bluuebunny/crossref_metadata_2025 huggingface dataset:
Embracing the complexity of genomic data for personalized medicine
Authors: West Mike , Ginsburg Geoffrey S. , Huang Andrew T. , Nevins Joseph R.
Published: May 2006

Numerous recent studies have demonstrated the use of genomic data, particularly gene expression signatures, as clinical prognostic factors in cancer and other complex diseases. Such studies herald the future of genomic medicine and the opportunity for personalized prognosis in a variety of clinical contexts that utilizes genome-scale molecular information. The scale, complexity, and information content of high-throughput gene expression data, as one example of complex genomic information, is often under-appreciated as many analyses continue to focus on defining individual rather than multiplex biomarkers for patient stratification. Indeed, this complexity of genomic data is often—rather paradoxically—viewed as a barrier to its utility. To the contrary, the complexity and scale of global genomic data, as representing the many dimensions of biology, must be embraced for the development of more precise clinical prognostics. The need is for integrated analyses—approaches that embrace the complexity of genomic data, including multiple forms of genomic data, and aim to explore and understand multiple, interacting, and potentially conflicting predictors of risk, rather than continuing on the current and traditional path that oversimplifies and ignores the information content in the complexity. All forms of potentially relevant data should be examined, with particular emphasis on understanding the interactions, complementarities, and possible conflicts among gene expression, genetic, and clinical markers of risk.
Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation
Authors: Rawal Pooja , Kummarasetti Veera Bhadra Rao , Ravindran Jinoy , Kumar Nirmal , Halder Kangkan , Sharma Rakesh , Mukerji Mitali , Das Swapan Kumar , Chowdhury Shantanu
Published: May 2006

The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of >61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins inEscherichia coli,which reveals significant (P< 0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD (σ70). These factors together control >1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for >30 operons inE. coli,and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation inE. coli.
The fate of laterally transferred genes: Life in the fast lane to adaptation or death
Authors: Hao Weilong , Golding G. Brian
Published: May 2006

Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.
A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome
Authors: Ohno Mizuki , Miura Tomofumi , Furuichi Masato , Tominaga Yohei , Tsuchimoto Daisuke , Sakumi Kunihiko , Nakabeppu Yusaku
Published: May 2006

8-Oxoguanine (8-oxoG), a major spontaneous form of oxidative DNA damage, is considered to be a natural cause of genomic diversity in organisms because of its mutagenic potential. The steady-state level of 8-oxoG in the nuclear genome of a human cell has been estimated to be several residues per 106 guanines. In the present study, to clarify the genome-wide distribution of 8-oxoG in the steady state, we performed fluorescence in situ detection of 8-oxoG on human metaphase chromosomes using a monoclonal antibody. Multiple dot-like signals were observed on each metaphase chromosome. We then mapped the position of the signal at megabase resolution referring to the cytogenetically identified chromosomal band, and demonstrated that 8-oxoG is unevenly distributed in the normal human genome and that the distribution pattern is conserved among different individuals. Moreover, we found that regions with a high frequency of recombination and single nucleotide polymorphisms (SNPs) are preferentially located within chromosomal regions with a high density of 8-oxoG. Our findings suggest that 8-oxoG is one of the main causes of frequent recombinations and SNPs in the human genome, which largely contribute to the genomic diversity in human beings.
Stimulation of chlorophyll synthesis by benzyladenine and potassium in excised and intact cucumber cotyledons
Authors: Arnold V. , Fletcher R. A.
Published: May 2006

Both benzyladenine (BA) and potassium (K) stimulated chlorophyll synthesis in cucumber (Cucumus sativus L. cv. National Pickling) cotyledons. However, differences existed between the effects of BA and K. Stimulation of chlorophyll synthesis by BA (1 mg l−1, 4.4 μM) was observed in excised cotyledons after 4 and 8 h of illumination but not after 24 h, whereas the stimulation caused by K (40 mM) continued. In contrast to BA, K was unable to eliminate the lag phase of chlorophyll production, and it also required light for its stimulation of cotyledon expansion. Both BA and K were required to maximize cotyledon expansion and chlorophyll production. In intact plants, K was not limiting for chlorophyll synthesis since foliar or soil pretreatments with K did not markedly stimulate greening. Foliar pretreatment with BA stimulated chlorophyll levels in intact plants, whereas soil pretreatment with BA inhibited chlorophyll production, probably because BA was not readily transported from the roots to the shoot and created a “sink” effect. Inhibitor studies showed that stimulation by K of greening did not depend on RNA or chloroplastic protein synthesis to the extent that has been reported for BA. Thus it appears that BA and K stimulate chlorophyll synthesis via different mechanisms, although both cytokinins and K are essential for maximum rates of greening.
Host water potentials may restrict development of snow mould fungi in low temperature‐hardened grasses
Authors: Tronsmo Anne Marte
Published: May 2006

