bluuebunny/crossref_metadata_2025 huggingface dataset:
THE COMPARATIVE BEHAVIOR OF MAMMALIAN EGGS IN VIVO AND IN VITRO
Authors: Pincus Gregory , Enzmann E. V.
Published: June 2004

1. A definite chronological sequence of events occurs in the eggs and follicles of rabbits after mating or after the injection of ovulation-inducing substances. The follicle secretes secondary liquor folliculi, and there occurs a separation of the corona radiata from strands connecting it to the follicle cells. The ovum goes through nuclear maturation with as climax the production of the first polar body by the 8th hour after copulation.

2. Thyroxin injections cause indirectly the same effects as mating or pituitary injections but no ovulation occurs. The thyroxin effect occurs later than the pituitary effect and is due to an initiation of atresia in the follicles.

3. Explantation of ova results in typical maturation phenomena which are apparently unaffected by the presence of pituitary hormones or of thyroxin in the culture medium.

4. It is concluded that maturation of the ovum can be obtained simply by isolating it from the normal follicular environment.

5. Normal fertilization can be secured with eggs removed from the follicles.
A QUANTITATIVE THEORY OF THE PRECIPITIN REACTION
Authors: Heidelberger Michael , Kendall Forrest E.
Published: June 2004

1. A quantitative theory of the precipitin reaction based on the laws of classical chemistry has now been found applicable to the crystalline egg albumin-antibody system. Equations derived from the theory permit the calculation of the behavior of an anti-egg albumin serum over most of the reaction range after a few quantitative analyses have been made for the nitrogen precipitated. Data of other workers also conform to the proposed equations.

2. The empirical relation, shown to have advantages in the dye antidye system, may also be used for the Ea-A reaction.

3. Serum from the same animal after successive courses exhibits progressive changes which have been described graphically and quantitatively. These changes are believed to consist in the formation of more and more antibody capable of reacting with a larger number of chemically different groupings in the antigen molecule.

4. Evidence is presented that anti-egg albumin is not homogeneous, and that even after prolonged immunization the antiserum contains much low-grade antibody, incapable of forming precipitates unless more reactive precipitin is present.

5. Factors affecting the equivalence point ratio are discussed.
SEROLOGICAL EVIDENCE OF IMMUNITY WITH COEXISTING SENSITIZATION IN A TYPE OF HUMAN ALLERGY (HAY FEVER)
Authors: Cooke Robert A. , Barnard James H. , Hebald Selian , Stull Arthur
Published: June 2004

Using ragweed hay fever as the representative of a certain type of allergy we have made studies to determine if possible the mechanism of the protection afforded by specific injections thus far established only by clinical observation.

1. Blood transfusions and serum injections from clinically immune, treated patients stopped the clinical reaction in untreated patients, thus indicating a transferable immunity.

2. The amount of skin sensitizing antibody in the serum was found to be practically unchanged by specific injections.

3. Injection of allergen-antibody mixtures into normal skin showed an immediate (1 hour) reaction when sites were made if serum of untreated cases (Serum A) was used but none or slight reaction if serum of treated cases (Serum P) was used.

4. When sites made with allergen-antibody mixtures were tested after 48 hours, reactions were absent with Serum A mixtures if enough allergen had been used, but were positive with mixtures of Serum P even though a much stronger allergen was contained in the mixture.

5. The primary inhibition of reactions with mixtures including Serum P was not due to antihistamine effect nor to binding of skin sensitizing antibody nor to binding or lysis of allergen.

6. The inhibiting antibody appears to be specific.

7. These serological studies supported by transfusion experiments have been interpreted by us as showing the development under treatment of a peculiar blocking or inhibiting type of immune antibody that prevented the action of allergen on the sensitizing antibody and hence showed in the type of human allergy under consideration (hay fever) the coexistence of sensitization and immunity.
CELLULAR REACTIONS TO WAX-LIKE MATERIALS FROM ACID-FAST BACTERIA
Authors: Sabin F. R. , Smithburn K. C. , Thomas R. M.
Published: June 2004

1. The unsaponifiable fractions of the Mycobacteria, though insoluble in water and extremely stable chemical compounds, are nevertheless remarkable stimulants of cells.

2. They give rise to new monocytes which surround these waxes and then fuse into giant cells which engulf them.

3. The property of acid-fastness of the waxes makes it possible to identify them within the giant cells which have phagocytized them.

4. Within the foreign body giant cells the waxes are slowly disintegrated. They appear not to damage the cells which engulf them, and hence one may infer that they take no part in caseation.

