bluuebunny/crossref_metadata_2025 huggingface dataset:
Protection mechanisms in the resurrection plant Xerophyta viscosa: cloning, expression, characterisation and role of XvINO1, a gene coding for a myo-inositol 1-phosphate synthase
Authors: Lehner Arnaud , Chopera Denis R. , Peters Shaun W. , Keller Felix , Mundree Sagadevan G. , Thomson Jennifer A. , Farrant Jill M.
Published: January 2008

We have used reverse transcription-PCR coupled with 5′- and 3′-RACE to isolate a full length INO1 cDNA (1692 bp with an ORF of 1530) from the resurrection plant Xerophyta viscosa Baker. XvINO1 encodes 510 amino acids, with a predicted MW of 56.7kD and contains four sequence motifs that are highly conserved in plant myo-inositol-1-phosphate synthases (MIPS, EC5.5.1.4), the enzyme that catalyses the first step in the formation of myo-inositol (Ino). Northern and western analyses show that the transcript and protein are constitutively present in leaves but their expression increases, temporarily, in response to both accumulative salt stress (~300 mM NaCl) and desiccation (to 5% relative water content). Leaf Ino concentration increases 40-fold during the first 6 h of salt stress, and levels of this and other carbohydrates (galactinol, sucrose, raffinose, stachyose and hexoses) remain elevated relative to control leaves for the duration of salt stress treatment. The timing and pattern of accumulation of these carbohydrates differ under desiccation stress and we propose that they perform different functions in the respective stresses. These are elaborated in discussion of our data.
Optically-assessed preformed flavonoids and susceptibility of grapevine to Plasmopara viticola under different light regimes
Authors: Agati Giovanni , Cerovic Zoran G. , Marta Anna Dalla , Di Stefano Valentina , Pinelli Patrizia , Traversi Maria Laura , Orlandini Simone
Published: January 2008

The role of flavonoids in the response of plants to Plasmopara viticola, the phytopathogen agent of downy mildew, was studied in the Vitis vinifera L. cultivar Sangiovese. Grapevines in the vineyard were exposed to two light regimes, 100% and 35% of full sunlight in order to induce differences in total leaf polyphenolic content. Epidermal leaf phenolic compounds were assessed optically, using the Dualex chlorophyll fluorescence-based portable leaf-clip. Dualex data were calibrated by means of HPLC analysis of extracts from the same measured leaves. Good correlations were obtained with total flavonoid contents, which consist mainly of quercetin 3-O-glucuronide. From the Dualex non-destructive measurements, we showed that full-sun exposed leaves contained 75% more flavonoids than shaded leaves. Inoculation of leaves with P. viticola sporangia resulted in a significantly lower infected leaf area in sun-lit leaves compared with shaded ones, as seen from subsequent analysis of the downy mildew severity. These results indicated an inverse relationship between preformed flavonoids and the susceptibility of grapevines to downy mildew. The rapid optical method for the non-destructive assessment of flavonoids presented here could be useful for large scale screening and predicting V. vinifera susceptibility to P. viticola.
Geochemistry of Cu, Zn and Fe in the Tambo River, Australia I. Oxidation of Fe(II)-rich water entering the river
Authors: Hart Barry T. , Hines Tina
Published: January 2008

The behaviour of Fe, Cu and Zn was studied during the laboratory oxidation of an acidic (pH 5.8) sample of naturally contaminated water from the Tambo River (Victoria, Australia). Changes in the concentrations of the dissolved, colloidal and particulate fractions of these metals were followed over 288 h. The initial concentrations of dissolved Cu (18.5 mg L–1) and Zn (22.6 mg L–1) were ~15-fold greater than that of the dissolved Fe (1.13 mg L–1). Dissolved Fe was completely removed from solution in 60 h, with removal following the well established first order oxidation kinetics for Fe(II). A relatively small amount of the dissolved Cu (18%) and dissolved Zn (14%) was removed from the solution, although the removal mechanisms appear to be different. A ‘co-precipitation-surface precipitation’ mechanism is proposed to explain the behaviour of the Cu and Zn, with Cu(II), Zn(II) and Fe(III) co-precipitating to form colloidal Fe(OH)3-Cu(OH)2-Zn(OH)2 particles following the initial oxidation of Fe(II) to Fe(III).
Geochemistry of Cu, Zn and Fe in the Tambo River, Australia II. Field investigation under low-flow conditions
Authors: Hart Barry T. , Hines Tina , Coller Bruce A.W.
Published: January 2008

