bluuebunny/crossref_metadata_2025 huggingface dataset:
Context-dependent perceptual modulation of single neurons in primate visual cortex
Authors: Maier Alexander , Logothetis Nikos K. , Leopold David A.
Published: March 2007

Some neurons in the visual cortex alter their spiking rate according to the perceptual interpretation of an observed stimulus, rather than its physical structure alone. Experiments in monkeys have suggested that, although the proportion of neurons showing this effect differs greatly between cortical areas, this proportion remains similar across different stimuli. These findings have raised the intriguing questions of whether the same neurons always participate in the disambiguation of sensory patterns and whether such neurons might represent a special class of cortical cells that relay perceptual signals to higher cortical areas. Here we explore this question by measuring activity in the middle temporal cortex of monkeys and asking to what degree the percept-related responses of individual neurons depend upon the specific sensory input. In contrast to our expectations, we found that even small differences in the stimuli led to significant changes in the signaling of the perceptual state by single neurons. We conclude that nearly all feature-responsive neurons in this area, rather than a select subset, can contribute to the resolution of sensory conflict, and that the role of individual cells in signaling the perceptual outcome is tightly linked to the fine details of the stimuli involved.
Dissection of complex protein dynamics in human thioredoxin
Authors: Qiu Weihong , Wang Lijuan , Lu Wenyun , Boechler Amanda , Sanders David A. R. , Zhong Dongping
Published: March 2007

We report our direct study of complex protein dynamics in human thioredoxin by dissecting into elementary processes and determining their relevant time scales. By combining site-directed mutagenesis with femtosecond spectroscopy, we have distinguished four partly time-overlapped dynamical processes at the active site of thioredoxin. Using intrinsic tryptophan as a molecular probe and from mutation studies, we ascertained the negligible contribution to solvation by protein sidechains and observed that the hydration dynamics at the active site occur in 0.47–0.67 and 10.8–13.2 ps. With reduced and oxidized states, we determined the electron-transfer quenching dynamics between excited tryptophan and a nearby disulfide bond in 10–17.5 ps for three mutants. A robust dynamical process in 95–114 ps, present in both redox states and all mutants regardless of neighboring charged, polar, and hydrophobic residues around the probe, is attributed to the charge transfer reaction with its adjacent peptide bond. Site-directed mutations also revealed the electronic quenching dynamics by an aspartate residue at a hydrogen bond distance in 275–615 ps. The local rotational dynamics determined by the measurement of anisotropy changes with time unraveled a relatively rigid local configuration but implies that the protein fluctuates on the time scale of longer than nanoseconds. These results elucidate the temporal evolution of hydrating water motions, electron-transfer reactions, and local protein fluctuations at the active site, and show continuously synergistic dynamics of biological function over wide time scales.
An explicit test of the phospholipid saturation hypothesis of acquired cold tolerance in
Caenorhabditis elegans
Authors: Murray Patricia , Hayward Scott A. L. , Govan Gregor G. , Gracey Andrew Y. , Cossins Andrew R.
Published: March 2007

Protection of poikilothermic animals from seasonal cold is widely regarded as being causally linked to changes in the unsaturation of membrane phospholipids, yet in animals this proposition remains formally untested. We have now achieved this by the genetic manipulation of lipid biosynthesis of
Caenorhabditis elegans
independent of temperature. Worms transferred from 25°C to 10°C develop over several days a much-increased tolerance of lethal cold (0°C) and also an increased phospholipid unsaturation, as in higher animal models. Of the three
C. elegans
Δ9-desaturases, transcript levels of
fat-7
only were up-regulated by cold transfer. RNAi suppression of
fat-7
caused the induction of
fat-5
desaturase, so to control desaturase expression we combined RNAi of
fat-7
with a
fat-5
knockout. These
fat-5
/
fat-7
manipulated worms displayed the expected negative linear relationship between lipid saturation and cold tolerance at 0°C, an outcome confirmed by dietary rescue. However, this change in lipid saturation explains just 16% of the observed difference between cold tolerance of animals held at 25°C and 10°C. Thus, although the manipulated lipid saturation affects the tolerable thermal window, and altered Δ9-desaturase expression accounts for cold-induced lipid adjustments, the effect is relatively small and none of the lipid manipulations were sufficient to convert worms between fully cold-sensitive and fully cold-tolerant states. Critically, transfer of 10°C-acclimated worms back to 25°C led to them restoring the usual cold-sensitive phenotype within 24 h despite retaining a lipid profile characteristic of 10°C worms. Other nonlipid mechanisms of acquired cold protection clearly dominate inducible cold tolerance.
Amphiregulin is an essential mediator of estrogen receptor α function in mammary gland development
Authors: Ciarloni Laura , Mallepell Sonia , Brisken Cathrin
Published: March 2007