The growth of the snow mould fungi Fusarium nivale (Fr.) Ces. and Typhula ishikariensis Imai at different water potentials was measured on potato dextrose broth supplemented with KCl or polyethylene glycol 6000. The dew point hygrometer method was used for determination of water potentials in both artificial growth media and plant material. Both fungi had a considerable decrease in dry weight production when water potentials of growth media were decreased from −0.7 to −3 MPa. Crown tissue from hardened plants of Phleum pratense L. (timothy, cvs Engmo, Grindstad) and Phalaris arundinacea L. (reed canary grass, cvs Hansvoll, American common, Vantage) showed a significant decrease in water potentials compared with unhardened plants. Thus, reduced availability of water may partly explain increased resistance to fungal pathogens in grasses after hardening.
Transient peaks in the delayed luminescence from Scenedesmus obtusiusculus induced by phosphorus starvation and carbon dioxide deficiency
Authors: Mellvig Staffan , Tillberg Jan‐Eric
Published: May 2006

Cells of the unicellular green alga Scenedesmus obtusiusculus (Chod.) were starved of phosphorus for 24, 48, 72 and 96 h, and the decay kinetics of the delayed luminescence from the differently starved cells was monitored for several minutes. Cells starved for 24 h showed similar delayed luminescence decay kinetics and accumulated output of photons as control cells after excitation with white light. Two transient peaks (with several components) in the decay kinetics of delayed luminescence were observed after 48 h of phosphorus starvation but not after 72 or 96 h. The amplitude of the transient peaks varied depending on the length of the excitation period with white light and on the length of the dark period preceding light excitation. High CO2 availability induced no transient peak, whereas low CO2 availability induced a high transient peak. Transient peaks could not be induced by excitation with light of 660 or 680 nm and only a single transient peak developed using 700 nm light. The kinetics of the delayed luminescence was changed, and the accumulated output of photons was decreased when the pH of the medium was changed from 7.2 to 9.5, both in cells starved for phosphorus for 96 h and in controls. The data indicate that a complicated metabolic pattern is involved in the mechanisms giving rise to the observed transient peaks in the delayed luminescence. The main factors may be a reduction in the translocation of trioses from chloroplasts, a concomitant reduction in Calvin cycle activities and changes in the amount of ATP and reducing agents available.
Organic acids reduce aluminum toxicity in maize root membranes
Authors: Suhayda Charles G. , Haug Alfred
Published: May 2006

Application of 10–50 μM Al ions to a plasma membrane‐enriched microsomal fraction, isolated from roots of maize (Zea mays L.), resulted in decreased Mg2‐ATPase activity. This was probably caused by changes in membrane structure as detected by the use of spin probes. Both enzymatic activity and membrane structure could in part be protected from Al injury when organic acids, similar to those found in maize root tissue, were administered prior to the metal. When stressed by application of Al ions, the Al‐tolerant maize hybrid, W64, maintained higher concentrations of organic acids, especially malic and trans‐aconitic, than the Al‐sensitive maize hybrid, A632. We hypothesize that citric and malic acid, because of their high stability constants with Al and/or the acid's concentration reduce Al toxicity in maize root tissue, especially in the Al‐tolerant line.
Maintenance of the diurnal petiolar movement by exogenous indole‐3‐acetic acid under day‐night cycles in Mimosa pudica
Authors: Morimoto Naoaki , Shichijo Chizuko , Watanabe Shinobu , Suda Shozo , Hashimoto Tohru
Published: May 2006

Effects of plant hormones on the diurnal movement of the petiole of Mimosa pudica L. were examined under the conditions of day‐night cycles. Surgical removal of the leaf at the middle of the petiole led to gradual loss of the movement. Aqueous solutions of indole‐3‐acetic acid (IAA) applied as a pulse each day 10 μl at (10−6−10−5M) or continuously (10−8−10−6M) to the cut end of the petiole maintained a diurnal movement that has the same phase of oscillation as that shown in the intact leaf. Pulse treatments given at different times of the day had no effect on the phase of the oscillation. Higher concentrations of the acid gave larger amplitudes. Other hormones such as gibberellic acid, kinetin and [R,S]‐abscisic acid or 1‐aminocyclopropane‐1‐carboxylic acid did not show diurnal movement‐maintaining activities of IAA. Gibberellic acid disturbed the phase of the diurnal movements and kept the petiole elevated at very high positions. A possible action mechanism of IAA is discussed.
Balance between anionic and cationic extracellular peroxidase activities in Sedum album leaves after ozone exposure. Analysis by high‐performance liquid chromatography
Authors: Castillo Federico J. , Greppin Hubert
Published: May 2006

Peroxidase activity was assayed with different electron donors (guaiacol, ascorbate, syringaldazine) in the intercellular fluid of Sedum album L. leaves after ozone exposure. Anionic and cationic peroxidases were separated and purified by high performance ion‐exchange and gel permeation chromatography. Both isoperoxidases were tested as regards their molecular weight and apparent kinetic constants with different substrates. Ascorbate peroxidase activity was rapidly stimulated after ozone exposure, whereas syringaldazine peroxidase activity reached its maximum 24 h later. Increases in ascorbate and syringaldazine peroxidase activities occurred simultaneously with increases in cationic and anionic peroxidase activities, respectively. Apparent Km values indicate a high affinity of cationic peroxidases for ascorbate and of anionic peroxidases for syringaldazine. The metabolic role of this balance between cationic and anionic peroxidases after ozone exposure is discussed.
Stress induction of abscisic acid in maize roots
Authors: Lachno D. R. , Baker D. A.
Published: May 2006

