A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population

With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. As an important crop and a model organism, rice provides major insights into gene functions important for crop growth or production. Phenomics with detailed information about tagged populations provides a good tool for functional genomics analysis. By a T-DNA insertional mutagenesis approach, we have generated a rice mutant population containing 55,000 promoter trap and gene activation or knockout lines. Approximately 20,000 of these lines have known integration sites. The T0 and T1 plants were grown in net "houses" for two cropping seasons each year since 2003, with the mutant phenotypes recorded. Detailed data describing growth and development of these plants, in 11 categories and 65 subcategories, over the entire four-month growing season are available in a searchable database, along with the genetic segregation information and flanking sequence data. With the detailed data from more than 20,000 T1 lines and 12 plants per line, we estimated the mutation rates of the T1 population, as well the frequency of the dominant T0 mutants. The correlations among different mutation phenotypes are also calculated. Together, the information about mutant lines, their integration sites, and the phenotypes make this collection, the Taiwan Rice Insertion Mutants (TRIM), a good resource for rice phenomics study. Ten T2 seeds per line can be distributed to researchers upon request.

A rice gene activation/knockout mutant resource for high throughput functional genomics

Using transfer DNA (T-DNA) with functions of gene trap and gene knockout and activation tagging, a mutant population containing 55,000 lines was generated. Approximately 81% of this population carries 1-2 T-DNA copies per line, and the retrotransposon Tos17 was mostly inactive in this population during tissue culture. A total of 11,992 flanking sequence tags (FSTs) have been obtained and assigned to the rice genome. T-DNA was preferentially ( approximately 80%) integrated into genic regions. A total of 19,000 FSTs pooled from this and another T-DNA tagged population were analyzed and compared with 18,000 FSTs from a Tos17 tagged population. There was difference in preference for integrations into genic, coding, and flanking regions, as well as repetitive sequences and centromeric regions, between T-DNA and Tos17; however, T-DNA integration was more evenly distributed in the rice genome than Tos17. Our T-DNA contains an enhancer octamer next to the left border, expression of genes within genetics distances of 12.5 kb was enhanced. For example, the normal height of a severe dwarf mutant, with its gibberellin 2-oxidase (GA2ox) gene being activated by T-DNA, was restored upon GA treatment, indicating GA2ox was one of the key enzymes regulating the endogenous level of GA. Our T-DNA also contains a promoterless GUS gene next to the right border. GUS activity screening facilitated identification of genes responsive to various stresses and those regulated temporally and spatially in large scale with high frequency. Our mutant population offers a highly valuable resource for high throughput rice functional analyses using both forward and reverse genetic approaches.

Computer-assisted automatic peak recognition and result evaluation for analysis of chlorinated hydrocarbons in environmental samples

A data manipulation method has been developed for automatic peak recognition and result evaluation in the analysis of organic chlorinated hydrocarbons with dual-column gas chromatography. Based on the retention times of two internal standards, pentachlorotoluene and decachlorobiphenyl, the retention times of chlorinated hydrocarbons can be calibrated automatically and accurately. It is very convenient to identify the peaks by comparing the retention times of samples with the calibrated retention times calculated from the relative retention indices of standards. Meanwhile, with a suggested two-step evaluation method the evaluation coefficients and the suitable quantitative results of each component can be automatically achieved for practical samples in an analytical system using two columns with different polarities and two internal standards.

A reevaluation and discussion on the threshold limit for hemolysis in a turbulent shear flow

One major factor of red blood cell damage induced by artificial heart valves is the magnitude of turbulent shear stresses in the flow field. An often-cited threshold for hemolysis is 400 N/m(2) (Sallam and Hwang, Biorheology 21 (1984) 783). This value, however, was measured with a one-component laser Doppler anemometer and was not calculated from the major principal Reynolds shear stress, therefore underestimating the threshold. This study performed flow field measurements under similar conditions, using a two-component laser Doppler anemometer and determining major principal Reynolds shear stress, to reevaluate the hemolytic threshold as 800 N/m(2) with an exposure time of 1 ms. The Kolmogorov length scales, approximately 9 microm, are capable of inflicting direct damage to the red blood cells. These results will serve as a more accurate reference in future heart valve design and testing.

Posterior corneal surface changes after refractive surgery

OBJECTIVE

To determine the frequency of changes in posterior corneal surface after laser in situ keratomileusis (LASIK) and photorefractive keratectomy (PRK).

DESIGN

Nonrandomized, comparative trial.

PARTICIPANTS

Ninety-five eyes (71 patients) that underwent PRK (n = 45) or LASIK (n = 50).

