bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging of the Yellow Cameleon 3.6 Indicator Reveals That Elevations in Cytosolic Ca2+ Follow Oscillating Increases in Growth in Root Hairs of Arabidopsis
Authors: Monshausen Gabriele B. , Messerli Mark A. , Gilroy Simon 
Published: June 2008

AbstractIn tip-growing cells, the tip-high Ca2+ gradient is thought to regulate the activity of components of the growth machinery, including the cytoskeleton, Ca2+-dependent regulatory proteins, and the secretory apparatus. In pollen tubes, both the Ca2+ gradient and cell elongation show oscillatory behavior, reinforcing the link between the two. We report that in growing root hairs of Arabidopsis (Arabidopsis thaliana), an oscillating tip-focused Ca2+ gradient can be resolved through imaging of a cytosolically expressed Yellow Cameleon 3.6 fluorescence resonance energy transfer-based Ca2+ sensor. Both elongation of the root hairs and the associated tip-focused Ca2+ gradient show a similar dynamic character, oscillating with a frequency of 2 to 4 min−1. Cross-correlation analysis indicates that the Ca2+ oscillations lag the growth oscillations by 5.3 ± 0.3 s. However, growth never completely stops, even during the slow cycle of an oscillation, and the concomitant tip Ca2+ level is always slightly elevated compared with the resting Ca2+ concentration along the distal shaft, behind the growing tip. Artificially increasing Ca2+ using the Ca2+ ionophore A23187 leads to immediate cessation of elongation and thickening of the apical cell wall. In contrast, dissipating the Ca2+ gradient using either the Ca2+ channel blocker La3+ or the Ca2+ chelator EGTA is accompanied by an increase in the rate of cell expansion and eventual bursting of the root hair tip. These observations are consistent with a model in which the maximal oscillatory increase in cytosolic Ca2+ is triggered by cell expansion associated with tip growth and plays a role in the subsequent restriction of growth.
Bridging the Gap between Plant and Mammalian Polyamine Catabolism: A Novel Peroxisomal Polyamine Oxidase Responsible for a Full Back-Conversion Pathway in Arabidopsis
Authors: Moschou Panagiotis N. , Sanmartin Maite , Andriopoulou Athina H. , Rojo Enrique , Sanchez-Serrano Jose J. , Roubelakis-Angelakis Kalliopi A. 
Published: June 2008

AbstractIn contrast to animals, where polyamine (PA) catabolism efficiently converts spermine (Spm) to putrescine (Put), plants have been considered to possess a PA catabolic pathway producing 1,3-diaminopropane, Δ 1-pyrroline, the corresponding aldehyde, and hydrogen peroxide but unable to back-convert Spm to Put. Arabidopsis (Arabidopsis thaliana) genome contains at least five putative PA oxidase (PAO) members with yet-unknown localization and physiological role(s). AtPAO1 was recently identified as an enzyme similar to the mammalian Spm oxidase, which converts Spm to spermidine (Spd). In this work, we have performed in silico analysis of the five Arabidopsis genes and have identified PAO3 (AtPAO3) as a nontypical PAO, in terms of homology, compared to other known PAOs. We have expressed the gene AtPAO3 and have purified a protein corresponding to it using the inducible heterologous expression system of Escherichia coli. AtPAO3 catalyzed the sequential conversion/oxidation of Spm to Spd, and of Spd to Put, thus exhibiting functional homology to the mammalian PAOs. The best substrate for this pathway was Spd, whereas the N 1-acetyl-derivatives of Spm and Spd were oxidized less efficiently. On the other hand, no activity was detected when diamines (agmatine, cadaverine, and Put) were used as substrates. Moreover, although AtPAO3 does not exhibit significant similarity to the other known PAOs, it is efficiently inhibited by guazatine, a potent PAO inhibitor. AtPAO3 contains a peroxisomal targeting motif at the C terminus, and it targets green fluorescence protein to peroxisomes when fused at the N terminus but not at the C terminus. These results reveal that AtPAO3 is a peroxisomal protein and that the C terminus of the protein contains the sorting information. The overall data reinforce the view that plants and mammals possess a similar PA oxidation system, concerning both the subcellular localization and the mode of its action.
The polybasic region of Rho GTPases defines the cleavage by Yersinia enterocolitica outer protein T (YopT)
Authors: Fueller Florian , Schmidt Gudula 
Published: June 2008

