three-dimensional chromosome structure.
The
Escherichia coli
Replisome Is Inherently DNA Damage Tolerant
Authors: Yeeles Joseph T. P. , Marians Kenneth J.
Published: October 2011

The core DNA replication machinery of
Escherichia coli
has an inherent ability to squeeze past DNA damage on the leading strand.
NMR Detection of Structures in the HIV-1 5′-Leader RNA That Regulate Genome Packaging
Authors: Lu Kun , Heng Xiao , Garyu Lianko , Monti Sarah , Garcia Eric L. , Kharytonchyk Siarhei , Dorjsuren Bilguujin , Kulandaivel Gowry , Jones Simonne , Hiremath Atheeth , Divakaruni Sai Sachin , LaCotti Courtney , Barton Shawn , Tummillo Daniel , Hosic Azra , Edme Kedy , Albrecht Sara , Telesnitsky Alice , Summers Michael F.
Published: October 2011

An RNA structural switch regulates whether the HIV genome is translated or dimerized and packaged.
Global Resilience of Tropical Forest and Savanna to Critical Transitions
Authors: Hirota Marina , Holmgren Milena , Van Nes Egbert H. , Scheffer Marten
Published: October 2011

Tree distributions across continents indicate three distinct stable states in tree cover―forest, savanna, and treeless.
Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis
Authors: Kuss Sharon K. , Best Gavin T. , Etheredge Chris A. , Pruijssers Andrea J. , Frierson Johnna M. , Hooper Lora V. , Dermody Terence S. , Pfeiffer Julie K.
Published: October 2011

Commensal microflora promote the pathogenesis of mucosally acquired viruses.
HIV Study Renews Scrutiny of Hormonal Contraception
Authors: Cohen Jon
Published: October 2011

Some researchers worry that a recent study that found that hormonal contraceptive use increases HIV risk will overshadow the many complexities in the data that leave open critical questions about whether injected contraceptives truly pose an HIV risk.
Comparison of Two Gamma Interferon Release Assays and Tuberculin Skin Testing for Tuberculosis Screening in a Cohort of Patients with Rheumatic Diseases Starting Anti-Tumor Necrosis Factor Therapy
Authors: Vassilopoulos Dimitrios , Tsikrika Stamatoula , Hatzara Chrisoula , Podia Varvara , Kandili Anna , Stamoulis Nikolaos , Hadziyannis Emilia
Published: October 2011

Gamma interferon release assays (IGRAs) are increasingly used for latentMycobacterium tuberculosisinfection (LTBI) screening in patients with rheumatic diseases starting anti-tumor necrosis factor (anti-TNF) therapies. We compared the performances of two IGRAs, an enzyme-linked immunospot release assay (T-SPOT.TB) and an enzyme-linked immunosorbent assay (QuantiFERON-TB Gold In Tube [QFT-GIT]), to that of tuberculin skin testing (TST) for LTBI screening of 157 consecutive rheumatic patients starting anti-TNF therapies. Among 155 patients with valid results, 58 (37%) were positive by TST, 39 (25%) by T-SPOT.TB assay, and 32 (21%) by QFT-GIT assay. IGRAs were associated more strongly with at least one risk factor for tuberculosis (TB) than TST. Risk factors for a positive assay included chest X-ray findings of old TB (TST), advanced age (both IGRAs), origin from a country with a high TB prevalence, and a positive TST (T-SPOT.TB assay). Steroid use was negatively associated with a positive QFT-GIT assay. The agreement rate between IGRAs was 81% (kappa rate = 0.47), which was much higher than that observed between an IGRA and TST. If positivity by either TST or an IGRA was required for LTBI diagnosis, then the rate of LTBI would have been 46 to 47%, while if an IGRA was performed only for TST-positive patients, the respective rate would have been 11 to 17%. In conclusion, IGRAs appear to correlate better with TB risk than TST and should be included in TB screening of patients starting anti-TNF therapies. In view of the high risk of TB in these patients, a combination of one IGRA and TST is probably more appropriate for LTBI diagnosis.
Generation and Characterization of a Live Attenuated Enterotoxigenic Escherichia coli Combination Vaccine Expressing Six Colonization Factors and Heat-Labile Toxin Subunit B
Authors: Turner Arthur K. , Stephens Jonathan C. , Beavis Juliet C. , Greenwood Judith , Gewert Cornelia , Randall Roger , Freeman Donna , Darsley Michael J.
Published: October 2011

