bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for evaluating the impacts of fishing mortality and stochastic influences on the demography of two long-lived shark stocks
Authors: McAuley Rory B. , Simpfendorfer Colin A. , Hall Norm G. 
Published: September 2007

Abstract
McAuley, R. B., Simpfendorfer, C. A., and Hall, N. G. 2007. A method for evaluating the impacts of fishing mortality and stochastic influences on the demography of two long-lived shark stocks. — ICES Journal of Marine Science, 64.
Stochastic demographic models were developed for Carcharhinus obscurus and C. plumbeus populations off the west coast of Australia by resampling the input parameters for life tables from empirical biological data collected from commercial target fisheries and fishery-independent surveys. The models were used to examine the effects of multiple scenarios of age-specific survival, derived from the fishing mortality rates estimated from a tagging study on sharks and indirect estimates of natural mortality. In the absence of fishing, median estimates of the rates of intrinsic population increase (r) were 0.025 for both species. Inclusion of the age-specific fishing mortality rates estimated for C. obscurus recruits born in 1994 and 1995 resulted in the median estimates of r declining to 0.007 and 0.012, respectively, suggesting that recent harvest levels of mainly neonates by the target fishery were probably sustainable. However, the model also suggested that the population was more susceptible to exploitation of older sharks than was previously believed. The C. plumbeus model indicated that fishing mortality between 2001 and 2004 was probably unsustainable. The increasingly negative trend in median r estimates (from –0.032 to –0.049), and the population’s apparently limited capacity for density-dependent compensation through changes in fecundity, somatic growth and longevity, suggests that management intervention is necessary to prevent continued stock depletion.
Reduced Expression of Succinyl-Coenzyme A Ligase Can Be Compensated for by Up-Regulation of theγ-Aminobutyrate Shunt in Illuminated Tomato Leaves
Authors: Studart-Guimarães Claudia , Fait Aaron , Nunes-Nesi Adriano , Carrari Fernando , Usadel Björn , Fernie Alisdair R. 
Published: September 2007

AbstractIncreasing experimental evidence suggests that the tricarboxylic acid cycle in plants is of greater importance in illuminated photosynthetic tissues than previously thought. In this study, transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the β-subunit of succinyl-coenzyme A ligase in either the antisense orientation or using the RNA interference approach, however, revealed little alteration in either photosynthesis or plant growth despite exhibiting dramatic reductions in activity. Moreover, the rate of respiration was only moderately affected in the transformants, suggesting that this enzyme does not catalyze a crucial step in mitochondrial respiration. However, metabolite and transcript profiling of these lines alongside enzyme and label redistribution experiments revealed that, whereas considerable activity of this enzyme appears to be dispensable, the reason for such a mild phenotype in extremely inhibited lines was an up-regulation of an alternative pathway for succinate production—that offered by the γ-aminobutyric acid shunt. When taken together, these data highlight the importance both of succinate production for mitochondrial metabolism and the interplay between various routes of its production. The results are discussed in the context of current models of plant respiration in mitochondrial and cellular metabolism of the illuminated leaf.
A Proteinaceous Elicitor Sm1 from the Beneficial FungusTrichoderma virensIs Required for Induced Systemic Resistance in Maize
Authors: Djonović Slavica , Vargas Walter A. , Kolomiets Michael V. , Horndeski Michelle , Wiest Aric , Kenerley Charles M. 
Published: September 2007

AbstractWe have previously shown that the beneficial filamentous fungus Trichoderma virens secretes the highly effective hydrophobin-like elicitor Sm1 that induces systemic disease resistance in the dicot cotton (Gossypium hirsutum). In this study we tested whether colonization of roots by T. virens can induce systemic protection against a foliar pathogen in the monocot maize (Zea mays), and we further demonstrated the importance of Sm1 during maize-fungal interactions using a functional genomics approach. Maize seedlings were inoculated with T. virens Gv29-8 wild type and transformants in which SM1 was disrupted or constitutively overexpressed in a hydroponic system or in soil-grown maize seedlings challenged with the pathogen Colletotrichum graminicola. We show that similar to dicot plants, colonization of maize roots by T. virens induces systemic protection of the leaves inoculated with C. graminicola. This protection was associated with notable induction of jasmonic acid- and green leaf volatile-biosynthetic genes. Neither deletion nor overexpression of SM1 affected normal growth or development of T. virens, conidial germination, production of gliotoxin, hyphal coiling, hydrophobicity, or the ability to colonize maize roots. Plant bioassays showed that maize grown with SM1-deletion strains exhibited the same levels of systemic protection as non-Trichoderma-treated plants. Moreover, deletion and overexpression of SM1 resulted in significantly reduced and enhanced levels of disease protection, respectively, compared to the wild type. These data together indicate that T. virens is able to effectively activate systemic disease protection in maize and that the functional Sm1 elicitor is required for this activity.
Phage-Type RNA Polymerase RPOTmp Transcribes the rrn Operon from the PC Promoter at Early Developmental Stages in Arabidopsis
Authors: Courtois Florence , Merendino Livia , Demarsy Emilie , Mache Régis , Lerbs-Mache Silva 
Published: September 2007

