bluuebunny/crossref_metadata_2025_split huggingface dataset:
Techniques to measure grain‐size distributions of loamy sediments: a comparative study of ten instruments for wet analysis
Authors: GOOSSENS DIRK 
Published: September 2007

AbstractTen instruments for measuring the grain‐size distribution of loamy sediments in water were tested in a comparative study. Instruments tested were: the Malvern Mastersizer S, the Coulter LS 200, the Fritsch Analysette 22 (version C), the Horiba Partica LA‐950, the Sedigraph 5100, the Atterberg cylinder, the Coulter Multisizer 3, the CIS‐100, the EyeTech and the image analysis software Histolab. The first four instruments use laser diffraction. The Sedigraph and Atterberg cylinder are based on sedimentation. The Coulter Multisizer 3 uses impedance measurements and the last three instruments use optical techniques. Grain‐size analyses were carried out on four sediments with median grain diameters of approximately 35, 30, 12 and 9 μm, respectively, and with no particles >90 μm. The laser diffraction instruments produced the best results for the various criteria considered in this study, followed by the Coulter Multisizer 3 (electrical sensing zone technique), the sedimentation techniques and the optical methods. However, the study also showed that there is no such thing as an ‘ideal’ method because techniques may score differently according to the criterion tested. An appropriate evaluation thus requires that various criteria be considered. Issues to be taken into account are: type of sediment, quantity of sediment available, speed of measurement, complexity of the measurement protocol, processing of the data, reproducibility of the results and the specific aims of the study undertaken.
The ancient subclasses of Arabidopsis ACTIN DEPOLYMERIZING FACTOR genes exhibit novel and differential expression
Authors: Ruzicka Daniel R. , Kandasamy Muthugapatti K. , McKinney Elizabeth C. , Burgos‐Rivera Brunilis , Meagher Richard B. 
Published: September 2007

SummaryThe Actin Depolymerizing Factor (ADF) gene family of Arabidopsis thaliana encodes 11 functional protein isovariants in four ancient subclasses. We report the characterization of the tissue‐specific and developmental expression of all Arabidopsis ADF genes and the subcellular localization of several protein isovariants. The four subclasses exhibited distinct expression patterns as examined by qRT‐PCR and histochemical assays of a GUS reporter gene under the control of individual ADF regulatory sequences. Subclass I ADFs were expressed strongly and constitutively in all vegetative and reproductive tissues except pollen. Subclass II ADFs were expressed specifically in mature pollen and pollen tubes or root epidermal trichoblast cells and root hairs, and these patterns evolved from an ancient dual expression pattern comprised of both polar tip growth cell types, still observed in the monocot Oryza sativa. Subclass III ADFs were expressed weakly in vegetative tissues, but were strongest in fast growing and/or differentiating cells including callus, emerging leaves, and meristem regions. The single subclass IV ADF was constitutively expressed at moderate levels in all tissues, including pollen. Immunocytochemical analysis with subclass‐specific monoclonal antibodies demonstrated that subclass I isovariants localize to both the cytoplasm and the nucleus of leaf cells, while subclass II isovariants predominantly localize to the cytoplasm at the tip region of elongating root hairs and pollen tubes. The distinct expression patterns of the ADF subclasses support a model of ADF s co‐evolving with the ancient and divergent actin isovariants.
PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis
Authors: Farré Eva M. , Kay Steve A. 
Published: September 2007

SummaryInterlocking transcriptional loops and regulated protein degradation are the principal mechanisms involved in the generation of self‐sustaining circadian rhythms in many organisms. In Arabidopsis the first proposed regulatory transcriptional loop involved the transcription factors CIRCADIAN CLOCK ASSOCIATED (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) and the pseudo‐response regulator TIMING OF CHLOROPHYLL A/B BINDING PROTEIN (TOC1/PRR1). Recent findings indicate that the TOC1 homologues PRR7 and PRR9 might also be involved in transcriptional regulatory loops with CCA1 and LHY. In this study we show that the overexpression of PRR7 in Arabidopsis leads to severely compromised circadian rhythms. These transgenic lines display significantly reduced levels of CCA1 and LHY RNA, providing further evidence for a transcriptional feedback loop between PRR7 and these transcription factors. In addition, we show that the PRR7 protein is phosphorylated in a circadian regulated manner and that its levels are post‐translationally regulated by both diurnal and circadian mechanisms. The Arabidopsis circadian oscillator is therefore likely to be entrained to light/dark cycles both through transcriptional and post‐transcriptional mechanisms.
The Pseudomonas syringae type III effector tyrosine phosphatase HopAO1 suppresses innate immunity in Arabidopsis thaliana
Authors: Underwood William , Zhang Shuqun , He Sheng Y. 
Published: September 2007

