bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of microsatellites for genetic variation and inbreeding analysis in Sarda sheep flocks of central Italy
Authors: Pariset L. , Savarese M. C. , Cappuccio I. , Valentini A.
Published: December 2003

A set of 11 polymorphic microsatellites has been used to assess the distribution of genetic variability in 17 flocks of the Sarda sheep breed in the Viterbo province, located in central Italy. The suitability of samples size and number of loci analysed were tested using a bootstrap procedure. The data obtained were used to estimate the genetic diversity within and among flocks, and to test the presence of inbreeding within flocks. To study the genetic relationship among flocks, a principal component analysis based on Nei standard distances was performed. The results of genetic analysis show a significant excess of homozygotes in some of the flocks. The use of genetic data for maximum likelihood tests of assignment is investigated in order to establish suitable breeding policies. This research represents a case study for the development of mating strategies suitable for incrementing genetic variability within flocks that can be applied in other domestic species showing similar breeding problems (goat, buffalo and small populations of cattle).
Development of a multigenic oligoligation assay test in relation to meat and carcass traits in cattle
Authors: Haegeman A. , Van Zeveren A. , Peelman L. J.
Published: December 2003

Simultaneous with the increased interest in the use of single nucleotide polymorphisms (SNPs) in genetic studies (such as association studies), the demand for high‐throughput SNP genotyping has risen. In order to accommodate the high throughput SNP analysis, the oligoligation assay (OLA) technique was adapted to genotype simultaneously 11 mutations in seven different candidate genes, related to meat and carcass traits in cattle. The accuracy of the multigenic test was determined by comparing the OLA data with previously obtained restriction fragment length polymorphism (RFLP) genotypes. Both data sets were 100% identical. The accuracy of the multigenic test coupled with the high throughput, relatively low cost (once optimized) and simplicity of test ensures that this test can be routinely used in each laboratory. Furthermore, the flexibility of this test means that genes can be replaced or that new ones can be added. Although initially this multigenic test was designed as a basic tool for association studies, it can be easily used as a diagnostic tool. The obtained genotype information can be integrated in breeding schemes in order to genetically enhance the herd.
Characterisation of a pine MYB that regulates lignification
Authors: Patzlaff Astrid , McInnis Stephanie , Courtenay Adrian , Surman Christine , Newman Lisa J. , Smith Caroline , Bevan Michael W. , Mansfield Shawn , Whetten Ross W. , Sederoff Ronald R. , Campbell Malcolm M.
Published: December 2003

A member of the R2R3‐MYB family of transcription factors was cloned from a cDNA library constructed from RNA isolated from differentiating pine xylem. This MYB, Pinus taeda MYB4 (PtMYB4), is expressed in cells undergoing lignification, as revealed by in situ RT‐PCR. Electrophoretic mobility shift assays (EMSAs) showed that recombinant PtMYB4 protein is able to bind to DNA motifs known as AC elements. AC elements are ubiquitous in the promoters of genes encoding lignin biosynthetic enzymes. Transcriptional activation assays using yeast showed that PtMYB4 could activate transcription in an AC‐element‐dependent fashion. Overexpression of PtMYB4 in transgenic tobacco plants altered the accumulation of transcripts corresponding to genes encoding lignin biosynthetic enzymes. Lignin deposition increased in transgenic tobacco plants that overexpressed PtMYB4, and extended to cell types that do not normally lignify. Taken together, these findings are consistent with the hypothesis that PtMYB4 is sufficient to induce lignification, and that it may play this role during wood formation in pine.
Identification of novel cis‐acting elements, IDE1 and IDE2, of the barley IDS2 gene promoter conferring iron‐deficiency‐inducible, root‐specific expression in heterogeneous tobacco plants
Authors: Kobayashi Takanori , Nakayama Yuko , Itai Reiko Nakanishi , Nakanishi Hiromi , Yoshihara Toshihiro , Mori Satoshi , Nishizawa Naoko K.
Published: December 2003

The molecular mechanisms of plant responses to iron (Fe) deficiency remain largely unknown. To identify the cis‐acting elements responsible for Fe‐deficiency‐inducible expression in higher plants, the barley IDS2 (iron deficiency specific clone no. 2) gene promoter was analyzed using a transgenic tobacco system. Deletion analysis revealed that the sequence between −272 and −91 from the translational start site (−272/−91) was both sufficient and necessary for specific expression in tobacco roots. Further deletion and linker‐scanning analysis of this region clearly identified two cis‐acting elements: iron‐deficiency‐responsive element 1 (IDE1) at −153/−136 (ATCAAGCATGCTTCTTGC) and IDE2 at −262/−236 (TTGAACGGCAAGTTTCACGCTGTCACT). The co‐existence of IDE1 and IDE2 was essential for specific expression when the −46/+8 region (relative to the transcriptional start site) of the CaMV 35S promoter was used as a minimal promoter. Expression occurred mainly in the root pericycle, endodermis, and cortex. When the −90/+8 region of the CaMV 35S promoter was fused, the −272/−227 region, which consists of IDE2 and an additional 19 bp, could drive Fe‐deficiency‐inducible expression without IDE1 throughout almost the entire root. The principal modules of IDE1 and IDE2 were homologous. Sequences homologous to IDE1 were also found in many other Fe‐deficiency‐inducible promoters, including: nicotianamine aminotransferase (HvNAAT)‐A, HvNAAT‐B, nicotianamine synthase (HvNAS1), HvIDS3, OsNAS1, OsNAS2, OsIRT1, AtIRT1, and AtFRO2, suggesting the conservation of cis‐acting elements in various genes and species. The identification of novel cis‐acting elements, IDE1 and IDE2, will provide powerful tools to clarify the molecular mechanisms regulating Fe homeostasis in higher plants.
Spermine signalling in tobacco: activation of mitogen‐activated protein kinases by spermine is mediated through mitochondrial dysfunction
Authors: Takahashi Yoshihiro , Berberich Thomas , Miyazaki Atsushi , Seo Shigemi , Ohashi Yuko , Kusano Tomonobu
Published: December 2003