Live attenuated oral enterotoxigenic
Escherichia coli
(ETEC) vaccines have been demonstrated to be safe and immunogenic in human volunteers and to provide a viable approach to provide protection against this important pathogen. This report describes the construction of new ETEC vaccine candidate strains from recent clinical isolates and their characterization. All known genes for ETEC toxins were removed, and attenuating deletion mutations were made in the
aroC
,
ompC
, and
ompF
chromosomal genes. An isolate expressing coli surface antigen 2 (CS2), CS3, heat-labile toxin (LT), heat-stable toxin (ST), and enteroaggregative
Escherichia coli
heat-stable toxin 1 (EAST1) was attenuated to generate ACAM2007. The subsequent insertion of the operon encoding CS1 created ACAM2017, and this was further modified by the addition of an expression cassette containing the
eltB
gene, encoding a pentamer of B subunits of LT (LTB), to generate ACAM2027. Another isolate expressing CS5, CS6, LT, ST, and EAST1 was attenuated to generate ACAM2006, from which a lysogenic prophage was deleted to create ACAM2012 and an LTB gene was introduced to form ACAM2022. Finally, a previously described vaccine strain, ACAM2010, had the
eltB
gene incorporated to generate ACAM2025. All recombinant genes were incorporated into the chromosomal sites of the attenuating mutations to ensure maximal genetic stability. The expression of the recombinant antigens and the changes in plasmids accompanying the deletion of toxin genes are described. Strains ACAM2025, ACAM2022, and ACAM2027 have been combined to create the ETEC vaccine formulation ACE527, which has recently successfully completed a randomized, double-blind, placebo-controlled phase I trial and is currently undergoing a randomized, double-blind placebo-controlled phase II challenge trial, both in healthy adult volunteers.
Case of Secondary Syphilis Presenting with Unusual Complications: Syphilitic Proctitis, Gastritis, and Hepatitis
Authors: Adachi Eisuke , Koibuchi Tomohiko , Okame Michio , Sato Hidenori , Imai Kentaro , Shimizu Shoichi , Tsurita Giichiro , Oyaizu Naoki , Iwamoto Aikichi , Fujii Takeshi
Published: October 2011

We report the first known case of syphilis with simultaneous manifestations of proctitis, gastritis, and hepatitis. The diagnosis of syphilitic proctitis and gastritis was established by the demonstration of spirochetes with anti-
Treponema pallidum
antibody staining in biopsy specimens. Unusual manifestations of secondary syphilis completely resolved after 4 weeks of antibiotic therapy.
Septic Arthritis Due to Cellulosimicrobium cellulans
Authors: Magro-Checa César , Chaves-Chaparro Lara , Parra-Ruiz Jorge , Peña-Monje Alejandro , Rosales-Alexander José Luis , Salvatierra Juan , Raya Enrique
Published: October 2011

Cellulosimicrobium cellulans
has been reported as a rare cause of human pathogenesis. Infections mainly occur in immunocompromised patients and very often are associated with a foreign body. We report the first case of septic arthritis caused by
C. cellulans
in an immunocompetent patient. Our patient suffered a penetrating palm tree thorn injury to his left knee 8 weeks before admission. Although no foreign objects were found, they were suspected because previous reports suggest a frequent association with this microorganism, and open debridament was performed. Removal of foreign bodies related to this organism must be considered a high-priority treatment in these patients to achieve a complete recovery.
Canadian Multicenter Laboratory Study for Standardized Second-Line Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis
Authors: Sharma Meenu , Thibert Louise , Chedore Pamela , Shandro Cary , Jamieson Frances , Tyrrell Gregory , Christianson Sara , Soualhine Hafid , Wolfe Joyce
Published: October 2011

The purpose of this study was to establish a standardized protocol for second-line antimicrobial susceptibility testing of
Mycobacterium tuberculosis
using the Bactec MGIT 960 system in Canadian laboratories. Four Canadian public health laboratories compared the susceptibility testing results of 9 second-line antimicrobials between the Bactec 460 and Bactec MGIT 960 systems. Based on the data generated, we have established that the Bactec MGIT 960 system provides results comparable to those obtained with the previous Bactec 460 method. The critical concentrations established for the testing of the antimicrobials used are as follows: amikacin, 1 μg/ml; capreomycin, 2.5 μg/ml; ethionamide, 5 μg/ml; kanamycin, 2.5 μg/ml; linezolid, 1 μg/ml; moxifloxacin, 0.25 μg/ml; ofloxacin, 2 μg/ml;
p
-aminosalicylic acid, 4 μg/ml; rifabutin, 0.5 μg/ml.
tuf
Gene Sequence Analysis Has Greater Discriminatory Power than 16S rRNA Sequence Analysis in Identification of Clinical Isolates of Coagulase-Negative Staphylococci
Authors: Hwang Sang Mee , Kim Myoung Shin , Park Kyoung Un , Song Junghan , Kim Eui-Chong
Published: October 2011