5. They have no effect on the resistance of the host.
CELLULAR REACTIONS TO WAXES FROM MYCOBACTERIUM LEPRAE
Authors: Sabin F. R. , Smithburn K. C. , Thomas R. M.
Published: June 2004

1. The waxes from the B. leprae, like those from tubercle bacilli, are remarkable stimulants of cells.

2. The crude wax separated from the B. leprae is a mixture of lipoids and other materials, and gives reactions that include the types of cells characteristic of the response to the tuberculo-polysaccharide, phosphatide, and wax.

3. The wax obtained from the purification of the lepra phosphatide shows similar cellular reactions but with a greater proportion of foreign body giant cells.

4. Leprosin, though a glyceride, corresponds in its physical properties to the unsaponifiable material from the tubercle bacillus. It stimulates two strains of cells, fibroblasts and monocytes. The monocytes fuse into foreign body giant cells to engulf the wax.

5. The cellular reaction to the leprosinic acid and to the crystalline alcohols is of one type only, represented by the foreign body giant cell.
THE DISTRIBUTION OF SWINE INFLUENZA VIRUS IN SWINE
Authors: Orcutt Marion L. , Shope Richard E.
Published: June 2004

Swine influenza virus was found to be regularly present in the turbinates, tracheal exudate and lungs of infected swine but not in the spleens, livers, kidneys, mesenteric lymph nodes, colon mucosae, brains or blood. It was present in low concentration in the bronchial lymph nodes of 2 out of 8 animals. This localization of the virus in swine accords with its classification as a pneumotropic virus.
THE EMIGRATION OF PNEUMOCOCCI TYPE III FROM THE BLOOD INTO THE THORACIC DUCT LYMPH OF RABBITS, AND THE SURVIVAL OF THESE ORGANISMS IN THE LYMPH FOLLOWING INTRAVENOUS INJECTION OF SPECIFIC ANTISERUM
Authors: Drinker Cecil K. , Enders John F. , Shaffer Morris F. , Leigh Octa C.
Published: June 2004

1. Rabbits injected intravenously with a large dose of a virulent Type III Pneumococcus develop a bacteremia, and within an hour organisms may be cultivated from the thoracic duct lymph. The rapidity with which entrance into the lymph occurs appears to be correlated with the size of the dose injected.

2. The organisms may become more numerous in the lymph than in the blood.

3. If homologous or heterologous antisera are injected, the blood may be sterilized, but though the organisms may be lessened in the lymph, sterilization at least within 4 hours is not secured, and in the intact animal living organisms must continue to enter the blood with the thoracic duct lymph.

4. In infected rabbits after intravenous injection of considerable quantities of antisera containing moderate amounts of agglutinin, no antibody appears in the thoracic duct lymph although the presence of horse serum may be detected.

The injection of a very large quantity of antiserum containing a high titre of agglutinin is followed by the penetration of antibody into the lymph. This, however, has failed to sterilize the lymph or to permanently affect the rate of multiplication of the pneumococci.
Plastidial α-Glucan Phosphorylase Is Not Required for Starch Degradation in Arabidopsis Leaves But Has a Role in the Tolerance of Abiotic Stress
Authors: Zeeman Samuel C. , Thorneycroft David , Schupp Nicole , Chapple Andrew , Weck Melanie , Dunstan Hannah , Haldimann Pierre , Bechtold Nicole , Smith Alison M. , Smith Steven M.
Published: June 2004

To study the role of the plastidial α-glucan phosphorylase in starch metabolism in the leaves of Arabidopsis, two independent mutant lines containing T-DNA insertions within the phosphorylase gene were identified. Both insertions eliminate the activity of the plastidial α-glucan phosphorylase. Measurement of other enzymes of starch metabolism reveals only minor changes compared with the wild type. The loss of plastidial α-glucan phosphorylase does not cause a significant change in the total accumulation of starch during the day or its remobilization at night. Starch structure and composition are unaltered. However, mutant plants display lesions on their leaves that are not seen on wild-type plants, and mesophyll cells bordering the lesions accumulate high levels of starch. Lesion formation is abolished by growing plants under 100% humidity in still air, but subsequent transfer to circulating air with lower humidity causes extensive wilting in the mutant leaves. Wilted sectors die, causing large lesions that are bordered by starch-accumulating cells. Similar lesions are caused by the application of acute salt stress to mature plants. We conclude that plastidial phosphorylase is not required for the degradation of starch, but that it plays a role in the capacity of the leaf lamina to endure a transient water deficit.
Homology Modeling of Representative Subfamilies of Arabidopsis Major Intrinsic Proteins. Classification Based on the Aromatic/Arginine Selectivity Filter
Authors: Wallace Ian S. , Roberts Daniel M.
Published: June 2004