Polyamines (PAs) play important roles in cell proliferation, growth and environmental stress responses of all living organisms. In this study, we examine whether these compounds act as signal mediators. Spermine (Spm) specifically activated protein kinases of tobacco leaves, which were identified as salicylic acid (SA)‐induced protein kinase (SIPK) and wound‐induced protein kinase (WIPK), using specific antibodies. Upon Spm treatment, upregulation of WIPK, but not SIPK, was observed. Spm‐induced mitogen‐activated protein kinases (MAPKs) activation and WIPK upregulation were prevented upon pre‐treatment with antioxidants and Ca2+ channel blockers. Additionally, Spm specifically stimulated expression of the alternative oxidase (AOX) gene, which was disrupted by these antioxidants and Ca2+ channel blockers. Bongkrekic acid (BK), an inhibitor of the opening of mitochondrial permeability transition (PT) pores, suppressed MAPKs activation and accumulation of WIPK and AOX mRNA. Our data collectively suggest that Spm causes mitochondrial dysfunction via a signalling pathway in which reactive oxygen species and Ca2+ influx are involved. As a result, the phosphorylation activities of the two MAPK enzymes SIPK and WIPK are stimulated.
Stress‐responsive zinc finger gene ZPT2‐3 plays a role in drought tolerance in petunia
Authors: Sugano Shoji , Kaminaka Hironori , Rybka Zbigniew , Catala Rafael , Salinas Julio , Matsui Kyoko , Ohme‐Takagi Masaru , Takatsuji Hiroshi
Published: December 2003

The petunia gene, ZPT2‐3, encodes a Cys2/His2‐type zinc finger protein. Here, we describe the expression of ZPT2‐3 in response to various stresses and the effects of ZPT2‐3 overexpression in transgenic petunia. Mechanical wounding induced accumulation of ZPT2‐3 transcript, and the activity of ZPT2‐3::luciferase was conferred by the 1668‐bp ZPT2‐3 upstream sequence, both locally and systemically. This induction was mediated by a jasmonic acid (JA)‐dependent and ethylene‐independent pathway. ZPT2‐3 expression was also induced by cold, drought, and heavy metal treatments. The same ZPT2‐3 promoter sequence showed similar responsiveness to wounding, cold, drought, and JA treatments in Arabidopsis when investigated in a β‐glucuronidase (GUS) reporter gene, indicating conservation of similar signaling pathways between the two plant species. ZPT2‐3 functioned as an active repressor in a transient assay using Arabidopsis leaves. Constitutive overexpression of ZPT2‐3 in transgenic petunia plants increased tolerance to dehydration. These results demonstrate the involvement of ZPT2‐3 in plant response to various stresses, and suggest its potential utility to improve drought tolerance.
Molecular cloning and characterization of a cDNA encoding ent‐cassa‐12,15‐diene synthase, a putative diterpenoid phytoalexin biosynthetic enzyme, from suspension‐cultured rice cells treated with a chitin elicitor
Authors: Cho Eun‐Min , Okada Atsushi , Kenmoku Hiromichi , Otomo Kazuko , Toyomasu Tomonobu , Mitsuhashi Wataru , Sassa Takeshi , Yajima Arata , Yabuta Goro , Mori Kenji , Oikawa Hideaki , Toshima Hiroaki , Shibuya Naoto , Nojiri Hideaki , Omori Toshio , Nishiyama Makoto , Yamane Hisakazu
Published: December 2003

We have isolated and characterized a cDNA encoding a novel diterpene cyclase, OsDTC1, from suspension‐cultured rice cells treated with a chitin elicitor. OsDTC1 functions as ent‐cassa‐12,15‐diene synthase, which is considered to play a key role in the biosynthesis of (−)‐phytocassanes recently isolated as rice diterpenoid phytoalexins. The expression of OsDTC1 mRNA was also confirmed in ultraviolet (UV)‐irradiated rice leaves. In addition, we identified ent‐cassa‐12,15‐diene, a putative diterpene hydrocarbon precursor of (−)‐phytocassanes, as an endogenous compound in the chitin‐elicited suspension‐cultured rice cells and the UV‐irradiated rice leaves. The OsDTC1 cDNA isolated here will be a useful tool to investigate the regulatory mechanisms of the biosyntheis of (−)‐phytocassanes in rice.
Characterisation of an Arabidopsis–Leptosphaeria maculans pathosystem: resistance partially requires camalexin biosynthesis and is independent of salicylic acid, ethylene and jasmonic acid signalling
Authors: Bohman Svante , Staal Jens , Thomma Bart P. H. J. , Wang Maolin , Dixelius Christina
Published: December 2003