Most mammary gland development occurs after birth under the control of systemic hormones. Estrogens induce mammary epithelial cell proliferation during puberty via epithelial estrogen receptor α (ERα) by a paracrine mechanism. Epidermal growth factor receptor (EGFR) signaling has long been implicated downstream of ERα signaling, and several EGFR ligands have been described as estrogen-target genes in tumor cell lines. Here, we show that amphiregulin is the unique EGF family member to be transcriptionally induced by estrogen in the mammary glands of puberal mice at a time of exponential expansion of the ductal system. In fact, we find that estrogens induce amphiregulin through the ERα and require amphiregulin to induce proliferation of the mammary epithelium. Like ERα, amphiregulin is required in the epithelium of puberal mice for epithelial proliferation, terminal end buds formation, and ductal elongation. Subsequent stages, such as side-branching and alveologenesis, are not affected. When amphiregulin
−/−
mammary epithelial cells are in close vicinity to wild-type cells, they proliferate and contribute to all cell compartments of the ductal outgrowth. Thus, amphiregulin is an important paracrine mediator of estrogen function specifically required for puberty-induced ductal elongation, but not for any earlier or later developmental stages.
SHP-2 tyrosine phosphatase inhibits p73-dependent apoptosis and expression of a subset of p53 target genes induced by EGCG
Authors: Amin A. R. M. Ruhul , Thakur Vijay S. , Paul Rajib K. , Feng Gen Sheng , Qu Cheng-Kui , Mukhtar Hasan , Agarwal Munna L.
Published: March 2007

Green tea polyphenol, epigallocatechin-3-gallate (EGCG) differentially regulates the cellular growth of cancer cells in a p53-dependent manner through apoptosis and/or cell cycle arrest. In an effort to further elucidate the mechanism of differential growth regulation by EGCG, we have investigated the role of the tyrosine phosphatase, SHP-2. Comparing the responses of mouse embryonic fibroblasts (MEFs), expressing either WT or functionally inactive/truncated SHP-2, we find that inactivation of SHP-2 remarkably sensitizes cells to EGCG-mediated killing. MEFs lacking functional SHP-2 undergo massive apoptosis upon treatment with EGCG. By comparing gene expression profiles, we have identified a set of transcriptional targets of p53 that are differentially modulated in cells undergoing apoptosis. Western blot and real-time PCR analyses of a select group of genes further confirm that the expression is SHP-2-dependent. Similar observations were made in MEFs lacking p53, confirming that the expression of these “p53 target genes” is p53-independent. In addition, EGCG treatment induced the expression of p73 mRNA and protein in both cell types, but not p63. Inactivation of p73 in cells expressing nonfunctional SHP-2 markedly inhibited apoptosis and p53 target gene expression. Although phosphorylation of JNK is differentially regulated by SHP2, it was found to be dispensable for EGCG-induced apoptosis and p53 target gene expression. Our results have identified SHP-2 as a negative regulator of EGCG-induced-apoptosis and have identified a subset of p53 target genes whose expression is paradoxically not mediated by p53 but by one of its family members, p73.
Arabidopsis
primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body
Authors: Song Liang , Han Meng-Hsuan , Lesicka Joanna , Fedoroff Nina
Published: March 2007

Small regulatory microRNAs (miRNAs) are encoded in long precursors and are released from them during processing by cleavage within partially duplexed stem–loop structures. In the present work we investigated the role of the
Arabidopsis
nuclear RNA-binding protein HYL1 and the nuclear RNase III enzyme DCL1 in processing of primary miRNA (pri-miR171a). The
miR171a
gene is complex, with multiple transcription start sites, as well as alternative splicing of exons and alternative polyadenylation sites. Both HYL1 and DCL1 proteins are required for processing of the major pri-miR171a, spliced and polyadenylated forms of which accumulate in plants homozygous for mutations in either gene, but not in wild-type plants. In transiently transfected
Arabidopsis
protoplasts, HYL1-mCherry and YFP-DCL1 fusion proteins colocalize to small nuclear bodies similar to Cajal bodies but lacking the Cajal body marker Atcoilin. The HYL1 protein coimmunoprecipitates with miR171a and miR159a precursors, indicating that it is an integral component of the precursor processing machinery. Thus, the distinct HYL1- and DCL1-containing nuclear bodies may be miRNA precursor processing sites. Alternatively, they may be assembly and storage sites for the miRNA precursor processing machinery.
Exchange of DNA polymerases at the replication fork of bacteriophage T7
Authors: Johnson Donald E. , Takahashi Masateru , Hamdan Samir M. , Lee Seung-Joo , Richardson Charles C.
Published: March 2007

T7 gene 5 DNA polymerase (gp5) and its processivity factor,
Escherichia coli
thioredoxin, together with the T7 gene 4 DNA helicase, catalyze strand displacement synthesis on duplex DNA processively (>17,000 nucleotides per binding event). The processive DNA synthesis is resistant to the addition of a DNA trap. However, when the polymerase–thioredoxin complex actively synthesizing DNA is challenged with excess DNA polymerase–thioredoxin exchange occurs readily. The exchange can be monitored by the use of a genetically altered T7 DNA polymerase (gp5-Y526F) in which tyrosine-526 is replaced with phenylalanine. DNA synthesis catalyzed by gp5-Y526F is resistant to inhibition by chain-terminating dideoxynucleotides because gp5-Y526F is deficient in the incorporation of these analogs relative to the wild-type enzyme. The exchange also occurs during coordinated DNA synthesis in which leading- and lagging-strand synthesis occur at the same rate. On ssDNA templates with the T7 DNA polymerase alone, such exchange is not evident, suggesting that free polymerase is first recruited to the replisome by means of T7 gene 4 helicase. The ability to exchange DNA polymerases within the replisome without affecting processivity provides advantages for fidelity as well as the cycling of the polymerase from a completed Okazaki fragment to a new primer on the lagging strand.
Exponential decay of
H
1
-localized solutions and stability of the train of
N
solitary waves for the Camassa–Holm equation
Authors: El Dika Khaled , Molinet Luc
Published: March 2007