Major intrinsic proteins (MIPs) are a family of membrane channels that facilitate the bidirectional transport of water and small uncharged solutes such as glycerol. The 35 full-length members of the MIP family in Arabidopsis are segregated into four structurally homologous subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic membrane proteins (NIPs), and small basic intrinsic proteins (SIPs). Computational methods were used to construct structural models of the putative pore regions of various plant MIPs based on homology modeling with the atomic resolution crystal structures of mammalian aquaporin 1 and the bacterial glycerol permease GlpF. Based on comparisons of the narrow selectivity filter regions (the aromatic/Arg [ar/R] filter), the members of the four phylogenetic subfamilies of Arabidopsis MIPs can be classified into eight groups. PIPs possess a uniform ar/R signature characteristic of high water transport aquaporins, whereas TIPs are highly diverse with three separate conserved ar/R regions. NIPs possess two separate conserved ar/R regions, one that is similar to the archetype, soybean (Glycine max) nodulin 26, and another that is characteristic of Arabidopsis NIP6;1. The SIP subfamily possesses two ar/R subgroups, characteristic of either SIP1 or SIP2. Both SIP ar/R residues are divergent from all other MIPs in plants and other kingdoms. Overall, these findings suggest that higher plant MIPs have a common fold but show distinct differences in proposed pore apertures, potential to form hydrogen bonds with transported molecules, and amphiphilicity that likely results in divergent transport selectivities.
Specification of the Peroxisome Targeting Signals Type 1 and Type 2 of Plant Peroxisomes by Bioinformatics Analyses
Authors: Reumann Sigrun
Published: June 2004

To specify the C-terminal peroxisome targeting signal type 1 (PTS1) and the N-terminal PTS2 for higher plants, a maximum number of plant cDNAs and expressed sequence tags that are homologous to PTS1- and PTS2-targeted plant proteins was retrieved from the public databases and the primary structure of their targeting domains was analyzed for conserved properties. According to their high overall frequency in the homologs and their widespread occurence in different orthologous groups, nine major PTS1 tripeptides ([SA][RK][LM]> without AKM> plus SRI> and PRL>) and two major PTS2 nonapeptides (R[LI]x5HL) were defined that are considered good indicators for peroxisomal localization if present in unknown proteins. A lower but significant number of homologs contained 1 of 11 minor PTS1 tripeptides or of 9 minor PTS2 nonapeptides, many of which have not been identified before in plant peroxisomal proteins. The region adjacent to the PTS peptides was characterized by specific conserved properties as well, such as a pronounced incidence of basic and Pro residues and a high positive net charge, which probably play an auxiliary role in peroxisomal targeting. By contrast, several peptides with assumed peroxisomal targeting properties were not found in any of the 550 homologs and hence play—if at all—only a minor role in peroxisomal targeting. Based on the definition of these major and minor PTS and on the recognition of additional conserved properties, the accuracy of predicting peroxisomal proteins can be raised and plant genomes can be screened for novel proteins of peroxisomes more successfully.
The Transcriptional Innate Immune Response to flg22. Interplay and Overlap with Avr Gene-Dependent Defense Responses and Bacterial Pathogenesis
Authors: Navarro Lionel , Zipfel Cyril , Rowland Owen , Keller Ingo , Robatzek Silke , Boller Thomas , Jones Jonathan D.G.
Published: June 2004

Animals and plants carry recognition systems to sense bacterial flagellin. Flagellin perception in Arabidopsis involves FLS2, a Leu-rich-repeat receptor kinase. We surveyed the early transcriptional response of Arabidopsis cell cultures and seedlings within 60 min of treatment with flg22, a peptide corresponding to the most conserved domain of flagellin. Using Affymetrix microarrays, approximately 3.0% of 8,200 genes displayed transcript level changes in flg22 elicited suspension cultures and seedlings. FLARE (Flagellin Rapidly Elicited) genes mostly encode signaling components, such as transcription factors, protein kinases/phosphatases, and proteins that regulate protein turnover. Approximately 80% of flg22-induced genes were also up-regulated in Arabidopsis seedlings treated with cycloheximide. This suggests that many FLARE genes are negatively regulated by rapidly turned-over repressor proteins. Twenty-one tobacco Avr9/Cf-9 rapidly elicited (ACRE) cDNA full-length sequences were used to search for their Arabidopsis orthologs (AtACRE). We identified either single or multiple putative orthologs for 17 ACRE genes. For 13 of these ACRE genes, at least one Arabidopsis ortholog was induced in flg22-elicited Arabidopsis suspension cells and seedlings. This result revealed a substantial overlap between the Arabidopsis flg22 response and the tobacco Avr9 race-specific defense response. We also compared FLARE gene sets and genes induced in basal or gene-for-gene interactions upon different Pseudomonas syringae treatments, and infer that Pseudomonas syringae pv tomato represses the flagellin-initiated defense response.
The Peroxisome Deficient Arabidopsis Mutant sse1 Exhibits Impaired Fatty Acid Synthesis
Authors: Lin Yun , Cluette-Brown Joanne E. , Goodman Howard M.
Published: June 2004