Out of 168 Arabidopsis accessions screened with isolates of Leptosphaeria maculans, one (An‐1) showed clear disease symptoms. In order to identify additional components involved in containment of L. maculans in Arabidopsis, a screen for L. maculans‐susceptible (lms) mutants was performed. Eleven lms mutants were isolated, which displayed differential susceptibility responses to L. maculans. lms1 was crossed with Columbia (Col‐0) and Ws‐0, and mapping data for both populations showed the highest linkage to a region on chromosome 2. Reduced levels of PR‐1 and PDF1.2 expression were found in lms1 compared to wild‐type plants 48 h after pathogen inoculation. In contrast, the lms1 mutant displayed upregulation of either marker gene upon chemical treatment, possibly as an effect of an altered ethylene (ET) response. To assess the contribution of different defence pathways, genotypes implicated in salicylic acid (SA) signalling plants expressing the bacterial salicylate hydroxylase (nahG) gene, non‐expressor of PR1 (npr1)‐1 and phytoalexin‐deficient (pad4‐1), jasmonic acid (JA) signalling (coronatine insensitive (coi)1‐16, enhanced disease susceptibility (eds)8‐1 and jasmonic acid resistant (jar)1‐1) and ET signalling (eds4‐1, ethylene insensitive (ein)2, ein3‐1 and ethylene resistant (etr)1‐1) were screened. All the genotypes screened were as resistant as wild‐type plants, demonstrating the dispensability of the pathways in L. maculans resistance. When mutants implicated in cell death responses were assayed, responsive to antagonist 1 (ran1)‐1 exhibited a weak susceptible phenotype, whereas accelerated cell death (acd)1‐20 showed a rapid lesion development. Camalexin is only partially responsible for L. maculans containment in Arabidopsis, as pad3‐1 and enhanced susceptibility to Alternaria (esa)1 clearly showed a susceptible response while wild‐type levels of camalexin were present in An‐1 and lms1. The data presented point to the existence of multiple defence mechanisms controlling the containment of L. maculans in Arabidopsis.
Potato lectin: an updated model of a unique chimeric plant protein
Authors: Van Damme Els J. M. , Barre Annick , Rougé Pierre , Peumans Willy J.
Published: December 2003

A complete cDNA encoding a potato tuber lectin has been identified and sequenced. Based on the deduced amino acid sequence, the still enigmatic molecular structure of the classical chimeric potato lectin could eventually be determined. Basically, the potato lectin consists of two nearly identical chitin‐binding modules, built up of two in‐tandem arrayed hevein domains that are interconnected by an extensin‐like domain of approximately 60 amino acid residues. Although this structure confirms the ‘canonical’ chimeric nature of the Solanaceae lectins, it differs fundamentally from all previously proposed models. The new insights in the structure are also discussed in view of the physiological role of the Solanaceae lectins.
Isolation of AtSUC2 promoter‐GFP‐marked companion cells for patch‐clamp studies and expression profiling
Authors: Ivashikina Natalya , Deeken Rosalia , Ache Peter , Kranz Erhard , Pommerrenig Benjamin , Sauer Norbert , Hedrich Rainer
Published: December 2003

K+ channels control K+ homeostasis and the membrane potential in the sieve element/companion cell complexes. K+ channels from Arabidopsis phloem cells expressing green fluorescent protein (GFP) under the control of the AtSUC2 promoter were analysed using the patch‐clamp technique and quantitative RT‐PCR. Single green fluorescent protoplasts were selected after being isolated enzymatically from vascular strands of rosette leaves. Companion cell protoplasts, which could be recognized by their nucleus, vacuole and chloroplasts, and by their expression of the phloem‐specific marker genes SUC2 and AHA3, formed the basis for a cell‐specific cDNA library and expressed sequence tag (EST) collection. Although we used primers for all members of the Shaker K+ channel family, we identified only AKT2, KAT1 and KCO6 transcripts. In addition, we also detected transcripts for AtPP2CA, a protein phosphatase, that interacts with AKT2/3. In line with the presence of the K+ channel transcripts, patch‐clamp experiments identified distinct K+ channel types. Time‐dependent inward rectifying K+ currents were activated upon hyperpolarization and were characterized by a pronounced Ca2+‐sensitivity and inhibition by protons. Whole‐cell inward currents were carried by single K+‐selective channels with a unitary conductance of approximately 4 pS. Outward rectifying K+ channels (approximately 19 pS), with sigmoidal activation kinetics, were elicited upon depolarization. These two dominant phloem K+ channel types provide a versatile mechanism to mediate K+ fluxes required for phloem action and potassium cycling.
Nuclear localization and in vivo dynamics of a plant‐specific serine/arginine‐rich protein
Authors: Ali Gul Shad , Golovkin Maxim , Reddy Anireddy S. N.
Published: December 2003

Serine/arginine‐rich (SR) proteins in non‐plant systems are known to play important roles in both constitutive and alternative splicing of pre‐messenger RNAs (pre‐mRNAs). Recently, we isolated a novel SR protein (SR45), which interacts with U1 snRNP 70K protein, a key protein involved in 5′ splice site recognition. SR45 is found only in plants and is unique in having two SR domains separated by an RNA recognition motif (RRM). To study the localization and dynamics of SR45, we expressed it as a fusion to green fluorescent protein (GFP) in cultured cells and transgenic Arabidopsis plants. The SR45 is localized exclusively to nuclei. In interphase nuclei, GFP–SR45 was found both in speckles and nucleoplasm. The speckles exhibited intranuclear movements and changes in morphology. Inhibition of transcription and protein phosphorylation resulted in redistribution of SR45 to bigger speckles. The change in the number and morphology of speckles caused by inhibition of transcription was blocked by an inhibitor of phosphatases. These results indicate that transcription activity of the cell and protein (de)phosphorylation regulate the intranuclear distribution of SR45.
KINKY POLLEN encodes a SABRE‐like protein required for tip growth in Arabidopsis and conserved among eukaryotes
Authors: Procissi A. , Guyon A. , Pierson E. S. , Giritch A. , Knuiman B. , Grandjean O. , Tonelli C. , Derksen J. , Pelletier G. , Bonhomme S.
Published: December 2003