Moderate water stresses in the range 0 to −0.6 MPa applied with PEG 6000 to excised roots of Zea mays L. var. LG 11 induced increases of up to four‐fold in the amount of abscisic acid (ABA) determined in the tissue after a 12 h period of xylem exudation. The ABA concentration of xylem exudate collected after a 2 h water stress also increased by up to four‐fold. Salt stresses, induced with NaCl solutions, resulted in similar increases in the ABA concentrations. ABA concentrations in both root tissue and xylem exudate were highest 4 h after removal of the stress and then declined over a subsequent 8 h period. These results are interpreted in support of the concept that root‐produced ABA may have a role in the fine control of the plant's water balance.
Incorporation of 5‐aminolevulinic acid into chlorophyll in darkness in barley
Authors: Packer Nicolle , Adamson Heather
Published: May 2006

The incorporation of radioactive aminolevulinic acid (ALA) into chlorophyll (Chl) a and b, as well as protochlorophyllide (Pchlide) in light‐grown barley seedlings (Hordeum vulgare L. cv. Clipper) transferred to darkness is demonstrated.

In the experiments described, 6‐day‐old, glasshouse‐grown seedlings were transferred to darkness and incubated in [14C]‐ or [3H]‐ ALA for 18 h.

Chl a and b were extracted and purified to constant specific radioactivity by HPLC and TLC of their magnesium‐free derivatives, pheophytin a and b. The presence of label in the tetrapyrrole ring of the Chls was established by removal of the phytol chain by alkaline hydrolysis and determination of the specific radioactivity of the chlorin e6 and rhodin g7 derivatives.

Barley seedlings that had been grown in darkness for 5 days, transferred to light for 20 h, and then returned to darkness in the presence of radioactive ALA also incorporated label into Chl. However, this was only apparent in intact seedlings. Excised leaves from greened etiolated plants did not incorporate ALA into Chl in darkness. This was consistent with the finding of Apel et al. (K. Apel, M. Motzkus and K. Dehesh, 1984. Planta 161: 550–554) and may account for their failure to obtain evidence for a light‐independent protochlorophyllide reductase in greening barley.

Although the incorporation of ALA into Chl compared to Pchlide was slight (5%), the presence of label in the tetrapyrrole nucleus of Chl a and b is unequivocal evidence of a light‐independent pathway of Chl biosynthesis in barley that has been exposed to light during development. Limited entry of exogenous labelled ALA into the precursor pools leading to the dark reduction of Pchlide is postulated.
Phytochrome in Norflurazon‐treated seedlings of Pharbitis nil
Authors: Rombach J.
Published: May 2006

The properties of phytochrome have been measured by dual‐wavelength spectropho‐tometry in the cotyledons of the short‐day plant Pharbitis nil Choisy cv. Violet, where it is known to play a role in flower induction. In plants de‐etiolated by a single white light period (4 h or longer), destruction of the far‐red absorbing form of phytochrome (Pfr) was twice as rapid as after 10 min red light. A small fraction of Pfr was stable. After de‐etiolation by a period of white light (6 h or longer) the rapid decrease of Pfr during the first 30 min was accompanied by a rapid increase of the red absorbing form of phytochrome (Pfr). This rapid increase of Pfr is probably due to dark reversion. Long term synthesis of phytochrome was inhibited by the presence of Pfr. Phytochrome synthesised in darkness showed the etiolated‐plant type characteristics and underwent rapid destruction upon photoconversion to Pfr. The stable Pfr identified here is possibly that pool of phytochrome associated with the long term promotive process in flower induction, and the rapidly reverting Pfr is that pool associated with the night break inhibition of flowering.
Metabolism of [13C]‐labelled photosynthate in plant cytosol and bacteroids of root nodules of Glycine max
Authors: Kouchi Hiroshi , Yoneyama Tadakatsu
Published: May 2006

Well‐nodulated soybean (Glycine max L. Merr. cv. Akisengoku) plants were allowed to assimilate 13CO2. Plant cytosol and bacteroid fractions were isolated from nodules, and the kinetics of [13C]‐labelling of soluble carbohydrates, organic acids and amino acids were investigated.

The concentrations of all metabolites, with the exception of trehalose and 3‐hydroxy‐butyrate, were 10‐ to 1000‐fold higher in plant cell cytosol than in bacteroids. The major portion of trehalose was found in bacteroids and 3‐hydroxybutyrate only in bacteroids. Sucrose was most highly labelled with 13C in nodules, and the levels and time‐course of labelling of sucrose were in good agreement with those of respired CO2 from the nodules. The levels and time‐courses of labelling of sucrose were closely similar in cytosol and bacteroids. Glucose was less labelled than sucrose and the level of labelling was consistently higher in cytosol than in bacteroids. The levels of [13C]‐labelling of organic acids and amino acids in nodules were lower than those of sucrose and of respired CO2. Tricarboxylic acid cycle intermediates, particularly succinate, were considerably less labelled in bacteroids than in the cytosol. All amino acids detected were also much more rapidly labelled in the cytosol. The results are discussed in relation to the utilization and possible compartmentation of carbon substrates in nodule tissues.
Histones and the first cell cycle in maize germination
Authors: Baíza A. , Aguilar R. , Sánchez‐de‐Jiménez E.
Published: May 2006