CONTROLS

Twenty nonsurgery eyes were used to validate the method of analysis of the posterior corneal curvature (PCC). Seventy nonsurgery eyes were used for comparisons.

METHODS

Float, apex-fixed best fit corneal curvature (ABC), and posterior elevation difference were evaluated in 20 elevation topography maps at 6 zone diameters (3-7 and 10 mm) and at two time points. Corneal elevation maps before and after PRK or LASIK were analyzed by the ABC and float methods and compared with a nonsurgery group.

MAIN OUTCOME MEASURES

Posterior corneal curvature change (mm) was classified as flattening, steepening, or no change.

RESULTS

Flattening of more than 0.12 mm was found in 22.2% of eyes (n = 10) in the PRK group, a change of +/-0.12 mm was found in 53.3% of eyes (n = 24), and steepening of more than 0.12 mm was found in 24.4% of eyes (n = 11) using the float method and in 28.9% of eyes (n = 13), 35.6% of eyes (n = 16), and 35.6% eyes (n = 16), respectively, using the ABC method. In the LASIK group, the float method registered flattening in 20% of eyes (n = 10), no change in 52% of eyes (n = 26), and steepening in 28% of eyes (n = 14), whereas the ABC method registered flattening in 30% of eyes (n = 15), no change in 40% of eyes (n = 20), and steepening in 30% of eyes (n = 15). The nonsurgery group showed a similar change in PCC at two different time points similar to that of the PRK and the LASIK groups.

CONCLUSIONS

The differences observed in the PCC after PRK or LASIK were not statistically significantly different from those observed over time in the nonsurgery control group.

Turbulence characteristics downstream of bileaflet aortic valve prostheses

This study was focused on a series of in vitro tests on the turbulent flow characteristics of three bileaflet aortic valves: St. Jude Medical (SJM), CarboMedics (CM), and Edwards Tekna (modified Duromedics, DM). The flow fields of the valves were measured in a pulsatile flow model with a laser-Doppler anemometer (LDA) at the aortic sinus area downstream of the valves. The heart rate was set at 70 beats per minute, the cardiac output was maintained at 5 liters per minute, and the aortic pressure wave forms were kept within the physiological range. Cycle-resolved analysis was applied to obtain turbulence data, including mean velocity, Reynolds stresses, autocorrelation coefficients, energy spectral density functions, and turbulence scales. The Reynolds shear stresses of all three valves induced only minor damage to red blood cells, but directly damaged the platelets, increasing the possibility of thrombosis. The smallest turbulence length scale, which offers a more reliable estimate of the effects of turbulence on blood cell damage, was three times the size of red blood cells and five times the size of platelets. This suggests that there is more direct interaction with the blood cells, thus causing more damage.

Prevalence of pre-eruptive intracoronal dentin defects from panoramic radiographs

PURPOSE

This investigation stemmed from preliminary clinical observations from a school dental clinic, which suggested that a proportion of clinically undetected, radiolucent lesions on radiographs may originate as pre-eruptive intracoronal dentin defects. This study investigated the prevalence of such defects in orthopantomograms from a group of children and young adults.

METHODS

A total of 1281 orthopantomograms with 11,767 unerupted permanent teeth were examined.

RESULTS

The prevalence of intracoronal dentin defects was 3% by subjects, and 0.5% by teeth; the highest prevalence being noted in the maxillary and mandibular first permanent molars. Most of the lesions occurred singly, and nearly half had extended to greater than two-thirds the width of dentin thickness. Ectopic positioning was significantly associated with this lesion.

CONCLUSIONS

Pre-eruptive intracoronal dentin defects occur at a significant prevalence rate. Increased awareness of this entity may improve diagnosis and allow early treatment.

Immunolocalization and gene expression of matrilysin during corneal wound healing

PURPOSE

To investigate the protein level of matrilysin and stromelysin-1 and the gene expression of matrilysin in rat corneas after excimer keratectomy using immunofluorescence staining, reverse transcriptase-polymerase Chain Reaction (RT-PCR), and in situ hybridization.

METHODS

Rat corneas were treated with 3-mm excimer laser keratectomy (193-nm ArF). Unwounded corneas served as controls. Confocal microscopy was used to immunolocalize matrilysin protein at 6 hours, 1 day, 3 days, 1 week, 4 weeks, and 8 weeks after surgery. RT-PCR was performed to analyze matrilysin mRNA in unwounded controls and in 3-day wounded corneas. In situ hybridization was performed to localize matrilysin mRNA.

