bluuebunny/crossref_metadata_2025 huggingface dataset:
Shade avoidance
Authors: Franklin Keara A.
Published: June 2008

The threat to plant survival presented by light limitation has driven the evolution of highly plastic adaptive strategies to either tolerate or avoid shading by neighbouring vegetation. When subject to vegetational shading, plants are exposed to a variety of informational signals, which include altered light quality and a reduction in light quantity. The former includes a decrease in the ratio of red to far‐red wavelengths (low R : FR) and is detected by the phytochrome family of plant photoreceptors. Monitoring of R : FR ratio can provide an early and unambiguous warning of the presence of competing vegetation, thereby evoking escape responses before plants are actually shaded. The molecular mechanisms underlying physiological responses to alterations in light quality have now started to emerge, with major roles suggested for the PIF (PHYTOCHROME INTERACTING FACTOR) and DELLA families of transcriptional regulators. Such studies suggest a complex interplay between endogenous and exogenous signals, mediated by multiple photoreceptors. The phenotypic similarities between physiological responses habitually referred to as ‘the shade avoidance syndrome’ and other abiotic stress responses suggest plants may integrate common signalling mechanisms to respond to multiple perturbations in their natural environment.

ContentsSummary930I.Introduction931II.Shade avoidance responses932III.Photoreceptor regulation of shade avoidance932IV.Molecular mechanisms in shade avoidance signalling934V.Crosstalk in shade avoidance signalling939VI.Future perspectives940Acknowledgements940References940
Hybridity and Change: Gamonales, Montoneros and Young Politicos in South‐Central Peru
Authors: RONSBO HENRIK
Published: June 2008

The article provides an analysis of three historical forms of political subjectivity in South‐Central Peru: the montoneros, the gamonales and the post‐conflict politicos. Based upon a historical sociology of puna–valley relations, the article suggests that subjectivities should be read not as emanating from either side of the racialised misti–Indio divide, but instead as fractals of this.
Thrombocytopenia in Patients Treated with Heparin, Combination Antiplatelet Therapy, and Intra‐Aortic Balloon Pump Counterpulsation
Authors: BREAM‐ROUWENHORST HEATHER R. , HOBBS RYAN A. , HORWITZ PHILLIP A
Published: June 2008

Objectives:

Determine the incidence and timing of intra‐aortic balloon pump (IABP)‐associated thrombocytopenia, if concomitant antiplatelet agents increase the incidence of thrombocytopenia, and the incidence of heparin‐induced thrombocytopenia (HIT) in a contemporary IABP population.

Background:

Previous studies predate the current practice of treating acute coronary syndrome patients with heparin and aspirin plus thienopyridines and glycoprotein IIb/IIIa receptor antagonists such that data are unavailable to determine if their co‐administration worsens IABP‐associated thrombocytopenia.

Methods:

A retrospective cohort study of adult IABP patients (n = 107) from 2002 to 2006 was performed to determine the indication for and duration of counterpulsation, platelet counts during and for 7 days postcounterpulsation, medications potentially contributing to thrombocytopenia, and HIT antibody results if obtained.

Results:

Thrombocytopenia, defined as platelets <150,000/mL or >50% decrease from baseline, occurred in 57.9% of patients. Overall, platelets declined to 60.2 ± 22.8% of baseline with the mean (± standard deviation) nadir on day 2.8 ± 2.0. Comparing patients who received heparin, aspirin, thienopyridines, and glycoprotein IIb/IIIa antagonists (n = 44) versus heparinized patients ± aspirin (n = 45), platelet nadirs were 62.7 ± 20.9% versus 58.3 ± 23.9% of baseline levels, respectively (P = 0.42). The incidence of HIT was 2.8% in the entire cohort.

Conclusions:

IABP‐associated thrombocytopenia occurred in 57.9% of this cohort. HIT was diagnosed in 2.8% and should be considered as a diagnosis if platelet counts do not stabilize or continue to fall after 3–4 days of counterpulsation. Increased use of antiplatelet therapy does not impact the degree of thrombocytopenia although the current practice of prompt IABP removal may offset this effect.
Clustering in the Presence of Scatter
Authors: Maitra Ranjan , Ramler Ivan P.
Published: June 2008

Summary:  A new methodology is proposed for clustering datasets in the presence of scattered observations. Scattered observations are defined as unlike any other, so traditional approaches that force them into groups can lead to erroneous conclusions. Our suggested approach is a scheme which, under assumption of homogeneous spherical clusters, iteratively builds cores around their centers and groups points within each core while identifying points outside as scatter. In the absence of scatter, the algorithm reduces to k‐means. We also provide methodology to initialize the algorithm and to estimate the number of clusters in the dataset. Results in experimental situations show excellent performance, especially when clusters are elliptically symmetric. The methodology is applied to the analysis of the United States Environmental Protection Agency's Toxic Release Inventory reports on industrial releases of mercury for the year 2000.
Immunohistochemical demonstration of D2‐40 in basal cell carcinomas of the skin
Authors: Ishida Mitsuaki , Kushima Ryoji , Okabe Hidetoshi
Published: June 2008

Background:  Recently, immunoreactivity to D2‐40, a monoclonal antibody to lymphatic endothelium, was shown in a subgroup of epidermal basal cells and the majority of squamous cell carcinomas, but the immunoreactivity to this antibody has not been examined in basal cell carcinomas (BCCs) of the skin.