The timing of the onset of cell division during seed germination in maize and the role of histones for this process have been studied. Embryonic axes of maize seeds (Zea mays L. hybrid H‐30) were incubated in a sterile nutrient medium for different periods of time. For some experiments putrescine was also added. Mesocotyl, root tip and scutellar node were dissected at specific periods after incubation and the mitotic indices were determined in these tissues. Embryonic axes were incubated in the same medium either with [14C]‐lysine or [32P]‐phosphate. The incorporation of either 14C or 32P into histones was followed, both in postribosomal supernatant and in nuclei. It was found that during germination, there is specific timing for meristematic cells entering into cell division. Among the tissues tested, the mesocotyl meristem was the first to initiate this process. De novo synthesis of histones was detected as early as after 6 h of imbibition and the rate increased up to 12 h. Putrescine stimulated cell division and phosphorylation of the histones. The implications of these findings are discussed.
Comparison of different enzyme immunoassays for measuring indole‐3‐acetic acid in vegetative citrus tissues
Authors: Sagee Oded , Maoz Arieh , Mertens Rudiger , Goren Raphael , Riov Joseph
Published: May 2006

An enzyme‐linked immunosorbent assay (ELISA) using polyclonal antibodies, which were raised against indole‐3‐acetic acid (IAA) conjugated to bovine serum albumin (BSA) via the indolic nitrogen (IAA‐N1‐BSA), has been developed. The sensitivity and specificity of these antibodies were compared to those of polyclonal and monoclonal antibodies raised against IAA conjugated to BSA via C1 of the carboxyl group (IAA‐C1‐BSA). The sensitivity of the assays improved in the following order: monoclonal antibodies > antibodies to IAA‐C1‐BSA > antibodies to IAA‐C1‐BSA. Antibodies against IAA‐C1‐BSA had less cross‐reactivity to indoles structurally related to IAA, excluding indole‐3‐pyruvic acid. A rapid and effective method for purification of IAA in citrus tissues before analysis by ELISA is described. Values of IAA in citrus (Citrus sinensis [L.] Osbeck cv. Shamouti orange) shoot tips obtained with all three antibodies were similar. However, in leaf tissues which contain lower amounts of IAA compared to shoot tips, monoclonal antibodies gave higher values of IAA than polyclonal antibodies. Estimation of free IAA levels in purified extracts of citrus shoot tips, very young leaves, and mature leaves was ca 380, 248, and 74 ng (g fresh weight)−1 respectively.
Patterns of adenine metabolism and caffeine biosynthesis in different parts of tea seedlings
Authors: Ashihara Hiroshi , Kubota Hiromi
Published: May 2006

Contents of purine alkaloids in different parts of tea (Camellia sinensis L. cv. Yabukita) seedlings, seeds and tissue cultures were determined with high‐performance liquid chromatography. More than 99% of the caffeine detected was in the leaves of the 4‐month‐old seedlings. The amount expressed per g fresh weight was higher in older leaves. Theobromine, a precursor of caffeine biosynthesis, was found only in younger leaves. Zero or only trace amounts of theophylline, a degradation product of caffeine, were found in the seedlings. Almost all the caffeine in tea seeds was found in the seed coats. Theobromine and theophilline could not be detected in any part of the seeds.

Tracer experiments using [8‐14C]‐adenine indicate that (i) caffeine biosynthesis from [8‐14C]‐adenine occurs only in younger leaves,(ii) “salvage” of [8‐14C]‐adenine for nucleic acid synthesis takes place in all parts of the seedlings, (iii) considerable degradation of [8‐14C]‐adenine by conventional purine degradation pathway via uric acid takes place in roots and lower parts of stem tissue.

The results strongly suggest that caffeine is synthesized in younger leaves and accumulated within the leaves. Both caffeine contents and its synthetic activity from adenine were extremely low in tissue culture of tea.
Role of water relations and photosynthesis in the release of buds from apical dominance and the early reinvigoration of decapitated poplars
Authors: Blake Terence John , Tschaplinski Timothy James
Published: May 2006

A decrease in xylem pressure potential starting 1 h after decapitation of young hybrid poplars (Populus deltoides Bartr. ×Populus nigra L. cv. DN22) reduced stomatal conductance and transpiration rates for the first 3 days after decapitation. This early moisture stress was alleviated 4 to 5 days after decapitation, resulting in substantial increases in stomatal aperture, transpiration and net photosynthetic rates which continued for the remainder of the one week measurement period. The results suggest the following sequence of events in the decapitated plant: After a brief moisture stress, decapitation increases moisture availability by increasing the root/shoot ratio and by reducing shoot competition for moisture. Improvement in hydration releases buds from apical dominance and increases stomatal conductance and rates of net photosynthesis. This, in turn, leads to the acceleration of growth observed when plants are reinvigorated by decapitation.
Effect of nitrate on acetylene reduction activity and carbohydrate composition of Phaseolus vulgaris nodules
Authors: Streeter John G.
Published: May 2006

