bluuebunny/crossref_metadata_2025 huggingface dataset:
Micromanaging Palate Development
Authors: Clouthier David E. , Gray Josie , Artinger Kristin Bruk
Published: October 2008

Development of the facial skeleton is one of the most intriguing and intricate events that occur during human development. Most of the bone, cartilage, and connective tissue that compose the face and neck arise from a class of cells, referred to as neural crest cells, which are initially located at some distance from the facial primordium. A complex set of events regulated by specific gene products direct the formation, migration, and differentiation of these cells, leading to what is viewed as “prototypical” adult facial features. These basic developmental processes are recapitulated during the formation of the palate, termed palatogenesis. In this review, we summarize the basic embryology leading to palate formation, discuss mechanisms that can lead to palatal dysmorphologies, and highlight a new interaction that has recently been demonstrated to play a role in palate development. This interaction, involving small non-coding RNAs referred to as microRNAs, not only establishes a new level of regulation to cellular development, but may also serve as attractive targets for future efforts directed at clinical treatment of birth defect syndromes.
Evaluation of tephra for removing phosphorus from dairy farm drainage waters
Authors: Hanly J. A. , Hedley M. J. , Horne D. J.
Published: October 2008

Research was conducted in the Manawatu region, New Zealand, to investigate the ability of Papakai tephra to remove phosphorus (P) from dairy farm mole and pipe drainage waters. The capacity of this tephra to adsorb P was quantified in the laboratory using a series of column experiments and was further evaluated in a field study. In a column experiment, the P adsorption capabilities of 2 particle size factions (0.25–1, 1–2 mm) of Papakai tephra were compared with that of an Allophanic Soil (Patua soil) known to have high P adsorption properties. The experiment used a synthetic P influent solution (12 mg P/L) and a solution residence time in the columns of c. 35 min. By the end of the experiment, the 0.25–1 mm tephra removed an estimated 2.6 mg P/g tephra at an average P removal efficiency of 86%. The 1–2 mm tephra removed 1.6 mg P/g tephra at an average removal efficiency of 58%. In comparison, the Patua soil removed 3.1 mg P/g soil at a P removal efficiency of 86%. Although, the Patua soil was sieved to 1–2 mm, this size range consisted of aggregates of finer particles, which is likely to have contributed to this material having a higher P adsorbing capacity. A field study was established on a Pallic Soil, under grazed dairy pastures, to compare drainage water P concentrations from standard mole and pipe drainage systems (control) and drainage systems incorporating Papakai tephra. The 2 tephra treatments involved filling mole channels with 1–4 mm tephra (Mole-fill treatment) or filling the trench above intercepting drainage pipes with ‘as received’ tephra (Back-fill treatment). Over an entire winter drainage season, the quantity of total P (TP) lost from the control treatment drainage system was 0.30 kg P/ha. The average TP losses for the Mole-fill and the Back-fill treatments were 45% and 47% lower than the control treatment, respectively.
Fate of biuret 15N and its effect on net mineralisation of native soil N in forest soils
Authors: Xue J. M. , Clinton P. W. , Sands R. , Payn T. W. , Skinner M. F.
Published: October 2008

Biuret (C2H5N3O2) priming effect on mineralisation of native soil N has not been precisely quantified in previous studies, although it is a potential microbial activity regulator and slow-release N fertiliser. Following application of biuret at concentrations of 0 (B0) and 100 (B100) mg/kg (oven-dried) soil, we measured the dynamics of biuret-derived 15N in soil N pools, soil C mineralisation, and microbial biomass C in a sandy loam and a silt loam during a 112-day-long incubation to investigate the fate of biuret 15N and its effect on net mineralisation of native soil N. Biuret was decomposed faster in the sandy loam soil than the silt loam soil. In the sandy loam soil, the stabilised N pool was a strong sink for the biuret-derived 15N and accumulated about half of the applied 15N at the end of incubation. In the silt loam soil, 68% of the 15N applied was recovered in the NO3−-N pool and the stabilised N pool accumulated only about 25% of the applied 15N at the end of incubation. Biuret addition increased the turnover rate constant of soil organic matter and caused a real priming effect on net mineralisation of native soil N in both soils. The additional mineralisation of native soil N was 20.1 mg/kg (equivalent to 27.3 kg N/ha) in the sandy loam soil and 20.5 mg/kg (equivalent to 57.3 kg N/ha) in the silt loam soil. Biuret priming effect was related to the acceleration of soil organic matter decomposition by increased microbial activity at an early stage and the death/decay of microbes at a later stage of incubation. The native soil N released through the priming effect was partially from soil non-biomass organic matter and partially from soil microbial biomass.
Use of alkaline flyash-based products to amend acid soils: Plant growth response and nutrient uptake
Authors: Spark K. M. , Swift R. S.
Published: October 2008