The behaviour of Fe, Cu and Zn, added to the upper Tambo River (Victoria, Australia) via a metal-enriched groundwater input, was studied during a period of very low river flow. Water samples were collected over a 1.3-km section of the river located immediately downstream of the spring input. Heavy metals were separated into three fractions (dissolved, colloidal and particulate) using tangential flow filtration. Within the ‘input region’, the pH was low (5.1–5.8) and sulphate (306–359 mg L–1), total Fe (2.81 mg L–1), total Cu (19.7 mg L–1) and total Zn (24.1 mg L–1) concentrations all increased significantly. Subsequently, the total metal concentrations reduced with distance downstream of the input, and approached values similar to those recorded upstream of the input region at the end of the study region. Most of the Fe was oxidised before it entered the river as a thick hydrous iron oxide floc that travelled downstream close to the riverbed. The remaining dissolved Fe (mainly Fe(II)) that entered the river largely controlled the behaviour of Cu and Zn in the ‘active region’ (75–400 m). This Fe(II) was rapidly oxidised to Fe(III), which then removed large amounts of the dissolved Cu (65%) and Zn (55%) into the colloidal fraction. Processes such as settling of particles, dilution by groundwater inputs and sorption of dissolved Cu and Zn onto sediments removed the remainder of the Cu and Zn.
Estimating prawn abundance and catchability from catch-effort data: comparison of fixed and random effects models using maximum likelihood and hierarchical Bayesian methods
Authors: Zhou Shijie , J. Vance David , Dichmont Catherine M. , Burridge Charis Y. , Toscas Peter J.
Published: January 2008

Abundance and catchability are crucial quantities in fisheries management, yet they are very difficult to estimate, particularly for short-lived invertebrates. Using two distinct approaches – a standard non-hierarchical model (NH) and a hierarchical Bayesian model (HB) – abundance and catchability coefficients from a fishery depletion process for banana prawns (Penaeus merguiensis) in northern Australia were estimated. Non-hierarchical models treated each stock and year separately and individually, whereas the hierarchical models assumed some form of common underlying population from which the parameters for the individual cases generated by the combination of stock and year were drawn. Two HBs were considered. In HB1 it was assumed that annual abundance and catchability parameters came from separate populations, or distributions, for each stock. In HB2 it was assumed that these stock region distributions were not separate, but had their parameters drawn from a common distribution. Thus in HB2 all stocks shared information at the regional level. The results for both NH and HB methods were similar in most cases, indicating a fair degree of stability irrespective of the particular form of model chosen. However, the NH method suffered because the data were analysed in generally small sections and in many cases these sections were too small to allow precise estimation of both parameters and confidence intervals. The deviations of point estimates between the HB1, HB2 and NH models were more marked in catchability coefficient estimates than in abundance estimates, and large relative deviations typically occurred in stock regions and years with low fishing efforts, low catch or poor depletion trends over time. We conclude that the combined analysis using HB was superior because it could handle limited data, yielded credible interval estimates for all parameters and was computationally more efficient.
Bacterial abundance and production, and their relation to primary production in tropical coastal waters of Peninsular Malaysia
Authors: Lee Choon Weng , Bong Chui Wei
Published: January 2008

In the present study, the relationship between bacteria and phytoplankton in tropical coastal waters was investigated. The bacterial abundance, bacterial production, chlorophyll a concentration and net primary production were measured at several locations in the coastal waters of Peninsular Malaysia. Chlorophyll a concentration ranged from 0.40 to 32.81 μg L–1, whereas bacterial abundance ranged from 0.1 to 97.5 × 106 cells mL–1. Net primary production ranged from 8.49 to 55.95 μg C L–1 h–1, whereas bacterial production ranged from 0.17 to 70.66 μg C L–1 h–1. In the present study, the carbon conversion factor used to convert bacterial production (cells mL–1 h–1) into carbon units ranged from 10 to 32.8 fg C cell–1, and was estimated from the bacterial size distribution measured at each location. Both phototrophic and heterotrophic biomass (bacteria–chlorophyll a) and activity (bacterial production–net primary production) were significantly correlated, although their correlation coefficients (r2) were relatively low (r2 = 0.188 and r2 = 0.218 respectively). Linear regression analyses provided the following equations to represent the relationship between: bacteria and chlorophyll a (Chl a), log Bacteria = 0.413 log Chl a + 6.057 (P = 0.003); and between bacterial production (BP) and net primary production (NPP), log BP = 0.896 log NPP – 0.394 (P = 0.004), which fitted with published results well. Comparison of annual carbon fluxes confirmed the prevalence of net heterotrophy in these coastal waters, and together with the low correlation coefficients, suggested the role of allochthonous organic matter in supporting heterotrophic activity.
A simple, cost-effective, morphometric marker for characterising abalone populations at multiple spatial scales
Authors: Saunders Thor M. , Mayfield Stephen , Hogg Andrew A.
Published: January 2008

The ability to identify and separately manage component populations is becoming increasingly important in guarding against overexploitation of many marine species. Blacklip abalone (Haliotis rubra) form isolated populations with variable life history characteristics as a result of the heterogenous areas they inhabit. Many of these populations are ‘stunted’, reaching a lower maximum size compared with those in adjacent areas. We obtained a range of morphological measurements from samples of ‘stunted’ and ‘non-stunted’ H. rubra collected from sites spread across broad (tens of kilometres) and fine (hundreds of metres) spatial scales in southern South Australia. The ratio between shell length and shell height showed clear and significant differences among samples from ‘stunted’ and ‘non-stunted’ sites. The morphometric collections from the sub-sites suggested that ‘stunted’ populations existed at smaller spatial scales (up to 400 m) compared with that for ‘non-stunted’ populations (at least 1000 m). The ‘morphometric marker’ developed in the present study has the potential to be used as a tool to identify individual populations rapidly and cost-effectively that can then be managed separately. Our approach is applicable to other species of abalone as well as other sedentary invertebrates with limited larval dispersal.
The lost origin of chemical ecology in the late 19th century
Authors: Hartmann Thomas
Published: January 2008

