Quantitative genetic analysis of grain yield in an Australian Brassica napus doubled-haploid population

The use of mo and cu monochromatic radiations for quantitative phase analysis: study of the accuracy

Cement hydration is a very complex process in which crystalline phases are dissolving in water and after supersaturation hydrated crystalline and amorphous phases precipitate. Great efforts are being made to develop analytical tools to accurately quantify these processes and X-ray Powder Diffraction (XRPD) combined with Rietveld methodology is a suitable tool to quantify these complex mixtures and their time evolutions. However, some problems/drawbacks should be overcome to fully apply it to cement pastes characterization in order to get accurate phase analyses. In order to tackle this issue, a comparison of the Rietveld quantitative phase analyses (RQPA) obtained using Cu-Kα1, Mo-Kα1, and synchrotron strictly monochromatic radiations of three set of mixtures with increasing amounts of a given phase (spiking-method) is presented. The main aim is to test a simple hypothesis: high energy Mo-radiation, combined with high resolution laboratory X-ray powder diffraction optics, could yield more accurate RQPA, for challenging samples, than well-established Cu-radiation procedure(s). Firstly, a series of crystalline inorganic phase mixtures with increasing amounts of an analyte was studied in order to determine if Mo-Kα1 methodology is as robust as the well-established Cu-Kα1 one. Secondly, a series of crystalline organic phase mixtures with increasing amounts of an organic compound was analyzed. This type of mixture can result in transparency problems in reflection and inhomogeneous loading in narrow capillaries for transmission studies. Finally, a third series with variable amorphous content was studied. Limit of detection in Cu-patterns, ~0.2 wt%, are slightly lower than those derived from Mo-patterns, ~0.3 wt%, for similar recording times and limit of quantification for a well crystallized inorganic phase using laboratory powder diffraction was established ~0.10 wt%. From the obtained results it is inferred that RQPA from Mo-Kα1 radiation have slightly better accuracies than those obtained from Cu-Kα1. The results obtained in the previous comparison have been taken into account to obtain accurate RQPA, including the amorphous component with internal standard methodology, of hydrating cement pastes. The final goal of this second study was understanding the early-stage hydration mechanisms of a variety of cementing systems (Ordinary Portland Cement or Belite Alite Ye’elimite cement) as a function of water content, superplasticizer additives and type and content of sulfate source. In order to do so, X-ray powder diffraction data were taken in-situ with the humidity chamber coupled to the Mo-Kα1 powder diffractometer. Some results of this ongoing investigation will be reported and discussed.

Optimized Fast-FISH with a-satellite probes: acceleration by microwave activation

It has been shown for several DNA probes that the recently introduced Fast-FISH (fluorescence in situ hybridization) technique is well suited for quantitative microscopy. For highly repetitive DNA probes the hybridization (renaturation) time and the number of subsequent washing steps were reduced considerably by omitting denaturing chemical agents (e.g., formamide). The appropriate hybridization temperature and time allow a clear discrimination between major and minor binding sites by quantitative fluorescence microscopy. The well-defined physical conditions for hybridization permit automatization of the procedure, e.g., by a programmable thermal cycler. Here, we present optimized conditions for a commercially available X-specific a-satellite probe. Highly fluorescent major binding sites were obtained for 74oC hybridization temperature and 60 min hybridization time. They were clearly discriminated from some low fluorescent minor binding sites on metaphase chromosomes as well as in interphase cell nuclei. On average, a total of 3.43 ± 1.59 binding sites were measured in metaphase spreads, and 2.69 ± 1.00 in interphase nuclei. Microwave activation for denaturation and hybridization was tested to accelerate the procedure. The slides with the target material and the hybridization buffer were placed in a standard microwave oven. After denaturation for 20 s at 900 W, hybridization was performed for 4 min at 90 W. The suitability of a microwave oven for Fast-FISH was confirmed by the application to a chromosome 1-specific a-satellite probe. In this case, denaturation was performed at 630 W for 60 s and hybridization at 90 W for 5 min. In all cases, the results were analyzed quantitatively and compared to the results obtained by Fast-FISH. The major binding sites were clearly discriminated by their brightness

Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.

