SeqLengthPlot v2.0: an all-in-one, easy-to-use tool for visualizing and retrieving sequence lengths from FASTA files.

Motivation: Accurate sequence length profiling is essential in bioinformatics, particularly in genomics and proteomics. Existing tools like SeqKit and the Trinity toolkit provide basic sequence statistics but often fall short in offering comprehensive analytics and plotting options. For instance, SeqKit is a very complete and fast tool for sequence analysis, delivering useful metrics (e.

Molecular evolution of ovothiol biosynthesis in animal life reveals diversity of the natural antioxidant ovothiols in Cnidaria.

Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs.

Oxidoreductases and metal cofactors in the functioning of the earth.

Life sustains itself using energy generated by thermodynamic disequilibria, commonly existing as redox disequilibria. Metals are significant players in controlling redox reactions, as they are essential components of the engine that life uses to tap into the thermodynamic disequilibria necessary for metabolism. The number of proteins that evolved to catalyze redox reactions is extraordinary, as is the diversification level of metal cofactors and catalytic domain structures involved.

Toxicological Impacts of Microplastics: Effects on Levels of Cellular Thiols in Mytilus galloprovincialis.

Over the last decade, the biological impact of microplastics in marine environments has become a serious global concern. Beyond their biological complexity, it is believed that many lethal and sublethal effects related to microplastic toxicity are triggered by oxidative stress and subsequently activated pathways. Thus, for marine organisms, having efficient mechanisms to fight the accumulation of oxidizing agents becomes indispensable to counteract the effects of microplastics.

The first genetic engineered system for ovothiol biosynthesis in diatoms reveals a mitochondrial localization for the sulfoxide synthase OvoA.

Diatoms represent one of the most abundant groups of microalgae in the ocean and are responsible for approximately 20% of photosynthetically fixed CO on Earth. Due to their complex evolutionary history and ability to adapt to different environments, diatoms are endowed with striking molecular biodiversity and unique metabolic activities. Their high growth rate and the possibility to optimize their biomass make them very promising 'biofactories' for biotechnological applications.

Cost analysis of extended half-life recombinant factor IX products in the treatment of haemophilia B in Italy: an update.

Haemophilia B (HB) is a rare disease which may lead to chronic disabling arthropathy, resulting in a significant clinical, social and economic impact. In recent years, new extended half-life (EHL) factor IX concentrates produced by recombinant technology (rFIX) have been developed. They have shown significantly prolonged half-life as compared to other rFIX products and improved bleeding control when used as prophylaxis.

Value assessment of medicinal products by the Italian Medicines Agency (AIFA) and French National Authority for Health (HAS): Similarities and discrepancies.

The evaluation of pharmaceutical innovation and therapeutic value is an increasingly complex exercise for which different approaches are adopted at the national level, despite the need for standardisation of processes and harmonisation of public health decisions. The objective of our analysis was to compare the approaches of the AIFA () and the HAS () in assessing the same medicinal products. In Italy, the 1525/2017 AIFA Deliberation introduces a transparent scheme for the evaluation of innovative status (innovative, conditional, not innovative) based on the therapeutic added value (TAV), therapeutic need, and quality of evidence.

A Survey on the Distribution of Ovothiol and Gene Expression in Different Tissues and Cells: A Comparative Analysis in Sea Urchins and Mussels.

Ovothiols are histidine-derived thiols produced by a variety of marine invertebrates, protists and bacteria. These compounds, which are among the strongest natural antioxidants, are involved in controlling the cellular redox balance due to their redox exchange with glutathione. Although ovothiols were initially reported as protective agents against environmental stressors, new evidence suggests that they can also act as pheromones and participate in fundamental biological processes such as embryogenesis.

First identification and characterization of detoxifying plastic-degrading DBP hydrolases in the marine diatom Cylindrotheca closterium.

Diatoms are photosynthetic organisms with potential biotechnological applications in the bioremediation sector, having shown the capacity to reduce environmental concentrations of different pollutants. The diatom Cylindrotheca closterium is known to degrade di-n-butyl phthalate (DBP), one of the most abundant phthalate esters in aquatic environments and a known endocrine-disrupting chemical. In this study, we present for the first time the in silico identification of two putative DBP hydrolases (provisionally called DBPH1 and DBPH2) in the transcriptome of C.

Milk Exosomes Transfer Oligosaccharides into Macrophages to Modulate Immunity and Attenuate Adherent-Invasive (AIEC) Infection.

Exosomes are abundance in human body fluids like urine, milk and blood. They act a critical role in extracellular and intracellular communication, intracellular trafficking and physiological regulation. Multiple immune-modulatory components, such as proteins, RNAs and carbohydrates (glycoproteins), have been found in human milk exosomes, which play immune-regulatory functions.

A Super Stable Mutant of the Plant Protein Monellin Endowed with Enhanced Sweetness.

Sweet proteins are a class of proteins with the ability to elicit a sweet sensation in humans upon interaction with sweet taste receptor T1R2/T1R3. Single-chain Monellin, MNEI, is among the sweetest proteins known and it could replace sugar in many food and beverage recipes. Nonetheless, its use is limited by low stability and high aggregation propensity at neutral pH.

Production and characterization of a fusion form of hepatitis E virus ORF2 capsid protein in .

Hepatitis E virus (HEV) is a nonenveloped virus causing an emerging zoonotic disease posing a severe threat to the public health in the world, especially to pregnant women. In this study, a truncated form (aa 368-606) of the open reading frame 2 of the capsid protein (ORF2-HEV), a major structural protein of HEV, was expressed in . This work characterizes for the first time, the fused Glutathione-S-Transferase-tagged ORF2 (GST-ORF2) and ORF2-HEV forms in .