Abstract
The plastid genome of higher plants is transcribed by two different types of RNA polymerases named nucleus encoded RNA polymerase (NEP) and plastid encoded RNA polymerase. Plastid encoded RNA polymerase is a multimeric enzyme comparable to eubacterial RNA polymerases. NEP enzymes represent a small family of monomeric phage-type RNA polymerases. Dicotyledonous plants harbor three different phage-type enzymes, named RPOTm, RPOTp, and RPOTmp. RPOTm is exclusively targeted to mitochondria, RPOTp is exclusively targeted to plastids, and RPOTmp is targeted to plastids as well as to mitochondria. In this article, we have made use of RPOTp and RPOTmp T-DNA insertion mutants to answer the question of whether both plastid-located phage-type RNA polymerases have overlapping or specific functions in plastid transcription. To this aim, we have analyzed accD and rpoB messenger RNAs (mRNA; transcribed from type I NEP promoters), clpP mRNA (transcribed from the −59 type II NEP promoter), and the 16S rRNA (transcribed from the exceptional PC NEP promoter) by primer extension. Results suggest that RPOTp represents the principal RNA polymerase for transcribing NEP-controlled mRNA genes during early plant development, while RPOTmp transcribes specifically the rrn operon from the PC promoter during seed imbibition.
Alteration of Organic Acid Metabolism in Arabidopsis Overexpressing the Maize C4 NADP-Malic Enzyme Causes Accelerated Senescence during Extended Darkness
Authors: Fahnenstich Holger , Saigo Mariana , Niessen Michaela , Zanor María I. , Andreo Carlos S. , Fernie Alisdair R. , Drincovich María F. , Flügge Ulf-Ingo , Maurino Verónica G. 
Published: September 2007

Abstract
The full-length cDNA encoding the maize (Zea mays) C4 NADP-malic enzyme was expressed in Arabidopsis (Arabidopsis thaliana) under the control of the cauliflower mosaic virus 35S promoter. Homozygous transgenic plants (MEm) were isolated with activities ranging from 6- to 33-fold of those found in the wild type. The transformants did not show any differences in morphology and development when grown in long days; however, dark-induced senescence progressed more rapidly in MEm plants compared to the wild type. Interestingly, senescence could be retarded in the transgenic lines by exogenously supplying glucose, sucrose, or malate, suggesting that the lack of a readily mobilized carbon source is likely to be the initial factor leading to the premature induction of senescence in MEm plants. A comprehensive metabolic profiling on whole rosettes allowed determination of approximately 80 metabolites during a diurnal cycle as well as following dark-induced senescence and during metabolic complementation assays. MEm plants showed no differences in the accumulation and degradation of carbohydrates with respect to the wild type in all conditions tested, but accumulated lower levels of intermediates used as respiratory substrates, prominently malate and fumarate. The data indicated that extremely low levels of malate and fumarate are responsible for the accelerated dark-induced senescence encountered in MEm plants. Thus, in prolonged darkness these metabolites are consumed faster than in the wild type and, as a consequence, MEm plants enter irreversible senescence more rapidly. In addition, the data revealed that both malate and fumarate are important forms of fixed carbon that can be rapidly metabolized under stress conditions in Arabidopsis.
Participation of the Arabidopsis bHLH Factor GL3 in Trichome Initiation Regulatory Events
Authors: Morohashi Kengo , Zhao Mingzhe , Yang Manli , Read Betsy , Lloyd Alan , Lamb Rebecca , Grotewold Erich 
Published: September 2007