When Phaseolus vulgaris L. cv. Kentucky Wonder plants were supplied with various levels of nitrate for 34 days, nodule weight (plant)−1, acetylene reduction activity (g nodule)−1, and sugar concentration in nodules were depressed >60% (7.5 mM nitrate vs nil nitrate). Starch concentration in nodules was more than double the sugar concentration and declined only slightly in response to nitrate level. At the highest level of nitrate, sugar concentration in nodules was 50% greater than that in roots and nodule starch was about 6‐fold greater than root starch on a fresh weight basis. When plants were grown with 1 mM nitrate and then supplied with 12 mM nitrate for 7 days, the rapid decline in acetylene reduction activity coincided with a decline in sucrose concentration. However, glucose and fructose concentrations declined only after the largest decrease in acetylene reduction had occurred, and the quantitative decrease in glucose and fructose in nodules was small relative to sucrose. Other results showed that the magnitude of the effect of nitrate on some nodule carbohydrate compounds depends on Rhizobium phaseoli strain and on whether plants were grown with or without nitrate prior to experimental treatments. Some of the results are consistent with the carbohydrate‐deprivation hypothesis for inhibition of legume nodules by nitrate. However, there are several complications involved in the interpretation of results of this type, and other possible explanations for the results are suggested.
Barley (Hordeum vulgare) seed dormancy as related to glumella characteristics
Authors: Lenoir C. , Corbineau F. , Côme D.
Published: May 2006

Dormancy of freshly harvested barley (Hordeum vulgare L. cv. Sonja) caryopses results mainly from glumellae which fix oxygen by polyphenol oxidase (EC 1.14.18.1)‐mediated oxidation of phenolic compounds present in high amounts. The breaking of dormancy during dry storage is not due to qualitative or quantitative modifications of the phenols or polyphenol oxidases. Glumellae of dormant caryopses start to take up oxygen at the beginning of inbibition, whereas those of non‐dormant caryopses start to take up oxygen only after about 10 h. That delay should allow germination.
K, Mg‐ATPase activity in guard cells of Commelina communis
Authors: Nejidat Ali , Roth‐Bejerano Nurit , Itai Chanan
Published: May 2006

A Mg2+‐dependent, K+‐stimulated ATPase activity was detected in microsomal preparations from guard cell protoplasts of Commelina communis L. The ATPase activity was oligomycin‐insensitive, highly specific for ATP and strongly inhibited by pentavanadate and CaSO4. It is possible that this ATPase is associated with the plasmalemma and its activity linked with K+ uptake by guard cells.
Senescence in cut carnation flowers: Temporal and physiological relationships among water status, ethylene, abscisic acid and membrane permeability
Authors: Eze J. M. O. , Mayak S. , Thompson J. E. , Dumbroff E. B.
Published: May 2006

Changes in water status, membrane permeability, ethylene production and levels of abscisic acid (ABA) were measured during senescence of cut carnation flowers (Dianthus caryophyllus L. cv. White Sim) in order to clarify the temporal sequence of physiological events during this post‐harvest period. Ethylene production and ABA content of the petal tissue rose essentially in parallel during natural senescence and after treatment of young flowers with exogenous ethylene, indicating that their syntheses are not widely separated in time. However, solute leakage, reflecting membrane deterioration, was apparent well before the natural rise in ethylene and ABA had begun. In addition, there were marked changes in water status of the tissue, including losses in water potential (ψw), and turgor (ψp), that preceded the rise in ABA and ethylene. As senescence progressed, ψw continued to decline, but ψp returned to normal levels. These temporal relationships were less well resolved when senescence of young flowers was induced by treatment with ethylene, presumably because the time‐scale had been shortened. Thus changes in membrane permeability and an associated water stress in petal tissue appear to be earlier symptoms of flower senescence than the rises in ABA or ethylene. These observations support the contention that the climacteric‐like rise in ethylene production is not the initial or primary event of senescence and that the rise in ABA titre may simply be a response to changes in water status.
Short‐term effects of infestation by two aphid species on plant growth and shoot respiration of three legumes
Authors: Hawkins C. D. B. , Aston M. J. , Whitecross M. I.
Published: May 2006

The short‐term effects of infestation by cowpea aphids (Aphis craccivora Koch) and pea aphids [Acyrthosiphon pisum (Harris)], both Homoptera: Aphididae, on plant growth and respiration of excised, intact shoots of cowpea [Vigna unguiculata (L.) Walp. cv. Caloona], broad bean (Vicia faba L. cv. Aquadulce) and garden pea (Pisum sativum L. cv. Victory Freezer) seedlings were investigated, but not all plant‐aphid combinations were utilized. Root, shoot and plant dry weights were significantly reduced within 10 days in the infested plants. Rates of total shoot respiration were significantly greater in infested plants within 10 days, and the increase was not due to increased alternative pathway activity but, rather, to increased cytochrome pathway activity. It is suggested that the aphid‐induced increase in shoot respiration may be due to increased rates of photosynthesis, to substances injected into the phloem by the aphids and/or delayed senescence. These data indicate that aphid‐infested shoots had a decreased carbon use efficiency.
Changes in the levels and composition of sterols in different tissues of Lolium temulentum plants during floral development
Authors: Garg Vipin K. , Paleg Leslie G.
Published: May 2006

Free, esterified and glycosylated sterols were analysed separately from the shoot apices, leaves, leaf sheaths and stems of Lolium temulentum L. (strain Ceres) plants during floral development. Short‐day grown plants (50 days old) were induced to flower by exposure to a single long day. The four major sterols found by GC‐MS analysis were sitosterol, cholesterol, campesterol and stigmasterol. The sterol levels in the shoot apex were much higher than those in the leaf, leaf sheath and stem. A much greater proportion of cholesterol was found in the shoot apex than in other tissues and this may reflect a specific association of cholesterol with meristematic and/or reproductive tissues.