Methods:  Expression of D2‐40 was analyzed together with that of cytokeratin (CK) 17, CK 19, CD34 and Ber‐EP4 by immunohistochemical methods in 10 non‐neoplastic skin tissue samples and 20 BCCs.

Results:  Immunoreactivity to D2‐40 was shown in the basal cells at the outer root sheath (ORS) of hair follicles, similar to the CK 19 expression pattern. CK 17 was strongly expressed in the suprabasal cells at the ORS. D2‐40 and CK 19 were focally expressed in 13/20 (65%) and 14/20 (70%) cases of BCCs, respectively, although the distributions of D2‐40 and CK 19 immunoreactivity were not always identical. However, BCC cells were constantly positive for CK 17 even tumor cells that were positive for D2‐40 and/or CK 19. Ber‐EP4 was diffusely expressed in all BCCs, and CD34 was focally expressed in 2/20 cases.

Conclusion:  Our results suggested that D2‐40 immunoreactivity in BCCs showed differentiation toward the ORS of hair follicles.
Molluscum‐like cutaneous cryptococcosis: a histopathological and pathogenetic appraisal
Authors: Ramdial Pratistadevi K. , Calonje Eduardo , Sing Yetish , Chotey Nivesh A. , Aboobaker Jamila
Published: June 2008

Background:  Molluscum‐like cutaneous cryptococcosis (MLCC) is characterized by hypopigmented or skin‐colored papules with central umbilication. The histomorphological nuances of Cryptococcus neoformans infection that effect mimicry of molluscum contagiosum are undocumented. This histopathological study was undertaken to assess the histopathological characteristics of MLCC and to determine potential evolutionary pathogenetic mechanisms and significance.

Methods:  A 5‐year retrospective re‐appraisal of cutaneous cryptococcosis biopsies with a clinical molluscum‐like appearance.

Results:  All 26 specimens with a molluscum‐like appearance showed a dome‐shaped architecture with central invagination and dermal C. neoformans of varying size and shape, with capsular fragmentation; 20 biopsies had a paucireactive appearance and 6 combined granulomatous and paucireactive foci. Twenty, two and four biopsies showed transepidermal, transfollicular and combined transepidermal and transfollicular elimination (TFE) of fungi, necrobiotic collagen and debris through the central invagination, respectively. Subepithelial neutrophils and collagen necrobiosis were identified in 8 and 14 cases each, respectively. Varying sized and shaped yeasts, capsules of varying width, capsular fragmentation and collagen necrobiosis were ultrastructurally confirmed.

Conclusion:  Transepithelial and TFE of C. neoformans, necrobiotic collagen, inflammatory cells and cellular debris account for the morphological attributes of MLCC. The eliminatory process is a potential public health hazard, serving as a vehicle for C. neoformans transfer to the exterior.
Comparative Policy Brief: Status of Intellectual Disabilities in the Republic of Haiti
Authors: Jacobson Erik
Published: June 2008

Abstract  An estimated 800,000 persons have disabilities in Haiti, but there are no data that refer specifically to those with intellectual disabilities. Traditional fears and stigma about disability are widespread. While the constitution supports the idea that people with disabilities should have autonomy and education, there are no laws to mandate implementation, nor is there a comprehensive strategy in place to promote social inclusion. Children with intellectual disabilities share the challenges faced by all children in Haiti where primary school enrollment covers just two‐thirds of all school‐aged children, rural areas lack any schools, and families are too poor to pay for uniforms or books or to release their children from work in order to attend school. For various social and economic reasons, most children with disabilities do not receive specialized education or social rehabilitation services, and some with more severe levels of disability may reside in institutions. In the absence of any welfare benefits, or laws mandating education or vocational training, adults with intellectual disabilities rely on their families or, if they cannot provide care, asylums or nursing homes. Against a background of economic and political instability, three key issues related to Haitians with intellectual disabilities are wider access to education; provision of specialized teaching for children and life‐skills training for adults; and co‐coordinated efforts to raise awareness and encourage more positive attitudes.
Comparative Policy Brief: Status of Intellectual Disabilities in Nepal
Authors: Crishna Brinda , Prajapati Surya Bhakta
Published: June 2008

Abstract  In Nepal, the estimates of the prevalence of disabilities vary, and there is sparse information specifically about people with intellectual disabilities (ID). Existing data suggest higher rates of prevalence of ID in the more remote northern area due to use of non‐iodized salt, lack of health facilities, and extreme poverty. Superstitious beliefs about the causes of ID are widespread. The most recent government plans addressing the situation of Nepalese people with disabilities endorse more robust data, coordination of ministries, allowances at local level, free education, and establishment of treatment centers. The government has also endorsed a policy of inclusive education: reports suggest that many children with ID have been integrated into mainstream schools. Many nongovernmental and governmental organizations have adopted community‐based rehabilitation as the leading model of intervention in the disability sector. Only a few families receive a government monthly allowance in support of their child with ID, and there are only a few government‐run homes for people with ID. A handful of sheltered workshops are located in larger towns, providing for a very small number of adults. Key issues are raising awareness and understanding about ID; development of care and rehabilitation programs specifically for people with ID; and a system to provide livelihood, employment, and some social security for adults.
A systematic review and meta‐analysis of the role of positron emission tomography in the follow up of head and neck squamous cell carcinoma following radiotherapy or chemoradiotherapy
Authors: Isles M.G. , McConkey C. , Mehanna H.M.
Published: June 2008

Objectives:  This review examines the effectiveness of positron emission tomography (PET) in the detection of recurrent or persistent head and neck squamous cell carcinoma after radiotherapy or chemoradiotherapy.