A metallurgical study of aluminium alloys used as aircraft components

The effects of heat treatment on morphologies and microstructures of Al 2024 and Al 7050 alloys, used as aircraft components, were studied by metallographic techniques. Light microscopy (LM) and quantitative image analysis were used to characterize the precipitate dispersion and morphology for these alloys. The application of the scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) combined techniques for studying these multiphase systems makes it possible to distinguish and quantify the different phases in the surface structure. Xray diffraction also permitted a qualitative comparison of the structures before and after heat treatments.

Predicting and monitoring cancer treatment response with diffusion-weighted MRI

An imaging biomarker that would provide for an early quantitative metric of clinical treatment response in cancer patients would provide for a paradigm shift in cancer care. Currently, nonimage based clinical outcome metrics include morphology, clinical, and laboratory parameters, however, these are obtained relatively late following treatment. Diffusion-weighted MRI (DW-MRI) holds promise for use as a cancer treatment response biomarker as it is sensitive to macromolecular and microstructural changes which can occur at the cellular level earlier than anatomical changes during therapy. Studies have shown that successful treatment of many tumor types can be detected using DW-MRI as an early increase in the apparent diffusion coefficient (ADC) values. Additionally, low pretreatment ADC values of various tumors are often predictive of better outcome. These capabilities, once validated, could provide for an important opportunity to individualize therapy thereby minimizing unnecessary systemic toxicity associated with ineffective therapies with the additional advantage of improving overall patient health care and associated costs. In this report, we provide a brief technical overview of DW-MRI acquisition protocols, quantitative image analysis approaches and review studies which have implemented DW-MRI for the purpose of early prediction of cancer treatment response.

Loss of tumor suppressor mir-203 mediates overexpression of LIM and SH3 Protein 1 (LASP1) in high-risk prostate cancer thereby increasing cell proliferation and migration

Several studies have linked overexpression of the LIM and SH3 domain protein 1 (LASP1) to progression of breast, colon, liver, and bladder cancer. However, its expression pattern and role in human prostate cancer (PCa) remained largely undefined. Analysis of published microarray data revealed a significant overexpression of LASP1 in PCa metastases compared to parental primary tumors and normal prostate epithelial cells. Subsequent gene-set enrichment analysis comparing LASP1-high and -low PCa identified an association of LASP1 with genes involved in locomotory behavior and chemokine signaling. These bioinformatic predictions were confirmed in vitro as the inducible short hairpin RNA-mediated LASP1 knockdown impaired migration and proliferation in LNCaP prostate cancer cells. By immunohistochemical staining and semi-quantitative image analysis of whole tissue sections we found an enhanced expression of LASP1 in primary PCa and lymph node metastases over benign prostatic hyperplasia. Strong cytosolic and nuclear LASP1 immunoreactivity correlated with PSA progression. Conversely, qRT-PCR analyses for mir-203, which is a known translational suppressor of LASP1 in matched RNA samples revealed an inverse correlation of LASP1 protein and mir-203 expression. Collectively, our results suggest that loss of mir-203 expression and thus uncontrolled LASP1 overexpression might drive progression of PCa.

Porosity contributions of radiolarians in ODP Site 110-671 and Hole 110-672A sediments

This study quantitatively addresses the significance of porosity within radiolarian tests in the décollement zone at the toe of the northern Barbados accretionary prism. Quantification was accomplished using scanning electron microscope images of core samples taken from Ocean Drilling Program (ODP) Sites 671 and 672, representing the décollement and proto-décollement, respectively. The décollement is localized to a radiolarian claystone, and its depth correlates with a low-density anomaly that has been attributed to high porosity at all relevant ODP drilling sites in the area (Moore, Klaus, et al., 1998, doi:10.2973/odp.proc.ir.171A.1998; Shipley, Ogawa, Blum, et al., 1995, doi:10.2973/odp.proc.ir.153.1995; Mascle, Moore, et al., 1988, doi:10.2973/odp.proc.ir.110.1988). Porosity in the décollement zone is presumably lost between Sites 672 and 671 because of shear enhanced consolidation (Moore et al., 1998, doi:10.1130/0091-7613(1998)026<0811:CPDIAE>2.3.CO;2).