Vast quantities of flyash are generated annually by the burning of coal in the power industry, with most of this material being stockpiled with little prospect of being utilised at present. Two alkaline flyash-based products (FAP) for use as soil amendments (FAP1 and FAP2) have been assessed using glasshouse pot trials to determine the suitability of using these products to treat acid soils. The products both contain ~80% flyash which originated from coal-fired electricity generation. The acid soils used in the study were 2 Podsols and a Ferrosol, all originating from south-east Queensland and ranging in pH (1 : 5 suspension in water) from 4 to 5.5. The flyash products when applied to the soil significantly enhanced growth of maize plants (Zea mays L.), with optimal application rates in the range 1.25–5% w/w. The FAP/soil mixtures and plants were analysed using a range of methods including extraction with DTPA, and plant biomass (aboveground dry matter). The results indicate that in addition to the liming effect, the flyash in the alkaline flyash products may enhance plant growth as a result of increasing the uptake of micro-nutrients such as copper, zinc, and manganese. The study suggests that flyash has the potential to be used as a base material in the production of soil amendment materials that can change soil pH and act as a fertiliser for certain soil micro-nutrients such as Cu, Mn, and Zn.
Use of alkaline flyash-based products to amend acid soils: Extractability of selected elements and their uptake by plants
Authors: Spark K. M. , Swift R. S.
Published: October 2008

In addition to promoting plant growth, the incorporation of flyash material into soil also has the potential to affect the solubility and plant availability of some elements. This paper reports on the effect of 2 flyash products (FAP) on the extractability and plant uptake as a function of pH of selected elements of concern in the environment: As, B, Cd, Co, Cu, Cr, Mn, Pb, Ni, and Zn. The results for the growth response of maize plants (Zea mays L.) in the FAP-amended soils have been reported in a companion paper. The addition of the FAP to the soils used in this study at rates up to 5% w/w resulted in increased levels of Cu, Mn, Ni, As, and Co in an acetic acid extract. The levels of Cr, Mn, Ni, Pb, Zn, As, and Co in these extracts all showed a dependency on pH for some soils. Maize plants grown in the amended soils exhibited an increase in the plant uptake of Cu, Mn, and Ni in some soils. However, none of the elements studied increased the plant uptake to levels which would generally be considered toxic to plants or cause problems in the food chain. The presence of the FAP decreased the plant availability of Ni at low pH and levels of Mn and Cd in the acetic acid extract were decreased, most likely due to sorption of these elements by the FAP.
There is no evidence that either the flyash alone, or the 2 FAP used in this study would pose a threat to plants or the environment when used at levels of up to 5% w/w. Possible beneficial effects for the environment were observed as the incorporation of FAP into soils has the capacity to reduce the uptake and potential toxicity of Cd, Ni, or Mn in some soils.
Understanding winter sodium deposition in Taranaki, New Zealand
Authors: Yates L. J. , Hedley M. J.
Published: October 2008

Research conducted in a limited number of regions has identified that Na deposition rate (kg Na/ha) is strongly influenced by 4 main factors: distance from coast, rainfall, wind speed, and wind direction. Despite the potential importance of Na deposition to the productivity of dairy farms, no comprehensive research has been conducted in Taranaki, New Zealand. Na, K, Ca, and Mg concentrations were determined in weekly rainwater samples collected in standard rain gauges erected at 15 sites, along 4 transects around Taranaki, between May and September 2006. Recorded Na concentrations ranged between 0.40 and 38 mg/L. High Na concentrations were associated with low rainfall volumes and proximity to the coast first receiving the prevailing wind, which was, during this period, the southern Taranaki coast. Na deposition ranged between 0.04 and 25 kg/ha.week. Equations were derived to predict the average Na concentration in rainwater and Na deposition in Taranaki for the 2006 winter period. The most influential factor explaining the variation in average Na concentration was the distance of the collector from the southern coast. Na and Mg depositions were highly correlated (R2 = 0.93; P < 0.01; n = 155), whereas correlations of Na with K or Ca were not as strong (R2 = 0.49 and 0.61, respectively). Measured Na deposition rates exceed those predicted by algorithms used in current nutrient budgeting software and could be used to improve this nutrient management software.
Carbon sequestration in urban landscapes: the example of a turfgrass system in New Zealand
Authors: Huh Keun Young , Deurer Markus , Sivakumaran Siva , McAuliffe Keith , Bolan Nanthi S.
Published: October 2008

Soil carbon sequestration was analysed in the topsoil (0–0.25 m) of putting greens of different ages (5, 9, 20, 30, 40 years) in a golf course in Palmerston North, New Zealand. The soil texture was the same for all putting greens and the intensive management guaranteed that the carbon (C) inputs to the soil were very similar for all ages. Significant and linear soil C sequestration rates occurred for 40 years. The soil C sequestration rate in 0–0.25 m depth was 69 ± 8 g/m2.year over a 40-year period totalling 28 t/ha over 40 years. The relative microbial activity (dehydrogenase activity/total soil C content) representing the bioavailability of soil C decreased by about 50% over 40 years. The C sequestration and decrease of bioavailability of soil C was much more pronounced in 0.1–0.25 m depth than in the top 0.1 m. In the top 0.1 m, very little C sequestration occurred, most probably due to the intensive soil management in this depth. We concluded that the C sequestration was mainly caused by the increasing humification of C in the undisturbed part of the soil (0.1–0.25 m depth) as was indicated by a significant decrease in the relative microbial activity. Turfgrass systems such as putting greens are well suited to sequester C in urban areas.
Nitrous oxide generation, denitrification, and nitrate removal in a seepage wetland intercepting surface and subsurface flows from a grazed dairy catchment
Authors: Zaman M. , Nguyen M. L. , Gold A. J. , Groffman P. M. , Kellogg D. Q. , Wilcock R. J.
Published: October 2008

