What if? Mouse proteomics after gene inactivation

The complex interactions among proteins and of proteins with small molecular weight protein ligands are overturned every time one of the components of the network is missing. For study purposes, animal models lacking one protein are obtained by experimental manipulation of the genome: in the knocking out approach, a gene is altered through the insertion of an artificial DNA sequence, which halts the transcription-translation sequence of events. In this review we have compiled the research papers that analyze the effects of knocking out individual genes on the proteomes of various tissues/organs throughout the body. We have gathered and organized all the available evidence and then compared the proteomic data in order to stress the context-specificity of the outcome every time two or more organs were investigated in the same KO mice. Finally, in a symmetrical approach to the above, we surveyed whether there is any obvious overlap among the effects of different KO on the same organ, marking affection of general pathways or lacking specificity of the gene targeting. Specific attention was put on the possible involvement of cellular stress markers

SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane \u3b1-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure-function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport

Increased serum OPG in atrophic nonunion shaft fractures

Background Bone repair alteration is hypothesized for nonunion fracture pathogenesis. Since it is involved in osteoclast regulation, the RANK/RANKL/OPG system (receptor activator of nuclear factor kB/its ligand/osteoprotegerin) may play a role. Materials and methods Serum OPG, free RANKL, bone alkaline phosphatase (BAP), osteocalcin (OC), and urinary deoxypyridinoline (DPD) were determined in 16 male patients (20\u201339 years) with long bone atrophic nonunion fractures. Serum markers were also measured in 18 agematched male controls who healed from the same type of fractures within six months, and in 14 age-matched male controls who were healing from the same fractures one month after injury. One-way ANOVA and Bonferroni\u2019s test were used for statistical analysis. Results Only OPG was significantly higher (0.56 sd 0.11 ng/ml) in the patients compared to healed (0.26 sd 0.04 ng/ml; P\0.001) and healing (0.29 sd 0.09 ng/ml; P\0.001) controls. The patients\u2019 DPD levels were normal. No correlations were found between bone markers and the characteristics of the subjects in all groups. Conclusions A normal steady state of bone metabolism seems to be present in patients with atrophic nonunion fractures, despite the high serum OPG. The reason for the inability of the patients\u2019 OPG to inhibit osteoclastic activity is unknown. Osteoblast activity also appears normal, so another cellular source of OPG can be hypothesized

In silico prioritization of endocrine active substances (EAS) and their in vitro validation

In silico molecular docking can be a cheap and fast strategy to estimate the binding free energies, and consequently the dissociation constants, for a set of compounds with respect to their putative targets. Interesting targets for EAS are the ligand binding domains (LBD) of the human nuclear receptors for the sex hormones, i.e. the estrogen, androgen, progesterone, and (gluco)corticoid receptor. The Horizon 2020 project EuroMix (http://euromixproject.eu) aims to establish and disseminate new, efficient and validated strategies for the risk assessment of mixtures, while limiting the use of test animals. The present presentation deals with a part of EuroMix that is intended to set up a testing approach for mixtures of endocrine disrupting chemicals, focusing on estrogenic and anti-androgenic effects. For that purpose, a combined Adverse Outcome Pathway (AOP) was constructed, including Molecular Initiating Events, Key Events, and Adverse Outcome (reproductive dysfunction). Using this combined AOP as framework, cognate in silico and in vitro tools as well as the in vivo confirmation studies were selected, i.e. in silico: h-ER and h-AR docking; in vitro: cell-based ER and AR transcriptional activation bioassays and the H295R steroidogenesis assay; and in vivo: the Fish Sexual Development Test (FSDT, OECD Test No. 234) and a rat study, examining in (male) offspring a number of parameters, such as anogenital distance, cryptorchidism, and nipple retention. Reference chemicals were selected and in silico and in vitro testing was started, showing that when testing single compounds, there is a very good correlation between the in silico determined binding energies and the in vitro measured hormonal activities

Deciphering and modelling remyelinating mechanisms induced by clinically-used azole antifungals with exploitable repurposing properties

Recent evidence demonstrated the ability of some antifungals to induce (re)myelination in speci c experimental models. These compounds, already marketed for di erent pathologies, are interesting candidates for a repurposing strategy in neurodegenerative diseases, like multiple sclerosis (MS), characterized by strong demyelination. Our preliminary results show that the inhibition of enzymes involved in retinoic acid (RA) catabolism (CYP26), by miconazole and other azole antifungals, induces an increase of cellular RA concentration and that this increase may be behind the observed oligodendrocyte precursor cell (OPC) maturation and di erentiation. On this basis, our proposal is aimed at studying the molecular mechanisms of azole antifungals used in human pharmacology, both in silico and in vitro, and at identifying the most promising ones according to their ability to increase Myelin Basic Protein (MBP) expression on OPCs and to promote their di erentiation and myelination. In our investigation, the ability of 7 azoles to inhibit CYP26 isozymes was evaluated through molecular docking: in silico results were the basis for the selection of the drugs for the in vitro experiments. The selected azoles were tested in three di erent cell models, characterized by increasing complexity: i) OPC cultures, a maturation assay for myelin-producing cells; ii) OPC-dorsal root ganglion (DRG) neuron co-cultures, a myelination assay; iii) cerebral micromass cultures, a cell di erentiation assay for CNS. In parallel, the e ects of exogenous RA and of an inhibitor of the synthesis of RA (citral), were evaluated as well. In the next phase of the project, the outcomes from the di erent in vitro models will be statistically correlated with the pharmacological treatments. Our results will be useful: 1) for identifying the most promising azole antifungals with respect to their pro-myelinating activity, 2) for clarifying the molecular mechanisms underlying their reparative e ect and 3) for formalizing mathematical models to identify the most active concentrations for the most potent azoles

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology

Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males: findings from a nested case-control study

Background: Recently, loss-of-function variants in TLR7 were identified in two families in which COVID-19 segregates like an X-linked recessive disorder environmentally conditioned by SARS-CoV-2. We investigated whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients.Methods: This is a nested case-control study in which we compared male participants with extreme phenotype selected from the Italian GEN-COVID cohort of SARS-CoV-2-infected participants (<60y, 79 severe cases versus 77 control cases). We applied the LASSO Logistic Regression analysis, considering only rare variants on young male subsets with extreme phenotype, picking up TLR7 as the most important susceptibility gene.Results: Overall, we found TLR7 deleterious variants in 2.1% of severely affected males and in none of the asymptomatic participants. The functional gene expression profile analysis demonstrated a reduction in TLR7-related gene expression in patients compared with controls demonstrating an impairment in type I and II IFN responses.Conclusion: Young males with TLR7 loss-of-function variants and severe COVID-19 represent a subset of male patients contributing to disease susceptibility in up to 2% of severe COVID-19