Fiber Confocal Back-Scattering Micro-Spectral Analysis for Single Cell

A fiber confocal back scattering micro-spectrometer (FCBS) was established, which combined fiber confocal microscopy with light scattering spectroscopy (LSS) for early diagnosis of the cancer cell at cellular level. An adherent monolayer human normal gastric epithelium line GES-1 and a carcinoma cell line NCI-N87 as well as a normal liver cell line L02 and a high-metastatic-potential hepatocellular carcinoma cell line HCC-LM3 were measured respectively. The spectral results showed that micro-back-scattering intensity from GES-1 cell and L02 cell possessed interesting oscillations in contrast to NCI-N87 and HCC-LM3 cells. There was significant difference between the spectra of the normal and the cancer cells (p < 0.001). This demonstrates that the FCBS system here is able to distinguish dysplastic cells from normal cells at cellular level.

First Report of Powdery Mildew on Euphorbia pekinensis Caused by Podosphaera euphorbiae-helioscopiae in China

Euphorbia pekinensis Rupr, the Peking spurge, is a perennial grass that is planted throughout northeast China. Its roots can be used as a Chinese medicine for diuretic or purgative purposes. Some diterpenoids isolated from Euphorbia spp. show strong antitumor, antivirus, skin-irritating, and tumor-promoting activities. Some species contain chemicals that can be used as pesticides. In September and October 2009, spurge plants were seriously infected by powdery mildew fungi in Changchun Agri-Expon, Jilin Province, China. White mildew colonies appeared in early autumn and initial colonies coalesced to cover the entire upper sides of leaves, stems, and petals 3 to 4 weeks after the disease was noticed. Until late October, chasmothecia were observed on leaves and stems and the infected areas also became dark brown. Mycelium was amphigenous, in patches, white, and persistent. Conidia with distinct fibrosin bodies were ellipsoid-cylindrical, 21.6 to 33.8 × 12 to 15.6 μm, and produced in chains. Germ tubes arose near a pole of the conidia and terminated in simple, unlobed apices. Conidiophores were 59.8 to 139.9 μm; foot cells were straight to slightly flexuous, followed by one to three cells, and 24 to 48 × 8.4 to 10.8 μm. Hyphal appressoria were papillate. Chasmothecia were 70 to 95 μm in diameter, averaging 79.4 μm, and were immersed in mycelia. Mycelioid appendages (5 to 12) occurred in the lower part of the chasmothecia and were flexuous, curved, thick walled, and strongly undulate. Appendages were long (349-) 490 to 1,000 (-1,300) μm, averaging 759.4 μm. They were often densely crowded around the chasmothecia. Asci were single, sessile or short stalked, 60 to 80 × 45 to 70 μm, and eight spored. Ascospores were ellipsoid-ovoid and 16.8 to 28.8 × 10.8 to 18 μm. The fungus was identified as Podosphaera euphorbiae-helioscopiae on the basis of morphological characteristics of the anamorphic and teleomorphic stages. An herbarium specimen was deposited in the Herbarium of Mycology of Jilin Agriculture University (CJLCC100). Genomic DNA was extracted from the chasmothecia, and the internal transcribed spacer region (ITS) and the D1/D2 domains of the 28S rDNA were amplified and sequenced (GenBank Nos. JF795490 and JF795491). The ITS sequence has 98% identity with those of Podosphaera lini, P. macularis, and P. spiraeae, and the D1-D2 sequence of 28S rDNA has 99% identity with those of P. negeri and P. spiraeae, which indicated that this fungus belongs to the genus Podosphaera, even though there is no direct sequence evidence that it is P. euphorbiae-helioscopiae. P. euphorbiae-helioscopiae has only been previously reported in Japan (2), occurring on Euphorbia helioscopia. This species is unique because of the long and curved, thick-walled appendages, and there is no comparable species (1). P. euphorbiae-hirtae and P. euphorbiae are reported to infect Euphorbiaceae plants. Both species differ from P. euphorbiae-helioscopiae in their conspicuously shorter appendages (1,3). To our knowledge, this is the first reported occurrence of powdery mildew on E. pekinensis, and P. euphorbiae-helioscopiae is new to China. This is also the first description of the anamorph of the fungus since there is no record in the Erysiphales Database. References: (1) U. Braun. Nova Hedwigia 89:1, 1987. (2) Y. Nomura. Taxonomical Study of Erysiphaceae of Japan. Yokendo LTD, Tokyo, 1997. (3) R. Y. Zheng and Y. N. Yu. Flora Fungorum Sinicorum. Vol. 1. Erysiphales. Science Press, Beijing, 1987.