Little is known about seepage wetlands, located within agricultural landscapes, with respect to removing nitrate (NO3−) from agricultural catchments, mainly through gaseous emissions of nitrous oxide (N2O) and dinitrogen (N2) via denitrification. These variables were quantified using a push–pull technique where we introduced a subsurface water plume spiked with 15N-enriched NO3− and 2 conservative tracers [bromide (Br−) and sulfur hexafluoride (SF6)] into each of 4 piezometers and extracted the plume from the same piezometers throughout a 48-h period. To minimise advective and dispersive flux, we placed each of these push–pull piezometers within a confined lysimeter (0.5 m diameter) installed around undisturbed wetland soil and vegetation. Although minimal dilution of the subsurface water plumes occurred, NO3−-N concentration dropped sharply in the first 4 h following dosing, such that NO3−-limiting conditions (<2 mg/L of NO3-N) for denitrification prevailed over the final 44 h of the experiment. Mean subsurface water NO3− removal rates during non-limiting conditions were 15.7 mg/L.day. Denitrification (based on the generation of isotopically enriched N2O plus N2) accounted for only 7% (1.1 mg/L.day) of the observed groundwater NO3− removal, suggesting that other transformation processes, such as plant uptake, were responsible for most of the NO3− removal. Although considerable increases in 15N-enriched N2O levels were initially observed following NO3− dosing, no net emissions were generated over the 48-h study. Our results suggest that this wetland may be a source of N2O emissions when NO3− concentrations are elevated (non-limited), but can readily remove N2O (function as a N2O sink) when NO3− levels are low. These results argue for the use of engineered bypass flow designs to regulate NO3− loading to wetland denitrification buffers during high flow events and thus enhance retention time and the potential for NO3−-limiting conditions and N2O removal. Although this type of management may reduce the full potential for wetland NO3− removal, it provides a balance between water quality goals and greenhouse gas emissions.
Effect of treated zeolite, iron waste, and liming on phytoavailability of Zn, Cu, and Ni in long-term biosolids-amended soils
Authors: Gheshlaghi Z. Talebi , McLaren R. G. , Adams J. A.
Published: October 2008

Two metal-contaminated biosolids-amended soils (moderately and highly contaminated) from the Bromley Sewage Treatment Farm, Christchurch, New Zealand, were used to evaluate the effect of remedial treatments on Ni, Zn, and Cu phytoavailability to sunflower (Helianthus annus L.). Two different chemical treatments (iron waste and treated zeolite), at 2 rates of application (5% and 10% w/w), in combination with 3 rates of a liming material (Ca(OH)2 at 0%, 0.33%, and 0.66% w/w) were evaluated for their metal remediation potential using pot experiments. Under the moderately acidic pH conditions of the original soils (pH 5.4–5.7), neither of the materials had substantial effects on plant metal concentrations, and the application of treated zeolite resulted in a large decrease in plant yield (>60% reduction). However, in the presence of Ca(OH)2, both materials showed some potential for reducing Ni and Zn concentrations in sunflowers compared with Ca(OH)2 alone. The best combinations of zeolite or iron waste with Ca(OH)2 resulted in reductions in shoot Ni concentrations to below the detection limit. For Zn, the best combinations of materials resulted in reductions in sunflower shoot Zn concentrations of 91% for the moderately contaminated soil and 75% for the highly contaminated soil. Combinations of iron waste and Ca(OH)2 in particular resulted in substantial decreases in soluble soil Zn concentrations (>90% reduction) and increases in plant yield (63% increase for highly contaminated soil), attributed to the remediation of Zn toxicity. There was little effect of any treatment on Cu concentration in the sunflower plants.
The use of diffuse reflectance spectroscopy for in situ carbon and nitrogen analysis of pastoral soils
Authors: Kusumo Bambang H. , Hedley C. B. , Hedley M. J. , Hueni A. , Tuohy M. P. , Arnold G. C.
Published: October 2008

A field method has been developed for rapid in situ assessment of soil carbon (C) and nitrogen (N) content using a portable spectroradiometer (ASD FieldSpecPro). The technique was evaluated at 7 field sites in permanent pasture, and in 1-year, 3-year, and 5-year pine-to-pasture conversions on Pumice, Allophanic, and Tephric Recent Soils in the Taupo and Rotorua region of New Zealand. A total of 210 samples were collected from 2 depths: 37.5 and 112.5 mm. Field measurement of diffuse spectral reflectance was recorded from a flat sectioned horizontal soil surface of a soil core using a purpose-built contact probe attached by fibre optic cable to the spectroradiometer. A 15-mm soil slice was collected from each cut surface for analysis of total C and N using a LECO Analyser. Soils had a wide range of total C and N (0.26–11.21% C, 0.02–1.01% N). Partial least-squares regression analysis was used to develop calibration models between smoothed-first derivative 5-nm-spaced spectral data and LECO-measured total C and N. The models successfully predicted total C and N in the validation sets with the best prediction for C (RPD 2.01, r2 0.75, RMSEP 1.21%) and N (RPD 2.66, r2 0.86, RMSEP 0.07%). Prediction accuracy using different selection methods of calibration and validation set is reported. This study indicates that in situ assessment of soil C and N by field spectroscopy has considerable potential for spatially rapid measurement of soil C and N in the landscape.
Mechanism of and exquisite selectivity for O–O bond formation by the heme-dependent chlorite dismutase
Authors: Lee Amanda Q. , Streit Bennett R. , Zdilla Michael J. , Abu-Omar Mahdi M. , DuBois Jennifer L.
Published: October 2008