SummaryThe bacterial pathogen Pseudomonas syringae pv. tomato (Pst) strain DC3000 infects tomato and Arabidopsis plants, and is a model for studying the molecular basis of bacterial disease. Pst DC3000 secretes a battery of largely uncharacterized effector proteins into host cells via a type‐III secretion system (TTSS). Little is currently known about the molecular mechanisms by which individual TTSS effectors promote virulence. The effector HopAO1 has similarity to protein tyrosine phosphatases, including a conserved catalytic site, and suppresses the hypersensitive response (HR) in some non‐host plants. Whether HopAO1 has a similar effect in the host Arabidopsis is not clear. Here, we show that transgenic expression of HopAO1 in Arabidopsis suppresses callose deposition elicited by the Pst DC3000 hrpA mutant, and allows the normally non‐pathogenic hrpA mutant to multiply within the leaf tissue. HopAO1 also suppresses resistance to Pst DC3000 induced by flg22, a pathogen‐associated molecular pattern (PAMP). However, HopAO1 does not suppress the HR triggered by several classical avirulence genes. These results suggest that HopAO1 targets primarily PAMP‐induced innate immunity in Arabidopsis. The virulence function of HopAO1 is dependent on an intact phosphatase catalytic site, as transgenic plants expressing a catalytically inactive derivative do not show these effects. Intriguingly, expression of the catalytically inactive HopAO1 has a dominant‐negative effect on the function of the wild‐type HopAO1. Analysis of mitogen‐activated protein kinase (MAPK) activity suggests that HopAO1 targets a step downstream or independent of MAPK activation. Genome‐wide expression analysis revealed that expression of several well‐known defense genes was suppressed in hrpA mutant‐infected HopAO1 transgenic plants.
Two genes in Arabidopsis thaliana encoding GDP‐l‐galactose phosphorylase are required for ascorbate biosynthesis and seedling viability
Authors: Dowdle John , Ishikawa Takahiro , Gatzek Stephan , Rolinski Susanne , Smirnoff Nicholas 
Published: September 2007

SummaryPlants synthesize ascorbate from guanosine diphosphate (GDP)‐mannose via l‐galactose/l‐gulose, although uronic acids have also been proposed as precursors. Genes encoding all the enzymes of the GDP‐mannose pathway have previously been identified, with the exception of the step that converts GDP‐l‐galactose to l‐galactose 1‐P. We show that a GDP‐l‐galactose phosphorylase, encoded by the Arabidopsis thaliana VTC2 gene, catalyses this step in the ascorbate biosynthetic pathway. Furthermore, a homologue of VTC2, At5g55120, encodes a second GDP‐l‐galactose phosphorylase with similar properties to VTC2. Two At5g55120 T‐DNA insertion mutants (vtc5‐1 and vtc5‐2) have 80% of the wild‐type ascorbate level. Double mutants were produced by crossing the loss‐of‐function vtc2‐1 mutant with each of the two vtc5 alleles. These show growth arrest immediately upon germination and the cotyledons subsequently bleach. Normal growth was restored by supplementation with ascorbate or l‐galactose, indicating that both enzymes are necessary for ascorbate generation. vtc2‐1 leaves contain more mannose 6‐P than wild‐type. We conclude that the GDP‐mannose pathway is the only significant source of ascorbate in A. thaliana seedlings, and that ascorbate is essential for seedling growth. A. thaliana leaves accumulate more ascorbate after acclimatization to high light intensity. VTC2 expression and GDP‐l‐galactose phosphorylase activity rapidly increase on transfer to high light, but the activity of other enzymes in the GDP‐mannose pathway is little affected. VTC2 and At5g55120 (VTC5) expression also peak in at the beginning of the light cycle and are controlled by the circadian clock. The GDP‐l‐galactose phosphorylase step may therefore play an important role in controlling ascorbate biosynthesis.
The soybean Dof‐type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants
Authors: Wang Hui‐Wen , Zhang Bo , Hao Yu‐Jun , Huang Jian , Tian Ai‐Guo , Liao Yong , Zhang Jin‐Song , Chen Shou‐Yi 
Published: September 2007

