bluuebunny/crossref_metadata_2025 huggingface dataset:
Untangling the positive genetic correlation between rainbow trout growth and survival
Authors: Vehviläinen Harri , Kause Antti , Kuukka‐Anttila Hanna , Koskinen Heikki , Paananen Tuija
Published: March 2012

Explanations for positive and negative genetic correlations between growth and fitness traits are essential for life‐history theory and selective breeding. Here, we test whether growth and survival display genetic trade‐off. Furthermore, we assess the potential of third‐party traits to explain observed genetic associations. First, we estimated genetic correlations of growth and survival of rainbow trout. We then explored whether these associations are explained by genetic correlations with health, body composition and maturity traits. Analysis included 14 traits across life stages and environments. Data were recorded from 249 166 individuals belonging to 10 year classes of a pedigreed population. The results revealed that rapid growth during grow‐out was genetically associated with enhanced survival (mean rG = 0.17). This resulted because genotypes with less nematode caused cataract grew faster and were more likely to survive. Fingerling survival was not genetically related to weight or to grow‐out survival. Instead, rapid fingerling growth made fish prone to deformations (rG = 0.18). Evolutionary genetics provides a theoretical framework to study variation in genetic correlations. This study demonstrates that genetic correlation patterns of growth and survival can be explained by a set of key explanatory traits recorded at different life stages and that these traits can be simultaneously improved by selective breeding.
Prognostic factors in lung cancer in a defined geographical area over two decades with a special emphasis on gender
Authors: Svensson Gunnar , Ewers Sven‐Börje , Ohlsson Ola , Olsson Håkan
Published: March 2012

Introduction:  Many studies over recent decades report an increasing incidence of lung cancer in female patients. Female gender is often reported as a good prognostic factor.

Objectives:  The aim of the present study was to investigate prognostic factors with a special emphasis on gender.

Methods:  During 1989–2008, 1497 patients in eastern Scania, a part of southern Sweden with 202 000 inhabitants, were referred to one Central Hospital and prospectively registered. All patients were grouped into four 5‐year periods and were analysed for occurrence of lung cancer, patient performance status, types and stages of lung cancer and the relation to gender.

Results:  The incidence of lung cancer more than doubled in women. The proportion of adenocarcinomas increased in females and in males to 57% (P = 0.028) and 42% (P = 0.001), respectively, while the frequency of small cell lung carcinomas (SCLCs) decreased in both genders to approximately 14%. Females had significantly more frequent stage 1 (16.6%) and higher surgery rate (23.1%) than males (12% and 18.2%, respectively). Females showed a higher 5‐year survival rate than males (20.1% and 11.5%, respectively; P < 0.001). Patients with non‐small cell lung carcinoma (NSCLC) had a higher 5‐year survival rate than those with SCLC (16.5% and 7.5%, respectively; P < 0.01); however, there was no significant survival difference in females between NSCLC and SCLC.

Conclusion:  Female patients exhibited longer survival than males for both NSCLC and SCLC, and this was not explained by a higher frequency of stage 1 or surgery in NSCLC.

Please cite this paper as: Svensson G., Ewers S.‐B., Ohlsson O. and Olsson H. Prognostic factors in lung cancer in a defined geographical area over two decades with a special emphasis on gender. Clin Respir J 2013; 7: 91–100.
Historical biogeography of the Angelica group (Apiaceae tribe Selineae) inferred from analyses of nrDNA and cpDNA sequences
Authors: LIAO Chen‐Yang , DOWNIE Stephen R. , YU Yan , HE Xing‐Jin
Published: March 2012

Abstract  Biogeographical patterns and diversification processes of Asia‐centered angiosperm groups have been significantly affected by the multistage uplift of the Himalayas–Tibetan Plateau since the Late Tertiary. The divergence time of the largely East Asian Angelica group (Apiaceae, subfamily Apioideae, tribe Selineae) was initially analyzed using Beast and nrDNA internal transcribed spacer sequence data from 96 representatives of tribe Selineae and relatives. Further analyses of the biogeographical history of the Angelica group were carried out using Beast, S‐Diva, Rasp, and Lagrange on datasets containing all or some of the following loci: nrDNA internal and external transcribed spacers; cpDNA rps16 intron; and cpDNA rps16‐trnK, rpl32‐trnL, and trnL‐trnT intergenic spacers. The results suggested that the Angelica group was originally present in the East Palearctic during the global cooling of the late Middle Miocene (13.6 Mya) and that the Angelica s.s. clade originated in the same region at 10.2 Mya. Subsequent diversifications of the Angelica s.s. clade intensified in the East Palearctic during the middle Late Miocene (10.0–7.0 Mya) and in the eastern Himalayan Zone during the late Pliocene and Pleistocene (<4.0 Mya). These diversifications likely corresponded with plateau uplift‐driven climatic changes. Considering elevational reconstructions, the differential responses to altitude appear to be the primary factor explaining the recent radiation of the group in the eastern Himalayas. The North American species of the Angelica group were retrieved as polyphyletic and their migrations involved six independent dispersals to North America at least since the middle Late Miocene, including four times from northeast Asia and twice from Europe.
Distinctive identification of Cladosporium sphaerospermum and Cladosporium halotolerans based on physiological methods
Authors: KOBAYASHI Naoki , WATANABE Maiko , HARA‐KUDO Yukiko
Published: March 2012