Design:  A systematic review and meta‐analysis of trials of PET for detecting residual/recurrent head and neck squamous cell carcinoma treated by radiotherapy or chemoradiotherapy. Trials were quality assessed using the Quality Assessment of Diagnostic Accuracy Studies tool for assessing diagnostic accuracy studies. Quantitative data were extracted and a bivariate random effects model used to calculate pooled sensitivity and specificity.

Setting:  Tertiary referral head and neck centre.

Participants:  Prospective and retrospective studies, excluding reviews, which included patients with head and neck squamous cell carcinoma who had fluorodeoxyglucose PET in the post‐treatment phase following primary treatment by radiotherapy or chemoradiotherapy.

Main outcomes measures:  Quality assessment, sensitivity, specificity, false positive rates, false negative rates, positive and negative predictive values.

Results:  Twenty‐seven of 1871 identified studies were eligible for inclusion. The pooled sensitivity and specificity of PET for detecting residual or recurrent head and neck squamous cell carcinoma were 94% [95% confidence interval (CI), 87–97%] and 82% (95% CI, 76–86%) respectively. Positive and negative predictive values were 75% (95% CI, 68–82%), and 95% (95% CI, 92–97%) respectively. Sensitivity was greater for scans performed 10 weeks or more after treatment.

Conclusions:  Positron emission tomography is highly accurate in this role. However it is less sensitive early after treatment and has poor anatomical detail. PET may reduce the requirement for check endoscopies and planned neck dissections. A protocol for its use in post‐treatment surveillance is proposed.
The tolerance of ambiguity in late cochlear‐implanted pre‐lingually deaf juveniles
Authors: Seifert E. , Kollbrunner J. , Mantokoudis G. , Vischer M. , Kompis M.
Published: June 2008

Objectives:  To examine the ambiguity tolerance, i.e. the ability to perceive new, contradictory and complex situations as positive challenges, of pre‐lingually deafened adolescents who received a cochlear implant after their eighth birthday and to identify those dimensions of ambiguity tolerance which correlate significantly with specific variables of their oral communication.

Design and setting:  Clinical survey at an academic tertiary referral center.

Participants and main outcome measures:  A questionnaire concerning communication and subjectively perceived changes compared to the pre‐cochlear implant situation was completed by 13 pre‐lingually deafened patients aged between 13 and 23 years, who received their cochlear implants between the ages of 8 and 17 years. The results were correlated with the ‘Inventory for Measuring Ambiguity Tolerance’.

Results:  The patients showed a lower ambiguity tolerance with a total score of 134.5 than the normative group with a score of 143.1. There was a positive correlation between the total score for ambiguity tolerance and the frequency of ‘use of oral speech’, as well as between the subscale ‘ambiguity tolerance towards apparently insoluble problems’ and all five areas of oral communication that were investigated. Comparison of two variables of oral communication, which shows a significant difference pre‐ and postoperatively, yields a positive correlation with the subscale ‘ambiguity tolerance towards the parental image’.

Conclusions:  Pre‐lingually deafened juveniles with cochlear implant who increasingly use oral communication seem to regard the limits of a cochlear implant as an interesting challenge rather than an insoluble problem.
Detection of lung tumours in patients with squamous cell carcinoma of the head and neck at the time of presentation
Authors: Ghosh S. , Kumar A. , Roland N. , Tandon S. , Lancaster J. , Jackson S. , Jones A. , Jones H.L. , Hanlon R. , Jones T.
Published: June 2008

Objectives.  Screening for synchronous pulmonary tumours at initial presentation of squamous cell carcinoma of the head and neck is important as detection may alter management. Currently no consensus exists regarding best practice.1 We present the largest series reported, and based on our data propose a pragmatic policy.

Methods.  Retrospective review of the findings of pulmonary imaging performed on all patients presenting with HNSCC between January 1996 and January 2007.

Results.  A total of 1882 patients were identified. Overall 66 (3.5%) presented with synchronous pulmonary tumours (bronchial carcinomas (1.4%), metastases (2.1%). In terms of numbers needed to scan (NNS) to detect one tumour, in the T1N0‐3 group, NNS = 70. For other stages NNS are 25.6, 26.3 and 17.5 for T2N0, T2N+ and T4N+ respectively. NNS for T0N+ lesions is 6.8. Considering site specific data, NNS is 4.6, 20.4, 42.2, 43.3 and 57.5 for oesophagus, hypopharynx, oropharynx, larynx and oral cavity respectively. No synchronous lesions were detected in our nasal cavity/paranasal sinus series (n = 51). Recurrent disease is highly significant for pulmonary lesions (P < 0.005).

Conclusions.  We propose the following protocol. Thoracic CT for all T0 tumours, T2–T4 tumours regardless of N stage, loco‐regional recurrent disease, where signs/symptoms of neoplastic chest disease exist, positive signs on staging CXR. Given that CXR has a NPV of 98.5% it can suffice as an investigation in T1 disease of any site excluding oesophagus, and potentially all lip/oral cavity and nasal cavity/ sinus tumours. If our series was investigated on this basis there would have been a potential cost saving of £61218.