AbstractThe development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis (Arabidopsis thaliana) provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. We show here that trichome initiation is triggered within 4 h of the induction of the GLABRA3 (GL3) basic helix-loop-helix transcription factor. Within this developmental window, GL3 binds to the promoters of at least three genes previously implicated in the development and patterning of trichomes (GL2, CAPRICE, and ENHANCER OF TRIPTYCHON AND CAPRICE1) and activates their transcription. The in vivo binding of GL3 to the promoters of these genes requires the presence of the R2R3-MYB factor GL1, supporting a model in which a GL3-GL1 complex is part of the trichome initiation enhanceosome. In contrast, GL3 is recruited to its own promoter in a GL1-independent manner, and this results in decreased GL3 expression, suggesting the presence of a GL3 negative autoregulatory loop. In support of genetic analyses indicating that ENHANCER OF GL3 (EGL3) is partially redundant with GL3, we show that EGL3 shares some direct targets with GL3. However, our results suggest that GL3 and EGL3 work independently of each other. Taken together, our results provide a regulatory framework to understand early events of epidermal cell differentiation.
yucca6, a Dominant Mutation in Arabidopsis, Affects Auxin Accumulation and Auxin-Related Phenotypes
Authors: Kim Jeong Im , Sharkhuu Altanbadralt , Jin Jing Bo , Li Pinghua , Jeong Jae Cheol , Baek Dongwon , Lee Sang Yeol , Blakeslee Joshua J. , Murphy Angus S. , Bohnert Hans J. , Hasegawa Paul M. , Yun Dae-Jin , Bressan Ray A. 
Published: September 2007

AbstractAuxin plays critical roles in many aspects of plant growth and development. Although a number of auxin biosynthetic pathways have been identified, their overlapping nature has prevented a clear elucidation of auxin biosynthesis. Recently, Arabidopsis (Arabidopsis thaliana) mutants with supernormal auxin phenotypes have been reported. These mutants exhibit hyperactivation of genes belonging to the YUCCA family, encoding putative flavin monooxygenase enzymes that result in increased endogenous auxin levels. Here, we report the discovery of fertile dominant Arabidopsis hypertall1-1D and hypertall1-2D (yucca6-1D, -2D) mutants that exhibit typical auxin overproduction phenotypic alterations, such as epinastic cotyledons, increased apical dominance, and curled leaves. However, unlike other auxin overproduction mutants, yucca6 plants do not display short or hairy root phenotypes and lack morphological changes under dark conditions. In addition, yucca6-1D and yucca6-2D have extremely tall (&gt;1 m) inflorescences with extreme apical dominance and twisted cauline leaves. Microarray analyses revealed that expression of several indole-3-acetic acid-inducible genes, including Aux/IAA, SMALL AUXIN-UP RNA, and GH3, is severalfold higher in yucca6 mutants than in the wild type. Tryptophan (Trp) analog feeding experiments and catalytic activity assays with recombinant YUCCA6 indicate that YUCCA6 is involved in a Trp-dependent auxin biosynthesis pathway. YUCCA6:GREEN FLUORESCENT PROTEIN fusion protein indicates YUCCA6 protein exhibits a nonplastidial subcellular localization in an unidentified intracellular compartment. Taken together, our results identify YUCCA6 as a functional member of the YUCCA family with unique roles in growth and development.
Differential Expansion and Expression ofα- andβ-Tubulin Gene Families inPopulus
Authors: Oakley Rodney V. , Wang Yuh-Shuh , Ramakrishna Wusirika , Harding Scott A. , Tsai Chung-Jui 
Published: September 2007

