Dispersion correction for optical coherence tomography by the stepped detection algorithm in the fractional Fourier domain.

Dispersion in optical coherence tomography (OCT) leads to a series of wavelength-dependent phase distortions, which cause degradation of axial resolution. Due to the lack of prior information or the complexity of an exhaustive search calculation, all-depth dispersion suppression can hardly be realized in practical cases, especially for high-speed processing and irregular-structure samples. This paper explores the understanding of the depth-dependent dispersion in the fractional Fourier domain (FRFD) and addresses a new method for dispersion correction based on the FRFD stepped detection algorithm that is able to adaptively compensate the dispersion at all depths of the sample. For the detection of each dispersion component, a coarse search followed by a localized fine search is presented in our algorithm to reduce the calculation complexity with high accuracy guaranteed. A signal separation method utilizing FRFD filtering is also designed to avoid the interference between the dispersion from different depths of the sample, which allows all-depth dispersion correction. The proposed algorithm is verified to be effective through the stratified media of ZnSe. The application of the proposed algorithm in OCT imaging of onion and human coronary artery also demonstrates the feasibility of our algorithm for dispersion correction in bio-tissues.

Onion Hybrid Seed Production: Relation with Nectar Composition and Flower Traits.

Onion (Allium cepa L.) is one of the main vegetable crops. Pollinators are required for onion seed production, being honeybees the most used. Around the world, two types of onion varieties are grown: open pollinated (OP) and hybrids. Hybrids offer numerous advantages to growers, but usually have lower seed yields than OP cultivars, which in many cases compromise the success of new hybrids. As pollination is critical for seed set, understanding the role of floral rewards and attractants to pollinator species is the key to improve crop seed yield. In this study, the correlation of nectar-analyzed compounds, floral traits, and seed yield under open field conditions in two experimental sites was determined. Nectar composition was described through the analysis of sugars, phenol, and alkaloid compounds. Length and width of the style and tepals of the flowers were measured to describe floral traits. Floral and nectar traits showed differences among the studied lines. For nectar traits, we found a significant influence of the environment where plants were cultivated. Nonetheless, flower traits were not influenced by the experimental sites. The OP and the male-sterile lines (MSLs) showed differences in nectar chemical composition and floral traits. In addition, there were differences between and within MSLs, some of which were correlated with seed yield, bringing the opportunity to select the most productive MSL, using simple determinations of morphological characters like the length of the style or tepals size.

Identifying subcellular protein localization with fluorescent protein fusions after transient expression in onion epidermal cells.

Most biochemical functions of plant cells are carried out by proteins which act at very specific places within these cells, for example, within different organelles. Identifying the subcellular localization of proteins is therefore a useful tool to narrow down the possible functions that a novel or unknown protein may carry out. The discovery of genetically encoded fluorescent markers has made it possible to tag specific proteins and visualize them in vivo under a variety of conditions. This chapter describes a simple method to use transient expression of such fluorescently tagged proteins in onion epidermal cells to determine their subcellular localization relative to known markers.

High-pressure freezing and low-temperature processing of plant tissue samples for electron microscopy.

Use of electron tomography methods improves image resolution of transmission electron microscopy especially in the z-direction, enabling determination of complicated 3D structures of organelles and cytoskeleton arrays. The increase in resolution necessitates preservation of cellular structures close to the native states with minimum artifacts. High-pressure freezing (HPF) that immobilizes molecules in the cell instantaneously has been used to avoid damages caused by convention chemical fixation. Despite the advantages of HPF, cells could still be damaged during dissection prior to HPF. Therefore, it is critical to isolate cells/tissues of interest quickly and carefully. The samples frozen by HPF are often processed by freeze substitution (FS), and FS should be carried out under appropriate conditions. Here we describe dissection, HPF, and FS methods that we have utilized to prepare plant samples for electron tomography/immuno-electron microscopy.

The effect of cultivar, sowing date and transplant location in field on bolting of Welsh onion (Allium fistulosum L.).

