miRNA detection and analysis from high-throughput small RNA sequencing data

Small RNAs (sRNAs) are a broad class of short regulatory non-coding RNAs. microRNAs (miRNAs) are a special class of -21-22 nucleotide sRNAs which are derived from a stable hairpin-like secondary structure. miRNAs have critical gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in both plants and animals. Next generation sequencing (NGS) technologies, which are often used for identifying miRNAs, are continuously evolving, generating datasets containing millions of sRNAs, which has led to new challenges for the tools used to predict miRNAs from such data. There are several tools for miRNA detection from NGS datasets, which we review in this thesis, identifying a number of potential shortcomings in their algorithms. In this thesis, we present a novel miRNA prediction algorithm, miRCat2. Our algorithm is more robust to variations in sequencing depth due to the fact that it compares aligned sRNA reads to a random uniform distribution to detect peaks in the input dataset, using a new entropy-based approach. Then it applies filters based on the miRNA biogenesis on the read alignment and on the computed secondary structure. Results show that miRCat2 has a better specificity-sensitivity trade-off than similar tools, and its predictions also contains a larger percentage of sequences that are downregulated in mutants in the miRNA biogenesis pathway. This con�rms the validity of novel predictions, which may lead to new miRNA annotations, expanding and contributing to the field of sRNA research

THE COMMUNICATION PROCESS IN THE BUSINESS ENVIRONMENT. ECONOMIC AND MORAL PRINCIPLES FROM THE PERSPECTIVE OF SUSTAINABLE DEVELOPMENT

The economic communication is more than a decade a point of interest due to the communication supports development and the diversity of information, on one hand, and due to the need for documentation and knowledge, both at the individual level and at the level of society, on the other hand. Thus the freedom into thinking and expression led to the development of communication activities and collecting them in a new vision. The process of communication has become, in a relatively short time, one of the engines of the economy, but also an integral part of what is meant to be today, the psycho-sociology of modern human societies. In this context, we propose an analysis of the communicative process that takes place in the economic environment, since the information and communication technology is, at present, a real factor in sustainable development. We start the analysis from the tight interdependence between the economic communication and the development of human culture as a basic factor for efficient management and for sustainable development overall

miRNA detection and analysis from high-throughput small RNA sequencing data

Small RNAs (sRNAs) are a broad class of short regulatory non-coding RNAs. microRNAs (miRNAs) are a special class of -21-22 nucleotide sRNAs which are derived from a stable hairpin-like secondary structure. miRNAs have critical gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in both plants and animals. Next generation sequencing (NGS) technologies, which are often used for identifying miRNAs, are continuously evolving, generating datasets containing millions of sRNAs, which has led to new challenges for the tools used to predict miRNAs from such data. There are several tools for miRNA detection from NGS datasets, which we review in this thesis, identifying a number of potential shortcomings in their algorithms. In this thesis, we present a novel miRNA prediction algorithm, miRCat2. Our algorithm is more robust to variations in sequencing depth due to the fact that it compares aligned sRNA reads to a random uniform distribution to detect peaks in the input dataset, using a new entropy-based approach. Then it applies filters based on the miRNA biogenesis on the read alignment and on the computed secondary structure. Results show that miRCat2 has a better specificity-sensitivity trade-off than similar tools, and its predictions also contains a larger percentage of sequences that are downregulated in mutants in the miRNA biogenesis pathway. This con�rms the validity of novel predictions, which may lead to new miRNA annotations, expanding and contributing to the field of sRNA research

THE ROMANIAN TOURISM IN THE CONTEXT OF SUSTAINABLE DEVELOPMENT

Currently tourism represents one of the basic elements for the sustainable development, considering that it is properly understood and implemented. To perform an analysis of tourism in this context, we must consider the three coordinates, interedependente, that influence and equally are influenced by the tourism activity. It is about the particularly impact that tourism has on living standards in areas with high potential for exploitation of tourism activities, about the impact and the effects generated in the economy and, not least, we discuss about the effects that tourism generates on the environment

The Management of Regional Biodiversity – Forest Potential

The considerations on the ability of forest to maintain ecological balance and numerous environmental protection functions require the exercise of a sensible management, consistent with regional development plans. This is the more necessary as, at this moment, we are situated well below the limit of a forestation, in terms of European woodland. The management of the forest biodiversity, seen as an economic and environmental manner, permits, among other things, a sustainable exploitation of the potential through specific actions, scheduled actions of timber production, deadlines of contraction, territorial redistribution of quotas of timber, a forestation measures.biodiversity; forest potential; management; durability.

THE IMPORTANCE OF THE ECONOMIC COMMUNICATION WITHIN THE ORGANIZATION

The current business climate is changing day by day with a greater speed than ever before. Businesses will always be affected by circumstances such as the economic enviromment or the market evolution. To do this it is important that the company is strong and with a healthy working enviromment. It is becoming more and more important that the organisation is strong so it maintains it’s place on the market. The main purpose of this article is the observation and the detailed analysis of the bonds between the concept of a business organisation, economical comunication inside the company and the strategies used by managers to create, develop and maintain a strong position for the company on the market

Corporate social responsibility and organizational identity in post-crisis economy

Today, building up organizational identity in post-crisis economy becomes a bet, as we are looking for new interpretative coordinates.First of all, we have to take into account the ability to communicate. Second in line, as an extension of the above mentioned ability, we have to highlight the corporate social responsibility (CSR).Nowadays, the road map of modern business environment can be identified only by a new philosophy of business administration. This is the result of try and error and/or success of companies, greater or smaller companies, about their ability to develop a dialogue with their own audience and corporate communities.This dialogue involves approaching the role of the social corporate responsibility (CSR), to create the fundamentals of public policies of modern organizations.Therefore, the new corporate identity, which is the object of our study, we believe it to be the result of the intensive development of corporate communication and the responsible approach of companies to the global issues of the world

The Management of Environmental Resources and its Regional Implications

The management of environmental resources at regional level is closely related to social, economic and community’s activities. Community’s activities should be led taking into account the environmental sustainability. Preserving and improving environment’s quality is one of the main national objectives in nowadays Romania. Under these circumstances the main purpose of our research is to highlight the major aspects of this debate. Therefore, the study of social and economic activities impact on the environment is a major issue that modern society has to face today. As a consequence there is necessary a well balanced management for the environment resources in accordance with certain rules and terms, not only at local level, but also at regional and national level

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs

Motivation: RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. Results: We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses