A comprehensive software suite for the analysis of cDNAs

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initia- tion and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http： / /www.g-language.org/ data/cdna/.     

Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles

Light is one of the most important environmental factors that determine the timing of a plant's transition from the vegetative to reproductive, or flowering, phase. Not only daylength but also the spectrum of light greatly affect flowering. The shade of nearby vegetation reduces the ratio of red to far-red light and can trigger shade avoidance responses, including stem elongation and the acceleration of flowering. Phytochrome B (phyB) acts as a photoreceptor for this response. Physiological studies have suggested that leaves can perceive and respond to shade. However, little is known about the mechanisms involved in the processing of light signals within leaves. In this study, we used an enhancer-trap system to establish Arabidopsis thaliana transgenic lines that express phyB-green fluorescent protein (GFP) fusion protein in tissue-specific manners. The analysis of these lines demonstrated that phyB-GFP in mesophyll cells affected flowering, whereas phyB-GFP in vascular bundles did not. Furthermore, mesophyll phyB-GFP suppressed the expression of a key flowering regulator, FLOWERING LOCUS T, in the vascular bundles of cotyledons. Hence, a novel intertissue signaling from mesophyll to vascular bundles is revealed as a critical step for the regulation of flowering by phyB.     

Florigen is involved in axillary bud development at multiple stages in Arabidopsis

The wide variety of plant architectures is largely based on diverse and flexible modes of axillary shoot development. In Arabidopsis, floral transition (flowering) stimulates axillary bud development. The mechanism that links flowering and axillary bud development is, however, largely unknown. We recently showed that FLOWERING LOCUS T (FT) protein, which acts as florigen, promotes the phase transition of axillary meristems, whereas BRANCHED1 (BRC1) antagonizes the florigen action in axillary buds. Here, we present evidences for another possible role of florigen in axillary bud development. Ectopic overexpression of FT or another florigen gene TWIN SISTER OF FT (TSF) with LEAFY (LFY) induces ectopic buds at cotyledonary axils, confirming the previous proposal that these genes are involved in formation of axillary buds. Taken together with our previous report that florigen promotes axillary shoot elongation, we propose that florigen regulates axillary bud development at multiple stages to coordinate it with flowering in Arabidopsis.     

Criterion and construct validity of the CogState Schizophrenia Battery in Japanese patients with schizophrenia

Background

The CogState Schizophrenia Battery (CSB), a computerized cognitive battery, covers all the same cognitive domains as the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) Consensus Cognitive Battery but is briefer to conduct. The aim of the present study was to evaluate the criterion and construct validity of the Japanese language version of the CSB (CSB-J) in Japanese patients with schizophrenia.

Methodology/Principal Findings

Forty Japanese patients with schizophrenia and 40 Japanese healthy controls with matching age, gender, and premorbid intelligence quotient were enrolled. The CSB-J and the Brief Assessment of Cognition in Schizophrenia, Japanese-language version (BACS-J) were performed once. The structure of the CSB-J was also evaluated by a factor analysis. Similar to the BACS-J, the CSB-J was sensitive to cognitive impairment in Japanese patients with schizophrenia. Furthermore, there was a significant positive correlation between the CSB-J composite score and the BACS-J composite score. A factor analysis showed a three-factor model consisting of memory, speed, and social cognition factors.

Conclusions/Significance

This study suggests that the CSB-J is a useful and rapid automatically administered computerized battery for assessing broad cognitive domains in Japanese patients with schizophrenia.     

Wounding-induced Enhancement of the Activity of Chromatin-bound DNA-Dependent RNA Polymerases in Sweet Potato Root

Chromatin fractions were isolated from intact and wounded sweet potato root tissues. The synthesis of RNA by the chromatin fractions was dependent on four ribonucleoside triphosphates and a divalent cation such as Mg²⁺ and Mn²⁺, Mn²⁺ being most effective. Whereas phosphate did not interfere with the polymerase reaction, it was totally blocked by pyrophosphate. The reaction was inhibited by DNase and actinomycin D as well as RNase and trypsin. The RNA polymerases of sweet potato root needed SH-groups for catalysis. Activity of chromatin-bound RNA polymerases (EC 2.7.7.6) promptly increased in the 6 hr after wounding and then decreased gradually up to 24 hr. Under the present experimental conditions it was mostly due to the activity of RNA polymerase I. RNA polymerase II contributed only about 5 to 15% to the total activity. The increase in the activity after wounding was completely inhibited by cycloheximide. Plant hormones such as 2,4-dichlorophenoxyacetic acid, gibberellic acid and dibutyryl cyclic adenosine 3′,5′-monophosphate stimulated the increase in RNA polymerases three to four times after wounding. Ethylene partially suppressed the wound-induced increase of RNA polymerases.     

DNA methylation imprints on the IG-DMR of the Dlk1-Gtl2 domain in mouse male germline

Mouse genomes show a large cluster of imprinted genes at the Dlk1-Gtl2 domain in the distal region of chromosome 12. An intergenic-differentially methylated region (IG-DMR) located between Dlk1 and Gtl2 is specifically methylated in the male germline; IG-DMR regulates the parental allele-specific expression of imprinted genes. Here, we show the resetting of IG-DMR methylation marks during male germ-cell differentiation. For parental allele-specific methylation analysis, polymorphisms were detected in a 2.6-kb IG-DMR in three mouse strains. Bisulfite methylation analysis showed erasure of the marks by E14 and re-establishment before birth. The IG-DMR methylation status was maintained in spermatogonia and spermatocytes of mature testes. The IG-DMR methylation status established before birth is thus maintained throughout the lifetime in the male germline.     

Binding between the integrin alphaXbeta2 (CD11c/CD18) and heparin

The interactions between cell surface receptors and sulfated glucosamineglycans serve ubiquitous roles in cell adhesion and receptor signaling. Heparin, a highly sulfated polymer of uronic acids and glucosamine, binds strongly to the integrin receptor alphaXbeta2 (p150,95, CD11c/CD18). Here, we analyze the structural motifs within heparin that constitute high affinity binding sites for the I domain of integrin alphaXbeta2. Heparin oligomers with chain lengths of 10 saccharide residues or higher provide strong inhibition of the binding by the alphaX I domain to the complement fragment iC3b. By contrast, smaller oligomers or the synthetic heparinoid fondaparinux were not able to block the binding. Semipurified heparin oligomers with 12 saccharide residues identified the fully sulfated species as the most potent antagonist of iC3b, with a 1.3 microM affinity for the alphaX I domain. In studies of direct binding by the alphaX I domain to immobilized heparin, we found that the interaction is conformationally regulated and requires Mg2+. Furthermore, the fully sulfated heparin fragment induced conformational change in the ectodomain of the alphaXbeta2 receptor, also demonstrating allosteric linkage between heparin binding and integrin conformation.     

Unsteady hydrodynamic forces acting on a robotic arm and its flow field: Application to the crawl stroke

This study aims to clarify the mechanisms by which unsteady hydrodynamic forces act on the hand of a swimmer during a crawl stroke. Measurements were performed for a hand attached to a robotic arm with five degrees of freedom independently controlled by a computer. The computer was programmed so the hand and arm mimicked a human performing the stroke. We directly measured forces on the hand and pressure distributions around it at 200 Hz; flow fields underwater near the hand were obtained via 2D particle image velocimetry (PIV). The data revealed two mechanisms that generate unsteady forces during a crawl stroke. One is the unsteady lift force generated when hand movement changes direction during the stroke, leading to vortex shedding and bound vortex created around it. This bound vortex circulation results in a lift that contributes to the thrust. The other occurs when the hand moves linearly with a large angle of attack, creating a Kármán vortex street. This street alternatively sheds clockwise and counterclockwise vortices, resulting in a quasi-steady drag contributing to the thrust. We presume that professional swimmers benefit from both mechanisms. Further studies are necessary in which 3D flow fields are measured using a 3D PIV system and a human swimmer.     