BACKGROUND: Bolting reduces the quality and commercial yield of Welsh onion (Allium fistulosum L.) in production. However, seed production is directly dependent on flower induction and bolting. The Welsh onion belongs to the green plant vernalisation type, specific seedling characteristics and sufficient accumulated time at low temperature are indispensible for the completion of its vernalisation process. Only if these conditions for vernalisation are fulfilled, the plants will bolt in the following year. The present investigation evaluated the effects of cultivar, sowing date and transplant location in field on the bolting of Welsh onion at the Horticultural Farm of the College of Horticulture, Northwest A&F University, Yangling, Shannxi Province, China in two succeeding production years: 2010-2011 and 2011-2012. A strip split plot layout within a randomised complete block design with three replications was used. RESULTS: The results revealed that all three factors (cultivar, sowing date and transplant location) and their interaction had significant effects on the initiation and final rate of bolting observed by 30 April. The earliest bolting date (14 February, 2011 and 15 February, 2012) and the highest bolting rate (100% in 2011 and 62% in 2012) occurred when the JinGuan cultivar was sown on 20 August and transplanted in a plastic tunnel, whereas the latest date and lowest rate (no bolting observed until 30 April) of bolting occurred when the XiaHei cultivar was sown on 29 September and transplanted in an open field. CONCLUSIONS: These results suggest that we can control bolting in Welsh onion production by choosing an appropriate cultivar, sowing date and transplant location. Choosing a late bolting cultivar, such as cultivar XiaHei, sowing around October, and transplanting in the open field can significantly delay bolting, while a sowing date in late August should be selected for seed production, and the seedlings should be transplanted in a plastic tunnel to accelerate development of the flower buds.

Megahertz streak-mode Fourier domain optical coherence tomography.

Here we present an ultrahigh-speed Fourier-domain optical coherence tomography (OCT) that records the OCT spectrum in streak mode with a high-speed area scan camera, which allows higher OCT imaging speed than can be achieved with a line-scan camera. Unlike parallel OCT techniques that also use area scan cameras, the conventional single-mode fiber-based point-scanning mechanism is retained to provide a confocal gate that rejects multiply scattered photons from the sample. When using a 1000 Hz resonant scanner as the streak scanner, 1,016,000 A-scans have been obtained in 1 s. This method's effectiveness has been demonstrated by recording in vivo OCT-image sequences of embryonic chick hearts at 1000 frames/s. In addition, 2-megahertz OCT data have been obtained with another high speed camera.

Standardization of bulb and root sample sizes for the Allium cepa test.

Although the Allium cepa test has been widely used to identify potentially cytotoxic and genotoxic pollutants in aquatic environments, variable non-standardized choices have been made regarding the number of plant bulbs and roots analyzed. We propose numbers for bulbs and roots per bulb when comparing the frequencies of micronuclei, mitotic anomalies and mitotic index with this test. Roots that had been treated with aqueous solutions, such as water samples collected in August 2007 from the Paraíba do Sul River at the Brazilian cities of Tremembé and Aparecida; negative and positive controls were used for bioassays. The presence of pollutants in the river water had been presumed based on our previous cytological data and an official report by the São Paulo State Environmental Agency (Brazil) on presence of fecal contaminants (Tremembé and Aparecida) and elevated dissolved aluminium (Aparecida) in the water under study. The sampling of ten bulbs and five roots per bulb was found adequate for comparative studies to evaluate with the A. cepa test the potential damage inflicted by pollutants in aquatic environments. Furthermore, even one bulb and one root per bulb was sufficient in discerning this damage, thereby shortening the time required to attain a statistically confident comparative evaluation. However, to allow for the use of statistical programs based on the evaluation of average values, and to avoid criticism based on genetic variability, we propose that three bulbs and three roots per bulb be considered as standard sample sizes for the A. cepa test.

Transport of intensity phase imaging in a volume holographic microscope.

We demonstrate a method for single-shot quantitative phase imaging based on the transport of intensity equation (TIE) in a volume holographic microscope (VHM). The VHM system uses a multiplexed volume hologram to laterally separate images from different focal planes. This axial intensity information is then used to solve the TIE and recover object phase quantitatively. Further, we show improved phase recovery by using five multiplexed gratings in one hologram.

Salt-induced abnormalities on root tip mitotic cells of Allium cepa: prevention by inositol pretreatment.

Salt-induced growth reduction of plants is a well-known phenomenon which poses major problem in crop productivity in places where vast majority of land plants are affected by salt. In this report, studies were carried out to reveal the effect of salt injury on the cell division pattern in roots and the role of myo-inositol in preventing the salt-induced ion disequilibrium on the chromosome and DNA degradation in roots. Present study revealed induction of various chromosomal abnormalities on the root tip mitotic cells of Allium cepa by treatment with different concentrations of NaCl (0-500 mM) for 24 h as also the amelioration of such effect by prior treatment of the roots with different concentration of myo-inositol (0-300 mM). Results showed that a narrow albeit definite range of extracellular myo-inositol (100-150 mM) is effective in preventing internucleosomal fragmentation which is the early response in roots under salt stress. Transgenic tobacco plants overexpressing Oryza (OsINO1) as well as Porteresia (PcINO1) cytosolic L: -myo-inositol-1-phosphate synthase coding genes can withstand and retain their chromosomal and DNA integrity in 100 mM NaCl solution and can subsequently prevent DNA fragmentation, caused by intracellular endonuclease activity at this salt concentration.

