Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Ropinirole alters gene expression profiles in SH-SY5Y cells: a whole genome microarray study

Ropinirole (ROP) is a dopamine agonist that has been used as therapy for Parkinson's disease. In the present study, we aimed to detect whether gene expression was modulated by ROP in SH-SY5Y cells. SH-SY5Y cell lines were treated with 10 µM ROP for 2 h, after which total RNA was extracted for whole genome analysis. Gene expression profiling revealed that 113 genes were differentially expressed after ROP treatment compared with control cells. Further pathway analysis revealed modulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway, with prominent upregulation of PIK3C2B. Moreover, batches of regulated genes, including PIK3C2B, were found to be located on chromosome 1. These findings were validated by quantitative RT-PCR and Western blot analysis. Our study, therefore, revealed that ROP altered gene expression in SH-SY5Y cells, and future investigation of PIK3C2B and other loci on chromosome 1 may provide long-term implications for identifying novel target genes of Parkinson's disease.

Invoice process analysis and development. Case: Power and automation technology company

This master’s thesis studies the case company’s current purchase invoice process and the challenges that are related to it. Like most of other master’s thesis this study consists of both theoretical- and empirical parts. The purpose of this work is to combine theoretical and empirical parts together so that the theoretical part brings value to the empirical case study. The case company’s main business is frequency converters for both low voltage AC & DC drives and medium voltage AC Drives which are used across all industries and applications. The main focus of this study is on the current invoice process modelling. When modelling the existing process with discipline and care, current challenges can be understood better. Empirical study relays heavily on interviews and existing, yet fragmented, data. This, along with own calculations and analysis, creates the foundation for the empirical part of this master’s thesis.

Lignin oxidation by PCD technology

The purpose of this study is to investigate whether commercial Kraft lignin can be treated with pulsed corona discharge apparatus so that it becomes active. Active lignin refers to the kind of lignin that can be precipitated on the surface of a fiber by lowering the pH. A secondary agenda here is to remove the pungent smell of kraft lignin, which is caused by organically bound sulfur. It is expected that the study will identify mild processing conditions and parameters for achievement of the desired outcome. In the literature review, the properties of lignin are explained, as is their impact on any further processing. In addition, a number of processes are described for the oxidation of lignin in a variety of applications. In the experimental part of the study, test runs were conducted to determine the effects of oxygen supply and pulse frequency on oxidation results, where the purpose is to produce reactive lignin and to find a process that is feasible at an industrial scale. Based on the reported experiments, lignin could not be made active or precipitated to the surface of the fiber. Actual changes in the structure of lignin were not observed, but the pungent smell of lignin was removed. The exact reason for this change could not be established because sulfur NMR analysis did not work for the lignin samples.

Development of an alternative technology for the oyster mushroom production using liquid inoculum

Pleurotus ostreatus, worldwide known as oyster mushroom, was cultivated in banana straw using inocula produced by two different processes - liquid inoculum and the traditionally used solid inoculum. Different ratios (5, 10, 15, and 20%) were tested. Biological efficiency, yield, productivity, organic matter loss, and moisture of fruiting bodies as well as physical-chemical characteristics of banana straw were studied. Significant differences were observed for cellulose, lignin, and hemicellulose content between one and two harvests for both solid and liquid inocula. It was observed that P. ostreatus growth promoted higher degradation of lignin (80.36%), followed by hemicellulose (78.64%) and cellulose (60.37%). Significant differences between one and two harvests were also observed for the production parameters (biological efficiency and yield) for both kinds of inocula, liquid and solid. However, significant differences in productivity between harvests were observed only for solid inoculum.

Jaboticaba peel for jelly preparation: an alternative technology

The peel of jaboticaba is attractive regarding its nutritional, functional and sensory aspects. However, its use for consumption is still restricted due to the need of technological development in order to obtain processed preparations for its inclusion in the human diet. The purpose of this study was to produce jelly using the peel of jaboticaba and to characterize it chemically and sensorially. Diferent formulations were prepared, all with 50% of sugar and with different proportions of peel, pulp and pectin. The formulations, which were tested for preference, were the following: F1a (80% of peel, 20% of pulp and 0.5% of pectin) and F3b (50% of peel, 50% pulp and 1.0% of pectin). These formulations showed chemical composition of 216.44 mg phenolic compounds, 148.00 mg gallic acid.100 g-1, 10.42 mg flavonoids, and 12.10 mg catechin.100 g-1, and 80% acceptability index. The peel presented higher levels of nutrients than the pulp, especially as source of fiber, carbohydrates and natural pigments. Results indicated the feasibility of technological nutritional harnessing of the jaboticaba peel in obtaining jelly. The results also indicated good sensory and nutritional characteristics, acceptability, and antioxidant properties of natural pigments.