The Arabidopsis Shrunken Seed 1 (SSE1) gene encodes a homolog of the peroxisome biogenesis factor Pex16p, and a loss-of-function mutation in this gene alters seed storage composition. Two lines of evidence support a function for SSE1 in peroxisome biogenesis: the peroxisomal localization of a green fluorescent protein-SSE1 fusion protein and the lack of normal peroxisomes in sse1 mutant embryos. The green fluorescent protein-SSE1 colocalizes with the red fluorescent protein (RFP)-labeled peroxisomal markers RFP-peroxisome targeting signal 1 and peroxisome targeting signal 2-RFP in transgenic Arabidopsis. Each peroxisomal marker exhibits a normal punctate peroxisomal distribution in the wild type but not the sse1 mutant embryos. Further studies reported here were designed toward understanding carbon metabolism in the sse1 mutant. A time course study of dissected embryos revealed a dramatic rate decrease in oil accumulation and an increase in starch accumulation. Introduction of starch synthesis mutations into the sse1 background did not restore oil biosynthesis. This finding demonstrated that reduction in oil content in sse1 is not caused by increased carbon flow to starch. To identify the blocked steps in the sse1 oil deposition pathway, developing sse1 seeds were supplied radiolabeled oil synthesis precursors. The ability of sse1 to incorporate oleic acid, but not pyruvate or acetate, into triacylglycerol indicated a defect in the fatty acid biosynthetic pathway in this mutant. Taken together, the results point to a possible role for peroxisomes in the net synthesis of fatty acids in addition to their established function in lipid catabolism. Other possible interpretations of the results are discussed.
A Novel Family of Cys-Rich Membrane Proteins Mediates Cadmium Resistance in Arabidopsis
Authors: Song Won-Yong , Martinoia Enrico , Lee Joohyun , Kim Dongwoo , Kim Do-Young , Vogt Esther , Shim Donghwan , Choi Kwan Sam , Hwang Inhwan , Lee Youngsook
Published: June 2004

Cadmium (Cd) is a widespread pollutant that is toxic to plant growth. However, only a few genes that contribute to Cd resistance in plants have been identified. To identify additional Cd(II) resistance genes, we screened an Arabidopsis cDNA library using a yeast (Saccharomyces cerevisiae) expression system employing the Cd(II)-sensitive yeast mutant ycf1. This screening process yielded a small Cys-rich membrane protein (Arabidopsis plant cadmium resistance, AtPcrs). Database searches revealed that there are nine close homologs in Arabidopsis. Homologs were also found in other plants. Four of the five homologs that were tested also increased resistance to Cd(II) when expressed in ycf1. AtPcr1 localizes at the plasma membrane in both yeast and Arabidopsis. Arabidopsis plants overexpressing AtPcr1 exhibited increased Cd(II) resistance, whereas antisense plants that showed reduced AtPcr1 expression were more sensitive to Cd(II). AtPcr1 overexpression reduced Cd uptake by yeast cells and also reduced the Cd contents of both yeast and Arabidopsis protoplasts treated with Cd. Thus, it appears that the Pcr family members may play an important role in the Cd resistance of plants.
Interaction between Wall Deposition and Cell Elongation in Dark-Grown Hypocotyl Cells in Arabidopsis
Authors: Refrégier Guislaine , Pelletier Sandra , Jaillard Danielle , Höfte Herman
Published: June 2004

A central problem in plant biology is how cell expansion is coordinated with wall synthesis. We have studied growth and wall deposition in epidermal cells of dark-grown Arabidopsis hypocotyls. Cells elongated in a biphasic pattern, slowly first and rapidly thereafter. The growth acceleration was initiated at the hypocotyl base and propagated acropetally. Using transmission and scanning electron microscopy, we analyzed walls in slowly and rapidly growing cells in 4-d-old dark-grown seedlings. We observed thick walls in slowly growing cells and thin walls in rapidly growing cells, which indicates that the rate of cell wall synthesis was not coupled to the cell elongation rate. The thick walls showed a polylamellated architecture, whereas polysaccharides in thin walls were axially oriented. Interestingly, innermost cellulose microfibrils were transversely oriented in both slowly and rapidly growing cells. This suggested that transversely deposited microfibrils reoriented in deeper layers of the expanding wall. No growth acceleration, only slow growth, was observed in the cellulose synthase mutant cesA6prc1-1 or in seedlings, which had been treated with the cellulose synthesis inhibitor isoxaben. In these seedlings, innermost microfibrils were transversely oriented and not randomized as has been reported for other cellulose-deficient mutants or following treatment with dichlorobenzonitrile. Interestingly, isoxaben treatment after the initiation of the growth acceleration in the hypocotyl did not affect subsequent cell elongation. Together, these results show that rapid cell elongation, which involves extensive remodeling of the cell wall polymer network, depends on normal cellulose deposition during the slow growth phase.
Plant Body Weight-Induced Secondary Growth in Arabidopsis and Its Transcription Phenotype Revealed by Whole-Transcriptome Profiling
Authors: Ko Jae-Heung , Han Kyung-Hwan , Park Sunchung , Yang Jaemo
Published: June 2004