We compared and analyzed 16S rRNA and
tuf
gene sequences for 97 clinical isolates of coagulase-negative staphylococci (CNS) by use of the GenBank, MicroSeq, EzTaxon, and BIBI databases. Discordant results for definitive identification were observed and differed according to the different databases and target genes. Although higher percentages of sequence identity were obtained with GenBank and MicroSeq for 16S rRNA analysis, the BIBI and EzTaxon databases produced less ambiguous results. Greater discriminatory power and fewer multiple probable identifications were observed with
tuf
gene analysis than with 16S rRNA analysis. The most pertinent results for
tuf
gene analysis were obtained with the GenBank database when the cutoff values for the percentage of identity were adjusted to be greater than or equal to 98.0%, with >0.8% separation between species. Analysis of the
tuf
gene proved to be more discriminative for certain CNS species; further, this method exhibited better distinction in the identification of CNS clinical isolates.
Age- and Gender-Associated Staphylococcus aureus spa Types Found among Nasal Carriers in a General Population: the Tromsø Staph and Skin Study
Authors: Sangvik Maria , Olsen Renate Slind , Olsen Karina , Simonsen Gunnar Skov , Furberg Anne-Sofie , Sollid Johanna U. Ericson
Published: October 2011

Staphylococcus aureus
nasal carriers risk autoinfection; however, knowledge about the factors that make specific strains successful colonizers is limited. This study was undertaken to identify the most successful
S. aureus
clones in nasal carriers and compare their distribution among host groups. The population structure of
S. aureus
isolates from healthy adults was investigated by
spa
typing 1,981 isolates from persistent and intermittent nasal carriers participating in a health survey. In the baseline screening (1,113 isolates), the most common
spa
types were t012 (8.4%), t084 (7.6%), and t065 (4.9%). Three large
spa
clonal complexes (
spa
CC012,
spa
CC065, and
spa
CC084) comprised 62.4% of the isolates. In multivariate models adjusted for age and smoking status, male sex was associated with higher risk for
spa
type t084 (odds ratio [OR], 1.72; 95% confidence interval [CI], 1.06 to 2.77), and lower risk of
spa
type t012 (OR, 0.60; 95% CI, 0.39 to 0.92) colonization. The prevalence of
spa
type t012 decreased significantly with increasing age (
P
= 0.03), with a prevalence almost twice as high in the youngest group (age 30 to 44 years, prevalence = 11.1%) as in the oldest group (age, 60 to 87 years; prevalence = 5.6%). Among baseline isolates,
spa
type t084 had a twofold-higher prevalence among intermittent carriers than among persistent carriers (10.6% versus 5.5%;
P
= 0.04). In summary, the two most prevalent
spa
types found in this study were significantly associated with age and/or gender. This may provide valuable clues to the multifactorial mechanisms, among them bacterial factors, involved in nasal colonization with
S. aureus
.
Evaluation of the Impact of Direct Plating, Broth Enrichment, and Specimen Source on Recovery and Diversity of Methicillin-Resistant Staphylococcus aureus Isolates among HIV-Infected Outpatients
Authors: McAllister S. K. , Albrecht V. S. , Fosheim G. E. , Lowery H. K. , Peters P. J. , Gorwitz R. , Guest J. L. , Hageman J. , Mindley R. , McDougal L. K. , Rimland D. , Limbago B.
Published: October 2011

We compared recovery of
Staphylococcus aureus
and methicillin-resistant
S. aureus
(MRSA) from nasal and groin swab specimens of 600 HIV-infected outpatients by selective and nonselective direct plating and broth enrichment. Swabs were collected at baseline, 6-month, and 12-month visits and cultured by direct plating to mannitol salt agar (MSA) and CHROMagar MRSA (CM) and overnight broth enrichment with subculture to MSA (broth). MRSA isolates were characterized by pulsed-field gel electrophoresis (PFGE), staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and PCR for the Panton-Valentine leukocidin. At each visit, 13 to 15% of patients were colonized with MRSA and 30 to 33% were colonized with methicillin-susceptible
S. aureus
(MSSA). Broth, CM, and MSA detected 95%, 82%, and 76% of MRSA-positive specimens, respectively. MRSA recovery was significantly higher from broth than CM (
P
≤ 0.001) or MSA (
P
≤ 0.001); there was no significant difference in recovery between MSA and CM. MSSA recovery also increased significantly when using broth than when using MSA (
P
≤ 0.001). Among specimens collected from the groin, broth, CM, and MSA detected 88%, 54%, and 49% of the MRSA-positive isolates, respectively. Broth enrichment had a greater impact on recovery of MRSA from the groin than from the nose compared to both CM (
P
≤ 0.001) and MSA (
P
≤ 0.001). Overall, 19% of MRSA-colonized patients would have been missed with nasal swab specimen culture only. USA500/Iberian and USA300 were the most common MRSA strains recovered, and USA300 was more likely than other strain types to be recovered from the groin than from the nose (
P
= 0.05).
Detection of an Unusual
van
Genotype in a Vancomycin-Resistant Enterococcus faecium Hospital Isolate
Authors: Teo Jeanette W. P. , Krishnan Prabha , Jureen Roland , Lin Raymond T. P.
Published: October 2011