Calcium-dependent enzyme activation and vacuole formation in the apical granular region of pancreatic acinar cells

The pancreatic acinar cell produces powerful digestive enzymes packaged in zymogen granules in the apical pole. Ca2+ signals elicited by acetylcholine or cholecystokinin (CCK) initiate enzyme secretion by exocytosis through the apical membrane. Intracellular enzyme activation is normally kept to a minimum, but in the often-fatal human disease acute pancreatitis, autodigestion occurs. How the enzymes become inappropriately activated is unknown. We monitored the cytosolic Ca2+ concentration ([Ca2+]i), intracellular trypsin activation, and its localization in isolated living cells with specific fluorescent probes and studied intracellular vacuole formation by electron microscopy as well as quantitative image analysis (light microscopy). A physiological CCK level (10 pM) eliciting regular Ca2+ spiking did not evoke intracellular trypsin activation or vacuole formation. However, stimulation with 10 nM CCK, evoking a sustained rise in [Ca2+]i, induced pronounced trypsin activation and extensive vacuole formation, both localized in the apical pole. Both processes were abolished by preventing abnormal [Ca2+]i elevation, either by preincubation with the specific Ca2+ chelator 1,2-bis(O-aminophenoxy)ethane-N,N-N′,N′-tetraacetic acid (BAPTA) or by removal of external Ca2+. CCK hyperstimulation evokes intracellular trypsin activation and vacuole formation in the apical granular pole. Both of these processes are mediated by an abnormal sustained rise in [Ca2+]i.

Quantitative analysis of photodynamic therapy effects in rat mammary tumor vascular density using image-pro plus software

Photodynamic therapy (PDT) is a treatment modality that has advanced rapidly in recent years. It causes tissue and vascular damage with the interaction of a photosensitizing agent (PS), light of a proper wavelength, and molecular oxygen. Evaluation of vessel damage usually relies on histopathology evaluation. Results are often qualitative or at best semi-quantitative based on a subjective system. The aim of this study was to evaluate, using CD31 immunohistochem- istry and image analysis software, the vascular damage after PDT in a well-established rodent model of chemically induced mammary tumor. Fourteen Sprague-Dawley rats received a single dose of 7,12-dimethylbenz(a)anthraxcene (80 mg/kg by gavage), treatment efficacy was evaluated by comparing the vascular density of tumors after treatment with Photogem® as a PS, intraperitoneally, followed by interstitial fiber optic lighting, from a diode laser, at 200 mW/cm and light dose of 100 J/cm directed against his tumor (7 animals), with a control group (6 animals, no PDT). The animals were euthanized 30 hours after the lighting and mammary tumors were removed and samples from each lesion were formalin-fixed. Immunostained blood vessels were quantified by Image Pro-Plus version 7.0. The control group had an average of 3368.6 ± 4027.1 pixels per picture and the treated group had an average of 779 ± 1242.6 pixels per area (P < 0.01), indicating that PDT caused a significant decrease in vascular density of mammary tumors. The combined immu- nohistochemistry using CD31, with selection of representative areas by a trained pathology, followed by quantification of staining using Image Pro-Plus version 7.0 system was a practical and robust methodology for vessel damage evalua- tion, which probably could be used to assess other antiangiogenic treatments.

Impact of optic media opacities and image compression on quantitative analysis of optical coherence tomography

To analyze the impact of opacities in the optical pathway and image compression of 32-bit raw data to 8-bit jpg images on quantified optical coherence tomography (OCT) image analysis.

Preliminary assessment of the quantitative relationships between testicular tissue composition and ultrasonographic image attributes in the ram

This study examined the relationships between gross chemical composition and ultrasonographic characteristics of the ram testes. Ten testes from sexually mature Karakul rams were scanned ex situ with an 8-MHz linear-array transducer, in a transverse and longitudinal plane. All ultrasonograms were saved as digital images and subjected to computerized analyses. Crude protein content was determined by the Kjeldahl method, moisture was determined with an oven-drying method, and fat was measured by the Soxhlet extraction of dried samples. Mean pixel values (r = -0.64, P = 0.04), pixel heterogeneity (standard deviation of pixel values; r = -0.64, P = 0.04) and maximum pixel intensity (r = -0.76, P = 0.01) were all negatively correlated with parenchymal protein content. Pixel heterogeneity correlated directly with extractable lipids (r = 0.66, P = 0.02). The quantitative correlations between echotextural and biochemical parameters found in the present experiment confirm the utility of ultrasonographic imaging combined with computer-assisted image analysis for determining changes in testicular histophysiology. © 2013 Elsevier Ltd. All rights reserved.