SummarySoybean is one of the most important leguminous seed crops among the oil crops. Although the pathways for lipid biosynthesis have been identified, the factors that regulate the biosynthetic pathways at the transcriptional level are largely unknown. Here, we report our findings on the involvement of soybean Dof‐type transcription factor genes in the regulation of the lipid content in soybean seeds. We identified 28 Dof‐type transcription factor genes in soybean plants, and these genes displayed diverse patterns of expression in various organs. Seven flower/pod‐specific genes and one constitutively expressed gene were further investigated. The proteins encoded by these seven genes were localized in the nucleus, and exhibited different abilities for transcriptional activation and DNA binding. Two genes, GmDof4 and GmDof11, were found to increase the content of total fatty acids and lipids in GmDof4 and GmDof11 transgenic Arabidopsis seeds. We also found that the 1000‐seed weight was increased in the GmDof4 and GmDof11 transgenic plants. Using microarray and DNA binding analysis, we found that the two Dof‐like proteins, GmDof4 and GmDof11, activated the acetyl CoA carboxylase gene and long‐chain‐acyl CoA synthetase gene, respectively, by direct binding to the cis‐DNA elements in their promoter regions. In addition, both proteins downregulated the storage protein gene, CRA1, through direct binding. These results suggest that the two GmDof genes may augment the lipid content of soybean seeds by upregulating genes that are associated with the biosynthesis of fatty acids.
Severing at sites of microtubule crossover contributes to microtubule alignment in cortical arrays
Authors: Wightman Raymond , Turner Simon R. 
Published: September 2007

SummaryThe cortical microtubule (MT) array and its organization is important in defining the growth axes of plant cells. In roots, the MT array exhibits a net‐like configuration in the division zone, and a densely‐packed transverse alignment in the elongation zone. This transition is essential for anisotropic cell expansion and consequently has been the subject of intense study. Cotyledons exhibit a net‐like array in pavement cells and a predominantly aligned array in the petioles, and provide an excellent system for determining the basis of plant MT organization. We show that in both kinds of MT array, growing MTs frequently encounter existing MTs. Although some steep‐angled encounters result in catastrophes, the most frequent outcome of these encounters is successful negotiation of the existing MT by the growing MT to form an MT crossover. Surprisingly, the outcome of such encounters is similar in both aligned and net‐like arrays. In contrast, aligned arrays exhibit a much higher frequency of MT severing events compared with net‐like arrays. Severing events occur almost exclusively at sites where MTs cross over one another. This process of severing at sites of MT crossover results in the removal of unaligned MTs, and is likely to form the basis for the difference between a net‐like and an aligned MT array.
The D‐lineage MADS‐box gene OsMADS13 controls ovule identity in rice
Authors: Dreni Ludovico , Jacchia Sara , Fornara Fabio , Fornari Monica , Ouwerkerk Pieter B. F. , An Gynheung , Colombo Lucia , Kater Martin M. 
Published: September 2007

SummaryGenes that control ovule identity were first identified in Petunia. Co‐suppression of both FLORAL BINDING PROTEIN 7 (FBP7) and FBP11, two D‐lineage genes, resulted in the homeotic transformation of ovules into carpelloid structures. Later in Arabidopsis it was shown that three genes, SHATTERPROOF1 (SHP1), SHP2, and SEEDSTICK (STK), redundantly control ovule identity, because in the stk shp1 shp2 triple mutant ovules lose identity and are transformed into carpel and leaf‐like structures. Of these three Arabidopsis genes STK is the only D‐lineage gene, and its expression, like FBP7 and FBP11, is restricted to ovules. OsMADS13 is the rice ortholog of STK, FBP7, and FBP11. Its amino acid sequence is similar to the Arabidopsis and Petunia proteins, and its expression is also restricted to ovules. We show that the osmads13 mutant is female sterile and that ovules are converted into carpelloid structures. Furthermore, making carpels inside carpels, the osmads13 flower is indeterminate, showing that OsMADS13 also has a function in floral meristem determinacy. OsMADS21 is most likely to be a paralog of OsMADS13, although its expression is not restricted to ovules. Interestingly, the osmads21 mutant did not show any obvious phenotype. Furthermore, combining the osmads13 and the osmads21 mutants did not result in any additive ovule defect, indicating that osmads21 does not control ovule identity. These results suggest that during evolution the D‐lineage gene OsMADS21 has lost its ability to determine ovule identity.
Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome‐wide transcriptional regulation
Authors: Potokina Elena , Druka Arnis , Luo Zewei , Wise Roger , Waugh Robbie , Kearsey Mike 
Published: September 2007