We highlight the detection of a rare
vanM
genotype in
Enterococcus faecium.
This isolate exhibited a VanB phenotype, with high levels of resistance to vancomycin (MIC, >256 mg/liter) and susceptibility to teicoplanin (MIC, 1 mg/liter). It was, however,
vanB
negative by PCR. Further screening for other
van
loci revealed the presence of a complete
vanM
operon.
Three-Year History of Transcription-Mediated Amplification-Based Trichomonas vaginalis Analyte-Specific Reagent Testing in a Subacute Care Patient Population
Authors: Napierala Maureen , Munson Erik , Munson Kimber L. , Kramme Timothy , Miller Cheryl , Burtch Jason , Olson Robin , Hryciuk Jeanne E.
Published: October 2011

A total of 7,899 specimens submitted for live clinical
Trichomonas vaginalis
analyte-specific reagent (ASR) screening from 2008 to 2010 were audited on the basis of patient gender, specimen source, molecular
Neisseria gonorrhoeae
and
Chlamydia trachomatis
results, and relative light unit (RLU) data yielded by
T. vaginalis
ASR. Only 1.4% of the screening was ordered by emergency department clinicians. The screening volume in 2010 was 126% higher than that in 2008. The proportions of annual female and male screening remained consistent throughout the 3-year interval (∼92 and 8%, respectively). Although 71.8 and 9.5% of screening was performed on endocervical and vaginal specimens, respectively, over the 3-year period, no significant difference was noted in the
T. vaginalis
detection rates (8.9 and 8.6%,
P
= 0.85). Increased
T. vaginalis
detection was derived from female urine specimens (12.6%) compared to female genital swabs (
P
= 0.0004). The proportion of female urine screening increased during the 3-year interval (
P
< 0.0002).
T. vaginalis
detection rate in males was 6.6%, with no difference between urethral and urine
T. vaginalis
detection (
P
= 0.53). The mean RLU value for 714 positive specimens was 3,971,441; analogous values for each female specimen source and combined male source testing showed no variance (
P
≥ 0.29). Combined-gender
T. vaginalis
detection rate (9.1%) was significantly greater than those of
C. trachomatis
(5.9%) and
N. gonorrhoeae
(1.5%;
P
< 0.0002). Equivocal results presented at a rate of 0.4%.
T. vaginalis
ASR is an increasingly utilized assay that yields higher detection rates than other sexually transmitted infection etiologies in this community subacute care setting.
Staphylococcus hyicus Bacteremia in a Farmer
Authors: Casanova Carlo , Iselin Lukas , von Steiger Niklaus , Droz Sara , Sendi Parham
Published: October 2011

Bacteria known in animal infectious diseases can cause challenges in human diagnostic laboratories. We present pitfalls in the identification and susceptibility testing ofStaphylococcus hyicus, a pathogen that typically causes exudative epidermitis in pigs. In this case, the coagulase-positive staphylococcus isolated from a septic patient was misidentified asStaphylococcus aureus.
Recurring Klebsiella pneumoniae Pyogenic Liver Abscesses in a Resident of San Diego, California, Due to a K1 Strain Carrying the Virulence Plasmid
Authors: Fierer Joshua , Walls Lorraine , Chu Pauline
Published: October 2011

We report a diabetic patient who had three episodes of cryptogenic liver abscess due to
Klebsiella pneumoniae
. He was a Caucasian who lived in California and had no epidemiological connection to East Asia. The isolate from his third episode was a hyperviscous K1 strain that carried the
Klebsiella
virulence plasmid.
Generation and Comprehensive Analysis of an Influenza Virus Polymerase Cellular Interaction Network
Authors: Tafforeau Lionel , Chantier Thibault , Pradezynski Fabrine , Pellet Johann , Mangeot Philippe E. , Vidalain Pierre-Olivier , Andre Patrice , Rabourdin-Combe Chantal , Lotteau Vincent
Published: October 2011