Abstract  We aimed to detect physiological characteristics that clearly varied among the closely‐related Cladosporium sphaerospermum‐like species. We isolated the fungi identified as C. sphaerospermum s.l. based on traditional morphological criteria from various locations and substrata, and redefined this initial identification by the molecular phylogenetic methods. The isolates were identified as only C. sphaerospermum and C. halotolerans. We analyzed the substrate‐utilization of 95 carbon sources using the Biolog system and made statistical comparisons of isolates by their abilities to grow at different osmolarities. The substrate‐utilization patterns separated the isolates into two groups corresponding to the molecular data, and the osmotolerance was different between the species. We first showed that C. sphaerospermum and C. halotolerans were diverse not only at the molecular level but also at the ecological and the physiological levels, by analyzing substrate‐utilization patterns and osmotolerance. Furthermore, we showed the potential utility of the Biolog system for discriminating among closely‐related fugal species.
Perfectionistic Self‐Presentation, Socially Prescribed Perfectionism, and Suicide in Youth: A Test of the Perfectionism Social Disconnection Model
Authors: Roxborough Heather M. , Hewitt Paul L. , Kaldas Janet , Flett Gordon L. , Caelian Carmen M. , Sherry Simon , Sherry Dayna L.
Published: March 2012

The role of interpersonal components of perfectionism in suicide outcomes among youth was assessed and the Perfectionism Social Disconnection Model (PSDM) was tested by determining whether the links between socially prescribed perfectionism (SPP) and perfectionistic self‐presentation (PSP) and suicide outcomes are mediated by experiences of social disconnection, as indicated by social hopelessness and being bullied. PSP, trait perfectionism, suicide outcomes, and experiences of being bullied and social hopelessness were measured in 152 psychiatric outpatient children and adolescents. Correlational tests confirmed that PSP and SPP were associated with suicide outcomes and these interpersonal perfectionism components were associated significantly with bullying and social hopelessness. Support was also obtained for the PSDM. The relationship between the PSP facets, particularly nondisplay of imperfections, and suicide outcomes were mediated by being bullied. Additionally, the relationship between all interpersonal components of perfectionism and suicide risk was mediated by social hopelessness. Theoretical and clinical implications of interpersonal components of perfectionism and social disconnection in suicide outcomes for youth are discussed.
Suicide Mortality of Suicide Attempt Patients Discharged from Emergency Room, Nonsuicidal Psychiatric Patients Discharged from Emergency Room, Admitted Suicide Attempt Patients, and Admitted Nonsuicidal Psychiatric Patients
Authors: Choi Jae W. , Park Subin , Yi Ki K. , Hong Jin P.
Published: March 2012

The suicide mortality rate and risk factors for suicide completion of patients who presented to an emergency room (ER) for suicide attempt and were discharged without psychiatric admission, patients who presented to an ER for psychiatric problems other than suicide attempt and were discharged without psychiatric admission, psychiatric inpatients admitted for suicide attempt, and psychiatric inpatients admitted for other reasons were examined. The records of 3,897 patients who were treated at a general hospital in Seoul, Korea, from July 2003 to December 2006 were reviewed. Forty‐three of the 3,897 subjects died by suicide during the 2.5‐year observation period. Compared to the general Korean population, the suicide mortality rate was 82‐fold higher for suicide attempt patients, admitted; 54‐fold higher for suicide attempt patients, discharged; 21‐fold higher for nonsuicidal patients, admitted; and 11‐fold higher for nonsuicidal patients, discharged. In all four groups, diagnosis of a depressive disorder and suicide attempt at presentation were each significant independent risk factors for suicide completion. These results highlight the need for suicide prevention strategies for depressed patients who present to the ER or are admitted to a psychiatric ward after a suicide attempt.
Inquiry Learning of High School Students Through a Problem‐Based Environmental Health Science Curriculum
Authors: Kang Nam‐Hwa , DeChenne Sue Ellen , Smith Grant
Published: March 2012

The purpose of this study was to examine the degree to which high school students improved their inquiry capabilities in relation to scientific literacy through their experience of a problem‐based environmental health science curriculum. The two inquiry capabilities studied were scientific questioning and approaches to inquiry into their own questions. A total of 129 high school students taught by two teachers in one school wrote responses to environmental health issues at the beginning and at the end of a 10‐week long inquiry curriculum. An additional group of 46 students of one of the two teachers learned an alternative curriculum and participated as a comparison group. The students using the inquiry curriculum performed significantly better than those using the alternative curriculum in posing active inquiry questions and generating hypothesis‐driven approaches to inquiry into their questions. The inquiry curriculum students also improved significantly from the pretest to the posttest in both measures of inquiry capacity. Among the students who were less prepared for inquiry in the beginning, 68% improved inquiry‐questioning capability, while among the students who were more prepared for inquiry, 36% improved in generating hypotheses‐driven approaches. Implications for curriculum design and implementation were provided along with further research suggestions.
Non‐Traditional Preservice Teachers and Their Mathematics Efficacy Beliefs
Authors: Brown Amy Bingham
Published: March 2012

