Recent Patents on Biotechnology - Volume 7, Issue 2, 2013

Patents in some biotechnological fields are controversial. Despite this fact, the number of patent applications increases every year. Total revenues in the global biotechnology market are expected to increase in the middle term. Nowadays, the bioeconomy is an important socio-economic area, which is reflected in the number of firms dedicated to or using biotechnology. The exploitation of biotechnological patents is an essential task in the management of intellectual capital. This paper explains the multiplicity of factors that influence the exploitation of biotechnological patents; specifically, the internal and external key points of patents exploitation. The external determining factors for patents are: (i) the market need for biotechnological products and services, (ii) the importance of the freedom to operate analysis before entering the market, and (iii) efficiency in prosecution by Patent Offices. This paper primarily focuses on the internal determining factors, more particularly, the characteristics that the patent’s owner must take into consideration in order to have a strong, broad subject-matter in the granted patent. The experimentation needed to obtain an adequate scope of the subject- matter in the claims is a critical issue in the exploitation of a patent or patent application.

Sarcomas are a class of tumors defined by their mesenchymal origin that comprise very different neoplasms. Although some sarcomas harbor pathogenomic molecular alterations (i.e. specific balanced translocations and their associated chimeric fusion genes), others still lack an ultimate diagnostic tool, which could be of great interest as in some cases different sarcomas share a similar clinical manifestation. High throughput tools are contributing new ways to molecularly delineate the boundaries of each sarcoma subtype. Moreover, they are also shedding light into other research subjects of immediate concern: (i) the elucidation of the molecular targets of chimeric fusion proteins and their interactome; (ii) the discovery of new biomarkers and therapeutic targets; and (iii) the delineation of the response to therapeutic agents. Here we review the application of proteomics approaches to sarcomas, with special emphasis in Ewing sarcoma. Proteomics strategies offer the focus, the analytical potential, and the high throughput capabilities to decipher the hidden agenda of the biology of sarcomas, a knowledge that will surely be the subject of future patents intended to develop new diagnostic and therapeutic tools.

The methodological aspects are here presented for the NAPPA (Nucleic Acid Programmable Protein Arrays) characterization by atomic force microscopy and anodic porous alumina. Anodic Porous Alumina represents also an advanced on chip laboratory for gene expression contained in an engineered plasmid vector. The results obtained with CdK2, CDKN1A, p53 and Jun test genes expressed on NAPPA and the future developments are discussed in terms of our pertinent and recent Patents and of their possibility to overcome some limitations of present fluorescence detection in probing protein-protein interaction in both basic sciences and clinical studies.

Protein function prediction is one of the most challenging problems in the post-genomic era. The number of newly identified proteins has been exponentially increasing with the advances of the high-throughput techniques. However, the functional characterization of these new proteins was not incremented in the same proportion. To fill this gap, a large number of computational methods have been proposed in the literature. Early approaches have explored homology relationships to associate known functions to the newly discovered proteins. Nevertheless, these approaches tend to fail when a new protein is considerably different (divergent) from previously known ones. Accordingly, more accurate approaches, that use expressive data representation and explore sophisticate computational techniques are required. Regarding these points, this review provides a comprehensible description of machine learning approaches that are currently applied to protein function prediction problems. We start by defining several problems enrolled in understanding protein function aspects, and describing how machine learning can be applied to these problems. We aim to expose, in a systematical framework, the role of these techniques in protein function inference, sometimes difficult to follow up due to the rapid evolvement of the field. With this purpose in mind, we highlight the most representative contributions, the recent advancements, and provide an insightful categorization and classification of machine learning methods in functional proteomics.

Over the last decade, proteomics has undergone remarkable progress thanks to the technical advances made in the field. Improvements in the design of the protein microarrays, including more types of chemical groups for surface functionalization, new capture agents and novel detection strategies, among others, have allowed the detection of proteins in a robust, specific, sensitive, real time and high throughput manner. However, there are still problems that hinder the analysis of low abundance proteins or those present in complex samples. For this reason, the development of patents related to the features mentioned above has an important relevance. In this review, we focus on the study of recently approved patents that try to solve the existing problems. Thanks to them, it is expected that the identification of disease biomarkers can be made in a suitable and reliable way, and above all, biocompatible and environmentally friendly.

Cordyceps, a well-known traditional Chinese medicine, is an endoparasitic and/or symbiotic macrofungus in the body of insect and other arthropod, and has received increasing attention worldwide due to its rarity and outstanding curative effects for different diseases. Recent years, however, the counterfeits and mimics of Cordyceps are frequently found in markets because of its scarce in nature and high in price. Therefore, quality control of Cordyceps and its bioproducts is very important to ensure their safety and efficacy. Nucleoside is recognized as a major active component of Cordyceps, and even is used as chemical marker for quality control of Cordyceps. In this present review, recent studies and associated patents, with regard to the chemical marker nucleosides for quality control of Cordyceps and its bioproducts, including nucleoside components, pharmacological activities, and analytical methods were reviewed and discussed thereof. Also, developing trends in the field have been appraised.