bluuebunny/crossref_metadata_2025 huggingface dataset:
Pb uptake by the freshwater alga Chlorella kesslerii in the presence of dissolved organic matter of variable composition
Authors: Lamenas Cristina , Slaveykova Vera I.
Published: October 2008

Environmental context. Dissolved organic matter (DOM) is of utmost importance for a toxic metal’s fate and ecotoxicity in the aquatic system, but the complex nature and variable composition of DOM makes the quantitative understanding of DOM’s role in the environment very difficult. We have demonstrated that the assumption that the properties of a DOM mixture are the sum of the properties of its individual fractions can capture the main trends characterising the role of DOM in lead speciation and adsorption by freshwater microalgae. This was done by mixing the isolated, well-characterised fractions of DOM and measuring levels of free lead ion and Pb adsorbed and internalised by algae.
Abstract. Dissolved organic matter (DOM) is a complex mixture of ill-defined components, which makes the quantitative understanding of DOM functions in aquatic systems a challenging task. The traditional approach for studying such complex mixtures involves their separation into groups of different components, while assuming minimal or no alteration of their properties. By mixing the pre-isolated and well-characterised individual fractions of the DOM, including humic, fulvic and alginic acids, we have demonstrated that the free Pb ion concentrations and the adsorbed Pb plus Pb internalised by the alga Chlorella kesslerii in the presence of DOM samples of different compositions can be predicted on the basis of the experiments performed in the presence of the individual DOM fractions. An additivity model assuming that the properties of the mixture can be considered as the sum of the properties of the individual components captured the Pb speciation and adsorption behaviour in the presence of DOM of variable compositions. Similarly to the results with the individual DOM fractions, internalised Pb concentrations in the presence of the reconstituted DOM were greater than that predicted by the corresponding free lead ion concentration. An improved fit between experimental observations and the model predictions of adsorbed plus internalised Pb in the presence of DOM of different compositions was observed by assuming that each individual component adsorbed by the algae gave access to additional binding sites for Pb. Furthermore, the contribution of the Pb–DOM complex to total cellular Pb was dominated by the humic and fulvic acids, whereas the contribution of alginate was minimal.
Provoking the air
Authors: Williams Jonathan
Published: October 2008

Environmental context. Understanding ozone chemistry has been the aim of atmospheric chemists for over 50 years. Although the chemical mechanisms in current models become increasingly detailed and complex, it is far from clear that our continued pursuit of ever more trace level products will improve our understanding of the underlying photochemistry. Here we suggest a new, innovative measurement approach by which the chemical component of models can be tested and on which policy strategy can be forged.
Identifying the incentives that graziers in central-western Queensland need to manage land for conservation outcomes
Authors: Rolfe John , McCosker Juliana , Windle Jill
Published: October 2008

Opportunities exist in rangeland areas for changed grazing management practices to have positive environmental outcomes. It is important to understand what productivity tradeoffs may be involved with these changes, so as to build trust with landholders, understand how incentives for different management systems might be structured, and predict (and ameliorate) potential socio-economic impacts on regional communities. However, the complexity of agricultural and natural systems and gaps in understanding and data mean that it is very difficult to predict accurately the economic impacts of changing management actions.
In this paper, the use of experimental auctions is reported as an alternative mechanism for predicting economic impacts. The methodology used was a series of field experiments, where landholders from the Desert Uplands region participated in conservation auction workshops, using ‘dummy’ properties to design proposals. Using their knowledge of the region, participants had to design a conservation area or corridor across their dummy property, and then identify what annual payment would be needed before they would enter into a five year conservation agreement. An evaluation of the bids shows that the bid values may be influenced by several socio-economic and attitudinal factors as well as the opportunity costs involved in changed production. The mechanism provides a promising way of evaluating the opportunity costs of changing management practices and trialling conservation auction approaches.
Safe pasture utilisation rates as a grazing management tool in extensively grazed tropical savannas of northern Australia
Authors: Hunt L. P.
Published: October 2008

The concept of safe pasture utilisation rates is frequently promoted as a tool for use in setting livestock numbers in perennial grass pastures in northern Australia’s tropical savannas to achieve a grazing intensity that is ecologically and economically sustainable. However, recommended pasture utilisation rates have been defined and applied in several ways, and this has led to some confusion among managers, researchers and advisers about their appropriate use. In order to reduce this confusion, this paper reviews the ecological basis and use of safe pasture utilisation rates as a management tool, concentrating on two common ways (i.e. strategic and tactical) in which they are applied. The main objective of both approaches is to limit the intensity of grazing of perennial grasses during the growing season when they are most sensitive to defoliation. When used in a strategic way, safe pasture utilisation rates provide an indication of long-term safe stocking rates that will avoid pasture deterioration in most years. Alternatively, they are used in a tactical sense to adjust stocking rates to track forage production, usually on an annual basis. Using the tactical approach, stocking rates are set at the end of the growing season in order to use a ‘safe’ proportion of the standing forage available at that time during the subsequent 12 months. Thus, stocking rates for one growing season are based on the quantity of forage available at the end of the previous growing season. In areas with high year-to-year variability in pasture growth this may lead to overgrazing during the growing season. This paper concludes by suggesting several strategies to better manage pasture utilisation levels under a tactical management approach to ensure that palatable perennial grass populations persist in the long term. A call is also made for researchers and land management advisers to be clear in the way recommended safe pasture utilisation rates are defined and intended to be used.
Economic analyses of options for weedy Sporobolus grass management
Authors: Bray Steven , Holmes Bill , Officer David
Published: October 2008