AbstractMicrotubule organization is intimately associated with cellulose microfibril deposition, central to plant secondary cell wall development. We have determined that a relatively large suite of eight α-TUBULIN (TUA) and 20 β-TUBULIN (TUB) genes is expressed in the woody perennial Populus. A number of features, including gene number, α:β gene representation, amino acid changes at the C terminus, and transcript abundance in wood-forming tissue, distinguish the Populus tubulin suite from that of Arabidopsis thaliana. Five of the eight Populus TUAs are unusual in that they contain a C-terminal methionine, glutamic acid, or glutamine, instead of the more typical, and potentially regulatory, C-terminal tyrosine. Both C-terminal Y-type (TUA1) and M-type (TUA5) TUAs were highly expressed in wood-forming tissues and pollen, while the Y-type TUA6 and TUA8 were abundant only in pollen. Transcripts of the disproportionately expanded TUB family were present at comparatively low levels, with phylogenetically distinct classes predominating in xylem and pollen. When tension wood induction was used as a model system to examine changes in tubulin gene expression under conditions of augmented cellulose deposition, xylem-abundant TUA and TUB genes were up-regulated. Immunolocalization of TUA and TUB in xylem and phloem fibers of stems further supported the notion of heavy microtubule involvement during cellulose microfibril deposition in secondary walls. The high degree of sequence diversity, differential expansion, and differential regulation of Populus TUA and TUB families may confer flexibility in cell wall formation that is of adaptive significance to the woody perennial growth habit.
A NEW METHOD FOR THE ESTIMATION OF CAPACITY UTILIZATION: THEORY AND EMPIRICAL EVIDENCE FROM 14 EU COUNTRIES
Authors: Dergiades Theologos , Tsoulfidis Lefteris 
Published: September 2007

ABSTRACTIn this paper, we develop a new and at the same time simple method of obtaining a measure of the rate of capacity utilization (CU) which makes use of the structural vector autoregression (SVAR) system of equation estimating technique with long‐run restrictions. The measure of CU that we derive for each of 14 EU countries replicates to a great extent the European Commission's Directorate General for Economic and Financial Affairs (ECFIN) measure. On closer examination we find that the in‐sample explanatory content with respect to the inflation rate of the SVAR measure exceeds more often than not that of the ECFIN's measure; however, the out‐of‐sample forecasting performance of the two models is approximately equivalent.
FIRM BEHAVIOUR AND FINANCIAL PRESSURE: EVIDENCE FROM SPANISH PANEL DATA
Authors: Benito Andrew , Hernando Ignacio 
Published: September 2007

ABSTRACTThis paper examines responses by firms in Spain to the experience of financial pressure. Using panel data methods applied to a large company panel, a number of aspects of corporate behaviour and the response of each to financial pressure are examined. We consider fixed investment, inventories, employment – distinguishing both permanent and temporary contract employees – and dividend policies. Our results include finding significant effects of financial pressure from borrowing costs on each outcome, particularly investment and employment. The effects on temporary employment are also found to be larger and work through more quickly than on permanent employment.
ADULT EDUCATION AND EARNINGS: EVIDENCE FROM BRITAIN
Authors: Silles Mary A. 
Published: September 2007

ABSTRACTThis paper uses the National Child Development Study to investigate the relationship between adult schooling and labour market earnings for men. In line with several other studies, the findings suggest that there are returns to all educational qualifications acquired early in life. A variety of statistical models are estimated to try to measure the causal effect of adult education on earnings. Careful analysis reveals that there are no genuine returns to additional qualifications awarded in middle adulthood. The central conclusion of this paper is that rates of return to human capital are greater for individuals who were educated early in life.
Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny
Authors: Bocakova Milada , Bocak Ladislav , Hunt Toby , Teraväinen Marianna , Vogler Alfried P. 
Published: September 2007

