bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for phosphonate usage in the coral holobiont
Authors: Thomas S , Burdett H , Temperton B , Wick R , Snelling D , McGrath J W , Quinn J P , Munn C , Gilbert J A 
Published: December 2009

Abstract
Phosphonates are characterized by a stable carbon–phosphorus bond and commonly occur as lipid conjugates in invertebrate cell membranes. Phosphonoacetate hydrolase encoded by the phnA gene, catalyses the cleavage of phosphonoacetate to acetate and phosphate. In this study, we demonstrate the unusually high phnA diversity in coral-associated bacteria. The holobiont of eight coral species tested positive when screened for phnA using degenerate primers. In two soft coral species, Sinularia and Discosoma, sequencing of the phnA gene showed 13 distinct groups on the basis of 90% sequence identity across 100% of the sequence. A total of 16 bacterial taxa capable of using phosphonoacetate as the sole carbon and phosphorus source were isolated; 8 of which had a phnA+ genotype. This study enhances our understanding of the wide taxonomic and environmental distribution of phnA, and highlights the importance of phosphonates in marine ecosystems.
Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan
Authors: Kimura Hiroyuki , Nashimoto Hiroaki , Shimizu Mikio , Hattori Shohei , Yamada Keita , Koba Keisuke , Yoshida Naohiro , Kato Kenji 
Published: December 2009

AbstractTo identify the methanogenic pathways present in a deep aquifer associated with an accretionary prism in Southwest Japan, a series of geochemical and microbiological studies of natural gas and groundwater derived from a deep aquifer were performed. Stable carbon isotopic analysis of methane in the natural gas and dissolved inorganic carbon (mainly bicarbonate) in groundwater suggested that the methane was derived from both thermogenic and biogenic processes. Archaeal 16S rRNA gene analysis revealed the dominance of H2-using methanogens in the groundwater. Furthermore, the high potential of methane production by H2-using methanogens was shown in enrichments using groundwater amended with H2 and CO2. Bacterial 16S rRNA gene analysis showed that fermentative bacteria inhabited the deep aquifer. Anaerobic incubations using groundwater amended with organic substrates and bromoethanesulfonate (a methanogen inhibitor) suggested a high potential of H2 and CO2 generation by fermentative bacteria. To confirm whether or not methane is produced by a syntrophic consortium of H2-producing fermentative bacteria and H2-using methanogens, anaerobic incubations using the groundwater amended with organic substrates were performed. Consequently, H2 accumulation and rapid methane production were observed in these enrichments incubated at 55 and 65 °C. Thus, our results suggested that past and ongoing syntrophic biodegradation of organic compounds by H2-producing fermentative bacteria and H2-using methanogens, as well as a thermogenic reaction, contributes to the significant methane reserves in the deep aquifer associated with the accretionary prism in Southwest Japan.
Current Trends in Knowledge Production: An Historical–Institutional Analysis
Authors: McNeely Ian F. 
Published: December 2009

Abstract
Building on the author’s recent survey of Western knowledge institutions since antiquity, this article assesses the impact of current trends in information technology, higher education, science, and the environment on knowledge production. Its focus on institutions diverges from conventional histories of ideas, media, and technologies but also from the understandings of knowledge and information prevalent among economists. It instead identifies patterns by which entirely new institutions of knowledge supersede their predecessors, reconceptualizing today’s changes around the fitful process by which the laboratory, broadly understood, outgrows the tutelage of the academic disciplines.
Knowledge Directed Economic Selection and Growth
Authors: Eliasson Gunnar 
Published: December 2009

Abstract
The single most important postulate in economics is what you assume about the totality of all possible states that the economy can be in (the state space). The assumption you make determines the costs of information and learning when exploring that state space, the nature of the equilibrating forces of the markets of the economy, towards what kind of equilibrium the economic system is heading and what that means for the modes of behavior of individuals and firms, in short the dynamics of the economy. The mainstream model of economics assumes a very narrow and, for all practical purposes, fully transparent state space and thus excludes all interesting dynamics from the analysis by assumption. I argue for the alternative assumption of a very large and non‐transparent state space, or investment opportunities space that takes us into the unpredictable world of an Experimentally Organized Economy that is more compatible with economic reality. In that brave new world of economics new answers to old questions appear. Above all, using the tools of analysis developed from, and for the mainstream neoclassical model to study the realities of an EOE will place the analyst in a misinformation situation. I illustrate that through simulation on the Swedish micro to macro (MM) model and with one Swedish business case.
Calorimetric studies of glass transition phenomenon in glassy Se80−
xTe20Snx alloys
Authors: Kumar H , Mehta N , Singh K 
Published: December 2009

Glass transition kinetics has been studied in a glassy Se80−

x
Te20Sn
x
(0 ⩽x ⩽10) system. Differential scanning calorimetry (DSC) runs were taken at four different heating rates (5, 10, 15 and 20 K min−1) for this purpose. The heating rate dependence of the glass transition temperature (T
g) has been studied using different non-isothermal methods. The activation energy of glass transition (E
g) has been evaluated using Kissinger's relation and the theory of Moynihan. The composition dependence of T
g and E
g has also been discussed.
Biochemical and Molecular Characterization of PvPAP3, a Novel Purple Acid Phosphatase Isolated from Common Bean Enhancing Extracellular ATP Utilization
Authors: Liang Cuiyue , Tian Jiang , Lam Hon-Ming , Lim Boon Leong , Yan Xiaolong , Liao Hong 
Published: December 2009

Abstract
Purple acid phosphatases (PAPs) play diverse physiological roles in plants. In this study, we purified a novel PAP, PvPAP3, from the roots of common bean (Phaseolus vulgaris) grown under phosphate (Pi) starvation. PvPAP3 was identified as a 34-kD monomer acting on the specific substrate, ATP, with a broad pH range and a high heat stability. The activity of PvPAP3 was insensitive to tartrate, indicating that PvPAP3 is a PAP-like protein. Amino acid sequence alignment and phylogenetic analysis suggest that PvPAP3 belongs to the group of plant PAPs with low molecular mass. Transient expression of 35S:PvPAP3-green fluorescent protein in onion (Allium cepa) epidermal cells verified that it might anchor on plasma membrane and be secreted into apoplast. Pi starvation led to induction of PvPAP3 expression in both leaves and roots of common bean, and expression of PvPAP3 was strictly dependent on phosphorus (P) availability and duration of Pi starvation. Furthermore, induction of PvPAP3 expression was more rapid and higher in a P-efficient genotype, G19833, than in a P-inefficient genotype, DOR364, suggesting possible roles of PvPAP3 in P efficiency in bean. In vivo analysis using a transgenic hairy root system of common bean showed that both growth and P uptake of bean hairy roots from the PvPAP3 overexpression transgenic lines were significantly enhanced when ATP was supplied as the sole external P source. Taken together, our results suggest that PvPAP3 is a novel PAP that might function in the adaptation of common bean to P deficiency, possibly through enhancing utilization of extracellular ATP as a P source.
An O-Acetylserine(thiol)lyase Homolog with l-Cysteine Desulfhydrase Activity Regulates Cysteine Homeostasis in Arabidopsis
Authors: Aݩlvarez Consolacioݩn , Calo Leticia , Romero Luis C. , Garciݩa Irene , Gotor Cecilia 
Published: December 2009

Abstract
Cysteine (Cys) occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis (Arabidopsis thaliana) cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of Cys. Because they are localized in the cytosol, plastids, and mitochondria, this results in multiple subcellular Cys pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (for Cys synthase-like; At5g28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of l-Cys to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel l-Cys desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in Cys metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total Cys desulfuration activity in leaves, and there is a concomitant increase in the total Cys content. As a consequence, the expression levels of sulfur-responsive genes are deregulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an l-Cys desulfhydrase involved in maintaining Cys homeostasis, mainly at late developmental stages or under environmental perturbations.
Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses
Authors: Walley Justin W. , Kelley Dior R. , Nestorova Gergana , Hirschberg David L. , Dehesh Katayoon 
Published: December 2009

AbstractTo maintain homeostasis in an ever-changing environment organisms have evolved mechanisms to reprogram gene expression. One central mechanism regulating gene expression is messenger RNA (mRNA) degradation, which is initiated by poly(A) tail shortening (deadenylation). The carbon catabolite repressor 4-CCR4 associated factor1 (CCR4-CAF1) complex is the major enzyme complex that catalyzes mRNA deadenylation and is conserved among eukaryotes. However, the components and functions of this global regulatory complex have not been well characterized in plants. Here we investigate the CAF1 family in Arabidopsis (Arabidopsis thaliana). We identify 11 AtCAF1 homologs and show that a subset of these genes are responsive to mechanical wounding, among them are AtCAF1a and AtCAF1b whose expression levels are rapidly and transiently induced by wounding. The differential expression profiles of the various AtCAF1s suggest that not all AtCAF1 genes are involved in stress-responsive regulation of transcript levels. Comparison of misexpressed genes identified via transcript profiling of Atcaf1a and Atcaf1b mutants at different time points before and after wounding suggests that AtCAF1a and AtCAF1b target shared and unique transcripts for deadenylation with temporal specificity. Consistent with the AtPI4Kγ3 transcript exhibiting the largest increase in abundance in Atcaf1b, AtCAF1b targets AtPI4Kγ3 mRNA for deadenylation. Stress-tolerance assays demonstrate that AtCAF1a and AtCAF1b are involved in mediating abiotic stress responses. However, AtCAF1a and AtCAF1b are not functionally redundant in all cases, nor are they essential for all environmental stresses. These findings demonstrate that these closely related proteins exhibit overlapping and distinct roles with respect to mRNA deadenylation and mediation of stress responses.
Severely degraded dunes of the southern Kalahari: local extinction, persistence and natural re‐establishment of plants
Authors: Rutherford Michael Charles , Powrie Leslie Ward 
Published: December 2009

AbstractThis study aimed to quantify and understand the impact of severe land degradation on plant attributes and diversity on dunes of the southern Kalahari. Heavy grazing pressure in particular resulted in a significant decline of canopy cover and species number in annual and perennial life forms; forb and graminoid growth forms; erect and prostrate habits; and leafy stem, tussock and stoloniferous architectures. However, no significant change was found in shrub and tree forms which persisted without apparent new recruitment. Under these conditions, species diversity dropped sharply and a number of species, mainly graminoids, became apparently locally extinct. The perennial shrub, Crotalaria cf. spartioides, showed the converse with a high frequency of establishing seedlings on the degraded dunes. Changes in relative dominance show that the extreme treatment favours perennial over annual, woody over graminoid and forb, erect over prostrate and leafy stem over stoloniferous and tussock. Some of these results and certain species and soil responses differ from those reported from grazing studies elsewhere, and are possibly no longer directly related to the impact of the primary grazing pressure but to the secondary effect of subsequent instability of the dunes.
Effect of intra‐operative pressure support vs pressure controlled ventilation on oxygenation and lung function in moderately obese adults*
Authors: Zoremba M. , Kalmus G. , Dette F. , Kuhn C. , Wulf H. 
Published: December 2009

SummaryObesity impairs peri‐operative lung function. To evaluate the impact of pressure support ventilation vs pressure controlled ventilation in moderately obese adults upon early postoperative lung function, we randomly assigned 68 moderately obese patients (body mass index 25–35 kg.m−2) undergoing minor surgery to receive intra‐operative ventilation either with pressure support or pressure controlled ventilation. We performed intra‐operative blood gas analysis and measured pulse oximetry saturation, spirometry values at pre‐operative assessment (baseline) and at 10 min, 30 min, 2 h and 24 h after extubation. The intra‐operative oxygenation index (arterial partial pressure of oxygen/fraction of inspired oxygen) in the pressure support ventilation group was significantly improved over time (p < 0.0001). Postoperatively, the pressure support ventilation group also had better lung function and oxygenation values than did the pressure controlled ventilation group (p < 0.005). We conclude that pressure support ventilation better maintains lung function than pressure controlled ventilation in moderately overweight patients scheduled for minor surgery.
Impact of dexamethasone responsiveness on long term outcome in patients with newly diagnosed multiple myeloma
Authors: Sinha Shirshendu , Vincent Rajkumar S. , Lacy Martha Q. , Hayman Suzanne R. , Buadi Francis K. , Dispenzieri Angela , Dingli David , Kyle Robert A. , Gertz Morie A. , Kumar Shaji 
Published: December 2009