During the inductive treatment, the sterol levels decreased in all four tissues. The major effect during early differentiation was the occurrence of transient increases in the free and esterified sterol levels in the leaf and the stem tissues. The steryl ester content peaked 24 h before the appearance of double ridges, followed by a peak in free sterol content at the double ridge stage. Similar changes could not be detected in the shoot apices. This is the first report of the sterol composition of developing shoot apices, and the results emphasize the dynamic nature of sterol metabolism during reproductive growth of L. temulentum.
Net CO2 output by CAM plants in the light: the role of leaf conductance
Authors: Frimert Volker , Kluge Manfred , Smith J. Andrew C.
Published: May 2006

The reasons for CO2 release by some CAM plants during the light period were investigated by comparative gas‐exchange studies with three leaf‐succulent species, Kalanchoë tubiflora Hamet, Sedum morganianum E. Walth. and Sempervivum tectorum L. Sempervivum showed net CO2 output during the day at constant day‐night temperatures of both 15 and 25°C, whereas Kalanchoë and Sedum showed no CO2 release at this time at either temperature. Net nocturnal CO2 uptake was markedly reduced at 25°C compared with 15°C in Kalanchoë and Sempervivum, while CO2 was released at night at higher temperature by Sedum if leaf/air vapour pressure difference was also increased.

Values for intercellular partial pressure of CO2 (piCO2) were calculated from leaf conductance and were characteristically lowest in the dark and highest in the light period. Maximum values of piCO2 ranged from 264 Pa in Sedum to 87 Pa in Kalanchoë, but were somewhat lower than those reported from direct measurements of the gas phase in other CAM plants. Leaf conductance declined with increasing piCO2 in all three species. Minimum values of approximately 0.2 mmol m−2 s−1 were observed at piCO2= 33 Pa in Kalanchoë and Sedum, with no further decrease at higher piCO2, implying that this largely represented the conductance of the cuticle. In Sempervivum, however, leaf conductance declined more gradually, and was as much as 0.8 mmol m−2 s−1 at the highest observed values of piCO2. The cause of net CO2 output in the light by Sempervivum thus appeared to be lower stomatal sensitivity to CO2, resulting in relatively high leaf conductance even at times when piCO2 greatly exceeded that of ambient air.
Selection, characterization and regeneration of hydroxyproline‐resistant cell lines of Solanum tuberosum: Tolerance to NaCl and freezing stress
Authors: van Swaaij A. C. , Jacobsen E. , Kiel J. A. K. W. , Feenstra W. J.
Published: May 2006

Sixty‐seven hydroxyproline‐resistant (hypr) cell lines were selected from cell suspensions of a diploid potato (Solanum tuberosum L., clone H2578) after plating on 5 and 10 mM hydroxyproline (hyp). Resistant colonies were obtained with a spontaneous frequency of 2.9×10−6. No clear influence could be shown from treatment with N‐ethyl‐N‐nitrosourea (10 or 50 μM). Ninety % of the variant lines contained more proline than the wild type when cells were grown away from hyp for 1 month. Total free amino acid content was increased 2.2 to 6.8 times. When the lines were grown for another 2–5 months on non‐selective medium, the content of proline and other amino acids and hyp resistance decreased. After this period the values were, however, still substantially higher than in the wild type. When tested for growth on media with other amino acid analogues (azetidine‐2‐carboxylic acid and dehydroproline, analogues of proline; aminoethyl‐cysteine, analogue of lysine and 3‐fluorotyrosine, analogue of tyrosine) and on media with inhibitory concentrations of lysine + threonine. lines H4a and H4b4 were cross resistant to these compounds. When tested on media with inhibitory NaCl concentrations, variant lines H2a, H4a, and H6 showed better tolerance than the wild type. One variant cell line (H4a) was successfully regenerated into plants. Preliminary results showed an increased frost tolerance in the leaves of these plants (−4.5°C compared to −3°C for the wild type), accompanied by a higher leaf proline content. Callus initiated from leaves of the regenerated clones was more resistant to hyp than wild type callus, indicating that the variant trait might be due to a mutation.
Cultivar differences in soluble sugar content of mature rice grain
Authors: Smyth Douglas A. , Repetto Barbara M. , Seidel Nancy E.
Published: May 2006