The origin of plant chemical ecology generally dates to the late 1950s, when evolutionary entomologists recognized the essential role of plant secondary metabolites in plant–insect interactions and suggested that plant chemical diversity evolved under the selection pressure of herbivory. However, similar ideas had already flourished for a short period during the second half of the 19th century but were largely forgotten by the turn of the century. This article presents the observations and studies of three protagonists of chemical ecology: Anton Kerner von Marilaun (1831–1898, Innsbruck, Austria, and Vienna, Austria), who mainly studied the impact of geological, climatic, and biotic factors on plant distribution and survival; Léo Errera (1858–1906, Brussels, Belgium), a plant physiologist who analyzed the localization of alkaloids in plant cells and tissues histochemically; and Ernst Stahl (1848–1919, Jena, Germany), likely the first experimental ecologist and who performed feeding studies with snails and slugs that demonstrated the essential role of secondary metabolites in plant protection against herbivores. All three, particularly Stahl, suggested that these “chemical defensive means” evolved in response to the relentless selection pressure of the heterotrophic community that surrounds plants. Although convincingly supported by observations and experiments, these ideas were forgotten until recently. Now, more than 100 years later, molecular analysis of the genes that control secondary metabolite production underscores just how correct Kerner von Marilaun, Errera, and, particularly, Stahl were in their view. Why their ideas were lost is likely a result of the adamant rejection of all things “teleological” by the physiologists who dominated biological research at the time.
The genome ofClostridium kluyveri, a strict anaerobe with unique metabolic features
Authors: Seedorf Henning , Fricke W. Florian , Veith Birgit , Brüggemann Holger , Liesegang Heiko , Strittmatter Axel , Miethke Marcus , Buckel Wolfgang , Hinderberger Julia , Li Fuli , Hagemeier Christoph , Thauer Rudolf K. , Gottschalk Gerhard
Published: January 2008

Clostridium kluyveriis unique among the clostridia; it grows anaerobically on ethanol and acetate as sole energy sources. Fermentation products are butyrate, caproate, and H2. We report here the genome sequence ofC. kluyveri, which revealed new insights into the metabolic capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB) coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for microcompartment proteins, suggesting that the two enzymes, which are isolated together in a macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe,C. kluyveriharbors three sets of genes predicted to encode for polyketide/nonribosomal peptide synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth conditions.
The endocochlear potential depends on two K
+
diffusion potentials and an electrical barrier in the stria vascularis of the inner ear
Authors: Nin Fumiaki , Hibino Hiroshi , Doi Katsumi , Suzuki Toshihiro , Hisa Yasuo , Kurachi Yoshihisa
Published: January 2008

An endocochlear potential (EP) of +80 mV is essential for audition. Although the regulation of K
+
concentration ([K
+
]) in various compartments of the cochlear stria vascularis seems crucial for the formation of the EP, the mechanism remains uncertain. We have used multibarreled electrodes to measure the potential, [K
+
], and input resistance in each compartment of the stria vascularis. The stria faces two fluids, perilymph and endolymph, and contains an extracelluar compartment, the intrastrial space (IS), surrounded by two epithelial layers, the marginal cell (MC) layer and that composed of intermediate and basal cells. Fluid in the IS exhibits a low [K
+
] and a positive potential, called the intrastrial potential (ISP). We found that the input resistance of the IS was high, indicating this space is electrically isolated from the neighboring extracellular fluids. This arrangement is indispensable for maintaining positive ISP. Inhibiting the K
+
transporters of the stria by anoxia, ouabain, or bumetanide caused the [K
+
] of the IS to increase and the intracellular [K
+
] of MCs to decrease, reducing both the ISP and the EP. Calculations indicate that the ISP represents the K
+
diffusion potential across the apical membranes of intermediate cells through Ba
2+
-sensitive K
+
channels. The K
+
diffusion potential across the apical membranes of MCs also contributes to the EP. Because the EP depends on two K
+
diffusion potentials and an electrical barrier in the stria vascularis, interference with any of these elements can interrupt hearing.
Sentence-phrase coordination in Hebrew and the syntax–pragmatics interface
Authors: Meir Irit
Published: January 2008

The coordination of a sentence and a phrase (Sentence-Phrase coordination, henceforth SPC) is a very widespread, though marked, construction in Modern Hebrew. It is characterized by special prosody in that it carries two sentential stresses, and is perceived as more forceful or emphatic than its non-conjoined counterpart. A full account of the properties and distribution of the construction involves both a syntactic and a pragmatic component. The analysis presented in the paper proposes that: (a) The conjunction imposes a propositional interpretation on the phrasal coordinand, thus enabling the speaker to convey two pieces of new information in one sentence. (b) Syntactically, the phrasal coordinand is best analyzed as an adjunct to the sentential coordinand. (c) The special discourse effect of the construction is to be analyzed as a case of independent strengthening (following Sperber & Wilson 1986, Blakemore & Carston 2005), whereby each coordinand leads independently to the same conclusion, thus providing cumulative evidence to the same purpose. (d) Although syntactically non-parallel, the two coordinands play a parallel inferential role in deriving cognitive effects of the utterance. Hence the use of the conjunction is taken as an instruction to the hearer to look for pragmatic parallelism between two constituents which are clearly non-like syntactically.
The irreality of alternatives
Authors: Mauri Caterina
Published: January 2008