For the Camassa–Holm equation with
κ
≥0, we first prove that any global solution that is
H
1
-localized and moves fast enough to the right decays exponentially in space uniformly with respect to time. We also prove that for
κ
>0, a train of
N
solitary waves, which are sufficiently decoupled, is orbitally stable in
H
1
(

).
Mad3p, a pseudosubstrate inhibitor of APCCdc20 in the spindle assembly checkpoint
Authors: Burton Janet L. , Solomon Mark J.
Published: March 2007

Inappropriate attachment/tension between chromosomal kinetochores and the kinetochore microtubules activates the spindle assembly checkpoint, which delays anaphase by blocking the ubiquitin-mediated degradation of securin/Pds1p by APCCdc20. The checkpoint proteins Mad2 and Mad3/BubR1 bind to Cdc20, although how they inhibit APCCdc20 is unclear. We investigated the roles of two evolutionarily conserved KEN boxes and a D box within Mad3/BubR1. Although such motifs usually mediate APC-substrate recognition and ubiquitination, they have no apparent role in Mad3p turnover in Saccharomyces cerevisiae. Instead, these motifs are important for Mad3p function in the checkpoint and for binding to Cdc20p. We show that the Mad3p D box and KEN boxes function together to mediate Cdc20p–Mad3p interaction and that Mad3p and an anaphase-promoting complex (APC) substrate, Hsl1p, compete for Cdc20p binding in a D-box- and KEN-box-dependent manner. In vivo, we observed an increased binding of Cdc20p to Mad3p and decreased binding to Hsl1p upon checkpoint activation. Furthermore, we demonstrate that Mad2p stimulates the association between Mad3p and Cdc20p and that this stimulated binding requires KEN box 1 within Mad3p. These findings implicate Mad3p as a pseudosubstrate inhibitor of APCCdc20, competing with APC substrates for Cdc20p binding. We present a model aimed at unifying previous analyses of checkpoint function by focusing on the Mad3–Cdc20 interaction.
Critical roles for Dicer in the female germline
Authors: Murchison Elizabeth P. , Stein Paula , Xuan Zhenyu , Pan Hua , Zhang Michael Q. , Schultz Richard M. , Hannon Gregory J.
Published: March 2007

Dicer is an essential component of RNA interference (RNAi) pathways, which have broad functions in gene regulation and genome organization. Probing the consequences of tissue-restricted Dicer loss in mice indicates a critical role for Dicer during meiosis in the female germline. Mouse oocytes lacking Dicer arrest in meiosis I with multiple disorganized spindles and severe chromosome congression defects. Oogenesis and early development are times of significant post-transcriptional regulation, with controlled mRNA storage, translation, and degradation. Our results suggest that Dicer is essential for turnover of a substantial subset of maternal transcripts that are normally lost during oocyte maturation. Furthermore, we find evidence that transposon-derived sequence elements may contribute to the metabolism of maternal transcripts through a Dicer-dependent pathway. Our studies identify Dicer as central to a regulatory network that controls oocyte gene expression programs and that promotes genomic integrity in a cell type notoriously susceptible to aneuploidy.
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
Authors: Ni Julie Z. , Grate Leslie , Donohue John Paul , Preston Christine , Nobida Naomi , O’Brien Georgeann , Shiue Lily , Clark Tyson A. , Blume John E. , Ares Manuel
Published: March 2007

Many alternative splicing events create RNAs with premature stop codons, suggesting that alternative splicing coupled with nonsense-mediated decay (AS-NMD) may regulate gene expression post-transcriptionally. We tested this idea in mice by blocking NMD and measuring changes in isoform representation using splicing-sensitive microarrays. We found a striking class of highly conserved stop codon-containing exons whose inclusion renders the transcript sensitive to NMD. A genomic search for additional examples identified >50 such exons in genes with a variety of functions. These exons are unusually frequent in genes that encode splicing activators and are unexpectedly enriched in the so-called “ultraconserved” elements in the mammalian lineage. Further analysis show that NMD of mRNAs for splicing activators such as SR proteins is triggered by splicing activation events, whereas NMD of the mRNAs for negatively acting hnRNP proteins is triggered by splicing repression, a polarity consistent with widespread homeostatic control of splicing regulator gene expression. We suggest that the extreme genomic conservation surrounding these regulatory splicing events within splicing factor genes demonstrates the evolutionary importance of maintaining tightly tuned homeostasis of RNA-binding protein levels in the vertebrate cell.
Maternal microRNAs are essential for mouse zygotic development
Authors: Tang Fuchou , Kaneda Masahiro , O’Carroll Dónal , Hajkova Petra , Barton Sheila C. , Sun Y. Andrew , Lee Caroline , Tarakhovsky Alexander , Lao Kaiqin , Surani M. Azim
Published: March 2007