In higher plants, pollen tubes and root hairs share an ancient growth process named tip growth. We have isolated three allelic Arabidopsis mutant lines showing kinky‐shaped pollen tubes and, when homozygous, showing shorter and thicker root hairs. The ultrastructure of pollen tubes in these kinky pollen (kip) mutants is similar to that of the wild type; however, time‐lapse studies suggest that aberrant pollen tube shape is caused by periodic growth arrests alternated with phases of tube axis reorientation. The KIP gene encodes a protein of 2587 amino acids that is predicted to be targeted to the secretory pathway. KIP mRNA was detected in all organs investigated but was most abundant in pollen and roots. KIP has putative homologues in many eukaryotes, including mammals and yeast, and is similar to the Arabidopsis SABRE gene, whose mutation causes a dwarf phenotype. The phenotype of the kip/sab double mutant suggests related functions for both genes, however, the KIP protein is mostly required for tip‐growth.
An ancient R gene from the wild potato species Solanum bulbocastanum confers broad‐spectrum resistance to Phytophthora infestans in cultivated potato and tomato
Authors: Van Der Vossen Edwin , Sikkema Anne , Hekkert Bas te Lintel , Gros Jack , Stevens Patricia , Muskens Marielle , Wouters Doret , Pereira Andy , Stiekema Willem , Allefs Sjefke
Published: December 2003

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease for potato cultivation. Here, we describe the positional cloning of the Rpi‐blb1 gene from the wild potato species Solanum bulbocastanum known for its high levels of resistance to late blight. The Rpi‐blb1 locus, which confers full resistance to complex isolates of P. infestans and for which race specificity has not yet been demonstrated, was mapped in an intraspecific S. bulbocastanum population on chromosome 8, 0.3 cM from marker CT88. Molecular analysis of a bacterial artificial chromosome (BAC) clone spanning the Rpi‐blb1 locus identified a cluster of four candidate resistance gene analogues of the coiled coil, nucleotide‐binding site, leucine‐rich repeat (CC‐NBS‐LRR) class of plant resistance (R) genes. One of these candidate genes, designated the Rpi‐blb1 gene, was able to complement the susceptible phenotype in a S. tuberosum and tomato background, demonstrating the potential of interspecific transfer of broad‐spectrum late blight resistance to cultivated Solanaceae from sexually incompatible host species. Paired comparisons of synonymous and non‐synonymous nucleotide substitutions between different regions of Rpi‐blb1 paralogues revealed high levels of synonymous divergence, also in the LRR region. Although amino acid diversity between Rpi‐blb1 homologues is centred on the putative solvent exposed residues of the LRRs, the majority of nucleotide differences in this region have not resulted in an amino acid change, suggesting conservation of function. These data suggest that Rpi‐blb1 is relatively old and may be subject to balancing selection.
CSP41a, a multifunctional RNA‐binding protein, initiates mRNA turnover in tobacco chloroplasts
Authors: Bollenbach Thomas J. , Tatman Dana A. , Stern David B.
Published: December 2003

Expression of chlorplast stem‐loop binding protein (CSP)41a, a highly conserved chloroplast endoribonuclease, was reduced >90% by the expression of antisense RNA in Nicotiana tabacum. The most striking effects of this silencing were two‐ to sevenfold decreases in the degradation rates of rbcL, psbA, and petD transcripts in lysed chloroplast extracts. These results are consistent with the hypothesis that CSP41a participates in initiating mRNA turnover through endonucleolytic cleavages. Surprisingly, rbcL and psbA mRNAs accumulated to similar levels in wild‐type and antisense lines. This suggested that decreased degradation was compensated by reduced transcription, which was confirmed using run‐on transcription assays. The collective accumulation of petD‐containing mRNAs in antisense plants decreased by 25% compared to wild‐type controls. However, the relative levels of petD processing intermediates in wild‐type and antisense plants did not differ, and there were no changes in petD 3′‐end maturation, suggesting that CSP41a is not required for petD RNA processing. CSP41a is a Mg2+‐dependent enzyme; therefore, extracts from antisense plants were tested at different Mg2+ concentrations. These experiments showed that the half‐life of rbcL decreased as the Mg2+ concentration was reduced, and at <1 mm free Mg2+, conditions where CSP41a is nearly inactive in vitro, the rbcL degradation rate was similar in wild‐type and antisense extracts, suggesting that CSP41a is normally bypassed under these conditions. Mg2+ has been shown to mediate RNA stability during chloroplast biogenesis, and our data suggest that regulation of CSP41a activity by Mg2+ is a component of this process.
Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants
Authors: Vannini Candida , Locatelli Franca , Bracale Marcella , Magnani Enrico , Marsoni Milena , Osnato Michela , Mattana Monica , Baldoni Elena , Coraggio Immacolata
Published: December 2003

The expression of the gene Osmyb4, detected at low level in rice (Oryza sativa) coleoptiles grown for 3 days at 29°C, is strongly induced by treatments at 4°C. At sublethal temperatures of 10 and 15°C, its expression in rice seedlings is already evident, but this effect cannot be vicariated by other stresses or ABA treatment. We demonstrate by transient expression that Myb4 transactivates the PAL2, ScD9 SAD and COR15a cold‐inducible promoters. The Osmyb4 function in vivo is demonstrated overexpressing its cDNA in Arabidopsis thaliana plants (ecotype Wassilewskija) under the control of the constitutive CaMV 35S promoter. Myb4 overexpressing plants show a significant increased cold and freezing tolerance, measured as membrane or Photosystem II (PSII) stability and as whole plant tolerance. Finally, in Osmyb4 transgenic plants, the expression of genes participating in different cold‐induced pathways is affected, suggesting that Myb4 represents a master switch in cold tolerance.
Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants
Authors: Ottenhof Harald H. , Ashurst Jennifer L. , Whitney Heather M. , Saldanha S. Adrian , Schmitzberger Florian , Gweon Hyun Soon , Blundell Tom L. , Abell Chris , Smith Alison G.
Published: December 2003