Weedy Sporobolus grasses have low palatability for livestock, with infestations reducing land condition and pastoral productivity. Control and containment options are available, but the cost of weed control is high relative to the extra return from livestock, thus, limiting private investment.
This paper outlines a process for analysing the economic consequences of alternative management options for weedy Sporobolus grasses. This process is applicable to other weeds and other pastoral degradation or development issues.
Using a case study property, three scenarios were developed. Each scenario compared two alternative management options and was analysed using discounted cash flow analysis. Two of the scenarios were based on infested properties and one scenario was based on a currently uninfested property but highly likely to become infested without active containment measures preventing weed seed transport and seedling establishment.
The analysis highlighted why particular weedy Sporobolus grass management options may not be financially feasible for the landholder with the infestation. However, at the regional scale, the management options may be highly worthwhile due to a reduction in weed seed movement and new weed invasions. Therefore, to encourage investment by landholders in weedy Sporobolus grass management the investment of public money on behalf of landholders with non-infested properties should be considered.
Soil disturbance by animals at varying spatial scales in a semi-arid Australian woodland
Authors: Eldridge David J. , Kwok Alan B. C.
Published: October 2008

We studied soil disturbance by rabbits, echidnas, goannas, ants and termites at three different spatial scales across four vegetation communities (dense woodland, open woodland, shrubland, grassland) in semi-arid rangeland in western NSW. For analyses, bare and litter-covered surfaces (micro-scale) were nested within canopy and open patches (intermediate scale), which were nested within vegetation communities (landscape scale). Landscape-scale disturbances (rabbit warrens) were six and three times more abundant in open woodlands and shrublands, respectively, than in dense woodlands. Although individual warrens had a similar mass of excavated soil across all vegetation communities, in total, more soil was excavated in the grasslands than in the dense woodlands or shrublands. There were four times as many intermediate-sized disturbances (foraging pits and resting sites) under canopies than out in the open, and this was consistent across all vegetation communities. Echidna foraging pits and kangaroo resting sites dominated the canopy patches. Intermediate-sized disturbances scaled up to the landscape scale were marginally more abundant in the dense and open woodlands than in grasslands and shrublands. However, total mass of soil moved by all species did not differ among vegetation communities. The density of small-scale disturbances (ant nests, termite foraging galleries) did not differ at the landscape-, intermediate- or micro-scales. Our study documents the extent of animal activity in the semi-arid woodlands, and reinforces the notion that, as soil disturbance is scale-dependent, differences among species, habitats and communities will depend on the scale at which disturbances are examined.
Visualizing myosin–actin interaction with a genetically-encoded fluorescent strain sensor
Authors: Iwai Sosuke , Uyeda Taro Q. P.
Published: October 2008

Many proteins have been shown to undergo conformational changes in response to externally applied force in vitro, but whether the force-induced protein conformational changes occur in vivo remains unclear. To reveal the force-induced conformational changes, or strains, within proteins in living cells, we have developed a genetically encoded fluorescent “strain sensor,” by combining the proximity imaging (PRIM) technique, which uses spectral changes of 2 GFP molecules that are in direct contact, and myosin–actin as a model system. The developed PRIM-based strain sensor module (PriSSM) consists of the tandem fusion of a normal and circularly permuted GFP. To apply strain to PriSSM, it was inserted between 2 motor domains of
Dictyostelium
myosin II. In the absence of strain, the 2 GFP moieties in PriSSM are in contact, whereas when the motor domains are bound to F-actin, PriSSM has a strained conformation, leading to the loss of contact and a concomitant spectral change. Using the sensor system, we found that the position of the lever arm in the rigor state was affected by mutations within the motor domain. Moreover, the sensor was used to visualize the interaction between myosin II and F-actin in
Dictyostelium
cells. In normal cells, myosin was largely detached from F-actin, whereas ATP depletion or hyperosmotic stress increased the fraction of myosin bound to F-actin. The PRIM-based strain sensor may provide a general approach for studying force-induced protein conformational changes in cells.
Genetic and environmental effects in L1 phonological acquisitionThe case of consonant harmony in Greek child speech
Authors: Tzakosta Marina
Published: October 2008

Consonant harmony (CH) is a phenomenon commonly found in child language. Cross-linguistically, Place of Articulation (PoA), specifically the Coronal Node, undergoes CH, while regressive harmony seems to be the preferred directionality that CH takes (cf. Goad 2001a, b; Levelt 1994; Rose 2000, 2001). In the present study, drawing on naturalistic data from nine children acquiring Greek L1, we place emphasis on the fact that multiple factors need to be considered in parallel, in order to account for CH patterns: Not only PoA, but also Manner of Articulation (MoA) contributes to CH; consequently, (de)voicing or continuity harmony emerges. Although regressive harmony is generally favoured, markedness scales and word stress highly affect directionality. Coronal, stop and voiceless segments trigger and undergo CH depending on their degree of prominence and their position in the word. Harmony can be partial or full, i.e. either place or manner or both place and manner of articulation are targeted. Progressive harmony emerges when the triggers belong to the stressed syllable or when they are stops. Cases of double, bidirectional and recursive harmony are also reported. In general, Greek CH patterns are the product of combined factors determined by phonological principles and input frequency in the ambient language. In other words, the degree to which Greek CH patterns are different from cross-linguistic findings depends on the combination of UG principles and language specific/environmental effects, as well as the prominence of certain of these factors over others.
On the inherently close relation of the verb and its direct object in ditransitive constructionsEvidence from Greek
Authors: Lascaratou Chryssoula , Georgiafentis Michalis
Published: October 2008