MicroRNAs (miRNAs) have important roles in diverse cellular processes, but little is known about their identity and functions during early mammalian development. Here, we show the effects of the loss of maternal inheritance of miRNAs following specific deletion of Dicer from growing oocytes. The mutant mature oocytes were almost entirely depleted of all miRNAs, and they failed to progress through the first cell division, probably because of disorganized spindle formation. By comparing single-cell cDNA microarray profiles of control and mutant oocytes, our data are compatible with the notion that a large proportion of the maternal genes are directly or indirectly under the control of miRNAs, which demonstrates that the maternal miRNAs are essential for the earliest stages of mouse embryonic development.
A novel checkpoint mechanism regulating the G1/S transition
Authors: Tvegård Tonje , Soltani Héla , Skjølberg Henriette C. , Krohn Marit , Nilssen Esben A. , Kearsey Stephen E. , Grallert Beáta , Boye Erik
Published: March 2007

Ultraviolet irradiation of fission yeast cells in G1 phase induced a delay in chromatin binding of replication initiation factors and, consistently, a transient delay in S-phase entry. The cell cycle delay was totally dependent on the Gcn2 kinase, a sensor of the nutritional status, and was accompanied by phosphorylation of the translation initiation factor eIF2α and by a general depression of translation. However, the G1-specific synthesis of factors required for DNA replication was not reduced by ultraviolet radiation. The cell cycle delay represents a novel checkpoint with a novel mechanism of action that is not activated by ionizing radiation.
MAM3 Catalyzes the Formation of All Aliphatic Glucosinolate Chain Lengths in Arabidopsis
Authors: Textor Susanne , de Kraker Jan-Willem , Hause Bettina , Gershenzon Jonathan , Tokuhisa James G.
Published: March 2007

Chain elongated, methionine (Met)-derived glucosinolates are a major class of secondary metabolites in Arabidopsis (Arabidopsis thaliana). The key enzymatic step in determining the length of the chain is the condensation of acetyl-coenzyme A with a series of ω-methylthio-2-oxoalkanoic acids, catalyzed by methylthioalkylmalate (MAM) synthases. The existence of two MAM synthases has been previously reported in the Arabidopsis ecotype Columbia: MAM1 and MAM3 (formerly known as MAM-L). Here, we describe the biochemical properties of the MAM3 enzyme, which is able to catalyze all six condensation reactions of Met chain elongation that occur in Arabidopsis. Underlining its broad substrate specificity, MAM3 also accepts a range of non-Met-derived 2-oxoacids, e.g. converting pyruvate to citramalate and 2-oxoisovalerate to isopropylmalate, a step in leucine biosynthesis. To investigate its role in vivo, we identified plant lines with mutations in MAM3 that resulted in a complete lack or greatly reduced levels of long-chain glucosinolates. This phenotype could be complemented by reintroduction of a MAM3 expression construct. Analysis of MAM3 mutants demonstrated that MAM3 catalyzes the formation of all glucosinolate chain lengths in vivo as well as in vitro, making this enzyme the major generator of glucosinolate chain length diversity in the plant. The localization of MAM3 in the chloroplast suggests that this organelle is the site of Met chain elongation.
Differential Effects of Sucrose and Auxin on Localized Phosphate Deficiency-Induced Modulation of Different Traits of Root System Architecture in Arabidopsis
Authors: Jain Ajay , Poling Michael D. , Karthikeyan Athikkattuvalasu S. , Blakeslee Joshua J. , Peer Wendy A. , Titapiwatanakun Boosaree , Murphy Angus S. , Raghothama Kashchandra G.
Published: March 2007

Phosphorus, one of the essential elements for plants, is often a limiting nutrient in soils. Low phosphate (Pi) availability induces sugar-dependent systemic expression of genes and modulates the root system architecture (RSA). Here, we present the differential effects of sucrose (Suc) and auxin on the Pi deficiency responses of the primary and lateral roots of Arabidopsis (Arabidopsis thaliana). Inhibition of primary root growth and loss of meristematic activity were evident in seedlings grown under Pi deficiency with or without Suc. Although auxin supplementation also inhibited primary root growth, loss of meristematic activity was observed specifically under Pi deficiency with or without Suc. The results suggested that Suc and auxin do not influence the mechanism involved in localized Pi sensing that regulates growth of the primary root and therefore delineates it from sugar-dependent systemic Pi starvation responses. However, the interaction between Pi and Suc was evident on the development of the lateral roots and root hairs in the seedlings grown under varying levels of Pi and Suc. Although the Pi+ Suc− condition suppressed lateral root development, induction of few laterals under the Pi− Suc− condition point to increased sensitivity of the roots to auxin during Pi deprivation. This was supported by expression analyses of DR5∷uidA, root basipetal transport assay of auxin, and RSA of the pgp19 mutant exhibiting reduced auxin transport. A significant increase in the number of lateral roots under the Pi− Suc− condition in the chalcone synthase mutant (tt4-2) indicated a potential role for flavonoids in auxin-mediated Pi deficiency-induced modulation of RSA. The study thus demonstrated differential roles of Suc and auxin in the developmental responses of ontogenetically distinct root traits during Pi deprivation. In addition, lack of cross talk between local and systemic Pi sensing as revealed by the seedlings grown under either the Pi− Suc− condition or in the heterogenous Pi environment highlighted the coexistence of Suc-independent and Suc-dependent regulatory mechanisms that constitute Pi starvation responses.
Increases in the Number of SNARE Genes Parallels the Rise of Multicellularity among the Green Plants
Authors: Sanderfoot Anton
Published: March 2007