SummaryDexamethasone (Dex), alone or in combination, is commonly used for treating multiple myeloma. Dex as single agent for initial therapy of myeloma results in overall response rates of 50–60%. It is unclear whether steroid responsiveness reflects any biological characteristic that impacts long‐term outcome. We studied a cohort of 182 patients with newly diagnosed myeloma seen between March 1998 and June 2007, initially treated with single‐agent Dex for at least 4 weeks. The median age at diagnosis was 63 years (range, 39–81) and the median estimated survival was 55 months. At a median duration of therapy of 15 weeks, 91 (50%) patients had a partial response or better, 80 (44%) had less than partial response and the remaining (6%) patients were not evaluable. The median overall survival from diagnosis for the responders was 75 months compared to 71 months for remaining patients, P = 0·6.There was no correlation between baseline disease characteristics and Dex responsiveness. While overall survival was longer for the 130 (70%) patients who proceeded to an autologous stem cell transplant, no correlation was found between survival and Dex responsiveness among either group. Among this cohort of patients with myeloma, failure to respond to single agent steroid did not have an adverse impact on eventual outcome.
The development and persistence of alternative ecosystem states in a large, shallow lake
Authors: WATERS MATTHEW N. , PIEHLER MICHAEL F. , SMOAK JOSEPH M. , MARTENS CHRISTOPHER S. 
Published: December 2009

Summary1. Palaeolimnological data were used to investigate drivers of the community of primary producers in Lake Mattamuskeet, North Carolina, U.S.A. This is a large, shallow lake with two basins currently dominated by phytoplankton and macrophytes. The two basins were divided in 1940 by the building of a roadway across the lake, which also corresponded with the divergence in their ecosystem state.2. Photosynthetic pigments, organic matter and nutrients (P, N, C, S) were analysed in sediment cores from each basin to reconstruct the primary producer community over the past c. 100 years. We sought to answer two questions. First, what changes to the ecosystem resulting from the building of the roadway caused the development of different primary producer communities in the two basins? Second, why have the alternative ecosystem states persisted despite a variety of human perturbations since 1940?3. K‐means cluster analysis and principal component analysis were applied to identify three sediment types based on photosynthetic pigment data: sediments indicating low productivity (low pigment concentrations), sediments associated with macrophytes (chlorophyll a and b) and with phytoplankton (alloxanthin and aphanizophyll). In addition, other palaeolimnological proxies measured, such as loss on ignition, total phosphorus, total organic carbon/total nitrogen and other nutrients, were different in post‐1940 sediments within the two basins.4. These differences suggest characteristics, such as nutrient cycling, water depth and other physical changes resulting from roadway construction, combined to establish and maintain the differing communities of primary producers in the two basins. Furthermore, Fe/S dynamics and waterfowl herbivory probably contributed to the development of the two ecosystem states.
Selection by sheep and goats for perennial ryegrass and white clover offered over a range of sward height contrasts
Authors: Concha M. A. , Nicol A. M. 
Published: December 2009