This paper deals with the close relation between the verb (V) and its direct object (DO) in Greek ditransitive structures, bringing together a formal analysis of the inherent nature of this special bond and a performance motivated treatment of factors determining variation in linearisation, i.e. the effects of performance principles on the permutation of the original order of arguments. Thus, first, by means of lexico-syntactic criteria, we propose that Greek –a relatively free word order language– exhibits the asymmetry between the DO and the IO which has also been observed in other languages (e.g. English, Icelandic, and Mainland Scandinavian languages). On the basis of such criteria, we conclude that in the underlying structure of both the PP Object Construction (PPOC) and the Double Object Construction (DOC), the DO is a sister to V. This structural relationship, represented in the single tree diagram we propose for the two constructions, reveals the V-DO special affinity. Second, we investigate the factors involved in the alternation from the basic to the derived orders both in the PPOC and the DOC. Thus, we suggest that the derivation of the orders V-NPacc-PP and V-NPacc-NPgen from V-PP-NPacc and V-NPgen-NPacc, respectively, is motivated by a number of largely interrelated factors (e.g. information focus, internal complexity, and syntactic weight), which may function either individually or compositionally. Finally, it is observed that the insights about the special affinity between the V and its DO expressed in our formal account of ditransitive orders are also captured in Lascaratou's (1994) performance principles motivated analysis of a small corpus of Greek ditransitive constructions, in terms of the strong preference of the DO to be linearised immediately after the verb.
Anal sphincter tears at spontaneous delivery: A comparison of five hospitals in Norway
Authors: VALBØ ANNELILL , GJESSING LEIF , HERZOG CHRISTINE , GODERSTAD JEANNE METTE , LAINE KATARIINA , VALSET ANNE MARTE
Published: October 2008

Objective. To analyze circumstances relating to severe anal sphincter tears occurring at spontaneous delivery, in view of reported differences in practice regarding manual perineal protection during delivery. Design. Cohort study of midwife‐conducted non‐operative vaginal deliveries. Setting. Five Norwegian hospitals with 12,438 consecutive deliveries during a 12‐month period. Methods. Data from 357 women sustaining third and fourth grade anal sphincter tears (2.9%) were analyzed. Main outcome measures. Different incidence of major perineal tears. Results. Sphincter tear incidence varied significantly between the five hospitals, from 1.3 to 4.7% (p <0.001, RR=3.14 (CI: 2.38–5.56)). There was no significant difference between the five hospitals when other risk variables were compared. Use of oxytocin in the second phase of labor and of epidural analgesia was significantly more often applied in the hospital with the lowest rate of sphincter tears. The midwives’ perception of having applied perineal support was not significantly different between the two hospitals with the highest and the lowest incidence of sphincter tear. Conclusion. The observed difference in incidence of sphincter tear between the hospitals remains unexplained, but could be due to different perineal protection handling techniques.
Thyroid peroxidase antibodies in pregnant women with type 1 diabetes: Impact on thyroid function, metabolic control and pregnancy outcome
Authors: VESTGAARD MARIANNE , NIELSEN LENE RINGHOLM , RASMUSSEN ÅSE KROGH , DAMM PETER , MATHIESEN ELISABETH R.
Published: October 2008

Objective. In pregnant women with type 1 diabetes, we evaluated whether the presence of thyroid peroxidase autoantibodies (anti‐TPO) was associated with changes in thyroid function, metabolic control and pregnancy outcome. Design/setting. Prospective study, Denmark. Population. Ninety‐six consecutive pregnant women with type 1 diabetes. Twenty‐five healthy pregnant controls. Methods. At 8, 14, 21, 27 and 33 weeks, the diabetic women self‐monitored plasma glucose (SMPG) (8/day) for 3 days and had blood samplings obtained. Main outcome measures. Thyroid‐stimulating hormone (TSH), free thyroxin (T4), hemoglobin A1C (HbA1C), anti‐TPO, pregnancy outcome. Results. Anti‐TPO was detected in 31 (32%) of the pregnant diabetic women compared with two women (8%) in the healthy controls (p = 0.015). The presence of anti‐TPO was associated with higher TSH at 8 (p <0.0001) and 14 weeks (p <0.05) and lower free T4 at 8 weeks (p <0.05) compared with anti‐TPO negative women. Twenty untreated anti‐TPO positive women had higher TSH compared with untreated, anti‐TPO negative women (p <0.05), but comparable free T4. At inclusion, 25% had TSH above the recommended treatment goal for levothyroxine (TSH>2.5 mIU/l), most prevalently among anti‐TPO positive women. Sixteen women (17%) were treated for thyroid disorder during pregnancy. No differences were detected between the diabetic women with and without anti‐TPO regarding HbA1C, insulin dose, median SMPG or pregnancy outcome. Conclusions. Anti‐TPO was present in one‐third of pregnant women with type 1 diabetes and associated with slightly higher TSH, but not poorer glycemic control or adverse birth outcome. A total of 17% of women with type 1 diabetes were treated for thyroid disorder during pregnancy.
Antiviral Therapy for Avian Influenza Virus (H5N1) Infection at 2 Thai Medical Centers: Survey Findings and Implications for Pandemic Preparedness
Authors: Apisarnthanarak Anucha , Mundy Linda M.
Published: October 2008

