Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration

Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf). To capture the underlying molecular changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf/ 120 h postfertilization (hpf) to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2,000 platform. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. Our analyses indicate that the RNA-Seq dataset was of high quality, and effectively captured the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration

Normalization of large-scale behavioural data collected from zebrafish

Many contemporary neuroscience experiments utilize high-throughput approaches to simultaneously collect behavioural data from many animals. The resulting data are often complex in structure and are subjected to systematic biases, which require new approaches for analysis and normalization. This study addressed the normalization need by establishing an approach based on linear-regression modeling. The model was established using a dataset of visual motor response (VMR) obtained from several strains of wild-type (WT) zebrafish collected at multiple stages of development. The VMR is a locomotor response triggered by drastic light change, and is commonly measured repeatedly from multiple larvae arrayed in 96-well plates. This assay is subjected to several systematic variations. For example, the light emitted by the machine varies slightly from well to well. In addition to the light-intensity variation, biological replication also created batch-batch variation. These systematic variations may result in differences in the VMR and must be normalized. Our normalization approach explicitly modeled the effect of these systematic variations on VMR. It also normalized the activity profiles of different conditions to a common baseline. Our approach is versatile, as it can incorporate different normalization needs as separate factors. The versatility was demonstrated by an integrated normalization of three factors: light-intensity variation, batch-batch variation and baseline. After normalization, new biological insights were revealed from the data. For example, we found larvae of TL strain at 6 days post-fertilization (dpf) responded to light onset much stronger than the 9-dpf larvae, whereas previous analysis without normalization shows that their responses were relatively comparable. By removing systematic variations, our model-based normalization can facilitate downstream statistical comparisons and aid detecting true biological differences in high-throughput studies of neurobehaviour

Statistical Analysis of Zebrafish Locomotor Response

Zebrafish larvae display rich locomotor behaviour upon external stimulation. The movement can be simultaneously tracked from many larvae arranged in multi-well plates. The resulting time-series locomotor data have been used to reveal new insights into neurobiology and pharmacology. However, the data are of large scale, and the corresponding locomotor behavior is affected by multiple factors. These issues pose a statistical challenge for comparing larval activities. To address this gap, this study has analyzed a visually-driven locomotor behaviour named the visual motor response (VMR) by the Hotelling's T-squared test. This test is congruent with comparing locomotor profiles from a time period. Different wild-type (WT) strains were compared using the test, which shows that they responded differently to light change at different developmental stages. The performance of this test was evaluated by a power analysis, which shows that the test was sensitive for detecting differences between experimental groups with sample numbers that were commonly used in various studies. In addition, this study investigated the effects of various factors that might affect the VMR by multivariate analysis of variance (MANOVA). The results indicate that the larval activity was generally affected by stage, light stimulus, their interaction, and location in the plate. Nonetheless, different factors affected larval activity differently over time, as indicated by a dynamical analysis of the activity at each second. Intriguingly, this analysis also shows that biological and technical repeats had negligible effect on larval activity. This finding is consistent with that from the Hotelling's T-squared test, and suggests that experimental repeats can be combined to enhance statistical power. Together, these investigations have established a statistical framework for analyzing VMR data, a framework that should be generally applicable to other locomotor data with similar structure

¹H-NMR based metabolomics reveals the nutrient differences of two kinds of freshwater fish soups before and after simulated gastrointestinal digestion

Soups show diverse health functions, which could be linked to their original nutrient profiles and metabolites derived from digestion. NMR spectroscopy is a robust and rapid method that unveils or identifies the chemical composition of food or food-derived metabolites. In the current study, 1H-NMR spectroscopy approach was applied to identify the differences in metabolic profiling of two kinds of home-cooked freshwater fish soups (crucian carp and snakehead fish) before and after in vitro gastrointestinal digestion. The nutritional profiles of these soups were studied using the 1H-NMR method for the first time. Two metabolomics methods -PCA (Principal Component Analysis) and OPLS-DA (Orthogonal Partial Least Squares Discriminant Analysis), were used to analyze the data. On the whole, levels of amino acid metabolites such as valine (Val), tyrosine, choline, taurine (Tau) and glycine were higher in the crucian carp soup, whereas higher levels of fatty acids and unsaturated fatty acids were found in the snakehead soup. Furthermore, the high content of seven metabolites valine, leucine, EPA C20:5 (PUFA eicosapentaenoic acid), acetic acid, taurine, GPCho (phosphatidylcholine) and creatine showed an upward trend after simulated gastrointestinal digestion. The results demonstrate that 1H-NMR metabolic profile of different fish soups can shed some light to our understanding of food functional properties and dietary therapy. Furthermore, changes of metabolites in digested fish soups could reveal information about chemical compounds which play important roles in the body

Intersymbol blind multiuser detection for CDMA systems

This thesis deals with the development of the blind multiuser detectors for various CDMA systems by using the intersymbol information between the consecutive received signals, which has been considered as a novel development for the detection of wireless communications systems.DOCTOR OF PHILOSOPHY (EEE

Intersymbol Decorrelating Detector for Asynchronous CDMA Networks with Multipath

<p>Most reported multiuser detection techniques for CDMA systems need the channel estimation including the delay spread and the parameters of the multipath channel of the desired user. This paper proposes an intersymbol decorrelating detector that makes use of the cross-correlation matrix constructed by the consecutively received symbols. The proposed detector is attractive for its simplicity because no channel estimation is required except for the synchronization of the desired user. Compared with other reported multiuser detectors, simulation results show that the proposed detector provides a good performance when the active users have significant intersymbol interference.</p

Preparation and characterization of cellulose nanofibers isolated from lettuce

Abstract: Cellulose nanofibers (CNFs) were isolated from lettuce peel using specific chemical treatments, i.e., NaOH alkali solution treatment, NaClO2 bleaching and sulfuric acid hydrolysis. Both cellulose and cellulose nanofibers were characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). Morphological features and particle size distribution of cellulose and nanostructures were explored using transmission electron microscopy (TEM), scanning electron microscope (SEM) and the Malvern laser particle size analyzer. Results showed that particle diameters of the majority of morphological nanofibrillated cellulose were in the range of 10 to 20 nm, and length between 190 to 460 nm. The crystallinity index reached 41.57%, which increased by 117.3% compared with the raw material. The crystalline type of lettuce peel nanofibers belongs to cellulose type I. Moreover，thermal degradation temperature of CNFs is 271.7 °C which is 47.3 °C higher than that of the untreated peel. The CNFs obtained from these treatments can be used as additional biocomposites in reinforced polymer manufacturing processes or the food industry

Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration

Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf). To capture the underlying molecular changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf/ 120 h postfertilization (hpf) to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2,000 platform. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. Our analyses indicate that the RNA-Seq dataset was of high quality, and effectively captured the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration

Changes in Nutrient Profile and Antioxidant Activities of Different Fish Soups, Before and After Simulated Gastrointestinal Digestion

Different kinds of freshwater fish soups show a diverse range of health functions, due to their different nutritional substances and corresponding bioactivities. In the current study, in order to learn the theoretical basis of the potential role fish soup plays in diet therapy functions, the changes of nutrient profiles and antioxidant activities in crucian carp soup and snakehead soup (before and after simulated gastrointestinal digestion) were investigated, such as chemical composition, free amino acids, mineral and fatty acid contents, DPPH radical scavenging activity, ferrous ion chelating activity, hydroxyl radical-scavenging activity and the reducing power effect. Results show that the content of mineral elements in snakehead fish soup was significantly higher than that of crucian carp soup, especially for the contents of Ca, Zn, Fe. The content of total amino acid (TAA) of crucian carp soup (82.51 mg/100 mL) was much higher than that of snakehead fish soup (47.54 mg/100 mL) (p &lt; 0.05). Furthermore, the antioxidant capacity of crucian carp soup was stronger than that of snakehead soup. The intensive profiles of nutritional composition and antioxidant activities of these two kinds of fish soups were expected to partly provide the theoretical basis of therapeutic effects