Reference.  1 Jackel M.C., Reischl A. & Huppert P. (2007) Efficacy of radiologic screening for distant metastases and second primaries in newly diagnosed patients with head and neck cancer. Laryngoscope 117, 242–247
The effect of Nutlin‐3 on laryngeal carcinoma cell lines with wild‐type p53: a promising treatment strategy for laryngeal carcinoma
Authors: Arya A.K. , El‐Fert A. , Devlin T. , Jones T.M. , Boyd M.T.
Published: June 2008

Objectives.  Abnormalities of the p53 gene are the commonest mutation found in all human cancers, and evidence suggests this may influence response to chemoradiotherapeutic agents. Nutlin‐3, the small molecule inhibitor of MDM2/p53 interaction, has been shown to be effective in prostate cancer and leukemia by inducing apoptosis in cells with functioning p53. It is this effect that we wished to demonstrate in laryngeal carcinoma.

Methods.  Eight cell lines derived from patients with laryngeal carcinoma were used in this study. Other cell lines from other sites of the head and neck were deliberately excluded to avoid using heterogeneous cell types. The p53 status of the cell lines was determined using direct sequence analysis of the entire coding length of the gene (exons 2–11). Cell lines were treated with Nutlin‐3 for 48 h and surviving cells were counted using the Beckman Coulter Counter. Flow cytometry was used to determine cell cycle characteristics.

Results.  Four cell lines harboured p53 mutations, four contained wild‐type p53. All cell lines with wild type p53 were sensitive to the effects of Nutlin‐3 in a time and dose dependant manner. Cell lines harbouring mutant p53 were resistant to Nutlin‐3. Flow cytometry demonstrated an increase in p53‐dependant apoptosis in responsive cell lines.

Conclusions.  This is the first study to demonstrate that Nutlin‐3 is effective in laryngeal cancer cell lines with wild‐type p53. The clinical application of Nutlin‐3 could provide a new and targeted treatment option for patients with laryngeal carcinoma.
Kinetic and Thermodynamic Parameters for Heat Denaturation of Cry1A(b) Protein from Transgenic Maize (Zea mays)
Authors: De Luis R. , Pérez M.D. , Sánchez L. , Lavilla M. , Calvo M.
Published: June 2008

ABSTRACT:  The effect of heat treatment on the denaturation of Cry1A(b) protein expressed in transgenic maize was studied over a temperature range of 69 to 77 °C. Denaturation of Cry1A(b) protein was measured by the loss of reactivity with its specific antibodies using a sandwich ELISA. The process of denaturation was studied by analyzing the values of inmunoreactive protein after each heat treatment by kinetic analysis. Denaturation of Cry1A(b) protein was best described assuming a reaction order of 1.5. D‐values calculated were 4338, 2350, 1272, 734, and 601 s at 69, 71, 73, 75, and 77 °C, respectively. Z‐value was estimated to be 9.0 °C and the activation energy value was 266.15 kJ/mol. Thermodynamic parameters for the process of denaturation of Cry1A(b) protein were also calculated. The high values of the enthalpy of activation and the positive values of the entropy of activation obtained for Cry1A(b) protein are typical of a reaction in which the denaturation of the protein is the rate‐determining process that predominates over an aggregation process during heating.
Effect of Continuous Flow High‐Pressure Throttling on Rheological and Ultrastructural Properties of Soymilk
Authors: Sivanandan L. , Toledo R.T. , Singh R.K.
Published: June 2008

ABSTRACT:  Soymilk processing uses a filtration or centrifugation step to remove coarse solids in the comminuted soy. The objective was to utilize the whole beans and determine the effect of continuous flow high pressure throttling (CFHPT) process in reducing particle size and narrowing down the particle size distribution. The rheological and ultrastructural properties of such soymilk were also determined. Whole dehulled soybeans and deionized water were ground in a food processor before comminution in a Megatron (process M) or a Fitzmill (process F) or a Stonemill (process S). The comminuted slurry was homogenized at pressures of 69, 103, 138, 207, and 276 MPa using a CFHPT system, heated to 80 °C in a tubular heat exchanger prior to depressurization, and held at elevated temperatures of 97, 106, 114, 131, and 148 °C, respectively, for each applied pressure after throttling. To avoid flashing, back pressure was applied after the holding tube and soymilk was cooled immediately. Process M produced soymilk with smallest particle size and the highest apparent viscosity. All soymilk samples showed non‐Newtonian pseudoplastic flow behavior. Ultrastructural images showed a clear protein network with very small fat globules entrapped in the protein matrix. Particles were uniformly distributed when the highest pressure treatment was applied for process M, which was considered as the best process.
Lead Isotope Homogeneity of NIST SRM 610 and 612 Glass Reference Materials: Constraints from Laser Ablation Multicollector ICP‐MS (LA‐MC‐ICP‐MS) Analysis
Authors: Kent Adam J.R.
Published: June 2008