Mature grain from 31 rice (Oryza sativa L.) cultivars grown in the same location was analyzed for soluble sugar content to determine quantitative differences in this parameter. Cultivar variation in caryopsis sucrose content was 4‐fold ranging from 15 to 59 μmol sucrose (g fresh weight)−1. Soluble reducing sugar ranged from 7 to 15 μmol hexose (g fresh weight)−1. Soluble sugar content was much greater in the outer part of the grain than in the endosperm. Caryopsis enzyme activities were measured in 8 cultivars having a range of grain sucrose content. No relationship between grain sucrose content of these cultivars and the level of enzymes of sucrose metabolism, glycolysis, and oxidative pentose pathway was established. Caryopsis respiration after 1 h of imbibition also was not related to the amount of soluble sugars available in the grain among these 8 cultivars. The results show that there are significant differences in the sugar‐accumulating capacity of the caryopsis of different rice cultivars. The detection of a fructose 2,6‐bisphosphate‐sensitive, PPi: fructose 6‐phosphate phosphototransferase (EC 2.7.1.90) in the endosperm suggests the presence of a regulatory mechanism for sucrose/starch partitioning established in other plant tissues.
Growth comparisons of a supernodulating soybean (Glycine max) mutant and its wild‐type parent
Authors: Day David A. , Lambers Hans , Bateman Jan , Carroll Bernard J. , Gresshoff Peter M.
Published: May 2006

The growth of a supernodulating, nitrate‐tolerant soybean [Glycine max (L.) Merr.] mutant nts382 (nitrate‐tolerant symbiosis) was compared to that of its wild‐type parent, cv. Bragg, over the first 50 days after sowing. Plants were grown either inoculated in the absence of an external nitrogen source or uninoculated in the presence of 5 mM KNO3. For both treatments, nts382 growth up to 13 days after planting was faster than that of cv. Bragg. Thereafter, supernodulation of inoculated nts382 occurred and growth of cv. Bragg was faster; shoot and root dry weight increments and leaf area were greater in cv. Bragg, but the N content of nts382 was higher. Relative growth and net assimilation rates were lower in nts382, which had faster shoot and root respiration rates. Shoot growth of uninoculated plants was similar for both mutant and wild‐type but roots of nts382 were slightly smaller than those of cv. Bragg. Total plant N content was similar in uninoculated cv. Bragg and nts382 but the latter had a higher leaf N content. Early lateral root formation (prior to nodule emergence) was greater in nts382 regardless of whether rhizobia or KJNO3 were present. We conclude that nts382 has some inherent differences from its parent but that supernodulation significantly retards plant growth.
Regulation of nitrate reductase in detached oat leaves by light and oxygen
Authors: Kenis J. D. , Trippi V. S.
Published: May 2006

Regulation of nitrate reductase (NR, EC 1.6.6.1) by oxygen concentration and light was studied in segments of oat (Avena sativa L. cv. Suregrain) leaves, using the in vivo nitrate reductase assay. The activity of NR decreased after excision in either light or darkness; the addition of cycloheximide prevented this decrease. Treatments that increased tissue permeability (anoxia, Triton X‐100) also increased NR activity. There was in general less NR activity in the light than in the dark and also less under aerobic (21–100% O2) than under anaerobic (0.3% O2) conditions. Treatments with antioxidants improved the activity in the light, but only at high O2 levels (21–100% O2).

The results suggest that NR may be regulated by inhibitory proteins synthesized in either light or darkness, by permeability changes and by light‐induced oxidations that occur when O2 is present. Oxygen may control the activity by stimulating the synthesis of inhibitory proteins in the light and in the dark and by promoting oxidation of SH‐groups in the light.
Changes in the pattern of protein synthesis during differentiation of the Ascomycete Sphaerostilbe repens
Authors: Hilbert Jean‐Louis , Botton Bernard
Published: May 2006

The vegetative mycelium of Sphaerostilbe repens Berkeley and Broome (strain CBS 275‐60) gives rise, within 48 h, to aggregated organs composed of coremia and rhi‐zomorphs. Developmental changes in polypeptide patterns were studied by one‐ and two‐dimensional polyacrylamide gel electrophoresis after cells had been induced to undergo synchronized differentiation. One‐dimensional gel electrophoresis revealed only minor changes during the morphogenesis. Of the 300 polypeptides resolved by two‐dimensional gel electrophoresis, nearly 12% either increased or decreased during coremium and rhizomorph differentiation. Some polypeptides appeared to be unique to one or the other of the cell preparations and represented apparent qualitative differences. During the first 24 h of differentiation, about 20 polypeptide spots appeared, 6 were enhanced, 4 were reduced and 32 disappeared. Over the next 24 h changes in the population of proteins were less marked: 14 new proteins were revealed and 9 increased in intensity while 15 declined and 9 were no longer detectable. Five proteins which were present at a significant level only during the first stages of differentiation, may therefore, putatively be designated as aggregation‐specific polypeptides.
The effect of the embryo axis and exogenous sucrose on lipolysis and glyoxysomal enzyme development in Ricinus communis (castor bean) endosperm and cotyledons
Authors: Tarpley Lee , Choinski J. S.
Published: May 2006