Chlorite dismutase (Cld) is a heme b-dependent, O–O bond forming enzyme that transforms toxic chlorite (ClO
2
−
) into innocuous chloride and molecular oxygen. The mechanism and specificity of the reaction with chlorite and alternate oxidants were investigated. Chlorite is the sole source of dioxygen as determined by oxygen-18 labeling studies. Based on ion chromatography and mass spectrometry results, Cld is highly specific for the dismutation of chlorite to chloride and dioxygen with no other side products. Cld does not use chlorite as an oxidant for oxygen atom transfer and halogenation reactions (using cosubstrates guaiacol, thioanisole, and monochlorodimedone, respectively). When peracetic acid or H
2
O
2
was used as an alternative oxidant, oxidation and oxygen atom transfer but not halogenation reactions occurred. Monitoring the reaction of Cld with peracetic acid by rapid-mixing UV-visible spectroscopy, the formation of the high valent compound I intermediate, [(Por
•+
)Fe
IV
= O], was observed [
k
1
= (1.28 ± 0.04) × 10
6
M
−1
s
−1
]. Compound I readily decayed to form compound II in a manner that is independent of peracetic acid concentration (
k
2
= 170 ± 20 s
−1
). Both compound I and a compound II-associated tryptophanyl radical that resembles cytochrome c peroxidase (Ccp) compound I were observed by EPR under freeze-quench conditions. The data collectively suggest an O–O bond-forming mechanism involving generation of a compound I intermediate via oxygen atom transfer from chlorite, and subsequent recombination of the resulting hypochlorite and compound I.
CaMKIIβ binding to stable F-actin
in vivo
regulates F-actin filament stability
Authors: Lin Yu-Chih , Redmond Lori
Published: October 2008

Ca2
+
/calmodulin-dependent protein kinase II (CaMKII) is a serine/threonine kinase that is best known for its role in synaptic plasticity and memory. Multiple roles of CaMKII have been identified in the hippocampus, yet its role in developing neurons is less well understood. We show here that endogenous CaMKIIβ, but not CaMKIIα, localized to prominent F-actin-rich structures at the soma in embryonic cortical neurons. Fluorescence recovery after photobleaching analyses of GFP-CaMKIIβ binding interactions with F-actin in this CaMKIIα-free system indicated CaMKIIβ binding depended upon a putative F-actin binding domain in the variable region of CaMKIIβ. Furthermore, CaMKIIα decreased CaMKIIβ binding to F-actin. We examined the interaction of CaMKIIβ with stable and dynamic actin and show that CaMKIIβ binding to F-actin was dramatically prolonged when F-actin was stabilized. CaMKIIβ binding to stable F-actin was disrupted when it was bound by Ca2
+
/calmodulin or when it was highly phosphorylated, but not by kinase inactivity. Whereas CaMKIIβ over-expression increased the prevalence of the F-actin-rich structures, disruption of CaMKIIβ binding to F-actin reduced them. Taken together, these data suggest that CaMKIIβ binding to stable F-actin is important for the
in vivo
maintenance of polymerized F-actin.
Retinoic acid regulates RARα-mediated control of translation in dendritic RNA granules during homeostatic synaptic plasticity
Authors: Maghsoodi Bita , Poon Michael M. , Nam Christine I. , Aoto Jason , Ting Pamela , Chen Lu
Published: October 2008

Homeostatic plasticity is thought to play an important role in maintaining the stability of neuronal circuits. During one form of homeostatic plasticity, referred to as synaptic scaling, activity blockade leads to a compensatory increase in synaptic transmission by stimulating in dendrites the local translation and synaptic insertion of the AMPA receptor subunit GluR1. We have previously shown that
all-trans
retinoic acid (RA) mediates activity blockade-induced synaptic scaling by activating dendritic GluR1 synthesis and that this process requires RARα, a member of the nuclear RA receptor family. This result raised the question of where RARα is localized in dendrites and whether its localization is regulated by RA and/or activity blockade. Here, we show that activity blockade or RA treatment in neurons enhances the concentration of RARα in the dendritic RNA granules and activates local GluR1 synthesis in these RNA granules. Importantly, the same RNA granules that contain RARα also exhibit an accumulation of GluR1 protein but with a much slower time course than that of RARα, suggesting that the former regulates the latter. Taken together, our results provide a direct link between dendritically localized RARα and local GluR1 synthesis in RNA granules during RA-mediated synaptic signaling in homeostatic synaptic plasticity.
Molecular code for protein insertion in the endoplasmic reticulum membrane is similar for N
in
–C
out
and N
out
–C
in
transmembrane helices
Authors: Lundin Carolina , Kim Hyun , Nilsson IngMarie , White Stephen H. , von Heijne Gunnar
Published: October 2008

Transmembrane α-helices in integral membrane proteins can have two orientations in the membrane: N
in
–C
out
or N
out
–C
in
. Previous studies of model N
out
–C
in
transmembrane segment have led to a detailed, quantitative picture of the “molecular code” that relates amino acid sequence to membrane insertion efficiency
in vivo
[Hessa T,
et al.
(2007) Molecular code for transmembrane helix recognition by the Sec61 translocon.
Nature
450:1026–1030], but whether the same code applies also to N
in
–C
out
transmembrane helices is unknown. Here, we show that the contributions of individual amino acids to the overall efficiency of membrane insertion are similar for the two kinds of helices and that the threshold hydrophobicity for membrane insertion can be up to ≈1 kcal/mol lower for N
in
–C
out
compared with N
out
–C
in
transmembrane helices, depending on the neighboring helices.
Probing the origin of tubulin rigidity with molecular simulations
Authors: Dima Ruxandra I. , Joshi Harshad
Published: October 2008