Fungi infecting cultivated moss can also cause diseases in crop plants

Bryophytes (mosses) are non‐vascular plants inhabited by a large number of fungal species, but whether mosses can act as reservoirs of fungal pathogens of crop plants has gained little attention. A few moss species including the Sunagoke moss (Racomitrium japonicum; family Grimmiaceae) are found to have modern economical applications in uses such as greening of urban environments. In a previous study, we identified fungi causing symptoms of varying severity in the commercially grown Sunagoke moss. The aim of this study was to test whether the same fungal isolates are pathogenic to vascular plants. An isolate of Fusarium avenaceum lethal to the Sunagoke moss caused root and crown rot in barley (Hordeum vulgare) and reduced germination of tomato (Solanum lycopersicum) and carrot (Daucus carota) grown in the infested soil. An isolate of Cladosporium oxysporum causing mild symptoms in moss reduced growth and caused reddening and premature death of carrot seedlings. On the other hand, isolates of Alternaria alternata and Fusarium oxysporum lethal to the Sunagoke moss caused no detectable symptoms in any tested vascular plant, suggesting specialisation of these isolates to moss. Chloroplast repositioning was observed in the neighbouring cells towards the initially infected cell following infection with F. avenaceum and A. alternata in Physcomitrella patens (family Funariaceae), a model moss used to study microscopic symptoms. Infection of P. patens with a non‐virulent Apiospora montagnei isolate induced formation of papillae in the moss cells, indicating activation of host defence as described in vascular plants. Results suggest that mosses and vascular plants may be linked by a common microbial interface constituted by pathogenic fungi. The findings have epidemiological implications that have gained little previous attention.     