Solution structure of insect CSP and OBPs by NMR.

Insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs) are proteins deputed to the solubilization, transport and stabilization of lipophilic and odorant compounds. These proteins have a conserved fold, which undergoes massive structural rearrangements in order to accommodate medium to large-sized lipophilic ligands. Solution NMR spectroscopy, due to its intrinsically dynamic nature, is the perfect technique to extrapolate structural information and dynamic parameters and to elucidate the conformational changes that occur upon ligand binding.

Understanding the self-assembly pathways of a single chain variant of monellin: A first step towards the design of sweet nanomaterials.

Peptides and proteins possess an inherent tendency to self-assemble, prompting the formation of amyloid aggregates from their soluble and functional states. Amyloids are linked to many devastating diseases, but self-assembling proteins can also represent formidable tools to produce new and sustainable biomaterials for biomedical and biotechnological applications. The mechanism of fibrillar aggregation, which influences the morphology and the properties of the protein aggregates, depend on factors such as pH, ionic strength, temperature, agitation, and protein concentration.

Probing structural changes during amyloid aggregation of the sweet protein MNEI.

Protein self-assembly is a ubiquitous phenomenon, traditionally studied for its links to amyloid pathologies, which has also gained attention as its physiological roles and possible biotechnological applications emerged over time. It is also known that varying the conditions to which proteins are exposed can lead to aggregate polymorphism. To understand the factors that trigger aggregation and/or direct it toward specific outcomes, we performed a multifaceted structural characterization of the thermally induced self-assembly process of MNEI, a model protein able to form amyloid aggregates under nondenaturing conditions.

Metabolic Effects of the Sweet Protein MNEI as a Sweetener in Drinking Water. A Pilot Study of a High Fat Dietary Regimen in a Rodent Model.

Sweeteners have become integrating components of the typical western diet, in response to the spreading of sugar-related pathologies (diabetes, obesity and metabolic syndrome) that have stemmed from the adoption of unbalanced dietary habits. Sweet proteins are a relatively unstudied class of sweet compounds that could serve as innovative sweeteners, but their introduction on the food market has been delayed by some factors, among which is the lack of thorough metabolic and toxicological studies. We have tried to shed light on the potential of a sweet protein, MNEI, as a fructose substitute in beverages in a typical western diet, by studying the metabolic consequences of its consumption on a Wistar rat model of high fat diet-induced obesity.

Insights into the G-rich VEGF-binding aptamer V7t1: when two G-quadruplexes are better than one!

The G-quadruplex-forming VEGF-binding aptamer V7t1 was previously found to be highly polymorphic in a K+-containing solution and, to restrict its conformational preferences to a unique, well-defined form, modified nucleotides (LNA and/or UNA) were inserted in its sequence. We here report an in-depth biophysical characterization of V7t1 in a Na+-rich medium, mimicking the extracellular environment in which VEGF targeting should occur, carried out combining several techniques to analyse the conformational behaviour of the aptamer and its binding to the protein. Our results demonstrate that, in the presence of high Na+ concentrations, V7t1 behaves in a very different way if subjected or not to annealing procedures, as evidenced by native gel electrophoresis, size exclusion chromatography and dynamic light scattering analysis.

Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera.

Structural roles of loop regions are frequently overlooked in proteins. Nevertheless, they may be key players in the definition of protein topology and in the self-assembly processes occurring through domain swapping. We here investigate the effects on structure and stability of replacing the loop connecting the last two β-strands of RNase A with the corresponding region of the more thermostable Onconase.

Disordered Peptides Looking for Their Native Environment: Structural Basis of CB1 Endocannabinoid Receptor Binding to Pepcans.

Endocannabinoid peptides, or "pepcans," are endogenous ligands of the CB1 cannabinoid receptor. Depending on their length, they display diverse activity: For instance, the nona-peptide Pepcan-9, also known as hemopressin, is a powerful inhibitor of CB1, whereas the longer variant Pepcan-12, which extends by only three amino acid residues at the N-terminus, acts on both CB1 and CB2 as an allosteric modulator, although with diverse effects. Despite active research on their pharmacological applications, very little is known about structure-activity relationships of pepcans.

Structural effects of methylglyoxal glycation, a study on the model protein MNEI.

The reaction of free amino groups in proteins with reactive carbonyl species, known as glycation, leads to the formation of mixtures of products, collectively referred to as advanced glycation endproducts (AGEs). These compounds have been implicated in several important diseases, but their role in pathogenesis and clinical symptoms' development is still debated. Particularly, AGEs are often associated to the formation of amyloid deposits in conformational diseases, such as Alzheimer's and Parkinson's disease, and it has been suggested that they might influence the mechanisms and kinetics of protein aggregation.

High-level production of single chain monellin mutants with enhanced sweetness and stability in tobacco chloroplasts.

Plastid-based MNEI protein mutants retain the structure, stability and sweetness of their bacterial counterparts, confirming the attractiveness of the plastid transformation technology for high-yield production of recombinant proteins. The prevalence of obesity and diabetes has dramatically increased the industrial demand for the development and use of alternatives to sugar and traditional sweeteners. Sweet proteins, such as MNEI, a single chain derivative of monellin, are the most promising candidates for industrial applications.

Structural organization of lipid-functionalized-Au nanoparticles.

Gold nanoparticles (AuNPs) are considered suitable systems for drug delivery and diagnostics with several applications in biomedicine. Size, shape and surface functionalization of these nanoparticles are important parameters influencing their behavior in a biological environment. This study describes the preparation and the characterization of lysophosphocholine coated AuNPs by means of Small Angle Neutron Scattering (SANS), Electron Paramagnetic Resonance (EPR) and Fluorescence Spectroscopy.