Expression of interleukin-22 in Sjögren's syndrome: significant correlation with disease parameters

Sjögren's syndrome (SS) is an autoimmune disease targeting the exocrine glands resulting in xerostomia/keratoconjunctivitis sicca. Presently, we examined the levels and clinical correlations of IL-22 in SS. Patients with SS together with normal controls were randomly selected. IL-22 was detected at significantly higher levels in sera of patients with SS. The levels of IL-22 present in sera showed statistically significant direct correlations with hyposalivation, anti-SSB, anti-SSA/SSB combined, hypergammaglobulinemia and rheumatoid factor. IL-22 showed a direct correlation with major clinical parameters. The data suggest that IL-22 plays a critical role in the development of SS, and further study is needed to examine its function in human SS.

Search for CP violation in τ±→K(S)0π±ντ decays at Belle

We report on a search for CP violation in τ(±)→K(S)(0)π(±)ν(τ) decays using a data sample of 699 fb(-1) collected by the Belle experiment at the KEKB electron-positron asymmetric-energy collider. The CP asymmetry is measured in four bins of the invariant mass of the K(S)(0)π(±) system and found to be compatible with zero with a precision of O(10(-3)) in each mass bin. Limits for the CP violation parameter Im(η(S)) are given at the 90% confidence level. These limits are |Im(η(S))| < 0.026 or better, depending on the parametrization used to describe the hadronic form factors, and improve upon previous limits by 1 order of magnitude.

An update on the dosimetric analysis of concurrent radiation therapy and trastuzumab on early cardiac events

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Background: The impact of radiation therapy (RT) with concurrent trastuzumab on early cardiac morbidity is relatively unknown. Trastuzumab’s radiosensitizing properties may augment both early and late effects of RT. This retrospective review update provides an analysis of cardiac event (CE) development in patients treated with concurrent RT and trastuzumab with a focus on RT heart dose.

Methods: Sixty-five patients treated with concurrent RT (30 left, 33 right, 2 bilateral) and trastuzumab at the University of Alabama at Birmingham were identified. Patient data for pre-existing heart disease, cardiac risk factors, drug regimen, and CEs were recorded. Dosimetric parameters of maximum heart dose, mean heart dose, heart volume receiving 5, 10, 15, 20 and 30Gy (V5, V10, V15, V20, V30) were also analyzed. Endpoints include the occurrence of CEs at any time in relation to RT and those specifically after the start of RT.

Results: In addition to receiving trastuzumab, 80% of patients received doxorubicin. 15.4% had preexisting heart disease. The mean heart dose for all patients was 248cGy. With a median follow-up of 24.5 months, six patients developed CEs (9.2%), and three of these cases occurred after RT initiation (4, 4, and 0.5 months post-RT). All six CEs occurred during treatment with trastuzumab and consisted of congestive heart failure. Analysis of the heart dose maximum, mean, V5, V10, V15, and V20, V30 were similar in patients with and without CEs, and small differences between groups did not reach statistical significance. CE incidence was significantly associated with smoking (p=0.0037) but not hypertension, diabetes or pre-existing heart disease.

Conclusions: This updated retrospective dosimetric analysis did not find a correlation between concurrent trastuzumab and RT on the development of early cardiac events. Modern era RT with 3D conformal planning, the use of heart blocks, and breath hold techniques will continue to decrease the dose to the heart. Longer follow-up will be needed for analysis of the impact of modern technologic advances and late cardiac morbidity.

Effective treatment of experimental ragweed-induced asthma with STAT-6-IP, a topically delivered cell-penetrating peptide

BACKGROUND

Treatment of allergic airways disease including asthma remains primarily local immunosuppression with topical corticosteroid and symptomatic management with antihistamines and anti-leucotrienes. We have developed a novel topical therapy designed to specifically inhibit the events associated with Th2 cell activation.