SummaryTranscript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome‐wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profile individuals from a segregating population to accurately identify robust polymorphic molecular genetic markers. We applied the method to identify more than 2000 genetic polymorphisms (transcript derived markers, TDMs) from an experiment involving two commercial varieties of barley (Hordeum vulgare; Steptoe and Morex) and their doubled‐haploid progeny. With this set of TDMs, we constructed a genetic map and used it for the genome‐wide eQTL analysis of about 16 000 genes in a relatively large population (n = 139). We identified 23 738 significant eQTLs at a genome‐wide significance (P ≤ 0.05), affecting the expression of 12 987 genes. Over a third of these genes with expression variation have only one identified eQTL while the rest have two to six. A large proportion of the quantitatively controlled transcripts appear to be regulated by both cis and trans effects. More than half of the quantitatively controlled transcripts appear to be primarily regulated by cis eQTLs in this population. We show that although there appear to be eQTL hotspots many of these are in chromosomal regions of low recombination, such as genetic centromeres, and so have a high gene density per centimorgan. Some chromosomal regions have a significant excess of eQTL over the number expected from gene density, and many of these are biased towards eQTL for which the allele from one particular parent increases the expression level.
Utilizing tiling microarrays for whole‐genome analysis in plants
Authors: Gregory Brian D. , Yazaki Junshi , Ecker Joseph R. 
Published: September 2007

SummaryThe recent explosion in available genome sequence data has ushered in an era in which analysis of a whole genome can be performed in a single experiment. While DNA microarrays have long been the established technology for measuring gene expression levels, standard expression arrays use relatively few probes for each gene and are typically biased toward known and predicted gene structures. Recently, with the availability of complete genome sequences for many organisms, very‐high‐density oligonucleotide‐based microarrays that span the entire genome have emerged as the preferred platform for genomic analysis. Whole‐genome tiling microarrays can be employed for a myriad of purposes, including empirical annotation of the transcriptome, chromatin immunoprecipitation–chip studies, analysis of alternative RNA splicing, characterization of the methylation state of cytosine bases throughout a genome (methylome), and DNA polymorphism discovery. Here, we review several applications of whole‐genome technology to obtain a variety of genomic‐scale information in plants.
CAUT lines: a novel resource for studies of cell autonomy in Arabidopsis
Authors: Furner Ian , Ellis Louise , Bakht Saleha , Mirza Bushra , Sheikh Mazhar 
Published: September 2007

SummaryPlant development is critically dependent on the interactions between clonally unrelated cell layers. The cross‐talk between layers can be addressed by studies of cell autonomy. Cell autonomy is a property of genetic mosaics composed of cells of differing genotypes. Broadly, if the phenotype of a mutant tissue reflects only its genotype and is unaffected by the presence of wild‐type tissue, the trait is cell‐autonomous. Conversely, if the phenotype of a mutant tissue reflects that of wild‐type tissue in the mosaic, the trait is non‐autonomous. Here we report a novel, versatile and robust method for studies of cell autonomy in Arabidopsis. Cell autonomy (CAUT) lines consist of a collection of homozygous stocks, each containing one of 76 mapped T‐DNA inserts, each of which corrects the yellow ch‐42 mutant to green (CH‐42) by complementation. This has the effect of translocating the colour marker to 76 new locations around the genome. X‐irradiation of heterozygous CAUT line seeds results in yellow sectors, with loss of the CH‐42 transgene and adjacent wild‐type genes. This property can be used to remove the wild‐type copy of developmental genes in appropriate heterozygotes, resulting in yellow (ch‐42) sectors that are hemizygous for the trait of interest. Such sectors can provide insight into cell autonomy. Experiments using the ap1, ap3, ag and clv1 mutants show that CAUT lines are useful in the study of cell autonomy.
26S proteasome regulatory particle mutants have increased oxidative stress tolerance
Authors: Kurepa Jasmina , Toh‐e Akio , Smalle Jan A. 
Published: September 2007