In Florida, recent legislative changes have granted community colleges the ability to offer baccalaureate degrees in education, frequently to non‐traditional students. Based on information obtained from the literature covering preservice teachers' math knowledge, teachers' efficacy beliefs about math, and high‐stakes mathematics testing, a study examined a population of preservice teachers in a new Florida teacher preparation program. The research investigated relationships surrounding non‐traditional preservice teachers' characteristics such as: ages, high‐stakes math failures, lower division mathematics history, and math methods course performance, in relation to their efficacy beliefs about mathematics. Results revealed that preservice teachers' ages, lower division mathematics history, and math methods course performance, did have a significant relationship with their math efficacy beliefs, as measured by the Mathematics Teaching Efficacy Beliefs Instrument (MTEBI); the variable of high‐stakes math failures did not. Additionally, a multiple regression model including the aforementioned variables did predict preservice teachers' MTEBI scores, but did not generalize to the greater population. The findings from this study can assist new teacher preparation programs in isolating variables that identify preservice teachers who are at risk for poor mathematical attitudes; can posit avenues for fostering positive math beliefs in preservice teachers; and can recommend further research in this area.
BASIC REASONS AND FIRST PHILOSOPHY: A COHERENTIST VIEW OF REASONS
Authors: POSTON TED
Published: March 2012

abstract

This paper develops and defends a coherentist account of reasons. I develop three core ideas for this defense: a distinction between basic reasons and noninferential justification, the plausibility of the neglected argument against first philosophy, and an emergent account of reasons. These three ideas form the backbone for a credible coherentist view of reasons. I work toward this account by formulating and explaining the basic reasons dilemma. This dilemma reveals a wavering attitude that coherentists have had toward basic reasons. More importantly, the basic reasons dilemma focuses our attention on the central problems that afflict coherentist views of basic beliefs. By reflecting on the basic reasons dilemma, I formulate three desiderata that any viable coherentist account of basic beliefs must satisfy. I argue that the account on offer satisfies these desiderata.
Parental interest in comprehensive care for children with attentional concerns
Authors: Banasiewicz Ben , Kemper Kathi J
Published: March 2012

Many families seek natural therapies for children. We describe what families want when they seek consultation for natural therapies for children with attention deficit hyperactivity disorder (ADHD). Our objective was to: a) describe the kinds of problems and therapies used by patients presenting with a concern about ADHD; b) assess interest in counselling about health promotion; and c) describe physician recommendations at the initial consultation about conventional and CAM therapies. We reviewed intake forms, physician reports and laboratory studies for new patients seen in an integrative paediatric clinic between January 2010 and June 2011. Of the 75 new patients, 23 (31%) families had concerns about ADHD. Of these, 70% were boys; the average age was 11.2 ± 3.1 years, and 80% received care from specialists. Eleven patients (48%) were taking a prescription medication, but only three (13%) were taking medicine for ADHD; dietary supplements were taken by 12 patients (52%). Most families were interested in health promotion information about diet (87%), exercise (78%), stress management (74%), and sleep (74%). Of 11 patients tested, 82% had low ferritin. Recommendations focused on health promotion (100%), dietary supplements, such as multivitamins/minerals (71%) and omega‐3 fatty acids (82%), and specialist referrals (30%). Families seeking natural therapies for children with ADHD have needs for health promotion and care coordination, which are well addressed using tools and skills already present in the medical home.
Protection against Lethal Leptospirosis after Vaccination with LipL32 Coupled or Coadministered with the B Subunit of Escherichia coli Heat-Labile Enterotoxin
Authors: Grassmann André A. , Félix Samuel R. , Ximendes dos Santos Carolina , Amaral Marta G. , Seixas Neto Amilton C. P. , Fagundes Michel Q. , Seixas Fabiana K. , da Silva Éverton F. , Conceição Fabricio R. , Dellagostin Odir A.
Published: March 2012

Leptospirosis, a worldwide zoonosis, lacks an effective, safe, and cross-protective vaccine. LipL32, the most abundant, immunogenic, and conserved surface lipoprotein present in all pathogenic species ofLeptospira, is a promising antigen candidate for a recombinant vaccine. However, several studies have reported a lack of protection when this protein is used as a subunit vaccine. In an attempt to enhance the immune response, we used LipL32 coupled to or coadministered with the B subunit of theEscherichia coliheat-labile enterotoxin (LTB) in a hamster model of leptospirosis. After homologous challenge with 5× the 50% lethal dose (LD50) ofLeptospira interrogans, animals vaccinated with LipL32 coadministered with LTB and LTB::LipL32 had significantly higher survival rates (P< 0.05) than animals from the control group. This is the first report of a protective immune response afforded by a subunit vaccine using LipL32 and represents an important contribution toward the development of improved leptospirosis vaccines.
Prediction System for Rapid Identification of Salmonella Serotypes Based on Pulsed-Field Gel Electrophoresis Fingerprints
Authors: Zou Wen , Lin Wei-Jiun , Hise Kelley B. , Chen Hung-Chia , Keys Christine , Chen James J.
Published: March 2012

A classification model is presented for rapid identification of
Salmonella
serotypes based on pulsed-field gel electrophoresis (PFGE) fingerprints. The classification model was developed using random forest and support vector machine algorithms and was then applied to a database of 45,923 PFGE patterns, randomly selected from all submissions to CDC PulseNet from 2005 to 2010. The patterns selected included the top 20 most frequent serotypes and 12 less frequent serotypes from various sources. The prediction accuracies for the 32 serotypes ranged from 68.8% to 99.9%, with an overall accuracy of 96.0% for the random forest classification, and ranged from 67.8% to 100.0%, with an overall accuracy of 96.1% for the support vector machine classification. The prediction system improves reliability and accuracy and provides a new tool for early and fast screening and source tracking of outbreak isolates. It is especially useful to get serotype information before the conventional methods are done. Additionally, this system also works well for isolates that are serotyped as “unknown” by conventional methods, and it is useful for a laboratory where standard serotyping is not available.
Ultrarapid Detection of
bla
KPC1/2-12
from Perirectal and Nasal Swabs by Use of Real-Time PCR
Authors: Richter Sara N. , Frasson Ilaria , Biasolo Maria Angela , Bartolini Andrea , Cavallaro Antonietta , Palù Giorgio
Published: March 2012