This paper investigates the variety of morphosyntactic strategies that languages use to encode the relation of alternative between states of affairs. A semantic deﬁnition of disjunction will be given, based on the notion of alternative meaning proposed by Dik 1968. After deﬁning the functional domain under investigation, it will be shown that languages encode the notion of alternative between states of affairs in different but non-random ways. Speciﬁcally, many languages do not have a disjunctive connective, but rather encode the concept of ‘alternative’ by means of the same strategies used for other irrealis domains, such as dubitative, hypothetical or interrogative. Two main implicational patterns will be identiﬁed, which will prove irreality to be a basic aspect of disjunction.
The syntax of intonation units in Sasak
Authors: Wouk Fay
Published: January 2008

In this paper I examine the syntactic nature of intonation units in Sasak, and compare the distribution of syntactic types with previously published work on other languages, in particular Mandarin, and to a lesser extent, Japanese. Sasak and Mandarin prove to have very similar frequencies of clausal IUs, but Sasak has far more complete clauses than Mandarin, which prefers elliptical clauses. Nominal IUs in the Sasak data are far more likely to be independent than in Japanese or Mandarin conversational data, and fulfill very different functions than those found in studies of Mandarin. I argue that cross-linguistic differences in the relative frequencies of different types of syntactic constituents are best explained partly in terms of the syntactic resources available in a given language, and partly in terms of cultural variation in conversational practice. Differences in the relative frequencies of various functions of nominal IUs, however, may relate more to genre than to language, but the limited corpora used in studies to date make this difficult to determine.
Hither and thither in Saramaccan Creole
Authors: McWhorter John
Published: January 2008

Manhattan Institute
A Sensor Network Architecture for Tsunami Detection and Response
Authors: Casey Kenan , Lim Alvin , Dozier Gerry
Published: January 2008

In this paper, we propose a sense and response system for tsunami detection and mitigation. We use the directed diffusion routing protocol as a baseline network protocol and develop several communication mechanisms to improve its performance. These include an efficient flooding technique, a route repair algorithm, and distributed services framework. We summarize the analysis mechanism used to predict tsunami propagation and briefly discuss the results of this algorithm. Finally, we describe potential barrier mechanisms and the real-time communication protocol that supports time-critical response of the system.
Cohort Study of the Pathogenesis and Molecular Epidemiology of Catheter-Related Bloodstream Infection in Neonates With Peripherally Inserted Central Venous Catheters
Authors: Garland Jeffery S. , Alex Colleen P. , Sevallius Jackie M. , Murphy Dawn M. , Good Mary J. , Volberding Annette M. , Hofer Leslie L. , Gordon Barbara J. , Maki Dennis G.
Published: January 2008

Objective.

To better define the pathogenesis of catheter-related bloodstream infection (BSI) in neonates with peripherally inserted central venous catheters (PICCs) to guide the development of more effective strategies for prevention.

Design.

Prospective nested cohort study.

Setting.

Level III neonatal intensive care unit in a community hospital.

Methods.

During a randomized trial to assess the safety and efficacy of a prophylactic vancomycin-heparin catheter-lock solution for the prevention of catheter-related BSI in neonates with PICCs, we performed cultures of peripheral and catheter-drawn blood samples, and quantitative cultures of catheter hub samples if BSI was suspected clinically. We performed semiquantitative cultures of the catheter tip and the catheter hub and the skin at the insertion site when the catheter was removed. Molecular subtyping by pulsed-field electrophoresis was used to determine the probable pathogenesis of all BSIs due to coagulase-negative staphylococci (CoNS); for BSIs caused by other microorganisms, epidemiologic concordance was based on speciation and antibiograms. Catheter-related BSI was considered extraluminally acquired if concordance was demonstrable solely between isolates recovered from the catheter tip and the blood, independent of concordance with isolates recovered from the insertion site. Catheter-related BSI was considered intraluminally acquired if concordance was demonstrated only between isolates recovered from the catheter hub and the blood. The source of the infection was considered indeterminate if both concordance patterns were present.

Results.

Nosocomial BSI was identified in 23 of the 82 neonates in the cohort. Fifteen of these infections, 14 of which were caused by CoNS, were considered definite or probable catheter-related BSIs. Catheter-related BSI was intraluminally acquired in 10 (67%) of 15 patients, extraluminally acquired in 3 (20%), and indeterminate in 2 (13%).

Conclusions.

Most catheter-related BSIs in neonates with PICCs are caused by CoNS and derive from intraluminal contamination. Strategies for prevention of catheter-related BSI directed at this predominant mechanism of infection are most likely to be effective.
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Authors: Stanke Mario , Diekhans Mark , Baertsch Robert , Haussler David
Published: January 2008

Motivation: Computational annotation of protein coding genes in genomic DNA is a widely used and essential tool for analyzing newly sequenced genomes. However, current methods suffer from inaccuracy and do poorly with certain types of genes. Including additional sources of evidence of the existence and structure of genes can improve the quality of gene predictions. For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes. Related genomes that have been sequenced, annotated, and aligned to the target genome provide evidence of existence and structure of genes.