AbstractPathogenic Yersinia strains evade the innate immune responses of the host by producing effector proteins (Yersinia outer proteins [Yops]), which are directly injected into mammalian cells by a type III secretion system (TTSS). One of these effector proteins (YopT) disrupts the actin cytoskeleton of the host cell resulting in cell rounding. YopT is a cysteine protease that cleaves Rho proteins directly upstream of the post‐translationally modified cysteine. Thereby, it releases the GTPases from the membrane leading to inactivation. Small GTPases are modified by isoprenylation of the cysteine of the CAAX box, cleavage of the –AAX tripeptide, and methylation of the cysteine. We have shown that isoprenylation and the endoproteolytic cleavage of the tripeptide of Rho GTPases are essential for YopT‐induced cleavage, whereas carboxyl methylation is not required. In the present study, we post‐translationally modified RhoA, Rac, Cdc42, and several mutants in vitro and characterized the YopT‐induced cleavage with recombinant YopT. We show that farnesylated RhoA is a preferred substrate of YopT compared with the geranylgeranylated GTPase. Geranylgeranylated RhoA, however, is the preferred substrate for YopT‐catalyzed cleavage with a threefold faster turnover rate over Rac and Cdc42. Moreover, our data indicate that the composition of the polybasic region of the GTPases defines the specificity and efficiency of the YopT‐induced cleavage, and that a space between the polybasic stretch of amino acids at the C terminus and the CAAX box enhances the turnover rate of YopT‐catalyzed cleavage.
Novel protein folds and their nonsequential structural analogs
Authors: Guerler Aysam , Knapp Ernst‐Walter 
Published: June 2008

AbstractNewly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three‐dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM‐align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu‐berlin.de/gplus for pairwise alignment, visualization, and database comparison.
Autopsy pathology of cocaine users from the Eastern district of London: a retrospective cohort study
Authors: Rajab R , Stearns E , Baithun S 
Published: June 2008

Aim:To establish the most frequent pathological findings encountered at postmortem examination during the investigation of a fatality with a history of cocaine abuse.Methods:Autopsied deaths investigated by the coroner for the Eastern district of London, between 2004 and 2007, in which the decedent had positive toxicology for cocaine were identified (n = 28). The autopsy records and histology of tissue taken at autopsy were retrieved and reviewed. Pathological findings (gross and microscopic, including cardiac, pulmonary, gastrointestinal, hepatobiliary, renal and neurological) were collated.Results:The main pathological findings at autopsy occurring in this cohort (comprising predominantly men, mean age 31 years), were cardiovascular: left ventricular hypertrophy (46%), multifocal myocardial fibrosis (21%), coronary artery disease (29%), cerebrovascular disease (36%) and pulmonary oedema (71%). Hepatic steatosis (29%) and gastrointestinal haemorrhage (18%), due mostly to gastric erosions/ulceration, were also frequent findings.Conclusions:During a coroner’s autopsy of a cocaine user, a thorough cardiac examination combined with cardiac tissue sampling for histology, are valuable investigations, which are most likely to help show pathology relevant to the cause of death.
High levels of expression of cytokeratin 5 are strongly correlated with poor survival in higher grades of mucoepidermoid carcinoma
Authors: Lueck N E , Robinson R A 
Published: June 2008

Aims:Mucoepidermoid carcinoma (MEC) is the most common malignant primary salivary gland tumour. Little is known about cytokeratin expression in MEC or how it may relate to survival. In this study, the aim was to determine the extent of cytokeratin 5 (CK5) expression in intermediate- and high-grade MEC and correlate expression with survival.Methods:Data on clinicopathological features including stage and survival outcome were collected on 29 patients with intermediate- or high-grade MEC that had follow-up for at least 4 years or until death. Staining with antibody to CK5 protein was carried out and tumour staining was stratified as 0–3 (0, no tumour cells staining; 1, 1–25% of tumour cells staining; 2, 26–75% of tumour cells staining; 3, >75% of tumour cells staining). Six patients had intermediate-grade tumours and 23 had high-grade tumours. The median patient follow-up was 33 months, and 11 patients were alive at the end of the study.Results:At the end of the study, 12/13 patients with the highest (>75%) CK5 expression were dead, while 6 of 18 patients with less than 75% expression were dead (p = 0.006, Fisher exact test). When compared with those patients whose tumours had less than 75% expression, patients whose tumours had greater than 75% CK5 expression had much poorer survival times (log-rank test; p ⩽ 0.001).Conclusions:The findings suggest that very high levels of CK5 expression may be a potential marker for worse outcome in intermediate- and high-grade MEC.
Kimberlite-sourced bentonite, its paleoenvironment and implications for the Late Cretaceous K14 kimberlite cluster, northern AlbertaThis article is one of a selection of papers published in this Special Issue on the themeGeology of northeastern British Columbia and northwestern Alberta: diamonds, shallow gas, gravel, and glaciers.
Authors: Eccles D. Roy , Heaman Larry M. , Sweet Arthur R. 
Published: June 2008

Kimberlite-sourced bentonite layers have been discovered in Late Cretaceous sedimentary drill cores located within the Buffalo Head Hills kimberlite field, north-central Alberta. Two bentonites are unambiguously differentiated from “common” intermediate to felsic volcanic-derived Alberta bentonite by having similar whole-rock geochemical composition to ultramafic rocks from the Buffalo Head Hills kimberlite field and worldwide crater-facies kimberlite. The results demonstrate that the geochemical analysis of bentonite can provide a quick, cost-effective means of testing for low-volume kimberlite volcanism. The kimberlite-sourced bentonite is associated with a cluster of Buffalo Head Hills kimberlites known as the K14 complex. The K14A kimberlite occurrence has a previously reported206Pb/238U perovskite emplacement age of 86.8 ± 2.1 Ma. This age is compatible with early or mid-Cenomanian (∼99–96 Ma) and mid-Coniacian to Santonian (∼88–84 Ma) palynological results for mudstone underlying and bracketing the K14A and K14B kimberlites, respectively. Conversely, biostratigraphically significant palynomorphs in host rock cores bracketing the K14C kimberlite indicate emplacement during the Cenomanian or Turonian (∼96–92 Ma). U–Pb detrital zircon ages from syndepositional kimberlite-sourced bentonite directly adjacent to the K14C kimberlite contains a high frequency of young (∼99–92 Ma) zircon with a best maximum206Pb/238U depositional age of 91.7 ± 2.9 Ma. Thus, this innovative approach may provide evidence of multiple episodes of kimberlite emplacement within or near the K14 complex.
Olenid-dominated trilobite fauna from the Shallow Bay Formation (Cow Head Group), Cambrian–Ordovician boundary interval, western Newfoundland
Authors: Karim Talia S. 
Published: June 2008

A single boulder (PH 8.14), recovered from unit 8 on the Point of Head, Cow Head Peninsula, Shallow Bay Formation (Cow Head Group), contains a unique olenid-dominated trilobite fauna composed of the following taxa: Boeckaspis geordii n. sp., Leiobienvillia terranovica (Rasetti, 1954), hystricurid n. gen. n. sp., Tulepyge sp. A, Tulepyge sp. B, Tulepyge? sp. C, and Symphysurina sp. The pelturine trilobite B. geordii dominates the assemblage. Boulder PH 8.14 consists of light grey-brown packstone to grainstone. This is atypical for olenid-dominated faunas, which usually occur in dark laminated limestones and shales. The fauna is likely earliest Ordovician in age, but a latest Cambrian age cannot be entirely ruled out. Regardless, this assemblage is unique in that it is the only known olenid-dominated fauna from Cambrian–Ordovician boundary sediments in Laurentia. A phylogenetic analysis of Boeckaspis and other putatively closely related taxa ( Westergaardia Raymond, 1924 and Jujuyaspis Kobayashi, 1936) was conducted. The results of the analysis indicate that Westergaardia is not monophyletic and as such it is considered a junior synonym of Boeckaspis herein.
Mountain permafrost probability mapping using the BTS method in two climatically dissimilar locations, northwest Canada
Authors: Bonnaventure Philip P. , Lewkowicz Antoni G. 
Published: June 2008

The Basal Temperature of Snow (BTS) method was used to predict permafrost distribution in two climatologically dissimilar mountain environments in northwest Canada. Permafrost probability maps with 30 m × 30 m grid cells were generated for part of the Ruby Range, Yukon Territory (425 km2), and for the Haines Summit area, northern British Columbia (536 km2), using winter BTS measurements in conjunction with late-summer ground truthing by probing and digging pits to physically verify the presence of permafrost. BTS values, and hence permafrost distribution, were modeled using elevation and potential incoming solar radiation (PISR) for the Ruby Range. PISR was not significant at Haines Summit, probably because persistent cloudiness associated with its more maritime climatic regime reduced aspect-induced variability in insolation. Probability maps indicate that ∼66% of the Ruby Range area and ∼43% of the Haines Summit area are underlain by permafrost. Therefore, the Ruby Range should be classified as extensive discontinuous permafrost, while Haines Summit is part of the sporadic discontinuous permafrost zone and not the isolated patches zone as portrayed on recent maps. Extensive ground truthing proved to be an essential part of the procedure because traditional BTS “rules-of-thumb” did not remain valid across the differing mountain climate zones.
Linking environmental gradients, species composition, and vegetation indicators of sugar maple health in the northeastern United States
Authors: Horsley Stephen B. , Bailey Scott W. , Ristau Todd E. , Long Robert P. , Hallett Richard A. 
Published: June 2008

Sugar maple ( Acer saccharum Marsh.) decline has occurred throughout its range over the past 50 years, although decline symptoms are minimal where nutritional thresholds of Ca, Mg, and Mn are met. Here, we show that availability of these elements also controls vascular plant species composition in northern hardwood stands and we identify indicator species of these nutrient thresholds. Presence and abundance of vascular plant species and data on 35 environmental variables were collected from 86 stands in New Hampshire and Vermont (NHVT) and Pennsylvania and New York (PANY). Nonmetric multidimensional scaling ordination was used to determine which variables affected presence and abundance of species; both measures gave similar results. A base cation – acid cation nutrient gradient on axis one accounted for 71.9% (NHVT) and 63.0% (PANY) of the variation in the nonmetric multidimensional scaling ordination. Measures of Ca, Mg, and pH formed the base end and Al, Mn, K, soil acidity, and organic matter the acid end in both subregions. In both subregions, sugar maple foliar Mg and Ca had the strongest association with the base end of axis 1; exchangeable Al in NHVT and foliar Mn in PANY were strongly associated with the acid end. McNemar’s exact test and indicator species analysis were used to determine which species were present in stands that met the nutritional thresholds for Ca, Mg, and Mn foliar chemistry. McNemar’s exact test identified 16 species in NHVT and PANY, 16 additional species in NHVT only, and 12 additional species in PANY only. Indicator species analysis identified a subset of these species with the highest frequency of occurrence. Indicator species could provide land managers with a diagnostic tool for determining where on the landscape sugar maple is “at risk” or likely to remain healthy in the face of stresses.
Quantifying the interrelationship between tree stand growth rate and water table level in drained peatland sites within Central Finland
Authors: Hökkä Hannu , Repola Jaakko , Laine Jukka 
Published: June 2008

The quantitative relationship between stand growth rate and water table level in peatland forest sites has not been fully ascertained in the literature. In this study, we investigated this relationship by means of a bivariate regression model. Tree and stand attributes, including volume and past 5-year volume growth as well as median water table depth (WTM) during the 1984 growing season, were observed in 69 Scots pine ( Pinus sylvestris L.) sample stands with three subplots established in each stand. All stands were located in deep-peated, moderately rich to poor organic soil sites in Central Finland (61°45′–62°26′N, 22°40′–28°29′E) that had been ditched for forestry about 25 years earlier (1959–1961). Prediction models for the fixed mean functions for 5-year volume growth and WTM as well as estimates for variances and the correlation of random effects at plot and subplot levels were estimated simultaneously using bivariate regression methods. The correlation of model residuals at the plot level was highly significant. The model was applied to simulate stand volume development for a period of 20 years. Simulations illustrated the dynamic interaction of stand volume, volume growth, and soil water levels: deep initial WTM resulted in stand growth and volume-development increases and subsequently further deepened the WTM in the stand. The model can be applied to southern boreal drained Scots pine peatlands to estimate the WTM in different stand volume conditions and to assess the effect of stand management on WTM.
Impact of a pine lappet (Dendrolimus pini) mass outbreak on C and N fluxes to the forest floor and soil microbial properties in a Scots pine forest in Germany
Authors: le Mellec Anne , Michalzik Beate 
Published: June 2008

Herbivorous insect infestations significantly alter element and nutrient cycling in forests, thus directly and indirectly affecting ecosystem functioning. In this paper, we report on the herbivore-mediated transfer of carbon (C) and nitrogen (N) from the canopy to the forest floor and its influence on soil microbial activity during a pine lappet ( Dendrolimus pini L.) infestation. Over the course of 6 months, we followed C and N fluxes in bulk deposition, throughfall, and green fall (green needle debris dropped during herbivory) together with solid frass (insect faeces) in an 80-year-old Scots pine ( Pinus silvestris L.) forest. Compared with the control, herbivore defoliation significantly doubled throughfall inputs of total and dissolved organic C and N over the study period. Frass plus green-fall C and N fluxes peaked in June–July at 110 kg C·ha–1and 2.3 kg N·ha–1, respectively. Randomized intervention analysis revealed no significant effects of herbivory on soil microbial properties, except for adenylate energy charge, which showed slightly higher values under herbivory. This study demonstrates the importance of canopy herbivory on overall C and N inputs to forest ecosystems, particularly in altering the timing and quality of the organic material reaching the forest floor and potentially affecting belowground processes.
Prediction ofPinus sylvestrisclear-wood properties using NIR spectroscopy and biorthogonal partial least squares regression
Authors: Lestander Torbjörn A. , Lindeberg Johan , Eriksson Daniel , Bergsten Urban 
Published: June 2008

Thirteen wood parameters were predicted using near infrared (NIR) spectra in the range 780–2380 nm modelled by biorthogonal partial least squares regression. The analysis of parameters and NIR measurements was done on clear-wood samples from the base and midstem of Scots pine ( Pinus sylvestris L.) from trees at two sites. Calibrations based on the measured parameters at seven growth rings (cambial age ranging between 6 and 42 years) could be divided into three groups: (i) the best accuracy was found for longitudinal modulus of elasticity (r > 0.9) followed by bending, compression, and cell length (0.8 < r < 0.9); (ii) microfibril angle, longitudinal hardness, proportion of latewood, and creep with correlations in the range of 0.7–0.8; and (iii) tangential hardness, cell diameter, and cell wall thickness with 0.4 < r < 0.7. It was also shown that juvenile (cambial age ≤20 years) and mature wood can be classified using NIR techniques.
Smaller longer, larger shorter: energy budget calculations explain intrapopulation variation in remigration intervals for loggerhead sea turtles (Caretta caretta)
Authors: Hatase Hideo , Tsukamoto Katsumi 
Published: June 2008

Adult female loggerhead sea turtles ( Caretta caretta (L., 1758)) show a size-related behavioural and trophic dichotomy within several populations: oceanic planktivory by small females and neritic benthivory by large females. Within a Japanese population, smaller females have longer remigration intervals (the intervals between successive nesting years) than larger females. We hypothesized that this is attributed to the size-related foraging dichotomy, and calculated energy budgets and food requirements for the small and large females. Total reproductive energy costs for the small and large females were 1003 and 434 MJ, equivalent to 4043 kg of planktonic items and 275 kg of benthic items, respectively. The minimum durations necessary for accumulating the total reproductive energy for the small and large females were 430 and 26 days, equivalent to remigration intervals of 2 years and 1 year taking into account the nesting and migration durations and seasonal reproduction. Therefore, it was theoretically demonstrated that the intrapopulation variation in remigration intervals for Japanese loggerheads could be caused by the difference in their feeding habits, implying that remigration dynamics in a sea turtle population that shows a foraging dichotomy is regulated by feeding conditions not in a single habitat but in multiple habitats.