The influenza virus transcribes and replicates its genome inside the nucleus of infected cells. Both activities are performed by the viral RNA-dependent RNA polymerase that is composed of the three subunits PA, PB1, and PB2, and recent studies have shown that it requires host cell factors to transcribe and replicate the viral genome. To identify these cellular partners, we generated a comprehensive physical interaction map between each polymerase subunit and the host cellular proteome. A total of 109 human interactors were identified by yeast two-hybrid screens, whereas 90 were retrieved by literature mining. We built the FluPol interactome network composed of the influenza virus polymerase (PA, PB1, and PB2) and the nucleoprotein NP and 234 human proteins that are connected through 279 viral-cellular protein interactions. Analysis of this interactome map revealed enriched cellular functions associated with the influenza virus polymerase, including host factors involved in RNA polymerase II-dependent transcription and mRNA processing. We confirmed that eight influenza virus polymerase-interacting proteins are required for virus replication and transcriptional activity of the viral polymerase. These are involved in cellular transcription (C14orf166, COPS5, MNAT1, NMI, and POLR2A), translation (EIF3S6IP), nuclear transport (NUP54), and DNA repair (FANCG). Conversely, we identified PRKRA, which acts as an inhibitor of the viral polymerase transcriptional activity and thus is required for the cellular antiviral response.
Complement-Dependent Lysis of Influenza A Virus-Infected Cells by Broadly Cross-Reactive Human Monoclonal Antibodies
Authors: Terajima Masanori , Cruz John , Co Mary Dawn T. , Lee Jane-Hwei , Kaur Kaval , Wilson Patrick C. , Ennis Francis A.
Published: October 2011

We characterized human monoclonal antibodies (MAbs) cloned from influenza virus-infected patients and from influenza vaccine recipients by complement-dependent lysis (CDL) assay. Most MAbs active in CDL were neutralizing, but not all neutralizing MAbs can mediate CDL. Two of the three stalk-specific neutralizing MAbs tested were able to mediate CDL and were more cross-reactive to temporally distant H1N1 strains than the conventional hemagglutination-inhibiting and neutralizing MAbs. One of the stalk-specific MAbs was subtype cross-reactive to H1 and H2 hemagglutinins, suggesting a role for stalk-specific antibodies in protection against influenza illness, especially by a novel viral subtype which can cause pandemics.
Selection with a Peptide Fusion Inhibitor Corresponding to the First Heptad Repeat of HIV-1 gp41 Identifies Two Genetic Pathways Conferring Cross-Resistance to Peptide Fusion Inhibitors Corresponding to the First and Second Heptad Repeats (HR1 and HR2) of gp41
Authors: Wang Wei , De Feo Christopher J. , Zhuang Min , Vassell Russell , Weiss Carol D.
Published: October 2011

We generated four HIV-1 cultures that are resistant to a peptide fusion inhibitor corresponding to the first heptad repeat of gp41 in order to study mechanisms of resistance and gain insights into envelope glycoprotein-mediated membrane fusion. Two genetic pathways emerged that were defined by acquisition of a specific mutation in either the first or second heptad repeat region of gp41 (HR1 or the HR2, respectively). Each pathway was enriched in mutations that clustered in either HR2 and V3 or in HR1 and residues in or near CD4 contact sites. The gp41 mutations in both pathways not only accounted for resistance to the selecting HR1 peptide but also conferred cross-resistance to HR2 peptide fusion inhibitors and enhanced the stability of the six-helix bundle formed by the self-assembly of HR1 and HR2. The gp120 mutations alone enhanced fusion but did not appear to directly contribute to resistance. The implications of these findings for resistance mechanisms and regulation of envelope-mediated fusion are discussed.
Promyelocytic Leukemia Isoform IV Confers Resistance to Encephalomyocarditis Virus via the Sequestration of 3D Polymerase in Nuclear Bodies
Authors: Maroui Mohamed Ali , Pampin Mathieu , Chelbi-Alix Mounira K.
Published: October 2011

Promyelocytic leukemia
(PML) protein is the organizer of nuclear matrix-associated nuclear bodies (NBs), and its conjugation to the small ubiquitin-like modifier (SUMO) is required for the formation of these structures. Several alternatively spliced PML transcripts from a single
PML
gene lead to the production of seven PML isoforms (PML isoform I [PMLI] to VII [PMLVII]), which all share a N-terminal region that includes the RBCC (RING, B boxes, and a α-helical coiled-coil) motif but differ in the C-terminal region. This diversity of PML isoforms determines the specific functions of each isoform. There is increasing evidence implicating PML in host antiviral defense and suggesting various strategies involving PML to counteract viral production. We reported that mouse embryonic fibroblasts derived from PML knockout mice are more sensitive than wild-type cells to infection with encephalomyocarditis virus (EMCV). Here, we show that stable expression of PMLIV or PMLIVa inhibited viral replication and protein synthesis, leading to a substantial reduction of EMCV multiplication. This protective effect required PMLIV SUMOylation and was not observed with other nuclear PML isoforms (I, II, III, V, and VI) or with the cytoplasmic PMLVII. We demonstrated that only PMLIV interacted with EMCV 3D polymerase (3Dpol) and sequestered it within PML NBs. The C-terminal region specific to PMLIV was required for both interaction with 3Dpol and the antiviral properties. Also, depletion of PMLIV by RNA interference significantly boosted EMCV production in interferon-treated cells. These findings indicate the mechanism by which PML confers resistance to EMCV. They also reveal a new pathway mediating the antiviral activity of interferon against EMCV.
Dysfunction of Autophagy Participates in Vacuole Formation and Cell Death in Cells Replicating Hepatitis C Virus
Authors: Taguwa Shuhei , Kambara Hiroto , Fujita Naonobu , Noda Takeshi , Yoshimori Tamotsu , Koike Kazuhiko , Moriishi Kohji , Matsuura Yoshiharu
Published: October 2011