Analysis of the metabolites in apical area of Allium cepa roots by high resolution NMR spectroscopy method.

Elucidation of the molecular mechanisms determining the formation of various tissues and organs is one of the central problems of cell biology. High-resolution NMR spectroscopy was applied for the analysis of the metabolites produced at the various areas of the apical part of the onion Allium cepa roots. To this end, three samples were extracted from the root apex (the root cap, the meristem region and the cell elongation zone). These samples were noticeably different in the number of mitoses and the sets of metabolites. Furthermore, the complete stasis of the plant roots and tops growth was registered in heavy water. Comparison of the morphological and NMR data revealed their perfect agreement with the cellular processes occurring in the root apex. The root cap sample was characterized by the greatest mitotic activity reflected in the great variability of the chemical compounds extracted from this area, the high level of energy consumption, and the increased synthesis of the phosphocholines needed for the cell fission. Sample containing the cell elongation zone possessed the high sugar content, which is required for the cell-wall growth. Therefore, our data show that high-resolution NMR spectroscopy can be used for the identification of chemical compounds in the various regions of the onion root apical area.

Identification of two novel inactive DFR-A alleles responsible for failure to produce anthocyanin and development of a simple PCR-based molecular marker for bulb color selection in onion (Allium cepa L.).

Two novel inactive alleles of Dihydroflavonol 4-reductase-A (DFR-A) were identified in yellow onion (Allium cepa L.) cultivars and breeding lines from Korea and Japan. Unlike the previously reported inactive yellow DFR-A allele, designated as DFR-A ( TRN ) , in which the 3' portion of the coding sequences was deleted, an allele containing a premature stop codon, DFR-A ( PS ) , was isolated from the majority of cultivars. Co-segregation of DFR-A ( PS ) and color phenotypes in the F(2) population from a cross between yellow and red parents showed that inactivation of DFR-A was responsible for lack of anthocyanin in these yellow onions. In addition, RT-PCR analysis of F(2) population showed that the transcription level of the DFR-A ( PS ) allele was significantly reduced owing to non-sense-mediated mRNA decay. A 20-bp deletion of a simple sequence repeat in the promoter region of the DFR-A ( PS ) allele was used to develop a simple PCR-based molecular marker for selection of the DFR-A ( PS ) allele. All genotypes of 138 F(2) individuals were clearly distinguished by this molecular marker. In addition to the DFR-A ( PS ) allele, another DFR-A allele, DFR-A ( DEL ) , was identified in some cultivars. In case of the DFR-A ( DEL ) allele, no PCR products were amplified throughout DFR-A sequences including promoter regions, suggesting deletion of the entire DFR-A gene. Co-segregation of the absence of DFR-A and color phenotypes was confirmed in another F(2) population. Furthermore, RT-PCR results showed that no DFR-A transcript was detected in any yellow F(2) individuals.

Inner epidermis of onion bulb scale: As natural support for immobilization of glucose oxidase and its application in dissolved oxygen based biosensor.

Inner epidermal membrane of the onion bulb scales was studied as a natural polymer support for immobilization of the glucose oxidase (GOD) enzyme for biosensor application. Onion epidermal membrane was used for immobilization of glucose oxidase and was associated with dissolved oxygen (DO) probe for biosensor reading. Glucose was detected on the basis of depletion of oxygen, when immobilized GOD oxidizes glucose into gluconolactone. A wide detection range between 22.5 and 450 mg/dl was estimated from calibration plot. A single membrane was reused for 127 reactions with retention of approximately 90% of its initial enzyme activity. Membrane was stable for 45 days ( approximately 90% activity) when stored in buffer at 4 degrees C. Surface structure studies of the immobilized membranes were carried under SEM. To our knowledge, this is the first report on employing inner epidermal membrane of onion bulb scales as the solid support for immobilization of enzyme.

Effects of mycorrhizal colonization on growth parameters of onion under different irrigation and soil conditions.