This contribution presents data for laser ablation multicollector ICP‐MS (LA‐MC‐ICP‐MS) analyses of NIST SRM 610 and 612 glasses with the express purpose of examining the Pb isotope homogeneity of these glasses at the ∼ 100 μm spatial scale, relevant to in situ analysis. Investigation of homogeneity at these scales is important as these glasses are widely used as calibrators for in situ measurements of Pb isotope composition. Results showed that at the levels of analytical uncertainty obtained, there was no discernable heterogeneity in Pb isotope composition of NIST SRM 610 and also most probably for NIST SRM 612. Traverses across the ∼ 1.5 mm glass wafers supplied by NIST, consisting of between 75 and 133 individual measurements, showed no compositional outliers at the two standard deviation level beyond those expected from population statistics. Overall, the measured Pb isotope ratios from individual traverses across NIST SRM 610 and 612 wafers closely approximate single normally‐distributed populations, with standard deviations similar to the average internal uncertainty for individual measurement blocks. Further, Pb isotope ratios do not correlate with Tl/Pb ratios measured during the analysis, suggesting that regions of volatile element depletion (marked by low Tl/Pb) in these glasses are not associated with changes in Pb isotope composition. For NIST SRM 610 there also appeared to be no variation in Pb isotope composition related to incomplete mixing of glass base and trace element spike during manufacture. For NIST SRM 612 there was some dispersion of measured ratios, including some in a direction parallel to the expected mixing line for base‐spike mixing. However, there was no significant correlation parallel to the mixing line. At this time this cannot be unequivocally demonstrated to result from glass heterogeneity, but it is suggested that NIST SRM 610 be preferred for standardising in situ Pb isotope measurements. Data from this study also showed significantly better accuracy and somewhat better precision for ratios corrected for mass bias by external normalisation to Pb isotope ratios measured in bracketing calibrators compared to mass bias corrected via internal normalisation to measured 205Tl/203Tl, although the Tl isotopic composition of both glasses appears to be homogeneous.
Total Sulfur Concentration in Geological Reference Materials by Elemental Infrared Analyser
Authors: Bédard L. Paul , Savard Dany , Barnes Sarah‐Jane
Published: June 2008

Total sulfur is an analyte for which there are few determinations published, despite the fact that it is a very important element (e.g., a major element in most ores, an important gas constituent in global warming, an active participant in acid drainage). Most geological reference materials have very poor quality sulfur results, that is with relative standard deviations (RSD) in the range of 30–50%, even for concentrations over 100 μg g−1 S, which compromises their use as calibrators. In order to provide modern results with low RSD, sulfur was determined in twenty‐nine geological reference materials with a state‐of‐the‐art elemental S/C analyser using metal chips (certified reference materials with a traceability link) and analytical grade sulfur for high concentration samples. Analytical parameters (sample mass, crucible degassing, calibration strategy, etc.) were optimised by testing. Our results agreed with reference material values provided by issuing bodies. Results for CCRMP SY‐2 (129 ± 13 μg g−1 S), which has been proposed as a sulfur reference material, were in agreement with the proposed modern value of 122 ± 3.7 μg g−1 S.
The antidepressant sertraline downregulates Akt and has activity against melanoma cells
Authors: Reddy Kalpana K. , Lefkove Benjamin , Chen Lan Bo , Govindarajan Baskaran , Carracedo Arkaitz , Velasco Guillermo , Carrillo Carol O. , Bhandarkar Sulochana S. , Owens Michael J. , Mechta‐Grigoriou Fatima , Arbiser Jack L.
Published: June 2008

Melanoma is a common malignancy which is poorly responsive to chemotherapy and radiation. One of the major reasons melanoma responds poorly to these modalities is constitutive expression of Akt, which protects against apoptosis. The antidepressant sertraline was found to be a potent cytotoxic agent against A375 human melanoma. To determine the mechanism by which sertraline kills melanoma cells, Western blot analysis of signaling molecules, including phosphorylated Akt, caspase 9 and phospho‐p70 S6 kinase was performed. Finally, the effects of sertraline on A375 xenografts in mice were assessed. Sertaline potently inhibited the phosphorylation of Akt, and caused cell death through induction of endoplasmic reticulum in vitro. Sertraline monotherapy demonstrated activity against A375 xenografts in vivo. Akt is a major cause of resistance of melanoma to current therapy. Antidepressants are commonly used to prevent interferon‐induced depression. Use of antidepressants that decrease Akt may improve the efficacy of interferon and other therapies against melanoma. Further studies are needed to elucidate whether sertraline acts as an Akt inhibitor in melanoma.
Use of Vaxfectin Adjuvant with DNA Vaccine Encoding the Measles Virus Hemagglutinin and Fusion Proteins Protects Juvenile and Infant Rhesus Macaques against Measles Virus
Authors: Pan Chien-Hsiung , Jimenez Gretchen S. , Nair Nitya , Wei Qun , Adams Robert J. , Polack Fernando P. , Rolland Alain , Vilalta Adrián , Griffin Diane E.
Published: June 2008

A measles virus vaccine for infants under 6 months of age would help control measles. DNA vaccines hold promise, but none has provided full protection from challenge. Codon-optimized plasmid DNAs encoding the measles virus hemagglutinin and fusion glycoproteins were formulated with the cationic lipid-based adjuvant Vaxfectin. In mice, antibody and gamma interferon (IFN-γ) production were increased by two- to threefold. In macaques, juveniles vaccinated at 0 and 28 days with 500 μg of DNA intradermally or with 1 mg intramuscularly developed sustained neutralizing antibody and H- and F-specific IFN-γ responses. Infant monkeys developed sustained neutralizing antibody and T cells secreting IFN-γ and interleukin-4. Twelve to 15 months after vaccination, vaccinated monkeys were protected from an intratracheal challenge: viremia was undetectable by cocultivation and rashes did not appear, while two naïve monkeys developed viremia and rashes. The use of Vaxfectin-formulated DNA is a promising approach to the development of a measles vaccine for young infants.
Mutagenesis and Nuclear Magnetic Resonance Analyses of the Fusion Peptide of
Helicoverpa armigera
Single Nucleocapsid Nucleopolyhedrovirus F Protein
Authors: Tan Ying , Jiang Ling , Wang Manli , Yin Feifei , Deng Fei , Liu Maili , Hu Zhihong , Wang Hualin
Published: June 2008