Hepatitis C virus (HCV) is a major cause of chronic liver diseases. A high risk of chronicity is the major concern of HCV infection, since chronic HCV infection often leads to liver cirrhosis and hepatocellular carcinoma. Infection with the HCV genotype 1 in particular is considered a clinical risk factor for the development of hepatocellular carcinoma, although the molecular mechanisms of the pathogenesis are largely unknown. Autophagy is involved in the degradation of cellular organelles and the elimination of invasive microorganisms. In addition, disruption of autophagy often leads to several protein deposition diseases. Although recent reports suggest that HCV exploits the autophagy pathway for viral propagation, the biological significance of the autophagy to the life cycle of HCV is still uncertain. Here, we show that replication of HCV RNA induces autophagy to inhibit cell death. Cells harboring an HCV replicon RNA of genotype 1b strain Con1 but not of genotype 2a strain JFH1 exhibited an incomplete acidification of the autolysosome due to a lysosomal defect, leading to the enhanced secretion of immature cathepsin B. The suppression of autophagy in the Con1 HCV replicon cells induced severe cytoplasmic vacuolation and cell death. These results suggest that HCV harnesses autophagy to circumvent the harmful vacuole formation and to maintain a persistent infection. These findings reveal a unique survival strategy of HCV and provide new insights into the genotype-specific pathogenicity of HCV.
Structural Characterization of the Viral and cRNA Panhandle Motifs from the Infectious Salmon Anemia Virus
Authors: Brinson Robert G. , Szakal Andrea L. , Marino John P.
Published: October 2011

Infectious salmon anemia virus (ISAV) has emerged as a virus of great concern to the aquaculture industry since it can lead to highly contagious and lethal infections in farm-raised salmon populations. While little is known about the transcription/replication cycle of ISAV, initial evidence suggests that it follows molecular mechanisms similar to those found in other orthomyxoviruses, which include the highly pathogenic influenza A (inf A) virus. During the life cycle of orthomyxoviruses, a panhandle structure is formed by the pairing of the conserved 5′ and 3′ ends of each genomic RNA. This structural motif serves both as a promoter of the viral RNA (vRNA)-dependent RNA polymerase and as a regulatory element in the transcription/replication cycle. As a first step toward characterizing the structure of the ISAV panhandle, here we have determined the secondary structures of the vRNA and the cRNA panhandles on the basis of solution nuclear magnetic resonance (NMR) and thermal melting data. The vRNA panhandle is distinguished by three noncanonical U·G pairs and one U·U pair in two stem helices that are linked by a highly stacked internal loop. For the cRNA panhandle, a contiguous stem helix with a protonated C·A pair near the terminus and tandem downstream U·U pairs was found. The observed noncanonical base pairs and base stacking features of the ISAV RNA panhandle motif provide the first insight into structural features that may govern recognition by the viral RNA polymerase.
Site-Specific Proteolytic Cleavage of the Amino Terminus of Herpes Simplex Virus Glycoprotein K on Virion Particles Inhibits Virus Entry
Authors: Jambunathan Nithya , Chowdhury Sona , Subramanian Ramesh , Chouljenko Vladimir N. , Walker Jason D. , Kousoulas Konstantin G.
Published: October 2011