Tubulin heterodimers are the building blocks of microtubules, a major component of the cytoskeleton, whose mechanical properties are fundamental for the life of the cell. We uncover the microscopic origins of the mechanical response in microtubules by probing features of the energy landscape of the tubulin monomers and tubulin heterodimer. To elucidate the structures of the unfolding pathways and reveal the multiple unfolding routes, we performed simulations of a self-organized polymer (SOP) model of tubulin. The SOP representation, which is a coarse-grained description of chains, allows us to perform force-induced simulations at loading rates and time scales that closely match those used in single-molecule experiments. We show that the forced unfolding of each monomer involves a bifurcation in the pathways to the stretched state. After the unfolding of the C-term domain, the unraveling continues either from the N-term domain or from the middle domain, depending on the monomer and the pathway. In contrast to the unfolding complexity of the monomers, the dimer unfolds according to only one route corresponding to the unraveling of the C-term domain and part of the middle domain of β-tubulin. We find that this surprising behavior is due to the viscoelastic properties of the interface between the monomers. We map precise features of the complex energy landscape of tubulin by surveying the structures of the various metastable intermediates, which, in the dimer case, are characterized only by changes in the β-tubulin monomer.
SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons
Authors: Kwan Kenneth Y. , Lam Mandy M. S. , Krsnik Željka , Kawasawa Yuka Imamura , Lefebvre Veronique , Šestan Nenad
Published: October 2008

Neocortical projection neurons exhibit layer-specific molecular profiles and axonal connections. Here we show that the molecular identities of early-born subplate and deep-layer neurons are not acquired solely during generation or shortly thereafter but undergo progressive postmitotic refinement mediated by SOX5.
Fezf2
and
Bcl11b
, transiently expressed in all subtypes of newly postmigratory early-born neurons, are subsequently downregulated in layer 6 and subplate neurons, thereby establishing their layer 5-enriched postnatal patterns. In
Sox5
-null mice, this downregulation is disrupted, and layer 6 and subplate neurons maintain an immature differentiation state, abnormally expressing these genes postnatally. Consistent with this disruption, SOX5 binds and represses a conserved enhancer near
Fezf2
. The
Sox5
-null neocortex exhibits failed preplate partition and laminar inversion of early-born neurons, loss of layer 5 subcerebral axons, and misrouting of subplate and layer 6 corticothalamic axons to the hypothalamus. Thus, SOX5 postmitotically regulates the migration, postmigratory differentiation, and subcortical projections of subplate and deep-layer neurons.
A chemical compound that stimulates the human homologous recombination protein RAD51
Authors: Jayathilaka Krishanthi , Sheridan Sean D. , Bold Tyler D. , Bochenska Katarzyna , Logan Hillary L. , Weichselbaum Ralph R. , Bishop Douglas K. , Connell Philip P.
Published: October 2008

RAD51 and other members of the RecA family of strand exchange proteins assemble on ssDNA to form presynaptic filaments, which carry out the central steps of homologous recombination. A microplate-based assay was developed for high-throughput measurement of hRAD51 filament formation on ssDNA. With this method, a 10,000 compound library was screened, leading to the identification of a small molecule (RS-1) that enhances hRAD51 binding in a wide range of biochemical conditions. Salt titration experiments showed that RS-1 can enhance filament stability. Ultrastructural analysis of filaments formed on ssDNA showed that RS-1 can increase both protein–DNA complex lengths and the pitch of helical filament turns. RS-1 stimulated hRAD51-mediated homologous strand assimilation (D-loop) activity by at least 5- to 11-fold, depending on the condition. This D-loop stimulation occurred even in the presence of Ca
2+
or adenylyl-imidodiphosphate, indicating that the mechanism of stimulation was distinct from that conferred by Ca
2+
and/or inhibition of ATPase. No D-loop activity was observed in the absence of a nucleotide triphosphate cofactor, indicating that the compound does not substitute for this requirement. These results indicate that RS-1 enhances the homologous recombination activity of hRAD51 by promoting the formation of active presynaptic filaments. Cell survival assays in normal neonatal human dermal fibroblasts demonstrated that RS-1 promotes a dose-dependent resistance to the cross-linking chemotherapeutic drug cisplatin. Given that RAD51-dependent recombination is a major determinant of cisplatin resistance, RS-1 seems to function
in vivo
to stimulate homologous recombination repair proficiency. RS-1 has many potential applications in both research and medical settings.
Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity
Authors: Koh Andrew S. , Kuo Alex J. , Park Sang Youn , Cheung Peggie , Abramson Jakub , Bua Dennis , Carney Dylan , Shoelson Steven E. , Gozani Or , Kingston Robert E. , Benoist Christophe , Mathis Diane
Published: October 2008