The effects of three Arbuscular Mycorrhizal Fungi (AMF), Glomus versiforme, G. intraradices and G. etonicatum) and three irrigation intervals (7, 9 and 11 days) on growth of onion (Allium cepa L.) cv. Red Azar Shahr were studied under two soil conditions (sterilized and non-sterilized). The results indicated that, AMF colonization improved plant height, Leaf Area Index (LAI), total biomass, bulb dry mass and diameter, Harvest Index (HI) and chlorophyll content (p < 0.001). Bulbing occurred 10-15 days earlier in mycorrhizal plants. Irrigation interval decreased biomass, LAI, Leaf Area Ratio (LAR), bulb diameter and dry mass and chlorophyll content (b and total) at 11 day irrigation interval. In term of interaction, G. versiforme at 9 day and non-mycorrhizal plants at 11 day produced the greatest and the lowest LAI (8.56 vs. 1.57), respectively. Mycorrhizal onions in contrary to non-mycorrhizal ones produced more LAI and biomass in sterilized soil and inoculation with G. etonicatum and the non-mycorrhizal onions in sterilized soil had the highest and the lowest biomass, respectively.

Genetic mapping of a major gene affecting onion bulb fructan content.

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry matter storage onion varieties and sweet, low dry matter varieties. When samples were analysed on a dry weight basis, reducing sugar and fructan content exhibited high negative correlations and bimodal segregation suggestive of the action of a major gene. A polymorphic SSR marker, ACM235, was identified which exhibited strong disequilibrium with bulb fructan content in F(2:3) families from the 'W202A' x 'Texas Grano 438' mapping population evaluated in two environments. This marker was mapped to chromosome 8 in the interspecific population 'Allium cepa x A. roylei'. Mapping in the 'Colossal Grano PVP' x 'Early Longkeeper P12' F2 population showed that a dominant major gene conditioning high-fructan content lay in the same genomic region. QTL analysis of total bulb fructan content in the intraspecific mapping population 'BYG15-23' x 'AC43' using a complete molecular marker map revealed only one significant QTL in the same chromosomal region. This locus, provisionally named Frc, may account for the major phenotypic differences in bulb carbohydrate content between storage and sweet onion varieties.

Salicylic acid triggers genotoxic adaptation to methyl mercuric chloride and ethyl methane sulfonate, but not to maleic hydrazide in root meristem cells of Allium cepa L.

Salicylic acid (SA), 0.01 mM, a signalling phytohormone, was tested for induction of adaptive response against genotoxicity of methyl mercuric chloride (MMCl), 0.013 mM; ethylmethane sulfonate (EMS), 2.5 mM, or maleic hydrazide (MH), 5 mM, in root meristem cells of Allium cepa. Induction of adaptive response to EMS by hydrogen peroxide (H2O2), 1 mM, and yet another secondary signal molecule was tested for comparison. Assessed by the incidence of mitoses with spindle and/or chromosome aberration and micronucleus, the findings provided evidence that SA-conditioning triggered adaptive response against the genotoxic-challenges of MMCl and EMS, but failed to do so against MH. H2O2, which is known to induce adaptive response to MMCl and MH, failed to induce the same against EMS in the present study. The findings pointed to the possible role of signal transduction in the SA-induced adaptive response to genotoxic stress that perhaps ruled out an involvement of H2O2.

Spectral shaping to improve the point spread function in optical coherence tomography.

We demonstrate inhibition of the sidelobes of the axial point spread function in optical coherence tomography by shaping the power spectrum of the light source with a remaining power of 4.54 mW. A broadband amplified spontaneous emission source radiating at 1565 +/- 40 nm is employed in a free-space optical coherence tomography system. The axial point spread functions before and after optical spectral shaping are presented. Results show that spectral shaping of the source can inhibit sidelobes of the point spread function up to 12.9 dB, with an associated small increase of 2.2 dB in noise floor in the far field. The effect of spectral shaping on axial resolution is demonstrated according to three metrics. Image quality improvement is also illustrated with optical coherence tomography images of an onion before and after spectral shaping.

The role of root system architecture and root hairs in promoting anchorage against uprooting forces in Allium cepa and root mutants of Arabidopsis thaliana.