OBJECTIVE

We assessed the efficacy of our cell-penetrating STAT-6 inhibitory peptide (STAT-6-IP), a novel treatment for allergic airways disease, in a model of chronic ragweed-induced asthma.

METHODS

Six- to eight-week-old mice were sensitized over 5 weeks with intranasal (IN) exposures to whole ragweed allergen without adjuvant. Mice were then IN challenged with Amba 1 with and without treatment IN with STAT-6-IP and allergic responses assessed. Two weeks later, some animals were rechallenged with Amba 1 with or without STAT-6-IP.

RESULTS

Animals exposed to IN ragweed developed significant airway hyperresponsiveness and airways inflammation upon challenge. Cell cultures showed increases in Th2 cytokines IL-4 and IL-13. Topical STAT-6-IP treatment reduced production of Th2 cytokines, demonstrated increased expression of IL-10 and reduced frequency of cultured IL-4 positive CD4+ T cells derived from treated mice, suggesting that STAT-6-IP treatment may be immunomodulatory. Airway responsiveness to methacholine challenge in the treatment group was similarly reduced to that of the non-allergic PBS-exposed animals. Importantly, STAT-6-IP-treated mice remained hyporesponsive following second ragweed challenge 2 weeks after treatment.

CONCLUSIONS AND CLINICAL RELEVANCE

These data suggest that topical application of the STAT-6-IP is sufficient to inhibit allergic airways responses in animals chronically sensitized and challenged with ragweed. Data show that a single topical treatment course is sufficient to block signs of allergic responses to ragweed in the airways for at least 2 weeks. STAT-6-IP is a novel potential treatment for chronic allergic asthma.

The use of mouse models to investigate shear bond strength in amelogenesis imperfecta

Patients with amelogenesis imperfecta (AI) have defective enamel; therefore, bonded restorations of patients with AI have variable success rates. To distinguish which cases of AI may have good clinical outcomes with bonded materials, we evaluated etching characteristics and bond strength of enamel in mouse models, comparing wild-type (WT) with those having mutations in amelogenin (Amelx) and matrix metalloproteinase-20 (Mmp20), which mimic 2 forms of human AI. Etched enamel surfaces were compared for roughness by scanning electron microscopy (SEM) images. Bonding was compared through shear bond strength (SBS) studies with 2 different systems (etch-and-rinse and self-etch). Etched enamel surfaces of incisors from Amelx knock-out (AmelxKO) mice appeared randomly organized and non-uniform compared with WT. Etching of Mmp20KO surfaces left little enamel, and the etching pattern was indistinguishable from unetched surfaces. SBS results were significantly different when AmelxKO and Mmp20KO enamel surfaces were compared. A significant increase in SBS was measured for all samples when the self-etch system was compared with the etch-and-rinse system. We have developed a novel system for testing shear bond strength of mouse incisors with AI variants, and analysis of these data may have important clinical implications for the treatment of patients with AI.

Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.)

Cytosine methylation is responsive to various biotic- and abiotic-stresses, which may produce heritable epialleles. Nitrogen (N)-deficiency is an abiotic stress being repeatedly experienced by plants. To address possible epigenetic consequences of N-deficiency-stress, we investigated the stability of cytosine methylation in rice (Oryza sativa L.) subsequent to a chronic (a whole-generation) N-deficiency at two levels, moderate (20mg/L) and severe (10mg/L), under hydroponic culture. MSAP analysis revealed that locus-specific methylation alteration occurred in leaf-tissue of the stressed plants (S(0)) experiencing either level of N-deficiency, which was validated by gel-blotting. Analysis on three non-stressed self-fed progenies (S(1), S(2) and S(3)) by gel-blotting indicated that ca. 50% of the altered methylation patterns in somatic cells (leaf) of the stressed S(0) plants were recaptured in S(1), which were then stably inherited to S(2) and S(3). Bisulfite sequencing of two variant MSAP loci with homology to low-copy retrotransposons on one stressed plant (S(0)) and its non-stressed progenies (S(1) and S(2)) showed that whereas one locus exhibited limited and non-heritable CHH methylation alteration, the other locus manifested dramatic heritable hypermethylation at nearly all cytosine sites within the assayed region. Intriguingly, when two groups of S(2) plants descended from the same N-deficiency-stressed S(0) plant were re-subjected to the stress, the group inheriting the modified methylation patterns showed enhanced tolerance to the N-deficiency-stress compared with the group bearing the original patterns. Our results thus demonstrate heritability of an acquired adaptive trait in rice, which was accompanied by epigenetic inheritance of modified cytosine methylation patterns, implicating an epigenetic basis underlying the inheritance of an acquired trait in plants.