Wood is an important raw material and environmentally cost-effective renewable source of energy. However, the molecular biology of wood formation (i.e. secondary growth) is surprisingly understudied. A novel experimental system was employed to study the molecular regulation of secondary xylem formation in Arabidopsis. First, we demonstrate that the weight carried by the stem is a primary signal for the induction of cambium differentiation and the plant hormone, auxin, is a downstream carrier of the signal for this process. We used Arabidopsis whole-transcriptome (23 K) GeneChip analysis to examine gene expression profile changes in the inflorescent stems treated for wood formation by cultural manipulation or artificial weight application. Many of the genes up-regulated in wood-forming stems had auxin responsive cis-acting elements in their promoter region, indicating auxin-mediated regulation of secondary growth. We identified 700 genes that were differentially expressed during the transition from primary growth to secondary growth. More than 40% of the genes that were up-regulated (>5×) were associated with signal transduction and transcriptional regulation. Biological significance of these regulatory genes is discussed in light of the induction and development of secondary xylem.
GCR1 Can Act Independently of Heterotrimeric G-Protein in Response to Brassinosteroids and Gibberellins in Arabidopsis Seed Germination
Authors: Chen Jin-Gui , Pandey Sona , Huang Jirong , Alonso José M. , Ecker Joseph R. , Assmann Sarah M. , Jones Alan M.
Published: June 2004

Signal recognition by seven-transmembrane (7TM) cell-surface receptors is typically coupled by heterotrimeric G-proteins to downstream effectors in metazoan, fungal, and amoeboid cells. Some responses perceived by 7TM receptors in amoeboid cells and possibly in human cells can initiate downstream action independently of heterotrimeric G-proteins. Plants use heterotrimeric G-protein signaling in the regulation of growth and development, particularly in hormonal control of seed germination, but it is not yet clear which of these responses utilize a 7TM receptor. Arabidopsis GCR1 has a predicted 7TM-spanning domain and other features characteristic of 7TM receptors. Loss-of-function gcr1 mutants indicate that GCR1 plays a positive role in gibberellin- (GA) and brassinosteroid- (BR) regulated seed germination. The null mutants of GCR1 are less sensitive to GA and BR in seed germination. This phenotype is similar to that previously observed for transcript null mutants in the Gα-subunit, gpa1. However, the reduced sensitivities toward GA and BR in the single gcr1, gpa1, and agb1 (heterotrimeric G-protein β-subunit) mutants are additive or synergistic in the double and triple mutants. Thus, GCR1, unlike a typical 7TM receptor, apparently acts independently of the heterotrimeric G-protein in at least some aspects of seed germination, suggesting that this alternative mode of 7TM receptor action also functions in the plant kingdom.
DELLA Proteins and Gibberellin-Regulated Seed Germination and Floral Development in Arabidopsis
Authors: Tyler Ludmila , Thomas Stephen G. , Hu Jianhong , Dill Alyssa , Alonso Jose M. , Ecker Joseph R. , Sun Tai-ping
Published: June 2004

RGA (repressor of ga1-3) and GAI (gibberellin insensitive) are negative regulators of plant hormone gibberellin (GA) signaling in Arabidopsis. The GA-deficient mutant ga1-3 is a nongerminating, extreme dwarf that flowers late and produces male-sterile flowers. The rga and gai null alleles interact synergistically to rescue vegetative growth and floral initiation in ga1-3, indicating that RGA and GAI are major repressors for these processes. However, rga and gai in combination cannot rescue seed germination or floral development in ga1-3. RGA and GAI belong to the DELLA subfamily within the GRAS family of plant regulatory proteins. Three additional DELLA proteins RGL1, RGL2, and RGL3 are present in Arabidopsis. Previous studies provided evidence that RGL2 and possibly RGL1 control seed germination. To investigate further the function of the RGL genes, we examined the expression profiles of all 5 DELLA protein genes by real-time PCR. RGA and, to a lesser extent, GAI mRNAs were expressed ubiquitously in all tissues, whereas RGL1, 2, and 3 transcripts were present at high levels only in germinating seeds and/or flowers and siliques. Using the newly isolated rgl1, rgl2, and rgl3 T-DNA insertion mutants, we demonstrated that RGL2 is the major repressor in seed germination. We further provided evidence that RGA, RGL1, and RGL2 are all involved in modulating floral development. Interestingly, RGL2 expression is regulated not only at the transcript level. We showed that RGL2 protein in imbibed seeds is rapidly degraded by GA treatment and that the F-box protein SLY1 is required for RGL2 degradation to occur.
Arabidopsis Trehalose-6-Phosphate Synthase 1 Is Essential for Normal Vegetative Growth and Transition to Flowering
Authors: Dijken Anja J.H. van , Schluepmann Henriette , Smeekens Sjef C.M.
Published: June 2004