RESULTS

Matrilysin was immunolocalized to the epithelial layers of unwounded and wounded corneas, predominantly to the leading edge at 6 hours and 1 day after wounding and to the epithelial layer at 3 to 7 days after surgery. Stromelysin-1 was expressed in the deep stromal layer in the first 3 days after wounding and in the area of newly synthesized stromal matrix 1 week after surgery. Upregulation of matrilysin expression 3 days after wounding was confirmed by RT-PCR. In situ hybridization revealed that the gene expression of matrilysin in rat corneas was upregulated during the migration phase (6 hours, 1 day) and that matrilysin mRNA was predominantly localized to the basal cell layers during the subsequent cell proliferation phase (7 and 14 days).

CONCLUSIONS

Basal epithelial cells express matrilysin during the migration proliferation phase of corneal wound healing after excimer keratectomy.

Immunoconfocal localization of gelatinase B expressed by migrating intrastromal epithelial cells after deep annular excimer keratectomy

PURPOSE

Intrastromal epithelial migration occurs following deep excimer annular keratectomy. Our purpose is to determine the localization of gelatinase B expression and its relationship to migrating intrastromal epithelial cells following deep annular excimer keratectomy.

METHODS

Rabbit corneas were treated with deep annular ablation and harvested 3, 5, 7 and 14 days following surgery. Histological examination was performed. Confocal microscopy was used to determine the time and the pattern of gelatinase B expression. This was compared to AE-5, vimentin, and alpha-smooth muscle actin immunolocalization.

RESULTS

Histologic examination revealed islands of epithelial cells within the corneal stroma after deep annular excimer ablation, whereas eyes treated with superficial annular keratectomy did not show intrastromal epithelial migration. Immunoconfocal microscopy using monoclonal anti-matrix metalloproteinase-9 (MMP-9) antibody demonstrated the presence of gelatinase B at the outer borders of the intrastromal epithelial islands following deep annular excimer keratectomy.

CONCLUSION

Gelatinase B may be involved in the process of intrastromal epithelial migration following deep annular excimer keratectomy.

Flavobacterium indologenes keratitis

Flavobacterium indologenes has recently been implicated in nosocomial or opportunistic infection. It has been isolated from lids, conjunctiva, and lacrimal system, and is resistant to most antibiotics. No previous cases of F. indologenes corneal ulcer have been reported in the literature. The natural habitat of Flavobacteria is soil, water, plants, and foodstuffs. In the hospital environment, these bacteria exist in water systems and on wet surfaces. They are not part of the normal ocular flora.

Computer-assisted peak recognition for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) in environmental samples

A software has been developed for the peak recognition of 136 polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) after high resolution gas chromatography coupled with mass spectrometry (HRGC/HRMS). Based on the retention times of (13)C labelled 2,3,7,8-substituted PCDD/F internal standards, the retention times of all PCDD and PCDF can be calibrated automatically and accurately. Therefore, it is very convenient to identify the peaks by comparing the retention of samples and the calibrated retention times of their chromatograms. Hence, this approach is very significant because it is impossible to obtain always a standard chromatogram and PCDD/F analysis are very expensive and time consuming. The calibration results can be transferred to Excel for calculation. The approach is a first step to store costly and environmentally relevant data for future application.

High performance liquid chromatographic determination of individual bile acids in serum for automatic diagnosis of various liver and biliary diseases

A reversed phase high performance liquid chromatographic method for the high sensitivity determination of individual bile acids in serum using a C18 column with a ternary solvent system combined with fluorometric techniques using immobilized enzymes is described. A computer-assisted diagnosis system using pattern recognition was developed to assist the clinical diagnosis of various liver and biliary diseases. A total consistency rate of 95% can be reached using this system.

The retention behaviour of conjugated bile acids in reversed phase high performance liquid chromatography

The retention behaviour of conjugated bile acids has been studied in a reversed phase high performance liquid chromatographic (RP-HPLC) system by using the mixture of methanol and aqueous phosphate buffer as the mobile phase. The retentions of the conjugates in RP-HPLC have been found to be mainly controlled by the glycine and taurine groups. The selectivity between five different glycine and taurine conjugated bile acids is a constant in RP-HPLC. This selectivity has been used for peak identification in the practical separation of conjugated bile acids.

A health hazard assessment in school arts and crafts

Unlike the cautious attitude being exercised toward generic chemicals, an off-guard behavior is often observed toward the same chemicals once they are recognized as a "common daily item." Students and instructors of arts and crafts classes alike are often unaware of the potential risks from exposure to some of the arts and crafts materials they use due to either the false security of "common daily item" or the lack of specific knowledge of the hazardous ingredients in those products. This unawareness of potential health hazards could lead to improper handling of these materials and result in unnecessary health risk during their use. A three-year study of college arts and crafts class students indicates a high incidence of allergic reactions among attending students for exposure of less than 70 hours within a period of 7 weeks. A self-evaluation method is developed to identify and minimize these health hazards associated with arts and crafts classes. This checklist of 15 pertinent parameters covers identifiable hazardous areas and situations in arts and crafts classrooms. Record keeping and promotion of student awareness are also addressed, so that instructors and students in an arts and crafts class can more readily recognize actual or potential hazards and act to prevent them.