The novel real-time PCR assay developed as described here was able to detect
bla
KPC1/2-12
(
bla
KPC-1/2
to
bla
KPC-12
) from easily available clinical specimens in less than 2 h. The genotypic assay was highly sensitive (100%) and specific (98%). In some cases, it was able to detect
bla
KPC
48 h before positive detection by standard phenotypic assay on patients who were monitored daily. The high sensitivity and rapidity of the molecular method make it the method of choice for KPC surveillance and, thus, containment purposes.
Mixed Tuberculosis Infections in Rural South Vietnam
Authors: Huyen Mai N. T. , Kremer Kristin , Lan Nguyen T. N. , Cobelens Frank G. J. , Buu Tran N. , Dung Nguyen H. , Caws Maxine , Tiemersma Edine W. , van Soolingen Dick
Published: March 2012

Tuberculosis patients may be infected with or have disease caused by more than one
Mycobacterium tuberculosis
strain, usually referred to as “mixed infections.” These have mainly been observed in settings with a very high tuberculosis incidence and/or high HIV prevalence. We assessed the rate of mixed infections in a population-based study in rural Vietnam, where the prevalences of both HIV and tuberculosis are substantially lower than those in previous studies looking at mixed infections. In total, 1,248
M. tuberculosis
isolates from the same number of patients were subjected to IS
6110
restriction fragment length polymorphism (RFLP) typing, spoligotyping, and variable-number-tandem-repeat (VNTR) typing. We compared mixed infections identified by the presence of (i) discrepant RFLP and spoligotype patterns in isolates from the same patient and (ii) double alleles at ≥2 loci by VNTR typing and assessed epidemiological characteristics of these infections. RFLP/spoligotyping and VNTR typing identified 39 (3.1%) and 60 (4.8%) mixed infections, respectively (Cohen's kappa statistic, 0.57). The number of loci with double alleles in the VNTR pattern was strongly associated with the proportion of isolates with mixed infections according to RFLP/spoligotyping (
P
< 0.001). Mixed infections occurred more frequently in newly treated than in previously treated patients, were significantly associated with minor X-ray abnormalities, and were almost significantly associated with lower sputum smear grades. Although the infection pressure in our study area is lower than that in previously studied populations, mixed
M. tuberculosis
infections do occur in rural South Vietnam in at least 3.1% of cases.
Novel Genetic Variation Identified at Fixed Loci in ORF62 of the Oka Varicella Vaccine and in a Case of Vaccine-Associated Herpes Zoster
Authors: Quinlivan Mark L. , Jensen Nancy J. , Radford Kay W. , Schmid D. Scott
Published: March 2012

The live attenuated Oka varicella vaccine (vOka), derived from clade 2 wild-type (wt) virus pOka, is used for routine childhood immunization in several countries, including the United States, which has caused dramatic declines in the incidence of varicella. vOka can cause varicella, establish latency, and reactivate to cause herpes zoster (HZ). Three loci in varicella-zoster virus (VZV) open reading frame 62 (ORF62) (106262, 107252, and 108111) are used to distinguish vOka from wt VZV. A fourth position (105705) is also fixed for the vOka allele in nearly all vaccine batches. These 4 positions and two vOka mutations (106710 and 107599) reportedly absent from Varivax were analyzed on Varivax-derived ORF62 TOPO TA clones. The wt allele was detected at positions 105705 and 107252 on 3% and 2% of clones, respectively, but was absent at positions 106262 and 108111. Position 106710 was fixed for the wt allele, whereas the vOka allele was present on 18.4% of clones at position 107599. We also evaluated the 4 vOka markers in an isolate obtained from a case of vaccine-caused HZ. The isolate carried the vOka allele at positions 105705, 106262, and 108111. However, at position 107252, the wt allele was present. Thus, all of the ORF62 vOka markers previously regarded as fixed occur as the wt allele in a small percentage of vOka strains. Characterization of all four vOka markers in ORF62 and of the clade 2 subtype marker in ORF38 is now necessary to confirm vOka adverse events.
Bacteriophage ϕ6 Nucleocapsid Surface Protein 8 Interacts with Virus-Specific Membrane Vesicles Containing Major Envelope Protein 9
Authors: Sarin L. Peter , Hirvonen Jari J. , Laurinmäki Pasi , Butcher Sarah J. , Bamford Dennis H. , Poranen Minna M.
Published: March 2012

Enveloped double-stranded RNA (dsRNA) bacterial virus
Pseudomonas
phage ϕ6 has been developed into an advanced assembly system where purified virion proteins and genome segments self-assemble into infectious viral particles, inferring the assembly pathway. The most intriguing step is the membrane assembly occurring inside the bacterial cell. Here, we demonstrate that the middle virion shell, made of protein 8, associates with the expanded viral core particle and the virus-specific membrane vesicle.
West Nile Virus Noncoding Subgenomic RNA Contributes to Viral Evasion of the Type I Interferon-Mediated Antiviral Response
Authors: Schuessler Andrea , Funk Anneke , Lazear Helen M. , Cooper Daphne A. , Torres Shessy , Daffis Stephane , Jha Babal Kant , Kumagai Yutaro , Takeuchi Osamu , Hertzog Paul , Silverman Robert , Akira Shizuo , Barton David J. , Diamond Michael S. , Khromykh Alexander A.
Published: March 2012