In a survey of 150 physicians from an area where avian influenza virus (H5N1) infection is endemic, practice location (adjusted odds ratio [aOR], 4.45 [95% confidence interval {CI}, 1.02–26.4]) and the belief that rapid tests reliably predicted H5N1 infection (aOR, 5.6 [95% CI, 1.14–33.6]) were associated with not prescribing antiviral therapy; the belief that antiviral therapy reduced mortality was associated with prescribing an antiviral agent (aOR, 0.56 [95% CI, 0.14–0.95]).00
The Anti-apoptotic Protein HAX-1 Interacts with SERCA2 and Regulates Its Protein Levels to Promote Cell Survival
Authors: Vafiadaki Elizabeth , Arvanitis Demetrios A. , Pagakis Stamatis N. , Papalouka Vasiliki , Sanoudou Despina , Kontrogianni-Konstantopoulos Aikaterini , Kranias Evangelia G.
Published: October 2008

Cardiac contractility is regulated through the activity of various key Ca2+-handling proteins. The sarco(endo)plasmic reticulum (SR) Ca2+transport ATPase (SERCA2a) and its inhibitor phospholamban (PLN) control the uptake of Ca2+by SR membranes during relaxation. Recently, the antiapoptotic HS-1–associated protein X-1 (HAX-1) was identified as a binding partner of PLN, and this interaction was postulated to regulate cell apoptosis. In the current study, we determined that HAX-1 can also bind to SERCA2. Deletion mapping analysis demonstrated that amino acid residues 575–594 of SERCA2's nucleotide binding domain are required for its interaction with the C-terminal domain of HAX-1, containing amino acids 203-245. In transiently cotransfected human embryonic kidney 293 cells, recombinant SERCA2 was specifically targeted to the ER, whereas HAX-1 selectively concentrated at mitochondria. On triple transfections with PLN, however, HAX-1 massively translocated to the ER membranes, where it codistributed with PLN and SERCA2. Overexpression of SERCA2 abrogated the protective effects of HAX-1 on cell survival, after hypoxia/reoxygenation or thapsigargin treatment. Importantly, HAX-1 overexpression was associated with down-regulation of SERCA2 expression levels, resulting in significant reduction of apparent ER Ca2+levels. These findings suggest that HAX-1 may promote cell survival through modulation of SERCA2 protein levels and thus ER Ca2+stores.
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data
Authors: Chen Ching-Tai , Yang Ei-Wen , Hsu Hung-Ju , Sun Yi-Kun , Hsu Wen-Lian , Yang An-Suei
Published: October 2008

Motivation: Regulatory proteases modulate proteomic dynamics with a spectrum of specificities against substrate proteins. Predictions of the substrate sites in a proteome for the proteases would facilitate understanding the biological functions of the proteases. High-throughput experiments could generate suitable datasets for machine learning to grasp complex relationships between the substrate sequences and the enzymatic specificities. But the capability in predicting protease substrate sites by integrating the machine learning algorithms with the experimental methodology has yet to be demonstrated.

Results: Factor Xa, a key regulatory protease in the blood coagulation system, was used as model system, for which effective substrate site predictors were developed and benchmarked. The predictors were derived from bootstrap aggregation (machine learning) algorithms trained with data obtained from multilevel substrate phage display experiments. The experimental sampling and computational learning on substrate specificities can be generalized to proteases for which the active forms are available for the in vitro experiments.

Availability:  http://asqa.iis.sinica.edu.tw/fXaWeb/

Contact:  hsu@iis.sinica.edu.tw; yangas@gate.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
Authors: Yagi Shintaro , Hirabayashi Keiji , Sato Shinya , Li Wei , Takahashi Yoko , Hirakawa Tsutomu , Wu Guoying , Hattori Naoko , Hattori Naka , Ohgane Jun , Tanaka Satoshi , Liu X. Shirley , Shiota Kunio
Published: October 2008

DNA methylation constitutes an important epigenetic regulation mechanism in many eukaryotes, although the extent of DNA methylation in the regulation of gene expression in the mammalian genome is poorly understood. We developed D-REAM, a genome-wide DNA methylation analysis method for tissue-dependent and differentially methylated region (T-DMR) profiling with restriction tag-mediated amplification in mouse tissues and cells. Using a mouse promoter tiling array covering a region from −6 to 2.5 kb (∼30,000 transcription start sites), we found that over 3000 T-DMRs are hypomethylated in liver compared to cerebrum. The DNA methylation profile of liver was distinct from that of kidney and spleen. This hypomethylation profile marked genes that are specifically expressed in liver, including key transcription factors such as Hnf1a and Hnf4a. Genes with T-DMRs, especially those lacking CpG islands and those with HNF-1A binding motifis in their promoters, showed good correlation between their tissue-specific expression and liver hypomethylation status. T-DMRs located downstream from their transcription start sites also showed tissue-specific gene expression. These data indicate that multilayered regulation of tissue-specific gene function could be elucidated by DNA methylation tissue profiling.
Whole population, genome-wide mapping of hidden relatedness
Authors: Gusev Alexander , Lowe Jennifer K. , Stoffel Markus , Daly Mark J. , Altshuler David , Breslow Jan L. , Friedman Jeffrey M. , Pe'er Itsik
Published: October 2008

