Recent Patents on Biotechnology (v.7, #2)

Patents in some biotechnological fields are controversial. Despite this fact, the number of patent applicationsincreases 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 orusing biotechnology. The exploitation of biotechnological patents is an essential task in the management of intellectualcapital. 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) themarket need for biotechnological products and services, (ii) the importance of the freedom to operate analysis before enteringthe market, and (iii) efficiency in prosecution by Patent Offices. This paper primarily focuses on the internal determiningfactors, more particularly, the characteristics that the patent’s owner must take into consideration in order to havea 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 associatedchimeric fusion genes), others still lack an ultimate diagnostic tool, which could be of great interest as in somecases different sarcomas share a similar clinical manifestation. High throughput tools are contributing new ways tomolecularly delineate the boundaries of each sarcoma subtype. Moreover, they are also shedding light into other researchsubjects 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 therapeuticagents. 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 hiddenagenda of the biology of sarcomas, a knowledge that will surely be the subject of future patents intended to develop newdiagnostic and therapeutic tools.

Atomic Force Microscopy and Anodic Porous Allumina of Nucleic Acid Programmable Protein Arrays by Claudio Nicolini, Tercio Bezerra Correia, Enrico Stura, Claudio Larosa, Rosanna Spera, Eugenia Pechkova (112-121).
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 advancedon chip laboratory for gene expression contained in an engineered plasmid vector. The results obtained withCdK2, CDKN1A, p53 and Jun test genes expressed on NAPPA and the future developments are discussed in terms of ourpertinent and recent Patents and of their possibility to overcome some limitations of present fluorescence detection inprobing protein-protein interaction in both basic sciences and clinical studies.

A Review of Protein Function Prediction Under Machine Learning Perspective by Juliana S. Bernardes, Carlos E. Pedreira (122-141).
Protein function prediction is one of the most challenging problems in the post-genomic era. The number ofnewly 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 thisgap, a large number of computational methods have been proposed in the literature. Early approaches have exploredhomology relationships to associate known functions to the newly discovered proteins. Nevertheless, these approachestend to fail when a new protein is considerably different (divergent) from previously known ones. Accordingly, moreaccurate approaches, that use expressive data representation and explore sophisticate computational techniques arerequired. Regarding these points, this review provides a comprehensible description of machine learning approaches thatare currently applied to protein function prediction problems. We start by defining several problems enrolled inunderstanding protein function aspects, and describing how machine learning can be applied to these problems. We aim toexpose, in a systematical framework, the role of these techniques in protein function inference, sometimes difficult tofollow up due to the rapid evolvement of the field. With this purpose in mind, we highlight the most representativecontributions, the recent advancements, and provide an insightful categorization and classification of machine learningmethods in functional proteomics.

Over the last decade, proteomics has undergone remarkable progress thanks to the technical advances made inthe field. Improvements in the design of the protein microarrays, including more types of chemical groups for surfacefunctionalization, new capture agents and novel detection strategies, among others, have allowed the detection of proteinsin a robust, specific, sensitive, real time and high throughput manner. However, there are still problems that hinder theanalysis of low abundance proteins or those present in complex samples. For this reason, the development of patents relatedto the features mentioned above has an important relevance. In this review, we focus on the study of recently approvedpatents that try to solve the existing problems. Thanks to them, it is expected that the identification of disease biomarkerscan 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 inthe body of insect and other arthropod, and has received increasing attention worldwide due to its rarity and outstandingcurative effects for different diseases. Recent years, however, the counterfeits and mimics of Cordyceps are frequentlyfound in markets because of its scarce in nature and high in price. Therefore, quality control of Cordyceps and its bioproductsis very important to ensure their safety and efficacy. Nucleoside is recognized as a major active component ofCordyceps, and even is used as chemical marker for quality control of Cordyceps. In this present review, recent studiesand 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 discussedthereof. Also, developing trends in the field have been appraised.

Patent Selections (167-169).