Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility

<p>Abstract</p> <p>Background</p> <p>Ratio-based analysis is the current standard for the analysis of dual-color microarray data. Indeed, this method provides a powerful means to account for potential technical variations such as differences in background signal, spot size and spot concentration. However, current high density dual-color array platforms are of very high quality, and inter-array variance has become much less pronounced. We therefore raised the question whether it is feasible to use an intensity-based analysis rather than ratio-based analysis of dual-color microarray datasets. Furthermore, we compared performance of both ratio- and intensity-based analyses in terms of reproducibility and sensitivity for differential gene expression.</p> <p>Results</p> <p>By analyzing three distinct and technically replicated datasets with either ratio- or intensity-based models, we determined that, when applied to the same dataset, intensity-based analysis of dual-color gene expression experiments yields 1) more reproducible results, and 2) is more sensitive in the detection of differentially expressed genes. These effects were most pronounced in experiments with large biological variation and complex hybridization designs. Furthermore, a power analysis revealed that for direct two-group comparisons above a certain sample size, ratio-based models have higher power, although the difference with intensity-based models is very small.</p> <p>Conclusions</p> <p>Intensity-based analysis of dual-color datasets results in more reproducible results and increased sensitivity in the detection of differential gene expression than the analysis of the same dataset with ratio-based analysis. Complex dual-color setups such as interwoven loop designs benefit most from ignoring the array factor. The applicability of our approach to array platforms other than dual-color needs to be further investigated.</p

Sunlight Powered Continuous Flow Reverse Water Gas Shift Process Using a Plasmonic Au/TiO₂ Nanocatalyst

The continuous flow reverse water gas shift (rWGS) process was efficiently catalyzed by a plasmonic Au/TiO2 nanocatalyst using sunlight as sole and sustainable energy source. The influence of the catalyst bed thickness on the CO production rate was studied, and three different catalytic regimes were identified as direct plasmon catalysis (DPC), shielded plasmon catalysis (SPC) and unused plasmon catalysis (UPC). The CO2 : H2 ratio was optimized to 4 : 1 and a maximum CO production rate of 7420 mmol ⋅ m−2 ⋅ h−1 was achieved under mild reaction conditions (p=3.5 bar, no external heating, Ee=14.0 kW ⋅ m−2), corresponding to an aparent quantum efficiency of 4.15%. The stability of the Au/TiO2 catalyst was studied for 110 h continuous operation, maintaining more than 82% of the initial CO production rate. On/off experiments mimicking discontinuous sunlight powered processing furthermore showed that the Au/TiO2 catalyst was stable for 8 consecutive runs.</p

Microarray and morphological analysis of early postnatal CRB2 mutant retinas on a pure C57BL/6J genetic background

In humans, the Crumbs homologue-1 (CRB1) gene is mutated in progressive types of autosomal recessive retinitis pigmentosa and Leber congenital amaurosis. Th

Gene Expression and Functional Annotation of the Human Ciliary Body Epithelia

Purpose: The ciliary body (CB) of the human eye consists of the non-pigmented (NPE) and pigmented (PE) neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma. Methods: We isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity. Results: The gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (N)PE of 35 genes previously implicated in molecular mechanisms related to glaucoma. Conclusion: Our gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma

A Ziegler-type spherical cap model reveals early stage ethylene polymerization growth versus catalyst fragmentation relationships

Polyolefin catalysts are characterized by their hierarchically complex nature, which complicates studies on the interplay between the catalyst and formed polymer phases. Here, the missing link in the morphology gap between planar model systems and industrially relevant spherical catalyst particles is introduced through the use of a spherical cap Ziegler-type catalyst model system for the polymerization of ethylene. More specifically, a moisture-stable LaOCl framework with enhanced imaging contrast has been designed to support the TiCl4 pre-active site, which could mimic the behaviour of the highly hygroscopic and industrially used MgCl2 framework. As a function of polymerization time, the fragmentation behaviour of the LaOCl framework changed from a mixture of the shrinking core (i.e., peeling off small polyethylene fragments at the surface) and continuous bisection (i.e., internal cleavage of the framework) into dominantly a continuous bisection model, which is linked to the evolution of the estimated polyethylene volume and the fraction of crystalline polyethylene formed. The combination of the spherical cap model system and the used advanced micro-spectroscopy toolbox, opens the route for high-throughput screening of catalyst functions with industrially relevant morphologies on the nano-scale

On the Fragmentation Behavior of Ziegler-Type Catalysts During the Early Stages of α-Olefin Polymerization

In this PhD Thesis the fragmentation behavior of Ziegler-type polyolefin catalysts was studied using advanced chemical imaging techniques. The fragmentation behavior plays a crucial part during the polymerization of a-olefins such as ethylene and propylene to ensure a well-controlled polymerization process, prevent reactor fouling and facilitate facile processing of the obtained polymer particles. For the first time, the fragmentation behavior of the highly moisture sensitive Ziegler-type catalyst particles was captured in 3-D over large field of views with high sub 100-nm spatial resolution using X-ray nanotomography. Additionally, a model system was developed to study the fragmentation behavior with surface sensitive techniques. This model system bridges the knowledge gap between planar thin films and industrially used spherical particles, through the use of spherical caps. These spherical caps therefore allow the research to mimic the shape of industrially relevant catalyst particles whilst being compatible with surface sensitive imaging techniques. The methodologies developed in this PhD Thesis to study the fragmentation behavior of Ziegler-type catalysts can be extended and applied to all other types of polyolefin catalysts such as the Phillips catalysts and immobilized metallocene catalysts

On the Fragmentation Behavior of Ziegler-Type Catalysts During the Early Stages of α-Olefin Polymerization

In this PhD Thesis the fragmentation behavior of Ziegler-type polyolefin catalysts was studied using advanced chemical imaging techniques. The fragmentation behavior plays a crucial part during the polymerization of a-olefins such as ethylene and propylene to ensure a well-controlled polymerization process, prevent reactor fouling and facilitate facile processing of the obtained polymer particles. For the first time, the fragmentation behavior of the highly moisture sensitive Ziegler-type catalyst particles was captured in 3-D over large field of views with high sub 100-nm spatial resolution using X-ray nanotomography. Additionally, a model system was developed to study the fragmentation behavior with surface sensitive techniques. This model system bridges the knowledge gap between planar thin films and industrially used spherical particles, through the use of spherical caps. These spherical caps therefore allow the research to mimic the shape of industrially relevant catalyst particles whilst being compatible with surface sensitive imaging techniques. The methodologies developed in this PhD Thesis to study the fragmentation behavior of Ziegler-type catalysts can be extended and applied to all other types of polyolefin catalysts such as the Phillips catalysts and immobilized metallocene catalysts

ONT read assembly of the black rhino genome

Abstract Objectives The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo’s often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced and assembled the genome of a captive male black rhino using ONT sequencing data only. Data description This work produced over 100 Gb whole genome sequencing reads from whole blood. These were assembled into a 2.47 Gb draft genome consisting of 834 contigs with an N50 of 29.53 Mb. The genome annotation was lifted over from an available genome annotation for black rhino, which resulted in the retrieval of over 99% of gene features. This new genome assembly will be a valuable resource in for conservation genetic research in this species. Keywords Black rhinoceros, Diceros bicornis, Genome assembly, Long reads, Whole genome sequencing