Flowering regulation by tissue specific functions of photoreceptors

Flowering is one of the most important steps in a plant life cycle. Plants utilize light as an informational source to determine the timing of flowering. In Arabidopsis, phytochrome A (phyA), phyB and cryptochrome2 (cry2) are major photoreceptors that regulate flowering. These photoreceptors perceive light stimuli by leaves for the regulation of flowering. A leaf is an organ consisting of different tissues such as epidermis, mesophyll and vascular bundles. In the present study, we examined in which tissue the light signals are perceived and how those signals are integrated within a leaf to regulate flowering. For this purpose, we established transgenic Arabidopsis lines that expressed a phyB-green fluorescent protein (GFP) fusion protein or a cry2-GFP fusion protein in organ/tissue-specific manners. Consequently, phyB was shown to perceive light stimuli in mesophyll. By contrast, cry2 functioned only in vascular bundles. We further confirmed that both phyB-GFP and cry2-GFP regulated flowering by altering the expression of a key flowering gene, FT, in vascular bundles. In summary, perception sites for different spectra of light are spatially separated within a leaf and the signals are integrated through the inter-tissue communication.Key words: photoreceptor, light, flowering, phytochrome, cryptochrome, inter-tissue signalThe timing of flowering is strictly regulated by environmental conditions such as light. Two aspects of light, spectral nature and photoperiod, dramatically affect flowering. In Arabidopsis, phyB and phyA/cry2 are the major photoreceptors mediating these responses. Although photoreceptors are expressed in almost all organs,¹ partial irradiation and grafting analyses have demonstrated that plants perceive light signals only in leaves.^2–4 However, roles for different tissues in a leaf remained unknown due to a lack of a proper method. To answer the question, we established Arabidopsis transgenic lines that expressed phyB-GFP or cry2-GFP on the respective mutant backgrounds. The resultant transgenic lines were examined for their flowering phenotype. Consequently, we found that phyB-GFP in mesophyll but not in other tissues regulated flowering.⁵ By contrast, cry2-GFP functioned only in vascular bundles.⁶A strong genetic interaction between phyB and cry2 in the regulation of flowering is known.^7,8 Cry2 regulates the flowering by suppressing the inhibitory effect of phyB on flowering. Hence, cry2 function is observed only in the presence of phyB. Conversely, the effect of phyB is exaggerated in the cry2 mutant, because phyB is not counteracted by cry2 in its absence. Here, we tested how phyB and cry2 in different tissues regulated flowering in the absence of the other photoreceptor. For this purpose, we took a physiological approach. Phenotype of the phyB-GFP lines was examined under monochromatic red light, in which phyB but not cyr2 is activated. As expected, phyB-GFP in mesophyll but not in vascular bundles strongly affected the flowering in this condition (Fig. 1A). We also tested the cry2-GFP function when phyB was not activated. Namely, plants were placed under blue light supplemented with strong far-red light. As expected, cry2-GFP failed to affect the flowering even under this condition regardless of where it was expressed (Fig. 1B).Open in a separate windowFigure 1FT expression under phyB or cry2 inactive conditions. Total RNA was extracted from the seedlings grown under long-day condition for 10 days and subjected to qRT-PCR for FT expression analysis. Data were normalized to the level of FT mRNA in (A) of the wild type, which was set to 1 arbitrary unit (a.u.). Mean ± SE (n = 4). WT, wild type. (A) Long-day red light, (16L 8D; 10 µmol m^-2 s^-1). WT, wild type; phyB, phyB mutant; Bpro, PHYB promoter-PHYB-GFP; PBT56, phyB-GFP in mesophyll; PBT239, phyB-GFP in vascular bundles.⁵ (B) Long-day blue and far-red light (16L 8D; blue light, 3 µmol m^-2 s^-1; far-red light, 10 µmol m^-2 s^-1). WT, wild type; cry2, cry2 mutant; pCRY-C2G, CRY2 promoter-CRY2-GFP; pCAB-C2G, CAB3 promoter-CRY2-GFP; pSUC-C2G, SUC2 promoter-CRY2-GFP.⁶Photoreceptors regulate flowering by altering the expression of a key flowering regulator, FT.^9,10 Interestingly, the FT gene is expressed specifically in vascular bundles.¹¹ Indeed, mesophyll phyB-GFP controlled the expression of FT in vascular bundles. Hence, there must be a mechanism by which the light signal is transduced from mesophyll to vascular bundles to regulate the FT expression in vascular bundles. It should be noted here that FT is not the sole factor involved in the light regulation of flowering. Factors such as CO, SPA, COP1 and PFT1 are known to link the photoreceptors and FT.^12–14 These factors most likely function in leaves. However, their function sites at the tissue level remain totally unknown except for CO. The biological clock is another class of machinery that is tightly related to the light signal transduction pathway.¹⁵ Unfortunately, function sites of the clock components for the regulation of flowering remain unclear. The future work should reveal those sites. Such analyses should finally provide a complete picture illustrating a network of the inter-tissue signaling for the regulation of flowering.The present work urges us to indentify the molecule that mediates the inter-tissue signaling between mesophyll and vascular bundles. Potential candidates include phytohormones, microRNA¹⁶ and peptides.¹⁷ Among phytohormones, gibberellin promotes flowering.¹⁸ However, gibberellin is probably not the answer because gibberellin does not alter the FT expression directly. Except gibberellin, no exogenously added phythromone dramatically affects flowering in Arabidopsis. It is known that microRNA such as miR172, miR159 and miR156 are involved in the regulation of flowering time.¹⁹ However, those microRNA''s neither regulate the FT expression nor are regulated by light. Since most of microRNA''s has not been intensively studied yet, it remains possible that one of them may mediate the above inter-tissue signal. Another potential candidate is a peptide. Although not much is known about peptide hormones in plants yet, peptides such as PSK,²⁰ xylogen²¹ and CLE²² have been shown to regulate cell growth and differentiation. Although none of peptides is known to regulate flowering in plants at present, a future work may reveal a novel peptide that mediates the inter-tissue signals for flowering.