We previously showed that a noncoding subgenomic flavivirus RNA (sfRNA) is required for viral pathogenicity, as a mutant West Nile virus (WNV) deficient in sfRNA production replicated poorly in wild-type mice. To investigate the possible immunomodulatory or immune evasive functions of sfRNA, we utilized mice and cells deficient in elements of the type I interferon (IFN) response. Replication of the sfRNA mutant WNV was rescued in mice and cells lacking interferon regulatory factor 3 (IRF-3) and IRF-7 and in mice lacking the type I alpha/beta interferon receptor (IFNAR), suggesting a contribution for sfRNA in overcoming the antiviral response mediated by type I IFN. This was confirmed by demonstrating rescue of mutant virus replication in the presence of IFNAR neutralizing antibodies, greater sensitivity of mutant virus replication to IFN-α pretreatment, partial rescue of its infectivity in cells deficient in RNase L, and direct effects of transfected sfRNA on rescuing replication of unrelated Semliki Forest virus in cells pretreated with IFN-α. The results define a novel function of sfRNA in flavivirus pathogenesis via its contribution to viral evasion of the type I interferon response.
The Intertransmembrane Region of Kaposi's Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation
Authors: Kajikawa Mizuho , Li Pai-Chi , Goto Eiji , Miyashita Naoyuki , Aoki-Kawasumi Masami , Mito-Yoshida Mari , Ikegaya Mika , Sugita Yuji , Ishido Satoshi
Published: March 2012

Kaposi's sarcoma-associated herpesvirus (KSHV), a human tumor virus, encodes two homologous membrane-associated E3 ubiquitin ligases, modulator of immune recognition 1 (MIR1) and MIR2, to evade host immunity. Both MIR1 and MIR2 downregulate the surface expression of major histocompatibility complex class I (MHC I) molecules through ubiquitin-mediated endocytosis followed by lysosomal degradation. Since MIR2 additionally downregulates a costimulatory molecule (B7-2) and an integrin ligand (intercellular adhesion molecule 1 [ICAM-1]), MIR2 is thought to be a more important molecule for immune evasion than MIR1; however, the molecular basis of the MIR2 substrate specificity remains unclear. To address this issue, we determined which regions of B7-2 and MIR2 are required for MIR2-mediated B7-2 downregulation. Experiments with chimeras made by swapping domains between human B7-2 and CD8α, a non-MIR2 substrate, and between MIR1 and MIR2 demonstrated a significant contribution of the juxtamembrane (JM) region of B7-2 and the intertransmembrane (ITM) region of MIR2 to MIR2-mediated downregulation. Structure prediction and mutagenesis analyses indicate that Phe119 and Ser120 in the MIR2 ITM region and Asp244 in the B7-2 JM region contribute to the recognition of B7-2 by MIR2. This finding provides new insight into the molecular basis of substrate recognition by MIR family members.
A Role of Template Cleavage in Reduced Excision of Chain-Terminating Nucleotides by Human Immunodeficiency Virus Type 1 Reverse Transcriptase Containing the M184V Mutation
Authors: Acosta-Hoyos Antonio J. , Matsuura Suzanne E. , Meyer Peter R. , Scott Walter A.
Published: March 2012

Resistance to nucleoside reverse transcriptase (RT) inhibitors is conferred on human immunodeficiency virus type 1 through thymidine analogue resistance mutations (TAMs) that increase the ability of RT to excise chain-terminating nucleotides after they have been incorporated. The RT mutation M184V is a potent suppressor of TAMs. In RT containing TAMs, the addition of M184V suppressed the excision of 3′-deoxy-3′-azidothymidine monophosphate (AZTMP) to a greater extent on an RNA template than on a DNA template with the same sequence. The catalytically inactive RNase H mutation E478Q abolished this difference. The reduction in excision activity was similar with either ATP or pyrophosphate as the acceptor substrate. Decreased excision of AZTMP was associated with increased cleavage of the RNA template at position −7 relative to the primer terminus, which led to increased primer-template dissociation. Whether M184V was present or not, RT did not initially bind at the −7 cleavage site. Cleavage at the initial site was followed by RT dissociation and rebinding at the −7 cleavage site, and the dissociation and rebinding were enhanced when the M184V mutation was present. In contrast to the effect of M184V, the K65R mutation suppressed the excision activity of RT to the same extent on either an RNA or a DNA template and did not alter the RNase H cleavage pattern. Based on these results, we propose that enhanced RNase H cleavage near the primer terminus plays a role in M184V suppression of AZT resistance, while K65R suppression occurs through a different mechanism.
Characterization of Novel Components of the Baculovirus
Per Os
Infectivity Factor Complex
Authors: Peng Ke , van Lent Jan W. M. , Boeren Sjef , Fang Minggang , Theilmann David A. , Erlandson Martin A. , Vlak Just M. , van Oers Monique M.
Published: March 2012