In resurrection plants and yeast, trehalose has a function in stress protection, but the absence of measurable amounts of trehalose in other plants precludes such a function. The identification of a trehalose biosynthetic pathway in angiosperms raises questions on the function of trehalose metabolism in nonresurrection plants. We previously identified a mutant in the Arabidopsis trehalose biosynthesis gene AtTPS1. Plants homozygous for the tps1 mutation do not develop mature seeds (Eastmond et al., 2002). AtTPS1 expression analysis and the spatial and temporal activity of its promoter suggest that this gene is active outside the seed-filling stage of development as well. A generally low expression is observed in all organs analyzed, peaking in metabolic sinks such as flower buds, ripening siliques, and young rosette leaves. The arrested tps1/tps1 embryonic state could be rescued using a dexamethasone-inducible AtTPS1 expression system enabling generation of homozygous mutant plants. When depleted in AtTPS1 expression, such mutant plants show reduced root growth, which is correlated with a reduced root meristematic region. Moreover, tps1/tps1 plants are retarded in growth and remain generative during their lifetime. Absence of Trehalose-6-Phosphate Synthase 1 in Arabidopsis plants precludes transition to flowering.
Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot
Authors: Nelson David R. , Schuler Mary A. , Paquette Suzanne M. , Werck-Reichhart Daniele , Bak Søren
Published: June 2004

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.
Cell Cycle Modulation in the Response of the Primary Root of Arabidopsis to Salt Stress
Authors: West Gerrit , Inzé Dirk , Beemster Gerrit T.S.
Published: June 2004

Salt stress inhibits plant growth and development. We investigated the importance of cell cycle regulation in mediating the primary root growth response of Arabidopsis to salt stress. When seedlings were transferred to media with increasing concentrations of NaCl, root growth rate was progressively reduced. At day 3 after transfer of seedlings to growth medium containing 0.5% NaCl the primary roots grew at a constant rate well below that prior to the transfer, whereas those transferred to control medium kept accelerating. Kinematic analysis revealed that the growth reduction of the stressed roots was due to a decrease in cell production and a smaller mature cell length. Surprisingly, average cell cycle duration was not affected. Hence, the reduced cell production was due to a smaller number of dividing cells, i.e. a meristem size reduction. To analyze the mechanism of meristem size adaptation prior to day 3, we investigated the short-term cell cycle events following transfer to saline medium. Directly after transfer cyclin-dependent kinase (CDK) activity and CYCB1;2 promoter activity were transiently reduced. Because protein levels of both CDKA;1 and CDKB1;1 were not affected, the temporary inhibition of mitotic activity that allows adaptation to the stress condition is most likely mediated by posttranslational control of CDK activity. Thus, the adaptation to salt stress involves two phases: first, a rapid transient inhibition of the cell cycle that results in fewer cells remaining in the meristem. When the meristem reaches the appropriate size for the given conditions, cell cycle duration returns to its default.
The Arabidopsis Genome Sequence as a Tool for Genome Analysis in Brassicaceae. A Comparison of the Arabidopsis and Capsella rubella Genomes
Authors: Boivin Karine , Acarkan Adile , Mbulu Rosa-Stella , Clarenz Oliver , Schmidt Renate
Published: June 2004

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.
Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies
Authors: Berardini Tanya Z. , Mundodi Suparna , Reiser Leonore , Huala Eva , Garcia-Hernandez Margarita , Zhang Peifen , Mueller Lukas A. , Yoon Jungwoon , Doyle Aisling , Lander Gabriel , Moseyko Nick , Yoo Danny , Xu Iris , Zoeckler Brandon , Montoya Mary , Miller Neil , Weems Dan , Rhee Seung Y.
Published: June 2004

Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species.
Functional Analysis of the Tandem-Duplicated P450 Genes SPS/BUS/CYP79F1 and CYP79F2 in Glucosinolate Biosynthesis and Plant Development by Ds Transposition-Generated Double Mutants
Authors: Tantikanjana Titima , Mikkelsen Michael Dalgaard , Hussain Mumtaz , Halkier Barbara Ann , Sundaresan Venkatesan
Published: June 2004