The selection by sheep (six Coopworth ewe hoggets, 44·3 ± 4·6 kg live weight) and goats (six Saanen/Anglo‐Nubian yearling males, 38·1 ± 3·8 kg live weight) for perennial ryegrass (Lolium perenne) and white clover (Trifolium repens) and for sward height was measured in two experiments involving paired turves. Pairs of turves with herbage of differing height and of either the same or different plant species were offered. One sward (fixed height species, FHS) was always offered at 130 mm and the other (variable height species, VHS) at 130, 90 or 50 mm. Turves (450 mm × 220 mm) were cut to a soil depth of 100–150 mm from areas of perennial ryegrass and white clover regrown to the desired height after previously being cut to 30 mm. Each turf in a pair was weighed (±1 g) before and after grazing by penned animals maintained on a barley‐based pelleted diet. The number of prehending bites taken from each turf was recorded over a grazing period (128 ± 12 s). Bite mass, bite rate and intake rate were calculated.As the sward height of the VHS turf declined, an increasing proportion of the diet was selected from the 130 mm turf. When averaged over all height contrasts, both animal species selected a higher proportion (0·776 ± 0·026) of their diet from 130‐mm white clover than from 130‐mm perennial ryegrass (0·591 ± 0·018) turves. On average, goats selected a higher proportion (0·721 ± 0·022) of their dry‐matter (DM) intake from the 130‐mm turf than sheep (0·646 ± 0·019), but the effect was not consistent. In contrasts with perennial ryegrass as the VHS (and both perennial ryegrass and white clover as FHS), the proportion of the diet selected from the 130‐mm turf was very similar for both animal species. However, with white clover as the VHS (and both perennial ryegrass and white clover as FHS), goats selected a higher proportion of their intake from the 130‐mm turf to the extent that in the 130‐mm perennial ryegrass/50‐mm white clover contrast sheep showed as strong selection for 50‐mm white clover as goats did for 130‐mm perennial ryegrass. This lesser selection of goats for white clover as its height in a sward declines is likely to contribute to the higher white clover content observed in swards grazed by goats.Bite mass was greater on white clover (246 ± 5 mg DM bite–1) than on perennial ryegrass (173 ± 5 mg DM bite–1) and was greater for goats (255 ± 6 mg DM bite–1) than for sheep (195 ± 5 mg DM bite–1). Bite rate was greater on perennial ryegrass (45·9 ± 1·0 bites min–1) than on white clover (39·9 ± 1·0 bites min–1) and was greater for sheep (45·5 ± 1·1 bites min–1) than for goats (42·5 ± 1·1 bites min–1). Apparent intake rate by both sheep and goats was lower (mean, 5·0 ± 0·29 g DM min–1) on 130 mm perennial ryegrass/white clover than on 130 mm perennial ryegrass/perennial ryegrass (7·0 ± 0·27 g DM min–1), but was higher (9·62 ± 0·29 g DM min–1) on 130‐mm white clover/perennial ryegrass than on 130‐mm white clover/white clover (8·2 ± 0·29 g DM min–1) combinations.
Calcium‐binding proteins in skeletal muscles of the mdx mice: potential role in the pathogenesis of Duchenne muscular dystrophy
Authors: Pertille Adriana , De Carvalho Candida Luiza Tonizza , Matsumura Cintia Yuri , Neto Humberto Santo , Marques Maria Julia 
Published: December 2009

SummaryDuchenne muscular dystrophy is one of the most common hereditary diseases. Abnormal ion handling renders dystrophic muscle fibers more susceptible to necrosis and a rise in intracellular calcium is an important initiating event in dystrophic muscle pathogenesis. In the mdx mice, muscles are affected with different intensities and some muscles are spared. We investigated the levels of the calcium‐binding proteins calsequestrin and calmodulin in the non‐spared axial (sternomastoid and diaphragm), limb (tibialis anterior and soleus), cardiac and in the spared extraocular muscles (EOM) of control and mdx mice. Immunoblotting analysis showed a significant increase of the proteins in the spared mdx EOM and a significant decrease in the most affected diaphragm. Both proteins were comparable to the cardiac muscle controls. In limb and sternomastoid muscles, calmodulin and calsequestrin were affected differently. These results suggest that differential levels of the calcium‐handling proteins may be involved in the pathogenesis of myonecrosis in mdx muscles. Understanding the signaling mechanisms involving Ca2+‐calmodulin activation and calsequestrin expression may be a valuable way to develop new therapeutic approaches to the dystrophinopaties.