Pantothenate (vitamin B5) is the precursor for the biosynthesis of the phosphopantetheine moiety of coenzyme A and acyl carrier protein, and is synthesised in Escherichia coli by four enzymic reactions. Ketopantoate hydroxymethyltransferase (KPHMT) and pantothenate synthetase (PtS) catalyse the first and last steps, respectively. Two genes encoding KPHMT and one for PtS were identified in the Arabidopsis thaliana genome, and cDNAs for all three genes were amplified by PCR. The cDNAs were able to complement their respective E. coli auxotrophs, demonstrating that they encoded functional enzymes. Subcellular localisation of the proteins was investigated using green fluorescent protein (GFP) fusions and confocal microscopy. The two KPHMT–GFP fusion proteins were targeted exclusively to mitochondria, whereas PtS–GFP was found in the cytosol. This implies that there must be transporters for pathway intermediates. KPHMT enzyme activity could be measured in purified mitochondria from both pea leaves and Arabidopsis suspension cultures. We investigated whether Arabidopsis encoded homologues of the remaining two pantothenate biosynthesis enzymes from E. coli, l‐aspartate‐α‐decarboxylase (ADC) and ketopantoate reductase (KPR). No homologue of ADC could be identified using either conventional blast or searches with the program fugue in which the structure of the E. coli ADC was compared to all the annotated proteins in Arabidopsis. ADC also appears to be absent from the genome of the yeast, Saccharomyces cerevisiae, by the same criteria. In contrast, a putative Arabidopsis oxidoreductase with some similarity to KPR was identified with fugue.
Dual functionality of a plant U‐rich intronic sequence element
Authors: Simpson Craig G. , Jennings S. Nikki , Clark Gillian P. , Thow Graham , Brown John W. S.
Published: December 2003

In potato invertase genes, the constitutively included, 9‐nucleotide (nt)‐long mini‐exon requires a strong branchpoint and U‐rich polypyrimidine tract for inclusion. The strength of these splicing signals was demonstrated by greatly enhanced splicing of a poorly spliced intron and by their ability to support splicing of an artificial mini‐exon, following their introduction. Plant introns also require a second splicing signal, UA‐rich intronic elements, for efficient intron splicing. Mutation of the branchpoint caused loss of mini‐exon inclusion without loss of splicing enhancement, showing that the same U‐rich sequence can function as either a polypyrimidine tract or a UA‐rich intronic element. The distinction between the splicing signals depended on intron context (the presence or absence of an upstream, adjacent and functional branchpoint), and on the sequence context of the U‐rich elements. Polypyrimidine tracts tolerated C residues while UA‐rich intronic elements tolerated As. Thus, in plant introns, U‐rich splicing elements can have dual roles as either a general plant U‐rich splicing signal or a polypyrimidine tract. Finally, overexpression of two different U‐rich binding proteins enhanced intron recognition significantly. These results highlight the importance of co‐operation between splicing signals, the importance of other nucleotides within U‐rich elements for optimal binding of competing splicing factors and effects on splicing efficiency of U‐rich binding proteins.
A mutation in the nuclear‐encoded plastid ribosomal protein S9 leads to early embryo lethality in maize
Authors: Ma Zhengrong , Dooner Hugo K.
Published: December 2003

Seeds of the lethal embryo 1 (lem1) mutant in maize (Zea mays) display a non‐concordant lethal phenotype: whereas the embryo aborts very early, before the transition stage, the endosperm develops almost normally. The mutant was identified in a collection of maize lines that carried the transposon Activation (Ac) at different locations in the genome. Co‐segregation and reversion analysis showed that lem1 was tagged by Ac. The lem1 gene encodes a protein that is highly similar to the rice plastid 30S ribosomal protein S9 (PRPS9). lem1 maps to chromosome 1L and appears to be the only copy of prps9 in the maize genome. Green fluorescent protein (GFP) fusion constructs containing only the putative transit peptide (TP) of LEM1 localize exclusively to the plastids, confirming that the LEM1 protein is a PRP. In contrast, GFP fusion constructs containing the entire LEM1 protein co‐localize to the plastids and to the nucleus, suggesting a possible dual function for this protein. Two alternative, although not mutually exclusive, explanations are considered for the lem phenotype of the lem1 mutant: (i) functional plastids are required for normal embryo development; and (ii) the PRPS9 has an extra‐ribosomal function required for embryogenesis.
Expression of cytokinin biosynthetic isopentenyltransferase genes in Arabidopsis: tissue specificity and regulation by auxin, cytokinin, and nitrate
Authors: Miyawaki Kaori , Matsumoto‐Kitano Miho , Kakimoto Tatsuo
Published: December 2003

The rate‐limiting step of cytokinin biosynthesis in Arabidopsis thaliana Heynh. is catalyzed by ATP/ADP isopentenyltransferases, A. thaliana IsoPentenyl Transferase (AtIPT)1, and AtIPT4, and by their homologs AtIPT3, AtIPT5, AtIPT6, AtIPT7, and AtIPT8. To understand the dynamics of cytokinins in plant development, we comprehensively analyzed the expression of isopentenyltransferase genes of Arabidopsis. Examination of their mRNA levels and the expression patterns of the beta‐glucuronidase (GUS) gene fused to the regulatory sequence of each AtIPT gene revealed a specific expression pattern of each gene. The predominant expression patterns were as follows: AtIPT1::GUS, xylem precursor cell files in the root tip, leaf axils, ovules, and immature seeds; AtIPT3::GUS, phloem tissues; AtIPT4::GUS and AtIPT8::GUS, immature seeds with highest expression in the chalazal endosperm (CZE); AtIPT5::GUS, root primordia, columella root caps, upper part of young inflorescences, and fruit abscission zones; AtIPT7::GUS, endodermis of the root elongation zone, trichomes on young leaves, and some pollen tubes. AtIPT1, AtIPT3, AtIPT5, and AtIPT7 were downregulated by cytokinins within 4 h. AtIPT5 and AtIPT7 was upregulated by auxin within 4 h in roots. AtIPT3 was upregulated within 1 h after an application of nitrate to mineral‐starved Arabidopsis plants. The upregulation by nitrate did not require de novo protein synthesis. We also examined the expression of two genes for tRNA isopentenyltransferases, AtIPT2 and AtIPT9, which can also be involved in cytokinin biosynthesis. They were expressed ubiquitously, with highest expression in proliferating tissues. These findings are discussed in relation to the role of cytokinins in plant development.
Hyperiid Amphipods (Crustacea: Peracarida) and Spring Mesoscale Features in the Gulf of Mexico
Authors: Gasca Rebeca
Published: December 2003

Abstract.  The distribution and abundance of the hyperiid amphipods collected during April–May 1986 was analysed in order to study their relationship to mesoscale features in the southern Gulf of Mexico. Hyperiids were represented by 79 species, Lestrigonus bengalensis (65% of total hyperiids), Primno abyssalis (4.3%), Anchylomera blossevillei (2.3%) and Lestrigonus schizogeneios (2.3%) being the most abundant. Several mesoscale features (two cyclonic and three anticyclonic eddies, two upwelling areas) were active in the surveyed area. Cluster analysis of density and composition produced five groups of stations that were found to be related to some of these features. Overall, the mesoscale features that most influenced the local hyperiid community were the upwelling areas; they were related both with the highest and the lowest hyperiid densities and with high and low diversity figures. Overall day/night variations were normal, with highest night‐time densities; this pattern was not consistent in the different mesoscale features studied. Reverse migrations were possibly occurring, or migration patterns were lacking, at some of these systems. The hyperiid community structure related to the anticyclonic eddies differed somewhat among the eddies; however, the oceanographic exchange with the surrounding gulf waters probably obscured sharper faunistic differences between the communities.
Coastal Fish Diversity in Three Marine Protected Areas and One Unprotected Area in the Gulf of Trieste (Northern Adriatic)
Authors: Lipej Lovrenc , Bonaca Martina Orlando , Šiško Milijan
Published: December 2003

Abstract.  The coastal fish assemblage in three protected sites and one unprotected area in the Slovenian part of the Gulf of Trieste (Northern Adriatic) was studied. Species composition and richness were comparable at all studied sites, including the control, unprotected area. Differences in fish density between the protected area of Debeli rtič and the unprotected area of Fiesa‐Pacug were revealed using correspondence analysis. Particularly the densities of certain labrid species (Symphodus cinereus and S. roissali) were higher in the protected area. Those differences are attributable to the extended and densely vegetated infralittoral belt of the Debeli rtič area rather than to its protected status.
Individual Variation in the Covering Behaviour of the Shallow Water Sea Urchin Paracentrotus lividus
Authors: Crook Anne C.
Published: December 2003

Abstract.  A number of recent field‐based studies have investigated the possible functions of covering behaviour in a range of echinoid species. Some of these have found important relationships between covering behaviour and environmental factors, such as light (in particular, ultra‐violet light) and covering item availability. However, these studies have often shown considerable within‐species variation, thus making covering functionality both within and between species difficult to interpret. The present study experimentally investigates individual variability in covering behaviour characteristics of the sea urchin Paracentrotus lividus (Lamarck). Data were collected bimonthly over a 1‐year period at Lough Hyne, Ireland, by observing P. lividus in outdoor aquaria. Significant variations in covering behaviour characteristics were observed as a function of individual size and mobility but not as a function of sex. A significant relationship between water temperature, mobility and covering behaviour was also found and is hypothesized to have implications for grazing activity in P. lividus. In contrast to previous field studies of P. lividus at Lough Hyne, no summer ‘peak’ in the proportion of individuals covering was observed. However, there was a significant relationship between local solar radiation and ‘time to first cover’. Overall, these data highlight (i) the ecological significance of individual variation in P. lividus covering behaviour and (ii) the importance of investigating multiple factors as potential determinants of echinoid covering behaviour.
Density‐Dependent Effects in Jehlius cirratus (Darwin, 1854) (Cirripedia: Chthamalidae) under Different Growth Conditions
Authors: López Daniel A. , González María L.
Published: December 2003

Abstract.  We analyse the effects of crowding (‘hummocking’) on the growth, reproduction and mortality of the chthamaloid barnacle Jehlius cirratus (Darwin, 1854) on the coast of Chile. Recruitment intensity, ranging from solitary individuals to dense groups, generates different growth conditions. Density‐dependent effects are reflected in the shape, growth parameters, fecundity, sexual maturity and mortality of solitary and crowded specimens. The skewing of size distribution during growth was not significant at the beginning of the growth period, irrespective of initial density. Nevertheless, skewness in size increased with time, both at high and low densities, indicating that the dominance and suppression exerted by larger specimens over smaller ones generate a density‐dependent effect on size during growth. Mortality was greatest when high‐density recruitment occurred immediately before the period when water temperature and food quantity are highest (spring), when it is assumed that growth is greatest; this seasonal effect was not detected at lower levels of recruitment density. Similarly, no differences in mortality were detected between recruitment densities during the period when temperatures are lowest (autumn) and growth is probably slower. In the middle‐high intertidal zone, where J. cirratus co‐exists with Notochthamalus scabrosus (Darwin, 1854), the proportion of dead J. cirratus specimens was directly related both to the relative abundance of N. scabrosus and the total barnacle density. Although the mortality of J. cirratus was density dependent, the increase in the number of N. scabrosus towards the lower section of the middle intertidal zone could have a greater effect on J. cirratus mortality than intra‐specific competition.
Compositional changes on GaN surfaces under low-energy ion bombardment studied by synchrotron-based spectroscopies
Authors: Deenapanray Prakash N. K. , Petravić M. , Kim K.-J. , Kim B. , Li G.
Published: December 2003

We have investigated compositional changes on GaN surfaces under Ar-ion bombardment using synchrotron-based high-resolution x-ray photoemission (PES) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy. The low-energy ion bombardment of GaN produces a Ga-rich surface layer which transforms into a metallic Ga layer at higher bombarding energies. At the same time, the photoemission spectra around N 1s core levels reveal the presence of both uncoordinated nitrogen and nitrogen interstitials, which we have analyzed in more details by x-ray absorption measurements at N K edge. We have demonstrated that PES and NEXAFS provide a powerful combination for studying the compositional changes on GaN surfaces. A mechanism for the relocation and loss of nitrogen during ion bombardment in agreement with some recent experimental and theoretical studies of defect formation in GaN has been proposed.
Polarized Raman scattering and localized embedded strain in self-organized Si/Ge nanostructures
Authors: Kamenev B. V. , Grebel H. , Tsybeskov L. , Kamins T. I. , Williams R. Stanley , Baribeau J. M. , Lockwood D. J.
Published: December 2003

Using polarized Raman spectroscopy, we examine different vibrational modes (i.e., Si–Si, Si–Ge, and Ge–Ge) in Si/Ge self-organized nanostructures. Here, we present unambiguous proof that multilayers of Ge nanometer-size, “dome-shaped” islands grown on a 〈100〉 Si substrate are nearly fully relaxed and that the built-in strain field is substantially localized in the surrounding Si matrix. In contrast, multilayers with “pyramid-shaped” islands do not show observable relaxation. The large strain in the Si layers of the multilayer dome samples correlates with the greater self-organization in these structures compared to the multilayer pyramid samples.
Computational analysis of the deformability of leukocytes modeled with viscous and elastic structural components
Authors: Marella Saikrishna V. , Udaykumar H. S.
Published: December 2003

The objective of this work is to systematically include non-Newtonian effects in a previous Newtonian model of the leukocyte and to study the effects thereof on leukocyte rheology. The standard Newtonian-drop model of the cell is enhanced in three respects: (1) The cortical layer is treated as an elastic membrane with a nonlinear stress–strain curve to simulate unfolding of the excess surface area of the membrane. (2) A power-law shear thinning fluid is used for the cytoplasm. (3) A three-layer or compound cell model is used, which is comprised of the membrane cortex, cytoplasm and nucleus. Combinations of these aspects are also investigated. The governing equations for this multifluid system are solved in the Stokes limit. The immersed boundary technique is used to simulate the interaction of the elastic membrane with the flow field. Results indicate that each of these additional elements in the leukocyte model yield significant deviations from the Newtonian deformation and recovery behavior of the leukocyte. However, the added modeling sophistication does not appear to be sufficient to fully capture all the distinctive responses of the leukocytes under a wide variety of deformation and recovery protocols. It is shown that although a comprehensive model for the leukocyte remains elusive, the three-layer leukocyte model with cortical elasticity is a promising candidate.
Unconventional polarization characteristic of rapid photoinduced material motion in liquid crystalline azobenzene polymer films
Authors: Zettsu Nobuyuki , Fukuda Takashi , Matsuda Hiro , Seki Takahiro
Published: December 2003

We carried out double-beam interference experiments using an argon ion laser with controlled polarization in order to cause the formation of photoinduced surface relief in liquid crystalline azobenzene polymer films. The irradiation was undertaken on a film in the cis-rich state obtained by a pre-exposure to ultraviolet light. In this procedure, the efficiency of the photoinduced mass transfer was high, more than 1000 times greater than hitherto reported for amorphous azobenzene polymers. This approach revealed the unusual nature of the migration process. Rapid mass migration is promoted by intensity holographic recording, independent of the polarization of the light used for the irradiation. This insensitivity with respect to the polarization of the light led us to the conclusion that rapid mass migration starting from a cis-rich azobenzene polymer is predominately driven by phototriggered elemental processes such as local dewetting, self-organizing motion, and translation diffusion.
Electronic gradiometer in cylindrical magnetic shield for compact magnetocardiograph
Authors: Tsukamoto A. , Saitoh K. , Takagi K. , Yokosawa K. , Suzuki D. , Ogata K. , Miyashita T. , Kandori A. , Tsukada K.
Published: December 2003

An electronic first-order gradiometer in a cylindrical magnetic shield was investigated in order to determine the best magnetometer configuration for a compact multichannel magnetocardiograph (MCG). It was found that a planar gradiometer is better in terms of noise reduction than an axial gradiometer. This is because the magnetic field inside the cylindrical magnetic shield exhibits an anisotropic distribution, which was confirmed by a numerical calculation using a three-dimensional finite element method. It was also found that MCG measurement in the cylindrical magnetic shield is possible by using a planar electronic gradiometer with high-Tc directly coupled magnetometers. This configuration can successfully detect the P-wave in MCG signal without the need for averaging.
Absolute densities of N and excited N2 in a N2 plasma
Authors: Agarwal Sumit , Hoex Bram , van de Sanden M. C. M. , Maroudas Dimitrios , Aydil Eray S.
Published: December 2003