Results: We incorporate several different evidence sources into the gene finder AUGUSTUS. The sources of evidence are gene and transcript annotations from related species syntenically mapped to the target genome using TransMap, evolutionary conservation of DNA, mRNA and ESTs of the target species, and retroposed genes. The predictions include alternative splice variants where evidence supports it. Using only ESTs we were able to correctly predict at least one splice form exactly correct in 57% of human genes. Also using evidence from other species and human mRNAs, this number rises to 77%. Syntenic mapping is well-suited to annotate genomes closely related to genomes that are already annotated or for which extensive transcript evidence is available. Native cDNA evidence is most helpful when the alignments are used as compound information rather than independent positionwise information.

Availability: AUGUSTUS is open source and available at http://augustus.gobics.de. The gene predictions for human can be browsed and downloaded at the UCSC Genome Browser (http://genome.ucsc.edu)

Contact:  mstanke@gwdg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion
Authors: Reinders Jon , Delucinge Vivier Céline , Theiler Grégory , Chollet Didier , Descombes Patrick , Paszkowski Jerzy
Published: January 2008

Methylation of cytosines (mC) is essential for epigenetic gene regulation in plants and mammals. Aberrant mC patterns are associated with heritable developmental abnormalities in plants and with cancer in mammals. We have developed a genome-wide DNA methylation profiling technology employing a novel amplification step for DNA subjected to bisulfite-mediated cytosine conversion. The methylation patterns detected are not only consistent with previous results obtained with mC immunoprecipitation (mCIP) techniques, but also demonstrated improved resolution and sensitivity. The technology, named BiMP (for Bisulfite Methylation Profiling), is more cost-effective than mCIP and requires as little as 100 ng of Arabidopsis DNA.
Comparative Genomic Sequence and Expression Analyses ofMedicago truncatulaand Alfalfa Subspeciesfalcata COLD-ACCLIMATION-SPECIFICGenes
Authors: Pennycooke Joyce C. , Cheng Hongmei , Stockinger Eric J.
Published: January 2008

In Arabidopsis (Arabidopsis thaliana) the low-temperature induction of genes encoding the C-REPEAT BINDING FACTOR (CBF) transcriptional activators is a key step in cold acclimation. CBFs in turn activate a battery of downstream genes known as the CBF regulon, which collectively act to increase tolerance to low temperatures. Fundamental questions are: What determines the size and scope of the CBF regulon, and is this is a major determinant of the low-temperature tolerance capacity of individual plant species? Here we have begun to address these questions through comparative analyses of Medicago truncatula and Medicago sativa subsp. falcata. M. truncatula survived to −4°C but did not cold acclimate, whereas Medicago falcata cold acclimated and survived −14°C. Both species possessed low-temperature-induced CBFs but differed in the expression of the COLD-ACCLIMATION-SPECIFIC (CAS) genes, which are candidate CBF targets. M. falcata CAS30 was robustly cold-responsive whereas the MtCAS31 homolog was not. M. falcata also possessed additional CAS30 homologs in comparison to the single CAS31 gene in M. truncatula. MfCAS30 possessed multiple pairs of closely spaced C-REPEAT/DEHYDRATION RESPONSIVE ELEMENT (CRT/DRE) motifs, the cognate CBF binding site in its upstream region whereas MtCAS31 lacked one CRT/DRE partner of the two proximal partner pairs. CAS genes also shared a promoter structure comprising modules proximal and distal to the coding sequence. CAS15, highly cold-responsive in both species, harbored numerous CRT/DRE motifs, but only in the distal module. However, fusion of the MtCAS15 promoter, including the distal module, to a reporter gene did not result in low-temperature responsiveness in stably transformed Arabidopsis. In contrast, both MtCAS31 and MfCAS30 promoter fusions were low-temperature responsive, although the MfCAS31 fusion was less robust than the MfCAS30 fusion. From these studies we conclude that CAS genes harbor CRT/DRE motifs, their proximity to one another is likely key to regulatory output in Medicago, and they may be located kilobases distal to the transcriptional start site. We hypothesize that these differences in CRT/DRE copy numbers in CAS30/CAS31 upstream regions combined with differences in gene copy numbers may be a factor in determining differences in low-temperature tolerance between M. truncatula and M. falcata.
Genome-Wide Expression Profiling Arabidopsis at the Stage ofGolovinomyces cichoracearumHaustorium Formation
Authors: Fabro Georgina , Di Rienzo Julio A. , Voigt Christian A. , Savchenko Tatyana , Dehesh Katayoon , Somerville Shauna , Alvarez María Elena
Published: January 2008