Aire induces ectopic expression of peripheral tissue antigens (PTAs) in thymic medullary epithelial cells, which promotes immunological tolerance. Beginning with a broad screen of histone peptides, we demonstrate that the mechanism by which this single factor controls the transcription of thousands of genes involves recognition of the amino-terminal tail of histone H3, but not of other histones, by one of Aire's plant homeodomain (PHD) fingers. Certain posttranslational modifications of H3 tails, notably dimethylation or trimethylation at H3K4, abrogated binding by Aire, whereas others were tolerated. Similar PHD finger–H3 tail-binding properties were recently reported for BRAF-histone deacetylase complex 80 and DNA methyltransferase 3L; sequence alignment, molecular modeling, and biochemical analyses showed these factors and Aire to have structure–function relationships in common. In addition, certain PHD1 mutations underlying the polyendocrine disorder autoimmune polyendocrinopathy–candidiases–ectodermaldystrophy compromised Aire recognition of H3.
In vitro
binding assays demonstrated direct physical interaction between Aire and nucleosomes, which was in part buttressed by its affinity to DNA.
In vivo
Aire interactions with chromosomal regions depleted of H3K4me3 were dependent on its H3 tail-binding activity, and this binding was necessary but not sufficient for the up-regulation of genes encoding PTAs. Thus, Aire's activity as a histone-binding module mediates the thymic display of PTAs that promotes self-tolerance and prevents organ-specific autoimmunity.
Crystal structure of the guanylyl cyclase Cya2
Authors: Rauch Annika , Leipelt Martina , Russwurm Michael , Steegborn Clemens
Published: October 2008

Cyclic GMP (cGMP) is an important second messenger in eukaryotes. It is formed by guanylyl cyclases (GCs), members of the nucleotidyl cyclases class III, which also comprises adenylyl cyclases (ACs) from most organisms. To date, no structures of eukaryotic GCs are available, and all bacterial class III proteins were found to be ACs. Here we describe the biochemical and structural characterization of the class III cyclase Cya2 from cyanobacteriumSynechocystis PCC6803. Cya2 shows high specificity for GTP versus ATP, revealing it to be the first bacterial GC, and sequence similarity searches indicate that GCs are also present in other bacteria. The crystal structure of Cya2 provides first structural insights into the universal GC family. Structure and mutagenesis studies show that a conserved glutamate, assisted by an interacting lysine, dominates substrate selection by forming hydrogen bonds to the substrate base. We find, however, that a second residue involved in substrate selection has an unexpected sterical role in GCs, different from its hydrogen bonding function in the related ACs. The structure identifies a tyrosine that lines the guanine binding pocket as additional residue contributing to substrate specificity. Furthermore, we find that substrate specificity stems from faster turnover of GTP, rather than different affinities for GTP and ATP, implying that the specificity-determining interactions are established after the binding step.
Exploring RNA transcription and turnover
in vivo
by using click chemistry
Authors: Jao Cindy Y. , Salic Adrian
Published: October 2008

We describe a chemical method to detect RNA synthesis in cells, based on the biosynthetic incorporation of the uridine analog 5-ethynyluridine (EU) into newly transcribed RNA, on average once every 35 uridine residues in total RNA. EU-labeled cellular RNA is detected quickly and with high sensitivity by using a copper (I)-catalyzed cycloaddition reaction (often referred to as “click” chemistry) with fluorescent azides, followed by microscopic imaging. We demonstrate the use of this method in cultured cells, in which we examine the turnover of bulk RNA after EU pulses of varying lengths. We also use EU to assay transcription rates of various tissues in whole animals, both on sections and by whole-mount staining. We find that total transcription rates vary greatly among different tissues and among different cell types within organs.
Strategies to Prevent Transmission of Methicillin-ResistantStaphylococcus aureusin Acute Care Hospitals
Authors: Calfee David P. , Salgado Cassandra D. , Classen David , Arias Kathleen M. , Podgorny Kelly , Anderson Deverick J. , Burstin Helen , Coffin Susan E. , Dubberke Erik R. , Fraser Victoria , Gerding Dale N. , Griffin Frances A. , Gross Peter , Kaye Keith S. , Klompas Michael , Lo Evelyn , Marschall Jonas , Mermel Leonard A. , Nicolle Lindsay , Pegues David A. , Perl Trish M. , Saint Sanjay , Weinstein Robert A. , Wise Robert , Yokoe Deborah S.
Published: October 2008

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections (HAIs). Our intent in this document is to highlight practical recommendations in a concise format to assist acute care hospitals in their efforts to prevent transmission of methicillin-resistantStaphylococcus aureus(MRSA). Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary, Introduction, and accompanying editorial for additional discussion.

1. Burden of HAIs caused by MRSA in acute care facilities

a. In the United States, the proportion of hospital-associatedS. aureusinfections that are caused by strains resistant to methicillin has steadily increased. In 2004, MRSA accounted for 63% ofS. aureusinfections in hospitals.

b. Although the proportion ofS. aureus–associated HAIs among intensive care unit (ICU) patients that are due to methicillin-resistant strains has increased (a relative measure of the MRSA problem), recent data suggest that the incidence of central line–associated bloodstream infection caused by MRSA (an absolute measure of the problem) has decreased in several types of ICUs since 2001. Although these findings suggest that there has been some success in preventing nosocomial MRSA transmission and infection, many patient groups continue to be at risk for such transmission.

c. MRSA has also been documented in other areas of the hospital and in other types of healthcare facilities, including those that provide long-term care.
Strategies to Prevent Surgical Site Infections in Acute Care Hospitals
Authors: Anderson Deverick J. , Kaye Keith S. , Classen David , Arias Kathleen M. , Podgorny Kelly , Burstin Helen , Calfee David P. , Coffin Susan E. , Dubberke Erik R. , Fraser Victoria , Gerding Dale N. , Griffin Frances A. , Gross Peter , Klompas Michael , Lo Evelyn , Marschall Jonas , Mermel Leonard A. , Nicolle Lindsay , Pegues David A. , Perl Trish M. , Saint Sanjay , Salgado Cassandra D. , Weinstein Robert A. , Wise Robert , Yokoe Deborah S.
Published: October 2008

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections. The intent of this document is to highlight practical recommendations in a concise format designed to assist acute care hospitals to implement and prioritize their surgical site infection (SSI) prevention efforts. Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary and Introduction and accompanying editorial for additional discussion.