Atomic N and excited N2 (N2*) play important roles in plasma-assisted synthesis of nitride materials, such as GaN. Absolute densities of N and N2* were measured at the substrate plane in an inductively coupled N2 plasma in the pressure range of 10 to 200 mTorr using modulated-beam line-of-sight threshold ionization mass spectrometry. The density of N increased with increasing pressure from 2.9×1018 to 1.8×1019 m−3, while the density of N2* was in the range of 9.7×1017 to 2.4×1018 m−3, with a maximum at 50 mTorr. Based on the appearance potential of N2* at ∼12 eV, we identify this excited molecule as long-lived N2 (A3Σu+) metastable.
Highly efficient pure blue electroluminescence from 1,4-bis[2-(3-N-ethylcarbazoryl)vinyl]benzene
Authors: Wu Y. Z. , Zheng X. Y. , Zhu W. Q. , Sun R. G. , Jiang X. Y. , Zhang Z. L. , Xu S. H.
Published: December 2003

An efficient blue organic light-emitting diode with 1,4-bis[2-(3-N-ethylcarbazoryl)vinyl]benzene doped into 4,4′-N,N′-dicarbazole-biphyenyl is reported. Maximum luminance and external quantum efficiency are 8500 cd/m2 and 2.6%. CIE-1931 coordinates are x=0.15, y=0.16. The device performance was further improved by introducing bis(2-methyl-8quinolinato)4-phenylphenolate aluminum to assist electron injection. The maximum luminance and quantum efficiency reached 11000 cd/m2 and 3.3%, respectively. Föster energy transfer and especially a carrier trapping mechanism are considered to dominate in the process of electroluminescence.
Nonperturbing observation of optical near field
Authors: Sekatskii S. K. , Dietler G. , Mironov B. N. , Kompanets V. O. , Matveets Yu. A. , Chekalin S. V. , Letokhov V. S.
Published: December 2003

The spatial distribution of light intensity in the near field is studied by observing the photoelectron projection images of a subwavelength nanoaperture. The imaging electrons are obtained as a result of a two-photon external photoelectric effect induced in the aperture formed at the end of an optical fiber by femtosecond pulses of the second-harmonic radiation (410 nm) of a Ti:sapphire laser. The light-field distribution in the aperture is not distorted by any near-by object (such as a medium containing fluorescent molecules), which allows nonperturbing measurement of such a distribution.
Experimental study of perpendicular transport in weakly coupled AlxGa1−xN/GaN superlattices
Authors: Waldron E. L. , Li Y.-L. , Schubert E. F. , Graff J. W. , Sheu J. K.
Published: December 2003

Perpendicular transport characteristics of n-type AlxGa1−xN/GaN superlattices are presented. Planar and mesa-etched superlattice structures are employed to identify the perpendicular resistance. Perpendicular transport measurements in Al0.22Ga0.78N/GaN superlattices display linear current–voltage characteristics with a resistivity that is a factor of 6.6 higher than for bulk material. A theoretical model is developed for perpendicular transport in AlxGa1−xN/GaN superlattices based on sequential tunneling. The model shows that short superlattice periods are required to minimize the perpendicular resistivity.
Oscillator strength for intraband transitions in (In,Ga)As/GaAs quantum dots
Authors: Stoleru V. G. , Towe E.
Published: December 2003

This letter reports on theoretical calculations of the oscillator strength associated with electron intraband transitions in (In,Ga)As/GaAs quantum dots. We study the effect of dot size and lateral separation between adjacent dots on the oscillator strength. The calculations indicate that transitions induced by p-polarized light from the electronic ground state to the first excited state are stronger than those induced by s-polarized light for large size dots with wide lateral interdot spacing. This situation changes, however, for small size dots in close proximity with one another. We discuss the relevance and implication of these results for applications in quantum-dot structures designed for mid-infrared detection.
Apertureless near-field optical microscopy: Tip–sample coupling in elastic light scattering
Authors: Raschke Markus B. , Lienau Christoph
Published: December 2003

For linear light scattering in apertureless scanning near-field optical microscopy, we have studied the correlations between the tip radius of the probe, signal strength, spatial resolution, and sample material. Pronounced variations of the near-field distance dependence on tip shape and dielectric function of the sample are observed. For very sharp metal tips, the scattered near-field signal decays on a 5 nm length scale. Despite this highly localized tip–sample coupling, the contrast is found to depend sensitively on the vertical composition of the sample on a length scale given by the penetration depth of the incident light. The resulting implications on the use of the technique as an analytic probe method are discussed.
Improving optical properties of 1.55 μm GaInNAs/GaAs multiple quantum wells with Ga(In)NAs barrier and space layer
Authors: Liu H. Y. , Hopkinson M. , Navaretti P. , Gutierrez M. , Ng J. S. , David J. P. R.
Published: December 2003

We present the 1.55 μm GaInNAs/GaAs multiple quantum well (QW) heterostructures with a GaNAs or a GaInNAs barrier and space layer (BSL). The stronger improvement of photoluminescence efficiency has been observed with increasing N concentration in a GaNAs BSL, instead of increasing N composition in GaInNAs QWs, to achieve room-temperature emission above 1.5 μm for GaInNAs/GaNAs multiple QW structure, when the nitrogen concentration in GaInNAs QW is as high as 3%. A further enhancement of photoluminescence intensity and a remarkable reduction of emission linewidth of GaInNAs multiple QWs have been demonstrated by using a GaInNAs quaternary BSL. These effects of a GaInNAs BSL could be understood in terms of the improvement of structural properties of GaInNAs QWs, resulting from the reduction of the strain at QW/BSL interface. These results present a variable approach to further developing GaAs-based light sources in the telecommunication-wavelength range near 1.55 μm.