A significant fraction (approximately 17%) of Arabidopsis genes are members of tandemly repeated families and pose a particular challenge for functional studies. We have used the Ac-Ds transposition system to generate single- and double-knockout mutants of two tandemly duplicated cytochrome P450 genes, SPS/BUS/CYP79F1 and CYP79F2. We have previously described the Arabidopsis supershoot mutants in CYP79F1 that exhibit massive overproliferation of shoots. Here we use a cytokinin-responsive reporter ARR5::uidA and an auxin-responsive reporter DR5::uidA in the sps/cyp79F1 mutant to show that increased levels of cytokinin, but not auxin, correlate well with the expression pattern of the SPS/CYP79F1 gene, supporting the involvement of this gene in cytokinin homeostasis. Further, we isolated Ds gene trap insertions in the CYP79F2 gene, and find these mutants to be defective mainly in the root system, consistent with a root-specific expression pattern. Finally, we generated double mutants in CYP79F1 and CYP79F2 using secondary transpositions, and demonstrate that the phenotypes are additive. Previous biochemical studies have suggested partially redundant functions for SPS/CYP79F1 and CYP79F2 in aliphatic glucosinolate synthesis. Our analysis shows that aliphatic glucosinolate biosynthesis is completely abolished in the double-knockout plants, providing genetic proof for the proposed biochemical functions of these genes. This study also provides further demonstration of how gluconisolate biosynthesis, regarded as secondary metabolism, is intricately linked with hormone homeostatis and hence with plant growth and development.
Arabidopsis to Rice. Applying Knowledge from a Weed to Enhance Our Understanding of a Crop Species
Authors: Rensink W.A. , Buell C. Robin
Published: June 2004

Although Arabidopsis is well established as the premiere model species in plant biology, rice (Oryza sativa) is moving up fast as the second-best model organism. In addition to the availability of large sets of genetic, molecular, and genomic resources, two features make rice attractive as a model species: it represents the taxonomically distinct monocots and is a crop species. Plant structural genomics was pioneered on a genome-scale in Arabidopsis and the lessons learned from these efforts were not lost on rice. Indeed, the sequence and annotation of the rice genome has been greatly accelerated by method improvements made in Arabidopsis. For example, the value of full-length cDNA clones and deep expressed sequence tag resources, obtained in Arabidopsis primarily after release of the complete genome, has been recognized by the rice genomics community. For rice >250,000 expressed sequence tags and 28,000 full-length cDNA sequences are available prior to the completion of the genome sequence. With respect to tools for Arabidopsis functional genomics, deep sequence-tagged lines, inexpensive spotted oligonucleotide arrays, and a near-complete whole genome Affymetrix array are publicly available. The development of similar functional genomics resources for rice is in progress that for the most part has been more streamlined based on lessons learned from Arabidopsis. Genomic resource development has been essential to set the stage for hypothesis-driven research, and Arabidopsis continues to provide paradigms for testing in rice to assess function across taxonomic divisions and in a crop species.
Molecular Characterization of an Arabidopsis Gene Encoding a Phospholipid-Specific Inositol Polyphosphate 5-Phosphatase
Authors: Ercetin Mustafa E. , Gillaspy Glenda E.
Published: June 2004

Phosphoinositides are important molecules that serve as second messengers and bind to a complex array of proteins modulating their subcellular location and activity. The enzymes that metabolize phosphoinositides can in some cases serve to terminate the signaling actions of phosphoinositides. The inositol polyphosphate 5-phosphatases (5PTases) comprise a large protein family that hydrolyzes 5-phosphates from a variety of inositol phosphate and phosphoinositide substrates. We previously reported the identification of 15 putative 5PTase genes in Arabidopsis and have shown that overexpression of the At5PTase1 gene can alter abscisic acid signaling. At5PTase1 and At5PTase2 have been shown to hydrolyze the 5-phosphate from inositol phosphate substrates. We have examined the substrate specificity of the At5PTase11 protein, which is one of the smallest predicted 5PTases found in any organism. We report here that the At5PTase11 gene encodes an active 5PTase enzyme that can only dephosphorylate phosphoinositide substrates containing a 5-phosphate. In addition to hydrolyzing known substrates of 5PTase enzymes, At5PTase11 also hydrolyzes the 5-phosphate from phosphatidylinositol (3,5) bisphosphate. We also show that the At5PTase11 gene is regulated by abscisic acid, jasmonic acid, and auxin, suggesting a role for phosphoinositide action in these signal transduction pathways.
Genome-Wide Analysis of the Cyclin Family in Arabidopsis and Comparative Phylogenetic Analysis of Plant Cyclin-Like Proteins
Authors: Wang Guanfang , Kong Hongzhi , Sun Yujin , Zhang Xiaohong , Zhang Wei , Altman Naomi , dePamphilis Claude W. , Ma Hong
Published: June 2004

Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.
Gene Expression Signatures from Three Genetically Separable Resistance Gene Signaling Pathways for Downy Mildew Resistance
Authors: Eulgem Thomas , Weigman Victor J. , Chang Hur-Song , McDowell John M. , Holub Eric B. , Glazebrook Jane , Zhu Tong , Dangl Jeffery L.
Published: June 2004

Resistance gene-dependent disease resistance to pathogenic microorganisms is mediated by genetically separable regulatory pathways. Using the GeneChip Arabidopsis genome array, we compared the expression profiles of approximately 8,000 Arabidopsis genes following activation of three RPP genes directed against the pathogenic oomycete Peronospora parasitica. Judicious choice of P. parasitica isolates and loss of resistance plant mutants allowed us to compare the responses controlled by three genetically distinct resistance gene-mediated signaling pathways. We found that all three pathways can converge, leading to up-regulation of common sets of target genes. At least two temporal patterns of gene activation are triggered by two of the pathways examined. Many genes defined by their early and transient increases in expression encode proteins that execute defense biochemistry, while genes exhibiting a sustained or delayed expression increase predominantly encode putative signaling proteins. Previously defined and novel sequence motifs were found to be enriched in the promoters of genes coregulated by the local defense-signaling network. These putative promoter elements may operate downstream from signal convergence points.
A Mutant of Arabidopsis Lacking the Triose-Phosphate/Phosphate Translocator Reveals Metabolic Regulation of Starch Breakdown in the Light
Authors: Walters Robin G. , Ibrahim Douglas G. , Horton Peter , Kruger Nicholas J.
Published: June 2004

The chloroplast envelope triose-phosphate/phosphate translocator (TPT) is responsible for carbohydrate export during photosynthesis. Using measurements of carbohydrates, partitioning of assimilated 14CO2, photosynthetic gas exchange, and chlorophyll fluorescence, we show that a mutant of Arabidopsis lacking the TPT increases synthesis of starch compared to the wild type, thereby compensating for a deficiency in its ability to export triose-phosphate from the chloroplast. However, during growth under high light, the capacity for starch synthesis becomes limiting so that the chloroplastic phosphate pool is depleted, resulting in a restriction on electron transport, a reduction in the rate of photosynthesis, and slowed plant growth. Under the same conditions but not under low light, we observe release of 14C label from starch, indicating that its synthesis and degradation occur simultaneously in the light. The induction of starch turnover in the mutant specifically under high light conditions leads us to conclude that it is regulated by one or more metabolic signals, which arise as a result of phosphate limitation of photosynthesis.
Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties
Authors: Sun Qi , Emanuelsson Olof , van Wijk Klaas J.
Published: June 2004

Carefully curated proteomes of the inner envelope membrane, the thylakoid membrane, and the thylakoid lumen of chloroplasts from Arabidopsis were assembled based on published, well-documented localizations. These curated proteomes were evaluated for distribution of physical-chemical parameters, with the goal of extracting parameters for improved subcellular prediction and subsequent identification of additional (low abundant) components of each membrane system. The assembly of rigorously curated subcellular proteomes is in itself also important as a parts list for plant and systems biology. Transmembrane and subcellular prediction strategies were evaluated using the curated data sets. The three curated proteomes differ strongly in average isoelectric point and protein size, as well as transmembrane distribution. Removal of the cleavable, N-terminal transit peptide sequences greatly affected isoelectric point and size distribution. Unexpectedly, the Cys content was much lower for the thylakoid proteomes than for the inner envelope. This likely relates to the role of the thylakoid membrane in light-driven electron transport and helps to avoid unwanted oxidation-reduction reactions. A rule of thumb for discriminating between the predicted integral inner envelope membrane and integral thylakoid membrane proteins is suggested. Using a combination of predictors and experimentally derived parameters, four plastid subproteomes were predicted from the fully annotated Arabidopsis genome. These predicted subproteomes were analyzed for their properties and compared to the curated proteomes. The sensitivity and accuracy of the prediction strategies are discussed. Data can be extracted from the new plastid proteome database (http://ppdb.tc.cornell.edu).
TILLING. Traditional Mutagenesis Meets Functional Genomics
Authors: Henikoff Steven , Till Bradley J. , Comai Luca
Published: June 2004

Most of the genes of an organism are known from sequence, but most of the phenotypes are obscure. Thus, reverse genetics has become an important goal for many biologists. However, reverse-genetic methodologies are not similarly applicable to all organisms. In the general strategy for reverse genetics that we call TILLING (for Targeting Induced Local Lesions in Genomes), traditional chemical mutagenesis is followed by high-throughput screening for point mutations. TILLING promises to be generally applicable. Furthermore, because TILLING does not involve transgenic modifications, it is attractive not only for functional genomics but also for agricultural applications. Here, we present an overview of the status of TILLING methodology, including Ecotilling, which entails detection of natural variation. We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems.