An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.     

K18- and CAG-hACE2 Transgenic Mouse Models and SARS-CoV-2: Implications for Neurodegeneration Research

COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic that might lead to very serious consequences. Notably, mental status change, brain confusion, and smell and taste disorders along with neurological complaints have been reported in patients infected with SARS-CoV-2. Furthermore, human brain tissue autopsies from COVID-19 patients show the presence of SARS-CoV-2 neuroinvasion, which correlates with the manifestation of meningitis, encephalitis, leukocyte infiltration, and neuronal damage. The olfactory mucosa has been suggested as a way of entry into the brain. SARS-CoV-2 infection is also known to provoke a hyper-inflammatory reaction with an exponential increase in the production of pro-inflammatory cytokines leading to systemic responses, even in the absence of direct infection of brain cells. Angiotensin-converting enzyme 2 (ACE2), the entry receptor of SARS-CoV-2, has been extensively demonstrated to be present in the periphery, neurons, and glial cells in different brain regions. To dissect the details of neurological complications and develop therapies helping COVID-19 survivors regain pre-infection quality of life, the development of robust clinical models is highly warranted. Several human angiotensin-converting enzyme 2 (hACE2) transgenic mouse models have been developed and used for antiviral drug screening and vaccine development, as well as for better understanding of the molecular pathogenetic mechanisms of SARS-CoV-2 infection. In this review, we summarize recent results from the studies involving two such mouse models, namely K18- and CAG-hACE2 transgenics, to evaluate the direct and indirect impact of SARS-CoV-2 infection on the central nervous system.     

Unconventional stereoselective one-pot synthesis of Knoevenagel-type indoles via in situ condensation of iminium salts with active methylene reagents

A simple one-pot procedure for the stereoselective synthesis of Knoevenagel-type indoles is described. The method is based on the in situ reaction of indole iminium salts (four of them are fully characterized) with acyclic symmetrical and unsymmetrical active methylene reagents in the presence of triethylamine. In general, the overall yields are moderate to good. Some of relevant reaction parameters and steric effects affecting stereoselectivity are discussed.     

Stratification of the Radiation Field Inside a Photobioreactor During Microalgae Growth

Light availability is a main issue in autotrophic growth of photosynthetic microorganisms. The change of the suspended cells concentration and that of their chlorophylls content during microalgal growth alters the optical properties of the aqueous suspension. This brings about changes in the properties of the radiation field inside the reactor. In this work, we have computed the evolution in time of the local volumetric rate of absorption of photons inside a photobioreactor by means of a Monte Carlo simulation algorithm previously developed. From this study, we have computed two operational variables that are useful tools for the analysis, performance comparison, optimization and scaling up of photobioreactors: the average rate of photon absorption and the volumetric distribution function of photons absorption rates. Based on these two variables, it is possible to systematically quantify the degree of stratification of the culture medium, which is a decisive aspect that hampers the reactor efficiency regarding the energy usage for biomass production.     

Shedding light on the mitochondrial matrix through a functional membrane transporter

The first fluorescent probes that are actively channeled into the mitochondrial matrix by a specific mitochondrial membrane transporter in living cells have been developed. The new functional probes (BCT) have a minimalist structural design based on the highly efficient and photostable BODIPY chromophore and carnitine as a biotargeting element. Both units are orthogonally bonded through the common boron atom, thus avoiding the use of complex polyatomic connectors. In contrast to known mitochondria-specific dyes, BCTs selectively label these organelles regardless of their transmembrane potential and in an enantioselective way. The obtained experimental evidence supports carnitine–acylcarnitine translocase (CACT) as the key transporter protein for BCTs, which behave therefore as acylcarnitine biomimetics. This simple structural design can be readily extended to other structurally diverse starting F-BODIPYs to obtain BCTs with varied emission wavelengths along the visible and NIR spectral regions and with multifunctional capabilities. BCTs are the first fluorescent derivatives of carnitine to be used in cell microscopy and stand as promising research tools to explore the role of the carnitine shuttle system in cancer and metabolic diseases. Extension of this approach to other small-molecule mitochondrial transporters is envisaged.

A BODIPY derivative of carnitine enters mitochondria regardless of their membrane potential and in an enantioselective way through a specific mitochondrial membrane transporter in living cells.     

Synthetic Route to a Benzooxazole Derivative with Heparanase Inhibitory Activity

The synthesis of a benzooxazol-5-yl acetic acid derivative (9) with strong heparanase and angiogenesis inhibitory activity, and thus possible commercial interest, is described in detail.     

Nanoparticles based on novel amphiphilic polyaspartamide copolymers

In this article, the synthesis of two amphiphilic polyaspartamide copolymers, useful to obtain polymeric nanoparticles without using surfactants or stabilizing agents, is described. These copolymers were obtained starting from α,β-poly-(N-2-hydroxyethyl)-dl-aspartamide (PHEA) by following a novel synthetic strategy. In particular, PHEA and its pegylated derivative (PHEA-PEG₂₀₀₀) were functionalized with poly(lactic acid) (PLA) through 1,1′-carbonyldiimidazole (CDI) activation to obtain PHEA–PLA and PHEA-PEG₂₀₀₀–PLA graft copolymers, respectively. These copolymers were properly purified and characterized by ¹H-NMR, FT-IR, and Size Exclusion Chromatography (SEC) analyses, which confirmed that derivatization reactions occurred. Nanoparticles were obtained from PHEA–PLA and PHEA-PEG₂₀₀₀–PLA graft copolymers by using the high pressure homogenization-solvent evaporation method, avoiding the use of surfactants or stabilizing agents. Polymeric nanoparticles were characterized by dimensional analysis, before and after freeze-drying process, and Scanning Electron Microscopy (SEM). Zeta potential measurements and X-ray Photoelectron Spectroscopy (XPS) analysis demonstrated the presence of PEG and/or PHEA onto the PHEA-PEG₂₀₀₀–PLA and PHEA–PLA nanoparticle surface, respectively.