We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals. We then expand these matches using dynamic programming to identify long, nearly identical segmental sharing that is indicative of relatedness. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We verify that GERMLINE is in concordance with other methods when they can process the data, and also facilitates analysis of larger scale studies. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for (1) identification and resolution of phasing errors and (2) exposing polymorphic deletions that are otherwise challenging to detect. This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE.
Bundle Sheath Leakiness and Light Limitation during C4 Leaf and Canopy CO2 Uptake
Authors: Kromdijk Johannes , Schepers Hans E. , Albanito Fabrizio , Fitton Nuala , Carroll Faye , Jones Michael B. , Finnan John , Lanigan Gary J. , Griffiths Howard
Published: October 2008

Perennial species with the C4 pathway hold promise for biomass-based energy sources. We have explored the extent that CO2 uptake of such species may be limited by light in a temperate climate. One energetic cost of the C4 pathway is the leakiness (ϕ) of bundle sheath tissues, whereby a variable proportion of the CO2, concentrated in bundle sheath cells, retrodiffuses back to the mesophyll. In this study, we scale ϕ from leaf to canopy level of a Miscanthus crop (Miscanthus × giganteus hybrid) under field conditions and model the likely limitations to CO2 fixation. At the leaf level, measurements of photosynthesis coupled to online carbon isotope discrimination showed that leaves within a 3.3-m canopy (leaf area index = 8.3) show a progressive increase in both carbon isotope discrimination and ϕ as light decreases. A similar increase was observed at the ecosystem scale when we used eddy covariance net ecosystem CO2 fluxes, together with isotopic profiles, to partition photosynthetic and respiratory isotopic flux densities (isofluxes) and derive canopy carbon isotope discrimination as an integrated proxy for ϕ at the canopy level. Modeled values of canopy CO2 fixation using leaf-level measurements of ϕ suggest that around 32% of potential photosynthetic carbon gain is lost due to light limitation, whereas using ϕ determined independently from isofluxes at the canopy level the reduction in canopy CO2 uptake is estimated at 14%. Based on these results, we identify ϕ as an important limitation to CO2 uptake of crops with the C4 pathway.
Aneuploidy Affects Proliferation and Spontaneous Immortalization in Mammalian Cells
Authors: Williams Bret R. , Prabhu Vineet R. , Hunter Karen E. , Glazier Christina M. , Whittaker Charles A. , Housman David E. , Amon Angelika
Published: October 2008

Aneuploidy, an incorrect number of chromosomes, is the leading cause of miscarriages and mental retardation in humans and is a hallmark of cancer. We examined the effects of aneuploidy on primary mouse cells by generating a series of cell lines that carry an extra copy of one of four mouse chromosomes. In all four trisomic lines, proliferation was impaired and metabolic properties were altered. Immortalization, the acquisition of the ability to proliferate indefinitely, was also affected by the presence of an additional copy of certain chromosomes. Our data indicate that aneuploidy decreases not only organismal but also cellular fitness and elicits traits that are shared between different aneuploid cells.
HARP Is an ATP-Driven Annealing Helicase
Authors: Yusufzai Timur , Kadonaga James T.
Published: October 2008

DNA-dependent adenosine triphosphatases (ATPases) participate in a broad range of biological processes including transcription, DNA repair, and chromatin dynamics. Mutations in the HepA-related protein (HARP) ATPase are responsible for Schimke immuno-osseous dysplasia (SIOD), but the function of the protein is unknown. We found that HARP is an ATP-dependent annealing helicase that rewinds single-stranded DNA bubbles that are stably bound by replication protein A. Other related ATPases, including the DNA translocase Rad54, did not exhibit annealing helicase activity. Analysis of mutant HARP proteins suggests that SIOD is caused by a deficiency in annealing helicase activity. Moreover, the pleiotropy of HARP mutations is consistent with the function of HARP as an annealing helicase that acts throughout the genome to oppose the action of DNA-unwinding activities in the nucleus.
Tracing the Origin and Fate of NO
x
in the Arctic Atmosphere Using Stable Isotopes in Nitrate
Authors: Morin Samuel , Savarino Joël , Frey Markus M. , Yan Nicolas , Bekki Slimane , Bottenheim Jan W. , Martins Jean M. F.
Published: October 2008

Atmospheric nitrogen oxides (NO
x
=NO+ NO
2
) play a pivotal role in the cycling of reactive nitrogen (ultimately deposited as nitrate) and the oxidative capacity of the atmosphere. Combined measurements of nitrogen and oxygen stable isotope ratios of nitrate collected in the Arctic atmosphere were used to infer the origin and fate of NO
x
and nitrate on a seasonal basis. In spring, photochemically driven emissions of reactive nitrogen from the snowpack into the atmosphere make local oxidation of NO
x
by bromine oxide the major contributor to the nitrate budget. The comprehensive isotopic composition of nitrate provides strong constraints on the relative importance of the key atmospheric oxidants in the present atmosphere, with the potential for extension into the past using ice cores.
Magnetism on the Angrite Parent Body and the Early Differentiation of Planetesimals
Authors: Weiss Benjamin P. , Berdahl James S. , Elkins-Tanton Linda , Stanley Sabine , Lima Eduardo A. , Carporzen Laurent
Published: October 2008