Baculovirus occlusion-derived virus (ODV) infects insect midgut cells under alkaline conditions, a process mediated by highly conserved
per os
infectivity factors (PIFs), P74 (PIF0), PIF1, PIF2, PIF3, PIF4, and PIF5 (ODV-E56). Previously, a multimolecular complex composed of PIF1, PIF2, PIF3, and P74 was identified which was proposed to play an essential role during ODV entry. Recently, more proteins have been identified that play important roles in ODV oral infectivity, including PIF4, PIF5, and SF58, which might work in concert with previously known PIFs to facilitate ODV infection. In order to understand the ODV entry mechanism, the identification of all components of the PIF complex is crucial. Hence, the aim of this study was to identify additional components of the PIF complex. Coimmunoprecipitation (CoIP) combined with proteomic analysis was used to identify the components of the
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) PIF complex. PIF4 and P95 (AC83) were identified as components of the PIF complex while PIF5 was not, and this was confirmed with blue native PAGE and a second CoIP. Deletion of the
pif4
gene impaired complex formation, but deletion of
pif5
did not. Differentially denaturing SDS-PAGE further revealed that PIF4 forms a stable complex with PIF1, PIF2, and PIF3. P95 and P74 are more loosely associated with this complex. Three other proteins, AC5, AC68, and AC108 (homologue of SF58), were also found by the proteomic analysis to be associated with the PIF complex. Finally the functional significance of the PIF protein interactions is discussed.
Identification of the Target Cells and Sequence of Infection during Experimental Infection of Ovine Fetuses with Cache Valley Virus
Authors: Rodrigues Hoffmann Aline , Welsh Christabel Jane , Varner Patricia Wilcox , de la Concha-Bermejillo Andres , Ball Judith Marchand , Ambrus Andy , Edwards John Francis
Published: March 2012

Cache Valley virus-induced malformations have been previously reproduced in ovine fetuses; however, no studies have established the course of infection of cells and tissues with Cache Valley virus. To address these questions, ovine fetuses at 35 days of gestation were inoculatedin uterowith Cache Valley virus and euthanized at 7, 10, 14, 21, and 28 days postinfection. On postmortem examination, arthrogryposis and oligohydramnios were observed in some infected fetuses. Morphological studies showed necrosis in the central nervous system and skeletal muscle of infected fetuses evaluated after 7 to 14 days postinfection, and hydrocephalus, micromyelia, and muscular loss were observed in infected fetuses after 21 to 28 days postinfection. Using immunohistochemistry andin situhybridization, intense Cache Valley virus antigen and RNA staining was detected in the brain, spinal cord, skeletal muscle, and, to a lesser degree, in fetal membranes and other tissues of infected fetuses. Viral antigen and RNA staining decreased in targeted and infected tissues with the progression of the infection.
Myxoma Virus M064 Is a Novel Member of the Poxvirus C7L Superfamily of Host Range Factors That Controls the Kinetics of Myxomatosis in European Rabbits
Authors: Liu Jia , Wennier Sonia , Moussatche Nissin , Reinhard Mary , Condit Richard , McFadden Grant
Published: March 2012

The myxoma virus (MYXV) carries three tandem C7L-like host range genes (M062R, M063R, and M064R). However, despite the fact that the sequences of these three genes are similar, they possess very distinctive functions
in vivo
. The role of M064 in MYXV pathogenesis was investigated and compared to the roles of M062 and M063. We report that M064 is a virulence factor that contributes to MYXV pathogenesis but lacks the host range properties associated with M062 and M063.
Acute and Chronic T Cell Dynamics in the Livers of Simian Immunodeficiency Virus-Infected Macaques
Authors: Ahsan Muhammad H. , Gill Amy F. , Lackner Andrew A. , Veazey Ronald S.
Published: March 2012

The mucosal immune system, particularly the gastrointestinal tract, is critically involved in the pathogenesis of human immunodeficiency virus (HIV) infection. Since the liver drains most of the substances coming from the intestinal tract, it may also play a role in the pathogenesis of HIV infection. Here we examined the percentages and absolute numbers of T cell subsets in the liver in normal and simian immunodeficiency virus (SIV)-infected macaques. Most of the T cells in the liver were CD8
+
memory cells, and most of these had an effector memory (CD95
+
CD28
−
) phenotype. CD4
+
T cells constituted approximately 20% of the liver T cell population, but the vast majority of these were also memory (CD95
+
) CCR5
+
cells, suggesting they were potential targets for viral infection. After SIV infection, CD4
+
T cells were markedly reduced, and increased proliferation and absolute numbers of CD8
+
T cells were detected in the liver. These data suggest that the liver is a major source of antigenic stimulation for promoting CD8
+
T cells and possibly a source for early CD4
+
T cell infection and destruction.
In Vitro
Epsilon RNA-Dependent Protein Priming Activity of Human Hepatitis B Virus Polymerase
Authors: Jones Scott A. , Boregowda Rajeev , Spratt Thomas E. , Hu Jianming
Published: March 2012

Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a pregenomic RNA (pgRNA) by using a multifunctional polymerase (HP). A critical function of HP is its specific recognition of a viral RNA signal termed ε (Hε) located on pgRNA, which is required for specific packaging of pgRNA into viral nucleocapsids and initiation of viral reverse transcription. HP initiates reverse transcription by using itself as a protein primer (protein priming) and Hε as the obligatory template. We have purified HP from human cells that retained Hε binding activity
in vitro
. Furthermore, HP purified as a complex with Hε, but not HP alone, displayed
in vitro
protein priming activity. While the HP-Hε interaction
in vitro
and
in vivo
required the Hε internal bulge, but not its apical loop, and was not significantly affected by the cap-Hε distance, protein priming required both the Hε apical loop and internal bulge, as well as a short distance between the cap and Hε, mirroring the requirements for RNA packaging. These studies have thus established new HBV protein priming and RNA binding assays that should greatly facilitate the dissection of the requirements and molecular mechanisms of HP-Hε interactions, RNA packaging, and protein priming.
Differentiation-Dependent Changes in Levels of C/EBPβ Repressors and Activators Regulate Human Papillomavirus Type 31 Late Gene Expression
Authors: Gunasekharan Vignesh , Haché Guylaine , Laimins Laimonis
Published: March 2012

The liver-enriched transcriptional activator protein (LAP) isoform of CCAAT/enhancer binding protein β (C/EBPβ) is shown to be a major activator of differentiation-dependent human papillomavirus (HPV) late gene expression, while the liver-enriched inhibitory protein (LIP) isoform negatively regulates late expression. In undifferentiated cells, LIPs act as dominant-negative repressors of late expression, and upon differentiation, LIP levels are significantly reduced, allowing LAP-mediated activation of the late promoter. Importantly, knockdown of C/EBPβ isoforms blocks activation of late gene expression from complete viral genomes upon differentiation.
Novel gene rearrangements in the mitochondrial genome of a webspinner, Aposthonia japonica (Insecta: Embioptera)
Authors: Kômoto Natuo , Yukuhiro Kenji , Tomita Shuichiro
Published: March 2012

Webspinners (order Embioptera) are polyneopteran insects characterized by enlarged foretarsi with silk glands, whose silk is used to produce galleries in which the insects live gregariously. The phylogenetic position of webspinners has been debated. In the present study, an almost complete mitochondrial DNA (mtDNA) sequence of Embioptera is reported for the first time. The mtDNA of a webspinner, Aposthonia japonica , has the 13 protein-coding genes (PCGs) generally found in metazoan mtDNA sequences. There is a translocation of a large region including atp6, atp8, cox3, nad3, and nad5 as well as a duplication of the 12S rRNA gene. The rearrangement does not seem to affect nucleotide composition, although amino acid composition in some parts of the mtDNA is biased compared with other Polyneoptera species. Based on phylogenetic analyses using nucleotide sequences of all PCGs concatenated with two rRNA genes and the amino acid sequences of all PCGs, A. japonica is sister to Verophasmatodea, a suborder of typical stick and leaf insects.
Reduction of TIP47 improves hepatic steatosis and glucose homeostasis in mice
Authors: Carr Rotonya M. , Patel Rajesh T. , Rao Vandana , Dhir Ravindra , Graham Mark J. , Crooke Rosanne M. , Ahima Rexford S.
Published: March 2012

Lipid droplets in the liver are coated with the perilipin family of proteins, notably adipocyte differentiation-related protein (ADRP) and tail-interacting protein of 47 kDa (TIP47). ADRP is increased in hepatic steatosis and is associated with hyperlipidemia, insulin resistance, and glucose intolerance. We have shown that reducing ADRP in the liver via antisense oligonucleotide (ASO) treatment attenuates steatosis and improves insulin sensitivity and glucose tolerance. We hypothesized that TIP47 has similar effects on hepatic lipid and glucose metabolism. We found that TIP47 mRNA and protein levels were increased in response to a high-fat diet (HFD) in C57BL/6J mice. TIP47 ASO treatment decreased liver TIP47 mRNA and protein levels without altering ADRP levels. Low-dose TIP47 ASO (15 mg/kg) and high-dose TIP47 ASO (50 mg/kg) decreased triglyceride content in the liver by 35% and 52%, respectively. Liver histology showed a drastic reduction in hepatic steatosis following TIP47 ASO treatment. The high dose of TIP47 ASO significantly blunted hepatic triglyceride secretion, improved glucose tolerance, and increased insulin sensitivity in liver, adipose tissue, and muscle. These findings show that TIP47 affects hepatic lipid and glucose metabolism and may be a target for the treatment of nonalcoholic fatty liver and related metabolic disorders.
Angiotensin II type 2 receptor-coupled nitric oxide production modulates free radical availability and voltage-gated Ca2+currents in NTS neurons
Authors: Wang Gang , Coleman Christal G. , Glass Michael J. , Zhou Ping , Yu Qi , Park Laibaik , Anrather Josef , Pickel Virginia M. , Iadecola Costantino
Published: March 2012