The role played by lateral roots and root hairs in promoting plant anchorage, and specifically resistance to vertical uprooting forces has been determined experimentally. Two species were studied, Allium cepa (onion) which has a particularly simple root system and two mutants of Arabidopsis thaliana, one without root hairs (rhd 2-1) and another with reduced lateral root branching (axr 4-2). Maximum strength of individual onion roots within a plant increased with plant age. In uprooting tests on onion seedlings, resistance to uprooting could be resolved into a series of events associated with the breakage of individual roots. Peak pulling resistance was explained in a regression model by a combination of a measure of plant size and the extent to which the uprooting resistance of individual roots was additive. This additive effect is termed root co-operation. A simple model is presented to demonstrate the role played by root co-operation in uprooting resistance. In similar uprooting tests on Arabidopsis thaliana, the mutant axr 4-2, with very restricted lateral development, showed a 14% reduction in peak pulling resistance when compared with the wild-type plants of similar shoot dry weight. The uprooting force trace of axr 4-2 was different to that of the wild type, and the main axis was a more significant contributor to anchorage than in the wild type. By contrast, the root hair-deficient mutant rhd 2-1 showed no difference in peak pulling resistance compared with the wild type, suggesting that root hairs do not normally play a role in uprooting resistance. The results show that lateral roots play an important role in anchorage, and that co-operation between roots may be the most significant factor.

Clastogenicity of pentachlorophenol, 2,4-D and butachlor evaluated by Allium root tip test.

The meristematic mitotic cells of Allium cepa is an efficient cytogenetic material for chromosome aberration assay on environmental pollutants. For assessing genotoxicity of pentachlorophenol (PCP), 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-chloro-2,6-diethyl-N-(butoxymethyl) acetanilide (butachlor), 50% effective concentration (EC(50)), c-mitosis, stickiness, chromosome breaks and mitotic index (MI) were used as endpoints of genotoxicity. EC(50) values for PCP and butachlor are 0.73 and 5.13 ppm, respectively. 2,4-D evidently induced morphological changes at higher concentrations. Some changes like crochet hooks, c-tumours and broken roots were unique to 2,4-D at 5-20 ppm. No such abnormalities were found in PCP and butachlor treated groups, however, root deteriorated and degenerated at higher concentrations (<3 ppm) in PCP. MI in 2,4-D showed a low average of 14.32% followed by PCP (19.53%), while in butachlor it was recorded 71.6%, which is near to the control value. All chemicals induced chromosome aberrations at statistically significant level. The highest chromosome aberration frequency (11.90%) was recorded in PCP at 3 ppm. Large number of c-mitotic anaphases indicated that butachlor acts as potent spindle inhibitor, whereas, breaks, bridges, stickiness and laggards were most frequently found in PCP showing that it is a potent clastogen.

Radial hydraulic conductivity along developing onion roots.

Although most studies have shown that water uptake varies along the length of a developing root, there is no consistent correlation of this pattern with root anatomy. In the present study, water movement into three zones of onion roots was measured by a series of mini-potometers. Uptake was least in the youngest zone (mean hydraulic conductivity, Lpr = 1.5 x 10(-7) +/- 0.34 x 10(-7) m MPa-1 s-1; +/- SE, n = 10 roots) in which the endodermis had developed only Casparian bands and the exodermis was immature. Uptake was significantly greater in the middle zone (Lpr = 2.4 x 10(-7) +/- 0.43 x 10(-7) m MPa-1 s-1; +/- SE, n = 10 roots) which had a mature exodermis with both Casparian bands and suberin lamellae, and continued at this level in the oldest zone in which the endodermis had also developed suberin lamellae (Lpr = 2.8 x 10(-7) +/- 0.30 x 10(-7) m MPa-1 s-1; +/- SE, n = 10 roots). Measurements of the hydraulic conductivities of individual cells (Lp) in the outer cortex using a cell pressure probe indicated that this parameter was uniform in all three zones tested (Lp = 1.3 x 10(-6) +/- 0.01 x 10(-6) m MPa-1 s-1; +/- SE, n = 60 cells). Lp of the youngest zone was lowered by mercuric chloride treatment, indicating the involvement of mercury-sensitive water channels (aquaporins). Water flow in the older two root zones measured by mini-potometers was also inhibited by mercuric chloride, despite the demonstrated impermeability of their exodermal layers to this substance. Thus, water channels in the epidermis and/or exodermis of the older regions were especially significant for water flow. The results of this and previous studies are discussed in terms of two models. The first, which describes maize root with an immature exodermis, is the 'uniform resistance model' where hydraulic resistances are evenly distributed across the root cylinder. The second, which describes the onion root with a mature exodermis, is the 'non-uniform resistance model' where resistances can be variable and are concentrated in a certain layer(s) on the radial path.