The green plant lineage is the second major multicellular expansion among the eukaryotes, arising from unicellular ancestors to produce the incredible diversity of morphologies and habitats observed today. In the unicellular ancestors, secretion of material through the endomembrane system was the major mechanism for interacting and shaping the external environment. In a multicellular organism, the external environment can be made of other cells, some of which may have vastly different developmental fates, or be part of different tissues or organs. In this context, a given cell must find ways to organize its secretory pathway at a level beyond that of the unicellular ancestor. Recently, sequence information from many green plants have become available, allowing an examination of the genomes for the machinery involved in the secretory pathway. In this work, the SNARE proteins of several green plants have been identified. While little increase in gene number was seen in the SNAREs of the early secretory system, many new SNARE genes and gene families have appeared in the multicellular green plants with respect to the unicellular plants, suggesting that this increase in the number of SNARE genes may have some relation to the rise of multicellularity in green plants.
Transcript Profiling of the Anoxic Rice Coleoptile
Authors: Lasanthi-Kudahettige Rasika , Magneschi Leonardo , Loreti Elena , Gonzali Silvia , Licausi Francesco , Novi Giacomo , Beretta Ottavio , Vitulli Federico , Alpi Amedeo , Perata Pierdomenico
Published: March 2007

Rice (Oryza sativa) seeds can germinate in the complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this article, we compared and investigated the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. The results allow drawing a detailed picture of the modulation of the transcripts involved in anaerobic carbohydrate metabolism, suggesting up-regulation of the steps required to produce and metabolize pyruvate and its derivatives. Sugars appear to play a signaling role under anoxia, with several genes indirectly up-regulated by anoxia-driven sugar starvation. Analysis of the effects of anoxia on the expansin gene families revealed that EXPA7 and EXPB12 are likely to be involved in rice coleoptile elongation under anoxia. Genes coding for ethylene response factors and heat shock proteins are among the genes modulated by anoxia in both rice and Arabidopsis (Arabidopsis thaliana). Identification of anoxia-induced ethylene response factors is suggestive because genes belonging to this gene family play a crucial role in rice tolerance to submergence, a process closely related to, but independent from, the ability to germinate under anoxia. Genes coding for some enzymes requiring oxygen for their activity are dramatically down-regulated under anoxia, suggesting the existence of an energy-saving strategy in the regulation of gene expression.
Genetic Interactions of TGA Transcription Factors in the Regulation of Pathogenesis-Related Genes and Disease Resistance in Arabidopsis
Authors: Kesarwani Meenu , Yoo Jungmin , Dong Xinnian
Published: March 2007

TGA transcription factors are implicated as regulators of pathogenesis-related (PR) genes because of their physical interaction with the known positive regulator, nonexpresser of PR gene1 (NPR1). A triple-knockout mutant tga2-1 tga5-1 tga6-1 was shown previously to be defective in the induction of PR genes and systemic acquired resistance, confirming their role in disease resistance. However, the contributions of individual TGA factors have been difficult to discern because of functional redundancy among these factors, as well as possible dual functions for some single factors. In this study, we characterized six TGA factors by reverse genetics. We show that TGA3 is required for both basal and 2,6-dichloroisonicotinic acid-induced transcription of PR genes. The tga3-1 mutants were found to be defective in basal pathogen resistance, whereas induced resistance was unaffected. TGA1 and TGA4 play partially redundant roles in regulation of basal resistance, having only moderate effects on PR gene expression. Additionally, an activation-tagged mutant of TGA6 was able to increase basal as well as induced expression of PR1, demonstrating a positive role for TGA6 on PR gene expression. In contrast, TGA2 has repressor activity on PR gene expression even though it can act as a positive regulator in the tga5-1 tga6-1 null mutant background. Finally, we examined the genetic interaction between tga2-2 and suppressor of npr1 inducible1 (sni1-1). TGA2's repressor activity overlaps with SNI1 because the tga2-2 sni1-1 double mutant shows a synergistic effect on PR gene expression.
The RiceYABBY1Gene Is Involved in the Feedback Regulation of Gibberellin Metabolism
Authors: Dai Mingqiu , Zhao Yu , Ma Qian , Hu Yongfeng , Hedden Peter , Zhang Qifa , Zhou Dao-Xiu
Published: March 2007

Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA20 and decreases of GA1 levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.
Cowpea Chloroplastic ATP Synthase Is the Source of Multiple Plant Defense Elicitors during Insect Herbivory
Authors: Schmelz Eric A. , LeClere Sherry , Carroll Mark J. , Alborn Hans T. , Teal Peter E.A.
Published: March 2007

In cowpea (Vigna unguiculata), fall armyworm (Spodoptera frugiperda) herbivory and oral secretions (OS) elicit phytohormone production and volatile emission due to inceptin [Vu-In; +ICDINGVCVDA−], a peptide derived from chloroplastic ATP synthase γ-subunit (cATPC) proteins. Elicitor-induced plant volatiles can function as attractants for natural enemies of insect herbivores. We hypothesized that inceptins are gut proteolysis products and that larval OS should contain a mixture of related peptides. In this study, we identified three additional cATPC fragments, namely Vu-GE+In [+GEICDINGVCVDA−], Vu-E+In [+EICDINGVCVDA−], and Vu-In−A [+ICDINGVCVD−]. Leaf bioassays for induced ethylene (E) production demonstrated similar effective concentration50 values of 68, 45, and 87 fmol leaf−1 for Vu-In, Vu-E+In, and Vu-GE+In, respectively; however, Vu-In−A proved inactive. Shortly following ingestion of recombinant proteins harboring cATPC sequences, larval OS revealed similar concentrations of the three elicitors with 80% of the potential inceptin-related peptides recovered. Rapidly shifting peptide ratios over time were consistent with continued proteolysis and preferential stability of inceptin. Likewise, larvae ingesting host plants with inceptin precursors containing an internal trypsin cleavage site rapidly lost OS-based elicitor activity. OS containing inceptin elicited a rapid and sequential induction of defense-related phytohormones jasmonic acid, E, and salicylic acid at 30, 120, and 240 min, respectively, and also the volatile (E)-4,8-dimethyl-1,3,7-nonatriene. Similar to established peptide signals such as systemin and flg22, amino acid substitutions of Vu-In demonstrate an essential role for aspartic acid residues and an unaltered C terminus. In cowpea, insect gut proteolysis following herbivory generates inappropriate fragments of an essential metabolic enzyme enabling plant non-self-recognition.
Oxylipins Produced by the 9-Lipoxygenase Pathway inArabidopsisRegulate Lateral Root Development and Defense Responses through a Specific Signaling Cascade
Authors: Vellosillo Tamara , Martínez Marta , López Miguel Angel , Vicente Jorge , Cascón Tomas , Dolan Liam , Hamberg Mats , Castresana Carmen
Published: March 2007

Arabidopsis thaliana seedling growth with pure oxylipins resulted in root waving, loss of root apical dominance, and decreased root elongation. 9-Hydroxyoctadecatrienoic acid (9-HOT) was a potent inducer of root waving. Studies with noxy2 (for nonresponding to oxylipins2), a new 9-HOT–insensitive mutant, and coronatine insensitive1-1 (jasmonate-insensitive) revealed at least three signaling cascades mediating the oxylipin actions. Treatment with 9-HOT resulted in a reduction in lateral roots and an increase in stage V primordia. Roots showed strong 9-lipoxygenase (9-LOX) activity, and root primordia expressed 9-LOX genes. These results, along with findings that noxy2 and mutants with defective 9-LOX activity showed increased numbers of lateral roots, suggest that 9-HOT, or a closely related 9-LOX product, is an endogenous modulator of lateral root formation. Histochemical and molecular analyses revealed that 9-HOT activated events common to development and defense responses. A subset of 9-HOT–responding root genes was also induced in leaves after 9-HOT treatment or pathogen inoculation. The results that noxy2 displayed altered root development, enhanced susceptibility to Pseudomonas, and reduced the activation of 9-HOT–responding genes are consistent with mechanistic links among these processes. The nature of the changes detected suggests that oxylipins from the 9-LOX pathway function in cell wall modifications required for lateral root development and pathogen arrest.
T-Loop Phosphorylation ofArabidopsisCDKA;1 Is Required for Its Function and Can Be Partially Substituted by an Aspartate Residue
Authors: Dissmeyer Nico , Nowack Moritz K. , Pusch Stefan , Stals Hilde , Inzé Dirk , Grini Paul E. , Schnittger Arp
Published: March 2007

As in other eukaryotes, progression through the cell cycle in plants is governed by cyclin-dependent kinases. Phosphorylation of a canonical Thr residue in the T-loop of the kinases is required for high enzyme activity in animals and yeast. We show that the Arabidopsis thaliana Cdc2+/Cdc28 homolog CDKA;1 is also phosphorylated in the T-loop and that phosphorylation at the conserved Thr-161 residue is essential for its function. A phospho-mimicry T161D substitution restored the primary defect of cdka;1 mutants, and although the T161D substitution displayed a dramatically reduced kinase activity with a compromised ability to bind substrates, homozygous mutant plants were recovered. The rescue by the T161D substitution, however, was not complete, and the resulting plants displayed various developmental abnormalities. For instance, even though flowers were formed, these plants were completely sterile as a result of a failure of the meiotic program, indicating that different requirements for CDKA;1 function are needed during plant development.
Crystallization shelf
Authors: Cabric B. , Janicijevic A.
Published: March 2007

A model of an air cooler (`crystallization shelf') installed in a laboratory furnace, which allows regulation and simultaneous crystallization of several substances at different temperature gradients, shapes of crystallization fronts and rate intervals, with the purpose of obtaining crystals, is presented.
Accurate determination and correction of the lattice parameter of LaB6(standard reference material 660) relative to that of Si (640b)
Authors: Chantler C. T. , Rae N. A. , Tran C. Q.
Published: March 2007

X-ray powder diffraction and synchrotron radiation have been used to determine the lattice parameter of the NIST standard reference material (SRM 660) LaB6as 4.156468 Å with an accuracy of 12 parts per million (p.p.m.), calibrated relative to the lattice parameter of the Si powder standard [a0= 5.430940 (11) Å, Si 640b]. A discrepancy of 0.00048 (5) Å, or nine standard deviations from the NIST reference, is observed between the currently accepted lattice spacing of LaB6and the measured value. Twelve different measurements of the lattice parameter were made at beam energies between 10 and 20 keV. The observed discrepancy in the lattice parameter is consistent for the different energies used. The absolute values of the mean difference between the measured and calculated 2θ centroids, \overline{\left| \delta 2 \theta \right|}, are highly consistent, between 0.0002 and 0.0004° for energies from 5 to 14 keV, and between 0.0005 and 0.0008° for energies from 15 to 20 keV. In order to determine the peak positions with high precision, account must be taken of the observed peak asymmetry. It is shown that significant asymmetry is due to peak broadening and must be taken into account in order to determine accurate peak locations and lattice spacings. The approach shows significant advantages over conventional analysis. The analysis of peak broadening is compared with models used in Rietveld analysis.
On the entropy to texture index relationship in quantitative texture analysis
Authors: Hielscher R. , Schaeben H. , Chateigner D.
Published: March 2007

This communication demonstrates a sharp inequality between the L^{2}-norm and the entropy of probability density functions. This inequality is applied to texture analysis, and the relationship between the entropy and the texture index of an orientation density function is characterized. More precisely, the orientation space is shown to allow for texture index and entropy variations of orientation probability density functions between an upper and a lower bound for the entropy. In this way, it is proved that there is no functional relationship between entropy and texture index of an orientation probability density function as conjectured previously on the basis of practical numerical texture analyses using the widely used pole-to-orientation probability density function reconstruction softwareWIMV, known by the initials of its authors and their ancestors (Williams–Imhof–Matthies–Vinel). Synthetic orientation probability density functions were then synthesized, covering a large domain of variation for texture index and entropy, and used to check the numerical results of the same software package.
X-ray bright-field imaging analyzes crystalline quality and defects of SiC wafers
Authors: Yi J. M. , Chu Y. S. , Zhong Y. , Je J. H. , Hwu Y. , Margaritondo G.
Published: March 2007

A new variety of the recently developed technique `X-ray bright-field imaging' is presented. In its basic version, this approach simultaneously yields diffraction-based information on lattice distortions and radiographic information on structural inhomogeneities, and is based on the detection of reversed diffraction contrast in transmission images. The new version extends the scope of the technique to the quantitative analysis of crystalline quality parameters such as the lattice plane curvature and mosaic distribution in SiC wafers, and makes it possible to correlate such parameters directly with defect (distortions/inhomogeneities) structures.
The Fortran90 source of the programPSILAM
Authors: Rossmanith Elisabeth
Published: March 2007

The Fortran90 source code of the programPSILAMhas been deposited with the IUCr.
Enantiomorph identification of crystals belonging to the point groups 321 and 312 by convergent-beam electron diffraction
Authors: Inui Haruyuki , Fujii Akihiro , Sakamoto Hiroki , Fujio Satoshi , Tanaka Katsushi
Published: March 2007

The recently proposed CBED (convergent-beam electron diffraction) method for enantiomorph identification has been successfully applied to crystals belonging to the point groups 321 and 312. The intensity asymmetry of zeroth-order Laue zone and/or first-order Laue zone reflections of Bijvoet pairs is easily recognized in CBED patterns with the incidence along appropriate zone-axis orientations for each member of the enantiomorphic pair. The intensity asymmetry with respect to the symmetry line is reversed upon changing the space group (handedness) from one to the other. Thus, enantiomorph identification can be easily performed in principle for all crystals belonging to the point groups 321 and 312.
Nondestructive quantitative synchrotron grazing incidence X-ray scattering analysis of cylindrical nanostructures in supported thin films
Authors: Yoon Jinhwan , Yang Seung Yun , Lee Byeongdu , Joo Wonchul , Heo Kyuyoung , Kim Jin Kon , Ree Moonhor
Published: March 2007

Nondestructive nanostructural analysis is indispensable in the development of nanomaterials and nanofabrication processes for use in nanotechnology applications. This paper demonstrates a quantitative, nondestructive analysis of nanostructured thin films supported on substrates and their templated nanopores by using grazing incidence X-ray scattering and data analysis with a derived scattering theory. The analysis disclosed that vertically oriented nanodomain cylinders had formed in 20–100 nm thick films supported on substrates, which consisted of a mixture of poly(styrene-b-methyl methacrylate) (PS-b-PMMA) and PMMA homopolymer, and that the PMMA nanodomain cylinders were selectively etched out by ultraviolet light exposure and a subsequent rinse with acetic acid, resulting in a well ordered nanostructure consisting of hexagonally packed cylindrical nanopores.
Diffraction profiles of elastically bent single crystals with constant strain gradients
Authors: Yan Hanfei , Kalenci Özgür , Noyan I. C.
Published: March 2007