Angrites are among the oldest known pristine basaltic meteorites and record the earliest stages of planet formation and differentiation. Our paleomagnetic analysis of three angrites found that they record a past magnetic field of ∼10 microteslas on the angrite parent body extending from 4564 to at least 4558 million years ago. Because the angrite paleomagnetic record extends beyond the expected lifetime of the early circumstellar disk, these paleofields were probably generated internally on the angrite parent body, possibly by an early dynamo in a rapidly formed metallic core.
Deletion of
Trpm7
Disrupts Embryonic Development and Thymopoiesis Without Altering Mg
2+
Homeostasis
Authors: Jin Jie , Desai Bimal N. , Navarro Betsy , Donovan Adriana , Andrews Nancy C. , Clapham David E.
Published: October 2008

The gene
transient receptor potential-melastatin-like 7
(
Trpm7
) encodes a protein that functions as an ion channel and a kinase. TRPM7 has been proposed to be required for cellular Mg
2+
homeostasis in vertebrates. Deletion of mouse
Trpm7
revealed that it is essential for embryonic development. Tissue-specific deletion of
Trpm7
in the T cell lineage disrupted thymopoiesis, which led to a developmental block of thymocytes at the double-negative stage and a progressive depletion of thymic medullary cells. However, deletion of
Trpm7
in T cells did not affect acute uptake of Mg
2+
or the maintenance of total cellular Mg
2+
.
Trpm7
-deficient thymocytes exhibited dysregulated synthesis of many growth factors that are necessary for the differentiation and maintenance of thymic epithelial cells. The thymic medullary cells lost signal transducer and activator of transcription 3 activity, which accounts for their depletion when Trpm7 is disrupted in thymocytes.
On Counterproductive Changes
Authors: Johnston Michael
Published: October 2008

The Hidden Costs of Clean Election Reform
.
By Frederic Charles Schaffer
. Cornell University Press, Ithaca, NY, 2008. 263 pp. $35, £17.95. ISBN 9780801441158.

In this consideration of detrimental effects of election reform, Schaffer discusses both what has gone wrong in the past and what can be done to head off potential problems in future changes.
Can We Trust the Machines?
Authors: Mebane Walter R.
Published: October 2008

Electronic Elections
. The Perils and Promises of Digital Democracy.
By R. Michael Alvarez and Thad E. Hall
. Princeton University Press, Princeton, NJ, 2008. 232 pp. $29.95, £17.95. ISBN 9780691125176.

Rejecting claims that new voting technologies foster tampering and fraud, Alvarez and Hall argue that with careful implementation computer-based solutions provide the best approach to voting.
Varicella-Zoster Virus Immediate-Early 63 Protein Interacts with Human Antisilencing Function 1 Protein and Alters Its Ability To Bind Histones H3.1 and H3.3
Authors: Ambagala Aruna P. , Bosma Trent , Ali Mir A. , Poustovoitov Maxim , Chen Jason J. , Gershon Michael D. , Adams Peter D. , Cohen Jeffrey I.
Published: October 2008

Varicella-zoster virus (VZV) immediate-early 63 protein (IE63) is abundantly expressed during both acute infection in vitro and latent infection in human ganglia. Using the yeast two-hybrid system, we found that VZV IE63 interacts with human antisilencing function 1 protein (ASF1). ASF1 is a nucleosome assembly factor which is a member of the H3/H4 family of histone chaperones. IE63 coimmunoprecipitated and colocalized with ASF1 in transfected cells expressing IE63 and in VZV-infected cells. IE63 also colocalized with ASF1 in both lytic and latently VZV-infected enteric neurons. ASF1 exists in two isoforms, ASF1a and ASF1b, in mammalian cells. IE63 preferentially bound to ASF1a, and the amino-terminal 30 amino acids of ASF1a were critical for its interaction with IE63. VZV IE63 amino acids 171 to 208 and putative phosphorylation sites of IE63, both of which are critical for virus replication and latency in rodents, were important for the interaction of IE63 with ASF1. Finally, we found that IE63 increased the binding of ASF1 to histone H3.1 and H3.3, which suggests that IE63 may help to regulate levels of histones in virus-infected cells. Since ASF1 mediates eviction and deposition of histones during transcription, the interaction of VZV IE63 with ASF1 may help to regulate transcription of viral or cellular genes during lytic and/or latent infection.
The M Type K15 Protein of Kaposi's Sarcoma-Associated Herpesvirus Regulates MicroRNA Expression via Its SH2-Binding Motif To Induce Cell Migration and Invasion
Authors: Tsai Yuan-Hau , Wu Min-Fen , Wu Yu-Hsuan , Chang Shing-Jyh , Lin Su-Fang , Sharp Tyson V. , Wang Hsei-Wei
Published: October 2008