[Experimental studies on immunostimulatory effects of the Isatis indigotica polysaccharide]

Polysaccharides extracted from the root of Isatis indigotica (IIP, 50 mg/kg.d, ipx8d) significantly increased the weight of spleen and number of white blood cell and lymphocyte in peripheral blood in normal ICR mice, and antagonized the immunosuppressive actions of hydrocortisone. There were marked potentiating effects on delayed hypersensitivity reaction induced by 2, 4-dinitrochlorobenzene in normal NIH mice treated with IIP as well as in immunodepressed mice induced by cyclophosphamide. By administration of IIP, the percentage of ANAE+ lymphocytes stained with acid alpha-naphthyl acetate esterase method were significantly increased in peripheral blood of normal ICR mice, and the decreases in number of ANAE+ lymphocytes in mice induced by hydrocortisone were prevented to a certain extent. But IIP could not enhance Con A-induced lymphocyte proliferation of C57BL mouse spleen cells in vitro measured with MTT colorimetric assay. In addition, the plaque forming cells in 5 x 10(6) splenocytes of NIH mice treated with IIP were higher than that of the control group (P less than 0.01). IIP could also elevate the clearance rate of intra-venous charcoal particles in normal mice, i.e., stimulated the phagocytic activity of macrophages. The result indicates that IIP is capable of increasing humoral and cellular immune functions and enhancing the functions of reticuloendothelial system, and might be a good immunopotentiator.

[Pharmacological localization of Horner's syndrome. Case report]

Horner's syndrome is derived from an interruption of the sympathetic pathway at any point along its course between the hypothalamus and the orbit. This pathway is generally considered to consist of three neurons. It had been suggested that the pupillary response to various pharmacologic agents will aid in localizing the lesioned neuron in the sympathetic pathway. We had the opportunity to observe a patient who developed Horner's syndrome as a consequence of pulmonary apex adenocarcinoma. Clinical, radiologic and pharmacologic studies are presented. The methods of pharmacologic localization are discussed.

A model investigation of the velocity and pressure spectra in vascular murmurs

A physical model consisting of an axisymmetrical jet in a rigid plexiglass pipe was used to study the flow and pressure fluctuations downstream from an aortic stenosis. The fluctuating velocity components, u and v, at several locations in the steady liquid jet were measured using a laser Doppler anemometer system. Simultaneous wall pressure fluctuations were monitored by an array of nine miniature pressure transducers wall mounted in the axial direction. This paper presents the detailed measurements of mean velocity profiles, turbulent intensity distributions and RMS pressure fluctuations. The energy spectra obtained for the pressure fluctuations and the u and v velocity components are compared. Contrary to earlier works, we found that the differences between peak frequencies of the pressure spectra and the characteristic frequencies of the velocity spectra vary with positions downstream from the nozzle. These differences are discussed in light of pseudosound generation by the eddy structures in the stenotic flow field.

Physical characteristics of pulmonary artery stenosis murmurs in calves

To better understnad the characteristics of cardiovascular murmurs and turbulent energy transmission, we made simultaneous measurements of pressure (sound) and velocity fluctuations in the vicinity of surgically produced stenoses in the pulmonary artery of calves. We did a spectral analysis of these data and found an identifiable break frequency at which the slopes of the pressure fluctuations changed. By use of these break frequencies and the corresponding blood jet velocity and vessel diameter measurements, Strouhal numbers were calculated. The jet velocity, Reynolds number, Strouhal number, and unsteadiness parameter values changed when the vessel was stenosed. When the power spectrum curves for the velocity fluctuations and the sound were compared, they tended to show a correlation between break frequencies. We speculate that this apparent correlation indicated a transfer from turbulent to acoustic energy.

The theoretical basis of column chromatography in multicomponent separation

Microparticulate packings (silica and chemically bonded silica) developed in our institute and produced in China have been evaluated by the method published previously with a column efficiency of 1,400 to 10,000 theoretical plates per 10 cm length for HPLC and 1,700 to 4,400 plates per 10 cm length for GC. By varying the surface area of silica and composition of the eluent, the linear relationship of capacity factor of various compounds and the high speed chromatograms of HPLC and HPGC have been given.