Compatibility between plants and obligate biotrophic fungi requires fungal mechanisms for efficiently obtaining nutrients and counteracting plant defenses under conditions that are expected to induce changes in the host transcriptome. A key step in the proliferation of biotrophic fungi is haustorium differentiation. Here we analyzed global gene expression patterns in Arabidopsis thaliana leaves during the formation of haustoria by Golovinomyces cichoracearum. At this time, the endogenous levels of salicylic acid (SA) and jasmonic acid (JA) were found to be enhanced. The responses of wild-type, npr1-1, and jar1-1 plants were used to categorize the sensitivity of gene expression changes to NPR1 and JAR1, which are components of the SA and JA signaling pathways, respectively. We found that the infection process was the major source of variation, with 70 genes identified as having similarly altered expression patterns regardless of plant genotype. In addition, principal component analysis (PCA) identified genes responding both to infection and to lack of functional JAR1 (17 genes) or NPR1 (18 genes), indicating that the JA and SA signaling pathways function as secondary sources of variation. Participation of these genes in the SA or JA pathways had not been described previously. We found that some of these genes may be sensitive to the balance between the SA and JA pathways, representing novel markers for the elucidation of cross-talk points between these signaling cascades. Conserved putative regulatory motifs were found in the promoter regions of each subset of genes. Collectively, our results indicate that gene expression changes in response to infection by obligate biotrophic fungi may support fungal nutrition by promoting alterations in host metabolism. In addition, these studies provide novel markers for the characterization of defense pathways and susceptibility features under this infection condition.
Tie-dyed2Functions withTie-dyed1to Promote Carbohydrate Export from Maize Leaves
Authors: Baker R. Frank , Braun David M.
Published: January 2008

Regulation of carbon partitioning is essential for plant growth and development. To gain insight into genes controlling carbon allocation in leaves, we identified mutants that hyperaccumulate carbohydrates. tie-dyed2 (tdy2) is a recessive mutant of maize (Zea mays) with variegated, nonclonal, chlorotic leaf sectors containing excess starch and soluble sugars. Consistent with a defect in carbon export, we found that a by-product of functional chloroplasts, likely a sugar, induces tdy2 phenotypic expression. Based on the phenotypic similarities between tdy2 and two other maize mutants with leaf carbon accumulation defects, tdy1 and sucrose export defective1 (sxd1), we investigated whether Tdy2 functioned in the same pathway as Tdy1 or Sxd1. Cytological and genetic studies demonstrate that Tdy2 and Sxd1 function independently. However, in tdy1/+; tdy2/+ F1 plants, we observed a moderate chlorotic sectored phenotype, suggesting that the two genes are dosage sensitive and have a related function. This type of genetic interaction is referred to as second site noncomplementation and has often, though not exclusively, been found in cases where the two encoded proteins physically interact. Moreover, tdy1; tdy2 double mutants display a synergistic interaction supporting this hypothesis. Additionally, we determined that cell walls of chlorotic leaf tissues in tdy mutants contain increased cellulose; thus, tdy mutants potentially represent enhanced feedstocks for biofuels production. From our phenotypic and genetic characterizations, we propose a model whereby TDY1 and TDY2 function together in a single genetic pathway, possibly in homo- and heteromeric complexes, to promote carbon export from leaves.
Ascorbate and Homoglutathione Metabolism in Common Bean Nodules under Stress Conditions and during Natural Senescence
Authors: Loscos Jorge , Matamoros Manuel A. , Becana Manuel
Published: January 2008

Ascorbate and glutathione are major antioxidants and redox buffers in plant cells but also play key functions in growth, development, and stress responses. We have studied the regulation of ascorbate and homoglutathione biosynthesis in common bean (Phaseolus vulgaris) nodules under stress conditions and during aging. The expression of five genes of the major ascorbate biosynthetic pathway was analyzed in nodules, and evidence was found that l-galactono-1,4-lactone dehydrogenase, the last committed step of the pathway, is posttranscriptionally regulated. Also, in nodules under stress conditions, γ-glutamylcysteine synthetase was translationally regulated, but homoglutathione synthetase (mRNA and activity) and homoglutathione (content and redox state) were not affected. Most interestingly, in nodules exposed to jasmonic acid, dehydroascorbate reductase activity was posttranslationally suppressed, ascorbate oxidase showed strong transcriptional up-regulation, and dehydroascorbate content increased moderately. These changes were not due to a direct effect of jasmonic acid on the enzyme activities but might be part of the signaling pathway in the response of nodules to stress. We determined ascorbate, homoglutathione, and ascorbate-glutathione pathway enzyme activities in two senescing stages of nodules undergoing oxidative stress. When all parameters were expressed on a nodule fresh weight basis, we found that in the first stage ascorbate decreased by 60% and homoglutathione and antioxidant activities remained fairly constant, whereas in the second stage ascorbate and homoglutathione, their redox states, and their associated enzyme activities significantly decreased. The coexistence in the same plants of nodules at different senescence stages, with different ascorbate concentrations and redox states, indicates that the life span of nodules is in part controlled by endogenous factors and points to ascorbate as one of the key players.
Characterization of the 4D5Flu single‐chain antibody with a stimulus‐responsive elastin‐like peptide linker: A potential reporter of peptide linker conformation
Authors: Blenner Mark A. , Banta Scott
Published: January 2008