Skin cancer concerns and genetic risk information-seeking in primary care

BACKGROUND

Genomic testing for common genetic variants associated with skin cancer risk could enable personalized risk feedback to motivate skin cancer screening and sun protection.

METHODS

In a cross-sectional study, we investigated whether skin cancer cognitions and behavioral factors, sociodemographics, family factors, and health information-seeking were related to perceived importance of learning about how (a) genes and (b) health habits affect personal health risks using classification and regression trees (CART).

RESULTS

The sample (n = 1,772) was collected in a large health maintenance organization as part of the Multiplex Initiative, ranged in age from 25-40, was 53% female, 41% Caucasian, and 59% African-American. Most reported that they placed somewhat to very high importance on learning about how genes (79%) and health habits (88%) affect their health risks. Social influence actors were associated with information-seeking about genes and health habits. Awareness of family history was associated with importance of health habit, but not genetic, information-seeking.

CONCLUSIONS

The investment of family and friends in health promotion may be a primary motivator for prioritizing information-seeking about how genes and health habits affect personal health risks and may contribute to the personal value, or personal utility, of risk information. Individuals who seek such risk information may be receptive to interventions aimed to maximize the social implications of healthy lifestyle change to reduce their health risks.

AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density

MOTIVATION

The area under the receiver operating characteristic (ROC) curve (AUC), long regarded as a 'golden' measure for the predictiveness of a continuous score, has propelled the need to develop AUC-based predictors. However, the AUC-based ensemble methods are rather scant, largely due to the fact that the associated objective function is neither continuous nor concave. Indeed, there is no reliable numerical algorithm identifying optimal combination of a set of biomarkers to maximize the AUC, especially when the number of biomarkers is large.

RESULTS

We have proposed a novel AUC-based statistical ensemble methods for combining multiple biomarkers to differentiate a binary response of interest. Specifically, we propose to replace the non-continuous and non-convex AUC objective function by a convex surrogate loss function, whose minimizer can be efficiently identified. With the established framework, the lasso and other regularization techniques enable feature selections. Extensive simulations have demonstrated the superiority of the new methods to the existing methods. The proposal has been applied to a gene expression dataset to construct gene expression scores to differentiate elderly women with low bone mineral density (BMD) and those with normal BMD. The AUCs of the resulting scores in the independent test dataset has been satisfactory.

CONCLUSION

Aiming for directly maximizing AUC, the proposed AUC-based ensemble method provides an efficient means of generating a stable combination of multiple biomarkers, which is especially useful under the high-dimensional settings.

CONTACT

lutian@stanford.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng

Panax ginseng C.A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

Observation of X(3872)→J/ψγ and search for X(3872)→ψ'γ in B decays

We report a study of B→(J/ψγ)K and B→(ψ'γ)K decay modes using 772×10⁶ B ̅B events collected at the Υ(4S) resonance with the Belle detector at the KEKB energy-asymmetric e(+)e(-) collider. We observe X(3872)→J/ψγ and report the first evidence for χ(c2)→J/ψγ in B→(X_{c ̅cγ)K decays, while in a search for X(3872)→ψ'γ no significant signal is found. We measure the branching fractions, B(B(±)→X(3872)K(±))B(X(3872)→J/ψγ)=(1.78(-0.44)(+0.48)±0.12)×10(-6), B(B(±)→χ(c2)K(±))=(1.11(-0.34)(+0.36)±0.09)×10(-5), B(B(±)→X(3872)K(±))B(X(3872)→ψ'γ)<3.45×10⁶ (upper limit at 90% C.L.), and also provide upper limits for other searches.