Post‐germinative growth in castor bean (Ricinus communis L. cv. Hale) seedlings was investigated to determine whether lipolytic enzyme synthesis and lipid breakdown was a function of the embryo axis or simply based on a source‐sink mechanism connected with sucrose produced during mobilization of storage lipid. Endosperm and cotyledons were excised from the embryo axis at 24 h intervals and were then incubated in Petri dishes containing water or 0.1 M sucrose for 24 h. Excised endosperm showed similar or higher malate synthase (MS, EC 4.1.3.2) and isocitrate lyase (ICL, EC 4.1.3.1) activities and increased lipolysis when compared with endosperm obtained from similarly intact seedlings of the same age. In contrast, cotyledonary ICL and MS activity was up to 50% lower and lipolysis was only slightly affected in excised material when compared with cotyledons obtained from intact seedlings. Incubating endosperm in sucrose had no effect on the development of the above enzyme activities or lipid content, when compared with material incubated in water only. In contrast, cotyledonary MS and ICL activities were up to 70% lower in sucrose and lipolysis substantially inhibited. Lipid breakdown and the development of lipolytic enzyme activity in cotyledons seem to be dependent on the presence of the endosperm. It is concluded that enzyme regulation in castor bean seedlings cannot entirely be explained by axis control or source‐sink relationships.
Endogenous levels of abscisic acid, indole‐3‐acetic acid, zeatin and zeatin‐riboside during the course of adventitious root formation in cuttings of Craigella and Craigella lateral suppressor tomatoes
Authors: Maldiney R. , Pelèse F. , Pilate G. , Sotta B. , Sossountzov L. , Miginiac E.
Published: May 2006

Indole acetic acid (IAA). abscisic acid (ABA), and zeatin plus zeatin riboside (Z + ZR) were determined daily in cuttings of Lycopersicon esculentum Mill. cv. Craigella (C) and the Craigella Lateral Suppressor (CLS) mutant during the first 5 days of the root‐forming process. A solid‐phase enzyme immunoassay using specific anti‐hormone antibodies was used following a one‐step HPLC purification procedure. The hormone measurements were made in cuttings divided into 4 parts. The main variations occurred in the terminal bud and in the basal part of the hypocotyl of the two tomato varieties, i.e. significant IAA and ABA increases during the first 2 days followed by a more or less fast return to the initial values at day 4 or 5. This is probably due to the ablation of the root system. Z + ZR levels dramatically decreased in the basal part of the Craigella hypocotyl 1 day after cutting. Contrary to CLS, C hypocotyls recovered the initial high levels when roots regenerated (day 5). This is probably linked to the greater ability of roots to produce cytokinins in C plants than in CLS ones. The first step of root formation (reactivation of the pericyclic cells and formation of root primordia) corresponded to a high IAA/Z + ZR ratio in the root‐forming tissue, whereas the second step (elongation of young roots) was characterized by a low ratio with low levels of hormones.
Uptake and translocation of [14C]‐labelled benzylaminopurine in apple shoots grown in vitro in relation to shoot development
Authors: Nordström Ann‐Caroline , Eliasson Lennart
Published: May 2006

Shoots of apple (rootstock A2, Malus sylvestris (L.) Mill var. domestica Borkh.) were grown in vitro on agar media containing 4.4 μM benzylaminopurine (BAP) during the whole of a 36‐day culture period or during the first 6 days of the period. Development of lateral shoots and an appreciable increase in fresh weight were obtained only when BAP was present during the whole period. Treatment for 6 days only was not sufficient for shoot proliferation although the transferred shoot continued its growth on fresh medium without BAP. Uptake of the cytokinin was studied by adding [8–14C]‐benzylaminopurine to the medium and then following the distribution of the isotope in the shoots during the 36‐day culture period. There was a steady, almost linear, uptake of 14C during the whole period. Most of the activity accumulated in the lower part of the shoot. It is concluded that BAP, due to slow translocation, is active mainly in the basal parts of the shoot where it stimulates formation and growth of buds. Its action is dependent on continuous supply of new BAP from the medium, indicating metabolism of BAP in the tissue.
Effect of steroidal glycoalkaloids of the potato on the permeability of liposome membranes
Authors: Roddick James G. , Rijnenberg Anna L.
Published: May 2006

At pH 7.2, the potato glycoalkaloid α‐chaconine caused release of entrapped peroxidase from phosphatidylcholine liposomes containing different free sterols but was ineffective against sterol‐free liposomes. The alkaloid was able to complex with all the tested sterols in vitro although there was no close correlation between the extent of sterol binding and liposome disruption. α‐Solanine also complexed with sterols in vitro but had no effects on sterol‐containing liposomes under these conditions. Both sterol concentration and alkaloid concentration were limiting factors in the action of chaconine but did not markedly affect that of solanine. Solanine destabilized liposome membranes only at pH values of 8 and above but was less effective than chaconine. The importance of the carbohydrate moiety of glycoalkaloids was further demonstrated by the inability of β2‐chaconine to complex with sterols or disrupt liposomes.
Protein synthesis and loss of viability of rice seeds: Effect of polyamines on in vitro translation
Authors: Mukhopadhyay A. , Ghosh B.
Published: May 2006

The capacity of rice (Oryza sativa L. cv. Rupsail) seeds to synthesize protein shows a gradual decline with loss of seed viability, and the lesion in post‐ribosomal fraction is greater than that of ribosome. Spermine (0.4 mM) is the most effective among the polyamines in enhancing the rate of protein synthesis. There are also indications that impairment of aminoacyl‐tRNA synthetase may be one of the causes for this decreasing ability in protein synthesis by aged seeds.