The entry of enveloped viruses into cells is normally mediated by fusion between viral and cellular membranes, in which the fusion peptide plays a crucial role. The fusion peptides of group II nucleopolyhedrovirus (NPV) F proteins are quite conserved, with a hydrophobic region located at the N terminal of the F
1
fragment. For this report, we used mutagenesis and nuclear magnetic resonance (NMR) to study the structure and function of the fusion peptide of the
Helicoverpa armigera
single-nucleocapsid NPV (HearNPV) F protein (HaF). Five mutations in the fusion peptide of HaF, N
1
G, N
1
L, I
2
N, G
3
L, and D
11
L, were generated separately, and the mutated
f
genes were transformed into the
f
-null HearNPV bacmid. The mutations N
1
L, I
2
N, and D
11
L were found to completely abolish the ability of the recombinant bacmids to produce infectious budded virus, while the mutations N
1
G and G
3
L did not. The low-pH-induced envelope fusion assay demonstrated that the N
1
G substitution increased the fusogenicity of HaF, while the G
3
L substitution reduced its fusogenicity. NMR spectroscopy was used to determine the structure of a synthetic fusion peptide of HaF in the presence of sodium dodecyl sulfate micelles at pH 5.0. The fusion peptide appeared to be an amphiphilic structure composed of a flexible coil in the N terminus from N
1
to N
5
, a 3
10
-helix from F
6
to G
8
, a turn at S
9
, and a regular α-helix from V
10
to D
19
. The data provide the first NMR structure of a baculovirus fusion peptide and allow us to further understand the relationship of structure and function of the fusion peptide.
Disparity between Levels of In Vitro Neutralization of Vaccinia Virus by Antibody to the A27 Protein and Protection of Mice against Intranasal Challenge
Authors: Fogg Christiana N. , Americo Jeffrey L. , Earl Patricia L. , Resch Wolfgang , Aldaz-Carroll Lydia , Eisenberg Roselyn J. , Cohen Gary H. , Moss Bernard
Published: June 2008

Immunization with recombinant proteins may provide a safer alternative to live vaccinia virus for prophylaxis of poxvirus infections. Although antibody protects against vaccinia virus infection, the mechanism is not understood and the selection of immunogens is daunting as there are dozens of surface proteins and two infectious forms known as the mature virion (MV) and the enveloped virion (EV). Our previous studies showed that mice immunized with soluble forms of EV membrane proteins A33 and B5 and MV membrane protein L1 or passively immunized with antibodies to these proteins survived an intranasal challenge with vaccinia virus. The present study compared MV protein A27, which has a role in virus attachment to glycosaminoglycans on the cell surface, to L1 with respect to immunogenicity and protection. Although mice developed similar levels of neutralizing antibody after immunizations with A27 or L1, A27-immunized mice exhibited more severe disease upon an intranasal challenge with vaccinia virus. In addition, mice immunized with A27 and A33 were not as well protected as mice receiving L1 and A33. Polyclonal rabbit anti-A27 and anti-L1 IgG had equivalent MV-neutralizing activities when measured by the prevention of infection of human or mouse cells or cells deficient in glycosaminoglycans or by adding antibody prior to or after virus adsorption. Nevertheless, the passive administration of antibody to A27 was poorly protective compared to the antibody to L1. These studies raise questions regarding the basis for antibody protection against poxvirus disease and highlight the importance of animal models for the early evaluation of vaccine candidates.
Molecular Characterization of the Heparin-Dependent Transduction Domain on the Capsid of a Novel Adeno-Associated Virus Isolate, AAV(VR-942)
Authors: Schmidt Michael , Govindasamy Lakshmanan , Afione Sandra , Kaludov Nick , Agbandje-McKenna Mavis , Chiorini John A.
Published: June 2008

A new adeno-associated virus (AAV), referred to as AAV(VR-942), has been isolated as a contaminant of adenovirus strain simian virus 17. The sequence of the
rep
gene places it in the AAV serotype 2 (AAV2) complementation group, while the capsid is only 88% identical to that of AAV2. High-level AAV(VR-942) transduction activity requires cell surface heparan sulfate proteoglycans, although AAV(VR-942) lacks residues equivalent to the AAV2 R585 and R588 amino acid residues essential for mediating the interaction of AAV2 with the heparan sulfate proteoglycan receptor. Instead, AAV(VR-942) uses a distinct transduction region. This finding shows that distinct domains on different AAV isolates can be responsible for the same activities.
Interaction of Hepatitis C Virus Nonstructural Protein 5A with Core Protein Is Critical for the Production of Infectious Virus Particles
Authors: Masaki Takahiro , Suzuki Ryosuke , Murakami Kyoko , Aizaki Hideki , Ishii Koji , Murayama Asako , Date Tomoko , Matsuura Yoshiharu , Miyamura Tatsuo , Wakita Takaji , Suzuki Tetsuro
Published: June 2008

Nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) possesses multiple and diverse functions in RNA replication, interferon resistance, and viral pathogenesis. Recent studies suggest that NS5A is involved in the assembly and maturation of infectious viral particles; however, precisely how NS5A participates in virus production has not been fully elucidated. In the present study, we demonstrate that NS5A is a prerequisite for HCV particle production as a result of its interaction with the viral capsid protein (core protein). The efficiency of virus production correlated well with the levels of interaction between NS5A and the core protein. Alanine substitutions for the C-terminal serine cluster in domain III of NS5A (amino acids 2428, 2430, and 2433) impaired NS5A basal phosphorylation, leading to a marked decrease in NS5A-core interaction, disturbance of the subcellular localization of NS5A, and disruption of virion production. Replacing the same serine cluster with glutamic acid, which mimics the presence of phosphoserines, partially preserved the NS5A-core interaction and virion production, suggesting that phosphorylation of these serine residues is important for virion production. In addition, we found that the alanine substitutions in the serine cluster suppressed the association of the core protein with viral genome RNA, possibly resulting in the inhibition of nucleocapsid assembly. These results suggest that NS5A plays a key role in regulating the early phase of HCV particle formation by interacting with core protein and that its C-terminal serine cluster is a determinant of the NS5A-core interaction.
Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors
Authors: Turnbough Charles L. , Switzer Robert L.
Published: June 2008

DNA-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (
pyr
) genes. Instead, bacterial
pyr
gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. Studies with
Escherichia coli
and
Bacillus subtilis pyr
genes reveal a variety of regulatory mechanisms. Transcription attenuation via UTP-sensitive coupled transcription and translation regulates expression of the
pyrBI
and
pyrE
operons in enteric bacteria, whereas nucleotide effects on binding of the PyrR protein to
pyr
mRNA attenuation sites control
pyr
operon expression in most gram-positive bacteria. Nucleotide-sensitive reiterative transcription underlies regulation of other
pyr
genes. With the
E. coli pyrBI
,
carAB
,
codBA
, and
upp-uraA
operons, UTP-sensitive reiterative transcription within the initially transcribed region (ITR) leads to nonproductive transcription initiation. CTP-sensitive reiterative transcription in the
pyrG
ITRs of gram-positive bacteria, which involves the addition of G residues, results in the formation of an antiterminator RNA hairpin and suppression of transcription attenuation. Some mechanisms involve regulation of translation rather than transcription. Expression of the
pyrC
and
pyrD
operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. In
Mycobacterium smegmatis
and other bacteria, PyrR modulates translation of
pyr
genes by binding to their ribosome binding site. Evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.
Evolutionary Persistence of the Molybdopyranopterin-Containing Sulfite Oxidase Protein Fold
Authors: Workun Gregory J. , Moquin Kamila , Rothery Richard A. , Weiner Joel H.
Published: June 2008

The importance of molybdoenzymes is exemplified both by the debilitating and fatal human diseases caused by their deficiency and by their persistence throughout evolution. Here, we show that the protein fold of the molybdopyranopterin-containing domain of sulfite oxidase (the SUOX fold) can be found in all three domains of life. Analyses of sequence data and protein structure comparisons (secondary structure matching) show that the SUOX fold is found in enzymes that have quite distinct macromolecular architectures comprising one or more domains and sometimes subsidiary subunits. These are summarized as follows: (i) animal SUOXs that contain an N-terminal cytochrome
b
5
domain and an SUOX fold fused to a C-terminal dimerization domain; (ii) plant SUOX that contains an SUOX fold fused to a C-terminal dimerization domain; (iii) the YedY protein from
Escherichia coli
, which comprises only the SUOX fold; (iv) the sulfite dehydrogenase from
Starkeya novella
that contains the SUOX fold, a dimerization domain, and an additional
c
-type cytochrome subunit; and (v) the plant-type nitrate reductases, exemplified by that of
Pichia angusta
, that contain an N-terminal SUOX fold, a dimerization domain, a cytochrome
b
5
domain, and a C-terminal NADH binding flavin adenine dinucleotide-containing domain. We used the primary sequences of the proteins containing an SUOX fold to mine 559 sequences of related proteins. A phylogeny of a nonredundant subset of these sequences was generated, and the resultant clades were categorized by sequence motif analyses in the context of the available protein structures. Based on the motif analyses, cladistics, and domain conservations, we are able to postulate a plausible pathway of SUOX fold enzyme evolution.
Ozone exposure, antioxidant genes, and lung function in an elderly cohort: VA normative aging study
Authors: Alexeeff S E , Litonjua A A , Wright R O , Baccarelli A , Suh H , Sparrow D , Vokonas P S , Schwartz J
Published: June 2008

Background:

Ozone (O3) exposure is known to cause oxidative stress. This study investigated the acute effects of O3on lung function in the elderly, a suspected risk group. It then investigated whether genetic polymorphisms of antioxidant genes (heme oxygenase-1 (HMOX1) and glutathioneS-transferase pi (GSTP1)) modified these associations.

Methods:

1100 elderly men from the Normative Aging Study were examined whose lung function (forced vital capacity (FVC) and forced expiratory volume in 1 second (FEV1)) was measured every 3 years from 1995 to 2005. The study genotyped theGSTP1Ile105Val and Ala114Val polymorphisms and the (GT)n repeat polymorphism in theHMOX1promoter, classifying repeats as short (n<25) or long (n⩾25). Ambient O3was measured continuously at locations in the Greater Boston area. Mixed linear models were used, adjusting for known confounders.

Results:

A 15 ppb increase in O3during the previous 48 h was associated with a 1.25% decrease in FEV1(95% CI: −1.96% to −0.54%). This estimated effect was worsened with either the presence of a long (GT)n repeat inHMOX1(−1.38%, 95% CI: −2.11% to −0.65%) or the presence of an allele coding for Val105 inGSTP1(−1.69%, 95% CI: −2.63% to −0.75%). A stronger estimated effect of O3on FEV1was found in subjects carrying both theGSTP1105Val variant and theHMOX1long (GT)n repeat (−1.94%, 95% CI: −2.89% to −0.98%). Similar associations were also found between FVC and O3exposure.

Conclusions:

Our results suggest that O3has an acute effect on lung function in the elderly, and the effects may be modified by the presence of specific polymorphisms in antioxidant genes.
Recent Changes in Age and Size of Chum Salmon (Oncorhynchus keta) in the North Pacific Ocean and Possible Causes
Authors: Ishida Yukimasa , Ito Soto-o , Kaeriyama Masahide , McKinnell Skip , Nagasawa Kazuya
Published: June 2008

Changes in age composition and size of adult chum salmon (Oncorhynchus keta) from rivers in Japan, Russia, and Canada were examined based on body weight and scale measurement data collected from 1953 to 1988. A significant increase in mean age was found in Japanese and Russian stocks after 1970 when the number of Japanese chum salmon began to increase exponentially, but not in the Canadian stock. Significant decreases in mean body weight, mean scale radius, and mean width of the third-year zones of age 4 chum salmon also occurred in Japanese and Russian stocks after 1970. Based on the Japanese salmon research vessel data from 1972 to 1988, significant negative relationships between catch-per-unit-effort and mean body weight of chum salmon were observed in summer in the central North Pacific Ocean where the distribution of Japanese and Russian stocks overlaps. These results suggest that density dependence is one of the possible causes for the recent changes in age and size of chum salmon in the North Pacific Ocean.
Use of Oyster Shell to Enhance Intertidal Habitat and Mitigate Loss of Dungeness Crab (Cancer magister) Caused by Dredging
Authors: Dumbauld Brett R. , Armstrong David A. , McDonald Trent L.
Published: June 2008

Juvenile Dungeness crab (Cancer magister) recruit to intertidal areas in estuaries along the Pacific Northwest coast of the United States in May and June of each year and survive best through their first summer in shell or eelgrass habitat. Experiments were initiated in Grays Harbor, Washington, to investigate the potential of using shell to enhance intertidal crab habitat as a means to augment the crab resource and mitigate losses from the subtidal population that occur during dredging. Experimental plots (225 m2) were constructed prior to crab settlement at each of three intertidal locations using three configurations of oyster shell (heavy layer, light scattering, and small piles of shell). Resulting crab densities were comparable with those found in naturally occurring shell with high numbers (20–60 crab∙m−2) observed during settlement that declined to a relatively stable density of 10 crab∙m−2 in July and August. Crab survival was highest in both heavy and pile configurations, but the heavy shell configuration remained intact the longest. This enhancement experiment has become the impetus for a large-scale (8 ha) mitigation program in 1992 as part of a dredging project completed in 1990 in Grays Harbor.
Manifestation of Lymphocystis Disease in American Plaice (Hippoglossoides platessoides) Exposed to Low Salinities
Authors: Berthiaume L. , Heppell J. , Désy M. , Leblanc L. , Lallier R. , Bailey R. , Dutil J.-D.
Published: June 2008

Lymphocystis disease virus (LDV), an iridovirus, is the aetiological agent of benign skin tumors observed in a wide variety of teleosts. The disease appears ubiquitous, but its manifestation is poorly understood because of the difficulty in isolation and cultivation of the virus in vitro. American plaice (Hippoglossoides platessoides) were trawled in the Gulf of St. Lawrence and acclimatized for at least 6 wk in captivity. Fish were then exposed to lower water salinities and examined regularly over a period of 6 wk. Lymphocystis tumors were recorded and samples prepared for electron microscopy. Statistical analysis revealed a significant increase of the occurrence of tumors in relation to decreases in salinity to 7 g/L and increases of exposure time up to 42 d. Iridoviruses were regularly observed in fish tumors by electron microscopy. Although plaice survived well, low salinities may have caused physiological stress which reactivated a latent iridovirus.
Molecular characteristics of penicillin-binding protein 2b, 2x, and 1a sequences in penicillin-nonsusceptible Streptococcus pneumoniae isolates in Shenyang, China
Authors: Tian Su Fei , Chu Yun Zhuo , Chen Bai Yi
Published: June 2008

The aim of this sudy was to investigate the nature of the amino acid motifs found in penicillin-binding proteins (PBP) 2b, 2x, and 1a of penicillin-nonsusceptible Streptococcus pneumoniae isolates from Shenyang, China, and to obtain information regarding the prevalence of alterations within the motifs or in positions flanking the motifs. For 18 clinical isolates comprising 4 penicillin-susceptible S. pneumoniae, 5 penicillin-intermediate S. pneumoniae, and 9 penicillin-resistant S. pneumoniae. the DNA sequences of PBP2b, PBP2x, and PBP1a transpeptidase domains were determined and then genotyped by multilocus sequence typing. Sequence analysis revealed that most penicillin-nonsusceptible S. pneumoniae isolates (penicillin MIC ≥ 1.5 μg/mL and cefotaxime MIC ≥ 2 μg/mL) shared identical PBP2b, PBP2x, and PBP1a amino acid profiles. Most penicillin-resistant S. pneumoniae isolates were ST320 (4-16-19-15-6-20-1), the double-locus variant of the Taiwan19F-14 clone. This study will serve as a basis for future monitoring of genetic changes associated with the emergence and spread of β-lactam resistance in Shenyang, China.