Single‐chain antibodies (scFvs) are comprised of IgG variable light and variable heavy domains tethered together by a peptide linker whose length and sequence can affect antigen binding properties. The ability to modulate antigen binding affinity through the use of environmental triggers would be of great interest for many biotechnological applications. We have characterized the antigen binding properties of an anti‐fluorescein scFv, 4D5Flu, containing stimulus‐responsive short elastin‐like peptide linkers and nonresponsive flexible linkers. Comparison of length‐matched flexible and short elastin‐like peptide linkers indicates that a stimulus‐responsive linker can confer stimulus‐responsive control of fluorescein binding. A linker length of either six or 10 amino acids proved to have the largest thermally induced response. Similar differences in binding free energy changes indicate a common underlying mechanism of thermal responsiveness. Contrary to the thermal behavior, the effect of salt, another elastin β‐turn‐inducing stimulus, stabilized antigen binding in the six‐ and 10‐amino‐acid linkers such that elastin‐like linkers became less stimulus‐responsive as compared with flexible linkers. Again, the thermodynamic analysis indicates a common mechanism of salt responsiveness. Characterization of the room‐temperature binding affinities and evidence indicating a dimeric state of the scFvs concomitantly suggest the major contribution to the stimulus‐responsive behavior derives from the perturbation of interdomain associations, rather than the linker‐constrained disruption of the intramolecular association. The ability to use stimulus‐responsive peptide modules to exert a novel control over protein function will likely find application in the creation of allosteric antibodies and scFv‐based biosensors, and as a platform to enable the evolution of new stimulus‐responsive peptides.
Rationalizing α‐helical membrane protein crystallization
Authors: Newstead Simon , Ferrandon Sébastien , Iwata So
Published: January 2008

X‐ray crystallography is currently the most successful method for determining the three‐dimensional structure of membrane proteins. Nevertheless, growing the crystals required for this technique presents one of the major bottlenecks in this area of structural biology. This is especially true for the α‐helical type membrane proteins that are of particular interest due to their medical relevance. To address this problem we have undertaken a detailed analysis of the crystallization conditions from 121 α‐helical membrane protein structures deposited in the Protein Data Bank. This information has been analyzed so that the success of different parameters can be easily compared for different membrane protein families. Concurrent with this analysis, we also present the new sparse matrix crystallization screen MemGold.
Enhancement of coenzyme binding by a single point mutation at the coenzyme binding domain of E. coli lactaldehyde dehydrogenase
Authors: Rodríguez‐Zavala José Salud
Published: January 2008

Phenylacetaldehyde dehydrogenase (PAD) and lactaldehyde dehydrogenase (ALD) share some structural and kinetic properties. One difference is that PAD can use NAD+ and NADP+, whereas ALD only uses NAD+. An acidic residue has been involved in the exclusion of NADP+ from the active site in pyridine nucleotide‐dependent dehydrogenases. However, other factors may participate in NADP+ exclusion. In the present work, analysis of the sequence of the region involved in coenzyme binding showed that residue F180 of ALD might participate in coenzyme specificity. Interestingly, F180T mutation rendered an enzyme (ALD‐F180T) with the ability to use NADP+. This enzyme showed an activity of 0.87 μmol/(min * mg) and Km for NADP+ of 78 μM. Furthermore, ALD‐F180T exhibited a 16‐fold increase in the Vm/Km ratio with NAD+ as the coenzyme, from 12.8 to 211. This increase in catalytic efficiency was due to a diminution in Km for NAD+ from 47 to 7 μM and a higher Vm from 0.51 to 1.48 μmol/(min * mg). In addition, an increased Kd for NADH from 175 (wild‐type) to 460 μM (mutant) indicates a faster product release and possibly a change in the rate‐limiting step. For wild‐type ALD it is described that the rate‐limiting step is shared between deacylation and coenzyme dissociation. In contrast, in the present report the rate‐limiting step in ALD‐F180T was determined to be exclusively deacylation. In conclusion, residue F180 participates in the exclusion of NADP+ from the coenzyme binding site and disturbs the binding of NAD+.
Effect of long‐term cabergoline therapy on the immunological pattern and pituitary function of patients with idiopathic hyperprolactinaemia positive for antipituitary antibodies
Authors: De Bellis A. , Colao A. , Savoia A. , Coronella C. , Pasquali D. , Conte M. , Pivonello R. , Bellastella A. , Sinisi A. A. , Bizzarro A. , Lombardi G. , Bellastella G.
Published: January 2008

Objective  The occurrence of antipituitary antibodies (APA) in patients with idiopathic hyperprolactinaemia (IH) and the effects of dopamine agonists on these antibodies and long‐term pituitary function outcome have been so far not evaluated. This longitudinal study was aimed at investigating, in patients with IH the occurrence of APA and the effect of cabergoline on the pituitary function and behaviour of APA.

Design  Sixty‐six patients with IH were studied. APA (by indirect immunofluorescence) and pituitary function were investigated every year for 3 years.

Results  Seventeen patients resulted APA positive (Group 1) and 49 APA negative (Group 2). Eight patients of Group 1 (Group 1a) and 24 of Group 2 (Group 2a) were asymptomatic and then not treated; instead, nine patients in Group 1 (Group 1b) and 25 in Group 2 (Group 2b), showing symptoms of hyperprolactinaemia, were treated with cabergoline for 2 years.

Among the untreated patients, during the follow‐up, those with APA positive (Group 1a) showed an increase of APA titres and PRL levels with partial pituitary impairment in some of them; instead those with APA negative (Group 2a) persisted negative with normal pituitary function despite persistent hyperprolactinaemia. Among the treated patients, those with APA positive (Group 1b) showed normalization of PRL levels, APA disappearance and recovery of pituitary function (when initially impaired) during cabergoline treatment, persisting also at last observation (off‐therapy). Instead all patients of Group 2b persisted with APA negative during the follow‐up with normalization of PRL levels and stable normal pituitary function during cabergoline therapy but showing a further increase of PRL at the last observation.