This work presents a set of equations that can be used to predict the dynamical diffraction profile from a non-transparent single crystal with a constant strain gradient examined in Bragg reflection geometry with a spherical incident X-ray beam. In agreement with previous work, the present analysis predicts two peaks: a primary diffraction peak, which would have still been observed in the absence of the strain gradient and which exits the specimen surface at the intersection point of the incident beam with the sample surface, and a secondary (mirage) peak, caused by the deflection of the wavefield within the material, which exits the specimen surface further from this intersection point. The integrated intensity of the mirage peak increases with increasing strain gradient, while its separation from the primary reflection peak decreases. The directions of the rays forming the mirage peak are parallel to those forming the primary diffraction peak. However, their spatial displacement might cause (fictitious) angular shifts in diffractometers equipped with area detectors or slit optics. The analysis results are compared with experimental data from an Si single-crystal strip bent in cantilever configuration, and the implications of the mirage peak for Laue analysis and high-precision diffraction measurements are discussed.
From CIF to virtual morphology using theWinXMorphprogram
Authors: Kaminsky Werner
Published: March 2007

Crystal morphologies are predicted from data stored in files in the CIF format (crystallographic information file standard of the International Union of Crystallography) on the basis of the Bravais–Friedel, Donnay–Harker model. Several simple improvements to the calculation are introduced withWinXMorph, version 1.4.9, in conjunction with illustrations of the morphologies of quartz, sucrose, lactose, pyrite and lysozyme. The morphologies of the recently discovered pentamorphs of 1,8-dihydroxyanthraquinone are predicted.WinXMorphis available free-of-charge for educational use.
The healing process for fractured tibia bones of sheep studied by neutron diffraction
Authors: Bacon G. E. , Goodship A. E.
Published: March 2007

Neutron diffraction has shown directly that the long bones of animals have thecaxes of their apatite crystals preferentially oriented to withstand stresses. When a sheep tibia is fractured and allowed to heal, the jointing material is initially randomly arranged, but a return of some orientation occurs after a few months. This orientation increases slowly with time. The growth of callus bone around the outside of the fracture becomes overshadowed by the appearance of poorly oriented internal bone. After 22 months, the end of this experiment, the process of bone restoration is still far from complete and it is evident that data after longer periods of time would be desirable. The current state of the structure at 22 months is shown in more detail by a two-dimensional neutron scan over a thin vertical section of bone cut through the centre of the fractured tibia.
Twin structure in the crystallite aggregation pattern
Authors: Zhao Shanrong , Wang Qinyan , Liu Rong , Lu Lian , Wang Jiyang
Published: March 2007

In this paper, the crystallographic relationships among all the NH4Cl crystallites in a zigzag aggregation pattern with local anisotropy, formed under low driving force, are analysed. It is found that all the crystallites in this aggregation are twinned with one another. The anisotropy of the zigzag pattern is controlled by the twin structure. The twin structure is of 6mmsymmetry. This twin structure is related to the crystal point groupm3m, so it is proposed that all crystals with point groupm3m(and even the similar point groups 432 andm3) have the possibility to form this zigzag pattern. It is illustrated that the crystal symmetry plays an important role in the crystallite aggregation pattern.
Anisotropic microstrain broadening due to field-tensor distributions
Authors: Leineweber Andreas
Published: March 2007

The anisotropic microstrain distribution resulting from an isotropic distribution of a field tensor (rank 0 or 2), the latter being connected with strain by an anisotropic property tensor (rank 2 or 4), is analyzed. It is shown that the anisotropy of the resulting line broadening is a direct consequence of the anisotropy of the property tensor. Various physical scenarios leading to such a type of line broadening are discussed.
Structure and microstructure evolution during martensitic transformation in wrought Fe–26Mn–0.14C austenitic steel: an effect of cooling rate
Authors: Sahu P. , Hamada A. S. , Ghosh Chowdhury S. , Karjalainen L. P.
Published: March 2007

Structure and microstructure evolution under various cooling rates of a wrought austenitic steel, Fe–26Mn–0.14C (composition in mass %), were studied by the Rietveld method of X-ray diffraction pattern fitting, grain boundary characterization by electron back-scattered diffraction (EBSD) and optical microscopy. Cooling rate, density of stacking faults, and austenite grain size and grain boundaries influence the observed γfcc→ ∊hcptransformation and lead to significant anisotropic X-ray line broadening. Depending on the cooling conditions, the grain boundaries are misoriented at both lower and higher angles. In the ∊-martensites, the dominant planar fault is twins (∼10−3). The austenite grains were found to contain low to moderate density of stacking faults (∼10−4–10−3), which act as efficient nucleation sites of the ∊-martensites. Both X-ray and EBSD analyses estimated negligible twins in the austenite. Approximate average dislocation densities have been estimated and correlated with the grain structure.
Diet, smoking and exercise: interrelationships between adolescent health behaviours
Authors: Coulson N S , Eiser C , Eiser J R
Published: March 2007

A questionnaire measuring smoking status, exercise and dietary behaviour was administered to 932 high school pupils during regular classroom periods. Pupils were taken from three year groups which included 327 year 8 (12–13 years), 313 year 9 (13–14 years) and 292 year 10 (14–15 years). Pupils also indicated whether they could recall classroom teaching on 15 food‐ and health‐related issues. Scores were derived representing self‐reported frequency of eating foods that were high in fat, and fresh fruits and vegetables. Smoking was found to be associated with lower levels of exercise, consumption of less fresh foods and greater consumption of fatty foods. In addition, consumption of fresh foods was found to be positively correlated with exercise. These findings have implications for the organization of school‐based health education efforts and suggest that health education programmes need to adopt an integrated approach rather than treat health behaviours in isolation from each other.