1. Burden of SSIs as complications in acute care facilities.

a. SSIs occur in 2%-5% of patients undergoing inpatient surgery in the United States.

b. Approximately 500,000 SSIs occur each year.

2. Outcomes associated with SSI

a. Each SSI is associated with approximately 7-10 additional postoperative hospital days.

b. Patients with an SSI have a 2-11 times higher risk of death, compared with operative patients without an SSI.

i. Seventy-seven percent of deaths among patients with SSI are direcdy attributable to SSI.

c. Attributable costs of SSI vary, depending on the type of operative procedure and the type of infecting pathogen; published estimates range from $3,000 to $29,000.

i. SSIs are believed to account for up to $10 billion annually in healthcare expenditures.

1. Definitions

a. The Centers for Disease Control and Prevention National Nosocomial Infections Surveillance System and the National Healthcare Safety Network definitions for SSI are widely used.

b. SSIs are classified as follows (Figure):

i. Superficial incisional (involving only skin or subcutaneous tissue of the incision)

ii. Deep incisional (involving fascia and/or muscular layers)

iii. Organ/space
Strategies to Prevent Clostridium difficile Infections in Acute Care Hospitals
Authors: Dubberke Erik R. , Gerding Dale N. , Classen David , Arias Kathleen M. , Podgorny Kelly , Anderson Deverick J. , Burstin Helen , Calfee David P. , Coffin Susan E. , Fraser Victoria , Griffin Frances A. , Gross Peter , Kaye Keith S. , Klompas Michael , Lo Evelyn , Marschall Jonas , Mermel Leonard A. , Nicolle Lindsay , Pegues David A. , Perl Trish M. , Saint Sanjay , Salgado Cassandra D. , Weinstein Robert A. , Wise Robert , Yokoe Deborah S.
Published: October 2008

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections. The intent of this document is to highlight practical recommendations in a concise format designed to assist acute care hospitals in implementing and prioritizing their Clostridium difficile infection (CDI) prevention efforts. Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary and Introduction and accompanying editorial for additional discussion.

1. Increasing rates of CDI

C. difficile now rivals methicillin-resistant Staphylococcus aureus (MRSA) as the most common organism to cause healthcare-associated infections in the United States.

a. In the United States, the proportion of hospital discharges in which the patient received the International Classification of Diseases, Ninth Revision discharge diagnosis code for CDI more than doubled between 2000 and 2003, and CDI rates continued to increase in 2004 and 2005 (L. C. McDonald, MD, personal communication, July 2007). These increases have been seen in pediatric and adult populations, but elderly individuals have been disproportionately affected. CDI incidence has also increased in Canada and Europe.

b. There have been numerous reports of an increase in CDI severity.

c. Most reports of increases in the incidence and severity of CDI have been associated with the BI/NAP1/027 strain of C. difficile. This strain produces more toxins A and B in vitro than do many other strains of C. difficile, produces a third toxin (binary toxin), and is highly resistant to fluoroquinolones.
Deuterium retention in ITER-grade austenitic stainless steel
Authors: Nemanič Vincenc , Žumer Marko , Zajec Bojan
Published: October 2008

In view of the construction of ITER, it is essential to confirm that the retention of tritium by the large interior surface area of stainless steel will not become an issue for safety or operating inventory reasons. Retention of deuterium in ITER-grade austenitic stainless steel samples was studied during t = 24 h exposures to pure gaseous deuterium at p = 0.01 mbar and 0.1 mbar and T = 100 °C, 250 °C and 400 °C, respectively. The required high sensitivity for distinguishing hydrogen isotopes involved in the process (H2, HD and D2) was gained after suppression of the native hydrogen concentration by a thermal treatment at T = 400 °C for t = 200 h. The quantity of retained deuterium was determined by measuring the absolute pressure change during the deuterium exposure and subsequent mass spectrometry revealing an intense isotope exchange reaction. The retained amount of 2.6 × 1016 D cm−2 was the highest at T = 400 °C and p = 0.1 mbar and noticeably less at lower deuterium pressure and temperature. Our results, when compared with similar tritium exposures, do not exceed the limits set in the generic safety analysis for the ITER. They manifest that an extremely high sensitivity for deuterium absorption and release can be gained with a precise pressure measuring technique, otherwise attributed exclusively to tritium scintillation methods.
The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola: Roles of Major Regulators and the Phytotoxin Coronatine
Authors: Wang Lin , Mitra Raka M. , Hasselmann Keegan D. , Sato Masanao , Lenarz-Wyatt Lisa , Cohen Jerry D. , Katagiri Fumiaki , Glazebrook Jane
Published: October 2008