AbstractPhylogenetic relationships in the coleopteran Series Elateriformia (click beetles, jewel beetles, fireflies and allies) were investigated using > 3800 nucleotides of partial nuclear (small and large subunit rRNA genes) and mitochondrial (large subunit rRNA and cytochrome oxidase subunit I) gene sequences. The Elateriformia includes several soft‐bodied lineages, some of which retain larviform features in the adult stage (neoteny), and several major bioluminescent groups, including the families Lampyridae (fireflies), Phengodidae and Rhagophthalmidae whose relationships have been contentious. All recognized superfamilies (Elateroidea, Cantharoidea, Byrrhoidea, Buprestoidea, Dascilloidea, Scirtoidea) and 28 of the 37 families, represented in 112 individuals, were included in the analysis. Sequence alignment was based on static and dynamic homology assignments and partial removal of sequences of uncertain homology. Alignment variable regions caused a great deal of uncertainty but also contributed much of the phylogenetic signal that was insufficient to resolve deep relationships when these were removed. The main features of most analyses were the monophyly of Elateroidea + Cantharoidea (= Elateroidea sensu lato), with Omethidae + Telegeusidae frequently occupying the basal node in this group; the affinities of Dascilloidea, Buprestoidea and a (broadly paraphyletic) Byrrhoidea, with unclear relationships among them; and the monophyly of Scirtoidea (including Decliniidae) as a rather distant outgroup to all others. When mapped on the resulting trees, soft‐bodied lineages were polyphyletic, contradicting the former Cantharoidea that had been united by this trait. Transitions to neoteny were either simultaneous with, or subsequent to, the origin of soft‐bodiedness in a minimum of seven lineages. The bioluminescent groups Lampyridae (including the enigmatic genus Drilaster) and the tightly allied Phengodidae + Rhagophthalmidae were never monophyletic. The former showed close relationship to the species‐rich, soft‐bodied families Lycidae and Cantharidae, while the latter grouped with poorly resolved lineages at the base of Elateridae (click beetles). Hence, although key features as soft‐bodiedness, neoteny and bioluminescence in Coleoptera are largely confined to the Elateriformia, they appear to result from multiple origins, showing the propensity of closely related lineages to acquire similar features independently.© The Willi Hennig Society 2007.
Phospholipid transfer protein activity is determined by type 2 diabetes mellitus and metabolic syndrome, and is positively associated with serum transaminases
Authors: Dullaart Robin P. F. , De Vries Rindert , Dallinga‐Thie Geesje M. , Sluiter Wim J. , Van Tol Arie 
Published: September 2007

SummaryBackground  The extent to which plasma phospholipid transfer protein (PLTP) activity is affected by type 2 diabetes mellitus (DM) and metabolic syndrome (MetS) is still unknown. PLTP is synthesized in the liver, and elevated serum transaminases are considered to predict nonalcoholic fatty liver disease (NAFLD). In this study, we examined the relationship between plasma PLTP activity and liver enzymes in subjects with and without DM and MetS.Design  Plasma PLTP activity, serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were measured in 71 subjects without DM or MetS, 21 without DM but with MetS, 26 with DM but without MetS and 55 with DM and MetS (WHO and NCEP‐ATP III criteria).Results  After controlling for age, sex and alcohol intake, PLTP activity was positively related to both MetS (P < 0·001) and DM (P = 0·001). Serum ALT (P = 0·006) and AST (P = 0·04) were both associated with MetS, but only ALT was associated with DM (P < 0·001). In multiple linear regression models, serum ALT and AST were positively and independently associated with PLTP activity (P < 0·01 for all), even when the presence of MetS and DM was taken into account, as well as after controlling for glycated haemoglobin (HbA1c), insulin resistance, triglycerides, free fatty acids (FFA), C‐reactive protein (CRP), leptin and adiponectin.Conclusions  Plasma PLTP activity is determined by MetS and by diabetes per se. Serum transaminases are independently associated with PLTP activity. We suggest that this lipid transfer protein may be a marker for NAFLD.
Do water molecules bridge soil organic matter molecule segments?
Authors: Schaumann G. E. , Bertmer M. 
Published: September 2007

SummaryOne of the most valuable ecological potentials of soil organic matter (SOM) is based on its highly dynamic nature, which enables flexible reactions to a variety of environmental conditions. SOM controls a large part of the processes occurring at biogeochemical interfaces in soil and may contribute to sequestration of organic chemicals. This contribution focuses on dynamics in SOM from a viewpoint that regards SOM as an amorphous matrix, in which weak intermolecular interactions rather than covalent binding are considered. This view is based on the conception of SOM as a supramolecular assembly, which was first suggested in studies by A. Piccolo and R. L. Wershaw. Based on our recent results on thermal analysis of SOM, our central hypothesis is that regardless of the individual molecular mass, SOM undergoes physicochemical matrix aging, driven by dynamics in intermolecular cross‐linking via bridges of water molecules. In this study, we have made the first efforts to evaluate the water‐bridge hypothesis with proton NMR relaxation and proton wideline NMR. The results clearly indicate changes in relaxation time and proton line shape induced by manipulations of thermal history, which suggests an increase in side‐chain mobility upon heating that remains after cooling. Side‐chain mobility slowly decreases again within at least 1–2 weeks. Our current results strongly suggest even longer aging periods. This observation supports the hypothesis that water molecules bridge molecular segments of SOM. The bridges may be easily disrupted, while re‐formation is slow due to diffusion limitation in the SOM matrix.