Herpes simplex virus 1 (HSV-1) glycoprotein K (gK) is expressed on virions and functions in entry, inasmuch as HSV-1(KOS) virions devoid of gK enter cells substantially slower than is the case for the parental KOS virus (T. P. Foster, G. V. Rybachuk, and K. G. Kousoulas, J. Virol. 75:12431–12438, 2001). Deletion of the amino-terminal 68-amino-acid (aa) portion of gK caused a reduction in efficiency and kinetics of virus entry similar to that of the gK-null virus in comparison to the HSV-1(F) parental virus. The UL20 membrane protein and gK were readily detected on double-gradient-purified virion preparations. Immuno-electron microscopy confirmed the presence of gK and UL20 on purified virions. Coimmunoprecipitation experiments using purified virions revealed that gK interacted with UL20, as has been shown in virus-infected cells (T. P. Foster, V. N. Chouljenko, and K. G. Kousoulas, J. Virol. 82:6310–6323, 2008). Scanning of the HSV-1(F) viral genome revealed the presence of a single putative tobacco etch virus (TEV) protease site within gD, while additional TEV predicted sites were found within the UL5 (helicase-primase helicase subunit), UL23 (thymidine kinase), UL25 (DNA packaging tegument protein), and UL52 (helicase-primase primase subunit) proteins. The recombinant virus gDΔTEV was engineered to eliminate the single predicted gD TEV protease site without appreciably affecting its replication characteristics. The mutant virus gK-V5-TEV was subsequently constructed by insertion of a gene sequence encoding a V5 epitope tag in frame with the TEV protease site immediately after gK amino acid 68. The gK-V5-TEV, R-gK-V5-TEV (revertant virus), and gDΔTEV viruses exhibited similar plaque morphologies and replication characteristics. Treatment of the gK-V5-TEV virions with TEV protease caused approximately 32 to 34% reduction of virus entry, while treatment of gDΔTEV virions caused slightly increased virus entry. These results provide direct evidence that the gK and UL20 proteins, which are genetically and functionally linked to gB-mediated virus-induced cell fusion, are structural components of virions and function in virus entry. Site-specific cleavage of viral glycoproteins on mature and fully infectious virions utilizing unique protease sites may serve as a generalizable method of uncoupling the roles of viral glycoproteins in virus entry and virion assembly.
Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion
Authors: Bose Sayantan , Welch Brett D. , Kors Christopher A. , Yuan Ping , Jardetzky Theodore S. , Lamb Robert A.
Published: October 2011

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 Å, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.
Prevalence and characterisation of, and producers' attitudes towards, hock lesions in UK dairy cattle
Authors: Potterton S. L. , Green M. J. , Millar K. M. , Brignell C. J. , Harris J. , Whay H. R. , Huxley J. N.
Published: October 2011

The objectives of this paper were to characterise lesions found at the hock and to establish their prevalence across a large sample of dairy cows in the UK. In addition, the study aimed to examine farmers' perceptions of these lesions. Seventy‐seven farms were visited; both hocks on a random sample of approximately 50 cows were scored on a categorical scale for hair loss, ulceration and swelling. In addition, the size and location of lesions were marked on a hock map. A questionnaire designed to explore attitudes towards lesions was conducted with the owner. Hair loss and ulceration were seen at five locations. Hair loss was identified on 5,619 of 6,896 hocks (mild: 43.7 per cent; moderate: 25.1 per cent; severe: 12.6 per cent) and 1,137 of 6,896 hocks had areas of ulceration (mild: 8.6 per cent; moderate: 5.8 per cent; severe: 2.1 per cent). The majority of lesions were small; however, a small proportion had extensive areas of hair loss (maximum size 113.3 cm2) and ulceration (maximum size 95.5 cm2). Moderate swelling was recorded on 20 per cent of hocks, and 2.0 per cent had severe swelling. Interview results suggested that more than 90 per cent of participants were aware of hock lesions and a third had sought treatment for them; most felt that lesions had at least some impact on productivity and welfare.
Palaeomagnetic results from Upper Triassic red-beds and CAMP lavas of the Argana Basin, Morocco
Authors: Deenen Martijn , Langereis Cor , Krijgsman Wout , Hachimi Hind El , Chellai El Hassane
Published: October 2011

The continental Argana Basin of Morocco is the trans-Atlantic counterpart of the extensively studied Fundy, Hartford and Newark basins in north-eastern America, that have provided the astrochronologically tuned geomagnetic polarity timescale (GPTS) for the late Triassic and earliest Jurassic. The Argana red-bed successions also show astronomically driven time control, which allowed trans-Atlantic correlations and revealed that the interval towards volcanism of the Central Atlantic Magmatic Province (CAMP) is without any significant hiatuses. Here, we present palaeomagnetic results from the cyclically bedded upper Triassic red-beds and the intercalated volcanics associated with CAMP. Our composite Argana section comprises an interval of 3.5–4.0 Ma, but its magnetostratigraphic pattern does not allow a straightforward correlation to the Newark GPTS. The continental red-bed deposits of the Bigoudine Formation demonstrate a dominant magnetic overprint that could only be removed at temperatures above 600 °C. We suggest that this overprint could have been caused by a period of (Jurassic,
c
. 170 Ma) magmatism that caused pervasive overprinting of the Triassic palaeomagnetic signal. Correlations between the sections in the Tazantoute region are not straightforward, hampered by the presence of a magmatic sill. The CAMP lava sequences of Tazantoute are all of normal polarity and record secular variation in a manner that agrees with short-lived pulses of CAMP activity in Morocco. Our results indicate that the sedimentary successions of the Argana Basin have the potential to evaluate the Newark GPTS, but that detailed palaeomagnetic analyses of more suitable sections with long(er) cyclostratigraphic records are required.
Towards a better understanding of African topography: a review of passive-source seismic studies of the African crust and upper mantle
Authors: Fishwick Stewart , Bastow Ian D.
Published: October 2011