Expression profiling of wild-type plants and mutants with defects in key components of the defense signaling network was used to model the Arabidopsis network 24 h after infection by Pseudomonas syringae pv. maculicola ES4326. Results using the Affymetrix ATH1 array revealed that expression levels of most pathogen-responsive genes were affected by mutations in coi1, ein2, npr1, pad4, or sid2. These five mutations defined a small number of different expression patterns displayed by the majority of pathogen-responsive genes. P. syringae pv. tomato strain DC3000 elicited a much weaker salicylic acid (SA) response than ES4326. Additional mutants were profiled using a custom array. Profiles of pbs3 and ndr1 revealed major effects of these mutations and allowed PBS3 and NDR1 to be placed between the EDS1/PAD4 node and the SA synthesis node in the defense network. Comparison of coi1, dde2, and jar1 profiles showed that many genes were affected by coi1 but very few were affected by dde2 or jar1. Profiles of coi1 plants infected with ES4326 were very similar to those of wild-type plants infected with bacteria unable to produce the phytotoxin coronatine, indicating that, essentially, all COI1-dependent gene expression changes in this system are caused by coronatine.
Characterization of Nonhost Resistance of Arabidopsis to the Asian Soybean Rust
Authors: Loehrer Marco , Langenbach Caspar , Goellner Katharina , Conrath Uwe , Schaffrath Ulrich
Published: October 2008

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is a devastating disease of soybean. We report the use of the nonhost plant Arabidopsis thaliana to identify the genetic basis of resistance to P. pachyrhizi. Upon attack by P. pachyrhizi, epidermal cells of wild-type Arabidopsis accumulated H2O2, which likely orchestrates the frequently observed epidermal cell death. However, even when epidermal cell death occurred, fungal hyphae grew on and infection was terminated at the mesophyll boundary. These events were associated with expression of PDF1.2, suggesting that P. pachyrhizi, an ostensible biotroph, mimics aspects of a necrotroph. Extensive colonization of the mesophyll occurred in Arabidopsis pen mutants with defective penetration resistance. Although haustoria were found occasionally in mesophyll cells, the successful establishment of biotrophy failed, as evidenced by the cessation of fungal growth. Double mutants affected in either jasmonic acid or salicylic acid signaling in the pen3-1 background revealed the involvement of both pathways in nonhost resistance (NHR) of Arabidopsis to P. pachyrhizi. Interestingly, expression of AtNHL10, a gene that is expressed in tissue undergoing the hypersensitive response, was only triggered in infected pen3-1 mutants. Thus, a suppression of P. pachyrhizi–derived effectors by PEN3 can be inferred. Our results demonstrate that Arabidopsis can be used to study mechanisms of NHR to ASR.
The Flagellar Sigma Factor FliA Is Required for Dickeya dadantii Virulence
Authors: Jahn Courtney E. , Willis David K. , Charkowski Amy O.
Published: October 2008

The genome sequence of the Enterobacteriaceae phytopathogen Dickeya dadantii (formerly Erwinia chrysanthemi) revealed homologs of genes required for a complete flagellar secretion system and one flagellin gene. We found that D. dadantii was able to swim and swarm but that ability to swarm was dependent upon both growth media and temperature. Mutation of the D. dadantii fliA gene was pleiotropic, with the alternate sigma factor required for flagella production and development of disease symptoms but not bacterial growth in Nicotiana benthamiana leaves. The flagellar sigma factor was also required for multiple bacterial phenotypes, including biofilm formation in culture, bacterial adherence to plant tissue, and full expression of pectate lyase activity (but not cellulase or protease activity). Surprisingly, mutation of fliA resulted in the increased expression of avrL (a gene of unknown function in D. dadantii) and two pectate lyase gene homologs, pelX and ABF-0019391. Because FliA is a key contributor to virulence in D. dadantii, it is a new target for disease control.
The Phytophthora infestans Avirulence Gene Avr4 Encodes an RXLR-dEER Effector
Authors: van Poppel Pieter M. J. A. , Guo Jun , van de Vondervoort Peter J. I. , Jung Maartje W. M. , Birch Paul R. J. , Whisson Stephen C. , Govers Francine
Published: October 2008

Resistance in potato against the oomycete Phytophthora infestans is conditioned by resistance (R) genes that are introgressed from wild Solanum spp. into cultivated potato. According to the gene-for-gene model, proteins encoded by R genes recognize race-specific effectors resulting in a hypersensitive response (HR). We isolated P. infestans avirulence gene PiAvr4 using a combined approach of genetic mapping, transcriptional profiling, and bacterial artificial chromosome marker landing. PiAvr4 encodes a 287-amino-acid-protein that belongs to a superfamily of effectors sharing the putative host-cell-targeting motif RXLR-dEER. Transformation of P. infestans race 4 strains with PiAvr4 resulted in transformants that were avirulent on R4 potato plants, demonstrating that PiAvr4 is responsible for eliciting R4-mediated resistance. Moreover, expression of PiAvr4 in R4 plants using PVX agroinfection and agroinfiltration showed that PiAvr4 itself is the effector that elicits HR on R4 but not r0 plants. The presence of the RXLR-dEER motif suggested intracellular recognition of PiAvr4. This was confirmed in agroinfiltration assays but not with PVX agroinfection. Because there was always recognition of PiAvr4 retaining the signal peptide, extracellular recognition cannot be excluded. Deletion of the RXLR-dEER domain neither stimulated nor prevented elicitor activity of PiAvr4. Race 4 strains have frame shift mutations in PiAvr4 that result in truncated peptides; hence, PiAvr4 is apparently not crucial for virulence.