BioChem, Volume 3, Issue 3 (September 2023) – 3 articles

The isothermal amplification of nucleic acids refers to processes that quickly increase the amount of DNA at a constant temperature. These methods are mainly developed as alternatives to PCR for cases in which the application of a thermal cycler is not possible or the assay method must be as rapid as possible. We have developed a new method of isothermal amplification based on the formation of hairpins at the ends of DNA fragments containing palindromic sequences and increased by the hydrolysis of one or both DNA strands by restriction endonuclease, known as hairpin-assisted isothermal reaction (HAIR). The key steps in HAIR are the formation of a self-complementary hairpin and the DNA breakage introduced by nickase. The end hairpins facilitate primer-free amplification, the amplicon strand cleavage by nickase produces additional 3′ ends that serve as new amplification points, and the amount of DNA can increase exponentially. The rate of amplification in HAIR is more than five times the rate of loop-mediated isothermal amplification (LAMP), and the total amount of DNA product of HAIR is more than double the amount of the LAMP product. Full article

Oncologic disease is a significant global health issue that causes thousands of deaths annually, and it has a significant impact on the quality of life of patients. Prostate cancer (PCa) is the second most diagnosed cancer and the fourth leading cause of cancer-related death in men in the Western world. Delineation of pathogenetic pathways and key driver molecular alterations involved in PCa development has provided a roadmap for the evaluation of biomarkers in predicting disease outcome and to identify potential therapeutic targets. Chemotherapeutic agents introduced from the 1990s include the taxanes (paclitaxel, docetaxel, and cabazitaxel), which are the anticancer drugs used most frequently for PCa treatment. This review presents the current knowledge about the onset and development of PCa, the state of the art of the use of taxane-based therapy, and their combination with targeting different transmembrane oncoproteins in PCa. The silencing of some transmembrane proteins can improve taxane sensitivity, and therefore may be a mechanism to improve the effectiveness of these drugs in PCa treatment. This combined therapy needs to be explored as a potential therapeutic agent for reducing cell proliferation, migration, and invasiveness in PCa. Full article

Despite decades of research on fish otoliths and their capacity to serve as biochronological recorders, much remains unknown about their protein composition, the mechanisms by which proteins are incorporated into the otolith matrix, or the potential for using otolith proteins to provide insight into aspects of fish life history. We examined the protein composition of Atlantic cod (Gadus morhua) otoliths using a state-of-the-art shotgun proteomics approach with liquid chromatography coupled to an electrospray ionization-orbitrap tandem mass spectrometer. In addition to previously known otolith matrix proteins, we discovered over 2000 proteins not previously identified in cod otoliths and more than 1500 proteins not previously identified in any fish otoliths. These included three novel proteins (Somatolactin, F-actin-capping protein subunit beta, Annexin) primarily involved in binding calcium ions and likely mediating crystal nucleation. However, most of the otolith proteins were not necessarily related to otolith formation but rather to other aspects of fish physiology. For example, we identified sex-related biomarkers for males (SPATA6 protein) and females (Vitellogenin-2-like protein). We highlight some noteworthy classes of proteins having diverse functions; however, the primary goal here is not to discuss each protein separately. The number and diverse roles of the proteins discovered in the otoliths suggest that proteomics could reveal critical life history information from archived otolith collections that could be invaluable for understanding aspects of fish biology and population ecology. This proof-of-concept methodology paper provides a novel methodology whereby otolith proteomics can be further explored. Full article