Kaposi's sarcoma (KS) associated herpesvirus (KSHV) is the etiological agent of KS. In vivo, KS is a tumor capable of spreading throughout the body, and pulmonary metastasis is observed clinically. In vitro, KSHV induces the invasiveness of endothelial cells. The KSHV open reading frame K15 is a KSHV-specific gene encoding a transmembrane protein. Two highly divergent forms of K15, the predominant (P) and minor (M) forms (K15P and K15M, respectively), have been identified in different KSHV strains. The two K15 alleles resemble the latent membrane protein 2A (LMP2A) gene of Epstein-Barr virus (EBV) in their genomic locations and protein topology. Also, both K15 proteins have motifs similar to those found in the EBV LMP1 protein. K15 therefore appears to be a hybrid of a distant evolutionary relative of EBV LMP1 and LMP2A. Since both LMP1 and LMP2A proteins are capable of inducing cell motility, we sought to determine whether K15 has similar abilities. In this study, we show that K15M is latently expressed in KSHV-positive PEL cells and knockdown of K15M in PEL cells reduces cell motility. K15M localizes to lysosomal membranes and induces cell migration, invasion, and NF-κB (but not AP-1) activity via its conserved SH2-binding motif. K15M also induces the expression of microRNAs miR-21 and miR-31 via this conserved motif, and knocking down both these microRNAs eliminates K15M-induced cell motility. Therefore, K15M may contribute to KSHV-mediated tumor metastasis and angiogenesis via regulation of miR-21 and miR-31, which we show here for the first time to be a specific regulator of cell migration. In light of these findings, the targeting of K15 or the downstream microRNAs regulated by it may represent novel therapies for treatment of KSHV-associated neoplasia.
Mechanism of NS2B-Mediated Activation of NS3pro in Dengue Virus: Molecular Dynamics Simulations and Bioassays
Authors: Zuo Zhili , Liew Oi Wah , Chen Gang , Chong Pek Ching Jenny , Lee Siew Hui , Chen Kaixian , Jiang Hualiang , Puah Chum Mok , Zhu Weiliang
Published: October 2008

The NS2B cofactor is critical for proteolytic activation of the flavivirus NS3 protease. To elucidate the mechanism involved in NS2B-mediated activation of NS3 protease, molecular dynamic simulation, principal component analysis, molecular docking, mutagenesis, and bioassay studies were carried out on both the dengue virus NS3pro and NS2B-NS3pro systems. The results revealed that the NS2B-NS3pro complex is more rigid than NS3pro alone due to its robust hydrogen bond and hydrophobic interaction networks within the complex. These potent networks lead to remodeling of the secondary and tertiary structures of the protease that facilitates cleavage sequence recognition and binding of substrates. The cofactor is also essential for proper domain motion that contributes to substrate binding. Hence, the NS2B cofactor plays a dual role in enzyme activation by facilitating the refolding of the NS3pro domain as well as being directly involved in substrate binding/interactions. Kinetic analyses indicated for the first time that Glu92 and Asp50 in NS2B and Gln27, Gln35, and Arg54 in NS3pro may provide secondary interaction points for substrate binding. These new insights on the mechanistic contributions of the NS2B cofactor to NS3 activation may be utilized to refine current computer-based search strategies to raise the quality of candidate molecules identified as potent inhibitors against flaviviruses.
Temporal Control of Message Stability in the Life Cycle of Double-Stranded RNA Bacteriophage Φ8
Authors: Qiao Xueying , Sun Yang , Qiao Jian , Mindich Leonard
Published: October 2008

The cystoviruses have genomes of three double-stranded RNA segments. The genes of the L transcript are expressed early in infection, while those of M and S are expressed late. In all cystovirus groups but one, the quantity of the L transcript late in infection is lower than those of the other two because of transcriptional control. In bacteriophage Φ8 and its close relatives, transcription of L is not controlled; instead, the L transcript is turned over rapidly late in infection. The three messages are produced in approximately equal amounts early in infection, but the amount of L is less than 10% of the amounts of the others late in infection. The decay of the Φ8 L message depends upon the production of protein Hb, which is encoded in segment L. It also depends upon a target site within the
H
gene region. Phage mutants lacking either the
Hb
gene or the target region do not show the late control of L message quantity. In addition to having a role as a negative regulator, Hb functions to neutralize the activity of protein J, encoded by segment S, which causes the degradation of all viral transcripts.
The p14 FAST Protein of Reptilian Reovirus Increases Vesicular Stomatitis Virus Neuropathogenesis
Authors: Brown Christopher W. , Stephenson Kyle B. , Hanson Stephen , Kucharczyk Michael , Duncan Roy , Bell John C. , Lichty Brian D.
Published: October 2008

The fusogenic orthoreoviruses express nonstructural fusion-associated small transmembrane (FAST) proteins that induce cell-cell fusion and syncytium formation. It has been speculated that the FAST proteins may serve as virulence factors by promoting virus dissemination and increased or altered cytopathology. To directly test this hypothesis, the gene encoding the p14 FAST protein of reptilian reovirus was inserted into the genome of a heterologous virus that does not naturally form syncytia, vesicular stomatitis virus (VSV). Expression of the p14 FAST protein by the VSV/FAST recombinant gave the virus a highly fusogenic phenotype in cell culture. The growth of this recombinant fusogenic VSV strain was unaltered in vitro but was significantly enhanced in vivo. The VSV/FAST recombinant consistently generated higher titers of virus in the brains of BALB/c mice after intranasal or intravenous infection compared to the parental VSV/green fluorescent protein (GFP) strain that expresses GFP in place of p14. The VSV/FAST recombinant also resulted in an increased incidence of hind-limb paralysis, it infected a larger volume of brain tissue, and it induced more extensive neuropathology, thus leading to a lower maximum tolerable dose than that for the VSV/GFP parental virus. In contrast, an interferon-inducing mutant of VSV expressing p14 was still attenuated, indicating that this interferon-inducing phenotype is dominant to the fusogenic properties conveyed by the FAST protein. Based on this evidence, we conclude that the reovirus p14 FAST protein can function as a bona fide virulence factor.
Activation of Pattern Recognition Receptor-Mediated Innate Immunity Inhibits the Replication of Hepatitis B Virus in Human Hepatocyte-Derived Cells
Authors: Guo Haitao , Jiang Dong , Ma Dongling , Chang Jinhong , Dougherty Anne Marie , Cuconati Andrea , Block Timothy M. , Guo Ju-Tao
Published: October 2008

