BioChem, Volume 2, Issue 1 (March 2022) – 8 articles

Simple biochemical concepts can be hard to grasp by non-specialists, even when they are related to practical contexts in industry, day-to-day activities, or well-acknowledged pathological conditions. This is especially important in instances where accurate communication of biochemical aspects for different types of stakeholders may be crucial. Examples include interacting with policymakers to establish guidelines, with patients (and/or caregivers) to identify key concepts in promoting awareness and adherence to therapeutic regimens, or with teachers and students for novel approaches in critical thinking. Focusing on our own work in developing communication tools for different purposes, in this review we will focus on some examples of how biochemical concepts can be effectively translated into illustrations and graphical narratives. For this purpose, engagement with target audiences in developing the materials themselves is key. We also discuss how specific projects can be tailored for different purposes, as well as evidence that comic-book strategies are effective in conveying biochemical and biomedical knowledge. Full article

Researchers at Universities generate and convey the knowledge acquired through communications in specialized (inter)national journals and congresses. An effort to share the scientific achievements with the general public is extremely important. For this purpose, we have launched the UALGORITMO, a journal freely accessible online, written in lay Portuguese language by Researchers of the University of the Algarve, to summarize recent communications published in peer reviewed journals. After submission, the manuscripts are revised by High Schools Students of the Algarve, under the guidance of a schoolteacher, for further simplification of the language and general improvement of the manuscript and figures. The revised manuscripts by the authors are edited and published, with an acknowledgment and a presentation of the reviewers at the end of each article. To maximize the outreach, the articles include a summarized biography of the authors, and links to their research centers and teaching courses. We believe that the UALGORITMO is a valuable instrument to promote scientific literacy and culture amongst all communities. Full article

PDZ domains are involved in many cellular processes and are key regulators of the cell physiology. A huge number of studies have investigated the binding specificity of PDZ domains to the carboxyl-terminal sequence of target proteins, while the molecular mechanisms that mediate the recognition of internal binding regions are largely unexplored. In the present study, we describe a ligand motif located in the catalytic domain of the phosphatase Dusp26 which mediates its binding to the PDZ-4 of Scribble. Site-directed mutagenesis identified a conserved tyrosine residue as relevant for the binding. The interaction with the PDZ domain could help the phosphatase to recruit its specific targets. Full article

Since the start of the COVID-19 outbreak, more than four million people have died of this disease. Given its ability to provide a precise response, mass spectrometry-based proteomics could represent a useful tool to study this pathology. To this end, an untargeted nLC-ESI-MS/MS-based method to characterise SARS-CoV-2 proteins, including possible variants, and investigate human saliva and plasma proteome in a single analysis was developed for further application in patients. Four SARS-CoV-2 recombinant proteins, three (S1–S2–RBD) belonging to the spike glycoprotein (S) and one corresponding to the nucleoprotein (N), were prepared and analysed with nLC-UHRTOF by injecting decreasing amounts to establish the limit of detection (LOD) of the method. This was determined as 10 pg for all the components of the S protein and for N (71 amol and 213 amol, respectively). Various viral inactivation strategies plus deglycosylation and digestion approaches were then tested in saliva and plasma spiked with different quantities of SARS-CoV-2 recombinant proteins. The limit of characterisation (LOC) in saliva for the N and S proteins was observed at 100 pg (coverage of 20% and 3%, respectively); instead, in plasma, it was 33 pg for N and 330 pg for the S protein, with a coverage of 4% for both. About 300 and 800 human proteins were identified in plasma and saliva, respectively, including several key effectors and pathways that are known to be altered in COVID-19 patients. In conclusion, this approach allows SARS-CoV-2 proteins and the human proteome to be simultaneously explored, both for plasma and saliva, showing a high relevant potential for retrospective studies aimed at investigating possible virus variants and for patient stratification. Full article

Sensing is an essential feature of life, where many systems have been developed. Diatomic molecules such as O₂, NO and CO exhibit an important role in life, which requires specialized sensors. Among the sensors discovered, heme-based gas sensors compose the largest group with at least eight different families. This large variety of proteins also exhibits many distinct ways of sensing diatomic molecules and promote a response for biological adaptation. Here, we briefly describe a story of two impressive systems of heme-based oxygen sensors, FixL from Rhizobium and DevS(DosS)/DosT from Mycobacterium tuberculosis. Beyond this, we also examined many applications that have emerged. These heme-based gas sensors have been manipulated to function as chemical and biochemical analytical systems to detect small molecules (O₂, CO, NO, CN⁻), fluorophores for imaging and bioanalysis, regulation of processes in synthetic biology and preparation of biocatalysts among others. These exciting features show the robustness of this field and multiple opportunities ahead besides the advances in the fundamental understanding of their molecular functioning. Full article

Infection and sepsis remain among the leading causes of neonatal mortality. The susceptibility of newborns to infection can be attributed to their immature immune system. Regarding immune response, monocytes represent a numerically minor population of leukocytes. However, they contribute to a variety of immunological demands, such as continuous replenishment of resident macrophages under non-infectious conditions and migration to inflamed sites where they neutralize pathogens and secrete cytokines. Further functions include the presentation of antigens and T-cell activation. Cytokines coordinate host responses to bacterial and viral infections and orchestrate ongoing physiological signaling between cells of non-immune tissues. A critical event is the skewing of the cytokine repertoire to achieve a resolution of infection. In this regard, monocytes may hold a key position as deciders in addition to their phagocytic activity, securing the extinction of pathogens to prevent broader organ damage by toxins and pro-inflammatory reactions. Neonatal monocytes undergo various regulatory and metabolic changes. Thus, they are thought to be vulnerable in anticipating pro-inflammatory conditions and cause severe progressions which increase the risk of developing sepsis. Furthermore, clinical studies have shown that exposure to inflammation puts neonates at a high risk for adverse pulmonary, immunological and other organ developments, which may result in multiorgan disease. This review discusses significant functions and impairments of neonatal monocytes that are decisive for the outcome of bacterial infections. Full article

Polyoxometalates (POMs) are clusters of units of oxoanions of transition metals, such as Mo, W, V and Nb, that can be formed upon acidification of neutral solutions. Once formed, some POMs have shown to persist in solution, even in the neutral and basic pH range. These inorganic clusters, amenable of a variety of structures, have been studied in environmental, chemical, and industrial fields, having applications in catalysis and macromolecular crystallography, as well as applications in biomedicine, such as cancer, bacterial and viral infections, among others. Herein, we connect recent POMs environmental applications in the decomposition of emergent pollutants with POMs’ biomedical activities and effects against cancer, bacteria, and viruses. With recent insights in POMs being pure, organic/inorganic hybrid materials, POM-based ionic liquid crystals and POM-ILs, and their applications in emergent pollutants degradation, including microplastics, are referred. It is perceived that the majority of the POMs studies against cancer, bacteria, and viruses were performed in the last ten years. POMs’ biological effects include apoptosis, cell cycle arrest, interference with the ions transport system, inhibition of mRNA synthesis, cell morphology changes, formation of reaction oxygen species, inhibition of virus binding to the host cell, and interaction with virus protein cages, among others. We additionally refer to POMs’ interactions with various proteins, including P-type ATPases, aquoporins, cinases, phosphatases, among others. Finally, POMs’ stability and speciation at physiological conditions are addressed. Full article

Bipolar Disorder (BD), a chronic mental illness, does not have an ideal treatment, and patients with BD have a higher chance of being diagnosed with alcohol abuse, liver disease, and diabetes. The goal of treatment is to prevent a relapse in BD episodes and find a new treatment. The research here looks at the genetics of BD and ignores environmental factors, as they are subjective. Therapy treats known environmental triggers and stressors and explores methods to reduce them. However, therapy alone cannot fully alleviate the symptoms of BD. My research employs text-mining as a primary strategy to obtain relevant genes and drugs pertaining to BD. The main gene involved is the Brain-Derived Neurotrophic Factor (BDNF). Popular drugs currently used for treatment of BD are Lithium and Carbamazepine. Using CMapPy to look at gene expression data, one sees a relationship between the two drug therapies and BDNF. Lithium fails to treat mania and Carbamazepine fails to treat depression, relatively speaking. When comparing gene expression data of Lithium and Carbamazepine with Ketamine, a newer therapy for BD, Ketamine, raises the BDNF level, keeps it elevated, and effectively controls BD episodes. Ketamine does not have the shortcomings that Lithium and Carbamazepine have. Next steps would include conducting a clinical trial with the hopeful application of Ketamine as a new treatment for BD. Full article