Conclusions  The presence of APA in some patients with IH suggests a possible occurrence of autoimmune hypophysitis at potential/subclinical stage; an early and prolonged cabergoline therapy could interrupt the progression to an overt clinical stage of the disease. However, the small amount of patients investigated suggests caution against generalization of our assumption and prompts to further controlled studies on a more numerous population to verify these conclusions.
Prevalence of GH and other anterior pituitary hormone deficiencies in adults with nonsecreting pituitary microadenomas and normal serum IGF‐1 levels
Authors: Yuen Kevin C. J. , Cook David M. , Sahasranam Prem , Patel Pragnesh , Ghods David E. , Shahinian Hrayr K. , Friedman Theodore C.
Published: January 2008

Objective  GH is usually the first pituitary hormone to be affected following a pathological insult to the pituitary; however, data on the prevalence of GH deficiency in patients with nonsecreting pituitary microadenomas and normal serum IGF‐1 levels are scarce. This study aims to evaluate the prevalence of GH and other anterior pituitary hormone deficiencies, and to determine whether microadenomas per se could be associated with reduced GH response rates to GHRH–arginine stimulation.

Design  Analytical, retrospective, two‐site case‐control study.

Patients and methods  Thirty‐eight patients with nonsecreting pituitary microadenomas (mean size 4·2 mm) and normal serum IGF‐1 levels were studied. Anterior pituitary function testing, including the GHRH–arginine test to examine GH reserve, was performed in all patients. Serum IGF‐1 levels and peak GH levels in the patients that passed the GHRH–arginine test were compared with 22 age‐ and BMI‐matched healthy controls.

Results  Nineteen patients (50%) failed the GHRH–arginine test and had higher body mass index (BMI) than those that passed the GHRH–arginine test and healthy controls. Peak GH levels in patients that passed the GHRH–arginine test were lower compared to healthy controls and 19 patients (50%) had at least one other pituitary hormone deficit. A negative correlation (r = –0·42, P < 0·01) between peak GH levels and BMI was identified, but no correlations were found between peak GH and serum IGF‐1 levels.

Conclusions  Our data demonstrated that a substantial number of patients with nonsecreting pituitary microadenomas failed the GHRH–arginine test despite normal serum IGF‐1 levels, and had at least one other pituitary hormone deficiency, suggesting that nonsecreting microadenomas may not be clinically harmless. We therefore recommend long‐term follow‐up with periodic basal pituitary function testing, and to consider dynamic pituitary testing should clinical symptoms arise in these patients.
Role of rapid virological response in prediction of sustained virological response to Peg‐IFN plus ribavirin in HCV /  HIV co‐infected individuals
Authors: Shea D. O. , Tuite H. , Farrell G. , Codd M. , Mulcahy F. , Norris S. , Bergin C.
Published: January 2008

Summary.  The objective of the study was to evaluate the role of rapid virological response (RVR) in predicting sustained virological response (SVR) rates to hepatitis C virus (HCV) therapy. 65 HIV / HCV co‐infected patients commenced HCV treatment per protocol. HIV / HCV patients with a mean CD4 count of 502 were treated for 24–48 weeks depending on genotype. Virological response was assessed at weeks 4 (RVR), 12 [early virological response (EVR)], 24, at end of treatment (EOTR) and 24 weeks post‐completion of treatment (SVR). Primary end‐point was defined as undetectable HCV RNA at 24 weeks post‐treatment completion. Fifty‐five per cent of co‐infected patients were on highly active anti‐retroviral therapy. A majority of patient group were male. 60% of HIV / HCV patients achieved SVR (35% genotype 1 / 4; 77% genotype 2 / 3). 24 HIV / HCV patients achieved undetectable HCV levels compared with baseline by week 4. The positive predictive value (PPV) of RVR at week 4 for subsequent SVR in HIV–HCV co‐infected patients was 100%; the negative predictive value (NPV) was 57%. Significant variables associated with SVR were: (i) lower median pre‐treatment HCV viral load, (ii) genotype 2 / 3 disease and (iii) achievement of RVR. Independent variables associated with RVR were low pre‐treatment HCV viral load and genotype 2 / 3 disease. Achievement of RVR, a negative HCV‐PCR, at week 4 of treatment is predictive of SVR in this cohort of patients. This may be used to guide optimal treatment duration in patient groups. More significantly, the data serve to highlight the subgroup of patients who, on achieving RVR, should be actively supported to complete HCV treatment with full dose therapy, especially patients co‐infected with G2 / 3 disease for whom 6 months’ full dose therapy may be sufficient to obtain a SVR.
Updating reviews: the experience of the Cochrane Neonatal Review Group
Authors: Soll Roger F.
Published: January 2008

Maintaining updated systematic reviews is one of the key goals of the Cochrane Collaboration. Reviews are meant to be updated at an interval of no more than 2 years. The Cochrane Neonatal Review (CNRG) is one of the most productive contributors to the Cochrane Collaboration. However, this means that the CNRG now has a more urgent need to address the issue of review updates. In order to do so, the CNRG has sought methods to prioritise and facilitate the review process.