Genetic and functional analysis of the bacillus subtilis BSP1 gam cluster

Mannans (linear mannan, glucomannan, galactomannan and galactoglucomannan) are the major constituents of the hemicellulose fraction in softwoods and show great importance as a renewable resource for fuel or feedstock applications. As complex polysaccharides, mannans can only be degraded through a synergistic action of different mannan-degrading enzymes, mannanases. Microbial mannanases are mainly extracellular enzymes that can act in wide range of pH and temperature, contributing to pulp and paper, pharmaceutical, food and feed, oil and textile successful industrial applications. Knowing and controlling these microbial mannan-degrading enzymes are essential to take advantage of their great biotechnological potential. The genome of the laboratory 168 strain of Bacillus subtilis carries genes gmuA-G dedicated to the degradation and utilization of glucomannan, including an extracellular -mannanase. Recently, the genome sequence of an undomesticated strain of B. subtilis, BSP1, was determined. In BSP1, the gmuA-G operon is maintained, interestingly, however, a second cluster of genes was found (gam cluster), which comprise a second putative extracellular β-mannanase, and most likely specify a system for the degradation and utilization of a different mannan polymer, galactoglucomannan. The genetic organization and function of the gam cluster, and whether its presence in BSP1 strain results in new hemicellulolytic capabilities, compared to those of the laboratory strain, was address in this work. In silico and in vivo mRNA analyses performed in this study revealed that the gam cluster, comprising nine genes, is organized and expressed in at least six different transcriptional units. Furthermore, cloning, expression, and production of Bbsp2923 in Escherichia coli was achieved and preliminary characterization shows that the enzyme is indeed a β-mannanase. Finally, the high hemicellulolytic capacity of the undomesticated B. subtilis BSP1, demonstrated in this work by qualitative analyses, suggests potential to be used in the food and feed industries.

Determination of the most suitable oil pipeline route using GIS least cost path analysis

The Keystone XL has a big role for transforming Canadian oil to the USA. The function of the pipeline is decreasing the dependency of the American oil industry on other countries and it will help to limit external debt. The proposed pipeline seeks the most suitable route which cannot damage agricultural and natural water recourses such as the Ogallala Aquifer. Using the Geographic Information System (GIS) techniques, the suggested path in this study got extremely high correct results that will help in the future to use the least cost analysis for similar studies. The route analysis contains different weighted overlay surfaces, each, was influenced by various criteria (slope, geology, population and land use). The resulted least cost path routes for each weighted overlay surface were compared with the original proposed pipeline and each displayed surface was more effective than the proposed Keystone XL pipeline.

Analysis of temporal and spatial variations of forest. A case of study in notheastern Armenia

The forest has a crucial ecological role and the continuous forest loss can cause colossal effects on the environment. As Armenia is one of the low forest covered countries in the world, this problem is more critical. Continuous forest disturbances mainly caused by illegal logging started from the early 1990s had a huge damage on the forest ecosystem by decreasing the forest productivity and making more areas vulnerable to erosion. Another aspect of the Armenian forest is the lack of continuous monitoring and absence of accurate estimation of the level of cuts in some years. In order to have insight about the forest and the disturbances in the long period of time we used Landsat TM/ETM + images. Google Earth Engine JavaScript API was used, which is an online tool enabling the access and analysis of a great amount of satellite imagery. To overcome the data availability problem caused by the gap in the Landsat series in 1988- 1998, extensive cloud cover in the study area and the missing scan lines, we used pixel based compositing for the temporal window of leaf on vegetation (June-late September). Subsequently, pixel based linear regression analyses were performed. Vegetation indices derived from the 10 biannual composites for the years 1984-2014 were used for trend analysis. In order to derive the disturbances only in forests, forest cover layer was aggregated and the original composites were masked. It has been found, that around 23% of forests were disturbed during the study period.

Microfluidics: a new look at cell migration analysis

This thesis explores the development and employment of microfluidic devices as a tool for studying the effect of the surrounding environment on embryonic stem cells during the migration phenomena. Different single-cell microchips were designed and manufactured to study mouse embryonic fibroblasts (MEFs) migration towards an environmental variation (increase of serum concentration in the culture medium) that was expected to function as a motility stimuli. Considering the experimental, cells were injected into the microchips chambers and individually isolated by dedicated cell traps with view to a single-cell analysis. Once fribroblasts were attached to the surface, culture medium with an increased serum level was subsequently injected in an adjacent chamber to promote the formation of a serum concentration gradient. The gradient established between the chambers could be sensed by the fibroblasts and thus triggered the cells mobilization towards and in the direction of the richer serum medium. Additionally, the experiment allowed the observation of MEFs’ structural reorganization when migrating through micro-tunnels containing widths below the cell size, suggesting a cytoskeleton rearrangement on account of the nutritional stimulus introduced. Furthermore, results indicate that fibronectin promotes MEFs adhesion to the substrate and that MEFs migration is characterized as haptotactic.

Visions on high-speed trains: a methodological analysis

Based on the report for the unit “Foresight Analysis Methods” of the PhD program on Technology Assessment in 2013. This unit was supervised by Prof. António Moniz. The paper had meanwhile contributions from the supervisor and Dr. Douglas Robinson.

A type system for value-dependent information flow analysis

Information systems are widespread and used by anyone with computing devices as well as corporations and governments. It is often the case that security leaks are introduced during the development of an application. Reasons for these security bugs are multiple but among them one can easily identify that it is very hard to define and enforce relevant security policies in modern software. This is because modern applications often rely on container sharing and multi-tenancy where, for instance, data can be stored in the same physical space but is logically mapped into different security compartments or data structures. In turn, these security compartments, to which data is classified into in security policies, can also be dynamic and depend on runtime data. In this thesis we introduce and develop the novel notion of dependent information flow types, and focus on the problem of ensuring data confidentiality in data-centric software. Dependent information flow types fit within the standard framework of dependent type theory, but, unlike usual dependent types, crucially allow the security level of a type, rather than just the structural data type itself, to depend on runtime values. Our dependent function and dependent sum information flow types provide a direct, natural and elegant way to express and enforce fine grained security policies on programs. Namely programs that manipulate structured data types in which the security level of a structure field may depend on values dynamically stored in other fields The main contribution of this work is an efficient analysis that allows programmers to verify, during the development phase, whether programs have information leaks, that is, it verifies whether programs protect the confidentiality of the information they manipulate. As such, we also implemented a prototype typechecker that can be found at http://ctp.di.fct.unl.pt/DIFTprototype/.

The reasons behind the progression in PISA scores: An education production function approach using semi-parametric techniques

Research Masters