The medial region of the nucleus tractus solitarius (mNTS) is a key brain stem site controlling cardiovascular function, wherein ANG II modulates neuronal L-type Ca2+currents via activation of ANG II type 1 receptors (AT1R) and production of reactive oxygen species (ROS). ANG II type 2 receptors (AT2R) induce production of nitric oxide (NO), which may interact with ROS and modulate AT1R signaling. We sought to determine whether AT2R-mediated NO production occurs in mNTS neurons and, if so, to elucidate the NO source and the functional interaction with AT1R-induced ROS or Ca2+influx. Electron microscopic (EM) immunolabeling showed that AT2R and neuronal NO synthase (nNOS) are coexpressed in neuronal somata and dendrites receiving synapses in the mNTS. In the presence of the AT1R antagonist losartan, ANG II increased NO production in isolated mNTS neurons, an effect blocked by the AT2R antagonist PD123319, but not the angiotensin (1–7) antagonist D-Ala. Studies in mNTS neurons of nNOS-null or endothelial NOS (eNOS)-null mice established nNOS as the source of NO. ANG II-induced ROS production was enhanced by PD123319, the NOS inhibitor NG-nitro-l-arginine (LNNA), or in nNOS-null mice. Moreover, in the presence of losartan, ANG II reduced voltage-gated L-type Ca2+current, an effect blocked by PD123319 or LNNA. We conclude that AT2R are closely associated and functionally coupled with nNOS in mNTS neurons. The resulting NO production antagonizes AT1R-mediated ROS and dampens L-type Ca2+currents. The ensuing signaling changes in the NTS may counteract the deleterious effects of AT1R on cardiovascular function.
Regulation of oxidative phosphorylation complex activity: effects of tissue-specific metabolic stress within an allometric series and acute changes in workload
Authors: Phillips Darci , Covian Raul , Aponte Angel M. , Glancy Brian , Taylor Joni F. , Chess David , Balaban Robert S.
Published: March 2012

The concentration of mitochondrial oxidative phosphorylation complexes (MOPCs) is tuned to the maximum energy conversion requirements of a given tissue; however, whether the activity of MOPCs is altered in response to acute changes in energy conversion demand is unclear. We hypothesized that MOPCs activity is modulated by tissue metabolic stress to maintain the energy-metabolism homeostasis. Metabolic stress was defined as the observed energy conversion rate/maximum energy conversion rate. The maximum energy conversion rate was assumed to be proportional to the concentration of MOPCs, as determined with optical spectroscopy, gel electrophoresis, and mass spectrometry. The resting metabolic stress of the heart and liver across the range of resting metabolic rates within an allometric series (mouse, rabbit, and pig) was determined from MPOCs content and literature respiratory values. The metabolic stress of the liver was high and nearly constant across the allometric series due to the proportional increase in MOPCs content with resting metabolic rate. In contrast, the MOPCs content of the heart was essentially constant in the allometric series, resulting in an increasing metabolic stress with decreasing animal size. The MOPCs activity was determined in native gels, with an emphasis on Complex V. Extracted MOPCs enzyme activity was proportional to resting metabolic stress across tissues and species. Complex V activity was also shown to be acutely modulated by changes in metabolic stress in the heart, in vivo and in vitro. The modulation of extracted MOPCs activity suggests that persistent posttranslational modifications (PTMs) alter MOPCs activity both chronically and acutely, specifically in the heart. Protein phosphorylation of Complex V was correlated with activity inhibition under several conditions, suggesting that protein phosphorylation may contribute to activity modulation with energy metabolic stress. These data are consistent with the notion that metabolic stress modulates MOPCs activity in the heart.
The brain matters: effects of descending signals on motor control
Authors: Mullins Olivia J. , Friesen W. Otto
Published: March 2012

The ability of nerve cords and spinal cords to exhibit fictive rhythmic locomotion in the absence of the brain is well-documented in numerous species. Although the brain is important for modulating the fictive motor output, it is broadly assumed that the functional properties of neuronal circuits identified in simplified preparations are conserved with the brain attached. We tested this assumption by examining the properties of a novel interneuron recently identified in the leech ( Hirudo verbana) nerve cord. This neuron, cell E21, initiates and drives stereotyped fictive swimming activity in preparations of the isolated leech nerve cord deprived of the head brain. We report that, contrary to expectation, the motor output generated when cell E21 is stimulated in preparations with the brain attached is highly variable. Swim frequency and episode duration are increased in some of these preparations and decreased in others. Cell E21 controls swimming, in part, via excitatory synaptic interactions with cells 204, previously identified gating neurons that reliably initiate and strongly enhance leech swimming activity when the brain is absent. We found that in preparations with the brain present, the magnitude of the synaptic interaction from cell E21 to cell 204 is reduced by 50% and that cell 204-evoked responses also were highly variable. Intriguingly, most of this variability disappeared in semi-intact preparations. We conclude that neuronal circuit properties identified in reduced preparations might be fundamentally altered from those that occur in more physiological conditions.
Cautious gait in relation to knowledge and vision of height: is altered visual information the dominant influence?
Authors: Tersteeg M. C. A. , Marple-Horvat Dilwyn E. , Loram Ian D.
Published: March 2012

For some people, visual exposure creates difficulty with movement and balance, yet the mechanisms causing this are poorly understood. The altered visual environment is an obvious possible cause of degraded balance. We studied locomotion in normal healthy adults along a 22-cm-wide walkway at ground level and at a height of 3.5 m. This produced substantial changes in gait progression (velocity reduced by 0.34 ms−1, P <0.01), proportion of time spent in double support more than doubled ( P <0.01), and galvanic skin conductance, a measure of physiological arousal, increased significantly ( P <0.01). Since increasing visual distance is known to destabilize balance, our primary question was whether the disturbing effects of height could be eliminated by replacing sight of the drop with a visual surround comparable to ground level while retaining the danger and knowledge of the risk. Removing visual exposure did not significantly change the gait progression ( P = 0.65) or double support duration ( P = 0.58) but produced a small, significant reduction in physiological arousal ( P = 0.04). In response to postural threat, knowledge of danger rather than current visual environment was the dominant cause of cautious gait and elevated physiological arousal in response to postural threat. We conclude that the mechanisms disturbing locomotion, balance, and autonomic response occur at a high task level which integrates cognition and prior experience with sensory input.