Recognition of virus infections by pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I), and melanoma differentiation associated gene 5 (MDA5), activates signaling pathways, leading to the induction of inflammatory cytokines that limit viral replication. To determine the effects of PRR-mediated innate immune response on hepatitis B virus (HBV) replication, a 1.3mer HBV genome was cotransfected into HepG2 or Huh7 cells with plasmid expressing TLR adaptors, myeloid differentiation primary response gene 88 (MyD88), and TIR-domain-containing adaptor-inducing beta interferon (TRIF), or RIG-I/MDA5 adaptor, interferon promoter stimulator 1 (IPS-1). The results showed that expressing each of the three adaptors dramatically reduced the levels of HBV mRNA and DNA in both HepG2 and Huh7 cells. However, HBV replication was not significantly affected by treatment of HBV genome-transfected cells with culture media harvested from cells transfected with each of the three adaptors, indicating that the adaptor-induced antiviral response was predominantly mediated by intracellular factors rather than by secreted cytokines. Analyses of involved signaling pathways revealed that activation of NF-κB is required for all three adaptors to elicit antiviral response in both HepG2 and Huh7 cells. However, activation of interferon regulatory factor 3 is only essential for induction of antiviral response by IPS-1 in Huh7 cells, but not in HepG2 cells. Furthermore, our results suggest that besides NF-κB, additional signaling pathway(s) are required for TRIF to induce a maximum antiviral response against HBV. Knowing the molecular mechanisms by which PRR-mediated innate defense responses control HBV infections could potentially lead to the development of novel therapeutics that evoke the host cellular innate antiviral response to control HBV infections.
Efficacy of intravitreal and periocular triamcinolone associated with photodynamic therapy for treatment of retinal angiomatous proliferation
Authors: Montero J A , Ruiz-Moreno J M , Sanabria M R , Fernandez-Munoz M
Published: October 2008

Aims:

To compare the relative efficacy of photodynamic therapy (PDT), PDT associated with intravitreal triamcinolone (PDT–IT) and PDT associated with periocular triamcinolone (PDT–PT) for treatment of retinal angiomatous proliferation (RAP) stage III.

Methods:

Retrospective, interventional, non-randomised multicentric study. The files, optical coherence tomography scans, indocyanine green and fluorescein angiograms of patients with RAP stage III who had been referred to a regional centre for PDT were retrospectively examined. Final visual acuity and chorioretinal atrophy were considered to be the main outcome indicators. The need to re-treat and recurrences were also considered.

Results:

Forty-two eyes were treated by PDT as monotherapy, 18 eyes by PDT–PT, and 19 eyes by PDT–IT. The mean (SD) age in each group was 79.1 (5.2), 77.0 (5.9) and 80.2 (5.1) years, respectively. The mean (SD) initial best corrected visual acuity (BCVA) was 0.17 (0.19), 0.21 (0.20) and 0.20 (0.18), respectively. Mean BCVA was 0.14 (0.19), 0.17 (0.15) and 0.17 (0.23), respectively, at 6 months (p = 0.27, 0.33 and 0.21, respectively) and 0.12 (0.18), 0.10 (0.10) and 0.17 (0.26), respectively, at 12 months (p = 0.12, 0.05 and 0.60, respectively, comparing vision at 6 months and 12 months with baseline; Student t test for paired data). Retinal pigment epithelium rips appeared in three eyes in group 1, in one eye in group 2, and in two eyes in group 3.

Conclusion:

Combined PDT–IT may offer better results than PDT monotherapy or PDT–PT in patients with RAP stage III.
Long-term control of choroidal neovascularisation secondary to angioid streaks treated with intravitreal bevacizumab (Avastin)
Authors: Neri P , Salvolini S , Mariotti C , Mercanti L , Celani S , Giovannini A
Published: October 2008

Aim:

To evaluate the efficacy of intravitreal bevacizumab (IB) in the long-term control of subfoveal choroidal neovascularisation (CNV) associated with angioid streaks (AS).

Methods:

Patients with unilateral active CNV associated with AS were enrolled. Exclusion criteria were previous treatment for CNV and comorbidity. Postoperative visual acuity was defined as a gain or loss of two or more lines of best-corrected visual acuity (BCVA). Post-treatment CNV size was dichotomised into “increased,” if the CNV area had grown by ⩾200 μm2, and “stable/reduced” if it had decreased by ⩾200 μm2 or had not changed by more than 200 μm2. Patients were retreated if no further improvement or worsening was noted.

Results:

Patients were five males and six females aged 33 to 58 years (mean 46.8 (SD 9.2)), who received a mean number of 3.5 (1.3) IB treatments (min: 2; max: 6). The mean retreatment interval was 3 (1.5) months (min: 1; max: 6). The mean follow-up duration was 23.8 (2.9) months. At 20 months all patients had stable/reduced CNV size and stable/improved BCVA. The mean BCVA rose significantly from 0.28 (0.2) at baseline to 0.56 (0.29) at 20 months (p<0.0001).

Conclusion:

IB is a promising tool for the long-term control of CNV in AS. Further studies are required to validate these findings.