Explaining the cause and support of Africa's varied topography remains a fundamental question for our understanding of the long-term evolution of the continent. As geodynamical modelling becomes more frequently used to investigate this problem, it is important to understand the seismological results that can be incorporated into these models. Crustal thickness estimates are crucial for calculating components of topography that are isostatically compensated. Variations in seismic velocity help constrain variations in subsurface temperature and density and thus buoyancy; measurements of anisotropy can also be used to determine the contribution of the mantle flow field to dynamic topography. In this light, we review the results of passive seismic studies across Africa. At the continental scale there are significant differences in crustal models, meaning large uncertainties in corrections for isostatic topography. In east Africa, multiple seismic experiments have provided firm constraints on crustal and mantle structure. Tomographic images illuminate a broad (
c.
500 km wide) low-velocity region in the upper mantle, with possible connection to the African Superplume in the lower mantle. These observations, alongside the variations in radial anisotropy, strongly suggest that the mantle flow field contributes significantly to the uplift of the region. Beneath southern Africa, low velocities are observed near the base of the continental lithosphere; the depth to transition zone discontinuities however suggests that they are not linked to the superplume beneath. It is thus less clear what role the sublithospheric mantle plays in supporting the region's high topography. Many of Africa's secondary topographic features (e.g. Atlas, Hoggar, Bie Dome) are underlain by slow velocities at depths of 100–150 km and are adjacent to rapid changes in lithospheric thickness. Whether these variations in lithospheric structure promote small-scale convection or simply guide the larger-scale mantle flow field remains ambiguous.
Tectonic evolution of the Central Steep Zone, Axum area, northern Ethiopia: inferences from magnetic and geochemical data
Authors: De Wall Helga , Dietl Carlo , Jungmann Olga , Tegene Ashenafi T. , Pandit Manoj K.
Published: October 2011

Northern Ethiopia is marked by a fanning system of thrust planes with NW-dipping structures in the east and southeast-dipping in the west. The central zone of this large-scale (200 km long) structure is formed by a
c.
10 km wide zone of localized strain and amphibolites facies metamorphic conditions (680 °C and 3.4 kbar) referred to as the Central Steep Zone (CSZ). The CSZ comprises a mafic rock assemblage of amphibolite, serpentinite showing ocean-floor characteristics and calc-silicate schist. A monzonite intrusion in the central part of the CSZ post-dates the deformation and is related to partial melting of the mafic rocks. Magnetic fabric measurements reveal NE-trending (043°) steep foliations in the CSZ with vertical orientation of lineation, parallel to the axes of micro-folds. This high-strain zone is interpreted as central zone of a positive flower structure on the basis of simultaneous flattening and shear movement, typical for transpressive kinematics. The CSZ has a northern continuation into the Nafka terrane of Eritrea where it can be traced over a distance of 200 km. This high-strain belt forms a major structure in the context of Arabian–Nubian Shield (ANS) collision tectonics during the closure of the Mozambique Ocean and assembly of Gondwana.
Constraining the timing of deformation in the southwestern Central Zone of the Damara Belt, Namibia
Authors: Longridge L. , Gibson R. L. , Kinnaird J. A. , Armstrong R. A.
Published: October 2011

Structural investigations and U–Pb sensitive high-resolution ion microprobe (SHRIMP) dating of rocks from the southwestern Central Zone of the Damara Belt, Namibia, reveal that a major SE-verging deformation event (D2) occurred at between 520 and 508 Ma. During D2, SE-verging simple shear and NE–SW pure shear extension in a constrictional stress field produced recumbent, south- to SE-verging, kilometre-scale folds and ductile shear zones, a NE–SW extensional lineation and conjugate shear bands, and was coeval with granitoid emplacement and high-grade metamorphism. The timing of this event is constrained by anatectic leucosomes in D2 shear zones (511±18 Ma) and extensional shear bands (508.4±8.7 Ma) as well as by syntectonic grey granites (520.4±4.2 Ma), and is similar to ages for high-grade metamorphism in the Central Zone. An upright folding event (D3) occurred at
c
. 508 Ma, resulting in the formation of basement-cored fold interference domes. The timing of deformation and metamorphism at 520–508 Ma in the mid-crustal SW Central Zone contrasts with ages of 560–540 Ma for shallow crustal NW-verging folding and thrusting elsewhere in the Central Zone that was concomitant with voluminous magmatism. This magmatism led to metamorphism and anatexis of the basement and the emplacement of anatectic red granites at 539±17 to 535.6±7.2 Ma, which contain 1013±21 Ma inherited zircons. The Central Zone therefore contains a record of crustal thickening, heating of the mid-crust, exhumation and orogen-parallel extension over the life of an orogen.