SummaryThe 26S proteasome (26SP) is a multi‐subunit, multi‐catalytic protease that is responsible for most of the cytosolic and nuclear protein turnover. The 26SP is composed of two sub‐particles, the 19S regulatory particle (RP) that binds and unfolds protein targets, and the 20S core particle (20SP) that degrades proteins into small peptides. Most 26SP targets are conjugated to a poly‐ubiquitin (Ub) chain that serves as a degradation signal. However, some targets, such as oxidized proteins, do not require a poly‐Ub tag for proteasomal degradation, and recent studies have shown that the main protease in this Ub‐independent pathway is free 20SP. It is currently unknown how the ratio of 26SP‐ to 20SP‐dependent proteolysis is controlled. Here we show that loss of function of the Arabidopsis RP subunits RPT2a, RPN10 and RPN12a leads to decreased 26SP accumulation, resulting in reduced rates of Ub‐dependent proteolysis. In contrast, all three RP mutants have increased 20SP levels and thus enhanced Ub‐independent protein degradation. As a consequence of this shift in proteolytic activity, mutant seedlings are hypersensitive to stresses that cause protein misfolding, and have increased tolerance to treatments that promote protein oxidation. Taken together, the data show that plant cells increase 20SP‐dependent proteolysis when 26SP activity is impaired.
Expectations held by type 1 and 2 diabetes mellitus patients and their relatives: the importance of facilitating the health‐care process
Authors: Escudero‐Carretero María J. , Prieto‐Rodríguez MaÁngeles , Fernández‐Fernández Isabel , March‐Cerdá Joan Carles 
Published: September 2007

AbstractAim  To understand the expectations held by type 1 and 2 diabetes mellitus (DM 1 & 2) patients and their relatives regarding the health‐care provided to them.Design  Qualitative. Focus groups.Setting and participants  Andalusia. A theoretical sample that includes the most characteristic profiles. Thirty‐one subjects with DM. Segmentation characteristics: receiving health‐care for DM in Primary or Specialized care, living in urban and rural areas, men and women, age, varying diagnosis times, DM course and consequences. Subjects were recruited by health‐care professionals at reference care centres.Results  Patients expect their health‐care professionals to be understanding, to treat them with kindness and respect, to have good communication skills, to provide information in a non‐authoritarian manner while fully acknowledging patients’ know‐how. Regarding the health‐care system, their expectations focus on the system’s ability to respond when required to do so, through a relevant professional, along with readily available equipment for treatment.The expectations of people affected by DM1 focus on leading a normal life and not having their educational, labour, social and family opportunities limited by the disease. Expectations in people with DM2 tend towards avoiding what they know has happened to other patients.Conclusions  ‘Facilitating’, is a key word. Both the health‐care system and its professionals must pay keener attention to the emotional aspects of the disease and its process, adopting a comprehensive approach to care. It is vital that health‐care professionals take an active interest in the course of their patient’s disease, promoting accessibility and an atmosphere of trust and flexibility.
The Analysis of Change, Newton’s Law of Gravity and Association Models
Authors: de Rooij Mark 
Published: September 2007

SummaryNewton’s law of gravity states that the force between two objects in the universe is equal to the product of the masses of the two objects divided by the square of the distance between the two objects. In the first part of the paper it is shown that a model with a ‘law-of-gravity’ interpretation applies well to the analysis of longitudinal categorical data where the number of people changing their behaviour or choice from one category to another is a measure of force and the goal is to obtain estimates of mass for the two categories and an estimate of the distance between them. To provide a better description of the data dynamic masses and dynamic positions are introduced. It is shown that this generalized law of gravity is equivalent to Goodman’s RC(M) association model. In the second part of the paper the model is generalized to two kinds of three-way data. The first case is when there are multiple two-way tables and in the second case we have change over three points of time. Conditional and partial association models are related to three-way distance models, like the INDSCAL model, and triadic distance models respectively.